TY - JOUR A1 - Tabatabaei, Iman A1 - Alseekh, Saleh A1 - Shahid, Mohammad A1 - Leniak, Ewa A1 - Wagner, Mateusz A1 - Mahmoudi, Henda A1 - Thushar, Sumitha A1 - Fernie, Alisdair R. A1 - Murphy, Kevin M. A1 - Schmöckel, Sandra M. A1 - Tester, Mark A1 - Müller-Röber, Bernd A1 - Skirycz, Aleksandra A1 - Balazadeh, Salma T1 - The diversity of quinoa morphological traits and seed metabolic composition JF - Scientific data N2 - Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa. Y1 - 2022 U6 - https://doi.org/10.1038/s41597-022-01399-y SN - 2052-4463 VL - 9 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Alshareef, Nouf Owdah A1 - Otterbach, Sophie L. A1 - Allu, Annapurna Devi A1 - Woo, Yong H. A1 - de Werk, Tobias A1 - Kamranfar, Iman A1 - Müller-Röber, Bernd A1 - Tester, Mark A1 - Balazadeh, Salma A1 - Schmöckel, Sandra M. T1 - NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis JF - Scientific reports N2 - Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-14429-x SN - 2045-2322 VL - 12 IS - 1 PB - Nature Research CY - Berlin ER - TY - JOUR A1 - Ralevski, Alexandra A1 - Apelt, Federico A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Rugarli, Elena I. A1 - Kragler, Friedrich A1 - Horvath, Tamas L. T1 - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice JF - Cellular and molecular life sciences N2 - Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals. KW - Arabidopsis thaliana KW - Mitochondria KW - FMT KW - Hyponasty KW - Mice KW - CLUH; KW - Locomotion Y1 - 2022 U6 - https://doi.org/10.1007/s00018-022-04382-3 SN - 1420-682X SN - 1420-9071 VL - 79 IS - 6 PB - Springer International Publishing AG CY - Cham (ZG) ER - TY - JOUR A1 - John, Sheeba A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd T1 - Regulation of alternative splicing in response to temperature variation in plants JF - Journal of experimental botany N2 - Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future. KW - alternative splicing KW - ambient temperature KW - cold KW - heat KW - plants KW - stress KW - adaptation Y1 - 2021 U6 - https://doi.org/10.1093/jxb/erab232 SN - 0022-0957 SN - 1460-2431 VL - 72 IS - 18 SP - 6150 EP - 6163 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Faisal, Muhammad B. A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Dijkwel, Paul P. T1 - Putative alternative translation start site-encoding nucleotides of CPR5 regulate growth and resistance JF - BMC plant biology N2 - Background The Arabidopsis CONSTITUTIVE EXPRESSER of PATHOGENESIS-RELATED GENES 5 (CPR5) has recently been shown to play a role in gating as part of the nuclear pore complex (NPC). Mutations in CPR5 cause multiple defects, including aberrant trichomes, reduced ploidy levels, reduced growth and enhanced resistance to bacterial and fungal pathogens. The pleiotropic nature of cpr5 mutations implicates that the CPR5 protein affects multiple pathways. However, little is known about the structural features that allow CPR5 to affect the different pathways. Results Our in silico studies suggest that in addition to three clusters of putative nuclear localization signals and four or five transmembrane domains, CPR5 contains two putative alternative translation start sites. To test the role of the methionine-encoding nucleotides implicated in those sites, metCPR5 cDNAs, in which the relevant nucleotides were changed to encode glutamine, were fused to the CPR5 native promoter and the constructs transformed to cpr5-2 plants to complement cpr5-compromised phenotypes. The control and metCPR5 constructs were able to complement all cpr5 phenotypes, although the extent of complementation depended on the specific complementing plant lines. Remarkably, plants transformed with metCPR5 constructs showed larger leaves and displayed reduced resistance when challenged to Pseudomonas syringae pv Pst DC3000, as compared to control plants. Thus, the methionine-encoding nucleotides regulate growth and resistance. We propose that structural features of the CPR5 N-terminus are implicated in selective gating of proteins involved in regulating the balance between growth and resistance. Conclusion Plants need to carefully balance the amount of resources used for growth and resistance. The Arabidopsis CPR5 protein regulates plant growth and immunity. Here we show that N-terminal features of CPR5 are involved in the regulation of the balance between growth and resistance. These findings may benefit efforts to improve plant yield, while maintaining optimal levels of disease resistance. KW - CPR5 KW - plant growth KW - disease resistance KW - cell death KW - arabidopsis thaliana KW - endoreduplication Y1 - 2020 U6 - https://doi.org/10.1186/s12870-020-02485-2 SN - 1471-2229 VL - 20 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Moreno Curtidor, Catalina A1 - Annunziata, Maria Grazia A1 - Gupta, Saurabh A1 - Apelt, Federico A1 - Richard, Sarah Isabel A1 - Kragler, Friedrich A1 - Müller-Röber, Bernd A1 - Olas, Justyna Jadwiga T1 - Physiological profiling of embryos and dormant seeds in two Arabidopsis accessions reveals a metabolic switch in carbon reserve accumulation JF - Frontiers in plant science N2 - In flowering plants, sugars act as carbon sources providing energy for developing embryos and seeds. Although most studies focus on carbon metabolism in whole seeds, knowledge about how particular sugars contribute to the developmental transitions during embryogenesis is scarce. To develop a quantitative understanding of how carbon composition changes during embryo development, and to determine how sugar status contributes to final seed or embryo size, we performed metabolic profiling of hand-dissected embryos at late torpedo and mature stages, and dormant seeds, in two Arabidopsis thaliana accessions with medium [Columbia-0 (Col-0)] and large [Burren-0 (Bur-0)] seed sizes, respectively. Our results show that, in both accessions, metabolite profiles of embryos largely differ from those of dormant seeds. We found that developmental transitions from torpedo to mature embryos, and further to dormant seeds, are associated with major metabolic switches in carbon reserve accumulation. While glucose, sucrose, and starch predominantly accumulated during seed dormancy, fructose levels were strongly elevated in mature embryos. Interestingly, Bur-0 seeds contain larger mature embryos than Col-0 seeds. Fructose and starch were accumulated to significantly higher levels in mature Bur-0 than Col-0 embryos, suggesting that they contribute to the enlarged mature Bur-0 embryos. Furthermore, we found that Bur-0 embryos accumulated a higher level of sucrose compared to hexose sugars and that changes in sucrose metabolism are mediated by sucrose synthase (SUS), with SUS genes acting non-redundantly, and in a tissue-specific manner to utilize sucrose during late embryogenesis. KW - carbon KW - embryo development KW - hexoses KW - metabolites KW - sucrose KW - synthase Y1 - 2020 U6 - https://doi.org/10.3389/fpls.2020.588433 SN - 1664-462X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Fichtner, Franziska A1 - Barbier, Francois F. A1 - Annunziata, Maria Grazia A1 - Feil, Regina A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Stitt, Mark A1 - Beveridge, Christine A. A1 - Lunn, John Edward T1 - Regulation of shoot branching in arabidopsis by trehalose 6-phosphate JF - New phytologist : international journal of plant science N2 - Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood. We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds. TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous Tre6P phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and upregulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds. These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT. KW - Arabidopsis thaliana (arabidopsis) KW - axillary bud KW - branching KW - sucrose KW - sugar signalling KW - trehalose 6‐ phosphate (Tre6P) Y1 - 2020 U6 - https://doi.org/10.1111/nph.17006 SN - 0028-646X SN - 1469-8137 VL - 229 IS - 4 SP - 2135 EP - 2151 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Hasnat, Muhammad Abrar A1 - Zupok, Arkadiusz A1 - Olas-Apelt, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Leimkühler, Silke T1 - A-type carrier proteins are involved in [4Fe-4S] cluster insertion into the radical S-adenosylmethionine protein MoaA for the synthesis of active molybdoenzymes JF - Journal of bacteriology N2 - Iron sulfur (Fe-S) clusters are important biological cofactors present in proteins with crucial biological functions, from photosynthesis to DNA repair, gene expression, and bioenergetic processes. For the insertion of Fe-S clusters into proteins, A-type carrier proteins have been identified. So far, three of them have been characterized in detail in Escherichia coli, namely, IscA, SufA, and ErpA, which were shown to partially replace each other in their roles in [4Fe-4S] cluster insertion into specific target proteins. To further expand the knowledge of [4Fe-4S] cluster insertion into proteins, we analyzed the complex Fe-S cluster-dependent network for the synthesis of the molybdenum cofactor (Moco) and the expression of genes encoding nitrate reductase in E. coli. Our studies include the identification of the A-type carrier proteins ErpA and IscA, involved in [4Fe-4S] cluster insertion into the radical Sadenosyl-methionine (SAM) enzyme MoaA. We show that ErpA and IscA can partially replace each other in their role to provide [4Fe-4S] clusters for MoaA. Since most genes expressing molybdoenzymes are regulated by the transcriptional regulator for fumarate and nitrate reduction (FNR) under anaerobic conditions, we also identified the proteins that are crucial to obtain an active FNR under conditions of nitrate respiration. We show that ErpA is essential for the FNR-dependent expression of the narGHJI operon, a role that cannot be compensated by IscA under the growth conditions tested. SufA does not appear to have a role in Fe-S cluster insertion into MoaA or FNR under anaerobic growth employing nitrate respiration, based on the low level of gene expression.
IMPORTANCE Understanding the assembly of iron-sulfur (Fe-S) proteins is relevant to many fields, including nitrogen fixation, photosynthesis, bioenergetics, and gene regulation. Remaining critical gaps in our knowledge include how Fe-S clusters are transferred to their target proteins and how the specificity in this process is achieved, since different forms of Fe-S clusters need to be delivered to structurally highly diverse target proteins. Numerous Fe-S carrier proteins have been identified in prokaryotes like Escherichia coli, including ErpA, IscA, SufA, and NfuA. In addition, the diverse Fe-S cluster delivery proteins and their target proteins underlie a complex regulatory network of expression, to ensure that both proteins are synthesized under particular growth conditions. KW - iron-sulfur clusters KW - Moco biosynthesis KW - MoaA KW - A-type carrier protein KW - FNR KW - nitrate reductase KW - molybdenum cofactor Y1 - 2021 U6 - https://doi.org/10.1128/JB.00086-21 SN - 1098-5530 VL - 203 IS - 12 PB - American Society for Microbiology CY - Washington ER - TY - JOUR A1 - Shubchynskyy, Volodymyr A1 - Boniecka, Justyna A1 - Schweighofer, Alois A1 - Simulis, Justinas A1 - Kvederaviciute, Kotryna A1 - Stumpe, Michael A1 - Mauch, Felix A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Boutrot, Freddy A1 - Zipfel, Cyril A1 - Meskiene, Irute T1 - Protein phosphatase AP2C1 negatively regulates basal resistance and defense responses to Pseudomonas syringae JF - Journal of experimental botany N2 - Mitogen-activated protein kinases (MAPKs) mediate plant immune responses to pathogenic bacteria. However, less is known about the cell autonomous negative regulatory mechanism controlling basal plant immunity. We report the biological role of Arabidopsis thaliana MAPK phosphatase AP2C1 as a negative regulator of plant basal resistance and defense responses to Pseudomonas syringae. AP2C2, a closely related MAPK phosphatase, also negatively controls plant resistance. Loss of AP2C1 leads to enhanced pathogen-induced MAPK activities, increased callose deposition in response to pathogen-associated molecular patterns or to P. syringae pv. tomato (Pto) DC3000, and enhanced resistance to bacterial infection with Pto. We also reveal the impact of AP2C1 on the global transcriptional reprogramming of transcription factors during Pto infection. Importantly, ap2c1 plants show salicylic acid-independent transcriptional reprogramming of several defense genes and enhanced ethylene production in response to Pto. This study pinpoints the specificity of MAPK regulation by the different MAPK phosphatases AP2C1 and MKP1, which control the same MAPK substrates, nevertheless leading to different downstream events. We suggest that precise and specific control of defined MAPKs by MAPK phosphatases during plant challenge with pathogenic bacteria can strongly influence plant resistance. KW - Callose KW - defense genes KW - MAPK KW - MAPK phosphatase KW - PAMP KW - PP2C phosphatase KW - Pseudomonas syringae KW - salicylic acid KW - transcription factors Y1 - 2017 U6 - https://doi.org/10.1093/jxb/erw485 SN - 0022-0957 SN - 1460-2431 VL - 68 IS - 5 SP - 1169 EP - 1183 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sharma, Niharika A1 - Dang, Trang Minh A1 - Singh, Namrata A1 - Ruzicic, Slobodan A1 - Müller-Röber, Bernd A1 - Baumann, Ute A1 - Heuer, Sigrid T1 - Allelic variants of OsSUB1A cause differential expression of transcription factor genes in response to submergence in rice JF - Rice N2 - Background: Flooding during seasonal monsoons affects millions of hectares of rice-cultivated areas across Asia. Submerged rice plants die within a week due to lack of oxygen, light and excessive elongation growth to escape the water. Submergence tolerance was first reported in an aus-type rice landrace, FR13A, and the ethylene-responsive transcription factor (TF) gene SUB1A-1 was identified as the major tolerance gene. Intolerant rice varieties generally lack the SUB1A gene but some intermediate tolerant varieties, such as IR64, carry the allelic variant SUB1A-2. Differential effects of the two alleles have so far not been addressed. As a first step, we have therefore quantified and compared the expression of nearly 2500 rice TF genes between IR64 and its derived tolerant near isogenic line IR64-Sub1, which carries the SUB1A-1 allele. Gene expression was studied in internodes, where the main difference in expression between the two alleles was previously shown. Results: Nineteen and twenty-six TF genes were identified that responded to submergence in IR64 and IR64-Sub1, respectively. Only one gene was found to be submergence-responsive in both, suggesting different regulatory pathways under submergence in the two genotypes. These differentially expressed genes (DEGs) mainly included MYB, NAC, TIFY and Zn-finger TFs, and most genes were downregulated upon submergence. In IR64, but not in IR64-Sub1, SUB1B and SUB1C, which are also present in the Sub1 locus, were identified as submergence responsive. Four TFs were not submergence responsive but exhibited constitutive, genotype-specific differential expression. Most of the identified submergence responsive DEGs are associated with regulatory hormonal pathways, i.e. gibberellins (GA), abscisic acid (ABA), and jasmonic acid (JA), apart from ethylene. An in-silico promoter analysis of the two genotypes revealed the presence of allele-specific single nucleotide polymorphisms, giving rise to ABRE, DRE/CRT, CARE and Site II cis-elements, which can partly explain the observed differential TF gene expression. Conclusion: This study identified new gene targets with the potential to further enhance submergence tolerance in rice and provides insights into novel aspects of SUB1A-mediated tolerance. KW - Submergence tolerance KW - SUB1A KW - Rice KW - Transcription factors Y1 - 2018 U6 - https://doi.org/10.1186/s12284-017-0192-z SN - 1939-8425 SN - 1939-8433 VL - 11 IS - 2 PB - Springer Open CY - London ER - TY - JOUR A1 - Durgud, Meriem A1 - Gupta, Saurabh A1 - Ivanov, Ivan A1 - Omidbakhshfard, Mohammad Amin A1 - Benina, Maria A1 - Alseekh, Saleh A1 - Staykov, Nikola A1 - Hauenstein, Mareike A1 - Dijkwel, Paul P. A1 - Hortensteiner, Stefan A1 - Toneva, Valentina A1 - Brotman, Yariv A1 - Fernie, Alisdair R. A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - Molecular Mechanisms Preventing Senescence in Response to Prolonged Darkness in a Desiccation-Tolerant Plant JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness. Y1 - 2018 U6 - https://doi.org/10.1104/pp.18.00055 SN - 0032-0889 SN - 1532-2548 VL - 177 IS - 3 SP - 1319 EP - 1338 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Hochrein, Lena A1 - Mitchell, Leslie A. A1 - Schulz, Karina A1 - Messerschmidt, Katrin A1 - Müller-Röber, Bernd T1 - L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast JF - Nature Communications N2 - The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a lightcontrolled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light. The extent of recombination depends on induction time and concentration of the chromophore phycocyanobilin (PCB), which can be easily adjusted. The tool presented here provides improved recombination control over the previously reported estradiol-dependent SCRaMbLE induction system, mediating a larger variety of possible recombination events in SCRaMbLE-ing a reporter plasmid. Thereby, L-SCRaMbLE boosts the potential for further customization and provides a facile application for use in the S. cerevisiae genome reengineering project Sc2.0 or in other recombination-based systems. Y1 - 2018 U6 - https://doi.org/10.1038/s41467-017-02208-6 SN - 2041-1723 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Naseri, Gita A1 - Behrend, Jessica A1 - Rieper, Lisa A1 - Müller-Röber, Bernd T1 - COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors JF - Nature Communications N2 - Balanced expression of multiple genes is central for establishing new biosynthetic pathways or multiprotein cellular complexes. Methods for efficient combinatorial assembly of regulatory sequences (promoters) and protein coding sequences are therefore highly wanted. Here, we report a high-throughput cloning method, called COMPASS for COMbinatorial Pathway ASSembly, for the balanced expression of multiple genes in Saccharomyces cerevisiae. COMPASS employs orthogonal, plant-derived artificial transcription factors (ATFs) and homologous recombination-based cloning for the generation of thousands of individual DNA constructs in parallel. The method relies on a positive selection of correctly assembled pathway variants from both, in vivo and in vitro cloning procedures. To decrease the turnaround time in genomic engineering, COMPASS is equipped with multi-locus CRISPR/Cas9-mediated modification capacity. We demonstrate the application of COMPASS by generating cell libraries producing n-carotene and co-producing p-ionone and biosensor-responsive naringenin. COMPASS will have many applications in synthetic biology projects that require gene expression balancing. