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Research Article

volume 53 issue 12 (december 2019) : 1607-1612,   Doi: 10.18805/ijar.B-3712

In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

P
P.R. Sahoo
S
S.R. Mishra
S
S. Mohapatra
S
Santoswini Sahu
G
G. Sahoo
P
P.C. Behera
1Department of Veterinary Physiology, College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar-751 003, Odisha, India.
Cite article:- Sahoo P.R., Mishra S.R., Mohapatra S., Sahu Santoswini, Sahoo G., Behera P.C. (2019). In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals. Indian Journal of Animal Research. 53(12): 1607-1612. doi: 10.18805/ijar.B-3712.

ABSTRACT

This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

REFERENCES

  1. Allen, M., Cox, C., Belbin, O., Ma, L., Bisceglio, G. D., Wilcox, S. L., Howell, C. C., et al. (2012). Association and heterogeneity at the GAPDH locus in Alzheimer’s disease. Neurobiology Aging, 33: e25–33. .
  2. Altschul, S. F., Wootton, J. C., Gertz, E. M., Agarwala, R., Morgulis, A., et al. (2005). Protein database searches using compositionally adjusted substitution matrices. FEBS J, 272: 5101-5109.
  3. Benkert, P., Tosatto, S. C. E., Schomburg, D. (2008).Qmean: A comprehensive scoring function for model quality assessment. Proteins, 71: 261-277.
  4. Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., et al. (2014).SWISS-MODEL: modeling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42: W252-W258.
  5. Bonafe, N., Gilmore-Hebert, M., Folk, N., Azodi, M., Zhou, Y., Chambers, S. (2005). Glyceraldehyde-3-phosphate dehydrogenase binds to the AU-rich 3¢ untranslated region of colony-stimulating factor-1 (CSF-1) messenger RNA in human ovarian cancer cells: Possible role of CSF-1 posttranscriptional regulation and tumor phenotype. Cancer Research, 65: 3762–3771.
  6. Choubey, J., Patel, A., Gupta, S., Verma, M. K.(2010). Homology modeling and binding site identification of 1deoxy d-xylulose 5 phosphate reductoisomerase of Plasmodium falciparum: New drug target for Plsmodium falciparum. International Journal    of Engineering, Science and Technology, 23468-3472.
  7. Garnier, J., Gibrat, J. F and Robson, B. (1996).GOR secondary structure prediction method version IV, Methods in Enzymolology, 266: 540-553.
  8. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M, R, Appel, R. D., Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. (In) John M. Walker (ed): The Proteomics Protocols Handbook, John M. Walker (ed): Humana Press. pp. 571-607.
  9. Greer, S., Honeywell, R., Geletu, M., Arulanandam, R., Raptis, L.(. (2010).Housekeeping genes; expression levels may change with density of cultured cells. Journal of Immunological Methods, 355: 76–79. 
  10. Guruprasad, K., Reddy, B. V. B., Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering Design and Selection, 4:155-161.
  11. Ikpeme, E. V., Udensi, O. U., Kooffreh, M. E., Etta, H. E., Ushie, B. B., Echea, E., Ozoje M. (2017). In silico analysis of BRCA1 gene and its phylogenetic relationship in some selected domestic animal species. Trends in Bioinformatics, 10: 1-10.
  12. Joshi, T. and Xu, D. (2007).Quantitative assessment of relationship between sequence similarity and function similarity.BMC Genomics, 8: 1471- 1481.
  13. Kanwar, M. and Kowluru,R. A.(2009). Role of Glyceraldehyde 3-Phosphate dehydrogenase in the development and progression of diabetic retinopathy.Diabetes, 58: 227–234.
