Submit

Full Research Article

Bhartiya Krishi Anusandhan Patrika, volume 37 issue 1 (march 2022) : 35-42

Genome-wide Identification, Characterization and Expression Profiling of bZIP Gene Family in Wheat using Bioinformatics Approach

Manoj Kumar Sharma, Sachin Kumar, Manoj Kumar Sharma
1Department of Botany, JV College, Baraut-250 611, Baghpat, Uttar Pradesh, India.

  • Submitted06-12-2021|

  • Accepted06-04-2022|

  • First Online 20-04-2022|

  • doi 10.18805/BKAP403

Cite article:- Sharma Kumar Manoj, Kumar Sachin, Sharma Kumar Manoj (2022). Genome-wide Identification, Characterization and Expression Profiling of bZIP Gene Family in Wheat using Bioinformatics Approach. Bhartiya Krishi Anusandhan Patrika. 37(1): 35-42. doi: 10.18805/BKAP403.

ABSTRACT

Background: The basic leucine zipper (bZIP) represents one of the largest as well as most diverse transcription factor (TFs) families, and well-studied for critical role in stress response, growth and sustainable devel opment of the plant.
Methods: In the current study a total of 266 bZIP genes were identified in wheat genome using BLAST algorithm against the fully annotated reference genome (International Wheat Genome Sequencing Consortium - IWGSC) available in Ensembl Plants 42.0 using AtbZIP11 protein from A. thaliana as a query. Coding sequence (CDS) analysis, physicochemical property analysis, homology model ling, structure validation, subcellular localization, phylogenetic analysis and expression profiling has been done to determine bZIP TFs in Triticum aestivum. Overall quality factor of protein has been studied using ERRAT, while expression profiling has been done using Wheat Expression Browser powered by expVIP.
Result: Sequence analysis revealed that the coding sequence (CDS) length of deduced TabZIP TFs genes ranged from 422 to 3669 bp and corresponding protein length ranged from 131 to 649aa. All the 266 genes were studied for the stability of their proteins. 26 out of them were considered further to study their overall quality factor using ERRAT and thereby 13 genes were found to have an ERRAT score of more than 95 for their deduced protein, further studied for their physicochemical properties revealed a molecular weight ranging from 18035.44 to 37304.66 and isoelectric point from 6.08 to 9.42. The subcellular location of all the encoding proteins is found in nucleus. RNA-Seq based expression profiling obtained through Wheat Expression Browser powered by expVIP reveals that many of the identified TabZIP were induced by heat and drought stress. Conclusively the discovered members of bZIP gene family may provide resource for genetic improvement and promote stress tolerance efficiency in wheat.

REFERENCES


  1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI -BLAST: A new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.

  2. Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006). The SWISS -MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics. 22: 195-201.

  3. Bhattacharjee, A., Khurana, J.P. and Jain, M. (2016). Characterization of rice homeobox genes, OsHOX22 and OsHOX24 and over-expression of OsHOX24 in transgenic arabidopsis suggest Their Role in Abiotic Stress Response. Front. Plant Sci. 7: 627. doi:10.3389/fpls.2016.00627.  

  4. Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L. and Schwede, T. (2014). SWISS -MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42: W252-258. doi: 10.1093/nar/gku340. 

  5. Bolser, D., Staines, D.M., Pritchard, E. and Kersey, P. (2016). Ensembl Plants: Integrating tools for visualization, mining and analyzing plant genomics data. Methods Mol. Biol. 1374: 115-140.  doi: 10.1007/978-1-4939-3167-5_6. 

  6. Borrill, P., Ramirez-Gonzalez, R., Uauy, C. (2016). expVIP: A customizable RNA-seq data analysis and visualization platform. Plant Physiology. 170: 2172-2186.

  7. Chou, K.C. and Shen, H.B. (2010). Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization. PLoS ONE. 5(6): e11335. https:/ /doi.org/10.1371/journal.pone.0011335.  

  8. Colovos, C. and Yeates, T.O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Sci. 2: 1511-1519. doi: 10.1002/pro.5560020916.

  9. Deinlein, U., Stephan, A.B., Horie, T., Luo, W., Xu, G. and Schroeder, J.I. (2014). Plant Salt-Tolerance Mechanisms. Trends in Plant Science. 19: 371-379.

  10. FAOSTAT. Food and Agriculture Organization of the United Nations (2020). Available online at: http://www.fao.org/faostat/en/ #data.

  11. Felsenstein, J. (1985). Confidence limits of phylogenies: An approach using the bootstrap. Evolution. 39: 783-791.

  12. Finn, R.D., Atwood, T.K., Babbitt, P.C., Bateman, A., Pork, P., Bridge, A.J., Chang, H.Y.  et al. (2017). InterPro in 2017-beyond protein family and domain annotations, Nucleic Acids Res. 45. D190-D199. https://doi.org/10.1093/nar/gkw1107.  