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-10224-x SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Yang, Lei A1 - Perrera, Valentina A1 - Saplaoura, Eleftheria A1 - Apelt, Federico A1 - Bahin, Mathieu A1 - Kramdi, Amira A1 - Olas, Justyna Jadwiga A1 - Müller-Röber, Bernd A1 - Sokolowska, Ewelina A1 - Zhang, Wenna A1 - Li, Runsheng A1 - Pitzalis, Nicolas A1 - Heinlein, Manfred A1 - Zhang, Shoudong A1 - Genovesio, Auguste A1 - Colot, Vincent A1 - Kragler, Friedrich T1 - m(5)C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants JF - Current biology N2 - In plants, transcripts move to distant body parts to potentially act as systemic signals regulating development and growth. Thousands of messenger RNAs (mRNAs) are transported across graft junctions via the phloem to distinct plant parts. Little is known regarding features, structural motifs, and potential base modifications of transported transcripts and how these may affect their mobility. We identified Arabidopsis thalianam RNAs harboring the modified base 5-methylcytosine (m(5)C) and found that these are significantly enriched in mRNAs previously described as mobile, moving over graft junctions to distinct plant parts. We confirm this finding with graft-mobile methylated mRNAs TRANSLATIONALLY CONTROLLED TUMOR PROTEIN 1 (TCTP1) and HEAT SHOCK COGNATE PROTEIN 70.1 (HSC70.1), whose mRNA transport is diminished in mutants deficient in m(5)C mRNA methylation. Together, our results point toward an essential role of cytosine methylation in systemic mRNA mobility in plants and that TCTP1 mRNA mobility is required for its signaling function. Y1 - 2019 U6 - https://doi.org/10.1016/j.cub.2019.06.042 SN - 0960-9822 SN - 1879-0445 VL - 29 IS - 15 SP - 2465 EP - 2476.e5 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Dong, Yanni A1 - Gupta, Saurabh A1 - Sievers, Rixta A1 - Wargent, Jason J. A1 - Wheeler, David A1 - Putterill, Joanna A1 - Macknight, Richard A1 - Gechev, Tsanko S. A1 - Müller-Röber, Bernd A1 - Dijkwel, Paul P. T1 - Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals environment JF - BMC genomics N2 - BackgroundPachycladon cheesemanii is a close relative of Arabidopsis thaliana and is an allotetraploid perennial herb which is widespread in the South Island of New Zealand. It grows at altitudes of up to 1000m where it is subject to relatively high levels of ultraviolet (UV)-B radiation. To gain first insights into how Pachycladon copes with UV-B stress, we sequenced its genome and compared the UV-B tolerance of two Pachycladon accessions with those of two A. thaliana accessions from different altitudes.ResultsA high-quality draft genome of P. cheesemanii was assembled with a high percentage of conserved single-copy plant orthologs. Synteny analysis with genomes from other species of the Brassicaceae family found a close phylogenetic relationship of P. cheesemanii with Boechera stricta from Brassicaceae lineage I. While UV-B radiation caused a greater growth reduction in the A. thaliana accessions than in the P. cheesemanii accessions, growth was not reduced in one P. cheesemanii accession. The homologues of A. thaliana UV-B radiation response genes were duplicated in P. cheesemanii, and an expression analysis of those genes indicated that the tolerance mechanism in P. cheesemanii appears to differ from that in A. thaliana.ConclusionAlthough the P. cheesemanii genome shows close similarity with that of A. thaliana, it appears to have evolved novel strategies allowing the plant to tolerate relatively high UV-B radiation. KW - Abiotic stress KW - Arabidopsis KW - Genome assembly KW - Pachycladon KW - UV-B tolerance Y1 - 2019 U6 - https://doi.org/10.1186/s12864-019-6084-4 SN - 1471-2164 VL - 20 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Naseri, Gita A1 - Balazadeh, Salma A1 - Machens, Fabian A1 - Kamranfar, Iman A1 - Messerschmidt, Katrin A1 - Müller-Röber, Bernd T1 - Plant-Derived Transcription Factors for Orthologous Regulation of Gene Expression in the Yeast Saccharomyces cerevisiae JF - ACS synthetic biology N2 - Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects for which a tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harboring cognate cis regulatory motifs driving a yEGFP reporter. Transcriptional output of the different driver/reporter combinations varied over a wide spectrum, with EDLL being a considerably stronger transcription activation domain in yeast than the GAL4 activation domain, in particular when fused to Arabidopsis NAC TFs. Notably, the strength of several NAC-EDLL fusions exceeded that of the strong yeast TDH3 promoter by 6- to 10-fold. We furthermore show that plant TFs can be used to build regulatory systems encoded by centromeric or episomal plasmids. Our library of TF-DNA binding site combinations offers an excellent tool for diverse synthetic biology applications in yeast. KW - Arabidopsis thaliana KW - artificial transcription factor KW - NAC transcription factor KW - synthetic biology KW - plant Y1 - 2017 U6 - https://doi.org/10.1021/acssynbio.7b00094 SN - 2161-5063 VL - 6 SP - 1742 EP - 1756 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Czarnocka, Weronika A1 - Van Der Kelen, Katrien A1 - Willems, Patrick A1 - Szechynska-Hebda, Magdalena A1 - Shahnejat-Bushehri, Sara A1 - Balazadeh, Salma A1 - Rusaczonek, Anna A1 - Müller-Röber, Bernd A1 - Van Breusegem, Frank A1 - Karpinski, Stanislaw T1 - The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator JF - Plant, cell & environment : cell physiology, whole-plant physiology, community physiology N2 - Since its discovery over two decades ago as an important cell death regulator in Arabidopsis thaliana, the role of LESION SIMULATING DISEASE 1 (LSD1) has been studied intensively within both biotic and abiotic stress responses as well as with respect to plant fitness regulation. However, its molecular mode of action remains enigmatic. Here, we demonstrate that nucleo-cytoplasmic LSD1 interacts with a broad range of other proteins that are engaged in various molecular pathways such as ubiquitination, methylation, cell cycle control, gametogenesis, embryo development and cell wall formation. The interaction of LSD1 with these partners is dependent on redox status, as oxidative stress significantly changes the quantity and types of LSD1-formed complexes. Furthermore, we show that LSD1 regulates the number and size of leaf mesophyll cells and affects plant vegetative growth. Importantly, we also reveal that in addition to its function as a scaffold protein, LSD1 acts as a transcriptional regulator. Taken together, our results demonstrate that LSD1 plays a dual role within the cell by acting as a condition-dependent scaffold protein and as a transcription regulator. KW - Arabidopsis KW - thaliana KW - dry weight KW - LSD1 KW - oxidative stress KW - protein interaction KW - transcription regulation Y1 - 2017 U6 - https://doi.org/10.1111/pce.12994 SN - 0140-7791 SN - 1365-3040 VL - 40 SP - 2644 EP - 2662 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Omranian, Nooshin A1 - Eloundou-Mbebi, Jeanne Marie Onana A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - Gene regulatory network inference using fused LASSO on multiple data sets JF - Scientific reports N2 - Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions. Y1 - 2016 U6 - https://doi.org/10.1038/srep20533 SN - 2045-2322 VL - 6 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - The plastid metalloprotease FtsH6 and small heat shock protein HSP21 jointly regulate thermomemory in Arabidopsis JF - Nature Communications N2 - Acquired tolerance to heat stress is an increased resistance to elevated temperature following a prior exposure to heat. The maintenance of acquired thermotolerance in the absence of intervening stress is called ‘thermomemory’ but the mechanistic basis for this memory is not well defined. Here we show that Arabidopsis HSP21, a plastidial small heat shock protein that rapidly accumulates after heat stress and remains abundant during the thermomemory phase, is a crucial component of thermomemory. Sustained memory requires that HSP21 levels remain high. Through pharmacological interrogation and transcriptome profiling, we show that the plastid-localized metalloprotease FtsH6 regulates HSP21 abundance. Lack of a functional FtsH6 protein promotes HSP21 accumulation during the later stages of thermomemory and increases thermomemory capacity. Our results thus reveal the presence of a plastidial FtsH6–HSP21 control module for thermomemory in plants. Y1 - 2016 U6 - https://doi.org/10.1038/ncomms12439 SN - 2041-1723 VL - 7 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Gupta, Saurabh A1 - Dong, Yanni A1 - Dijkwel, Paul P. A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation JF - International Journal of Molecular Sciences N2 - Abiotic stress is one of the major threats to plant crop yield and productivity. When plants are exposed to stress, production of reactive oxygen species (ROS) increases, which could lead to extensive cellular damage and hence crop loss. During evolution, plants have acquired antioxidant defense systems which can not only detoxify ROS but also adjust ROS levels required for proper cell signaling. Ascorbate peroxidase (APX), glutathione peroxidase (GPX), catalase (CAT) and superoxide dismutase (SOD) are crucial enzymes involved in ROS detoxification. In this study, 40 putative APX, 28 GPX, 16 CAT, and 41 SOD genes were identified from genomes of the resurrection species Boea hygrometrica, Selaginella lepidophylla, Xerophyta viscosa, and Oropetium thomaeum, and the mesophile Selaginella moellendorffi. Phylogenetic analyses classified the APX, GPX, and SOD proteins into five clades each, and CAT proteins into three clades. Using co-expression network analysis, various regulatory modules were discovered, mainly involving glutathione, that likely work together to maintain ROS homeostasis upon desiccation stress in resurrection species. These regulatory modules also support the existence of species-specific ROS detoxification systems. The results suggest molecular pathways that regulate ROS in resurrection species and the role of APX, GPX, CAT and SOD genes in resurrection species during stress. KW - abiotic stress KW - desiccation KW - resurrection plants KW - ROS KW - ascorbate peroxidase KW - glutathione peroxidase KW - catalase KW - superoxide dismutase Y1 - 2019 U6 - https://doi.org/10.3390/ijms20123101 SN - 1422-0067 SN - 1661-6596 VL - 20 IS - 12 PB - Molecular Diversity Preservation International CY - Basel ER - TY - JOUR A1 - Machens, Fabian A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Messerschmidt, Katrin T1 - Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae JF - Frontiers in Bioengineering and Biotechnology N2 - Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host’s endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400. The broad spectrum of expression strengths that is achieved will be useful for various experimental setups, e.g., the transcriptional balancing of expression levels within heterologous pathways or the construction of artificial regulatory networks. Furthermore, our analyses reveal simple rules that enable the tuning of synTF expression output, thereby allowing easy modification of a given synTF/synP pair. This will make it easier for researchers to construct tailored transcriptional control systems. KW - JUB1 KW - synthetic biology KW - transcriptional regulation KW - gene expression KW - synthetic circuits KW - dead Cas9 KW - chimeric transcription factors Y1 - 2017 U6 - https://doi.org/10.3389/fbioe.2017.00063 SN - 2296-4185 VL - 5 SP - 1 EP - 11 PB - Frontiers CY - Lausanne ER - TY - JOUR A1 - Proost, Sebastian A1 - Van Bel, Michiel A1 - Vaneechoutte, Dries A1 - Van de Peer, Yves A1 - Inze, Dirk A1 - Müller-Röber, Bernd A1 - Vandepoele, Klaas T1 - PLAZA 3.0: an access point for plant comparative genomics JF - Nucleic acids research N2 - Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. Y1 - 2015 U6 - https://doi.org/10.1093/nar/gku986 SN - 0305-1048 SN - 1362-4962 VL - 43 IS - D1 SP - D974 EP - D981 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Alseekh, Saleh A1 - Tohge, Takayuki A1 - Wendenberg, Regina A1 - Scossa, Federico A1 - Omranian, Nooshin A1 - Li, Jie A1 - Kleessen, Sabrina A1 - Giavalisco, Patrick A1 - Pleban, Tzili A1 - Müller-Röber, Bernd A1 - Zamir, Dani A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. T1 - Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato JF - The plant cell N2 - A large-scale metabolic quantitative trait loci (mQTL) analysis was performed on the well-characterized Solanum pennellii introgression lines to investigate the genomic regions associated with secondary metabolism in tomato fruit pericarp. In total, 679 mQTLs were detected across the 76 introgression lines. Heritability analyses revealed that mQTLs of secondary metabolism were less affected by environment than mQTLs of primary metabolism. Network analysis allowed us to assess the interconnectivity of primary and secondary metabolism as well as to compare and contrast their respective associations with morphological traits. Additionally, we applied a recently established real-time quantitative PCR platform to gain insight into transcriptional control mechanisms of a subset of the mQTLs, including those for hydroxycinnamates, acyl-sugar, naringenin chalcone, and a range of glycoalkaloids. Intriguingly, many of these compounds displayed a dominant-negative mode of inheritance, which is contrary to the conventional wisdom that secondary metabolite contents decreased on domestication. We additionally performed an exemplary evaluation of two candidate genes for glycolalkaloid mQTLs via the use of virus-induced gene silencing. The combined data of this study were compared with previous results on primary metabolism obtained from the same material and to other studies of natural variance of secondary metabolism. Y1 - 2015 U6 - https://doi.org/10.1105/tpc.114.132266 SN - 1040-4651 SN - 1532-298X VL - 27 IS - 3 SP - 485 EP - 512 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Köslin-Findeklee, Fabian A1 - Rizi, Vajiheh Safavi A1 - Becker, Martin A. A1 - Parra-Londono, Sebastian A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Kunze, Reinhard A1 - Horst, Walter J. T1 - Transcriptomic analysis of nitrogen starvation- and cultivar-specific leaf senescence in winter oilseed rape (Brassica napus L.) JF - Plant science : an international journal of experimental plant biology N2 - High nitrogen (N) efficiency, characterized by high grain yield under N limitation, is an important agricultural trait in Brassica napus L. cultivars related to delayed senescence of older leaves during reproductive growth (a syndrome called stay-green). The aim of this study was thus to identify genes whose expression is specifically altered during N starvation-induced leaf senescence and that can be used as markers to distinguish cultivars at early stages of senescence prior to chlorophyll loss. To this end, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analyzed 4 days after the induction of senescence by either N starvation, leaf shading or detaching. In addition to N metabolism genes, N starvation mostly (and specifically) repressed genes related to photosynthesis, photorespiration and cell-wall structure, while genes related to mitochondrial electron transport and flavonoid biosynthesis were predominately up-regulated. A kinetic study over a period of 12 days with four B. napus cultivars differing in their stay-green characteristics confirmed the cultivar-specific regulation of six genes in agreement with their senescence behavior: the senescence regulator ANAC029, the anthocyanin synthesis-related genes ANS and DFR-like1, the ammonium transporter AMT1:4, the ureide transporter UPSS, and SPS1 involved in sucrose biosynthesis. The identified genes represent markers for the detection of cultivar-specific differences in N starvation-induced leaf senescence and can thus be employed as valuable tools in B. napus breeding. (C) 2015 Elsevier Ireland Ltd. All rights reserved. KW - Brassica napus KW - Genotypic differences KW - Leaf senescence KW - Molecular marker KW - N efficiency KW - Stay-green Y1 - 2015 U6 - https://doi.org/10.1016/j.plantsci.2014.11.018 SN - 0168-9452 VL - 233 SP - 174 EP - 185 PB - Elsevier CY - Clare ER - TY - JOUR A1 - Sree, K. Sowjanya A1 - Keresztes, Aron A1 - Müller-Röber, Bernd A1 - Brandt, Ronny A1 - Eberius, Matthias A1 - Fischer, Wolfgang A1 - Appenroth, Klaus-J. T1 - Phytotoxicity of cobalt ions on the duckweed Lemna minor - Morphology, ion uptake, and starch accumulation JF - Chemosphere : chemistry, biology and toxicology as related to environmental problems N2 - Cobalt (Co2+) inhibits vegetative growth of Lemna minor gradually from 1 mu M to 100 mu M. Fronds accumulated up to 21 mg Co2+ g(-1) dry weight at 10 mu M external Co2+ indicating hyperaccumulation. Interestingly, accumulation of Co2+ did not decrease the iron (Fe) content in fronds, highlighting L. minor as a suitable system for studying effects of Co2+ undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co2+ treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4 d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co2+-treated daughter fronds, indicating that Co2+ inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4 d of Co2+ treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter. (C) 2015 Elsevier Ltd. All rights reserved. KW - Chloroplast KW - Cobalt KW - Lemnaceae KW - Lemna minor KW - Phytotoxicity KW - Starch accumulation Y1 - 2015 U6 - https://doi.org/10.1016/j.chemosphere.2015.03.008 SN - 0045-6535 SN - 1879-1298 VL - 131 SP - 149 EP - 156 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Proost, Sebastian A1 - Fujikura, Ushio A1 - Müller-Röber, Bernd T1 - Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology JF - Molecular plant N2 - Growth-regulating factors (GRFs) are plant-specific transcription factors that were originally identified for their roles in stem and leaf development, but recent studies highlight them to be similarly important for other central developmental processes including flower and seed formation, root development, and the coordination of growth processes under adverse environmental conditions. The expression of several GRFs is controlled by microRNA miR396, and the GRF-miRNA396 regulatory module appears to be central to several of these processes. In addition, transcription factors upstream of GRFs and miR396 have been discovered, and gradually downstream target genes of GRFs are being unraveled. Here, we review the current knowledge of the biological functions performed by GRFs and survey available molecular data to illustrate how they exert their roles at the cellular level. KW - abiotic stress KW - chromatin remodeling KW - flower development KW - growth regulation KW - leaf development KW - miRNA Y1 - 2015 U6 - https://doi.org/10.1016/j.molp.2015.01.013 SN - 1674-2052 SN - 1752-9867 VL - 8 IS - 7 SP - 998 EP - 1010 PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Garapati, Prashanth A1 - Feil, Regina A1 - Lunn, John Edward A1 - Van Dijck, Patrick A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - Transcription Factor Arabidopsis Activating Factor1 Integrates Carbon Starvation Responses with Trehalose Metabolism JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Plants respond to low carbon supply by massive reprogramming of the transcriptome and metabolome. We show here that the carbon starvation-induced NAC (for NO APICAL MERISTEM/ARABIDOPSIS TRANSCRIPTION ACTIVATION FACTOR/CUP-SHAPED COTYLEDON) transcription factor Arabidopsis (Arabidopsis thaliana) Transcription Activation Factor1 (ATAF1) plays an important role in this physiological process. We identified TREHALASE1, the only trehalase-encoding gene in Arabidopsis, as a direct downstream target of ATAF1. Overexpression of ATAF1 activates TREHALASE1 expression and leads to reduced trehalose-6-phosphate levels and a sugar starvation metabolome. In accordance with changes in expression of starch biosynthesis-and breakdown-related genes, starch levels are generally reduced in ATAF1 overexpressors but elevated in ataf1 knockout plants. At the global transcriptome level, genes affected by ATAF1 are broadly associated with energy and carbon starvation responses. Furthermore, transcriptional responses triggered by ATAF1 largely overlap with expression patterns observed in plants starved for carbon or energy supply. Collectively, our data highlight the existence of a positively acting feedforward loop between ATAF1 expression, which is induced by carbon starvation, and the depletion of cellular carbon/energy pools that is triggered by the transcriptional regulation of downstream gene regulatory networks by ATAF1. