35362
2013
2013
eng
46
54
9
1
6
article
Southern Cross Publ.
Lismore
1
--
--
--
In search for new players of the oxidative stress network by phenotyping an Arabidopsis T-DNA mutant collection on reactive oxygen species-eliciting chemicals
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.
Plant omics
1836-0661
wos:2011-2013
WOS:000317715600006
Petrov, V (reprint author), Paisij Hilendarski Univ Plovdiv, Dept Mol Biol & Plant Physiol, 24 Tsar Assen Str, BG-4000 Plovdiv, Bulgaria., vpetrov@plantgene.cn
EC FR7 [245588]
Veselin Petrov
Jos Schippers
Maria Benina
Ivan Minkov
Bernd Müller-Röber
Tsanko S. Gechev
eng
uncontrolled
growth
eng
uncontrolled
image analysis
eng
uncontrolled
methyl viologen
eng
uncontrolled
LemnaTec
eng
uncontrolled
screening
eng
uncontrolled
superoxide
Institut für Biochemie und Biologie
Referiert
35249
2013
2013
eng
689
709
21
4
70
article
Springer
Basel
1
--
--
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Molecular mechanisms of desiccation tolerance in the resurrection glacial relic Haberlea rhodopensis
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.
Cellular and molecular life sciences
10.1007/s00018-012-1155-6
1420-682X
wos:2011-2013
WOS:000314044900006
Gechev, TS (reprint author), Paisij Hilendarski Univ Plovdiv, Dept Plant Physiol & Plant Mol Biol, 24 Tsar Assen Str, BG-4000 Plovdiv, Bulgaria., tsangech@uni-plovdiv.bg
National Science Fund of Bulgaria [DO02-071]; EC [245588]; UK BBSRC
Tsanko S. Gechev
Maria Benina
Toshihiro Obata
Takayuki Tohge
Sujeeth Neerakkal
Ivan Minkov
Jacques Hille
Mohamed-Ramzi Temanni
Andrew S. Marriott
Ed Bergström
Jane Thomas-Oates
Carla Antonio
Bernd Müller-Röber
Jos H. M. Schippers
Alisdair R. Fernie
Valentina Toneva
eng
uncontrolled
Antioxidant genes
eng
uncontrolled
Catalase
eng
uncontrolled
Desiccation tolerance
eng
uncontrolled
Drought stress
eng
uncontrolled
Metabolome analysis
eng
uncontrolled
Resurrection plants
Institut für Biochemie und Biologie
Referiert
35128
2013
2013
eng
25
36
12
1
74
article
Wiley-Blackwell
Hoboken
1
--
--
--
An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana
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.
The plant journal
10.1111/tpj.12097
0960-7412
wos:2011-2013
WOS:000316618500003
Schippers, JHM (reprint author), Univ Potsdam, Dept Mol Biol, Inst Biochem & Biol, Karl Liebknecht Str 24-25,Haus 20, D-14476 Potsdam, Germany., schippers@mpimp-golm.mpg.de; bmr@uni-potsdam.de
Bundesministerium fur Bildung und Forschung; FKZ [0313924]; Vietnam Ministry of Education and Training; Max Planck Society
Hung M. Nguyen
Jos H. M. Schippers
Oscar Goni-Ramos
Mathias P. Christoph
Hakan Dortay
Renier A. L. van der Hoorn
Bernd Müller-Röber
eng
uncontrolled
Arabidopsis thaliana
eng
uncontrolled
organ size
eng
uncontrolled
evolution
eng
uncontrolled
leaf development
eng
uncontrolled
proteasome
eng
uncontrolled
gene regulatory network
Institut für Biochemie und Biologie
Referiert
35121
2013
2013
eng
382
388
7
4
14
article
Nature Publ. Group
London
1
--
--
--
ORE1 balances leaf senescence against maintenance by antagonizing G2-like-mediated transcription
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.
EMBO reports
10.1038/embor.2013.24
1469-221X
wos:2011-2013
WOS:000316981700017
Mueller-Roeber, B (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25,Haus 20, D-14476 Potsdam, Germany., bmr@uni-potsdam.de; balazadeh@mpimp-golm.mpg.de
Deutsche Forschungsgemeinschaft [FOR 948, MU 1199/14-1]
Mamoona Rauf
Muhammad Arif
Hakan Dortay
Lilian P. Matallana-Ramirez
Mark T. Waters
Hong Gil Nam
Pyung-Ok Lim
Bernd Müller-Röber
Salma Balazadeh
eng
uncontrolled
transcription factor
eng
uncontrolled
senescence
eng
uncontrolled
chloroplast
eng
uncontrolled
protein-protein interaction
Institut für Biochemie und Biologie
Referiert
35014
2013
2013
eng
10
5
8
article
PLoS
San Fransisco
1
--
--
--
Network-based segmentation of biological multivariate time series
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.
PLoS one
10.1371/journal.pone.0062974
1932-6203
wos:2011-2013
WOS:000319654700090
Nikoloski, Z (reprint author), Max Planck Inst Mol Plant Physiol, Syst Biol & Math Modeling Grp, Potsdam, Germany., nikoloski@mpimp-golm.mpg.de
Nooshin Omranian
Sebastian Klie
Bernd Müller-Röber
Zoran Nikoloski
Institut für Biochemie und Biologie
Referiert
Open Access
34981
2013
2013
eng
842
857
16
2
162
article
American Society of Plant Physiologists
Rockville
1
--
--
--
EBE, an AP2/ERF transcription factor highly expressed in proliferating cells, affects shoot architecture in arabidopsis
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.
Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
10.1104/pp.113.214049
0032-0889
wos:2011-2013
WOS:000319819900024
Mueller-Roeber, B (reprint author), Max Planck Inst Mol Plant Physiol, Cooperat Res Grp, D-14476 Golm, Germany., bmr@uni-potsdam.de
Mohammad Mehrnia
Salma Balazadeh
Maria-Ines Zanor
Bernd Müller-Röber
Institut für Biochemie und Biologie
Referiert
34954
2013
2013
eng
2115
2131
17
6
25
article
American Society of Plant Physiologists
Rockville
1
--
--
--
Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice
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.
The plant cell
10.1105/tpc.113.113068
1040-4651
wos:2011-2013
WOS:000322371500019
Schippers, JHM (reprint author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany., schippers@mpimp-golm.mpg.de
Bundesministerium fur Bildung und Forschung (BMBF) in Germany
[0313993A]; Agence Nationale de la Recherche in France
[ANR-06-ERAPG-005-01]; Ministerio de Educacion y Ciencia in Spain
[GEN2006-27794-C4-1-E]; Agropolis Foundation; FAZIT Stiftung
Romy Schmidt
Delphine Mieulet
Hans-Michael Hubberten
Toshihiro Obata
Rainer Höfgen
Alisdair R. Fernie
Joachim Fisahn
Blanca San Segundo
Emmanuel Guiderdoni
Jos H. M. Schippers
Bernd Müller-Röber
Institut für Biochemie und Biologie
Referiert
34902
2013
2013
eng
1290
1310
21
3
162
article
American Society of Plant Physiologists
Rockville
1
--
--
--
Comprehensive dissection of spatiotemporal metabolic shifts in primary, secondary, and lipid metabolism during developmental senescence in arabidopsis
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.
Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
10.1104/pp.113.217380
0032-0889
wos:2011-2013
WOS:000321325700007
Watanabe, M (reprint author), Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany., watanabe@mpimp-golm.mpg.de
Deutsche Forschungsgemeinschaft [FOR 948, MU 1199/14-1, MU 1199/14-2, BA4769/1-2]; Max Planck Society
Mutsumi Watanabe
Salma Balazadeh
Takayuki Tohge
Alexander Erban
Patrick Giavalisco
Joachim Kopka
Bernd Müller-Röber
Alisdair R. Fernie
Rainer Höfgen
Institut für Biochemie und Biologie
Referiert
34867
2013
2013
eng
209
213
5
7457
499
article
Nature Publ. Group
London
Emiliania Huxleyi Annotation
1
--
--
--
Pan genome of the phytoplankton Emiliania underpins its global distribution
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.
Nature : the international weekly journal of science
10.1038/nature12221
0028-0836
1476-4687
wos:2011-2013
WOS:000321557600062
Read, BA (reprint author), Calif State Univ San Marcos, Dept Biol Sci, San Marcos, CA 92096 USA., bread@csusm.edu
Office of Science of the US Department of Energy (DOE)
[7DE-AC02-05CH11231]
Betsy A. Read
Jessica Kegel
Mary J. Klute
Alan Kuo
Stephane C. Lefebvre
Florian Maumus
Christoph Mayer
John Miller
Adam Monier
Asaf Salamov
Jeremy Young
Maria Aguilar
Jean-Michel Claverie
Stephan Frickenhaus
Karina Gonzalez
Emily K. Herman
Yao-Cheng Lin
Johnathan Napier
Hiroyuki Ogata
Analissa F. Sarno
Jeremy Shmutz
Declan Schroeder
Colomban de Vargas
Frederic Verret
Peter von Dassow
Klaus Valentin
Yves Van de Peer
Glen Wheeler
Joel B. Dacks
Charles F. Delwiche
Sonya T. Dyhrman
Gernot Glöckner
Uwe John
Thomas Richards
Alexandra Z. Worden
Xiaoyu Zhang
Igor V. Grigoriev
Andrew E. Allen
Kay Bidle
M. Borodovsky
C. Bowler
Colin Brownlee
J. Mark Cock
Marek Elias
Vadim N. Gladyshev
Marco Groth
Chittibabu Guda
Ahmad Hadaegh
Maria Debora Iglesias-Rodriguez
J. Jenkins
Bethan M. Jones
Tracy Lawson
Florian Leese
Erika Lindquist
Alexei Lobanov
Alexandre Lomsadze
Shehre-Banoo Malik
Mary E. Marsh
Luke Mackinder
Thomas Mock
Bernd Müller-Röber
Antonio Pagarete
Micaela Parker
Ian Probert
Hadi Quesneville
Christine Raines
Stefan A. Rensing
Diego Mauricio Riano-Pachon
Sophie Richier
Sebastian Rokitta
Yoshihiro Shiraiwa
Darren M. Soanes
Mark van der Giezen
Thomas M. Wahlund
Bryony Williams
Willie Wilson
Gordon Wolfe
Louie L. Wurch
Institut für Biochemie und Biologie
Referiert
34859
2013
2013
eng
20
7
8
article
PLoS
San Fransisco
1
--
--
--
Extensive Modulation of the Transcription Factor Transcriptome during Somatic Embryogenesis in Arabidopsis thaliana
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.
PLoS one
10.1371/journal.pone.0069261
1932-6203
wos:2011-2013
e69261
WOS:000322000600049
Gaj, MD (reprint author), Univ Silesia, Dept Genet, Katowice, Poland., malgorzata.gaj@us.edu.pl
Polish Ministry of Science and Higher Education [N N301 283537]
Marta Gliwicka
Katarzyna Nowak
Salma Balazadeh
Bernd Müller-Röber
Malgorzata D. Gaj
Institut für Biochemie und Biologie
Referiert
Open Access