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volume 49 issue 2 (april 2015) : 180-186,   Doi: 10.5958/0976-0555.2015.00110.7

Prediction of structure and functions from full length coding sequence of SRY gene in crossbred and Indicine bulls

A
Ayan Mukherjee*
S
Sachinandan De
A
Arpana Verma
G
Gulshan Dass
D
Dibyendu Chakraborty
1Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal-132 001, India.
Cite article:- Mukherjee* Ayan, De Sachinandan, Verma Arpana, Dass Gulshan, Chakraborty Dibyendu (2025). Prediction of structure and functions from full length coding sequence of SRY gene in crossbred and Indicine bulls. Indian Journal of Animal Research. 49(2): 180-186. doi: 10.5958/0976-0555.2015.00110.7.

ABSTRACT

Sex-determining Region on Y chromosome (SRY) is testis determining factor in mammalian species. It encodes a protein that possess high mobility group (HMG) DNA-binding domain and acts as an architectural transcription factor. Mutation in this gene causes sex-reversal in many mammalian species. Detailed structure and exact biological functions of this protein in bovine species are not known. In the present study the full length coding sequences of the gene from crosssbred and indicine bulls were amplified, translated in silico and 3D model of the protein were predicted from the amino acid sequences. Predicted structure-activity relationship of the protein states that the protein is subcellular, essential, N-glycosylated in nature and is involved in sex determination and neuroendocrine functioning in central and peripheral nervous systems. The proteins have also plausible role in RNA metabolism, transition-metal and calmodulin binding. Overall this structural and functional information about the protein in bovine species will reinforce the understanding of domain-specific role of this protein and development of diagnostics for sex-determination in bovine species.

REFERENCES

  1. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, and Stockinger H. (2012). ExPASy: SIB bioinformatics resource portal, Nucleic Acids Research 40(W1):W597-W603.
  2. Desclozeaux M, Poulat F, de Santa Barbara P, Capony JP, Turowski P, Jay P, Mejean C, Moniot B, Boizet B and Berta P. (1998). Phosphorylation of an N-terminal motif enhances DNA-binding activity of the human SRY protein. Journal of Biological Chemistry 273:7988-7995.
  3. 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. Edited by Walker JM. Humana Press; 571-607.
  4. Gubbay J, Collignon J, Koopman P, Capel B, Economou A, Munsterberg A, Vivian N, Goodfellow P and Lovell-Badge R. (1990). A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature 346:245-250.
  5. Gupta R and Brunak S. (2002). Prediction of glycosylation across the human proteome and the correlation to protein function. Pacific Symposium on Biocomputing 7:310-322.
  6. Hanover, J A, Love D C, DeAngelis N, O’Kane M E, Lima-Miranda R, Schulz T, Yen Y M, Johnson R C and Prinz W A. (2007). The High Mobility Group Box Transcription Factor Nhp6Ap Enters the Nucleus by a Calmodulin-dependent, Ran-independent Pathway. Journal of Biological Chemistry 282:33743-33751.
  7. Hawkins T, Luban S and Kihara D. (2006). Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Science 15:1550-1556.
  8. Harley V R, Layfield S, Mitchell C L, Forwood J K, John A P, Briggs L J, McDowall S G and Jans D A. (2003). Defective importin â recognition and nuclear import of the sex-determining factor SRY are associated with XY sex-reversing mutations. Proceedings of National Academy of Science USA 100:7045-7050.
  9. Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu Hui and Xu J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols 7: 1511-1522.
  10. Kashimada K and Koopman P. (2010). Sry: the master switch in mammalian sex determination. Development 137(23): 3921-3930.
  11. Knower K C, Kelly S and Harley V R. (2003). Turning on the male-SRY, SOX9 and sex determination in mammals. Cytogenetics Genome Research 101: 185-198.
  12. Marchler-Bauer A, Lu S, Anderson J B, Chitsaz F, Derbyshire M K, DeWeese- Scott C, Fong J H, Geer L Y, Geer R C, Gonzales N R, Gwadz M, Hurwitz D I, Jackson J D, Ke Z, Lanczycki C J, Lu F, Marchler G H, Mullokandov M, Omelchenko M V, Robertson C L, Song J S, Thanki N, Yamashita R A, Zhang D, Zhang N, Zheng C and Bryant S.
  13. H. (2011). CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Research 39: D225-D229.
  14. Mitchell C L and Harley V R. (2002). Biochemical defects in eight SRY missense mutations causing XY gonadal dysgenesis. Molecular Genetics Metabolism 77: 217-225.
  15. Oh H J, Li Y and Lau Y F. (2005). Sry associates with the heterochromatin protein 1 complex by interacting with a KRAB domain protein. Biology of Reproduction 72: 407-415.
  16. Pal D and Eisenberg D. (2005). Inference of protein functions from protein structure. Structure 13: 121-130.
  17. Polanco J C and Koopman P. (2007). Sry and the hesitant beginnings of male development. Developmental Biology, 302(1):13-24.
  18. Sambrook Jand Russell D. (2001). Molecular cloning. A laboratory manual 3rd ed. (Cold Spring Harbor Press,Cold Spring Harbor N.Y.)
  19. Sekido R and Lovell-Badge R. (2008). Sex determination involves synergistic action of SRY and SF1 on a specific Sox9 enhancer. Nature 453: 930-934.
  20. Sim H, Rimmer K, Kelly S, Ludbrook L M, Clayton A H and Harley V R. (2005). Defective Calmodulin-Mediated Nuclear Transport of the Sex-Determining Region of the Y Chromosome (SRY) in XY Sex ReversalMolecular Endocrinology 19: 1884-1892.
  21. Stott K, Tang G S, Lee K B and Thomas J O. (2006). Structure of complex of tandem HMG boxes and DNA. Journal of Molecular Biology 360: 90-104.
  22. Sweitzer T D and Hanover J A. (1996). Calmodulin activates nuclear protein import: A link between signal transduction and nuclear transport. Proceedings of National Academy of Science USA. 93: 14574-14579.
  23. Tucker P K and Lundrigan B L. (1993). Rapid evolution of the sex determining locus in old world mice and rats. Nature 364:715-717.
  24. Turner ME, Ely D, Prokop J and Milsted A. (2011). Sry, more than testis determination? American Journal of Physiology, Regulatory, integrative and comparative Physiology. 301(3):R561-71.
  25. Whitfield L S, Lovell-Badge R and Goodfellow P N. (1993). Rapid sequence evolution of the mammalian sex-determining gene SRY. Nature 364:713-715.
  26. Wilhelm D, Palmer S and Koopman P. (2007). Sex determination and gonadal development in mammals. Physiological Review 87:1-28.
  27. Wu J B, Chen K, Li Y, Lau Y F and Shih J C. (2009). Regulation of monoamine oxidase A by the SRY gene on the Y chromosome. FASEB Journal 23: 4029-4938.
  28. Yuan X, Lu M L, Li T and Balk S P. (2001). SRY interacts with and negatively regulates androgen receptor transcriptional activity. Journal of Biological Chemistry 276: 46647-46654.Top of Form
  29. Zdobnov E M and Apweiler R. (2001). InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
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Indian Journal of Animal Research
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    volume 49 issue 2 (april 2015) : 180-186,   Doi: 10.5958/0976-0555.2015.00110.7

