Inhibition of the growth of Bacillus subtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome

References

• Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995; 59: 143-69; PMID:7535888.
   PubMedGoogle Scholar
• Beja O, Koonin EV, Aravind L, Taylor LT, Seitz H, Stein JL, Bensen DC, Feldman RA, Swanson RV, DeLong EF. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol 2002; 68: 335-45; PMID:11772643; http://dx.doi.org/10.1128/AEM.68.1.335-345.2002
   PubMed Web of Science ®Google Scholar
• Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 2004; 305: 1457-62; PMID:15353801; http://dx.doi.org/10.1126/science.1100025
   PubMed Web of Science ®Google Scholar
• Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA MacNeil IA, Minor C, et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 2000; 66: 2541-7; PMID:10831436; http://dx.doi.org/10.1128/AEM.66.6.2541-2547.2000
   PubMed Web of Science ®Google Scholar
• Treusch AH, Kletzin A, Raddatz G, Ochsenreiter T, Quaiser A, Meurer G, Schuster SC, Schleper C. Characterization of large-insert DNA libraries from soil for environmental genomic studies of archaea. Environ Microbiol 2004; 6: 970-80; PMID:15305922; http://dx.doi.org/10.1111/j.1462-2920.2004.00663.x
   PubMedGoogle Scholar
• Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004; 428: 37-43; PMID:14961025; http://dx.doi.org/10.1038/nature02340
   PubMed Web of Science ®Google Scholar
• Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the sargasso sea. Science 2004; 304: 66-74; PMID:15001713; http://dx.doi.org/10.1126/science.1093857
   PubMed Web of Science ®Google Scholar
• Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P. Metagenomic gene discovery: past, present and future. Trends Biotechnol 2005; 23: 321-9; PMID:15922085; http://dx.doi.org/10.1016/j.tibtech.2005.04.001
   PubMed Web of Science ®Google Scholar
• Kennedy J, Marchesi JR, Dobson AD. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl Microbiol Biotechnol 2007; 75: 11-20; PMID:17318533; http://dx.doi.org/10.1007/s00253-007-0875-2
   PubMedGoogle Scholar
• Kim YJ, Choi GS, Kim SB, Yoon GS, Kim YS, Ryu YW. Screening and characterization of a novel esterase from a metagenomic library. Protein Expr Purif 2006; 45: 315-23; PMID:16061395; http://dx.doi.org/10.1016/j.pep.2005.06.008
   PubMed Web of Science ®Google Scholar
• Lorenz P, Eck J. Metagenomics and industrial applications. Nat Rev Microbiol 2005; 3: 510-6; PMID:15931168; http://dx.doi.org/10.1038/nrmicro1161
   PubMed Web of Science ®Google Scholar
• Lorenz P, Liebeton K, Niehaus F, Eck J. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 2002; 13: 572-7; PMID:12482516; http://dx.doi.org/10.1016/S0958-1669(02)00345-2
   PubMed Web of Science ®Google Scholar
• Selvin J, Kennedy J, Lejon DP, Kiran S, Dobson AD. Isolation identification and biochemical characterization of a novel halo-tolerant lipase from the metagenome of the marine sponge haliclona simulans. Microb Cell Fact 2012; 11: 72; PMID:22657530; http://dx.doi.org/10.1186/1475-2859-11-72
   PubMedGoogle Scholar
• Chang FY, Brady SF. Cloning and characterization of an environmental DNA-derived gene cluster that encodes the biosynthesis of the antitumor substance BE-54017. J Am Chem Soc 2011; 133: 9996-9; PMID:21542592; http://dx.doi.org/10.1021/ja2022653
   PubMed Web of Science ®Google Scholar
• Iqbal HA, Feng Z, Brady SF. Biocatalysts and their small molecule products from metagenomic studies. Curr Opin Chem Biol 2012; 16: 109-16; PMID:22455793; http://dx.doi.org/10.1016/j.cbpa.2012.02.015
   PubMed Web of Science ®Google Scholar