  14. Kosova, A.A., Khodyreva, S. N., Lavrik, O. I. (2017). Role of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in DNA Repair. Biochemistry (Mosc),82:643-654.
  15. Kyte, J. and Doolittle, R. E. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 105-132. 
  16. Lesh, A. M. (2002).Introduction to Bioinformatics. 2nd Edn, Oxford University Press, Oxford, Pages: 255.
  17. Nicholls, C., Li, H., Liu, J. P. (2012). GAPDH: a common enzyme with uncommon functions. Clinical and Experimental Pharmacology and Physiology, 39: 674–9. 
  18. Phadke, M., Krynetskaia, N., Mishra, A., Krynetskiy, E. (2011). Accelerated cellular senescence phenotype of GAPDH-depleted human lung carcinoma cells. Biochemical and Biophysical Research Communications, 411: 409–15.
  19. Qvit, N., Joshi, A. U., Cunningham, A. D., Ferreira, J. C., Mochly R. D.(2016). Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Protein-protein interaction inhibitor reveals a non-catalytic role for GAPDH oligomerization in cell death. Journal of Biological Chemistry, 291: 13608-21.
  20. Ramos, D., Pellín-Carcelén, A., Agustí, J., Murgui, A., Jordá, E., Pellín, A., Monteagudo, C. (2015).Deregulation of glyceraldehyde-    3-phosphate dehydrogenase expression during tumor progression of human cutaneous melanoma. Anticancer Research, 35: 439–44. 
  21. Roger, A. J., Smith, M. W., Doolittle, R. F., Doolittle W. F.(1996). Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase. Journal of Eukaryotic Microbiology,43: 475-85.
  22. Stone, A. C., Battistuzzi, F. U., Kubatko, L. S., Perry, G. H., Trudeau, E., Lin, H., Kumar, S.(2010). More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical transactions of the Royal Society of London. Series B, Biological Ssciences, 365: 3277-3288.
  23. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and Maximum parsimony methods. Molecular Biology and Evolution, 28: 2731-2739.
  24. Tarze, A., Deniaud, A., Le, B. M., Maillier, E., Molle, D., Larochette, N., Zamzami, N., Jan, G., Kroemer, G., Brenner, C. (2007).GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization. Oncogene, 26: 2606–20. 
  25. Thakkar, A. and Saraf, M. (2017).Molecular cloning and insilico analysis of cellulose gene from Bacillus amyloliquefaciens MBAA3. The Indian Journal of Biotechnology, 16: 487-494.
  26. Thompson, J. D., Higgins, D. G., Gibson, T. J.(1994). CLUSTAL W.: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680. 
  27. Wang, D., Moothart, D. R, Lowy, D. R., Qian, X. (2013).The expression of glyceraldehyde-3-phosphate dehydrogenase associated cell cycle (GACC) genes correlates with cancer stage and poor survival in patients with solid tumors. PLoS One, 8: e61262.
  28. Whelan, S. and Goldman, N. (2001).A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution,18, 18: 691–699. 
  29. Zhang, X. H., Dai, Z. X., Zhang, G. H., Han, J. B., Zheng, Y. T.(2013). Molecular characterization, balancing selection, and genomic organization of the tree shrew (Tupaia belangeri) MHC class I gene. Gene, 522:147–155.
  30. Zheng, Y., Wang, Q., Yun, C., Wang, Y., Smith, W. W, Leng, J. (2014).Identification of glyceraldehyde 3-Phosphate dehydrogenase sequence and expression profiles in tree shrew (Tupaia belangeri). PLoS One, 9: e98552. 
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Indian Journal of Animal Research
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    Research Article

