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Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 37 issue 3 (september 2017) : 185-190,   Doi: 10.18805/asd.v37i03.8986

In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris 
 

M
Meenu Goyal
S
Sugandh Chauhan
P
Pardeep Kumar
1Department of Biotechnology, Central University of Haryana, Mahendergarh 123 031, Haryana, India.
Cite article:- Goyal Meenu, Chauhan Sugandh, Kumar Pardeep (2017). In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris. Agricultural Science Digest. 37(3): 185-190. doi: 10.18805/asd.v37i03.8986.

ABSTRACT

The 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is one of the essential enzymes of shikimate pathway and is verified as a specific target of broad-spectrum herbicide glyphosate. It is important to get insights into three-dimensional (3D) structure of this enzyme for engineering new herbicides as well as herbicide resistant crops. The information about 3D structure of EPSP synthase enzyme is not yet available in protein database for any of the plant species. Therefore, we revealed the homology model of Phaseolus vulgaris EPSP synthase protein using the structure of EPSP synthase from E. coli as template. The resulting model structure was refined by RAMPAGE server, ERRAT and Verify3D. Ramachandran plot analysis showed that conformations for 95.6% of amino acid residues are within the most favoured region. The phylogenetic tree (constructed using MAFFT) separated EPSP synthases of bacteria, monocot and dicot plants into distinct clusters. Our study generated reliable 3D model structure of EPSP synthase in P. vulgaris, which can be used for future studies.

REFERENCES

  1. Arnold, K., Bordoli, L., Kopp, J., Schwede, T. (2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics, 22: 195-201.
  2. Baerson, S.R., Rodriguez, D.J., Tran, M., Feng, Y., Biest, N.A. et al. (2002). Glyphosate resistant goose grass. Identification of a mutation in the target enzyme EPSP synthase. Plant Physiol., 129: 1265-1275.
  3. Buxbaum, E. (2007). Fundamentals of Protein Structure and Function. Springer Science and Business Media, LLC, New York.
  4. Cedano, J., Aloy, P., Perez-Pons, J.A., Querol, E. (1997). Relation between amino acid composition and cellular location of proteins. J. Mol. Biol., 266: 594-600.
  5. Colovos, V.C. and Yeates, T.O. (1993). Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Sci., 2: 1511–1519.
  6. Comai, L., Facciotti, D., Hiatt, W.R., Thompson, G., Rose, R.E. et al. (2012). Expression in plants of a mutant aroA gene from Salmonella typhimurium confers tolerance to glyphosate. Nature, 317: 741-744.
  7. Eisenberg, D., Luthy, R., Bowie, J.U. (1997). VERIFY3D: Assessment of protein models with three dimensional profiles. Methods Enzymol., 277: 396–404.
  8. Funke, T., Han, H., Healy-Fried, M.L., Fischer, M. and Schonbrunn, E. (2006). Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. USA, 103: 13010-13015.
  9. Garg, B., Vaid, N., and Tuteja, N. (2014). In-silico analysis and expression profiling implicate diverse role of EPSPS family genes in regulating developmental and metabolic processes. BMC Research Notes, 7(1): 58.
  10. Geourjon, C. and Deleage, G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput. Appl. Biosci., 11: 681-684.
  11. Gill, S.C. and von Hippel, P.H. (1989). Extinction coefficient. Anal Biochem., 182: 319-328.
  12. Guruprasad, K., Reddy, B.V.P., 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. Prot. Eng., 4: 155-164.
  13. Ikai, A.J. (1980). Thermo stability and aliphatic index of globular proteins. J. Biochem., 88: 1895-1898.
  14. Kyte, J. and Doolottle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157: 105-132.
  15. Sanbagavalli, S., Kandasamy, O.S., Ganesan, K. (2000). Herbicide resistance in weeds: a review. Agric. Rev., 21(2): 80-88.
  16. Schonbrunn, E., Eschenburg, S., Shuttleworth, W.A., Schloss, J.V., Amrhein, N., Evans, J.N.S., Kabsch, W. (2001). Interaction of the herbicide glyphosate with its target enzyme EPSP synthase in atomic detail. Proc. Natl. Acad. Sci. USA, 98: 1376-1380.
  17. Zhou, M., Xu, H., Wei, X., Ye, Z., Wei, L., Gong, W., Wang, Y., Zhu, Z. (2006). Identification of a resistant mutant of rice 5-    enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol., 140: 184-195.
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    Research Article

    volume 37 issue 3 (september 2017) : 185-190,   Doi: 10.18805/asd.v37i03.8986

    In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris 
     

    M
    Meenu Goyal
    S
    Sugandh Chauhan
    P
    Pardeep Kumar
    1Department of Biotechnology, Central University of Haryana, Mahendergarh 123 031, Haryana, India.
    Cite article:- Goyal Meenu, Chauhan Sugandh, Kumar Pardeep (2017). In silico analysis, structural modeling and phylogenetic analysis of EPSP synthase of Phaseolus vulgaris. Agricultural Science Digest. 37(3): 185-190. doi: 10.18805/asd.v37i03.8986.

