In silico studies predict role of PgUCP1 from Pennisetum glaucum in heat stress tolerance

ALBERT MAIBAM; HARINDER VISHWAKARMA; JASDEEP CHATRATH PADARIA

doi:10.56093/ijas.v89i10.94632

Authors

ALBERT MAIBAM PhD Scholar, ICAR-IARI, New Delhi
HARINDER VISHWAKARMA Research Associate, ICAR-National Institute for Plant Biotechnology, New Delhi 110 012, India
JASDEEP CHATRATH PADARIA Principal Scientist, ICAR-National Institute for Plant Biotechnology, New Delhi 110 012, India

https://doi.org/10.56093/ijas.v89i10.94632

Keywords:

3-Dimensional structure, Heat stress, Pennisetum glaucum, Phylogenetic, Uncharacterized protein

Abstract

Heat stress adversely affects crop plants leading to high yield losses. To protect themselves, plants respond by expressing large number of genes. This includes reported/known genes as well as hypothetical or uncharacterized genes. Genes for uncharacterized or hypothetical proteins form a major proportion of data generated by different functional genomic approaches. It is quite important to assign function to these stress responsive uncharacterized genes for better understanding of stress responsive molecular mechanisms. In the present study, full length coding sequence of a gene for an uncharacterized protein1 PgUCP1 (624 bp) was cloned from pearl millet genotype 841-B (ICMB841) at National Institute for Plant Biotechnology, New Delhi in year 2017â€“18. The gene PgUCP1(Accession number MK33595) was identified in the heat responsive transcriptome data generated in leaf tissue of P. glaucum plants grown in National Phytotron Facility,IARI, New Delhi. The CDS was successfully isolated and cloned in pGEM-T easy vector. The predicted 3-Dimensional structure of PgUCP1 showed that it is able to interact with ligands [AMP (Adenosine monophosphate), ADP (Adenosine diphosphate), ATP (Adenosine triphosphate)] depicting presence of active site residues. Phylogenetic analysis showed PgUCP1 to be closely related to zinc finger protein of Setaria italica. The predicted transcript in this study clearly indicated its role in providing heat stress tolerance. Further, the role of identified transcript can be validated in model plant system under abiotic stress conditions. The gene may be a potent prospective resource for development of abiotic stress tolerant crops.

Downloads

Download data is not yet available.

References

Altschul S F, Gish W, Miller W, Myers E W and Lipman D J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3): 403–10. DOI: https://doi.org/10.1016/S0022-2836(05)80360-2

Artimo P, Jonnalagedda M, Arnold K et al. 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research. 40(Web Server issue):W597-603. DOI: https://doi.org/10.1093/nar/gks400

Chen P H, Chi J T and Boyce M. 2018. Functional crosstalk among oxidative stress and O-GlcNAc signaling pathways. Glycobiology 28(8): 556–64. DOI: https://doi.org/10.1093/glycob/cwy027

Chomczynski P and Sacchi N. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry 162(1): 156–9. DOI: https://doi.org/10.1016/0003-2697(87)90021-2

Craig E A, Gambill B D and Nelson R J. 1993. Heat shock proteins: molecular chaperones of protein biogenesis. Microbiological Reviews 57(2): 402–14. DOI: https://doi.org/10.1128/mr.57.2.402-414.1993

Dang F F, Wang Y N, Yu L. 2013. CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacearum infection. Plant, Cell and Environment 36(4): 757–74. DOI: https://doi.org/10.1111/pce.12011

Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792–7. DOI: https://doi.org/10.1093/nar/gkh340

Gourcilleau D, Lenne C, Armenise C, Moulia B, Julien J, et al. 2011. Phylogenetic study of plant Q-type C2H2 zinc finger proteins and expression analysis of poplar genes in response to osmotic, cold and mechanical stresses. DNA Research 18: 77–92. DOI: https://doi.org/10.1093/dnares/dsr001

Hasanuzzaman M, Nahar K, Alam M M, Roychowdhury R and Fujita M. 2013. Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants. International Journal of Molecular Science 14(5): 9643–84. DOI: https://doi.org/10.3390/ijms14059643

Kodaira K, Qin F, Tran L P, Maruyama K, Kidokoro S. 2011. Arabidopsis Cys2/His2 zinc-finger proteins AZF1 and AZF2 negatively regulate abscisic acid-repressive and auxin-inducible genes under abiotic stress conditions. Plant Physiology 157: 742–56. DOI: https://doi.org/10.1104/pp.111.182683

Kolahi M, Yazdi M, Goldson-Barnaby A and Tabandeh MR. 2018. In silico prediction, phylogenetic and bioinformatic analysis of SoPCS gene, survey of its protein characterization and gene expression in response to cadmium in Saccharum officinarum. Ecotoxicology and Environmental Safety 163: 7–18. DOI: https://doi.org/10.1016/j.ecoenv.2018.07.032

Kolker E, Picone A F and Galperin M Y. 2005. Global profiling of Shewanella oneidensis MR-1: Expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences 102(6): 2099–104. DOI: https://doi.org/10.1073/pnas.0409111102

Kumar S, Stecher G and Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Molecular Biology and Evolution 33(7): 1870–4. DOI: https://doi.org/10.1093/molbev/msw054

Liu H C, Liao H T and Charng Y Y. 2011. The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis. Plant Cell and Environment 34(5): 738–51. DOI: https://doi.org/10.1111/j.1365-3040.2011.02278.x

Maibam A and Padaria J C. 2015. Pearl millet : A Genetic resource for abiotic tolerant transgenics. Biotech Today 5(1): 21–4. DOI: https://doi.org/10.5958/2322-0996.2015.00003.4

Mackay JP and Crossley M. 1998. Zinc fingers are sticking together. Trends in Biochemical Sciences 23: 1–4. DOI: https://doi.org/10.1016/S0968-0004(97)01168-7

McGuffin L J, Bryson K and Jones DT. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16(4): 404–5. DOI: https://doi.org/10.1093/bioinformatics/16.4.404

Ogiso H, Kagi N, Matsumoto E. 2004. Phosphorylation analysis of 90 kDa heat shock protein within the cytosolic arylhydrocarbon receptor complex. Biochemistry 43(49): 15510-15519. DOI: https://doi.org/10.1021/bi048736m

Padaria J C, Vishwakarma H, Biswas K, Jasrotia R S and Singh G P. 2014. Molecular cloning and in silico characterization of high temperature stress responsive pAPX gene isolated from heat tolerant Indian wheat cv. Raj 3765. BMC Research Notes 7(1):713. DOI: https://doi.org/10.1186/1756-0500-7-713

Parthasarathy S and Murthy M R. 2000. Protein thermal stability: Insights from atomic displacement parameters (B values). Protein Engineering 13: 9–13. DOI: https://doi.org/10.1093/protein/13.1.9

Singh SD, Singh P, Rai KN and Andrews DJ. 1990. Registration of ICMA 841 and ICMB 841. Crop Science 36(6): 1378. DOI: https://doi.org/10.2135/cropsci1990.0011183X003000060081x

Wahid A, Gelani S, Ashraf M and Foolad M R. 2007. Heat tolerance in plants: An overview. Environmental and Experimental Botany 61(3):199–223. DOI: https://doi.org/10.1016/j.envexpbot.2007.05.011

Zhang X N, Mount S M. 2009. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development. Plant Physiology 150(3): 1450–8. DOI: https://doi.org/10.1104/pp.109.138180