Development of resistance against blackleg disease in Brassica oleracea var. botrytis through in silico methods

Fungal Genetics and Biology

Volumn 47, Issue 10, 2010, Pages 800-808

  Srivastava, Mugdha ^a,c   Akhoon, Bashir A ^b   Gupta, Shishir Kumar ^c   Gupta, Shailendra K ^d  

^a DOEACC Center of Bioinformatics   (India)

^b SHRI MATA VAISHNO DEVI UNIVERSITY   (India)

^c Society for Biological Research and Rural Development   (India)

^d CSIR INDIAN INSTITUTE OF TOXICOLOGY RESEARCH   (India)

Author keywords

Blackleg; Brassica oleracea; Cloning; Isocitrate lyase; Leptosphaeria maculans; Modelling; Peptide designing; Resistance; Superposition

Indexed keywords

GLYOXYLIC ACID; ISOCITRATE LYASE; ISOCITRIC ACID; PEPTIDE;

AMINO ACID METABOLISM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CAULIFLOWER; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; DISEASE PREDISPOSITION; DISEASE RESISTANCE; ENERGY CONSERVATION; FUNGAL METABOLISM; FUNGAL PLANT DISEASE; FUNGAL VIRULENCE; FUNGUS; LEPTOSPHAERIA MACULANS; MOLECULAR CLONING; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; PLANT FUNGUS INTERACTION; PRIORITY JOURNAL; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; ASCOMYCOTA; BRASSICA; COMPUTER SIMULATION; GENETIC ENGINEERING; ISOCITRATE LYASE; ISOCITRATES; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; PEPTIDES; PLANT DISEASES; PLANTS, GENETICALLY MODIFIED; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN; TEMPLATES, GENETIC;

BRASSICA OLERACEA; BRASSICA OLERACEA VAR. BOTRYTIS; BRASSICACEAE; LEPTOSPHAERIA MACULANS;

EID: 77956342932     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2010.06.014     Document Type: Article

References (56)

