International E-publication: Publish Projects, Dissertation, Theses, Books, Souvenir, Conference Proceeding with ISBN.  International E-Bulletin: Information/News regarding: Academics and Research

Molecular Modeling and Docking Studies of PirB Fusion Protein from Photorhabdus Luminescens

Author Affiliations

  • 1 Department of Biotechnology, Center for Postgraduate studies, Jain University, Bangalore – 560011 INDIA

Int. Res. J. Biological Sci., Volume 1, Issue (8), Pages 7-18, December,10 (2012)

Abstract

Genetic engineering of Cry proteins from Bacillus thuringiensis (BT) has resulted in the synthesis of various novel toxin proteins which exhibits increased insecticidal activity and highly specificity towards different insect pests. The present study focused on computational studies on PirB sequence from Photorhabdus luminescens. The consensus tree generated by PHYLIP for the PirB sequence revealed that this toxin sequence does not share any ancestral relationship with other Cry toxins from Bacillus thuringiensis considered in this study. Molecular modeling of PirB was followed by construction of two fusion proteins: Type I (PirB-Cry2AaII-Cry2AaIII) and Type II (PirB-Cry2AaII-Garlic lectin). Comparison of the 3D model of PirB with X-ray structure of N-terminal domain 1I5P_A revealed both the structures shared similar architecture. Validation of the tertiary structure of PirB by the structural assessment tools such as ProSA, ERRAT and PROCHECK suggested that the predicted structure was of reasonable quality. Docking studies carried out onto the cadherin receptor showed that Type II fusion protein had a greater affinity, suggesting the possibility of using this fusion protein as a potential bio-pesticide.