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00917 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 1 SP - 379 EP - 390 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Engqvist, Martin K. M. A1 - Schmitz, Jessica A1 - Gertzmann, Anke A1 - Florian, Alexandra A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Maurino, Veronica G. T1 - GLYCOLATE OXIDASE3, a Glycolate Oxidase Homolog of Yeast L-Lactate Cytochrome c Oxidoreductase, Supports L-Lactate Oxidation in Roots of Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - In roots of Arabidopsis (Arabidopsis thaliana), L-lactate is generated by the reduction of pyruvate via L-lactate dehydrogenase, but this enzyme does not efficiently catalyze the reverse reaction. Here, we identify the Arabidopsis glycolate oxidase (GOX) paralogs GOX1, GOX2, and GOX3 as putative L-lactate-metabolizing enzymes based on their homology to CYB2, the L-lactate cytochrome c oxidoreductase from the yeast Saccharomyces cerevisiae. We found that GOX3 uses L-lactate with a similar efficiency to glycolate; in contrast, the photorespiratory isoforms GOX1 and GOX2, which share similar enzymatic properties, use glycolate with much higher efficiencies than L-lactate. The key factor making GOX3 more efficient with L-lactate than GOX1 and GOX2 is a 5- to 10-fold lower Km for the substrate. Consequently, only GOX3 can efficiently metabolize L-lactate at low intracellular concentrations. Isotope tracer experiments as well as substrate toxicity tests using GOX3 loss-of-function and overexpressor plants indicate that L-lactate is metabolized in vivo by GOX3. Moreover, GOX3 rescues the lethal growth phenotype of a yeast strain lacking CYB2, which cannot grow on L-lactate as a sole carbon source. GOX3 is predominantly present in roots and mature to aging leaves but is largely absent from young photosynthetic leaves, indicating that it plays a role predominantly in heterotrophic rather than autotrophic tissues, at least under standard growth conditions. In roots of plants grown under normoxic conditions, loss of function of GOX3 induces metabolic rearrangements that mirror wild-type responses under hypoxia. Thus, we identified GOX3 as the enzyme that metabolizes L-lactate to pyruvate in vivo and hypothesize that it may ensure the sustainment of low levels of L-lactate after its formation under normoxia. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.01003 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1042 EP - 1061 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Wang, Ting A1 - Tohge, Takayuki A1 - Ivakov, Alexander A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Mutwil, Marek A1 - Schippers, Jos H. M. A1 - Persson, Staffan T1 - Salt-Related MYB1 Coordinates Abscisic Acid Biosynthesis and Signaling during Salt Stress in Arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Abiotic stresses, such as salinity, cause global yield loss of all major crop plants. Factors and mechanisms that can aid in plant breeding for salt stress tolerance are therefore of great importance for food and feed production. Here, we identified a MYB-like transcription factor, Salt-Related MYB1 (SRM1), that negatively affects Arabidopsis (Arabidopsis thaliana) seed germination under saline conditions by regulating the levels of the stress hormone abscisic acid (ABA). Accordingly, several ABA biosynthesis and signaling genes act directly downstream of SRM1, including SALT TOLERANT1/NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3, RESPONSIVE TO DESICCATION26, and Arabidopsis NAC DOMAIN CONTAINING PROTEIN19. Furthermore, SRM1 impacts vegetative growth and leaf shape. We show that SRM1 is an important transcriptional regulator that directly targets ABA biosynthesis and signaling-related genes and therefore may be regarded as an important regulator of ABA-mediated salt stress tolerance. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00962 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 2 SP - 1027 EP - + PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Lotkowska, Magda E. A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - The Arabidopsis Transcription Factor MYB112 Promotes Anthocyanin Formation during Salinity and under High Light Stress JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - MYB transcription factors (TFs) are important regulators of flavonoid biosynthesis in plants. Here, we report MYB112 as a formerly unknown regulator of anthocyanin accumulation in Arabidopsis (Arabidopsis thaliana). Expression profiling after chemically induced overexpression of MYB112 identified 28 up-and 28 down-regulated genes 5 h after inducer treatment, including MYB7 and MYB32, which are both induced. In addition, upon extended induction, MYB112 also positively affects the expression of PRODUCTION OF ANTHOCYANIN PIGMENT1, a key TF of anthocyanin biosynthesis, but acts negatively toward MYB12 and MYB111, which both control flavonol biosynthesis. MYB112 binds to an 8-bp DNA fragment containing the core sequence (A/T/G)(A/C) CC(A/T)(A/G/T)(A/C)(T/C). By electrophoretic mobility shift assay and chromatin immunoprecipitation coupled to quantitative polymerase chain reaction, we show that MYB112 binds in vitro and in vivo to MYB7 and MYB32 promoters, revealing them as direct downstream target genes. We further show that MYB112 expression is up-regulated by salinity and high light stress, environmental parameters that both require the MYB112 TF for anthocyanin accumulation under these stresses. In contrast to several other MYB TFs affecting anthocyanin biosynthesis, MYB112 expression is not controlled by nitrogen limitation or an excess of carbon. Thus, MYB112 constitutes a regulator that promotes anthocyanin accumulation under abiotic stress conditions. Y1 - 2015 U6 - https://doi.org/10.1104/pp.15.00605 SN - 0032-0889 SN - 1532-2548 VL - 169 IS - 3 SP - 1862 EP - 1880 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Schmidt, Romy A1 - Schippers, Jos H. M. A1 - Mieulet, Delphine A1 - Watanabe, Mutsumi A1 - Hoefgen, Rainer A1 - Guiderdoni, Emmanuel A1 - Müller-Röber, Bernd T1 - Salt-Rresponsive ERF1 is a negative regulator of grain filling and gibberellin-mediated seedling establishment in rice JF - Molecular plant N2 - Grain quality is an important agricultural trait that is mainly determined by grain size and composition. Here, we characterize the role of the rice transcription factor (TF) SALT-RESPONSIVE ERF1 (SERF1) during grain development. Through genome-wide expression profiling and chromatin immunoprecipitation, we found that SERF1 directly regulates RICE PROLAMIN-BOX BINDING FACTOR (RPBF), a TF that functions as a positive regulator of grain filling. Loss of SERF1 enhances RPBF expression resulting in larger grains with increased starch content, while SERF1 overexpression represses RPBF resulting in smaller grains. Consistently, during grain filling, starch biosynthesis genes such as GRANULE-BOUND STARCH SYNTHASEI (GBSSI), STARCH SYNTHASEI (SSI), SSIIIa, and ADP-GLUCOSE PYROPHOSPHORYLASE LARGE SUBUNIT2 (AGPL2) are up-regulated in SERF1 knockout grains. Moreover, SERF1 is a direct upstream regulator of GBSSI. In addition, SERF1 negatively regulates germination by controlling RPBF expression, which mediates the gibberellic acid (GA)-induced expression of RICE AMYLASE1A (RAmy1A). Loss of SERF1 results in more rapid seedling establishment, while SERF1 overexpression has the opposite effect. Our study reveals that SERF1 represents a negative regulator of grain filling and seedling establishment by timing the expression of RPBF. KW - RPBF KW - rice KW - grain filling KW - germination KW - SERF1 KW - gibberellic acid Y1 - 2014 U6 - https://doi.org/10.1093/mp/sst131 SN - 1674-2052 SN - 1752-9867 VL - 7 IS - 2 SP - 404 EP - 421 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Auxin and its role in plant senescence JF - Journal of plant growth regulation N2 - Leaf senescence represents a key developmental process through which resources trapped in the photosynthetic organ are degraded in an organized manner and transported away to sustain the growth of other organs including newly forming leaves, roots, seeds, and fruits. The optimal timing of the initiation and progression of senescence are thus prerequisites for controlled plant growth, biomass accumulation, and evolutionary success through seed dispersal. Recent research has uncovered a multitude of regulatory factors including transcription factors, micro-RNAs, protein kinases, and others that constitute the molecular networks that regulate senescence in plants. The timing of senescence is affected by environmental conditions and abiotic or biotic stresses typically trigger a faster senescence. Various phytohormones, including for example ethylene, abscisic acid, and salicylic acid, promote senescence, whereas cytokinins delay it. Recently, several reports have indicated an involvement of auxin in the control of senescence, however, its mode of action and point of interference with senescence control mechanisms remain vaguely defined at present and contrasting observations regarding the effect of auxin on senescence have so far hindered the establishment of a coherent model. Here, we summarize recent studies on auxin-related genes that affect senescence in plants and highlight how these findings might be integrated into current molecular-regulatory models of senescence. KW - ARF KW - Auxin KW - Chloroplast KW - Development KW - Leaf KW - SAUR KW - Senescence KW - Signaling KW - Transcription factor KW - YUCCA Y1 - 2014 U6 - https://doi.org/10.1007/s00344-013-9398-5 SN - 0721-7595 SN - 1435-8107 VL - 33 IS - 1 SP - 21 EP - 33 PB - Springer CY - New York ER - TY - JOUR A1 - Lu, Dandan A1 - Wang, Ting A1 - Persson, Staffan A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. T1 - Transcriptional control of ROS homeostasis by KUODA1 regulates cell expansion during leaf development JF - Nature Communications N2 - The final size of an organism, or of single organs within an organism, depends on an intricate coordination of cell proliferation and cell expansion. Although organism size is of fundamental importance, the molecular and genetic mechanisms that control it remain far from understood. Here we identify a transcription factor, KUODA1 (KUA1), which specifically controls cell expansion during leaf development in Arabidopsis thaliana. We show that KUA1 expression is circadian regulated and depends on an intact clock. Furthermore, KUA1 directly represses the expression of a set of genes encoding for peroxidases that control reactive oxygen species (ROS) homeostasis in the apoplast. Disruption of KUA1 results in increased peroxidase activity and smaller leaf cells. Chemical or genetic interference with the ROS balance or peroxidase activity affects cell size in a manner consistent with the identified KUA1 function. Thus, KUA1 modulates leaf cell expansion and final organ size by controlling ROS homeostasis. Y1 - 2014 U6 - https://doi.org/10.1038/ncomms4767 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Omidbakhshfard, Mohammad Amin A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Riano-Pachon, Diego M. A1 - Müller-Röber, Bernd T1 - A step-by-step protocol for formaldehyde-assisted isolation of regulatory elements from Arabidopsis thaliana JF - Journal of integrative plant biology N2 - The control of gene expression by transcriptional regulators and other types of functionally relevant DNA transactions such as chromatin remodeling and replication underlie a vast spectrum of biological processes in all organisms. DNA transactions require the controlled interaction of proteins with DNA sequence motifs which are often located in nucleosome-depleted regions (NDRs) of the chromatin. Formaldehyde-assisted isolation of regulatory elements (FAIRE) has been established as an easy-to-implement method for the isolation of NDRs from a number of eukaryotic organisms, and it has been successfully employed for the discovery of new regulatory segments in genomic DNA from, for example, yeast, Drosophila, and humans. Until today, however, FAIRE has only rarely been employed in plant research and currently no detailed FAIRE protocol for plants has been published. Here, we provide a step-by-step FAIRE protocol for NDR discovery in Arabidopsis thaliana. We demonstrate that NDRs isolated from plant chromatin are readily amenable to quantitative polymerase chain reaction and next-generation sequencing. Only minor modification of the FAIRE protocol will be needed to adapt it to other plants, thus facilitating the global inventory of regulatory regions across species. KW - Arabidopsis thaliana KW - chromatin KW - cis-regulatory elements KW - epigenomics KW - FAIRE-qPCR KW - FAIRE-seq KW - gene expression KW - gene regulatory network KW - transcription factor Y1 - 2014 U6 - https://doi.org/10.1111/jipb.12151 SN - 1672-9072 SN - 1744-7909 VL - 56 IS - 6 SP - 527 EP - 538 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Mettler, Tabea A1 - Mühlhaus, Timo A1 - Hemme, Dorothea A1 - Schöttler, Mark Aurel A1 - Rupprecht, Jens A1 - Idoine, Adam A1 - Veyel, Daniel A1 - Pal, Sunil Kumar A1 - Yaneva-Roder, Liliya A1 - Winck, Flavia Vischi A1 - Sommer, Frederik A1 - Vosloh, Daniel A1 - Seiwert, Bettina A1 - Erban, Alexander A1 - Burgos, Asdrubal A1 - Arvidsson, Samuel Janne A1 - Schoenfelder, Stephanie A1 - Arnold, Anne A1 - Guenther, Manuela A1 - Krause, Ursula A1 - Lohse, Marc A1 - Kopka, Joachim A1 - Nikoloski, Zoran A1 - Müller-Röber, Bernd A1 - Willmitzer, Lothar A1 - Bock, Ralph A1 - Schroda, Michael A1 - Stitt, Mark T1 - Systems analysis of the response of photosynthesis, metabolism, and growth to an increase in irradiance in the photosynthetic model organism chlamydomonas reinhardtii JF - The plant cell N2 - We investigated the systems response of metabolism and growth after an increase in irradiance in the nonsaturating range in the algal model Chlamydomonas reinhardtii. In a three-step process, photosynthesis and the levels of metabolites increased immediately, growth increased after 10 to 15 min, and transcript and protein abundance responded by 40 and 120 to 240 min, respectively. In the first phase, starch and metabolites provided a transient buffer for carbon until growth increased. This uncouples photosynthesis from growth in a fluctuating light environment. In the first and second phases, rising metabolite levels and increased polysome loading drove an increase in fluxes. Most Calvin-Benson cycle (CBC) enzymes were substrate-limited in vivo, and strikingly, many were present at higher concentrations than their substrates, explaining how rising metabolite levels stimulate CBC flux. Rubisco, fructose-1,6-biosphosphatase, and seduheptulose-1,7-bisphosphatase were close to substrate saturation in vivo, and flux was increased by posttranslational activation. In the third phase, changes in abundance of particular proteins, including increases in plastidial ATP synthase and some CBC enzymes, relieved potential bottlenecks and readjusted protein allocation between different processes. Despite reasonable overall agreement between changes in transcript and protein abundance (R-2 = 0.24), many proteins, including those in photosynthesis, changed independently of transcript abundance. Y1 - 2014 U6 - https://doi.org/10.1105/tpc.114.124537 SN - 1040-4651 SN - 1532-298X VL - 26 IS - 6 SP - 2310 EP - 2350 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Balazadeh, Salma A1 - Schildhauer, Joerg A1 - Araujo, Wagner L. A1 - Munne-Bosch, Sergi A1 - Fernie, Alisdair R. A1 - Proost, Sebastian A1 - Humbeck, Klaus A1 - Müller-Röber, Bernd T1 - Reversal of senescence by N resupply to N-starved Arabidopsis thaliana: transcriptomic and metabolomic consequences JF - Journal of experimental botany N2 - Leaf senescence is a developmentally controlled process, which is additionally modulated by a number of adverse environmental conditions. Nitrogen shortage is a well-known trigger of precocious senescence in many plant species including crops, generally limiting biomass and seed yield. However, leaf senescence induced by nitrogen starvation may be reversed when nitrogen is resupplied at the onset of senescence. Here, the transcriptomic, hormonal, and global metabolic rearrangements occurring during nitrogen resupply-induced reversal of senescence in Arabidopsis thaliana were analysed. The changes induced by senescence were essentially in keeping with those previously described; however, these could, by and large, be reversed. The data thus indicate that plants undergoing senescence retain the capacity to sense and respond to the availability of nitrogen nutrition. The combined data are discussed in the context of the reversibility of the senescence programme and the evolutionary benefit afforded thereby. Future prospects for understanding and manipulating this process in both Arabidopsis and crop plants are postulated. KW - Arabidopsis KW - gene expression KW - metabolomics KW - nitrogen limitation KW - senescence KW - transcriptome Y1 - 2014 U6 - https://doi.org/10.1093/jxb/eru119 SN - 0022-0957 SN - 1460-2431 VL - 65 IS - 14 SP - 3975 EP - 3992 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Arvidsson, Samuel Janne A1 - Perez-Rodriguez, Paulino A1 - Müller-Röber, Bernd T1 - A growth phenotyping pipeline for Arabidopsis thaliana integrating image analysis and rosette area modeling for robust quantification of genotype effects JF - New phytologist : international journal of plant