    volume 53 issue 12 (december 2019) : 1607-1612,   Doi: 10.18805/ijar.B-3712

    In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals

    P
    P.R. Sahoo
    S
    S.R. Mishra
    S
    S. Mohapatra
    S
    Santoswini Sahu
    G
    G. Sahoo
    P
    P.C. Behera
    1Department of Veterinary Physiology, College of Veterinary Science and Animal Husbandry, Odisha University of Agriculture and Technology, Bhubaneswar-751 003, Odisha, India.
    Cite article:- Sahoo P.R., Mishra S.R., Mohapatra S., Sahu Santoswini, Sahoo G., Behera P.C. (2019). In silico structural and phylogenetic analysis of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in domestic animals. Indian Journal of Animal Research. 53(12): 1607-1612. doi: 10.18805/ijar.B-3712.

    ABSTRACT

    This study has been able to determine the physiochemical properties, secondary and tertiary structure, and phylogenetic analysis of GAPDH among domestic animals under in silico platform. Eighteen nucleotide and protein sequence of GAPDH gene of different mammalian species were retrieved from National Centre for Biotechnology information (NCBI). The percentage of identity and similarity was done by Basic Local Alignment Search Tool (BLAST), physiochemical properties were analyzed by ExPASy”s ProtParam tool, the secondary and 3-D structure was predicted by GOR IV and Swiss modeling respectively. Phylogenetic analysis among the animals was done by Molecular Evolutionary Genetics Analysis. It was found that the percentage of identity and similarity among all animals were almost more than 90%. The physiochemical analysis showed this protein is very stable, hydrophilic and intracytoplasmic in nature. The secondary structure analysis showed that GAPDH has more number of random coil (49.85%) Extended strand (27.93%), alpha helix (22.22%) of the protein. The QMEAN Z score was found 0.33 under protein modeling which interfered that this protein is of comparable quality. The phylogenetic analysis of this gene showed that the highest time of divergence occurred between sheep and common chimpanzee but least time of divergence observed between killer whale and dolphin. So it can be concluded that the GAPDH gene is highly conserved along all animal species.

