Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses

[1]  J. Callis,et al.  Identification and biochemical characterization of the fructokinase gene family in Arabidopsis thaliana , 2017, BMC Plant Biology.

[2]  J. Thelen,et al.  The proteome of higher plant mitochondria. , 2017, Mitochondrion.

[3]  K. Krupinska,et al.  Knockdown of WHIRLY1 Affects Drought Stress-Induced Leaf Senescence and Histone Modifications of the Senescence-Associated Gene HvS40 , 2016, Plants.

[4]  Liisa Holm,et al.  Dali server update , 2016, Nucleic Acids Res..

[5]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[6]  Hsien-Da Huang,et al.  PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants , 2015, Nucleic Acids Res..

[7]  Quan Zhang,et al.  Elevation of Pollen Mitochondrial DNA Copy Number by WHIRLY2: Altered Respiration and Pollen Tube Growth in Arabidopsis1 , 2015, Plant Physiology.

[8]  Don C. Jones,et al.  Small RNA sequencing identifies miRNA roles in ovule and fibre development. , 2015, Plant biotechnology journal.

[9]  G. Hensel,et al.  WHIRLY1 is a major organizer of chloroplast nucleoids , 2014, Front. Plant Sci..

[10]  C. Foyer,et al.  The functions of WHIRLY1 and REDOX-RESPONSIVE TRANSCRIPTION FACTOR 1 in cross tolerance responses in plants: a hypothesis , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.

[11]  J. Franco-Zorrilla,et al.  DNA-binding specificities of plant transcription factors and their potential to define target genes , 2014, Proceedings of the National Academy of Sciences.

[12]  N. Yadav,et al.  MYB transcription factor genes as regulators for plant responses: an overview , 2013, Physiology and Molecular Biology of Plants.

[13]  A. Dziembowski,et al.  The RNA exosome complex central channel controls both exonuclease and endonuclease Dis3 activities in vivo and in vitro , 2013, Nucleic acids research.

[14]  R. Sunkar,et al.  Functions of microRNAs in plant stress responses. , 2012, Trends in plant science.

[15]  A. Fukushima,et al.  Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches1[C][W][OA] , 2012, Plant Physiology.

[16]  H. Koop,et al.  Recombinant Whirly1 translocates from transplastomic chloroplasts to the nucleus , 2012, FEBS letters.

[17]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[18]  A. K. Swami,et al.  Differential proteomic analysis of salt stress response in Sorghum bicolor leaves , 2011 .

[19]  Patrick Xuechun Zhao,et al.  psRNATarget: a plant small RNA target analysis server , 2011, Nucleic Acids Res..

[20]  P. Duque A role for SR proteins in plant stress responses , 2011, Plant signaling & behavior.

[21]  Yoshiyuki Ogata,et al.  Coexpression Analysis of Tomato Genes and Experimental Verification of Coordinated Expression of Genes Found in a Functionally Enriched Coexpression Module , 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.

[22]  Christopher S. Brown,et al.  Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato. , 2010, Plant biotechnology journal.

[23]  Staffan Persson,et al.  Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. , 2009, Plant, cell & environment.

[24]  Yang Xu,et al.  Carbon nanotubes are able to penetrate plant seed coat and dramatically affect seed germination and plant growth. , 2009, ACS nano.

[25]  A. Hitmi,et al.  Expression of stress-related genes in tomato plants exposed to arsenic and chromium in nutrient solution. , 2009, Journal of plant physiology.

[26]  A. Powell,et al.  Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene1[W][OA] , 2009, Plant Physiology.

[27]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[28]  G. Friso,et al.  A member of the Whirly family is a multifunctional RNA- and DNA-binding protein that is essential for chloroplast biogenesis , 2008, Nucleic acids research.

[29]  Peter Widmayer,et al.  Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes , 2008, Adv. Bioinformatics.

[30]  Jean-Sébastien Parent,et al.  Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function , 2008, BMC Plant Biology.

[31]  I. Meier,et al.  Anchorage of Plant RanGAP to the Nuclear Envelope Involves Novel Nuclear-Pore-Associated Proteins , 2007, Current Biology.

[32]  C. J. Adams-Collier,et al.  WoLF PSORT: protein localization predictor , 2007, Nucleic Acids Res..

[33]  V. Valpuesta,et al.  TPR Proteins in Plant Hormone Signaling , 2006, Plant signaling & behavior.

[34]  S. Moss,et al.  Annexins: linking Ca2+ signalling to membrane dynamics , 2005, Nature Reviews Molecular Cell Biology.

[35]  J. Skolnick,et al.  TM-align: a protein structure alignment algorithm based on the TM-score , 2005, Nucleic acids research.

[36]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[37]  D. Desveaux,et al.  Whirly transcription factors: defense gene regulation and beyond. , 2005, Trends in plant science.

[38]  Homin K. Lee,et al.  Coexpression analysis of human genes across many microarray data sets. , 2004, Genome research.

[39]  J. Reyes,et al.  The GATA Family of Transcription Factors in Arabidopsis and Rice1 , 2004, Plant Physiology.

[40]  J. Dangl,et al.  A "Whirly" transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis. , 2004, Developmental cell.

[41]  V. Ambros,et al.  Role of MicroRNAs in Plant and Animal Development , 2003, Science.

[42]  David S. Wishart,et al.  VADAR: a web server for quantitative evaluation of protein structure quality , 2003, Nucleic Acids Res..

[43]  J. Sygusch,et al.  A new family of plant transcription factors displays a novel ssDNA-binding surface , 2002, Nature Structural Biology.

[44]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[45]  D. Desveaux,et al.  PBF-2 Is a Novel Single-Stranded DNA Binding Factor Implicated in PR-10a Gene Activation in Potato , 2000, Plant Cell.

[46]  D. Landsman,et al.  AT-hook motifs identified in a wide variety of DNA-binding proteins. , 1998, Nucleic acids research.

[47]  Christophe Geourjon,et al.  SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments , 1995, Comput. Appl. Biosci..

[48]  R. Dobson,et al.  Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution. , 2017, Sub-cellular biochemistry.

[49]  Q. Meng,et al.  Overexpression of tomato WHIRLY protein enhances tolerance to drought stress and resistance to Pseudomonas solanacearum in transgenic tobacco , 2017, Biologia Plantarum.

[50]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[51]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[52]  T. A. Hall,et al.  BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT , 1999 .

[53]  L. Pauling,et al.  Evolutionary Divergence and Convergence in Proteins , 1965 .

[54]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .