Indian Journal of Animal Research

  • Chief EditorK.M.L. Pathak

  • Print ISSN 0367-6722

  • Online ISSN 0976-0555

  • NAAS Rating 6.43

  • SJR 0.263

  • Impact Factor 0.5 (2023)

Frequency :
Monthly (January, February, March, April, May, June, July, August, September, October, November and December)
Indexing Services :
Science Citation Index Expanded, BIOSIS Preview, ISI Citation Index, Biological Abstracts, Scopus, AGRICOLA, Google Scholar, CrossRef, CAB Abstracting Journals, Chemical Abstracts, Indian Science Abstracts, EBSCO Indexing Services, Index Copernicus
Indian Journal of Animal Research, volume 51 issue 1 (february 2017) : 44-51

Impact analysis of missense variants on heat shock protein of farmed carp rohu, Labeo rohita (Hamilton, 1822)

Prajna Pradhan, Kiran Dashrath Rasal*, Dibyashree Swain, Pranati Swain, Jitendra Kumar Sundaray, Pallipuram Jayasankar
1<p>ICAR - Central Institute of Freshwater Aquaculture,&nbsp;Bhubaneswar 751 002, Odisha, India.</p>
Cite article:- Pradhan Prajna, Rasal* Dashrath Kiran, Swain Dibyashree, Swain Pranati, Sundaray Kumar Jitendra, Jayasankar Pallipuram (2016). Impact analysis of missense variants on heat shock protein offarmed carp rohu, Labeo rohita (Hamilton, 1822) . Indian Journal of Animal Research. 51(1): 44-51. doi: 10.18805/ijar.9645.

The progress in the computational field is advantageous for investigating the impact of missense variants/mutation on the protein structure-function. The impact analyses of variants on the genes/proteins using in vivo laboratory methods are laborious and time consuming. Thus, the present study was performed for investigating the impact of missense mutations on the Heat-shock proteins (HSP70) of farmed carp, rohu, Labeo rohita. We have used several sequence-based computational tools/algorithms such as SIFT, PANTHER, PROVEAN and I-Mutant2.0. We have depicted that all mutations (p.G6V, p.A56I, and p.A159T) in the HSP70 were deleterious. The 3D model of HSP70 of rohu was generated using Modeller9.14 and subsequently validated using SAVEs server. The Ramachandran plot shown that shifting of residues in the mutant structure towards the disallowed region due to mutation as compared to native counterpart. The ERAT score and PROSA score, also given clues of deteriorating quality of mutant protein HSP70. Moreover, STRING9.1 shown that HSP70 protein interacting with several proteins and strong association was observed with two proteins, hsp90 and dnajb (Hsp40 homolog). The RMSD was obtained 0.04Å between native and mutant structure. The present study will helpful for understanding the impact of missense mutations on the HSP70 of rohu using in vivo methods. This study enriched for further exploring disturbances of protein-protein interaction mechanism as well as associated molecular pathways. 

  1. Arai, A., Naruse, K., Mitani, H. and Shima, A., (1995) Cloning and characterization of cDNAs for 70-kDa heat-shock proteins (Hsp70) from two fish species of the genus Oryzias. Jpn J Genet. 70: 423-433.

  2. Basu, N., Kennedy, C.J. and Iwama, G.K., (2003) The effects of stress on the association between hsp70 and the glucocorticoid receptor in rainbow trout. Comp Biochem Physiol A Mol Integr Physiol. 134: 655-663.

  3. Basu, N., Todgham, A.E., Ackerman, P.A., Bibeau, M.R., Nakano, K., Schulte, P.M. and Iwama, G.K., (2002) Heat shock protein genes and their functional significance in fish. Gene. 295: 173-183.

  4. Capriotti, E., Fariselli, P. and Casadio, R., (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33: W306-310.

  5. Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. and Chan, A.P., (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE. 7: e46688.

  6. Davis, J.E., Voisine, C. and Craig, E.A., (1999) Intragenic suppressors of Hsp70 mutants: interplay between the ATPase- and peptide-binding domains. Proc Natl Acad Sci U S A. 96: 9269-9276.

  7. Feder, M.E. and Hofmann, G.E., (1999) Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. Annu Rev Physiol. 61: 243-282.

  8. George Priya Doss, C. and Rajith, B., (2012) Computational refinement of functional single nucleotide polymorphisms associated with ATM gene. PLoS ONE. 7: e34573.

  9. Hallare, A.V., Kohler, H.R. and Triebskorn, R., (2004) Developmental toxicity and stress protein responses in zebrafish embryos after exposure to diclofenac and its solvent. DMSO, Chemosphere. 56: 659-666.

  10. Han, J.H., Kerrison, N., Chothia, C. and Teichmann, S.A., (2006) Divergence of interdomain geometry in two-domain proteins. Structure. 14: 935-945.

  11. Javid, B., MacAry, P.A., Oehlmann, W., Singh, M. and Lehner, P.J., (2004) Peptides complexed with the protein HSP70 generate efficient human cytolytic T-lymphocyte responses. Biochem Soc Trans. 32: 622-625.

