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Theoretical structure prediction of TcaA from Photorhabdus luminescens and aminopeptidase N receptor from Helicoverpa armigera

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Author Affiliations

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

Res. J. Recent Sci., Volume 2, Issue (2), Pages 40-49, February,2 (2013)

Abstract

Due to resistance developed by various agricultural pests towards Bacillus thuringiensis (BT) toxins, there is a necessity of developing alternative biopesticide. The TcaA toxin produced by Photorhabdus luminescens is a high molecular weight insecticidal toxin having toxicity against wide range of agricultural pests. Phylogenetic tree constructed for TcaA revealed that this toxin does not have any ancestral relationship with BT toxins. Present study focused on the modeling the TcaA toxin from Photorhabdus luminescens and aminopeptidase N receptor from Helicoverpa armigera using various computational approaches. Structural validation using various tools such as ProSA and PROCHECK revealed that and angles of these theoretical models were present in the core and allowed region. The theoretical toxin structure was subsequently docked onto the homology modeled aminopeptidase N receptor. Outcome of the docking study showed that first domain of TcaA had highest docking energy when compared to remaining domains.

References

  1. Roush R., Can we slow adaptation by pests to insect transgenic crops? In: Parsley GJ (ed) Biotechnology and integrated pest management. CAB International, Willinford. (1996)
  2. 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)
  3. Wirth M. C., Georghiou G. P., and Federici, B. A., Cyt A enables CryIV endotoxins of BT to overcome high levels of CryIV resistance in the mosquito, Culex quinquefasciatus, Proc. Natl. Acad. Sci, 94, 10536-10540. (1997)
  4. Gould F. Anderson A. Jones A. Sumerford D. Heckel D. Lopez, J., et al. Initial frequency of alleles for resistance to Bacillus thuringiensis toxins in field populations of Heliothis virescens. Proc. Natl. Acad. Sci, 94, 3519-3523(1997)
  5. Liu Y. B. Tabashnik B. Dennehy T. Patin A. and Bartlet A., Development time and resistance to Bt crops, Nature, 400, 519 (1999)
  6. Frutos R. Rang C. and Royer M., Managing Insect Resistance to Plants Producing Bacillus thuringiensis Toxins, Crit. Rev. Biotechnol, 19(3), 227-276 (1999)
  7. Tabashnik B., Delaying Insect Adaptation to Transgenic Plants: Seed Mixtures and Refugia Reconsidered, Proc. R. Soc. Lond., 255(1342) , 7-12 (1994)
  8. Blackburn M. Golubeva E. Bowen D. and Ffrench-Constant R., A novel insecticidal toxin from photorhabdus luminescens, toxin complex a (Tca), and its histopathological effects on the midgut of manduca sexta, Applied and environmental microbiology, 64(8), 3036-3041(1998)
  9. Han R. and Ehlers R. U., Effect of Photorhabdus luminescens phase variants on the in vivo and in vitro development and reproduction of the entomopathogenic nematodes Heterorhabditis bacteriophora and Steinernema carpocapsae, FEMS microbiology ecology, 35(3), 239-247 (2001)
  10. Knight P. J. Crickmore N. 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. 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)
  14. 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)
  15. Guo S. Ye S. Liu Y. Wei L. Xue J. Wu H. Song F. Zhang J. Wu X. Huang D. 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)
  16. Grochulski P. Masson L. Borisova S. Pusztai-Carey M. Schwartz J. L. Brousseau R. Cygler M., Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation, J Mol Biol.254, 447-464 (1995)
  17. 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)
  18. 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)
  19. Morse R. J. Yamamoto T. and Stroud R. M., Structure of Cry2Aa suggests an unexpected receptor binding epitope, Structure 9, 409-417 (2001)
  20. 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)
  21. Felsenstein J. Inferring phylogeny, Sinauer Associates, Sunderland, MA (2003)
  22. Servant F.C. Bru E. Courcelle J. Gouzy D. Peyruc D. and Kahn D., ProDom: Automated clustering of homologous domains, Briefings in Bioinformatic,3, 246-251(2002)
  23. 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)
  24. Schwede T.Kopp J. Guex N. andPeitsch M. C.,SWISS-MODEL: an automated protein homology-modeling serve,. Nucl. Acids Res, 31, 3381-3385 (2003)
  25. Zhang Y., I-TASSER server for protein 3D structure prediction, BMC bioinformatics, 9, 40-47 (2008)
  26. Colovos C. and Yeates T. O., Verification of protein structures: Patterns of nonbonded atomic interactions, Protein Science,2,1511-1519 (1993)
  27. 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)
  28. 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)
  29. Fiser A. Do R. K. and Sali A. Modeling of loops in protein structures. Protein Science9, 1753-1773(2000)
  30. Holm L. and Rosenstrom P. Dali server: conservation mapping in 3D, Nucl Acids Res38, 545-549 (2010)
  31. Ritchie D. W., Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2. Proteins, Structure, Function, and Bioinformatics,52, 98–106 (2003)
  32. Nguyen T. T. Chang S. Evnouchidou I. York I. A. et al., Structural Basis For Antigenic Peptide Precursor Processing by the Endoplasmic Reticulum Aminopeptidase ERAP1, Nat Struct Mol Biol. 18, 604-613 (2011)
  33. Calhoun J. R. Liu W. Spiegel K. et al., Solution NMR Structure of a Designed Metalloprotein and Complementary Molecular Dynamics Refinement, Structure16, 210–215 (2008)
  34. Iyer S. Holloway D. E. Kumar K. Shapiro R. and Acharya K. R., Molecular Recognition of Human Eosinophil-derived Neurotoxin (RNase 2) by Placental Ribonuclease Inhibitor, J. Mol. Biol.347, 637–655 (2005)
  35. Spahr H. Samuelsson T, Hällberg B. M. and Gustafsson C. M., Structure of mitochondrial transcription termination factor 3 reveals a novel nucleic acid-binding domain, Biochem. Biophys. Res. Commun. 397, 386–390 (2010)