science N2 - To gain a deeper understanding of the mechanisms behind biomass accumulation, it is important to study plant growth behavior. Manually phenotyping large sets of plants requires important human resources and expertise and is typically not feasible for detection of weak growth phenotypes. Here, we established an automated growth phenotyping pipeline for Arabidopsis thaliana to aid researchers in comparing growth behaviors of different genotypes. The analysis pipeline includes automated image analysis of two-dimensional digital plant images and evaluation of manually annotated information of growth stages. It employs linear mixed-effects models to quantify genotype effects on total rosette area and relative leaf growth rate (RLGR) and ANOVAs to quantify effects on developmental times. Using the system, a single researcher can phenotype up to 7000 plants d(-1). Technical variance is very low (typically < 2%). We show quantitative results for the growth-impaired starch-excessmutant sex4-3 and the growth-enhancedmutant grf9. We show that recordings of environmental and developmental variables reduce noise levels in the phenotyping datasets significantly and that careful examination of predictor variables (such as d after sowing or germination) is crucial to avoid exaggerations of recorded phenotypes and thus biased conclusions. KW - development KW - growth KW - leaf area KW - modeling KW - phenotyping Y1 - 2011 U6 - https://doi.org/10.1111/j.1469-8137.2011.03756.x SN - 0028-646X VL - 191 IS - 3 SP - 895 EP - 907 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Lai, Alvina G. A1 - Denton-Giles, Matthew A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. A1 - Dijkwel, Paul P. T1 - Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of arabidopsis thaliana JF - Genome biology and evolution N2 - Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality-drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a similar to 371-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (> 100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions. KW - haplotype KW - allelic variants KW - drafted genomes KW - genome partitioning KW - comparative genomics Y1 - 2011 U6 - https://doi.org/10.1093/gbe/evr038 SN - 1759-6653 VL - 3 IS - 1-2 SP - 627 EP - 640 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Balazadeh, Salma A1 - Kwasniewski, Miroslaw A1 - Caldana, Camila A1 - Mehrnia, Mohammad A1 - Zanor, Maria Ines A1 - Xue, Gang-Ping A1 - Müller-Röber, Bernd T1 - ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana JF - Molecular plant N2 - We report here that ORS1, a previously uncharacterized member of the NAC transcription factor family, controls leaf senescence in Arabidopsis thaliana. Overexpression of ORS1 accelerates senescence in transgenic plants, whereas its inhibition delays it. Genes acting downstream of ORS1 were identified by global expression analysis using transgenic plants producing dexamethasone-inducible ORS1-GR fusion protein. Of the 42 up-regulated genes, 30 (similar to 70%) were previously shown to be up-regulated during age-dependent senescence. We also observed that 32 (similar to 76%) of the ORS1-dependent genes were induced by long-term (4 d), but not short-term (6 h) salinity stress (150 mM NaCl). Furthermore, expression of 16 and 24 genes, respectively, was induced after 1 and 5 h of treatment with hydrogen peroxide (H2O2), a reactive oxygen species known to accumulate during salinity stress. ORS1 itself was found to be rapidly and strongly induced by H2O2 treatment in both leaves and roots. Using in vitro binding site selection, we determined the preferred binding motif of ORS1 and found it to be present in half of the ORS1-dependent genes. ORS1 is a paralog of ORE1/ANAC092/AtNAC2, a previously reported regulator of leaf senescence. Phylogenetic footprinting revealed evolutionary conservation of the ORS1 and ORE1 promoter sequences in different Brassicaceae species, indicating strong positive selection acting on both genes. We conclude that ORS1, similarly to ORE1, triggers expression of senescence-associated genes through a regulatory network that may involve cross-talk with salt- and H2O2-dependent signaling pathways. KW - NAC transcription factor KW - leaf senescence KW - gene expression KW - gene regulatory network KW - hydrogen peroxide Y1 - 2011 U6 - https://doi.org/10.1093/mp/ssq080 SN - 1674-2052 VL - 4 IS - 2 SP - 346 EP - 360 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Kwasniewski, Miroslaw A1 - Wienkoop, Stefanie A1 - Müller-Röber, Bernd T1 - An optimized method for the isolation of nuclei from chlamydomas Reinhardtii (Chlorophyceae) JF - Journal of phycology N2 - The cell nucleus harbors a large number of proteins involved in transcription, RNA processing, chromatin remodeling, nuclear signaling, and ribosome assembly. The nuclear genome of the model alga Chlamydomonas reinhardtii P. A. Dang. was recently sequenced, and many genes encoding nuclear proteins, including transcription factors and transcription regulators, have been identified through computational discovery tools. However, elucidating the specific biological roles of nuclear proteins will require support from biochemical and proteomics data. Cellular preparations with enriched nuclei are important to assist in such analyses. Here, we describe a simple protocol for the isolation of nuclei from Chlamydomonas, based on a commercially available kit. The modifications done in the original protocol mainly include alterations of the differential centrifugation parameters and detergent-based cell lysis. The nuclei-enriched fractions obtained with the optimized protocol show low contamination with mitochondrial and plastid proteins. The protocol can be concluded within only 3 h, and the proteins extracted can be used for gel-based and non-gel-based proteomic approaches. KW - 2D gel electrophoresis KW - algae KW - Chlamydomonas KW - nuclear proteins KW - nucleus KW - proteomics Y1 - 2011 U6 - https://doi.org/10.1111/j.1529-8817.2011.00967.x SN - 0022-3646 VL - 47 IS - 2 SP - 333 EP - 340 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Zhang, Gong A1 - Lukoszek, Radoslaw A1 - Müller-Röber, Bernd A1 - Ignatova, Zoya T1 - Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation JF - Nucleic acids research N2 - In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues. Y1 - 2011 U6 - https://doi.org/10.1093/nar/gkq1257 SN - 0305-1048 VL - 39 IS - 8 SP - 3331 EP - 3339 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Dortay, Hakan A1 - Akula, Usha Madhuri A1 - Westphal, Christin A1 - Sittig, Marie A1 - Müller-Röber, Bernd T1 - High-throughput protein expression using a combination of ligation-independent cloning (LIC) and infrared fluorescent protein (IFP) detection JF - PLoS one N2 - Protein expression in heterologous hosts for functional studies is a cumbersome effort. Here, we report a superior platform for parallel protein expression in vivo and in vitro. The platform combines highly efficient ligation-independent cloning (LIC) with instantaneous detection of expressed proteins through N- or C-terminal fusions to infrared fluorescent protein (IFP). For each open reading frame, only two PCR fragments are generated (with three PCR primers) and inserted by LIC into ten expression vectors suitable for protein expression in microbial hosts, including Escherichia coli, Kluyveromyces lactis, Pichia pastoris, the protozoon Leishmania tarentolae, and an in vitro transcription/translation system. Accumulation of IFP-fusion proteins is detected by infrared imaging of living cells or crude protein extracts directly after SDS-PAGE without additional processing. We successfully employed the LIC-IFP platform for in vivo and in vitro expression of ten plant and fungal proteins, including transcription factors and enzymes. Using the IFP reporter, we additionally established facile methods for the visualisation of protein-protein interactions and the detection of DNA-transcription factor interactions in microtiter and gel-free format. We conclude that IFP represents an excellent reporter for high-throughput protein expression and analysis, which can be easily extended to numerous other expression hosts using the setup reported here. Y1 - 2011 U6 - https://doi.org/10.1371/journal.pone.0018900 SN - 1932-6203 VL - 6 IS - 4 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Banks, Jo Ann A1 - Nishiyama, Tomoaki A1 - Hasebe, Mitsuyasu A1 - Bowman, John L. A1 - Gribskov, Michael A1 - dePamphilis, Claude A1 - Albert, Victor A. A1 - Aono, Naoki A1 - Aoyama, Tsuyoshi A1 - Ambrose, Barbara A. A1 - Ashton, Neil W. A1 - Axtell, Michael J. A1 - Barker, Elizabeth A1 - Barker, Michael S. A1 - Bennetzen, Jeffrey L. A1 - Bonawitz, Nicholas D. A1 - Chapple, Clint A1 - Cheng, Chaoyang A1 - Correa, Luiz Gustavo Guedes A1 - Dacre, Michael A1 - DeBarry, Jeremy A1 - Dreyer, Ingo A1 - Elias, Marek A1 - Engstrom, Eric M. A1 - Estelle, Mark A1 - Feng, Liang A1 - Finet, Cedric A1 - Floyd, Sandra K. A1 - Frommer, Wolf B. A1 - Fujita, Tomomichi A1 - Gramzow, Lydia A1 - Gutensohn, Michael A1 - Harholt, Jesper A1 - Hattori, Mitsuru A1 - Heyl, Alexander A1 - Hirai, Tadayoshi A1 - Hiwatashi, Yuji A1 - Ishikawa, Masaki A1 - Iwata, Mineko A1 - Karol, Kenneth G. A1 - Koehler, Barbara A1 - Kolukisaoglu, Uener A1 - Kubo, Minoru A1 - Kurata, Tetsuya A1 - Lalonde, Sylvie A1 - Li, Kejie A1 - Li, Ying A1 - Litt, Amy A1 - Lyons, Eric A1 - Manning, Gerard A1 - Maruyama, Takeshi A1 - Michael, Todd P. A1 - Mikami, Koji A1 - Miyazaki, Saori A1 - Morinaga, Shin-ichi A1 - Murata, Takashi A1 - Müller-Röber, Bernd A1 - Nelson, David R. A1 - Obara, Mari A1 - Oguri, Yasuko A1 - Olmstead, Richard G. A1 - Onodera, Naoko A1 - Petersen, Bent Larsen A1 - Pils, Birgit A1 - Prigge, Michael A1 - Rensing, Stefan A. A1 - Mauricio Riano-Pachon, Diego A1 - Roberts, Alison W. A1 - Sato, Yoshikatsu A1 - Scheller, Henrik Vibe A1 - Schulz, Burkhard A1 - Schulz, Christian A1 - Shakirov, Eugene V. A1 - Shibagaki, Nakako A1 - Shinohara, Naoki A1 - Shippen, Dorothy E. A1 - Sorensen, Iben A1 - Sotooka, Ryo A1 - Sugimoto, Nagisa A1 - Sugita, Mamoru A1 - Sumikawa, Naomi A1 - Tanurdzic, Milos A1 - Theissen, Guenter A1 - Ulvskov, Peter A1 - Wakazuki, Sachiko A1 - Weng, Jing-Ke A1 - Willats, William W. G. T. A1 - Wipf, Daniel A1 - Wolf, Paul G. A1 - Yang, Lixing A1 - Zimmer, Andreas D. A1 - Zhu, Qihui A1 - Mitros, Therese A1 - Hellsten, Uffe A1 - Loque, Dominique A1 - Otillar, Robert A1 - Salamov, Asaf A1 - Schmutz, Jeremy A1 - Shapiro, Harris A1 - Lindquist, Erika A1 - Lucas, Susan A1 - Rokhsar, Daniel A1 - Grigoriev, Igor V. T1 - The selaginella genome identifies genetic changes associated with the evolution of vascular plants JF - Science N2 - Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes. Y1 - 2011 U6 - https://doi.org/10.1126/science.1203810 SN - 0036-8075 VL - 332 IS - 6032 SP - 960 EP - 963 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - JOUR A1 - Dortay, Hakan A1 - Schmöckel, Sandra M. A1 - Fettke, Jörg A1 - Müller-Röber, Bernd T1 - Expression of human c-reactive protein in different systems and its purification from Leishmania tarentolae JF - Protein expression and purification N2 - With its homo-pentameric structure and calcium-dependent specificity for phosphocholine (PCh), human c-reactive protein (CRP) is produced by the liver and secreted in elevated quantities in response to inflammation. CRP is widely accepted as a cardiac marker, e.g. in point-of-care diagnostics, however, its heterologous expression has proven difficult. Here, we demonstrate the expression of CRP in different Escherichia coli strains as well as by in vitro transcription/translation. Although expression in these systems was straightforward, most of the protein that accumulated was insoluble. We therefore expanded our study to include the expression of CRP in two eukaryotic hosts, namely the yeast Kluyveromyces lactis and the protozoon Leishmania tarentolae. Both expression systems are optimized for secretion of recombinant proteins and here allowed successful expression of soluble CRP. We also demonstrate the purification of recombinant CRP from Leishmania growth medium; the purification of protein expressed from K. lactis was not successful. Functional and intact CRP pentamer is known to interact with PCh in Ca(2+)-dependent manner. In this report we verify the binding specificity of recombinant CRP from L tarentolae (2 mu g/mL culture medium) for PCh. KW - C-reactive protein KW - Protein expression KW - Leishmania KW - In vitro expression KW - Protein purification Y1 - 2011 U6 - https://doi.org/10.1016/j.pep.2011.03.010 SN - 1046-5928 VL - 78 IS - 1 SP - 55 EP - 60 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Maitrejean, Marie A1 - Wudick, Michael M. A1 - Völker, Camilla A1 - Prinsi, Bhakti A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Pedrazzini, Emanuela A1 - Vitale, Alessandro T1 - Assembly and sorting of the tonoplast potassium channel AtTPK1 and its turnover by internalization into the Vacuole JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - The assembly, sorting signals, and turnover of the tonoplast potassium channel AtTPK1 of Arabidopsis (Arabidopsis thaliana) were studied. We used transgenic Arabidopsis expressing a TPK1-green fluorescent protein (GFP) fusion or protoplasts transiently transformed with chimeric constructs based on domain exchange between TPK1 and TPK4, the only TPK family member not located at the tonoplast. The results show that TPK1-GFP is a dimer and that the newly synthesized polypeptides transiently interact with a thus-far unidentified 20-kD polypeptide. A subset of the TPK1-TPK4 chimeras were unable to assemble correctly and these remained located in the endoplasmic reticulum where they interacted with the binding protein chaperone. Therefore, TPK1 must assemble correctly to pass endoplasmic reticulum quality control. Substitution of the cytosolic C terminus of TPK4 with the corresponding domain of TPK1 was sufficient to allow tonoplast delivery, indicating that this domain contains tonoplast sorting information. Pulse-chase labeling indicated that TPK1-GFP has a half-life of at least 24 h. Turnover of the fusion protein involves internalization into the vacuole where the GFP domain is released. This indicates a possible mechanism for the turnover of tonoplast proteins. Y1 - 2011 U6 - https://doi.org/10.1104/pp.111.177816 SN - 0032-0889 VL - 156 IS - 4 SP - 1783 EP - 1796 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Parlitz, Steffi A1 - Kunze, Reinhard A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Regulation of photosynthesis and transcription factor expression by leaf shading and re-illumination in Arabidopsis thaliana leaves JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Leaf senescence of annual plants is a genetically programmed developmental phase. The onset of leaf senescence is however not exclusively determined by tissue age but is modulated by various environmental factors. Shading of individual attached leaves evokes dark-induced senescence. The initiation and progression of dark-induced senescence depend on the plant and the age of the affected leaf, however. In several plant species dark-induced senescence is fully reversible upon re-illumination and the leaves can regreen, but the regreening ability depends on the duration of dark incubation. We studied the ability of Arabidopsis thaliana leaves to regreen after dark-incubation with the aim to identify transcription factors (TFs) that are involved in the regulation of early dark-induced senescence and regreening. Two days shading of individual attached leaves triggers the transition into a pre-senescence state from which the leaves can largely recover. Longer periods of darkness result in irreversible senescence. Large scale qRT-PCR analysis of 1872 TF genes revealed that 649 of them are regulated in leaves during normal development, upon shading or re-illumination. Leaf shading triggered upregulation of 150 TF genes, some of which are involved in controlling senescence. Of those, 39 TF genes were upregulated after two days in the dark and regained pre-shading expression level after two days of re-illumination. Furthermore, a larger number of 422 TF genes were down regulated upon shading. In TF gene clusters with different expression patterns certain TF families are over-represented. KW - Arabidopsis thaliana KW - Dark-induced senescence KW - Expression profiling KW - Regreening KW - Transcription factor Y1 - 2011 U6 - https://doi.org/10.1016/j.jplph.2011.02.001 SN - 0176-1617 VL - 168 IS - 12 SP - 1311 EP - 1319 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair R. T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Balazadeh, Salma A1 - Jaspert, Nils A1 - Arif, Muhammad A1 - Müller-Röber, Bernd A1 - Maurino, Veronica G. T1 - Expression of ROS-responsive genes and transcription factors after metabolic formation of H2O2 in chloroplasts JF - Frontiers in plant science N2 - Glycolate oxidase (GO) catalyses the oxidation of glycolate to glyoxylate, thereby consuming O-2 and producing H2O2. In this work, Arabidopsis thaliana plants expressing GO in the chloroplasts (GO plants) were used to assess the expressional behavior of reactive oxygen species (ROS)-responsive genes and transcription factors (TFs) after metabolic induction of H2O2 formation in chloroplasts. In this organelle, GO uses the glycolate derived from the oxygenase activity of RubisCO. Here, to identify genes responding to an abrupt production of H2O2 in chloroplasts we used quantitative real-time PCR (qRT-PCR) to test the expression of 187 ROS-responsive genes and 1880 TFs after transferring GO and wild-type (WT) plants grown at high CO2 levels to ambient CO2 concentration. Our data revealed coordinated expression changes of genes of specific functional networks 0.5 h after metabolic induction of H2O2 production in GO plants, including the induction of indole glucosinolate and camalexin biosynthesis genes. Comparative analysis using available microarray data suggests that signals for the induction of these genes through H2O2 may originate in the chloroplast. The TF profiling indicated an up-regulation in GO plants of a group of genes involved in the regulation of proanthocyanidin and anthocyanin biosynthesis. Moreover, the upregulation of expression of IF and IF interacting proteins affecting development (e.g., cell division, stem branching, flowering time, flower development) would impact growth and reproductive capacity, resulting in altered development under conditions that promote the formation of H2O2. KW - glycolate oxidase KW - H2O2 KW - ROS-responsive genes KW - transcription factors Y1 - 2012 U6 - https://doi.org/10.3389/fpls.2012.00234 SN - 1664-462X VL - 3 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Winck, Flavia V. A1 - Riano-Pachon, Diego M. A1 - Sommer, Frederik A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - The nuclear proteome of the green alga Chlamydomonas reinhardtii JF - Proteomics N2 - Nuclear proteins play a central role in regulating gene expression. Their identification is important for understanding how the nuclear