Comprehensive Analysis of Distinctive Polyketide and Nonribosomal Peptide Structural Motifs Encoded in Microbial Genomes

Journal of Molecular Biology

Volumn 368, Issue 5, 2007, Pages 1500-1517

  Minowa, Yohsuke ^a   Araki, Michihiro ^b   Kanehisa, Minoru ^a,b  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

antibiotics; motif extraction of chemical structures; nonribosomal peptide; pathogenicity; polyketide

Indexed keywords

CARBONYL DERIVATIVE; NONRIBOSOMAL PEPTIDE; PEPTIDE DERIVATIVE; POLYKETIDE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CLUSTER ANALYSIS; GENE CLUSTER; MICROBIAL GENETICS; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; VIRULENCE;

BURKHOLDERIA; PSEUDOMONAS;

EID: 34247279292     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.02.099     Document Type: Article

References (51)

1. Menzella H.G., Reid R., Carney J.R., Chandran S.S., Reisinger S.J., Patel K.G., et al. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nature Biotechnol. 23 (2005) 1171-1176
2. Doekel S., and Marahiel M.A. Dipeptide formation on engineered hybrid peptide synthetases. Chem. Biol. 7 (2000) 373-384
3. Gokhale R.S., Tsuji S.Y., Cane D.E., and Khosla C. Dissecting and exploiting intermodular communication in polyketide synthases. Science 284 (1999) 482-485
4. McDaniel R., Thamchaipenet A., Gustafsson C., Fu H., Betlach M., and Ashley G. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products. Proc. Natl Acad. Sci. USA 96 (1999) 1846-1851
5. Gonzalez-Lergier J., Broadbelt L.J., and Hatzimanikatis V. Theoretical considerations and computational analysis of the complexity in polyketide synthesis pathways. J. Am. Chem. Soc. 127 (2005) 9930-9938
6. Kamra P., Gokhale R.S., and Mohanty D. SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. Nucl. Acids Res. 33 (2005) W220-W225
7. Lautru S., Deeth R.J., Bailey L.M., and Challis G.L. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nature Chem. Biol. 1 (2005) 265-269
8. Rausch C., Weber T., Kohlbacher O., Wohlleben W., and Huson D.H. Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucl. Acids Res. 33 (2005) 5799-5808
9. Ansari M.Z., Yadav G., Gokhale R.S., and Mohanty D. NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucl. Acids Res. 32 (2004) W405-W413
10. Yadav G., Gokhale R.S., and Mohanty D. Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J. Mol. Biol. 328 (2003) 335-363
11. Keatinge-Clay A.T., Shelat A.A., Savage D.F., Tsai S.C., Miercke L.J., O'Connell III J.D., et al. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147-154
12. Challis G.L., Ravel J., and Townsend C.A. Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem. Biol. 7 (2000) 211-224
13. Stachelhaus T., Mootz H.D., and Marahiel M.A. The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem. Biol. 6 (1999) 493-505
14. Conti E., Stachelhaus T., Marahiel M.A., and Brick P. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16 (1997) 4174-4183
15. Serre L., Verbree E.C., Dauter Z., Stuitje A.R., and Derewenda Z.S. The Escherichia coli malonyl-CoA:acyl carrier protein transacylase at 1.5-A resolution. Crystal structure of a fatty acid synthase component. J. Biol. Chem. 270 (1995) 12961-12964
16. Hahn M., and Stachelhaus T. Harnessing the potential of communication-mediating domains for the biocombinatorial synthesis of nonribosomal peptides. Proc. Natl Acad. Sci. USA 103 (2006) 275-280
17. Lai J.R., Fischbach M.A., Liu D.R., and Walsh C.T. A protein interaction surface in nonribosomal peptide synthesis mapped by combinatorial mutagenesis and selection. Proc. Natl Acad. Sci. USA 103 (2006) 5314-5319
18. Hahn M., and Stachelhaus T. Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains. Proc. Natl Acad. Sci. USA 101 (2004) 15585-15590
19. Liu F., Garneau S., and Walsh C.T. Hybrid nonribosomal peptide-polyketide interfaces in epothilone biosynthesis: minimal requirements at N and C termini of EpoB for elongation. Chem. Biol. 11 (2004) 1533-1542
20. Moss S.J., Martin C.J., and Wilkinson B. Loss of co-linearity by modular polyketide synthases: a mechanism for the evolution of chemical diversity. Nature Prod. Rep. 21 (2004) 575-593
21. Broadhurst R.W., Nietlispach D., Wheatcroft M.P., Leadlay P.F., and Weissman K.J. The structure of docking domains in modular polyketide synthases. Chem. Biol. 10 (2003) 723-731
22. Kumar P., Li Q., Cane D.E., and Khosla C. Intermodular communication in modular polyketide synthases: structural and mutational analysis of linker mediated protein-protein recognition. J. Am. Chem. Soc. 125 (2003) 4097-4102
23. Linne U., Stein D.B., Mootz H.D., and Marahiel M.A. Systematic and quantitative analysis of protein-protein recognition between nonribosomal peptide synthetases investigated in the tyrocidine biosynthetic template. Biochemistry 42 (2003) 5114-5124
