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  -