repertoire changes over time under different conditions. Nuclear proteins are often underrepresented in proteomic studies due to the frequently low abundance of proteins involved in regulatory processes. So far, only few studies describing the nuclear proteome of plant species have been published. Recently, the genome sequence of the unicellular green alga Chlamydomonas reinhardtii has been obtained and annotated, allowing the development of further detailed studies for this organism. However, a detailed description of its nuclear proteome has not been reported so far. Here, we present an analysis of the nuclear proteome of the sequenced Chlamydomonas strain cc503. Using LC-MS/MS, we identified 672 proteins from nuclei isolates with a maximum 1% peptide spectrum false discovery rate. Besides well-known proteins (e.g. histones), transcription factors and other transcriptional regulators (e.g. tubby and HMG) were identified. The presence of protein motifs in nuclear proteins was investigated by computational tools, and specific over-represented protein motifs were identified. This study provides new insights into the complexity of the nuclear environment and reveals novel putative protein targets for further studies of nuclear mechanisms. KW - Nuclear proteomics KW - Plant proteomics KW - Systems biology KW - Transcription factor Y1 - 2012 U6 - https://doi.org/10.1002/pmic.201000782 SN - 1615-9853 VL - 12 IS - 1 SP - 95 EP - 100 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Wang, Wei-Hong A1 - Köhler, Barbara A1 - Cao, Feng-Qiu A1 - Liu, Guo-Wei A1 - Gong, Yuan-Yong A1 - Sheng, Song A1 - Song, Qi-Chao A1 - Cheng, Xiao-Yuan A1 - Garnett, Trevor A1 - Okamoto, Mamoru A1 - Qin, Rui A1 - Müller-Röber, Bernd A1 - Tester, Mark A1 - Liu, Lai-Hua T1 - Rice DUR3 mediates high-affinity urea transport and plays an effective role in improvement of urea acquisition and utilization when expressed in Arabidopsis JF - New phytologist : international journal of plant science N2 - Despite the great agricultural and ecological importance of efficient use of urea-containing nitrogen fertilizers by crops, molecular and physiological identities of urea transport in higher plants have been investigated only in Arabidopsis. We performed short-time urea-influx assays which have identified a low-affinity and high-affinity (Km of 7.55 mu M) transport system for urea-uptake by rice roots (Oryza sativa). A high-affinity urea transporter OsDUR3 from rice was functionally characterized here for the first time among crops. OsDUR3 encodes an integral membrane-protein with 721 amino acid residues and 15 predicted transmembrane domains. Heterologous expression demonstrated that OsDUR3 restored yeast dur3-mutant growth on urea and facilitated urea import with a Km of c. 10 mu M in Xenopus oocytes. Quantitative reverse-transcription polymerase chain reaction (qPCR) analysis revealed upregulation of OsDUR3 in rice roots under nitrogen-deficiency and urea-resupply after nitrogen-starvation. Importantly, overexpression of OsDUR3 complemented the Arabidopsis atdur3-1 mutant, improving growth on low urea and increasing root urea-uptake markedly. Together with its plasma membrane localization detected by green fluorescent protein (GFP)-tagging and with findings that disruption of OsDUR3 by T-DNA reduces rice growth on urea and urea uptake, we suggest that OsDUR3 is an active urea transporter that plays a significant role in effective urea acquisition and utilisation in rice. KW - high-affinity transporter KW - leaf senescence KW - nitrogen remobilization KW - OsDUR3 KW - overexpression KW - rice plant KW - urea transport and utilization Y1 - 2012 U6 - https://doi.org/10.1111/j.1469-8137.2011.03929.x SN - 0028-646X VL - 193 IS - 2 SP - 432 EP - 444 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Omranian, Nooshin A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - PageRank-based identification of signaling crosstalk from transcriptomics data the case of Arabidopsis thaliana JF - Molecular BioSystems N2 - The levels of cellular organization, from gene transcription to translation to protein-protein interaction and metabolism, operate via tightly regulated mutual interactions, facilitating organismal adaptability and various stress responses. Characterizing the mutual interactions between genes, transcription factors, and proteins involved in signaling, termed crosstalk, is therefore crucial for understanding and controlling cells' functionality. We aim at using high-throughput transcriptomics data to discover previously unknown links between signaling networks. We propose and analyze a novel method for crosstalk identification which relies on transcriptomics data and overcomes the lack of complete information for signaling pathways in Arabidopsis thaliana. Our method first employs a network-based transformation of the results from the statistical analysis of differential gene expression in given groups of experiments under different signal-inducing conditions. The stationary distribution of a random walk (similar to the PageRank algorithm) on the constructed network is then used to determine the putative transcripts interrelating different signaling pathways. With the help of the proposed method, we analyze a transcriptomics data set including experiments from four different stresses/signals: nitrate, sulfur, iron, and hormones. We identified promising gene candidates, downstream of the transcription factors (TFs), associated to signaling crosstalk, which were validated through literature mining. In addition, we conduct a comparative analysis with the only other available method in this field which used a biclustering-based approach. Surprisingly, the biclustering-based approach fails to robustly identify any candidate genes involved in the crosstalk of the analyzed signals. We demonstrate that our proposed method is more robust in identifying gene candidates involved downstream of the signaling crosstalk for species for which large transcriptomics data sets, normalized with the same techniques, are available. Moreover, unlike approaches based on biclustering, our approach does not rely on any hidden parameters. Y1 - 2012 U6 - https://doi.org/10.1039/c2mb05365a SN - 1742-206X VL - 8 IS - 4 SP - 1121 EP - 1127 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schmidt, Romy A1 - Schippers, Jos H. M. A1 - Welker, Annelie A1 - Mieulet, Delphine A1 - Guiderdoni, Emmanuel A1 - Müller-Röber, Bernd T1 - Transcription factor OsHsfC1b regulates salt tolerance and development in Oryza sativa ssp japonica JF - AoB PLANTS N2 - Background and aims Salt stress leads to attenuated growth and productivity in rice. Transcription factors like heat shock factors (HSFs) represent central regulators of stress adaptation. Heat shock factors of the classes A and B are well established as regulators of thermal and non-thermal stress responses in plants; however, the role of class C HSFs is unknown. Here we characterized the function of the OsHsfC1b (Os01g53220) transcription factor from rice. Methodology We analysed the expression of OsHsfC1b in the rice japonica cultivars Dongjin and Nipponbare exposed to salt stress as well as after mannitol, abscisic acid (ABA) and H2O2 treatment. For functional characterization of OsHsfC1b, we analysed the physiological response of a T-DNA insertion line (hsfc1b) and two artificial micro-RNA (amiRNA) knock-down lines to salt, mannitol and ABA treatment. In addition, we quantified the expression of small Heat Shock Protein (sHSP) genes and those related to signalling and ion homeostasis by quantitative real-time polymerase chain reaction in roots exposed to salt. The subcellular localization of OsHsfC1b protein fused to green fluorescent protein (GFP) was determined in Arabidopsis mesophyll cell protoplasts. Principal results Expression of OsHsfC1b was induced by salt, mannitol and ABA, but not by H2O2. Impaired function of OsHsfC1b in the hsfc1b mutant and the amiRNA lines led to decreased salt and osmotic stress tolerance, increased sensitivity to ABA, and temporal misregulation of salt-responsive genes involved in signalling and ion homeostasis. Furthermore, sHSP genes showed enhanced expression in knock-down plants under salt stress. We observed retarded growth of hsfc1b and knock-down lines in comparison with control plants under non-stress conditions. Transient expression of OsHsfC1b fused to GFP in protoplasts revealed nuclear localization of the transcription factor. Conclusions OsHsfC1b plays a role in ABA-mediated salt stress tolerance in rice. Furthermore, OsHsfC1b is involved in the response to osmotic stress and is required for plant growth under non-stress conditions. Y1 - 2012 U6 - https://doi.org/10.1093/aobpla/pls011 SN - 2041-2851 IS - 3 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wu, Anhui A1 - Allu, Annapurna Devi A1 - Garapati, Prashanth A1 - Siddiqui, Hamad A1 - Dortay, Hakan A1 - Zanor, Maria-Ines A1 - Asensi-Fabado, Maria Amparo A1 - Munne-Bosch, Sergi A1 - Antonio, Carla A1 - Tohge, Takayuki A1 - Fernie, Alisdair R. A1 - Kaufmann, Kerstin A1 - Xue, Gang-Ping A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Jungbrunnen1, a reactive oxygen species-responsive NAC transcription factor, regulates longevity in arabidopsis JF - The plant cell N2 - The transition from juvenility through maturation to senescence is a complex process that involves the regulation of longevity. Here, we identify JUNGBRUNNEN1 (JUB1), a hydrogen peroxide (H2O2)-induced NAC transcription factor, as a central longevity regulator in Arabidopsis thaliana. JUB1 overexpression strongly delays senescence, dampens intracellular H2O2 levels, and enhances tolerance to various abiotic stresses, whereas in jub1-1 knockdown plants, precocious senescence and lowered abiotic stress tolerance are observed. A JUB1 binding site containing a RRYGCCGT core sequence is present in the promoter of DREB2A, which plays an important role in abiotic stress responses. JUB1 transactivates DREB2A expression in mesophyll cell protoplasts and transgenic plants and binds directly to the DREB2A promoter. Transcriptome profiling of JUB1 overexpressors revealed elevated expression of several reactive oxygen species-responsive genes, including heat shock protein and glutathione S-transferase genes, whose expression is further induced by H2O2 treatment. Metabolite profiling identified elevated Pro and trehalose levels in JUB1 overexpressors, in accordance with their enhanced abiotic stress tolerance. We suggest that JUB1 constitutes a central regulator of a finely tuned control system that modulates cellular H2O2 level and primes the plants for upcoming stress through a gene regulatory network that involves DREB2A. Y1 - 2012 U6 - https://doi.org/10.1105/tpc.111.090894 SN - 1040-4651 VL - 24 IS - 2 SP - 482 EP - 506 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Ribeiro, Dimas M. A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis JF - Journal of experimental botany N2 - Although gibberellins (GAs) are well known for their growth control function, little is known about their effects on primary metabolism. Here the modulation of gene expression and metabolic adjustment in response to changes in plant (Arabidopsis thaliana) growth imposed on varying the gibberellin regime were evaluated. Polysomal mRNA populations were profiled following treatment of plants with paclobutrazol (PAC), an inhibitor of GA biosynthesis, and gibberellic acid (GA(3)) to monitor translational regulation of mRNAs globally. Gibberellin levels did not affect levels of carbohydrates in plants treated with PAC and/or GA(3). However, the tricarboxylic acid cycle intermediates malate and fumarate, two alternative carbon storage molecules, accumulated upon PAC treatment. Moreover, an increase in nitrate and in the levels of the amino acids was observed in plants grown under a low GA regime. Only minor changes in amino acid levels were detected in plants treated with GA(3) alone, or PAC plus GA(3). Comparison of the molecular changes at the transcript and metabolite levels demonstrated that a low GA level mainly affects growth by uncoupling growth from carbon availability. These observations, together with the translatome changes, reveal an interaction between energy metabolism and GA-mediated control of growth to coordinate cell wall extension, secondary metabolism, and lipid metabolism. KW - Gibberellin KW - growth KW - paclobutrazol KW - primary metabolism KW - translatome Y1 - 2012 U6 - https://doi.org/10.1093/jxb/err463 SN - 0022-0957 VL - 63 IS - 7 SP - 2769 EP - 2786 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Brotman, Yariv A1 - Landau, Udi A1 - Pnini, Smadar A1 - Lisec, Jan A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Zilberstein, Aviah A1 - Willmitzer, Lothar A1 - Chet, Ilan A1 - Viterbo, Ada T1 - The LysM Receptor-Like Kinase LysM RLK1 is required to activate defense and abiotic-stress responses induced by overexpression of fungal chitinases in arabidopsis plants JF - Molecular plant N2 - Application of crab shell chitin or pentamer chitin oligosaccharide to Arabidopsis seedlings increased tolerance to salinity in wild-type but not in knockout mutants of the LysM Receptor-Like Kinase1 (CERK1/LysM RLK1) gene, known to play a critical role in signaling defense responses induced by exogenous chitin. Arabidopsis plants overexpressing the endochitinase chit36 and hexoaminidase excy1 genes from the fungus Trichoderma asperelleoides T203 showed increased tolerance to salinity, heavy-metal stresses, and Botrytis cinerea infection. Resistant lines, overexpressing fungal chitinases at different levels, were outcrossed to lysm rlk1 mutants. Independent homozygous hybrids lost resistance to biotic and abiotic stresses, despite enhanced chitinase activity. Expression analysis of 270 stress-related genes, including those induced by reactive oxygen species (ROS) and chitin, revealed constant up-regulation (at least twofold) of 10 genes in the chitinase-overexpressing line and an additional 76 salt-induced genes whose expression was not elevated in the lysm rlk1 knockout mutant or the hybrids harboring the mutation. These findings elucidate that chitin-induced signaling mediated by LysM RLK1 receptor is not limited to biotic stress response but also encompasses abiotic-stress signaling and can be conveyed by ectopic expression of chitinases in plants. KW - abiotic stress KW - chitin-induced signaling KW - chitinases KW - LysM receptor kinase KW - Trichoderma Y1 - 2012 U6 - https://doi.org/10.1093/mp/sss021 SN - 1674-2052 VL - 5 IS - 5 SP - 1113 EP - 1124 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Mehterov, Nikolay A1 - Balazadeh, Salma A1 - Hille, Jacques A1 - Toneva, Valentina A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - Oxidative stress provokes distinct transcriptional responses in the stress-tolerant atr7 and stress-sensitive loh2 Arabidopsis thaliana mutants as revealed by multi-parallel quantitative real-time PCR analysis of ROS marker and antioxidant genes JF - Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology N2 - The Arabidopsis thaliana atr7 mutant is tolerant to oxidative stress induced by paraquat (PQ) or the catalase inhibitor aminotriazole (AT), while its original background loh2 and wild-type plants are sensitive. Both, AT and PQ which stimulate the intracellular formation of H2O2 or superoxide anions, respectively, trigger cell death in loh2 but do not lead to visible damage in atr7. To study gene expression during oxidative stress and ROS-induced programmed cell death, two platforms for multi-parallel quantitative real-time PCR (qRT-PCR) analysis of 217 antioxidant and 180 ROS marker genes were employed. The qRT-PCR analyses revealed AT- and PQ-induced expression of many ROS-responsive genes mainly in loh2, confirming that an oxidative burst plays a role in the activation of the cell death in this mutant. Some of the genes were specifically regulated by either AT or PQ serving as markers for particular types of ROS. Genes significantly induced by both AT and PQ in loh2 included transcription factors (ANAC042/JUB1, ANAC102, DREB19, HSFA2, RRTF1, ZAT10, ZAT12, ethylene-responsive factors), signaling compounds, ferritins, alternative oxidases, and antioxidant enzymes. Many of these genes were upregulated in atr7 compared to loh2 under non-stress conditions at the first time point, indicating that higher basal levels of ROS and higher antioxidant capacity in atr7 are responsible for the enhanced tolerance to oxidative stress and suggesting a possible tolerance against multiple stresses of this mutant. KW - Antioxidant genes KW - Reactive oxygen species KW - Stress tolerance KW - Transcription analysis Y1 - 2012 U6 - https://doi.org/10.1016/j.plaphy.2012.05.024 SN - 0981-9428 VL - 59 SP - 20 EP - 29 PB - Elsevier CY - Paris ER - TY - JOUR A1 - Lai, Alvina Grace A1 - Doherty, Colleen J. A1 - Müller-Röber, Bernd A1 - Kay, Steve A. A1 - Schippers, Jos H. M. A1 - Dijkwel, Paul P. T1 - CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in Arabidopsis thaliana. ROS-responsive genes exhibit a time-of-day-specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of EARLY FLOWERING 3, LUX ARRHYTHMO, and TIMING OF CAB EXPRESSION 1 affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by CCA1 and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses. KW - redox homeostasis KW - transcriptional coordination Y1 - 2012 U6 - https://doi.org/10.1073/pnas.1209148109 SN - 0027-8424 VL - 109 IS - 42 SP - 17129 EP - 17134 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Ribeiro, Dimas M. A1 - Araujo, Wagner L. A1 - Fernie, Alisdair R. A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Action of Gibberellins on growth and metabolism of arabidopsis plants Associated with high concentration of carbon dioxide JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Although the positive effect of elevated CO2 concentration [CO2] on plant growth is well known, it remains unclear whether global climate change will positively or negatively affect crop yields. In particular, relatively little is known about the role of hormone pathways in controlling the growth responses to elevated [CO2]. Here, we studied the impact of elevated [CO2] on plant biomass and metabolism in Arabidopsis (Arabidopsis thaliana) in relation to the availability of gibberellins (GAs). Inhibition of growth by the GA biosynthesis inhibitor paclobutrazol (PAC) at ambient [CO2] (350 mu mol CO2 mol(-1)) was reverted by elevated [CO2] (750 mu mol CO2 mol(-1)). Thus, we investigated the metabolic adjustment and modulation of gene expression in response to changes in growth of plants imposed by varying the GA regime in ambient and elevated [CO2]. In the presence of PAC (low-GA regime), the activities of enzymes involved in photosynthesis and inorganic nitrogen assimilation were markedly increased at elevated [CO2], whereas the activities of enzymes of organic acid metabolism were decreased. Under ambient [CO2], nitrate, amino acids, and protein accumulated upon PAC treatment; however, this was not the case when plants were grown at elevated [CO2]. These