Mining microbial genomes for new natural products and biosynthetic pathways

被引:174
作者
Challis, Gregory L. [1 ]
机构
[1] Univ Warwick, Dept Chem, Coventry CV4 7AL, W Midlands, England
来源
MICROBIOLOGY-SGM | 2008年 / 154卷
基金
英国生物技术与生命科学研究理事会; 英国惠康基金;
关键词
D O I
10.1099/mic.0.2008/018523-0
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Analyses of microbial genome sequences have revealed numerous examples of 'cryptic' or 'orphan' biosynthetic gene clusters, with the potential to direct the production of novel, structurally complex natural products. This article summarizes the various methods that have been developed for discovering the products of cryptic biosynthetic gene clusters in microbes and gives an account of my group's discovery of the products of two such gene clusters in the model actinomycete Streptomyces coelicolor M145. These discoveries hint at new mechanisms, roles and specificities for natural product biosynthetic enzymes. Our efforts to elucidate these are described. The identification of new secondary metabolites of S. coelicolor raises the question: what is their biological function? Progress towards answering this question is also summarized.
引用
收藏
页码:1555 / 1569
页数:15
相关论文
共 67 条
[51]  
MULLER G, 1984, J BACTERIOL, V160, P304
[52]   Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection [J].
Nguyen, Tuanh ;
Ishida, Keishi ;
Jenke-Kodama, Holger ;
Dittmann, Elke ;
Gurgui, Cristian ;
Hochmuth, Thomas ;
Taudien, Stefan ;
Platzer, Matthias ;
Hertweck, Christian ;
Piel, Joern .
NATURE BIOTECHNOLOGY, 2008, 26 (02) :225-233
[53]   Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338 [J].
Oliynyk, Markiyan ;
Samborskyy, Markiyan ;
Lester, John B. ;
Mironenko, Tatiana ;
Scott, Nataliya ;
Dickens, Shilo ;
Haydock, Stephen F. ;
Leadlay, Peter F. .
NATURE BIOTECHNOLOGY, 2007, 25 (04) :447-453
[54]   Genome sequence of an industrial microorganism Streptomyces avermitilis:: Deducing the ability of producing secondary metabolites [J].
Omura, S ;
Ikeda, H ;
Ishikawa, J ;
Hanamoto, A ;
Takahashi, C ;
Shinose, M ;
Takahashi, Y ;
Horikawa, H ;
Nakazawa, H ;
Osonoe, T ;
Kikuchi, H ;
Shiba, T ;
Sakaki, Y ;
Hattori, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (21) :12215-12220
[55]   Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5 [J].
Paulsen, IT ;
Press, CM ;
Ravel, J ;
Kobayashi, DY ;
Myers, GSA ;
Mavrodi, DV ;
DeBoy, RT ;
Seshadri, R ;
Ren, QH ;
Madupu, R ;
Dodson, RJ ;
Durkin, AS ;
Brinkac, LM ;
Daugherty, SC ;
Sullivan, SA ;
Rosovitz, MJ ;
Gwinn, ML ;
Zhou, LW ;
Schneider, DJ ;
Cartinhour, SW ;
Nelson, WC ;
Weidman, J ;
Watkins, K ;
Tran, K ;
Khouri, H ;
Pierson, EA ;
Pierson, LS ;
Thomashow, LS ;
Loper, JE .
NATURE BIOTECHNOLOGY, 2005, 23 (07) :873-878
[56]   GERMICIDIN, AN AUTOREGULATIVE GERMINATION INHIBITOR OF STREPTOMYCES-VIRIDOCHROMOGENES NRRL B-1551 [J].
PETERSEN, F ;
ZAHNER, H ;
METZGER, JW ;
FREUND, S ;
HUMMEL, RP .
JOURNAL OF ANTIBIOTICS, 1993, 46 (07) :1126-1138
[57]   A polyketide synthase in glycopeptide biosynthesis -: The biosynthesis of the non-proteinogenic amino acid (S)-3,5-dihydroxyphenylglycine [J].
Pfeifer, V ;
Nicholson, GJ ;
Ries, J ;
Recktenwald, J ;
Schefer, AB ;
Shawky, RM ;
Schröder, J ;
Wohlleben, W ;
Pelzer, S .
JOURNAL OF BIOLOGICAL CHEMISTRY, 2001, 276 (42) :38370-38377
[58]   Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs) [J].
Rausch, C ;
Weber, T ;
Kohlbacher, O ;
Wohlleben, W ;
Huson, DH .
NUCLEIC ACIDS RESEARCH, 2005, 33 (18) :5799-5808
[59]   A model of structure and catalysis for ketoreductase domains in modular polyketide synthases [J].
Reid, R ;
Piagentini, M ;
Rodriguez, E ;
Ashley, G ;
Viswanathan, N ;
Carney, J ;
Santi, DV ;
Hutchinson, CR ;
McDaniel, R .
BIOCHEMISTRY, 2003, 42 (01) :72-79
[60]   Type III polyketide synthase β-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining [J].
Song, Lijiang ;
Barona-Gomez, Francisco ;
Corre, Christophe ;
Xiang, Longkuan ;
Udwary, Daniel W. ;
Austin, Michael B. ;
Noel, Joseph P. ;
Moore, Bradley S. ;
Challis, Gregory L. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2006, 128 (46) :14754-14755