Molecular cloning of a novel bioH gene from an environmental metagenome encoding a carboxylesterase with exceptional tolerance to organic solvents

BMC Biotechnology

Yuping Shi¹  Yingjie Pan¹  Bailin Li¹  Wei He²  Qunxin She³  Lanming Chen¹ 

[1] Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Engineering Centre for Quality Control and Risk Assessment of Aquatic Products, College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, 201306, Shanghai, P. R. China

[2] Shanghai Hanyu Bio-lab, 151 Ke Yuan Road, 201203, Shanghai, P.R. China

[3] Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 N, Copenhagen, Denmark

关键词: Aqueous environment;    Metagenome;    Carboxylesterase;    Biotin biosynthetic pathway;    BioH;   

Others  :  1131098
DOI  :  10.1186/1472-6750-13-13

 received in 2012-10-09, accepted in 2013-01-25,  发布年份 2013

【 摘 要 】

Background

BioH is one of the key enzymes to produce the precursor pimeloyl-ACP to initiate biotin biosynthesis de novo in bacteria. To date, very few bioH genes have been characterized. In this study, we cloned and identified a novel bioH gene, bioHx, from an environmental metagenome by a functional metagenomic approach. The bioHx gene, encoding an enzyme that is capable of hydrolysis of p-nitrophenyl esters of fatty acids, was expressed in Escherichia coli BL21 using the pET expression system. The biochemical property of the purified BioHx protein was also investigated.

Results

Screening of an unamplified metagenomic library with a tributyrin-containing medium led to the isolation of a clone exhibiting lipolytic activity. This clone carried a 4,570-bp DNA fragment encoding for six genes, designated bioF, bioHx, fabG, bioC, orf5 and sdh, four of which were implicated in the de novo biotin biosynthesis. The bioHx gene encodes a protein of 259 aa with a calculated molecular mass of 28.60 kDa, displaying 24-39% amino acid sequence identity to a few characterized bacterial BioH enzymes. It contains a pentapeptide motif (Gly₇₆-Trp₇₇-Ser₇₈-Met₇₉-Gly₈₀) and a catalytic triad (Ser₇₈-His₂₃₀-Asp₂₀₂), both of which are characteristic for lipolytic enzymes. BioHx was expressed as a recombinant protein and characterized. The purified BioHx protein displayed carboxylesterase activity, and it was most active on p-nitrophenyl esters of fatty acids substrate with a short acyl chain (C4). Comparing BioHx with other known BioH proteins revealed interesting diversity in their sensitivity to ionic and nonionic detergents and organic solvents, and BioHx exhibited exceptional resistance to organic solvents, being the most tolerant one amongst all known BioH enzymes. This ascribed BioHx as a novel carboxylesterase with a strong potential in industrial applications.

Conclusions

This study constituted the first investigation of a novel bioHx gene in a biotin biosynthetic gene cluster cloned from an environmental metagenome. The bioHx gene was successfully cloned, expressed and characterized. The results demonstrated that BioHx is a novel carboxylesterase, displaying distinct biochemical properties with strong application potential in industry. Our results also provided the evidence for the effectiveness of functional metagenomic approach for identifying novel bioH genes from complex ecosystem.