  13. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D. and Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. In: The Proteomics Protocols Handbook. Springer Protocols Handbooks. [Walker J.M. (eds)]. Humana Press. https://doi.org/10. 1385/1-59259-890-0:571. 

  14. Gupta, P.K., Mir, R.R., Mohan, A. and Kumar, J. (2008). Wheat genomics: Present status and future prospects. International Journal of Plant Genomics. 896451 https://doi.org/10.1155/ 2008/896451.  

  15. Hurst, H.C. (1995). Transcription factors 1: bZIP proteins. Protein Profile. 2(2): 101-68. PMID: 7780801.

  16. Jakoby, M. Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., et al. (2002). bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7(3): 106-11. 

  17. Joshi, R., Wani, S.H., Singh, B., Bohra, A., Dar, Z.A., Lone, A.A., Pareek, A. and Singla-Pareek, S.L. (2016). Transcription factors and plants response to drought stress: Current understanding and future directions. Frontiers in Plant Science. 7: 1029. https://doi.org/10.3389/fpls.2016.01029. 

  18. Kajla, M., Yadav, V.K., Khokhar, J., Singh, S., Chhokar, R.S., Meena, R.P. et al. (2015). Increase in wheat production through management of abiotic stresses: A review, J. Appl. Nat. Sci. 7: 1070-1080.  

  19. Kumar, A., Batra, R., Gahlaut, V., Gautam, T., Kumar, S., Sharma, M., Tyagi, S., Singh, K.P., Balyan, H.S., Pandey, R. and Gupta, P.K. (2018). Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PLoS One. 12;13 (12): e0208409. https://doi.org/10.1371/journal.pone.0208409. 

  20. Kumar, A., Kumar, S., Kumar, A., Sharma, N., Sharma, M., Singh, K.P., Rathore, M. and Gajula, M.N.V.P. (2018). Homology Modeling, Molecular Docking and Molecular Dynamics Based Functional Insights into Rice Urease Bound to Urea. Proceedings of the National Academy of Sciences, India Section B: Biological Sciences. 88: 1539-1548. https:// doi.org/10.1007/s40011-017-0898-0. 

  21. Kumar, A., Kumar, S., Kumar, U., Suravajhala, P. and Gajula, M.N.V.P. (2016). Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach. Computational Biology and Chemistry. 64: 217-226. https://doi.org/ 10.1016/j.compbiolchem.2016.07.008. 

  22. Kumar, A., Mishra, D.C., Rai, A., Sharma, M.K. and Gajula, M.N.V.P. (2013). In -silico analysis of protein-protein interaction between resistance and virulence protein during leaf rust disease in wheat (Triticum aestivum L). World Research Journal of Peptide and Protein. 2: 52-58. 

  23. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics. 23: 2947-2948. 

  24. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993). PROCHECK: A program to check the stereochemical quality of protein structure, J. Appl. Cryst. 26: 283-291. https://doi.org/10.1107/S0021889892009944.

  25. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993). PROCHECK: A programto check the stereochemical quality of protein structure. Journal of Applied Crystallography. 26: 283-291. https://doi.org/10.1107/S0021889892009944. 

  26. Meraj, T.A., Fu, J., Raza, M.A., Zhu, C., Shen, Q., Xu, D. and Wang, Q. (2020). Transcriptional Factors Regulate Plant Stress Responses Through Mediating Secondary Metabolism. Genes. 11: 346. https://doi.org/10.3390/genes11040346. 

  27. Nei, M. and Kumar, S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York. 

  28. Nijhawan, A., Jain, M., Tyagi, A.K. and Khurana, J.P. (2008). Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiology. 146(2): 333-350. 

  29. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. and Ferrin, T.E. (2004). UCSF Chimera visualization system for exploratory research and analysis. Journal of Computational Chemistry. 25: 1605-1612. 

  30. Saitou, N. and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4(4): 406-425. https://doi.org/ 10.1093/oxfordjournals.molbev.a040454.  

  31. Savojardo, C., Martelli, P.L., Fariselli, P., Profiti, G. and Casadio, R. (2018) BUSCA: An integrative web server to predict subcellular localization of proteins. Nucleic Acids Research. 46: W459-466. 

  32. Tamura, K.G. Stecher, D. Peterson, A. Filipski, S. Kumar, MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution. 30(12): 2725-2729. https://doi.org/10.1093/molbev/mst197.   

  33. Wani, S.H., Tripathi, P., Zaid, A., Challa, G.S., Kumar, A., Kumar, V., Upadhyay, J., Joshi, R. and Bhatt, M. (2018). Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.). Plant Molecular Biology. 97: 469-487.
Reviewed By

Download Article
In this Article
    Contact us
    Follow us

    Editorial Board

    View all (0)