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  - Scarpeci, Telma E.
A1  - Zanor, Maria I.
A1  - Müller-Röber, Bernd
A1  - Valle, Estela M.
T1  - Overexpression of AtWRKY30 enhances abiotic stress tolerance during
 early growth stages in Arabidopsis thaliana
JF  - PLANT MOLECULAR BIOLOGY
N2  - AtWRKY30 belongs to a higher plant transcription factor superfamily, which responds to pathogen attack. In previous studies, the AtWRKY30 gene was found to be highly and rapidly induced in Arabidopsis thaliana leaves after oxidative stress treatment. In this study, electrophoretic mobility shift assays showed that AtWRKY30 binds with high specificity and affinity to the WRKY consensus sequence (W-box), and also to its own promoter. Analysis of the AtWRKY30 expression pattern by qPCR and using transgenic Arabidopsis lines carrying AtWRKY30 promoter-beta-glucuronidase fusions showed transcriptional activity in leaves subjected to biotic or abiotic stress. Transgenic Arabidopsis plants constitutively overexpressing AtWRKY30 (35S::W30 lines) were more tolerant than wild-type plants to oxidative and salinity stresses during seed germination. The results presented here show that AtWRKY30 is responsive to several stress conditions either from abiotic or biotic origin, suggesting that AtWRKY30 could have a role in the activation of defence responses at early stages of Arabidopsis growth by binding to W-boxes found in promoters of many stress/developmentally regulated genes.
KW  - Antioxidant response
KW  - Chloroplast
KW  - Germination
KW  - Oxidative stress
KW  - Stress signaling
Y1  - 2013
U6  - https://doi.org/10.1007/s11103-013-0090-8
SN  - 0167-4412
VL  - 83
IS  - 3
SP  - 265
EP  - 277
PB  - SPRINGER
CY  - DORDRECHT
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  -