ABSTRACT It is becoming more and more apparent that most genetic disorders are caused by biochemical abnormalities. Recent advances in human genome project and related research have showed us to detect and understand most of the inborn errors of metabolism. These are often caused by point mutations manifested as single-nucleotide-polymorphisms (SNPs). The GSS gene inquested in this work was analyzed for potential mutations with the help of computational tools like SIFT, PolyPhen and UTRscan. It was noted that 84.38% nsSNPs were found to be deleterious by the sequence homology based tool (SIFT), 78.13% by the structure homology based tool (PolyPhen) and 75% by both the SIFT and PolyPhen servers. Two major mutations occurred in the native protein (2HGS) coded by GSS gene at positions R125C and R236Q. Then a modeled structure for the mutant proteins (R125C and R236Q) was proposed and compared with that of the native protein. It was found that the total energy of the mutant (R125C and R236Q) proteins were -31893.846 and -31833.818 Kcal/mol respectively and that of the native protein was -31977.365 Kcal/mol. Also the RMSD values between the native and mutant (R125C and R236Q) type proteins were 1.80Å and 1.54Å. Hence, we conclude based on our study that the above mutations could be the major target mutations in causing the glutathione synthetase deficiency.
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nullKanthappan, R. and Sethumadhavan, R. (2010) Identification of structurally and functionally significant deleterious nsSNPs of GSS gene: in silico analysis. Advances in Bioscience and Biotechnology, 1, 361-366. doi: 10.4236/abb.2010.14048.
 Krawezak, M., Reiss, J. and Cooper, D.N. (1992) The mutational spectrum of single base-pair substitutions in mRNA splice junctions of human genes: causes and consequences. Human Genetics, 90(1-2), 41-54.
Pitarque, M., vonRichter, O., Oke, B., Berkkan, H., Oscarson, M. and Ingelman-Sundberg, M. (2001) Identification of a single nucleotide polymorphism in the TATA box of the CYP2A6 gene: impairment of its promoter activity. Biochemical Biophysical Research Communications, 284(2), 455-460.
LeVan, T.D., Bloom, J.W., Bailey, T.J., Karp, C.L., Halonen, M., Martinez, F.D. and Vercelli, D. (2001) A common single nucleotide polymorphism in the CD14 promoter decreases the affinity of Sp protein binding and enhances transcriptional activity. The Journal of Immunology, 167(10), 5838-5844.
Collins, F.S., Guyer, M.S. and Charkravarti, A. (1997) Variations on a theme: cataloging human DNA sequence variation. Science, 278(5343), 1580-1581.
Syvanen, A.C., Landegren, U., Isaksson, A., Gyllensten, U. and Brookes, A.J. (1999) Enthusiasm mixed with skepticism about singlenucleotide polymorphism markers for dissecting complex disorders. The European Journal of Human Genetics, 7, 98-101.
Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L. and Shen, N. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nature Genetics, 22(3), 239-247.
Brookes, A.J. (1999) The essence of SNPs. Gene, 234(2), 177-186.
Larsson, A. and Anderson, M. (2001) Glutathione synthetase deficiency and other disorders of the gamma-glutamyl cycle. 8th Edition, Mc Graw Hill, New York.
Taniguchi, N., Higashi, T., Sakamoto, Y. and Meister, A. (1989) Gluthatione cennential: Molecular perspectives and clinical implications. Academic Press, New York.
Gali, R.R and Board, P.G. (1995) Sequencing and expression of a cDNA for human glutathione synthetase. Biochemical journal, 310(pt1), 353-358.
Ristoff, E., Mayatepek, E.and Larsson, A. (2001) Long-term clinical outcome in patients with glutathione synthetase deficiency. The Journal of Pediatrics, 139(1), 79-84.
Shi, Z.Z., Habib, G.M., Rhead, W.J. Gahl, W.A., He, X., Sazer, S. and Lieberman, M.W. (1996) Mutations in the glutathione synthetase gene cause 5-oxoprolinuria. Nature Genetics, 14(3), 361-365.