    REFERENCES

    1. Allen, M., Cox, C., Belbin, O., Ma, L., Bisceglio, G. D., Wilcox, S. L., Howell, C. C., et al. (2012). Association and heterogeneity at the GAPDH locus in Alzheimer’s disease. Neurobiology Aging, 33: e25–33. .
    2. Altschul, S. F., Wootton, J. C., Gertz, E. M., Agarwala, R., Morgulis, A., et al. (2005). Protein database searches using compositionally adjusted substitution matrices. FEBS J, 272: 5101-5109.
    3. Benkert, P., Tosatto, S. C. E., Schomburg, D. (2008).Qmean: A comprehensive scoring function for model quality assessment. Proteins, 71: 261-277.
    4. Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., et al. (2014).SWISS-MODEL: modeling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42: W252-W258.
    5. Bonafe, N., Gilmore-Hebert, M., Folk, N., Azodi, M., Zhou, Y., Chambers, S. (2005). Glyceraldehyde-3-phosphate dehydrogenase binds to the AU-rich 3¢ untranslated region of colony-stimulating factor-1 (CSF-1) messenger RNA in human ovarian cancer cells: Possible role of CSF-1 posttranscriptional regulation and tumor phenotype. Cancer Research, 65: 3762–3771.
    6. Choubey, J., Patel, A., Gupta, S., Verma, M. K.(2010). Homology modeling and binding site identification of 1deoxy d-xylulose 5 phosphate reductoisomerase of Plasmodium falciparum: New drug target for Plsmodium falciparum. International Journal    of Engineering, Science and Technology, 23468-3472.
    7. Garnier, J., Gibrat, J. F and Robson, B. (1996).GOR secondary structure prediction method version IV, Methods in Enzymolology, 266: 540-553.
    8. Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M, R, Appel, R. D., Bairoch, A. (2005). Protein Identification and Analysis Tools on the ExPASy Server. (In) John M. Walker (ed): The Proteomics Protocols Handbook, John M. Walker (ed): Humana Press. pp. 571-607.
    9. Greer, S., Honeywell, R., Geletu, M., Arulanandam, R., Raptis, L.(. (2010).Housekeeping genes; expression levels may change with density of cultured cells. Journal of Immunological Methods, 355: 76–79. 
    10. Guruprasad, K., Reddy, B. V. B., Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering Design and Selection, 4:155-161.
    11. Ikpeme, E. V., Udensi, O. U., Kooffreh, M. E., Etta, H. E., Ushie, B. B., Echea, E., Ozoje M. (2017). In silico analysis of BRCA1 gene and its phylogenetic relationship in some selected domestic animal species. Trends in Bioinformatics, 10: 1-10.
    12. Joshi, T. and Xu, D. (2007).Quantitative assessment of relationship between sequence similarity and function similarity.BMC Genomics, 8: 1471- 1481.
    13. Kanwar, M. and Kowluru,R. A.(2009). Role of Glyceraldehyde 3-Phosphate dehydrogenase in the development and progression of diabetic retinopathy.Diabetes, 58: 227–234.
    14. Kosova, A.A., Khodyreva, S. N., Lavrik, O. I. (2017). Role of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in DNA Repair. Biochemistry (Mosc),82:643-654.
    15. Kyte, J. and Doolittle, R. E. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 105-132. 
    16. Lesh, A. M. (2002).Introduction to Bioinformatics. 2nd Edn, Oxford University Press, Oxford, Pages: 255.
    17. Nicholls, C., Li, H., Liu, J. P. (2012). GAPDH: a common enzyme with uncommon functions. Clinical and Experimental Pharmacology and Physiology, 39: 674–9. 
    18. Phadke, M., Krynetskaia, N., Mishra, A., Krynetskiy, E. (2011). Accelerated cellular senescence phenotype of GAPDH-depleted human lung carcinoma cells. Biochemical and Biophysical Research Communications, 411: 409–15.
    19. Qvit, N., Joshi, A. U., Cunningham, A. D., Ferreira, J. C., Mochly R. D.(2016). Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH) Protein-protein interaction inhibitor reveals a non-catalytic role for GAPDH oligomerization in cell death. Journal of Biological Chemistry, 291: 13608-21.
    20. Ramos, D., Pellín-Carcelén, A., Agustí, J., Murgui, A., Jordá, E., Pellín, A., Monteagudo, C. (2015).Deregulation of glyceraldehyde-    3-phosphate dehydrogenase expression during tumor progression of human cutaneous melanoma. Anticancer Research, 35: 439–44. 
    21. Roger, A. J., Smith, M. W., Doolittle, R. F., Doolittle W. F.(1996). Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase. Journal of Eukaryotic Microbiology,43: 475-85.
    22. Stone, A. C., Battistuzzi, F. U., Kubatko, L. S., Perry, G. H., Trudeau, E., Lin, H., Kumar, S.(2010). More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philosophical transactions of the Royal Society of London. Series B, Biological Ssciences, 365: 3277-3288.
    23. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and Maximum parsimony methods. Molecular Biology and Evolution, 28: 2731-2739.
    24. Tarze, A., Deniaud, A., Le, B. M., Maillier, E., Molle, D., Larochette, N., Zamzami, N., Jan, G., Kroemer, G., Brenner, C. (2007).GAPDH, a novel regulator of the pro-apoptotic mitochondrial membrane permeabilization. Oncogene, 26: 2606–20. 
    25. Thakkar, A. and Saraf, M. (2017).Molecular cloning and insilico analysis of cellulose gene from Bacillus amyloliquefaciens MBAA3. The Indian Journal of Biotechnology, 16: 487-494.
    26. Thompson, J. D., Higgins, D. G., Gibson, T. J.(1994). CLUSTAL W.: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680. 
    27. Wang, D., Moothart, D. R, Lowy, D. R., Qian, X. (2013).The expression of glyceraldehyde-3-phosphate dehydrogenase associated cell cycle (GACC) genes correlates with cancer stage and poor survival in patients with solid tumors. PLoS One, 8: e61262.
    28. Whelan, S. and Goldman, N. (2001).A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution,18, 18: 691–699. 
    29. Zhang, X. H., Dai, Z. X., Zhang, G. H., Han, J. B., Zheng, Y. T.(2013). Molecular characterization, balancing selection, and genomic organization of the tree shrew (Tupaia belangeri) MHC class I gene. Gene, 522:147–155.
    30. Zheng, Y., Wang, Q., Yun, C., Wang, Y., Smith, W. W, Leng, J. (2014).Identification of glyceraldehyde 3-Phosphate dehydrogenase sequence and expression profiles in tree shrew (Tupaia belangeri). PLoS One, 9: e98552. 
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