  12. Johnson, M.M., Houck, J. and Chen, C., (2005) Screening for deleterious nonsynonymous single-nucleotide polymorphisms in genes involved in steroid hormone metabolism and response. Cancer Epidemiol Biomarkers Prev. 14: 1326-1329.

  13. Kamaraj, B. and Purohit, R., (2013) In silico screening and molecular dynamics simulation of disease-associated nsSNP in TYRP1 gene and its structural consequences in OCA3. Biomed Res Int. 2013: 697051.

  14. Keller, J.M., Escara-Wilke, J.F. and Keller, E.T., (2008) Heat stress-induced heat shock protein 70 expression is dependent on ERK activation in zebrafish (Danio rerio) cells. Comp Biochem Physiol A Mol Integr Physiol. 150: 307-314.

  15. Kumar, P., Henikoff, S. and Ng, P.C., (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 4: 1073-1081.

  16. Mao, L., Bryantsev, A.L., Chechenova, M.B. and Shelden, E.A., (2005) Cloning, characterization, and heat stress-induced redistribution of a protein homologous to human hsp27 in the zebrafish Danio rerio. Exp Cell Res. 306: 230-241.

  17. Milarski, K.L. and Morimoto, R.I., (1989) Mutational analysis of the human HSP70 protein: distinct domains for nucleolar localization and adenosine triphosphate binding. J Cell Biol. 109: 1947-1962.

  18. Mohamoud, H.S., Hussain, M.R., El-Harouni, A.A., Shaik, N.A., Qasmi, Z.U., Merican, A.F., Baig, M., Anwar, Y., Asfour, H., Bondagji, N. et al., (2014) First comprehensive in silico analysis of the functional and structural consequences of SNPs in human GalNAc-T1 gene. Comput Math Methods Med. 2014: 904052.

  19. Molina, A., Biemar, F., Muller, F., Iyengar, A., Prunet, P., Maclean, N., Martial, J.A. and Muller, M., (2000) Cloning and expression analysis of an inducible HSP70 gene from tilapia fish. FEBS Lett. 474: 5-10.

  20. Multhoff, G., (2007) Heat shock protein 70 (Hsp70): membrane location, export and immunological relevance. Methods. 43: 229-237.

  21. Ng, P.C. and Henikoff, S., (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31: 3812-3814.

  22. Ng, P.C. and Henikoff, S., (2006) Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet. 7: 61-80.

  23. Park, J.W., Moon, C., Yun, S., Kim, S.Y., Bae, Y.C., Chun, M.H. and Moon, J.I., (2007) Differential expression of heat shock protein mRNAs under in vivo glutathione depletion in the mouse retina. Neurosci Lett. 413: 260-264.

  24. Radford, N.B., Fina, M., Benjamin, I.J., Moreadith, R.W., Graves, K.H., Zhao, P., Gavva, S., Wiethoff, A., Sherry, A.D., Malloy, C.R. et al., (1996) Cardioprotective effects of 70-kDa heat shock protein in transgenic mice. Proc Natl Acad Sci U S A. 93: 2339-2342.

  25. Ran, R., Zhou, G., Lu, A., Zhang, L., Tang, Y., Rigby, A.C. and Sharp, F.R., (2004) Hsp70 mutant proteins modulate additional apoptotic pathways and improve cell survival. Cell Stress Chaperones. 9: 229-242.

  26. Rasal, K.D., Chakrapani, V., Patra, S.K., Jena, S., Mohapatra, S.D., Nayak, S., Sundaray, J.K., Jayasankar, P. and Barman, H.K., (2015a) Identification and prediction of consequences of non-synonymous SNP in glyceraldehyde 3-    Phosphate Dehydrogenase (GAPDH) gene of zebrafish. Danio rerio, Turk J of Biol.

  27. Rasal, K.D., Shah, T.M., Vaidya, M., Jakhesara, S.J. and Joshi, C.G., (2015b) Analysis of consequences of non-synonymous SNP in feed conversion ratio associated TGF-â receptor type 3 gene in chicken. Metagene. 4: 107-117.

  28. Thomas, P.D., Campbell, M.J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A. and Narechania, A., (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res. 13: 2129-2141.

  29. Thomas, P.D. and Kejariwal, A., (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects, Proc Natl Acad Sci U S A. 101: 15398-15403.

  30. Thomas, R., McConnell, R., Whittacker, J., Kirkpatrick, P., Bradley, J. and Sandford, R., (1999) Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene, PKD1, by long-range PCR. Am J Hum Genet. 65: 39-49.

  31. Turturici, G., Sconzo, G. and Geraci, F., (2011) Hsp70 and its molecular role in nervous system diseases. Biochem Res Int. 2011: 618127.

  32. Wang, Z., Gerstein, M. and Snyder, M., (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 10: 57-63.

  33. Wang, Z. and Moult, J., (2001) SNPs, protein structure, and disease, Hum Mutat. 17: 263-270.

  34. Wiederstein, M. and Sippl, M.J., (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 35: W407-410.

  35. Zafarullah, M., Wisniewski, J., Shworak, N.W., Schieman, S., Misra, S. and Gedamu, L., (1992) Molecular cloning and characterization of a constitutively expressed heat-shock-cognate hsc71 gene from rainbow trout. Eur J Biochem. 204: 893-900.

Editorial Board

View all (0)