24. Keating T.A., Marshall C.G., Walsh C.T., and Keating A.E. The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains. Nature Struct. Biol. 9 (2002) 522-526
25. Marshall C.G., Burkart M.D., Meray R.K., and Walsh C.T. Carrier protein recognition in siderophore-producing nonribosomal peptide synthetases. Biochemistry 41 (2002) 8429-8437
26. Wu N., Cane D.E., and Khosla C. Quantitative analysis of the relative contributions of donor acyl carrier proteins, acceptor ketosynthases, and linker regions to intermodular transfer of intermediates in hybrid polyketide synthases. Biochemistry 41 (2002) 5056-5066
27. Tsuji S.Y., Cane D.E., and Khosla C. Selective protein-protein interactions direct channeling of intermediates between polyketide synthase modules. Biochemistry 40 (2001) 2326-2331
28. Wu N., Tsuji S.Y., Cane D.E., and Khosla C. Assessing the balance between protein-protein interactions and enzyme-substrate interactions in the channeling of intermediates between polyketide synthase modules. J. Am. Chem. Soc. 123 (2001) 6465-6474
29. Zhang Y.M., Rao M.S., Heath R.J., Price A.C., Olson A.J., Rock C.O., et al. Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III. J. Biol. Chem. 276 (2001) 8231-8238
30. Haydock S.F., Appleyard A.N., Mironenko T., Lester J., Scott N., and Leadlay P.F. Organization of the biosynthetic gene cluster for the macrolide concanamycin A in Streptomyces neyagawaensis ATCC 27449. Microbiology 151 (2005) 3161-3169
31. Di Vincenzo L., Grgurina I., and Pascarella S. In silico analysis of the adenylation domains of the freestanding enzymes belonging to the eucaryotic nonribosomal peptide synthetase-like family. FEBS J. 272 (2005) 929-941
32. Landgraf R., Fischer D., and Eisenberg D. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 12 (1999) 943-951
33. McAlpine J.B., Bachmann B.O., Piraee M., Tremblay S., Alarco A.M., Zazopoulos E., et al. Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. J. Nature Prod. 68 (2005) 493-496
34. Miao V., Coeffet-Legal M.F., Brian P., Brost R., Penn J., Whiting A., et al. Daptomycin biosynthesis in Streptomyces roseosporus: cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology 151 (2005) 1507-1523
35. Wu K., Chung L., Revill W.P., Katz L., and Reeves C.D. The FK520 gene cluster of Streptomyces hygroscopicus var. ascomyceticus (ATCC 14891) contains genes for biosynthesis of unusual polyketide extender units. Gene 251 (2000) 81-90
36. Borgos S.E., Tsan P., Sletta H., Ellingsen T.E., Lancelin J.M., and Zotchev S.B. Probing the structure-function relationship of polyene macrolides: engineered biosynthesis of soluble nystatin analogues. J. Med. Chem. 49 (2006) 2431-2439
37. Enright A.J., Illopoulos I., Kyrpides N.C., and Ouzounis A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402 (1999) 86-90
38. Marcotte E.M., Pellegrini M., Ng H., Rice D.W., Yeates T.O., and Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 285 (1999) 751-753
39. Bringmann G., Noll T.F., Gulder T.A.M., Grune M., Dreyer M., Wilde C., et al. Different polyketide folding modes converge to an identical molecular architecture. Nature Chem. Biol. 2 (2006) 429-433
40. Agnoli K., Lowe C.A., Farmer K.L., Husnain S.I., and Thomas M.S. The ornibactin biosynthesis and transport genes of Burkholderia cenocepacia are regulated by an extracytoplasmic function sigma factor which is a part of the Fur regulon. J. Bacteriol. 188 (2006) 3631-3644
41. Oka M., Yaginuma K., Numata K., Konishi M., Oki T., and Kawaguchi H. Glidobactins A, B and C, new antitumor antibiotics. II. Structure elucidation. J. Antibiot (Tokyo) 41 (1988) 1338-1350
42. Terui Y., Nishikawa J., Hinoo H., Kato T., and Shoji J. Structures of cepafungins I, II and III. J. Antibiot. (Tokyo) 43 (1990) 788-795
43. Amrein H., Makart S., Granado J., Shakya R., Schneider-Pokorny J., and Dudler R. Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301 D-R. Mol. Plant Microbe Interact. 17 (2004) 90-97
44. Roongsawang N., Hase K., Haruki M., Imanaka T., Morikawa M., and Kanaya S. Cloning and characterization of the gene cluster encoding arthrofactin synthetase from Pseudomonas sp. MIS38. Chem. Biol. 10 (2003) 869-880
45. Rodrigues L., Banat I.M., Teixeira J., and Oliveira R. Biosurfactants: potential applications in medicine. J. Antimicrob. Chemother. 57 (2006) 609-618
46. Paulsen I.T., Press C.M., Ravel J., Kobayashi D.Y., Myers G.S., Mavrodi D.V., et al. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnol. 23 (2005) 873-878
47. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
48. Eddy S.R. Profile hidden Markov models. Bioinformatics 14 (1998) 755-763
49. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
50. Kimura M. The Neutral Theory of Evolution (1983), Cambridge University Press, Cambridge, UK
51. Hattori M., Okuno Y., Goto S., and Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125 (2003) 11853-11865