• Felczykowska A, Dydecka A, Bohdanowicz M, Gasior T, Sobon M, Kobas J, Bloch S, Nejman-Falenczyk B, Wegrzyn G. The use of fosmid metagenomic libraries in preliminary screening for various biological activities. Micro Cell Factories 2014; 13:105; PMID:25048369; http://dx.doi.org/10.1186/s12934-014-0105-4
   PubMedGoogle Scholar
• Daniel R. The soil metagenome - a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 2004; 15: 199-204; PMID:15193327; http://dx.doi.org/10.1016/j.copbio.2004.04.005
   PubMed Web of Science ®Google Scholar
• Craig JW, Chang FY, Kim JH, Obiajulu SC, Brady SF. Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental DNA libraries in diverse proteobacteria. Appl Environ Microbiol 2010; 76: 1633-41; PMID:20081001; http://dx.doi.org/10.1128/AEM.02169-09
   PubMed Web of Science ®Google Scholar
• Daniel R. The metagenomics of soil. Nat Rev Microbiol 2005; 3: 470-8; PMID:15931165; http://dx.doi.org/10.1038/nrmicro1160
   PubMed Web of Science ®Google Scholar
• Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998; 5: R245-249; PMID:9818143; http://dx.doi.org/10.1016/S1074-5521(98)90108-9
   PubMed Web of Science ®Google Scholar
• Chung EJ, Lim HK, Kim JC, Choi GJ, Park EJ, Lee MH, Chung YR, Lee SW. Forest soil metagenome gene cluster involved in antifungal activity expression in escherichia coli. Appl Environ Microbiol 2008; 74: 723-30; PMID:18065615; http://dx.doi.org/10.1128/AEM.01911-07
   PubMed Web of Science ®Google Scholar
• Kim SJ, Lee CM, Han BR, Kim MY, Yeo YS, Yoon SH, Koo BS, Jun HK. Characterization of a gene encoding cellulase from uncultured soil bacteria. FEMS Microbiol Lett 2008; 282: 44-51; PMID:18355282; http://dx.doi.org/10.1111/j.1574-6968.2008.01097.x
   PubMed Web of Science ®Google Scholar
• van Elsas JD, Speksnijder AJ, van Overbeek LS. A procedure for the metagenomics exploration of disease-suppressive soils. J Microbiol Methods 2008; 75: 515-22; PMID:18778739; http://dx.doi.org/10.1016/j.mimet.2008.08.004
   PubMedGoogle Scholar
• Steinberg C, Edel-Hermann V, Alabouvette C, Lemanceau P. Soil suppressiveness to plant disease. In: van Elsas JD, Jansson JK, Trevors JT, editors. Modern Soil Microbiology. Boca Raton: Taylor & Francis; 2006; 455-78.
   Google Scholar
• van Elsas JD, Costa R, Jansson J, Sjoling S, Bailey M, Nalin R, Vogel TM, van Overbeek L. The metagenomics of disease-suppressive soils - experiences from the METACONTROL project. Trends Biotechnol 2008; 26: 591-601; PMID:18774191; http://dx.doi.org/10.1016/j.tibtech.2008.07.004
   PubMedGoogle Scholar
• Mendes R, Kruijt M, de Bruijn I, Dekkers E, van der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA et al. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011; 332: 1097-100; PMID:21551032; http://dx.doi.org/10.1126/science.1203980
   PubMed Web of Science ®Google Scholar
• Reddy BV, Kallifidas D, Kim JH, Charlop-Powers Z, Feng Z, Brady SF. Natural product biosynthetic gene diversity in geographically distinct soil microbiomes. Appl Environ Microbiol 2012; 78: 3744-52; PMID:22427492; http://dx.doi.org/10.1128/AEM.00102-12
   PubMed Web of Science ®Google Scholar
• Lim HK, Chung EJ, Kim JC, Choi GJ, Jang KS, Chung YR, Cho KY, Lee SW. Characterization of a forest soil metagenome clone that confers indirubin and indigo production on escherichia coli. Appl Environ Microbiol 2005; 71: 7768-77; PMID:16332749; http://dx.doi.org/10.1128/AEM.71.12.7768-7777.2005
   PubMedGoogle Scholar
• Guan C, Ju J, Borlee BR, Williamson LL, Shen B, Raffa KF, Handelsman J. Signal mimics derived from a metagenomic analysis of the gypsy moth gut microbiota. Appl Environ Microbiol 2007; 73: 3669-76; PMID:17435000; http://dx.doi.org/10.1128/AEM.02617-06
   PubMed Web of Science ®Google Scholar
• Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 2002; 68: 4301-6; PMID:12200279; http://dx.doi.org/10.1128/AEM.68.9.4301-4306.2002
   PubMed Web of Science ®Google Scholar
• Brady SF, Chao CJ, Handelsman J, Clardy J. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett 2001; 3: 1981-4; PMID:11418029; http://dx.doi.org/10.1021/ol015949k
   PubMedGoogle Scholar
• Brady SF, Clardy J. Palmitoylputrescine, an antibiotic isolated from the heterologous expression of DNA extracted from bromeliad tank water. J Nat Prod 2004; 67: 1283-6; PMID:15332842; http://dx.doi.org/10.1021/np0499766
   PubMedGoogle Scholar
• Wang GY, Graziani E, Waters B, Pan W, Li X, McDermott J, Meurer G, Saxena G, Andersen RJ, Davies J. Novel natural products from soil DNA libraries in a streptomycete host. Org Lett 2000; 2: 2401-4; PMID:10956506; http://dx.doi.org/10.1021/ol005860z
   PubMed Web of Science ®Google Scholar
• Kallifidas D, Kang HS, Brady SF. Tetarimycin A, an MRSA-active antibiotic identified through induced expression of environmental DNA gene clusters. J Am Chem Soc 2012; 134: 19552-5; PMID:23157252; http://dx.doi.org/10.1021/ja3093828
   PubMed Web of Science ®Google Scholar
• King RW, Bauer JD, Brady SF. An environmental DNA-derived type II polyketide biosynthetic pathway encodes the biosynthesis of the pentacyclic polyketide erdacin. Angew Chem Int Ed Engl 2009; 48: 6257-61; PMID:19621341; http://dx.doi.org/10.1002/anie.200901209
   PubMedGoogle Scholar
• Feng Z, Kim JH, Brady SF. Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster. J Am Chem Soc 2010; 132: 11902-3; PMID:20690632; http://dx.doi.org/10.1021/ja104550p
   PubMedGoogle Scholar
• Iqbal HA, Craig JW, Brady SF. Antibacterial enzymes from the functional screening of metagenomic libraries hosted in ralstonia metallidurans. FEMS Microbiol Letts 2014; 354: 19-26; PMID:24661178; http://dx.doi.org/10.1111/1574-6968.12431
   PubMedGoogle Scholar
• Chang FY, Brady SF. Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening. Proc Natl Acad Sci USA 2013; 110: 2473-83; PMID:23302687.
   PubMedGoogle Scholar
• Feng Z, Chakraborty D, Dewell SB, Reddy BV, Brady SF. Environmental DNA encoded antibiotics fasamycins A and B inhibit FabF in type II fatty acid biosynthesis. Am Chem Soc 2012; 134: 2981-7; PMID:22224500; http://dx.doi.org/10.1021/ja207662w
   PubMed Web of Science ®Google Scholar
• Kant R, van Passel MW, Sangwan P, Palva A, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Dalin E, Tice H, et al. Genome sequence of "pedosphaera parvula" Ellin514, an aerobic verrucomicrobial isolate from pasture soil. J Bacteriol 2011; 193: 2900-1; PMID:21460084; http://dx.doi.org/10.1128/JB.00299-11
   PubMedGoogle Scholar
• Arpigny JL, Jaeger KE. Bacterial lipolytic enzymes: classification and properties. Biochem J 1999; 343: 177-83; PMID:10493927; http://dx.doi.org/10.1042/0264-6021:3430177
   PubMed Web of Science ®Google Scholar
• Yu EY, Kwon MA, Lee M, Oh JY, Choi JE, Lee JY, Song BK, Hahm DH, Song JK. Isolation and characterization of cold-active family VIII esterases from an arctic soil metagenome. Appl Microbiol Biotechnol 2011; 90: 573-81; PMID:21318360; http://dx.doi.org/10.1007/s00253-011-3132-7
   PubMed Web of Science ®Google Scholar
• Levett PN, Morey RE, Galloway R, Steigerwalt AG, Ellis WA. Reclassification of leptospira parva hovind-hougen et al. 1982 as turneriella parva gen. nov., comb. nov. Int J Syst Evol Microbiol 2005; 55: 1497-9; PMID:16014471; http://dx.doi.org/10.1099/ijs.0.63088-0
   PubMed Web of Science ®Google Scholar