1. Akhoon B.A., Gupta S.K., Verma V., Dhaliwal G., Srivastava M., Gupta S.K., Ahmad R.F. In silico designing and optimization of anti-breast cancer antibody mimetic oligopeptide targeting HER-2 in women. J. Mol. Graphics Modell. 2010, 28:664-669.
2. Altschul S.F., Thomas L.M., Alejandro A.S., Jinghui Z., Zheng Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Ananga A.O., Cebert E., Soliman K., Kantety R., Pacumbaba R.P., Konan K. RAPD markers associated with resistance to blackleg disease in Brassica species. Afr. J. Biotechnol. 2006, 5:2041-2048.
4. Appelt K., Bacquet R.J., Bartlett C.A., Booth C.L.J., Freer S.T., Fuhry M.A.M., Gehring M.R., Herrmann S.M., Howland E.F. Design of enzyme inhibitors using iterative protein crystallographic analysis. J. Med. Chem. 1991, 34:1925-1934.
5. Balesdent M., Attard H., Ansan-Melayah D., Delourme D., Renard R., Rouxel M. Genetic control and host range of avirulence toward Brassica napus cultivars Quinta and Jet Neuf in Leptosphaeria maculans. Phytopathology 2001, 91:70-76.
6. Bhalla P.L., Smith N. Agrobacterium tumefaciens-mediated transformation of cauliflower, Brassica oleracea var. botrytis. Mol. Breed. 1998, 4:531-541.
7. Bhattacharyra R.C., Maheshwari M., Dineshkumar V., Kirti P.B., Bhat S.R., Chopra V.L. Transformation of Brassica oleracea var. capitata with bacterial betA gene enhances tolerance to salt stress. Sci. Hort. 2004, 100:215-227.
8. Bokor A., Barbetti M.J., Brown A.G.P., MacNish G.C., Poole M.L., Wood P.McR. Blackleg-a major hazard to the rapeseed industry. J. Agric. 1975, 16:7-10.
9. Bruns T.D., Bidartondo M.I., Taylor D.L. Host specificity in ectomycorrhizal communities: what do the exceptions tell us?. Integr. Comp. Biol. 2002, 42:352-359.
10. Camproux A.C., Tuffery P., Chevrolat J.P., Boisvieux J.F., Hazout S. Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng. 1999, 12:1063-1073.
11. Camproux A.C., Gautier R., Tuffery P. A hidden markov model derived structural alphabet for proteins. J. Mol. Biol. 2004, 339:591-605.
12. Cardoza V., Stewart C.N. Brassica biotechnology: progress in cellular and molecular biology. In Vitro Cell. Dev. Biol. Plants 2004, 40:542-551.
13. Carne W.M. A preliminary census of plant diseases of south-western Australia. Fungal and bacterial diseases of plants in Western Australia. J. Roy. Soc. West Aust. 1925, 11:43-68.
14. Chen C.Y., Howlett J.B. Rapid necrosis of guard cells is associated with the arrest of fungal growth in leaves of Indian mustard (Brassica juncea) inoculated with avirulent isolates of Leptosphaeria maculans. Physiol. Mol. Plant Pathol. 1996, 48:73-81.
15. Chen P.Y., Wang C.K., Soong S.C., To K.Y. Complete sequence of the binary vector pBI121 and its application in cloning T-DNA insertion from transgenic plants. Mol. Breed. 2003, 11:287-293.
16. Chen H.-J., Wang S.-J., Chen C.-C., Yeh K.-W. New gene construction strategy in T-DNA vector to enhance expression level of sweet potato sporamin and insect resistance in transgenic Brassica oleracea. Plant Sci. 2006, 171:367-374.
17. Dash C., Ahmad A., Nath D., Rao M. Novel bifunctional inhibitor of xylanase and aspartic protease: implications for inhibition of fungal growth antimicrobial agents and chemotherapy. Antimicrob. Agents Chemother. 2001, 45:2008-2017.
18. Eswar N., Marti-Renom M.A., Webb B., Madhusudhan M.S., Eramian D., Shen M., Pieper U., Sali A. Comparative protein structure modeling with MODELLER. Curr. Protoc. Bioinf. 2006, (Suppl. 15):5.6.1-5.6.30.
19. Frappat L., Minichini C., Sciarrino A., Sorba P. Universality and Shannon entropy of codon usage. Phys. Rev. E: Stat. Nonlinear Soft Matter Phys. 2003, 68:061910.
20. Garcia-Calvo M., Peterson E.P., Leiting B., Ruel R., Nicholson D.W., Thornberry N.A. Inhibition of human caspases by peptide-based and macromolecular inhibitors. J. Biol. Chem. 1998, 273:32608-32613.
21. Gelvin S.B. Agrobacterium and plant genes involved in T-DNA transfer and integration. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2000, 51:223-256.
22. Greiner S., Krausgrill S., Rausch T. Cloning of a tobacco apoplasmic invertase inhibitor proof of function of the recombinant protein and expression analysis during plant development. Plant Physiol. 1998, 116:733-742.
23. Higgins J., Newbury H., Barbara D., Muthumeenakshi S., Puddephat I. The production of marker-free genetically engineered Broccoli with sense and antisense ACC synthase 1 and ACC oxidases 1 and 2 to extend shelf-life. Mol. Breed. 2006, 17:7-20.
24. Idnurm A., Howlett B.J. Isocitrate lyase is essential for pathogenicity of the fungus Leptosphaeria maculans to Canola (Brassica napus). Eukaryot. Cell 2002, 1:719-724.
