Interactions among plant transcription factors regulating expression of stress-responsive genes

Bioinformatics and Biology Insights

Volumn 8, Issue , 2014, Pages 193-198

  Malhotra, Sony ^a   Sowdhamini, R ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

Arabidopsis thaliana; Docking; Protein protein interactions; Stress conditions; Transcription factors

Indexed keywords

ABSCISIC ACID; ARF PROTEIN; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; PROTEIN MYB; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR BHLH; TRANSCRIPTION FACTOR EREBP; TRANSCRIPTION FACTOR HSF; TRANSCRIPTION FACTOR WRKY; UNCLASSIFIED DRUG;

ARABIDOPSIS THALIANA; ARTICLE; BINDING SITE; COLD STRESS; CONTROLLED STUDY; DROUGHT STRESS; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE INTERACTION; LIGHT STRESS; MOLECULAR DOCKING; NONHUMAN; PLANT GENE; PLANT RESPONSE; PLANT STRESS; PROTEIN PROTEIN INTERACTION; SALT STRESS; SCORING SYSTEM;

EID: 84907615017     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: 10.4137/BBI.S16313     Document Type: Article

References (38)

1. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S. NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res. 2004;32(Database issue):D575–7.
2. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004;136(1):2621–32.
3. Sakurai T, Satou M, Akiyama K, et al. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res. 2005;33(Database issue):D647–50.
4. Button DK, Gartland KMA, Ball LD, Natanson L, Gartland JS, Lyon GD. DRASTIC – INSIGHTS: querying information in a plant gene expression database. Nucleic Acids Res. 2006;34(suppl 1):D712–6.
5. Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA. PLEXdb: gene expression resources for plants and plant pathogens. Nucleic Acids Res. 2011;40(D1):D1194–201.
6. Shinozaki K, Yamaguchi-Shinozaki K. Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol. 2000;3(3):217–23.
7. Chinnusamy V, Schumaker K, Zhu J-K. Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. J Exp Bot. 2004;55(395):225–36.
8. Ludwig AA, Saitoh H, Felix G, et al. Ethylene-mediated cross-talk between calcium-dependent protein kinase and MAPK signaling controls stress responses in plants. Proc Natl Acad Sci U S A. 2005;102(30):10736–41.
9. Smékalová V, Doskočilová A, Komis G, Samaj J. Crosstalk between secondary messengers, hormones and MAPK modules during abiotic stress signalling in plants. Biotechnol Adv. 2014;32(1):2–11.
10. Xiao J, Cheng H, Li X, Xiao J, Xu C, Wang S. Rice WRKY13 regulates cross talk between abiotic and biotic stress signaling pathways by selective binding to different cis-elements. Plant Physiol. 2013;163(4):1868–82.
11. Sharma R, De Vleesschauwer D, Sharma MK, Ronald PC. Recent advances in dissecting stress-regulatory crosstalk in rice. Mol Plant. 2013;6(2):250–60.
12. O’Brien JA, Benková E. Cytokinin cross-talking during biotic and abiotic stress responses. Front Plant Sci. 2013;4:451.
13. Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R. STIFDB-Arabidopsis stress responsive transcription factor database. Int J Plant Genomics. 2009;2009:583429.
14. Sundar AS, Varghese SM, Shameer K, Karaba N, Udayakumar M, Sowdhamini R. STIF: identification of stress-upregulated transcription factor binding sites in Arabidopsis thaliana. Bioinformation. 2008;2(10):431–7.
15. Reményi A, Schöler HR, Wilmanns M. Combinatorial control of gene expression. Nat Struct Mol Biol. 2004;11(9):812–5.
16. Hussain SS, Kayani MA, Amjad M. Transcription factors as tools to engineer enhanced drought stress tolerance in plants. Biotechnol Prog. 2011;27(2):297–306.
17. Levine M, Tjian R. Transcription regulation and animal diversity. Nature. 2003;424(6945):147–51.
18. Hu Z, Gallo SM. Identification of interacting transcription factors regulating tissue gene expression in human. BMC Genomics. 2010;11(1):49.
19. Agarwal PK, Agarwal P, Reddy MK, Sopory SK. Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep. 2006;25(12):1263–74.
20. Singh K, Foley RC, Oñate-Sánchez L. Transcription factors in plant defense and stress responses. Curr Opin Plant Biol. 2002;5(5):430–6.
21. Vinocur B, Altman A. Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol. 2005;16(2):123–32.
22. Malhotra S, Sankar K, Sowdhamini R. Structural interface parameters are discriminatory in recognising near-native poses of protein-protein interactions. PLoS One. 2014;9(2):e80255.
23. Marinescu VD, Kohane IS, Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2005;33(suppl 1):D91–7.
24. Riva A. The MAPPER2 database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res. 2012;40(Database issue):D155–61.
25. Hannenhalli S, Levy S. Predicting transcription factor synergism. Nucleic Acids Res. 2002;30(19):4278–84.
26. Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res. 2000;28(1):235–42.
27. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779–815.
28. Shen M, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15(11):2507–24.
29. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(2):283–91.
30. Tovchigrechko A, Vakser IA. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res. 2006;34(Web Server issue):W310–4.
31. Kuras L, Barbey R, Thomas D. Assembly of a bZIP—bHLH transcription activation complex: formation of the yeast Cbf1–Met4–Met28 complex is regulated through Met28 stimulation of Cbf1 DNA binding. EMBO J. 1997;16(9):2441–51.
32. Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006;34(suppl 1):D535–9.
33. Arabidopsis Interactome Mapping Consortium. Evidence for network evolution in an Arabidopsis interactome map. Science. 2011;333(6042):601–7.
34. Miller G, Mittler R. Could heat shock transcription factors function as hydrogen peroxide sensors in plants? Ann Bot. 2006;98(2):279–88.
35. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 2010;38(suppl 2):W529–33.
36. Pattanaik S, Xie CH, Yuan L. The interaction domains of the plant Myc-like bHLH transcription factors can regulate the transactivation strength. Planta. 2008;227(3):707–15.
37. Shin R, Burch AY, Huppert KA, et al. The Arabidopsis transcription factor MYB77 modulates auxin signal transduction. Plant Cell. 2007;19(8):2440–53.
38. Naika M, Shameer K, Mathew OK, Gowda R, Sowdhamini R. STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol. 2013;54(2):e8.