References

  1. Poinar G.O., Thomas G.M. and Hess R., Characteristics of the specific bacterium associated with Heterorhabditis bacteriophora (Heterorhabditidae: Rhabditida), Nematologica.,23, 97–102 (1977)
  2. Chattopadhyay A. Bhatnagar N. and Bhatnagar R., Bacterial insecticidal toxins, Crit. Rev. Microbiol.,30, 33–54 (2004)
  3. Daborn P.J., Waterfield N.R., Silva C.P., Au C.P., Sharma S. and Ffrench-Constant R.H., A single Photorhabdus gene, makes caterpillars floppy (mcf), allows Escherichia coli to persist within and kill insects, Proc. Natl. Acad. Sci USA,99, 10742–10747 (2002)
  4. Duchaud E et al., The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens, Nat. Biotechnol,21, 1307–1313 (2003)
  5. Waterfield N.R., Hares M., Yang G., Dowling A. and ffrench-Constant R.H., Potentiation and cellular phenotypes of the insecticidal toxin complexes of Photorhabdus bacteria, Cell Microbiol7, 373–382 (2005 a)
  6. ffrench-Constant R. H., Dowling A. and Waterfield N. R., Insecticidal toxins from Photorhabdus bacteria and their potential use in agriculture, Toxicon49, 436–451(2007)
  7. Yang G., Dowling J., Gerike U., ffrench-Contant R. H. and Waterfield N. R., Photorhabdus virulence cassettes confer injectable insecticidal activity against the wax moth, J. Bacteriol188, 2254–2261 (2006)
  8. Waterfield N. R., Kamita S. G., Hammock B. D. and ffrench-Constant R. H., The Photorhabdus Pir toxins are similar to a developmentally regulated insect protein but show no juvenile hormone esterase activity, FEMS Microbiol.Lett 245, 47–52 (2005 b)
  9. Wilkinson P., Waterfield N. R., Crossman L., Corton G., Sanchez-Contreras M. et al. Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens. BMC Genomics10, 302-323 (2009)
  10. Knight P. J., Crickmore N. and Ellar D. J., The receptor for Bacillus thuringiensis CrylA(c) delta-endotoxin in the brush border membrane of the lepidopteran Manduca sexta is aminopeptidase N, Mol. Microbiol11, 429–436 (1994)
  11. Francis B.R. and Bulla Jr L.A., Further characterization of BT-R1, the cadherin- like receptor for Cry1Ab toxin in tobacco hornworm (Manduca sexta) midgets, Insect Biochem. Mol.Biol, 27, 541–550 (1997)
  12. Knight P.J., Carroll J. and Ellar D.J., Analysis of glycan structures on the 120 kDa aminopeptidase N of Manduca sexta and their interactions with Bacillus thuringiensis Cry1Ac toxin, Insect Biochem. Mol. Biol34, 101–112 (2004)
  13. Lee M.K., You T.H., Gould F.L. and Dean D.H., Identification of residues in domain III of Bacillus thuringiensis Cry1Ac toxin that affect binding and toxicity, Appl. Environ. Microbiol65, 4513–4520 (1999)
  14. Bharathi Y., Reddy T.P., Reddy V.D. and Rao K.V., Plant lectins and their utilization for development of insect resistant transgenic crop plants, in: Pests and Pathogens: Management Strategies, BS Publications, 457–489 (2010)
  15. Ho N.H., Oliva B.N., Datta K., Frutos R. and Datta S.K., Translational fusion hybrid Bt genes confer resistance against yellow stem borer in transgenic elite vietnamese rice (Oryza sativa L.) cultivars, Crop Sci.46, 781–789 (2006)
  16. Honee G., Vriezen W. and Visser B., A translation fusion product of two different insecticidal crystal protein genes of Bacillus thuringiensis exhibits an enlarged insecticidal spectrum, Appl. Environ. Microbiol.56, 823–825 (1990)
  17. Harper B.K., Mabon S.A., Leffel S.M., Halfhill M.D., Richards H.A. and Moyer K.A. et al., Green fluorescent protein as a marker for expression of a second gene in transgenic plants, Nat. Biotechnol17, 1125–1129 (1999)
  18. de Maagd R.A., Kwa M.S., van der Klei H., Yamamoto T., Schipper N., Vlak J.M. et al., Domain III substitution in Bacillus thuringiensis delta-endotoxin CryIA(b) results in superior toxicity for Spodoptera exigua and altered membrane protein recognition, Appl. Environ. Microbiol62, 1537–1543 (1996)
  19. Hoy M.A., Myths, models and mitigation of resistance to pesticides, Phil. Trans. R. Soc. Lond. B353, 1787–1795 (1998)
  20. Michaud D., Avoiding protease mediated resistance in herbivorous pests. Trends Biotech 15, 4–6 (1997)
  21. Li J.D., Carroll J. and Ellar D.J., Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 A resolution, Nature,353, 815-821 (1991)
  22. Galitsky N., Cody V., Wojtczak A., Ghosh D., Luft J. R., Pangborn W. and English L., Structure of the insecticidal bacterial delta-endotoxin Cry3Bb1 of Bacillus thuringiensis, Acta crystallogr D Biol Crystallogr57, 1101-1109 (2001)
