Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii

BMC Microbiology

Xue-Chang Wu²  Ou Li²  Wen-Peng Zhao²  Rui Ding²  Shuang-Lin Zhou¹  Tian-Zhe Liu²  Chao-Dong Qian² 

[1] Zhejiang Pharmaceutical College, Ningbo, Zhejiang Province, P.R.China;Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, P.R.China

关键词: Antimicrobial agent;    Gene cluster;    Biosynthesis;    Non-ribosomal peptide;   

Others  :  1221767
DOI  :  10.1186/1471-2180-12-197

 received in 2012-06-12, accepted in 2012-08-29,  发布年份 2012

【 摘 要 】

Background

Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway.

Results

A potential pelgipeptin synthetase gene cluster (plp) was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs), with one, seven, and one module(s), respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1) provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis.

Conclusions

In this study, a gene cluster (plp) responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.

【 授权许可】

   
2012 Qian et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1 .

Figure 2 .

【 参考文献 】

• [1]Wu XC, Shen XB, Ding R, Qian CD, Fang HH, Li O: Isolation and partial characterization of antibiotics produced by Paenibacillus elgii B69. FEMS Microbiol Lett 2010, 310(1):32-38.
• [2]Arguelles-Arias A, Ongena M, Halimi B, Lara Y, Brans A, Joris B, Fickers P: Bacillus amyloliquefaciens GA 1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens. Microb Cell Fact 2009, 8(63):1-12.
• [3]Ding R, Wu XC, Qian CD, Teng Y, Li O, Zhan ZJ, Zhao YH: Isolation and identification of lipopeptide antibiotics from Paenibacillus elgii B69 with inhibitory activity against methicillin-resistant Staphylococcus aureus. J Microbiol 2011, 49(6):942-949.
• [4]Finking R, Marahiel MA: Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 2004, 58:453-488.
• [5]Schwarzer D, Finking R, Marahiel MA: Nonribosomal peptides: from genes to products. Nat Prod Rep 2003, 20(3):275-287.
• [6]Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
• [7]Bachmann BO, Ravel J: Methods for In Silico Prediction of Microbial Secondary Metabolic Pathways from DNA Sequence Data. Methods Enzymol 2009, 458:181-217.
• [8]Rausch C, Weber T, Kohlbacher O, Wohlleben W, Huson DH: Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs). Nucleic Acids Res 2005, 33(18):5799.
• [9]Wen Y, Wu X, Teng Y, Qian C, Zhan Z, Zhao Y, Li O: Identification and analysis of the gene cluster involved in biosynthesis of paenibactin, a catecholate siderophore produced by Paenibacillus elgii B69. Environ Microbiol 2011, 13(10):2726-2737.
• [10]McQuade TJ, Shallop AD, Sheoran A, Delproposto JE, Tsodikov OV, Garneau-Tsodikova S: A nonradioactive high-throughput assay for screening and characterization of adenylation domains for nonribosomal peptide combinatorial biosynthesis. Anal Biochem 2009, 386(2):244-250.
• [11]Ding R, Li Y, Qian C, Wu X: Draft Genome Sequence of Paenibacillus elgii B69, a Strain with Broad Antimicrobial Activity. J Bacteriol 2011, 193(17):4537.
• [12]Choi SK, Park SY, Kim R, Kim SB, Lee CH, Kim JF, Park SH: Identification of a polymyxin synthetase gene cluster of Paenibacillus polymyxa and heterologous expression of the gene in Bacillus subtilis. J Bacteriol 2009, 191(10):3350-3358.
• [13]Rausch C, Hoof I, Weber T, Wohlleben W, Huson D: Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evol Biol 2007, 7(1):78. BioMed Central Full Text
• [14]Kessler N, Schuhmann H, Morneweg S, Linne U, Marahiel MA: The linear pentadecapeptide gramicidin is assembled by four multimodular nonribosomal peptide synthetases that comprise 16 modules with 56 catalytic domains. Journal Biol Chem 2004, 279(9):7413-7419.
• [15]Saum SH, Muller V: Growth phase-dependent switch in osmolyte strategy in a moderate halophile: ectoine is a minor osmolyte but major stationary phase solute in Halobacillus halophilus. Environ Microbiol 2008, 10(3):716-726.
• [16]Vandenende CS, Vlasschaert M, Seah SYK: Functional characterization of an aminotransferase required for pyoverdine siderophore biosynthesis in Pseudomonas aeruginosa PAO1. J Bacteriol 2004, 186(17):5596-5602.
• [17]Tjalsma H, Bolhuis A, Jongbloed JDH, Bron S, Van Dijl JM: Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome. Microbiol Mol Biol R 2000, 64(3):515.
• [18]Jaeger KE, Ransac S, Koch HB, Ferrato F, Dijkstra BW: Topological characterization and modeling of the 3D structure of lipase from Pseudomonas aeruginosa. FEBS Lett 1993, 332(1–2):143-149.
• [19]Eggert T, Pencreac’h G, Douchet I, Verger R, Jaeger KE: A novel extracellular esterase from Bacillus subtilis and its conversion to a monoacylglycerol hydrolase. Eur J Biochem 2000, 267(21):6459-6469.
• [20]Arpigny JL, Jaeger KE: Bacterial lipolytic enzymes: classification and properties. Biochem J 1999, 343(Pt 1):177.
• [21]Hashizume H, Nosaka C, Hirosawa S, Igarashi M, Nishimura Y, Akamatsu Y: Production of tripropeptins in media supplemented with precursors based on the biosynthetic pathway. ARKIVOC 2007, 7:241-253.
• [22]Kagami S, Esumi Y, Nakakoshi M, Yoshihama M, Kimura KI: Control of liposidomycin production through precursor-directed biosynthesis. J Antibiot 2003, 56(6):552-556.
• [23]Copp JN, Neilan BA: The phosphopantetheinyl transferase superfamily: phylogenetic analysis and functional implications in cyanobacteria. Appl Environ Microbiol 2006, 72(4):2298-2305.
• [24]Cosmina P, Rodriguez F, de Ferra F, Grandi G, Perego M, Venema G, van Sinderen D: Sequence and analysis of the genetic locus responsible for surfactin synthesis in Bacillus subtilis. Mol Microbiol 1993, 8(5):821-831.
• [25]Yakimov MM, Kroger A, Slepak TN, Giuliano L, Timmis KN, Golyshin PN: A putative lichenysin A synthetase operon in Bacillus licheniformis: initial characterization. Biochim Biophys Acta 1998, 1399(2–3):141-153.
• [26]Tosato V, Albertini AM, Zotti M, Sonda S, Bruschi CV: Sequence completion, identification and definition of the fengycin operon in Bacillus subtilis 168. Microbiology 1997, 143(Pt 11):3443-3450.
• [27]Li J, Jensen SE: Nonribosomal biosynthesis of fusaricidins by Paenibacillus polymyxa PKB1 involves direct activation of a D-amino acid. Chem Biol 2008, 15(2):118-127.
• [28]Steller S, Sokoll A, Wilde C, Bernhard F, Franke P, Vater J: Initiation of surfactin biosynthesis and the role of the SrfD-thioesterase protein. Biochemistry 2004, 43(35):11331-11343.