【 授权许可】

   
2013 Shi et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Tong L: Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012. in press
• [2]Cronan JE, Lin S: Synthesis of the α, ω-dicarboxylic acid precursor of biotin by the canonical fatty acid biosynthetic pathway. Curr Opin Chem Biol 2011, 15:407-413.
• [3]Lin S, Hanson RE, Cronan JE: Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat Chem Biol 2010, 6(9):682-688.
• [4]Bower S, Perkins JB, Yocum RR, Howitt CL, Rahaim P, Pero J: Cloning, sequencing, and characterization of the Bacillus subtilis biotin biosynthetic operon. J Bacteriol 1996, 178:4122-4130.
• [5]Shapiro MM, Chakravartty V, Cronan JE: Remarkable diversity in the enzymes catalyzing the last step in synthesis of the pimelate moiety of biotin. PLoS One 2012, 7(11):e49440.
• [6]Min-A K, Kim HS, Oh JY, Song BK, Song JK: Gene cloning, expression, and characterization of a new carboxylesterase from Serratia sp. SES-01: comparison with Escherichia coli BioHe Enzyme. J Microbiol Biotechnol 2009, 19(2):147-154.
• [7]Akatsuka H, Kawai E, Imai Y, Sakurai N, Omori K: The Serratia marcescens bioH gene encodes an esterase. Gene 2003, 302:185-192.
• [8]Tomczyk NH, Nettleship JE, Baxter RL, Crichton HJ, Webster SP, Campopiano DJ: Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway. FEBS Lett 2002, 513:299-304.
• [9]Kiyasu T, Nagahashi Y, Hoshino T: Cloning and characterization of biotin biosynthetic genes of Kurthia sp. Gene 2001, 265:103-113.
• [10]Ollis DL, Cheah E, Cygler M, Dijkstra BW, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J, Sussman JL, Verschueren KHG, Goldman A: The alpha/beta hydrolase fold. Protein Eng 1992, 5:197-211.
• [11]Arpigny JL, Jaeger K-E: Bacterial lipolytic enzymes: classification and properties. Biochem J 1999, 343:177-183.
• [12]Sanishvilia R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM: Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem 2003, 278(28):26039-26045.
• [13]Sharmaa R, Chistib Y, Banerjee UC: Production, purification, characterization, and applications of lipases. Biotechnol Adv 2001, 19:627-662.
• [14]Amann RI, Ludwig W, Schleifer KH: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169.
• [15]Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM: Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 2000, 66:2541-2547.
• [16]Chu X, He H, Guo C, Sun B: Identification of two novel esterases from a marine metagenomic library derived from South China Sea. Appl Microbiol Biotechnol 2008, 80(4):615-625.
• [17]Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D, Santos VA, Strompl C, Elborough K, Jarvis G, Neef A, Yakimov MM, Timmis KN, Golyshin PN: Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ Microbiol 2005, 7(12):1996-2010.
• [18]Hong KS, Lim HK, Chung EJ, Park EJ, Lee MH, Kim JC, Choi GJ, Cho KY, Lee SW: Selection and characterization of forest soil metagenome genes encoding lipolytic enzymes. J Microbiol Biotechnol 2007, 17(10):1655-1660.
• [19]Kang C-H, Oh K-H, Lee M-H, Oh T-K, Kim BH, Yoon J-H: A novel family VII esterase with industrial potential from compost metagenomic library. Microbial Cell Factories 2011, 10:41. BioMed Central Full Text
• [20]Berg G, Roskot N, Smalla K: Genotypic and phenotypic relationships between clinical and environmental isolates of Stenotrophomonas maltophilia. J Clin Microbiol 1999, 37(11):3594-6000.
• [21]Rodionov DA, Mironov AA, Gelfand MS: Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 2002, 12:1507-1516.
• [22]Sambrook J, Russell DW: Molecular Cloning: A Laboratory Manual. New York: Cold Spring Harbor Press; 2001.
• [23]Zhou J, Bruns MA, Tiedje JM: DNA Recovery from soils of diverse composition. Appl Environ Microbiol 1996, 62(2):316-322.
• [24]Larkin MA, Blackshields G, Brown NP, Chenna R, NcGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
• [25]Tamura K, Dudley J, Nei M, Kumar S: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007, 24:1596-1599.
• [26]Watanabe H, Shiratori T, Shoji H, Miyatake S, Okazaki Y, Ikuta K, Sato T, Saito T: A Novel acyl-CoA Thioesterase Enhances Its Enzymatic Activity by Direct Binding with HIV Nef. Biochem Biophys Res Commun 1997, 238:234-239.