• Yung PY, Burke C, Lewis M, Kjelleberg S, Thomas T. Novel antibacterial proteins from the microbial communities associated with the sponge cymbastela concentrica and the green alga ulva australis. Appl Environ Microbiol 2011; 77: 1512-5; PMID:21183639; http://dx.doi.org/10.1128/AEM.02038-10
   PubMedGoogle Scholar
• Petersen EI, Valinger G, Solkner B, Stubenrauch G, Schwab H. A novel esterase from burkholderia gladioli which shows high deacetylation activity on cephalosporins is related to β-lactamases and DD-peptidases. J Biotechnol 2001; 89: 11-25; PMID:11472796; http://dx.doi.org/10.1016/S0168-1656(01)00284-X
   PubMedGoogle Scholar
• Wagner UG, Petersen EI, Schwab H, Kratky C. EstB from burkholderia gladioli: a novel esterase with a β-lactamase fold reveals steric factors to discriminate between esterolytic and β-lactam cleaving activity. Protein Sci 2002; 11: 467-78; PMID:11847270; http://dx.doi.org/10.1110/ps.33002
   PubMedGoogle Scholar
• Belardinelli M, Fausto AM, Guerra L, Buonocore F, Bongiorno G, Maroli M, Mazzini M. Lipase and antibacterial activities of a recombinant protein from the accessory glands of female phlebotomus papatasi (diptera: psychodidae). Ann Trop Med Parasitol 2005; 99: 673-82; PMID:16212801; http://dx.doi.org/10.1179/136485905X51472
   PubMed Web of Science ®Google Scholar
• Desbois AP, Smith VJ. Antibacterial free fatty acids: activities, mechanisms of action and biotechnological potential. Appl Microbiol Biotechnol 2010; 85: 1629-42; PMID:19956944; http://dx.doi.org/10.1007/s00253-009-2355-3
   PubMed Web of Science ®Google Scholar
• Drake DR, Brogden KA, Dawson DV, Wertz PW. Thematic review series: skin lipids. antimicrobial lipids at the skin surface. J Lipid Res 2008; 49: 4-11; PMID:17906220; http://dx.doi.org/10.1194/jlr.R700016-JLR200
   PubMed Web of Science ®Google Scholar
• Parsons JB, Yao J, Frank MW, Jackson P, Rock CO. Membrane disruption by antimicrobial fatty acids releases low-molecular-weight proteins from staphylococcus aureus. J Bacteriol 2012; 194: 5294-304; PMID:22843840; http://dx.doi.org/10.1128/JB.00743-12
   PubMed Web of Science ®Google Scholar
• Tao W, Lee MH, Yoon MY, Kim JC, Malhotra S, Wu J, Hwang EC, Lee SW. Characterization of two metagenome-derived esterases that reactivate chloramphenicol by counteracting chloramphenicol acetyltransferase. J Microbiol Biotechnol 2011; 21: 1203-10; PMID:22210605; http://dx.doi.org/10.4014/jmb.1107.07034
   PubMed Web of Science ®Google Scholar
• Brady SF. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2007; 2: 1297-305; PMID:17546026; http://dx.doi.org/10.1038/nprot.2007.195
   PubMed Web of Science ®Google Scholar
• Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 2006; 34: 5623-30; PMID:17028096; http://dx.doi.org/10.1093/nar/gkl723
   PubMed Web of Science ®Google Scholar
• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215 403-10; PMID:2231712; http://dx.doi.org/10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 2011; 39: D225-9; PMID:21109532; http://dx.doi.org/10.1093/nar/gkq1189
   PubMed Web of Science ®Google Scholar
• Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPasy server. In: Walker JM, editor. The Proteomics Protocols Handbook. New York: Taylor & Francis; 2005; 571-607.
   Google Scholar
• Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 2011; 8: 785-6; PMID:21959131; http://dx.doi.org/10.1038/nmeth.1701
   PubMed Web of Science ®Google Scholar
• Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24: 1596-9; PMID:17488738; http://dx.doi.org/10.1093/molbev/msm092
   PubMed Web of Science ®Google Scholar
• Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007; 17: 377-86; PMID:17255551; http://dx.doi.org/10.1101/gr.5969107
   PubMed Web of Science ®Google Scholar