Network Analysis of ABA-dependent and ABA-independent Drought Responsive Genes in Arabidopsis Thaliana

Overview

Journal Genet Mol Biol

Specialty Genetics

Date 2018 Jul 26

PMID 30044467

Citations 41

Authors

Shiwei Liu

Zongyou Lv

Yihui Liu

Ling Li

Lida Zhang

Affiliations

Soon will be listed here.

Abstract

Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

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References

Yoshida T, Mogami J, Yamaguchi-Shinozaki K . ABA-dependent and ABA-independent signaling in response to osmotic stress in plants. Curr Opin Plant Biol. 2014; 21:133-139. DOI: 10.1016/j.pbi.2014.07.009. View

Xiong L, Wang R, Mao G, Koczan J . Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic Acid. Plant Physiol. 2006; 142(3):1065-74. PMC: 1630748. DOI: 10.1104/pp.106.084632. View

Xu Z, Kim S, Hyeon D, Kim D, Dong T, Park Y . The Arabidopsis NAC transcription factor ANAC096 cooperates with bZIP-type transcription factors in dehydration and osmotic stress responses. Plant Cell. 2013; 25(11):4708-24. PMC: 3875745. DOI: 10.1105/tpc.113.119099. View

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C . Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMC: 3685583. DOI: 10.1038/nprot.2007.324. View

Zhang F, Liu S, Li L, Zuo K, Zhao L, Zhang L . Genome-Wide Inference of Protein-Protein Interaction Networks Identifies Crosstalk in Abscisic Acid Signaling. Plant Physiol. 2016; 171(2):1511-22. PMC: 4902594. DOI: 10.1104/pp.16.00057. View

Jin Z, Xue S, Luo Y, Tian B, Fang H, Li H . Hydrogen sulfide interacting with abscisic acid in stomatal regulation responses to drought stress in Arabidopsis. Plant Physiol Biochem. 2012; 62:41-6. DOI: 10.1016/j.plaphy.2012.10.017. View

Harb A, Krishnan A, Ambavaram M, Pereira A . Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiol. 2010; 154(3):1254-71. PMC: 2971604. DOI: 10.1104/pp.110.161752. View

Livak K, Schmittgen T . Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2002; 25(4):402-8. DOI: 10.1006/meth.2001.1262. View

10.

Lee S, Kang J, Park H, Kim M, Bae M, Choi H . DREB2C interacts with ABF2, a bZIP protein regulating abscisic acid-responsive gene expression, and its overexpression affects abscisic acid sensitivity. Plant Physiol. 2010; 153(2):716-27. PMC: 2879808. DOI: 10.1104/pp.110.154617. View

11.

Lin M, Zhou X, Shen X, Mao C, Chen X . The predicted Arabidopsis interactome resource and network topology-based systems biology analyses. Plant Cell. 2011; 23(3):911-22. PMC: 3082272. DOI: 10.1105/tpc.110.082529. View

12.

Choi H, Im M, Kim S . Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. Plant Cell. 2002; 14(2):343-57. PMC: 152917. DOI: 10.1105/tpc.010362. View

13.

Cui J, Li P, Li G, Xu F, Zhao C, Li Y . AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2007; 36(Database issue):D999-1008. PMC: 2238993. DOI: 10.1093/nar/gkm844. View

14.

Christmann A, Moes D, Himmelbach A, Yang Y, Tang Y, Grill E . Integration of abscisic acid signalling into plant responses. Plant Biol (Stuttg). 2006; 8(3):314-25. DOI: 10.1055/s-2006-924120. View

15.

Aoki Y, Okamura Y, Tadaka S, Kinoshita K, Obayashi T . ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. Plant Cell Physiol. 2015; 57(1):e5. PMC: 4722172. DOI: 10.1093/pcp/pcv165. View

16.

Peleg Z, Blumwald E . Hormone balance and abiotic stress tolerance in crop plants. Curr Opin Plant Biol. 2011; 14(3):290-5. DOI: 10.1016/j.pbi.2011.02.001. View

17.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

18.

Sharma R, De Vleesschauwer D, Sharma M, Ronald P . Recent advances in dissecting stress-regulatory crosstalk in rice. Mol Plant. 2013; 6(2):250-60. DOI: 10.1093/mp/sss147. View

19.

Zentella R, Zhang Z, Park M, Thomas S, Endo A, Murase K . Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell. 2007; 19(10):3037-57. PMC: 2174696. DOI: 10.1105/tpc.107.054999. View

20.

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. View