    ABSTRACT

    The 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase is one of the essential enzymes of shikimate pathway and is verified as a specific target of broad-spectrum herbicide glyphosate. It is important to get insights into three-dimensional (3D) structure of this enzyme for engineering new herbicides as well as herbicide resistant crops. The information about 3D structure of EPSP synthase enzyme is not yet available in protein database for any of the plant species. Therefore, we revealed the homology model of Phaseolus vulgaris EPSP synthase protein using the structure of EPSP synthase from E. coli as template. The resulting model structure was refined by RAMPAGE server, ERRAT and Verify3D. Ramachandran plot analysis showed that conformations for 95.6% of amino acid residues are within the most favoured region. The phylogenetic tree (constructed using MAFFT) separated EPSP synthases of bacteria, monocot and dicot plants into distinct clusters. Our study generated reliable 3D model structure of EPSP synthase in P. vulgaris, which can be used for future studies.

    REFERENCES

    1. Arnold, K., Bordoli, L., Kopp, J., Schwede, T. (2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics, 22: 195-201.
    2. Baerson, S.R., Rodriguez, D.J., Tran, M., Feng, Y., Biest, N.A. et al. (2002). Glyphosate resistant goose grass. Identification of a mutation in the target enzyme EPSP synthase. Plant Physiol., 129: 1265-1275.
    3. Buxbaum, E. (2007). Fundamentals of Protein Structure and Function. Springer Science and Business Media, LLC, New York.
    4. Cedano, J., Aloy, P., Perez-Pons, J.A., Querol, E. (1997). Relation between amino acid composition and cellular location of proteins. J. Mol. Biol., 266: 594-600.
    5. Colovos, V.C. and Yeates, T.O. (1993). Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Sci., 2: 1511–1519.
    6. Comai, L., Facciotti, D., Hiatt, W.R., Thompson, G., Rose, R.E. et al. (2012). Expression in plants of a mutant aroA gene from Salmonella typhimurium confers tolerance to glyphosate. Nature, 317: 741-744.
    7. Eisenberg, D., Luthy, R., Bowie, J.U. (1997). VERIFY3D: Assessment of protein models with three dimensional profiles. Methods Enzymol., 277: 396–404.
    8. Funke, T., Han, H., Healy-Fried, M.L., Fischer, M. and Schonbrunn, E. (2006). Molecular basis for the herbicide resistance of Roundup Ready crops. Proc. Natl. Acad. Sci. USA, 103: 13010-13015.
    9. Garg, B., Vaid, N., and Tuteja, N. (2014). In-silico analysis and expression profiling implicate diverse role of EPSPS family genes in regulating developmental and metabolic processes. BMC Research Notes, 7(1): 58.
    10. Geourjon, C. and Deleage, G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput. Appl. Biosci., 11: 681-684.
    11. Gill, S.C. and von Hippel, P.H. (1989). Extinction coefficient. Anal Biochem., 182: 319-328.
    12. Guruprasad, K., Reddy, B.V.P., 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. Prot. Eng., 4: 155-164.
    13. Ikai, A.J. (1980). Thermo stability and aliphatic index of globular proteins. J. Biochem., 88: 1895-1898.
    14. Kyte, J. and Doolottle, R.F. (1982). A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157: 105-132.
    15. Sanbagavalli, S., Kandasamy, O.S., Ganesan, K. (2000). Herbicide resistance in weeds: a review. Agric. Rev., 21(2): 80-88.
    16. Schonbrunn, E., Eschenburg, S., Shuttleworth, W.A., Schloss, J.V., Amrhein, N., Evans, J.N.S., Kabsch, W. (2001). Interaction of the herbicide glyphosate with its target enzyme EPSP synthase in atomic detail. Proc. Natl. Acad. Sci. USA, 98: 1376-1380.
    17. Zhou, M., Xu, H., Wei, X., Ye, Z., Wei, L., Gong, W., Wang, Y., Zhu, Z. (2006). Identification of a resistant mutant of rice 5-    enolpyruvylshikimate 3-phosphate synthase using a directed evolution strategy. Plant Physiol., 140: 184-195.
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