TRANSCRIPTOME-WIDE ANALYSIS OF NFX1 TRANSCRIPTION FACTORS IN WHEAT (TRITICUM AESTIVUM L.) AND THEIR LEAF RUST RESPONSIVE EXPRESSION PROFILING
Objective: The purpose of this study was to identify and characterize NFX1 transcription factors (TFs) in wheat and study their expression profiles in response to leaf rust infection.
Methods: NFX1 transcription factors were identified by in silico data-mining, followed by characterisation using different bioinformatics tool. The evolutionary relationship was established by constructing a phylogenetic tree with Arabidopsis NFX1 proteins using Molecular Evolutionary Genetic Analysis (MEGA5). Expression analysis of identified TaNFX1 TFs in wheat was performed using CLC Genomics Workbench.
Results: Nine NFX1 transcription factors were identified in wheat. Evolutionary analysis revealed their classification into group 1, 2 and 4 type NFX1 zinc finger. Tag based expression analysis revealed that based on the fold change values, the maximum level of expression was observed in TaNFX1-3 and 7 whereas, the minimum level of expression was observed in TaNFX1-2 in response to leaf rust pathogenesis. Chromosomal localization predicted that identified NFX1 sequences belonged to 3A, 3B, 3D and 7D chromosomes.
Conclusion: Using transcriptomic approach nine NFX1 TF proteins are predicted that regulate gene expression in response to leaf rust disease in wheat which has not been reported or studied before. Functional and bioinformatics-based exploration of wheat NFX1 TFs in related monocots might provide subsets of candidate target genes to improve agronomic traits related to biotic stress tolerance.
2. Manickavelu A, Kawaura K, Oishi K, Shin IT, Kohara Y, Yahiaoui N, et al. Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum). DNA Res 2012;19:165â€“77.
3. Okay S, Derelli E, Unver T. Transcriptome-wide identification of bread wheat WRKY transcription factors in response to drought stress. Mol Genet Genomics 2014;289:765-81.
4. Aasland R, Gibson TJ, Stewart AF. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci 1995;20:56â€“9.
5. Lisso J, Altmann T, Mussig C. The AtNFXL1 gene encodes a NFX1 type zinc finger protein required for growth under salt stress. FEBS Lett 2006;580:4851-6.
6. Mussig C, Schroder F, Usadel P, Lisso J. Structure and putative function of NFX1-like proteins in plants. Plant Biol 2009;12:381-94.
7. Borden KLB. RING domains: master builders of molecular scaffolds. J Mol Biol 2000;295:1103â€“12.
8. Katoh S, Hong C, Tsunoda Y, Murata K, Takai R, Minami E, et al. High-precision NMR structure and function of the RING-H2 finger domain of EL5, a rice protein whose expression is increased upon exposure to pathogen derived oligosaccharides. J Biol Chem 2003;278:15341â€“8.
9. Mercier P, Lewis MJ, Hau DD, Saltibus LF, Xiao W, Spyracopoulos L. Structure, interactions, and dynamics of the RING domain from human TRAF6. Protein Sci 2007;16:602â€“14.
10. Dodd RB, Allen MD, Brown SE, Sanderson CM, Duncan LM, Lehner PJ, et al. Solution structure of the kaposiâ€™s sarcoma-associated herpesvirus K3 N-terminal domain reveals a novel E2-binding C3HC4-type RING domain. J Biol Chem 2004:279:53840â€“7.
11. Kostic M, Matt T, Martinez-Yamouta MA, Dysona HJ, Wright PE. Solution structure of the Hdm2 C2H2C4 RING, a domain critical for ubiquitination of p53. J Mol Biol 2006;363:433â€“50.
12. Kellenberger E, Dominguez C, Fribourg S, Wasielewski E, Moras D, Poterszman A, et al. Solution structure of the C-terminal domain of TFIIH P44 subunit reveals a novel type of C4C4 ring domain involved in proteinâ€“protein interactions. J Biol Chem 2005;280:20785â€“92.
13. Niu C, Wei W, Zhou Q, Tian A, Hao Y, Zhang W, et al. Wheat WRKY genes TaWRKY2 and TaWRKY19 regulate abiotic stress tolerance in transgenic Arabidopsis plants. Plant Cell Environ 2012;35:1156-70.
14. Xiaoming S, Gaofeng L, Weike D, Tongkun L, Zhinan H, Jun R, et al. Genome-wide identification, classification and expression analysis of the heat shock transcription factor family in Chinese cabbage. Mol Genet Genomics 2014;289:541-51.
15. Satapathy L, Singh D, Ranjan P, Kumar D, Kumar M, Prabhu KV, et al. Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling. Mol Genet Genomics 2014;289:1289-306.
16. Tamura K, Peterson D, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731-9.
17. Bjellqvist B, Basse B, Olsen E, Celis JE. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994;15:529-39.
18. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server. The proteomics protocols handbook, Humana Press; 2005.
19. Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 1999;294:1351-62.
20. Gupta R, Jung E, Brunak S. Prediction of N-glycosylation sites in human proteins. Pac Symp Biocomput 2004;7:310-22.
21. Garg B, Puranik S, Misra S, Tripathy BN, Prasad M. Transcript profiling identifies novel transcripts with unknown functions as primary response components to osmotic stress in wheat (Triticum aestivum L.). Plant Cell Tissue Organ Cult 2013;113:91-101.
22. Nguyen BAN, Pogoutse A, Provart N, Moses AM. NL Stradamus: a simple hidden markov model for nuclear localization signal prediction. BMC Bioinf 2009;10:202.
23. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013;41:808-15.
24. Bipinraj A, Honrao B, Prashar M, Bhardwaj S, Rao S, Tamhankar S. Validation and identification of molecular markers linked to the leaf rust resistance gene Lr28 in wheat. J Appl Genet 2011;52:171-5.
25. Singh D, Bhaganagare G, Bandopadhyay R, Prabhu KV, Gupta PK, Mukhopadhyay K. Targeted spatiotemporal expression based characterization of the state of infection and time-point of maximum defense in wheat NILs during leaf rust infection. Mol Biol Rep 2012;39:9373-82.