Ristoff, E. and Larsson, A. (1998) Patients with genetics defects in the g-glutamyl cycle. Chemico Biological Interactions, 111-112(24), 113-121.
Meister, A.and Larsson, A. (1995) Metabolic and molecular bases of inherited disease. In: Scriver, C.F., Beaudet, A.L., Sly, W.S. and Valle, D. Eds., 7th Edition, McGraw Hill, New York, 1461-1477.
Dahl, N., Pigg, M., Ristoff, E., Gali, R., Carlsson, B., Mannervik, B., Larsson, A. and Board, P. (1997) Missense mutations in the human glutathione synthetase gene result in severe metabolic acidosis, 5-oxoprolinuria, hemolytic anemia and neurological dysfunction. Human Molecular Genetics, 6(7), 1147-1152.
Runa, N., Katarina, C., Birgit, O., Birgit, C., Lel, W., Galina, P., Michael, W.P., Svante, N., Bengt, M., Philip, G.B. and Agne, L. (2000) Kinetic properties of missense mutations in patients with glutathione synthetase deficiency. Biochemical Journal, 349(pt1), 275-279.
Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M. and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308-311.
Pauline, N.C. and Henikoff, S. (2003) SIFT: Predicting amino acid changes that affect protein function. 2003, Nucleic Acids Research, 31(13), 3812-3814.
Pauline, N.C. and Henikoff, S. (2001) Predicting deleterious amino acid substitutions. Genome Research, 11(5), 863-874.
Ramensky, V., Pork, P. and Sunyaev, S. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Research, 30(17), 3894-3900.
Pesole, G. and Liuni, S. (1999) Internet resources for the functional analysis of 5’ and 3’ untranslated regions of eukaryotic mRNAs. Trends in Genetics, 15(9), 378.
Sonenberg, N. (1994) mRNA translation: influence of the 5’ and 3’ untranslated regions. Current Opinion in Genetics, 4(2), 310-315.
Nowak, R. (1994) Mining treasures from ‘junk DNA’. Science, 263(5147), 608-610.
Pesole, G., Liuni, S., Grillo, G., Licciulli, F., Mignone, F., Gissi, C. and Saccone, C. (2002) UTRdb and UTRsite: specialized databases of sequences and functional elements of 5’ and 3’ untranslated regions of eukaryotic mRNAs. Nucleic Acids Research, 30, 335-340.
Cavallo, A. and Martin, A.C. (2005) Mapping SNPs to protein sequence and structure data. Bioinformatics, 21(8), 1443-1450.
Lindahl, E., Azuara, C., Koehl, P. and Delarue, M. (2006) NOMAD-Ref: Visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Research, 34(suppl 2), W52-W56.
Delarue, M. and Dumas, P. (2004) On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models. Proceedings of the National Academy of Sciences, 101(18), 6957-6962.
Van, D.S. (2000) Cytokine and cytokine receptor polymorphisms in infectious disease. Intensive Care Medicine, 26(suppl 1), S98-S102.
Becky, M.P. and Anne, E.W. (2005) The implications of structured 5’ untranslated regions on translation and disease. Cell and Developmental Biology, 16(1), 39-47.
Kaspar, R.L., Kakegawa, T., Cranston, H., Morris, D.R. and White, M.W. (1992) A regulatory cis element and a specific binding factor involved in the mitogenic control of murine ribosomal protein L32 translation. Journal of Biological Chemistry, 267(1), 508-514.
Kaspar, R.L., Morris, D.R. and White, M.W. (1993) Control of ribosomal protein synthesis in eukaryotic cells. In: Ilan, J. Ed., Translational Regulation of Gene Expression 2, Plenum Press, New York, 335-348.
Parsch, J., Russell, J.A., Beerman, I., Hartl, D.L. and Stephan, W. (2000) Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased alcohol dehydrogenase activity but also delays development. Genetics, 156(1), 219-227.
Lai, E.C., Burks, C. and Posakony, J.W. (1998) The K box, a conserved 3’ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development, 125(20), 4077-40 88.