    Prediction of structure and functions from full length coding sequence of SRY gene in crossbred and Indicine bulls

    A
    Ayan Mukherjee*
    S
    Sachinandan De
    A
    Arpana Verma
    G
    Gulshan Dass
    D
    Dibyendu Chakraborty
    1Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal-132 001, India.
    Cite article:- Mukherjee* Ayan, De Sachinandan, Verma Arpana, Dass Gulshan, Chakraborty Dibyendu (2025). Prediction of structure and functions from full length coding sequence of SRY gene in crossbred and Indicine bulls. Indian Journal of Animal Research. 49(2): 180-186. doi: 10.5958/0976-0555.2015.00110.7.

    ABSTRACT

    Sex-determining Region on Y chromosome (SRY) is testis determining factor in mammalian species. It encodes a protein that possess high mobility group (HMG) DNA-binding domain and acts as an architectural transcription factor. Mutation in this gene causes sex-reversal in many mammalian species. Detailed structure and exact biological functions of this protein in bovine species are not known. In the present study the full length coding sequences of the gene from crosssbred and indicine bulls were amplified, translated in silico and 3D model of the protein were predicted from the amino acid sequences. Predicted structure-activity relationship of the protein states that the protein is subcellular, essential, N-glycosylated in nature and is involved in sex determination and neuroendocrine functioning in central and peripheral nervous systems. The proteins have also plausible role in RNA metabolism, transition-metal and calmodulin binding. Overall this structural and functional information about the protein in bovine species will reinforce the understanding of domain-specific role of this protein and development of diagnostics for sex-determination in bovine species.

    REFERENCES

    1. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, and Stockinger H. (2012). ExPASy: SIB bioinformatics resource portal, Nucleic Acids Research 40(W1):W597-W603.
    2. Desclozeaux M, Poulat F, de Santa Barbara P, Capony JP, Turowski P, Jay P, Mejean C, Moniot B, Boizet B and Berta P. (1998). Phosphorylation of an N-terminal motif enhances DNA-binding activity of the human SRY protein. Journal of Biological Chemistry 273:7988-7995.
    3. 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. Edited by Walker JM. Humana Press; 571-607.
    4. Gubbay J, Collignon J, Koopman P, Capel B, Economou A, Munsterberg A, Vivian N, Goodfellow P and Lovell-Badge R. (1990). A gene mapping to the sex-determining region of the mouse Y chromosome is a member of a novel family of embryonically expressed genes. Nature 346:245-250.
    5. Gupta R and Brunak S. (2002). Prediction of glycosylation across the human proteome and the correlation to protein function. Pacific Symposium on Biocomputing 7:310-322.
    6. Hanover, J A, Love D C, DeAngelis N, O’Kane M E, Lima-Miranda R, Schulz T, Yen Y M, Johnson R C and Prinz W A. (2007). The High Mobility Group Box Transcription Factor Nhp6Ap Enters the Nucleus by a Calmodulin-dependent, Ran-independent Pathway. Journal of Biological Chemistry 282:33743-33751.
    7. Hawkins T, Luban S and Kihara D. (2006). Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Science 15:1550-1556.
    8. Harley V R, Layfield S, Mitchell C L, Forwood J K, John A P, Briggs L J, McDowall S G and Jans D A. (2003). Defective importin â recognition and nuclear import of the sex-determining factor SRY are associated with XY sex-reversing mutations. Proceedings of National Academy of Science USA 100:7045-7050.
    9. Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu Hui and Xu J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols 7: 1511-1522.
    10. Kashimada K and Koopman P. (2010). Sry: the master switch in mammalian sex determination. Development 137(23): 3921-3930.
    11. Knower K C, Kelly S and Harley V R. (2003). Turning on the male-SRY, SOX9 and sex determination in mammals. Cytogenetics Genome Research 101: 185-198.
    12. Marchler-Bauer A, Lu S, Anderson J B, Chitsaz F, Derbyshire M K, DeWeese- Scott C, Fong J H, Geer L Y, Geer R C, Gonzales N R, Gwadz M, Hurwitz D I, Jackson J D, Ke Z, Lanczycki C J, Lu F, Marchler G H, Mullokandov M, Omelchenko M V, Robertson C L, Song J S, Thanki N, Yamashita R A, Zhang D, Zhang N, Zheng C and Bryant S.
    13. H. (2011). CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Research 39: D225-D229.
    14. Mitchell C L and Harley V R. (2002). Biochemical defects in eight SRY missense mutations causing XY gonadal dysgenesis. Molecular Genetics Metabolism 77: 217-225.
    15. Oh H J, Li Y and Lau Y F. (2005). Sry associates with the heterochromatin protein 1 complex by interacting with a KRAB domain protein. Biology of Reproduction 72: 407-415.
    16. Pal D and Eisenberg D. (2005). Inference of protein functions from protein structure. Structure 13: 121-130.
    17. Polanco J C and Koopman P. (2007). Sry and the hesitant beginnings of male development. Developmental Biology, 302(1):13-24.
    18. Sambrook Jand Russell D. (2001). Molecular cloning. A laboratory manual 3rd ed. (Cold Spring Harbor Press,Cold Spring Harbor N.Y.)
    19. Sekido R and Lovell-Badge R. (2008). Sex determination involves synergistic action of SRY and SF1 on a specific Sox9 enhancer. Nature 453: 930-934.
    20. Sim H, Rimmer K, Kelly S, Ludbrook L M, Clayton A H and Harley V R. (2005). Defective Calmodulin-Mediated Nuclear Transport of the Sex-Determining Region of the Y Chromosome (SRY) in XY Sex ReversalMolecular Endocrinology 19: 1884-1892.
    21. Stott K, Tang G S, Lee K B and Thomas J O. (2006). Structure of complex of tandem HMG boxes and DNA. Journal of Molecular Biology 360: 90-104.
    22. Sweitzer T D and Hanover J A. (1996). Calmodulin activates nuclear protein import: A link between signal transduction and nuclear transport. Proceedings of National Academy of Science USA. 93: 14574-14579.
    23. Tucker P K and Lundrigan B L. (1993). Rapid evolution of the sex determining locus in old world mice and rats. Nature 364:715-717.
    24. Turner ME, Ely D, Prokop J and Milsted A. (2011). Sry, more than testis determination? American Journal of Physiology, Regulatory, integrative and comparative Physiology. 301(3):R561-71.
    25. Whitfield L S, Lovell-Badge R and Goodfellow P N. (1993). Rapid sequence evolution of the mammalian sex-determining gene SRY. Nature 364:713-715.
    26. Wilhelm D, Palmer S and Koopman P. (2007). Sex determination and gonadal development in mammals. Physiological Review 87:1-28.
    27. Wu J B, Chen K, Li Y, Lau Y F and Shih J C. (2009). Regulation of monoamine oxidase A by the SRY gene on the Y chromosome. FASEB Journal 23: 4029-4938.
    28. Yuan X, Lu M L, Li T and Balk S P. (2001). SRY interacts with and negatively regulates androgen receptor transcriptional activity. Journal of Biological Chemistry 276: 46647-46654.Top of Form
    29. Zdobnov E M and Apweiler R. (2001). InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
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