results suggest that only under ambient [CO2] is GA required for the integration of carbohydrate and nitrogen metabolism underlying optimal biomass determination. Our results have implications concerning the action of the Green Revolution genes in future environmental conditions. Y1 - 2012 U6 - https://doi.org/10.1104/pp.112.204842 SN - 0032-0889 VL - 160 IS - 4 SP - 1781 EP - 1794 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Petrov, Veselin A1 - Schippers, Jos A1 - Benina, Maria A1 - Minkov, Ivan A1 - Müller-Röber, Bernd A1 - Gechev, Tsanko S. T1 - In search for new players of the oxidative stress network by phenotyping an Arabidopsis T-DNA mutant collection on reactive oxygen species-eliciting chemicals JF - Plant omics N2 - The ability of some chemical compounds to cause oxidative stress offers a fast and convenient way to study the responses of plants to reactive oxygen species (ROS). In order to unveil potential novel genetic players of the ROS-regulatory network, a population of similar to 2,000 randomly selected Arabidopsis thaliana T-DNA insertion mutants was screened for ROS sensitivity/resistance by growing seedlings on agar medium supplemented with stress-inducing concentrations of the superoxide-eliciting herbicide methyl viologen or the catalase inhibitor 3-amino-triazole. A semi-robotic setup was used to capture and analyze images of the chemically treated seedlings which helped interpret the screening results by providing quantitative information on seedling area and healthy-to-chlorotic tissue ratios for data verification. A ROS-related phenotype was confirmed in three of the initially selected 33 mutant candidates, which carry T-DNA insertions in genes encoding a Ring/Ubox superfamily protein, ABI5 binding protein 1 (AFP1), previously reported to be involved in ABA signaling, and a protein of unknown function, respectively. In addition, we identified six mutants, most of which have not been described yet, that are related to growth or chloroplast development and show defects in a ROS-independent manner. Thus, semi-automated image capturing and phenotyping applied on publically available T-DNA insertion collections adds a simple means for discovering novel mutants in complex physiological processes and identifying the genes involved. KW - growth KW - image analysis KW - methyl viologen KW - LemnaTec KW - screening KW - superoxide Y1 - 2013 SN - 1836-0661 VL - 6 IS - 1 SP - 46 EP - 54 PB - Southern Cross Publ. CY - Lismore ER - TY - JOUR A1 - Gechev, Tsanko S. A1 - Benina, Maria A1 - Obata, Toshihiro A1 - Tohge, Takayuki A1 - Neerakkal, Sujeeth A1 - Minkov, Ivan A1 - Hille, Jacques A1 - Temanni, Mohamed-Ramzi A1 - Marriott, Andrew S. A1 - Bergström, Ed A1 - Thomas-Oates, Jane A1 - Antonio, Carla A1 - Müller-Röber, Bernd A1 - Schippers, Jos H. M. A1 - Fernie, Alisdair R. A1 - Toneva, Valentina T1 - Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis JF - Cellular and molecular life sciences N2 - Haberlea rhodopensis is a resurrection plant with remarkable tolerance to desiccation. Haberlea exposed to drought stress, desiccation, and subsequent rehydration showed no signs of damage or severe oxidative stress compared to untreated control plants. Transcriptome analysis by next-generation sequencing revealed a drought-induced reprogramming, which redirected resources from growth towards cell protection. Repression of photosynthetic and growth-related genes during water deficiency was concomitant with induction of transcription factors (members of the NAC, NF-YA, MADS box, HSF, GRAS, and WRKY families) presumably acting as master switches of the genetic reprogramming, as well as with an upregulation of genes related to sugar metabolism, signaling, and genes encoding early light-inducible (ELIP), late embryogenesis abundant (LEA), and heat shock (HSP) proteins. At the same time, genes encoding other LEA, HSP, and stress protective proteins were constitutively expressed at high levels even in unstressed controls. Genes normally involved in tolerance to salinity, chilling, and pathogens were also highly induced, suggesting a possible cross-tolerance against a number of abiotic and biotic stress factors. A notable percentage of the genes highly regulated in dehydration and subsequent rehydration were novel, with no sequence homology to genes from other plant genomes. Additionally, an extensive antioxidant gene network was identified with several gene families possessing a greater number of antioxidant genes than most other species with sequenced genomes. Two of the transcripts most abundant during all conditions encoded catalases and five more catalases were induced in water-deficient samples. Using the pharmacological inhibitor 3-aminotriazole (AT) to compromise catalase activity resulted in increased sensitivity to desiccation. Metabolome analysis by GC or LC-MS revealed accumulation of sucrose, verbascose, spermidine, and gamma-aminobutyric acid during drought, as well as particular secondary metabolites accumulating during rehydration. This observation, together with the complex antioxidant system and the constitutive expression of stress protective genes suggests that both constitutive and inducible mechanisms contribute to the extreme desiccation tolerance of H. rhodopensis. KW - Antioxidant genes KW - Catalase KW - Desiccation tolerance KW - Drought stress KW - Metabolome analysis KW - Resurrection plants Y1 - 2013 U6 - https://doi.org/10.1007/s00018-012-1155-6 SN - 1420-682X VL - 70 IS - 4 SP - 689 EP - 709 PB - Springer CY - Basel ER - TY - JOUR A1 - Nguyen, Hung M. A1 - Schippers, Jos H. M. A1 - Goni-Ramos, Oscar A1 - Christoph, Mathias P. A1 - Dortay, Hakan A1 - van der Hoorn, Renier A. L. A1 - Müller-Röber, Bernd T1 - An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana JF - The plant journal N2 - In both animal and plant kingdoms, body size is a fundamental but still poorly understood attribute of biological systems. Here we report that the Arabidopsis NAC transcription factor Regulator of Proteasomal Gene Expression' (RPX) controls leaf size by positively modulating proteasome activity. We further show that the cis-element recognized by RPX is evolutionarily conserved between higher plant species. Upon over-expression of RPX, plants exhibit reduced growth, which may be reversed by a low concentration of the pharmacological proteasome inhibitor MG132. These data suggest that the rate of protein turnover during growth is a critical parameter for determining final organ size. KW - Arabidopsis thaliana KW - organ size KW - evolution KW - leaf development KW - proteasome KW - gene regulatory network Y1 - 2013 U6 - https://doi.org/10.1111/tpj.12097 SN - 0960-7412 VL - 74 IS - 1 SP - 25 EP - 36 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Rauf, Mamoona A1 - Arif, Muhammad A1 - Dortay, Hakan A1 - Matallana-Ramirez, Lilian P. A1 - Waters, Mark T. A1 - Nam, Hong Gil A1 - Lim, Pyung-Ok A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription JF - EMBO reports N2 - Leaf senescence is a key physiological process in all plants. Its onset is tightly controlled by transcription factors, of which NAC factor ORE1 (ANAC092) is crucial in Arabidopsis thaliana. Enhanced expression of ORE1 triggers early senescence by controlling a downstream gene network that includes various senescence-associated genes. Here, we report that unexpectedly ORE1 interacts with the G2-like transcription factors GLK1 and GLK2, which are important for chloroplast development and maintenance, and thereby for leaf maintenance. ORE1 antagonizes GLK transcriptional activity, shifting the balance from chloroplast maintenance towards deterioration. Our finding identifies a new mechanism important for the control of senescence by ORE1. KW - transcription factor KW - senescence KW - chloroplast KW - protein-protein interaction Y1 - 2013 U6 - https://doi.org/10.1038/embor.2013.24 SN - 1469-221X VL - 14 IS - 4 SP - 382 EP - 388 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Omranian, Nooshin A1 - Klie, Sebastian A1 - Müller-Röber, Bernd A1 - Nikoloski, Zoran T1 - Network-based segmentation of biological multivariate time series JF - PLoS one N2 - Molecular phenotyping technologies (e.g., transcriptomics, proteomics, and metabolomics) offer the possibility to simultaneously obtain multivariate time series (MTS) data from different levels of information processing and metabolic conversions in biological systems. As a result, MTS data capture the dynamics of biochemical processes and components whose couplings may involve different scales and exhibit temporal changes. Therefore, it is important to develop methods for determining the time segments in MTS data, which may correspond to critical biochemical events reflected in the coupling of the system's components. Here we provide a novel network-based formalization of the MTS segmentation problem based on temporal dependencies and the covariance structure of the data. We demonstrate that the problem of partitioning MTS data into k segments to maximize a distance function, operating on polynomially computable network properties, often used in analysis of biological network, can be efficiently solved. To enable biological interpretation, we also propose a breakpoint-penalty (BP-penalty) formulation for determining MTS segmentation which combines a distance function with the number/length of segments. Our empirical analyses of synthetic benchmark data as well as time-resolved transcriptomics data from the metabolic and cell cycles of Saccharomyces cerevisiae demonstrate that the proposed method accurately infers the phases in the temporal compartmentalization of biological processes. In addition, through comparison on the same data sets, we show that the results from the proposed formalization of the MTS segmentation problem match biological knowledge and provide more rigorous statistical support in comparison to the contending state-of-the-art methods. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0062974 SN - 1932-6203 VL - 8 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Mehrnia, Mohammad A1 - Balazadeh, Salma A1 - Zanor, Maria-Ines A1 - Müller-Röber, Bernd T1 - EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - We report about ERF BUD ENHANCER (EBE; At5g61890), a transcription factor that affects cell proliferation as well as axillary bud outgrowth and shoot branching in Arabidopsis (Arabidopsis thaliana). EBE encodes a member of the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor superfamily; the gene is strongly expressed in proliferating cells and is rapidly and transiently up-regulated in axillary meristems upon main stem decapitation. Overexpression of EBE promotes cell proliferation in growing calli, while the opposite is observed in EBE-RNAi lines. EBE overexpression also stimulates axillary bud formation and outgrowth, while repressing it results in inhibition of bud growth. Global transcriptome analysis of estradiol-inducible EBE overexpression lines revealed 48 EBE early-responsive genes, of which 14 were up-regulated and 34 were downregulated. EBE activates several genes involved in cell cycle regulation and dormancy breaking, including D-type cyclin CYCD3; 3, transcription regulator DPa, and BRCA1-ASSOCIATED RING DOMAIN1. Among the down-regulated genes were DORMANCY-ASSOCIATED PROTEIN1 (AtDRM1), AtDRM1 homolog, MEDIATOR OF ABA-REGULATED DORMANCY1, and ZINC FINGER HOMEODOMAIN5. Our data indicate that the effect of EBE on shoot branching likely results from an activation of genes involved in cell cycle regulation and dormancy breaking. Y1 - 2013 U6 - https://doi.org/10.1104/pp.113.214049 SN - 0032-0889 VL - 162 IS - 2 SP - 842 EP - 857 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Schmidt, Romy A1 - Mieulet, Delphine A1 - Hubberten, Hans-Michael A1 - Obata, Toshihiro A1 - Höfgen, Rainer A1 - Fernie, Alisdair R. A1 - Fisahn, Joachim A1 - Segundo, Blanca San A1 - Guiderdoni, Emmanuel A1 - Schippers, Jos H. M. A1 - Müller-Röber, Bernd T1 - Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice JF - The plant cell N2 - Early detection of salt stress is vital for plant survival and growth. Still, the molecular processes controlling early salt stress perception and signaling are not fully understood. Here, we identified SALT-RESPONSIVE ERF1 (SERF1), a rice (Oryza sativa) transcription factor (TF) gene that shows a root-specific induction upon salt and hydrogen peroxide (H2O2) treatment. Loss of SERF1 impairs the salt-inducible expression of genes encoding members of a mitogen-activated protein kinase (MAPK) cascade and salt tolerance-mediating TFs. Furthermore, we show that SERF1-dependent genes are H2O2 responsive and demonstrate that SERF1 binds to the promoters of MAPK KINASE KINASE6 (MAP3K6), MAPK5, DEHYDRATION-RESPONSIVE ELEMENT BINDING2A (DREB2A), and ZINC FINGER PROTEIN179 (ZFP179) in vitro and in vivo. SERF1 also directly induces its own gene expression. In addition, SERF1 is a phosphorylation target of MAPK5, resulting in enhanced transcriptional activity of SERF1 toward its direct target genes. In agreement, plants deficient for SERF1 are more sensitive to salt stress compared with the wild type, while constitutive overexpression of SERF1 improves salinity tolerance. We propose that SERF1 amplifies the reactive oxygen species-activated MAPK cascade signal during the initial phase of salt stress and translates the salt-induced signal into an appropriate expressional response resulting in salt tolerance. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.113068 SN - 1040-4651 VL - 25 IS - 6 SP - 2115 EP - 2131 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Watanabe, Mutsumi A1 - Balazadeh, Salma A1 - Tohge, Takayuki A1 - Erban, Alexander A1 - Giavalisco, Patrick A1 - Kopka, Joachim A1 - Müller-Röber, Bernd A1 - Fernie, Alisdair R. A1 - Höfgen, Rainer T1 - Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in arabidopsis JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Developmental senescence is a coordinated physiological process in plants and is critical for nutrient redistribution from senescing leaves to newly formed sink organs, including young leaves and developing seeds. Progress has been made concerning the genes involved and the regulatory networks controlling senescence. The resulting complex metabolome changes during senescence have not been investigated in detail yet. Therefore, we conducted a comprehensive profiling of metabolites, including pigments, lipids, sugars, amino acids, organic acids, nutrient ions, and secondary metabolites, and determined approximately 260 metabolites at distinct stages in leaves and siliques during senescence in Arabidopsis (Arabidopsis thaliana). This provided an extensive catalog of metabolites and their spatiotemporal cobehavior with progressing senescence. Comparison with silique data provides clues to source-sink relations. Furthermore, we analyzed the metabolite distribution within single leaves along the basipetal sink-source transition trajectory during senescence. Ceramides, lysolipids, aromatic amino acids, branched chain amino acids, and stress-induced amino acids accumulated, and an imbalance of asparagine/aspartate, glutamate/glutamine, and nutrient ions in the tip region of leaves was detected. Furthermore, the spatiotemporal distribution of tricarboxylic acid cycle intermediates was already changed in the presenescent leaves, and glucosinolates, raffinose, and galactinol accumulated in the base region of leaves with preceding senescence. These results are discussed in the context of current models of the metabolic shifts occurring during developmental and environmentally induced senescence. As senescence processes are correlated to crop yield, the metabolome data and the approach provided here can serve as a blueprint for the analysis of traits and conditions linking crop yield and senescence. Y1 - 2013 U6 - https://doi.org/10.1104/pp.113.217380 SN - 0032-0889 VL - 162 IS - 3 SP - 1290 EP - 1310 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Read, Betsy A. A1 - Kegel, Jessica A1 - Klute, Mary J. A1 - Kuo, Alan A1 - Lefebvre, Stephane C. A1 - Maumus, Florian A1 - Mayer, Christoph A1 - Miller, John A1 - Monier, Adam A1 - Salamov, Asaf A1 - Young, Jeremy A1 - Aguilar, Maria A1 - Claverie, Jean-Michel A1 - Frickenhaus, Stephan A1 - Gonzalez, Karina A1 - Herman, Emily K. A1 - Lin, Yao-Cheng A1 - Napier, Johnathan A1 - Ogata, Hiroyuki A1 - Sarno, Analissa F. A1 - Shmutz, Jeremy A1 - Schroeder, Declan A1 - de Vargas, Colomban A1 - Verret, Frederic A1 - von Dassow, Peter A1 - Valentin, Klaus A1 - Van de Peer, Yves A1 - Wheeler, Glen A1 - Dacks, Joel B. A1 - Delwiche, Charles F. A1 - Dyhrman, Sonya T. A1 - Glöckner, Gernot A1 - John, Uwe A1 - Richards, Thomas A1 - Worden, Alexandra Z. A1 - Zhang, Xiaoyu A1 - Grigoriev, Igor V. A1 - Allen, Andrew E. A1 - Bidle, Kay A1 - Borodovsky, M. A1 - Bowler, C. A1 - Brownlee, Colin A1 - Cock, J. Mark A1 - Elias, Marek A1 - Gladyshev, Vadim N. A1 - Groth, Marco A1 - Guda, Chittibabu A1 - Hadaegh, Ahmad A1 - Iglesias-Rodriguez, Maria Debora A1 - Jenkins, J. A1 - Jones, Bethan M. A1 - Lawson, Tracy A1 - Leese, Florian A1 - Lindquist, Erika A1 - Lobanov, Alexei A1 - Lomsadze, Alexandre A1 - Malik, Shehre-Banoo A1 - Marsh, Mary E. A1 - Mackinder, Luke A1 - Mock, Thomas A1 - Müller-Röber, Bernd A1 - Pagarete, Antonio A1 - Parker, Micaela A1 - Probert, Ian A1 - Quesneville, Hadi A1 - Raines, Christine A1 - Rensing, Stefan A. A1 - Riano-Pachon, Diego Mauricio A1 - Richier, Sophie A1 - Rokitta, Sebastian A1 - Shiraiwa, Yoshihiro A1 - Soanes, Darren M. A1 - van der Giezen, Mark A1 - Wahlund, Thomas M. A1 - Williams, Bryony A1 - Wilson, Willie A1 - Wolfe, Gordon A1 - Wurch, Louie L. T1 - Pan genome of the phytoplankton Emiliania underpins its global distribution JF - Nature : the international weekly journal of science N2 - Coccolithophores have influenced the global climate for over 200 million years(1). These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems(2). They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space(3). Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean(4). Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions. Y1 - 2013 U6 - https://doi.org/10.1038/nature12221 SN - 0028-0836 SN - 1476-4687 VL - 499 IS - 7457 SP - 209 EP - 213 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Gliwicka, Marta A1 - Nowak, Katarzyna A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd A1 - Gaj, Malgorzata D. T1 - Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana JF - PLoS one N2 - Molecular mechanisms controlling plant totipotency are largely unknown and studies on somatic embryogenesis (SE), the process through which already differentiated cells reverse their developmental program and become embryogenic, provide a unique means for deciphering molecular mechanisms controlling developmental plasticity of somatic cells. Among various factors essential for embryogenic transition of somatic cells transcription factors (TFs), crucial regulators of genetic programs, are believed to play a central role. Herein, we used quantitative real-time polymerase chain reaction (qRT-PCR) to identify TF genes affected during SE induced by in vitro culture in Arabidopsis thaliana. Expression profiles of 1,880 TFs were evaluated in the highly embryogenic Col-0 accession and the non-embryogenic tanmei/emb2757 mutant. Our study revealed 729 TFs whose expression changes during the 10-days incubation period of SE; 141 TFs displayed distinct differences in expression patterns in embryogenic versus non-embryogenic cultures. The embryo-induction stage of SE occurring during the first 5 days of culture was associated with a robust and dramatic change of the TF transcriptome characterized by the drastic up-regulation of the expression of a great majority (over 80%) of the TFs active during embryogenic culture. In contrast to SE induction, the advanced stage of embryo formation showed attenuation and stabilization of transcript levels of many TFs. In total, 519 of the SE-modulated TFs were functionally annotated and transcripts related with plant development, phytohormones and stress responses were found to be most abundant. The involvement of selected TFs in SE was verified using T-DNA insertion lines and a significantly reduced embryogenic response was found for the majority of them. This study provides comprehensive data focused on the expression of TF genes during SE and suggests directions for further research on functional genomics of SE. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0069261 SN - 1932-6203 VL - 8 IS - 7 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Matallana-Ramirez, Lilian P. A1 - Rauf, Mamoona A1 - Farage-Barhom, Sarit A1 - Dortay, Hakan A1 - Xue, Gang-Ping A1 - Droege-Laser, Wolfgang A1 - Lers, Amnon A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis JF - Molecular plant N2 - The NAC transcription factor ORE1 is a key regulator of senescence in Arabidopsis thaliana. Here, we demonstrate that senescence-induced and cell death-associated BIFUNCTIONAL NUCLEASE1 (BFN1) is a direct downstream target of ORE1, revealing a previously unknown regulatory cascade.Senescence is a highly regulated process that involves the action of a large number of transcription factors. The NAC transcription factor ORE1 (ANAC092) has recently been shown to play a critical role in positively controlling senescence in Arabidopsis thaliana; however, no direct target gene through which it exerts its molecular function has been identified previously. Here, we report that BIFUNCTIONAL NUCLEASE1 (BFN1), a well-known senescence-enhanced gene, is directly regulated by ORE1. We detected elevated expression of BFN1 already 2 h after induction of ORE1 in estradiol-inducible ORE1 overexpression lines and 6 h after transfection of Arabidopsis mesophyll cell protoplasts with a 35S:ORE1 construct. ORE1 and BFN1 expression patterns largely overlap, as shown by promoterreporter gene (GUS) fusions, while BFN1 expression in senescent leaves and the abscission zones of maturing flower organs was virtually absent in ore1 mutant background. In vitro binding site assays revealed a bipartite ORE1 binding site, similar to that of ORS1, a paralog of ORE1. A bipartite ORE1 binding site was identified in the BFN1 promoter; mutating the cis-element within the context of the full-length BFN1 promoter drastically reduced ORE1-mediated transactivation capacity in transiently transfected Arabidopsis mesophyll cell protoplasts. Furthermore, chromatin immunoprecipitation (ChIP) demonstrates in vivo binding of ORE1 to the BFN1 promoter. We also demonstrate binding of ORE1 in vivo to the promoters of two other senescence-associated genes, namely SAG29/SWEET15 and SINA1, supporting the central role of ORE1 during senescence. KW - Arabidopsis thaliana KW - senescence KW - transcription factor KW - ORE1 KW - BFN1 KW - promoter Y1 - 2013 U6 - https://doi.org/10.1093/mp/sst012 SN - 1674-2052 VL - 6 IS - 5 SP - 1438 EP - 1452 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Schmidt, Romy A1 - Schippers, Jos H. M. A1 - Mieulet, Delphine A1 - Obata, Toshihiro A1 - Fernie, Alisdair R. A1 - Guiderdoni, Emmanuel A1 - Müller-Röber, Bernd T1 - Multipass, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways JF - The plant journal N2 - Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth. KW - development KW - expansin KW - transcription KW - Oryza sativa KW - hormone KW - abiotic stress Y1 - 2013 U6 - https://doi.org/10.1111/tpj.12286 SN - 0960-7412 SN - 1365-313X VL - 76 IS - 2 SP - 258 EP - 273 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Winck, Flavia Vischi A1 - Arvidsson, Samuel Janne A1 - Mauricio Riano-Pachon, Diego A1 - Hempel, Sabrina A1 - Koseska, Aneta A1 - Nikoloski, Zoran A1 - Urbina Gomez, David Alejandro A1 - Rupprecht, Jens A1 - Müller-Röber, Bernd T1 - Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation JF - PLoS one N2 - The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas. Y1 - 2013 U6 - https://doi.org/10.1371/journal.pone.0079909 SN - 1932-6203 VL - 8 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Lukoszek, Radoslaw A1 - Müller-Röber, Bernd A1 - Ignatova, Zoya T1 - Interplay between polymerase II- and polymerase III-assisted expression of overlapping genes JF - FEBS letters : the journal for rapid publication of short reports in molecular biosciences N2 - Up to 15% of the genes in different genomes overlap. This architecture, although beneficial for the genome size, represents an obstacle for simultaneous transcription of both genes. Here we analyze the interference between RNA-polymerase II (Pol II) and RNA-polymerase III (Pol III) when transcribing their target genes encoded on opposing strands within the same DNA fragment in Arabidopsis thaliana. The expression of a Pol II-dependent protein-coding gene negatively correlated with the transcription of a Pol III-dependent, tRNA-coding gene set. We suggest that the architecture of the overlapping genes introduces an additional layer of control of gene expression. (C) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. KW - Gene expression KW - Transcription KW - tRNA KW - Nested and overlapping genes KW - Arabidopsis thaliana Y1 - 2013 U6 - https://doi.org/10.1016/j.febslet.2013.09.033 SN - 0014-5793 SN - 1873-3468 VL - 587 IS - 22 SP - 3692 EP - 3695 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Rauf, Mamoona A1 - Arif, Muhammad A1 - Fisahn, Joachim A1 - Xue, Gang-Ping A1 - Balazadeh, Salma A1 - Müller-Röber, Bernd T1 - NAC transcription factor speedy hyponastic growth regulates flooding-induced leaf movement in arabidopsis JF - The plant cell N2 - In rosette plants, root flooding (waterlogging) triggers rapid upward (hyponastic) leaf movement representing an important architectural stress response that critically determines plant performance in natural habitats. The directional growth is based on localized longitudinal cell expansion at the lower (abaxial) side of the leaf petiole and involves the volatile phytohormone ethylene (ET). We report the existence of a transcriptional core unit underlying directional petiole growth in Arabidopsis thaliana, governed by the NAC transcription factor SPEEDY HYPONASTIC GROWTH (SHYG). Overexpression of SHYG in transgenic Arabidopsis thaliana enhances waterlogging-triggered hyponastic leaf movement and cell expansion in abaxial cells of the basal petiole region, while both responses are largely diminished in shyg knockout mutants. Expression of several EXPANSIN and XYLOGLUCAN ENDOTRANSGLYCOSYLASE/HYDROLASE genes encoding cell wall-loosening proteins was enhanced in SHYG overexpressors but lowered in shyg. We identified ACC OXIDASE5 (ACO5), encoding a key enzyme of ET biosynthesis, as a direct transcriptional output gene of SHYG and found a significantly reduced leaf movement in response to root flooding in aco5 T-DNA insertion mutants. Expression of SHYG in shoot tissue is triggered by root flooding and treatment with ET, constituting an intrinsic ET-SHYG-ACO5 activator loop for rapid petiole cell expansion upon waterlogging. Y1 - 2013 U6 - https://doi.org/10.1105/tpc.113.117861 SN - 1040-4651 SN - 1532-298X VL - 25 IS - 12 SP - 4941 EP - 4955 PB - American Society of Plant Physiologists CY - Rockville ER - TY - JOUR A1 - Skirycz, Aleksandra A1 - Reichelt, Michael A1 - Burow, Meike A1 - Birkemeyer, Claudia Sabine A1 - Rolcik, Jacub A1 - Kopka, Joachim A1 - Zanor, Maria Ines A1 - Gershenzon, Jonathan A1 - Strnad, Miroslav A1 - Szopa, Jan A1 - Müller-Röber, Bernd A1 - Witt, Isabell T1 - DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis N2 - Glucosinolates are a group of secondary metabolites that function as defense substances against herbivores and micro-organisms in the plant order Capparales. Indole glucosinolates (IGS), derivatives of tryptophan, may also influence plant growth and development. In Arabidopsis thaliana, indole-3-acetaldoxime (IAOx) produced from tryptophan by the activity of two cytochrome P450 enzymes, CYP79B2 and CYP79B3, serves as a precursor for IGS biosynthesis but is also an intermediate in the biosynthetic pathway of indole-3-acetic acid (IAA). Another cytochrome P450 enzyme, CYP83B1, funnels IAOx into IGS. Although there is increasing information about the genes involved in this biochemical pathway, their regulation is not fully understood. OBP2 has recently been identified as a member of the DNA-binding-with-one- finger (DOF) transcription factors, but its function has not been studied in detail so far. Here we report that OBP2 is expressed in the vasculature of all Arabidopsis organs, including leaves, roots, flower stalks and petals. OBP2 expression is induced in response to a generalist herbivore, Spodoptera littoralis, and by treatment with the plant signalling molecule methyl jasmonate, both of which also trigger IGS accumulation. Constitutive and inducible over- expression of OBP2 activates expression of CYP83B1. In addition, auxin concentration is increased in leaves and seedlings of OBP2 over-expression lines relative to wild-type, and plant size is diminished due to a reduction in cell size. RNA interference-mediated OBP2 blockade leads to reduced expression of CYP83B1. Collectively, these data provide evidence that OBP2 is part of a regulatory network that regulates glucosinolate biosynthesis in Arabidopsis Y1 - 2006 UR - http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2006.02767.x/full ER - TY - JOUR A1 - Kreft, Oliver A1 - Georgieva, Radostina A1 - Bäumler, Hans A1 - Steup, Martin A1 - Müller-Röber, Bernd A1 - Sukhorukov, Gleb B. A1 - Möhwald, Helmuth T1 - Red blood cell templated polyelectrolyte capsules : a novel vehicle for the stable encapsulation of DNA and proteins N2 - A novel method for the encapsulation of biomacromolecules, such as nucleic acids and proteins, into polyelectrolyte microcapsules is described. Fluorescence-labelled double-stranded DNA and human serum albumin (HSA) are used as model substances for encapsulation in hollow microcapsules templated on human erythrocytes. The encapsulation procedure involves an intermediate drying C, step. The accumulation of DNA and HSA in the capsules is observed by confocal laser scanning microscopy, UV spectroscopy, and flourimetry. The mechanism of encapsulation is discussed Y1 - 2006 UR - http://www3.interscience.wiley.com/cgi-bin/jhome/10003270 U6 - https://doi.org/10.1002/marc.200500777 SN - 1022-1336 ER - TY - JOUR A1 - Dortay, Hakan A1 - Müller-Röber, Bernd T1 - A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker N2 - Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L Y1 - 2010 UR - http://www.microbialcellfactories.com/home/ U6 - https://doi.org/10.1186/1475-2859-9-29 SN - 1475-2859 ER - TY - JOUR A1 - Balazadeh, Salma A1 - Siddiqui, Hamad A1 - Allu, Annapurna Devi A1 - Matallana-Ramirez, Lilian Paola A1 - Caldana, Camila A1 - Mehrnia, Mohammad A1 - Zanor, Maria-Inés A1 - Koehler, Barbara A1 - Müller-Röber, Bernd T1 - A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence N2 - P>The onset and progression of senescence are under genetic and environmental control. The Arabidopsis thaliana NAC transcription factor ANAC092 (also called AtNAC2 and ORE1) has recently been shown to control age-dependent senescence, but its mode of action has not been analysed yet. To explore the regulatory network administered by ANAC092 we performed microarray-based expression profiling using estradiol-inducible ANAC092 overexpression lines. Approximately 46% of the 170 genes up-regulated upon ANAC092 induction are known senescence-associated genes, suggesting that the NAC factor exerts its role in senescence through a regulatory network that includes many of the genes previously reported to be senescence regulated. We selected 39 candidate genes and confirmed their time-dependent response to enhanced ANAC092 expression by quantitative RT-PCR. We also found that the majority of them (24 genes) are up-regulated by salt stress, a major promoter of plant senescence, in a manner similar to that of ANAC092, which itself is salt responsive. Furthermore, 24 genes like ANAC092 turned out to be stage-dependently expressed during seed growth with low expression at early and elevated expression at late stages of seed development. Disruption of ANAC092 increased the rate of seed germination under saline conditions, whereas the opposite occurred in respective overexpression plants. We also detected a delay of salinity-induced chlorophyll loss in detached anac092-1 mutant leaves. Promoter-reporter (GUS) studies revealed transcriptional control of ANAC092 expression during leaf and flower ageing and in response to salt stress. We conclude that ANAC092 exerts its functions during senescence and seed germination through partly overlapping target gene sets. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0960-7412 U6 - https://doi.org/10.1111/j.1365-313X.2010.04151.x SN - 0960-7412 ER - TY - JOUR A1 - Naso, Alessia A1 - Dreyer, Ingo A1 - Pedemonte, Laura A1 - Testa, Ilaria A1 - Gomez-Porras, Judith Lucia A1 - Usai, Cesare A1 - Müller-Röber, Bernd A1 - Diaspro, Alberto A1 - Gambale, Franco A1 - Picco, Cristiana T1 - The role of the C-terminus for functional heteromerization of the plant channel KDC1 N2 - Voltage-gated potassium channels are formed by the assembly of four identical (homotetramer) or different (heterotetramer) subunits. Tetramerization of plant potassium channels involves the C-terminus of the protein. We investigated the role of the C-terminus of KDC1, a Shaker-like inward-rectifying K+ channel that does not form functional homomeric channels, but participates in the formation of heteromeric complexes with other potassium alpha- subunits when expressed in Xenopus oocytes. The interaction of KDC1 with KAT1 was investigated using the yeast two- hybrid system, fluorescence and electrophysiological studies. We found that the KDC1-EGFP fusion protein is not targeted to the plasma membrane of Xenopus oocytes unless it is coexpressed with KAT1. Deletion mutants revealed that the KDC1 C- terminus is involved in heteromerization. Two domains of the C-terminus, the region downstream the putative cyclic nucleotide binding domain and the distal part of the C-terminus called K-HA domain, contributed to a different extent to channel assembly. Whereas the first interacting region of the C-terminus was necessary for channel heteromerization, the removal of the distal KHA domain decreased but did not abolish the formation of heteromeric complexes. Similar results were obtained when coexpressing KDC1 with the KAT1-homolog KDC2 from carrots, thus indicating the physiological significance of the KAT1/KDC1 characterization. Electrophysiological experiments showed furthermore that the heteromerization capacity of KDC1 was negatively influenced by the presence of the enhanced green fluorescence protein fusion. Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/00063495 U6 - https://doi.org/10.1016/j.bpj.2009.02.055 SN - 0006-3495 ER - TY - JOUR A1 - Müller-Röber, Bernd A1 - Arvidsson, Samuel Janne T1 - Fertility control : the role of magnesium transporters in pollen development Y1 - 2009 UR - http://www.nature.com/cr/archive/index.html U6 - https://doi.org/10.1038/Cr.2009.82 SN - 1001-0602 ER - TY - JOUR A1 - Gajdanowicz, Pawel A1 - Garcia-Mata, Carlos A1 - Gonzalez, Wendy A1 - Morales-Navarro, Samuel Elïas A1 - Sharma, Tripti A1 - Gonzalez-Nilo, Fernando Danilo A1 - Gutowicz, Jan A1 - Müller-Röber, Bernd A1 - Blatt, Michael R. A1 - Dreyer, Ingo T1 - Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity N2 - The family of voltage-gated potassium channels in plants presumably evolved from a common ancestor and includes both inward-rectifying (K-in) channels that allow plant cells to accumulate K+ and outward-rectifying (K-out) channels that mediate K+ efflux. Despite their close structural similarities, the activity of Kin channels is largely independent of K+ and depends only on the transmembrane voltage, whereas that of K-out channels responds to the membrane voltage and the prevailing extracellular K+ concentration. Gating of potassium channels is achieved by structural rearrangements within the last transmembrane domain (S6). Here we investigated the functional equivalence of the S6 helices of the Kin channel KAT1 and the K-out channel SKOR by domain-swapping and site-directed mutagenesis. Channel mutants and chimeras were analyzed after expression in Xenopus oocytes. We identified two discrete regions that influence gating differently in both channels, demonstrating a lack of functional complementarity between KAT1 and SKOR. Our findings are supported by molecular models of KAT1 and SKOR in the open and closed states. The role of the S6 segment in gating evolved differently during specialization of the two channel subclasses, posing an obstacle for the transfer of the K+-sensor from K-out to K-in channels. Y1 - 2009 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0028-646X U6 - https://doi.org/10.1111/j.1469-8137.2008.02749.x SN - 0028-646X ER - TY - JOUR A1 - Voelker, Camilla A1 - Gomez-Porras, Judith Lucia A1 - Becker, Dirk A1 - Hamamoto, Shin A1 - Uozumi, Nobuyuki A1 - Gambale, Franco A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Dreyer, Ingo T1 - Roles of tandem-pore K plus channels in plants : a puzzle still to be solved N2 - The group of voltage-independent K+ channels in Arabidopsis thaliana consists of six members, five tandem-pore channels (TPK1-TPK5) and a single K-ir-like channel (KCO3). All TPK/KCO channels are located at the vacuolar membrane except for TPK4, which was shown to be a plasma membrane channel in pollen. The vacuolar channels interact with 14-3-3 proteins (also called General Regulating Factors, GRFs), indicating regulation at the level of protein-protein interactions. Here we review current knowledge about these ion channels and their genes, and highlight open questions that need to be urgently addressed in future studies to fully appreciate the physiological functions of these ion channels. Y1 - 2010 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=1435-8603 U6 - https://doi.org/10.1111/j.1438-8677.2010.00353.x SN - 1435-8603 ER - TY - JOUR A1 - Gliwicka, Marta A1 - Balazadeh, Salma A1 - Caldana, Camila A1 - Müller-Röber, Bernd