25. Jin R.G., Liu Y.-B., Tabashnik B.E., Borthakur D. Development of transgenic cabbage (Brassica oleracea var. capitata) for insect resistance by Agrobacterium tumefaciens-mediated transformation. In Vitro Cell. Dev. Biol.-Plants 2000, 36:231-237.
26. Kaplan W., Littlejohn T.G. Swiss-PDB viewer (deep view). Brief Bioinf. 2001, 2:195-197.
27. Kaur H., Garg A., Raghava G.P. PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept. Lett. 2007, 14:626-631.
28. Kelly B.G., Wall D.M., Boland C.A., Meijer W.G. Isocitrate lyase of the facultative intracellular pathogen Rhodococcus equi. Microbiology 2002, 148:793-798.
29. Kornberg H.L., Krebs H.A. Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle. Nature 1957, 179:988-991.
30. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
31. Latham P.W. Therapeutic peptides revisited. Nat. Biotechnol. 1999, 17:755-757.
32. Lee H.S., Lee T.H., Ji H.L., Chae C.S., Chung S.C., Shin D.S., Shin J., Oh K.B. Inhibition of the pathogenicity of Magnaporthe grisea by bromophenols, isocitrate lyase inhibitors, from the red Alga Odonthalia corymbifera. J. Agric. Food Chem. 2007, 55:6923-6928.
33. Lorenz M.C., Fink G.R. The glyoxylate cycle is required for fungal virulence. Nature 2001, 412:83-86.
34. Maupetit J., Tuffery P., Derreumaux P. A coarse-grained protein force field for folding and structure prediction. Proteins 2007, 69:394-408.
35. Maupetit J., Derreumaux P., Tuffery P. PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res. 2009, 37:498-503.
36. Maupetit J., Derreumaux P., Tuffery P. A fast and accurate method for large-scale de novo peptide structure prediction. J. Comput. Chem. 2009.
37. Mayerhofer R., Wilde K., Mayerhofer M., Lydiate D., Bansal V.K., Good A.G., Parkin I.A. Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus. Genetics 2005, 171:1977-1988.
38. McKinney J.D., Hoener zu Bentrup K., Munoz-Elias E.J., Miczak A., Chen B., Chan W.T., Swenson D., Sacchettini J.C., Jacobs W.R., Russell D.G. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 2000, 406:735-738.
39. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19:1639-1662.
40. Nakamura Y., Gojobori T., Ikemura T. Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 1998, 26:334-335.
41. Oyedotun K.S., Lemire B.D. The quaternary structure of the Saccharomyces cerevisiae succinate dehydrogenase. J. Biol. Chem. 2004, 279:9424-9431.
42. Parang K., Till J.H., Ablooglu A.J., Kohanski R.A., Hubbard S.R., Cole P.A. Mechanism-based design of a protein kinase inhibitor. Nat. Struct. Biol. 2001, 8:37-41.
43. Peter R., Ian L., Alan B. EMBOSS: the European molecular biology open suite. Trends Genet. 2000, 16:276-277.
44. Rao G.S., Ramachandran M.V., Bajaj J.S. In silico structure-based design of a potent and selective small peptide inhibitor of protein tyrosine phosphatase 1B, a novel therapeutic target for obesity and Type 2 diabetes mellitus: a computer modeling approach. J. Biomol. Struct. Dyn. 2006, 23:377-384.
45. Rimmer S.R., Van Den Berg C.G.J. Resistance of oilseed Brassica spp. to blackleg caused by Leptosphaeria maculans. Can. J. Plant Pathol. 1992, 14:56-66.
46. Ritchie D.W., Kemp G.J.L. Protein docking using spherical polar fourier correlations. PROTEINS: Struct. Funct. Genet. 2000, 39:178-194.
47. Rose J.K.C., Ham K.-S., Darvill A.G., Albersheim P. Molecular cloning and characterization of glucanase inhibitor proteins: coevolution of a counterdefense mechanism by plant pathogens. The Plant Cell 2002, 14:1329-1345.
48. Roy N.N. Interspecific transfer of Brassica juncea type high blackleg resistance to Brassica napus. Euphytica 1984, 33:295-303.
49. Sanner M.F. Python: a programming language for software integration and development. J. Mol. Graphics Modell. 1999, 17:57-61.
50. Scott W.R.P., Hünenberger P.H., Tironi I.G., Mark A.E., Billeter S.R., Fennen J., Torda A.E., Huber T., Krüger P., van Gunsteren W.F. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 1999, 103:3596-3607.
51. Sivasithamparam K., Barbetti M.J., Li H. Recurring challenges from a Necrotrophic fungal plant pathogen: a case study with Leptosphaeria maculans (causal agent of blackleg disease in brassicas) in Western Australia. Ann. Bot. 2005, 96:363-377.
52. Steinmetz K.A., Potter J.D. Vegetables, fruit, and cancer prevention: a review. J. Am. Diet. Assoc. 1996, 96:1027-1039.
53. Tuffery P., Derreumaux P. Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm. Proteins 2005, 61:732-740.
54. Tuffery P., Guyon F., Derreumaux P. Improved greedy algorithm for protein structure reconstruction. J. Comput. Chem. 2005, 26:506-513.
55. U, N. Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jpn. J. Bot. 1935, 7:389-452.
56. Yagi Y., Terada K., Noma T., Ikebukuro K., Sode K. In silico panning for a non-competitive peptide inhibitor. BMC Bioinf. 2007, 8:1-11.