  23. Guo S., Ye S., Liu Y., Wei L., Xue J., Wu H., Song F., Zhang J., Wu X., Huang D. and Rao Z., Crystal structure of Bacillus thuringiensis Cry8Ea1: An insecticidal toxin toxic to underground pests, the larvae of Holotrichiaparallela, J struct Biol , 168, 259-266 (2009)
  24. Grochulski P., Masson L., Borisova S., Pusztai-Carey M., Schwartz J. L., Brousseau R. and Cygler M., Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation, J Mol Biol.254, 447-464 (1995)
  25. Int. Res. J. Biological Sci. International Science Congress Association 1825.Boonserm P., Mo M., Angsuthanasombat C. and Lescar J., Structure of the functional form of the mosquito larvicidal Cry4Aa toxin from Bacillus thuringiensis at a 2.8-angstrom resolution, J Bacteriol.188, 3391-3401 (2006)
  26. Boonserm P., Davis P., Ellar D. J. and Li J., Crystal structure of the mosquito-larvicidal toxin Cry4Ba and its biological implications, J Mol Biol, 348, 363-382 (2005)
  27. Morse R. J., Yamamoto T. and Stroud R. M., Structure of Cry2Aa suggests an unexpected receptor binding epitope, Structure9, 409-417 (2001)
  28. Thompson J. D., Higgins D. G. and Gibson T. J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res , 22, 4673-4680 (1994)
  29. Felsenstein J. Inferring phylogeny, Sinauer Associates, Sunderland, MA (2003)
  30. Altschul S.F., Madden T.L., Schäffer1 A. A., Zhang J., Zhang Z., Miller W. and Lipman D. J., Gapped BLAST Nucleic Acids Res and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res, 17, 3389-3402 (1997)
  31. Schwede T.,Kopp J., Guex N. andPeitsch M. C., SWISS-MODEL: an automated protein homology-modeling serve,. Nucl. Acids Res, 31, 3381-3385 (2003)
  32. Zhang Y., I-TASSER server for protein 3D structure prediction, BMC bioinformatics, 9, 40-47 (2008)
  33. Colovos C. and Yeates T. O., Verification of protein structures: Patterns of nonbonded atomic interactions, Protein Science,2,1511-1519 (1993)
  34. Fiser A., Do R. K. and Sali A., Modeling of loops in protein structures. Protein Science9, 1753-1773(2000)
  35. Guex N. and Peitsch M. C., SWISS-MODE: and the Swiss-PdbViewer: An environment for comparative protein modeling, Electrophoresis, 18, 2714-2723 (1997)
  36. Holm L. and Rosenstrom P. Dali server: conservation mapping in 3D, Nucl Acids Res38, 545-549 (2010)
  37. Laskowski R. A. MacArthur M. W. Moss D. and Thornton J. M., PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Cryst,26, 283-291(1993)
  38. Wiederstein M. and Sippl M. J., ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins, Nucleic Acids Res , 35, W407-W410 (2007)
  39. Ritchie D.W., Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2. Proteins, Structure, Function, and Bioinformatics52, 98–106 (2003)
  40. Ramachandraiah G., Chandra N. R., Surolia A. and Vijayan M., Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin, Acta Crystallogr D Biol crtstallogr, 58, 414-420 (2002)
  41. Burton S. L., Ellar D. J., Li J. and Derbyshire D. J., N-acetylgalactosamine on the putative insect receptor aminopeptidase N is recognised by a site on the domain III lectin-like fold of a Bacillus thuringiensis insecticidal toxin, J. Mol. Biol.287, 1011–1022 (1999)
  42. Hofmann C., Vanderbruggen H., Hofte H., Van Rie J., Jansens S. and Van Mel- laert H., Specificity of Bacillus thuringiensis delta-endotoxins is correlated with the presence of high-affinity binding sites in the brush border membrane of target insect midgets, Proc. Natl. Acad. Sci 85,7844–7848 (1988)
  43. Jin X., Walker M. A., Felsovalyi K., Vendome J., Bahna F., Mannepalli S., Cosmanescu F., Ahlsen G., Honig B. and Shapiro L., Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers, Proc Natl Acad Sci, U S A 3, 127-134 (2012)
  44. Gribskov M., McLachlan A. D. and Eisenberg D., Profile analysis: Detection of distantly related proteins, Proc. Natl. Acad. Sci.84, 4355-4358 (1987)
  45. Krogh A., Brown M., Mian I. S., Sjolander K. and Haussler D., Hidden Markov models in computational biology: Applications to protein modeling, J. Mol. Biol.235, 1501-1531 (1994)
  46. Eddy S. R., Hidden Markov models, Curr. Opin. Struct. Biol.6, 361-365 (1996)
  47. Kashyap S., Singh B.D. and Amla D.V., Homology modeling deduced structure of the Cry1Ab22 toxin, Indian journal of biotechnology,10, 202-206 (2011)
  48. Tanje S., Sanam R., Gundla R., Gandhi N.S., Mancera R.L., Boddupally D., Vudem D. R. and Khareedu V. R., Molecular modeling of Bt Cry1Ac (DI-DII)-ASAL (Allium sativum lectin)-fusion protein and its interaction with aminopeptidase N (APN) receptor of Manduca sexta, J. Mol. Graphics Modell, 33, 61-76 (2012)