A1 - Gaj, Malgorzata D. T1 - The use of multi-qPCR platform and tan1 mutant in identification of TF genes involved in somatic embryogenesis in Arabidopsis Y1 - 2009 UR - http://www.ib.uj.edu.pl/abc/index.php?d=06 SN - 0001-5296 ER - TY - JOUR A1 - Dreyer, Ingo A1 - Poree, Fabien A1 - Schneider, A. A1 - Mittelstadt, J. A1 - Bertl, Adam A1 - Sentenac, H. A1 - Thibaud, Jean-Baptiste A1 - Müller-Röber, Bernd T1 - Assembly of plant Shaker-like K-out channels requires two distinct sites of the channel alpha-subunit N2 - SKOR and GORK are outward-rectifying plant potassium channels from Arabidopsis thaliana. They belong to the Shaker superfamily of voltage-dependent K+ channels. Channels of this class are composed of four alpha-subunits and subunit assembly is a prerequisite for channel function. In this study the assembly mechanism of SKOR was investigated using the yeast two-hybrid system and functional assays in Xenopus oocytes and in yeast. We demonstrate that SKOR and GORK physically interact and assemble into heteromeric K-out channels. Deletion mutants and chimeric proteins generated from SKOR and the K-in channel alpha-subunit KAT1 revealed that the cytoplasmic C-terminus of SKOR determines channel assembly. Two domains thatchannel a-subunit KAT1 revealed that the cytoplasmic C-terminus of SKOR determines channel assembly. Two domains that are crucial for channel assembly were identified: i), a proximal interacting region comprising a putative cyclic nucleotide-binding domain together with 33 amino acids just upstream of this domain, and ii), a distal interacting region showing some resemblance to the K-T domain of KAT1. Both regions contributed differently to channel assembly. Whereas the proximal interacting region was found to be active on its own, the distal interacting region required an intact proximal interacting region to be active. K-out alpha-subunits did not assemble with K-in alpha-subunits because of the absence of interaction between their assembly sites Y1 - 2004 SN - 0006-3495 ER - TY - JOUR A1 - Becker, Dirk A1 - Geiger, D. A1 - Dunkel, M. A1 - Roller, A. A1 - Bertl, Adam A1 - Latz, A. A1 - Carpaneto, Armando A1 - Dietrich, Peter A1 - Roelfsema, M. R. G. A1 - Voelker, C. A1 - Schmidt, D. A1 - Müller-Röber, Bernd A1 - Czempinski, Katrin A1 - Hedrich, R. T1 - AtTPK4, an Arabidopsis tandem-pore K+ channel, poised to control the pollen membrane voltage in a pH- and Ca2+- dependent manner N2 - The Arabidopsis tandem-pore K+ (TPK) channels displaying four transmembrane domains and two pore regions share structural homologies with their animal counterparts of the KCNK family. In contrast to the Shaker-like Arabidopsis channels (six transmembrane domains/one pore region), the functional properties and the biological role of plant TPK channels have not been elucidated yet. Here, we show that AtTPK4 (KCO4) localizes to the plasma membrane and is predominantly expressed in pollen. AtTPK4 (KCO4) resembles the electrical properties of a voltage-independent K+ channel after expression in Xenopus oocytes and yeast. Hyperpolarizing as well as depolarizing membrane voltages elicited instantaneous K+ currents, which were blocked by extracellular calcium and cytoplasmic protons. Functional complementation assays using a K+ transport-deficient yeast confirmed the biophysical and pharmacological properties of the AtTPK4 channel. The features of AtTPK4 point toward a role in potassium homeostasis and membrane voltage control of the growing pollen tube. Thus, AtTPK4 represents a member of plant tandem-pore-K+ channels, resembling the characteristics of its animal counterparts as well as plant-specific features with respect to modulation of channel activity by acidosis and calcium Y1 - 2004 SN - 0027-8424 ER - TY - JOUR A1 - Kohler, B. A1 - Müller-Röber, Bernd T1 - Remote control - cell and organ communication within plants Y1 - 2004 ER - TY - JOUR A1 - Gomez-Merino, Fernando Carlos A1 - Brearley, C. A. A1 - Ornatowska, Magdalena A1 - Abdel-Haliem, Mahmoud E. F. A1 - Zanor, Maria Ines A1 - Müller-Röber, Bernd T1 - AtDGK2, a novel diacylglycerol kinase from Arabidopsis thaliana, phosphorylates 1-stearoyl-2-arachidonoyl-sn- glycerol and 1,2-dioleoyl-sn-glycerol and exhibits cold-inducible gene expression N2 - Diacylglycerol kinase (DGK) phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). Both DAG and PA are implicated in signal transduction pathways. DGKs have been widely studied in animals, but their analysis in plants is fragmentary. Here, we report the cloning and biochemical characterization of AtDGK2, encoding DGK from Arabidopsis thaliana. AtDGK2 has a predicted molecular mass of 79.4 kDa and, like AtDGK1 previously reported, harbors two copies of a phorbol ester/DAG-binding domain in its N-terminal region. AtDGK2 belongs to a family of seven DGK genes in A. thaliana. AtDGK3 to AtDGK7 encode similar to55-kDa DGKs that lack a typical phorbol ester/DAG-binding domain. Phylogenetically, plant DGKs fall into three clusters. Members of all three clusters are widely expressed in vascular plants. Recombinant AtDGK2 was expressed in Escherichia coli and biochemically characterized. The enzyme phosphorylated 1,2-dioleoyl-sn-glycerol to yield PA, exhibiting Michaelis-Menten type kinetics. Estimated K-m and V-max values were 125 muM for DAG and 0.25 pmol of PA min(-1) mug(-1), respectively. The enzyme was maximally active at pH 7.2. Its activity was Mg2+-dependent and affected by the presence of detergents, salts, and the DGK inhibitor R59022, but not by Ca2+. AtDGK2 exhibited substrate preference for unsaturated DAG analogues (i.e. 1-stearoyl-2-arachidonoyl-sn-glycerol and 1,2- dioleoyl-sn-glycerol). The AtDGK2 gene is expressed in various tissues of the Arabidopsis plant, including leaves, roots, and flowers, as shown by Northern blot analysis and promoter-reporter gene fusions. We found that AtDGK2 is induced by exposure to low temperature (4degreesC), pointing to a role in cold signal transduction Y1 - 2004 SN - 0021-9258 ER - TY - JOUR A1 - Witt, Isabell A1 - Zanor, Maria Ines A1 - Müller-Röber, Bernd T1 - Transcription factor function search : how do individual factors regulate agronomical important processes in plants? (Subproject A) Y1 - 2004 SN - 3-00-011587-0 ER - TY - JOUR A1 - Xu, J. A1 - Brearley, C. A. A1 - Lin, W. H. A1 - Wang, Y. A1 - Ye, R. A1 - Müller-Röber, Bernd A1 - Xu, Z. H. A1 - Xue, H. W. T1 - A role of Arabidopsis inositol polyphosphate kinase, AtIPK2 alpha, in pollen germination and root growth N2 - Inositol polyphosphates, such as inositol trisphosphate, are pivotal intracellular signaling molecules in eukaryotic cells. In higher plants the mechanism for the regulation of the type and the level of these signaling molecules is poorly understood. In this study we investigate the physiological function of an Arabidopsis (Arabidopsis thaliana) gene encoding inositol polyphosphate kinase (AtIPK2alpha), which phosphorylates inositol 1,4,5-trisphosphate successively at the D-6 and D-3 positions, and inositol 1,3,4,5-tetrakisphosphate at D-6, resulting in the generation of inositol 1,3,4,5,6-pentakisphosphate. Semiquantitative reverse transcription-PCR and promoter-beta-glucuronidase reporter gene analyses showed that AtIPK2alpha is expressed in various tissues, including roots and root hairs, stem, leaf, pollen grains, pollen tubes, the flower stigma, and siliques. Transgenic Arabidopsis plants expressing the AtIPK2alpha antisense gene under its own promoter were generated. Analysis of several independent transformants exhibiting strong reduction in AtIPK2alpha transcript levels showed that both pollen germination and pollen tube growth were enhanced in the antisense lines compared to wild-type plants, especially in the presence of nonoptimal low Ca2+ concentrations in the culture medium. Furthermore, root growth and root hair development were also stimulated in the antisense lines, in the presence of elevated external Ca2+ concentration or upon the addition of EGTA. In addition, seed germination and early seedling growth was stimulated in the antisense lines. These observations suggest a general and important role of AtIPK2alpha, and hence inositol polyphosphate metabolism, in the regulation of plant growth most likely through the regulation of calcium signaling, consistent with the well-known function of inositol trisphosphate in the mobilization of intracellular calcium stores Y1 - 2005 SN - 0032-0889 ER - TY - JOUR A1 - Riano-Pachon, Diego Mauricio A1 - Dreyer, Ingo A1 - Müller-Röber, Bernd T1 - Orphan transcripts in Arabidopsis thaliana : identification of several hundred previously unrecognized genes N2 - Expressed sequence tags (ESTs) represent a huge resource for the discovery of previously unknown genetic information and functional genome assignment. In this study we screened a collection of 178 292 ESTs from Arabidopsis thaliana by testing them against previously annotated genes of the Arabidopsis genome. We identified several hundreds of new transcripts that match the Arabidopsis genome at so far unassigned loci. The transcriptional activity of these loci was independently confirmed by comparison with the Salk Whole Genome Array Data. To a large extent, the newly identified transcriptionally active genomic regions do not encode 'classic' proteins, but instead generate non-coding RNAs and/or small peptide-coding RNAs of presently unknown biological function. More than 560 transcripts identified in this study are not represented by the Affymetrix GeneChip arrays currently widely used for expression profiling in A. thaliana. Our data strongly support the hypothesis that numerous previously unknown genes exist in the Arabidopsis genome Y1 - 2005 SN - 0960-7412 ER - TY - JOUR A1 - Lin, W. H. A1 - Wang, Y. A1 - Müller-Röber, Bernd A1 - Brearley, C. A. A1 - Xu, Z. H. A1 - Xue, H. W. T1 - At5PTase13 modulates cotyledon vein development through regulating auxin homeostasis N2 - Phosphatidylinositol signaling pathway and the relevant metabolites are known to be critical to the modulation of different aspects of plant growth, development, and stress responses. Inositol polyphosphate 5-phosphatase is a key enzyme involved in phosphatidylinositol metabolism and is encoded by an At5PTase gene family in Arabidopsis thaliana. A previous study shows that At5PTase11 mediates cotyledon vascular development probably through the regulation of intracellular calcium levels. In this study, we provide evidence that At5PTase13 modulates the development of cotyledon veins through its regulation of auxin homeostasis. A T-DNA insertional knockout mutant, At5pt13-1, showed a defect in development of the cotyledon vein, which was rescued completely by exogenous auxin and in part by brassinolide, a steroid hormone. Furthermore, the mutant had reduced auxin content and altered auxin accumulation in seedlings revealed by the DR5:beta-glucuronidase fusion construct in seedlings. In addition, microarray analysis shows that the transcription of key genes responsible for auxin biosynthesis and transport was altered in At5pt13-1. The At5pt13-1 mutant was also less sensitive to auxin inhibition of root elongation. These results suggest that At5PTase13 regulates the homeostasis of auxin, a key hormone controlling vascular development in plants Y1 - 2005 SN - 0032-0889 ER - TY - JOUR A1 - Gomez-Merino, Fernando Carlos A1 - Arana-Ceballos, Fernando Alberto A1 - Trejo-Tellez, L. I. A1 - Skirycz, Aleksandra A1 - Brearley, C. A. A1 - Dormann, P. A1 - Müller-Röber, Bernd T1 - Arabidopsis AtDGK7, the smallest member of plant diacylglycerol kinases (DGKs), displays unique biochemical features and saturates at low substrate concentration : the DGK inhibitor R59022 differentially affects AtDGK2 and AtDGK7 activity in vitro and alters plant growth and development N2 - Diacylglycerol kinase (DGK) regulates the level of the second messenger diacylglycerol and produces phosphatidic acid (PA), another signaling molecule. The Arabidopsis thaliana genome encodes seven putative diacylglycerol kinase isozymes (named AtDGK1 to -7), structurally falling into three major clusters. So far, enzymatic activity has not been reported for any plant Cluster II DGK. Here, we demonstrate that a representative of this cluster, AtDGK7, is biochemically active when expressed as a recombinant protein in Escherichia coli. AtDGK7, encoded by gene locus At4g30340, contains 374 amino acids with an apparent molecular mass of 41.2 kDa. AtDGK7 harbors an N-terminal catalytic domain, but in contrast to various characterized DGKs (including AtDGK2), it lacks a cysteine-rich domain at its N terminus, and, importantly, its C-terminal DGK accessory domain is incomplete. Recombinant AtDGK7 expressed in E. coli exhibits Michaelis-Menten type kinetics with 1,2-dioleoyl-sn-glycerol as substrate. AtDGK7 activity was affected by pH, detergents, and the DGK inhibitor R59022. We demonstrate that both AtDGK2 and AtDGK7 phosphorylate diacylglycerol molecular species that are typically found in plants, indicating that both enzymes convert physiologically relevant substrates. AtDGK7 is expressed throughout the Arabidopsis plant, but expression is strongest in flowers and young seedlings. Expression of AtDGK2 is transiently induced by wounding. R59022 at similar to 80 mu M inhibits root elongation and lateral root formation and reduces plant growth, indicating that DGKs play an important role in plant development Y1 - 2005 SN - 0021-9258 ER - TY - JOUR A1 - Michard, Erwan A1 - Lacombe, Benoît A1 - Poree, Fabien A1 - Müller-Röber, Bernd A1 - Sentenac, Hervé A1 - Thibaud, Jean-Baptiste A1 - Dreyer, Ingo T1 - A unique voltage sensor sensitizes the potassium channel AKT2 to phosphoregulation N2 - Among all voltage-gated K+ channels from the model plant Arabidopsis thaliana, the weakly rectifying K+ channel (K-weak channel) AKT2 displays unique gating properties. AKT2 is exceptionally regulated by phosphorylation: when nonphosphorylated AKT2 behaves as an inward-rectifying potassium channel; phosphorylation of AKT2 abolishes inward rectification by shifting its activation threshold far positive (>200 mV) so that it closes only at voltages positive of + 100 mV. In its phosphorylated form, AKT2 is thus locked in the open state in the entire physiological voltage range. To understand the molecular grounds of this unique gating behavior, we generated chimeras between AKT2 and the conventional inward-rectifying channel KAT1. The transfer of the pore from KAT1 to AKT2 altered the permeation properties of the channel. However, the gating properties were unaffected, suggesting that the pore region of AKT2 is not responsible for the unique K-weak gating. Instead, a lysine residue in S4, highly conserved among all K-weak channels but absent from other plant K+ channels, was pinpointed in a site-directed mutagenesis approach. Substitution of the lysine by serine or aspartate abolished the "open-lock" characteristic and converted AKT2 into an inward- rectifying channel. Interestingly, phosphoregulation of the mutant AKT2-K197S appeared to be similar to that of the K-in channel KAT1: as suggested by mimicking the phosphorylated and dephosphorylated states, phosphorylation induced a shift of the activation threshold of AKT2-K197S by about +50 mV. We conclude that the lysine residue K197 sensitizes AKT2 to phosphoregulation. The phosphorylation-induced reduction of the activation energy in AKT2 is similar to 6 kT larger than in the K197S mutant. It is discussed that this hypersensitive response of AKT2 to phosphorylation equips a cell with the versatility to establish a potassium gradient and to make efficient use of it Y1 - 2005 ER - TY - JOUR A1 - Johansson, Ingela A1 - Wulfetange, Klaas A1 - Poree, Fabien A1 - Michard, Erwan A1 - Gajdanowicz, Pawel A1 - Lacombe, Benoit A1 - Sentenac, Herve A1 - Thibaud, Jean-Baptiste A1 - Müller-Röber, Bernd A1 - Blatt, Michael R. A1 - Dreyer, Ingo T1 - External K+ modulates the activity of the Arabidopsis potassium channel SKOR via an unusual mechanism N2 - Plant outward-rectifying K+ channels mediate K+ efflux from guard cells during stomatal closure and from root cells into the xylem for root-shoot allocation of potassium (K). Intriguingly, the gating of these channels depends on the extracellular K+ concentration, although the ions carrying the current are derived from inside the cell. This K+ dependence confers a sensitivity to the extracellular K+ concentration ([K+]) that ensures that the channels mediate K+ efflux only, regardless of the [K+] prevailing outside. We investigated the mechanism of K+-dependent gating of the K+ channel SKOR of Arabidopsis by site-directed mutagenesis. Mutations affecting the intrinsic K+ dependence of gating were found to cluster in the pore and within the sixth transmembrane helix (S6), identifying an 'S6 gating domain' deep within the membrane. Mapping the SKOR sequence to the crystal structure of the voltage-dependent K+ channel KvAP from Aeropyrum pernix suggested interaction between the S6 gating domain and the base of the pore helix, a prediction supported by mutations at this site. These results offer a unique insight into the molecular basis for a physiologically important K+-sensory process in plants Y1 - 2006 UR - http://www3.interscience.wiley.com/cgi-bin/issn?DESCRIPTOR=PRINTISSN&VALUE=0960-7412 U6 - https://doi.org/10.1111/j.1365-313X.2006.02690.X SN - 0960-7412 ER - TY - JOUR A1 - Feng, Xiao-Li A1 - Ni, Wei-Min A1 - Elge, Stephan A1 - Müller-Röber, Bernd A1 - Xu, Zhi-Hong A1 - Xue, Hong-Wei T1 - Auxin flow in anther filaments is critical for pollen grain development through regulating pollen mitosis N2 - It was well known that auxin is critical for anther/pollen grain development, however, the clear distribution and detailed effects of auxin during floral development are still unclear. We have shown here that, through analyzing GUS activities of Arabidopsis lines harboring auxin response elements DR5-GUS, auxin was mainly accumulated in the anther during flower stages 10-12. Further studies employing the indoleacetic acid-lysine synthetase (iaaL) coding gene from Pseudomonas syringae subsp. savastanoi under control of the promoter region of Arabidopsis phosphatidylinositol monophosphate 5-kinase 1 gene, which conducts the anther filament-specific expression, showed that block of auxin flow of filaments resulted in shortened filaments and significantly defective pollen grains. Similar phenotype was observed in tobacco plants transformed with the same construct, confirming the effects of auxin flow in filaments on anther development. Detailed studies further revealed that the meiosis process of pollen grain was normal while the mitosis at later stage was significantly defected, indicating the effects of auxin flow in filaments on pollen grain mitosis process. Analysis employing [C-14]IAA, as well as the observation on the expression of AtPIN1, coding for auxin efflux carrier, demonstrated the presence of polar auxin transport in anther filaments and pollen grains Y1 - 2006 UR - http://www.springerlink.com/content/100330 U6 - https://doi.org/10.1007/s11103-006-0005-z SN - 0167-4412 ER -