Wang P, Guo Q, Ma Y, Li S, Lu X, Zhang X, Ma P. DegQ regulates the production of fengycins and biofilm formation of the biocontrol agent Bacillus subtilis NCD-2. Microbiol Res. 2015;178:42–50.
CAS
Google Scholar
Fan H, Ru J, Zhang Y, Wang Q, Li Y. Fengycin produced by Bacillus subtilis 9407 plays a major role in the biocontrol of apple ring rot disease. Microbiol Res. 2017;199:89–97.
CAS
Google Scholar
Wu Y, Wang Y, Zou H, Wang B, Sun Q, Fu A, Wang Y, Wang Y, Xu X, Li W. Bacillus amyloliquefaciens probiotic SC06 induces autophagy to protect against pathogens in macrophages. Front Microbiol. 2017;8:469.
Google Scholar
Sonenshein AL. Control of sporulation initiation in Bacillus subtilis. Curr Opin Microbiol. 2000;3(6):561–6.
CAS
Google Scholar
Moszer I, Jones L, Moreira S, Fabry C, Danchin A. SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res. 2002;30(1):62–5.
CAS
Google Scholar
Torres MJ, Brandan CP, Sabate DC, Petroselli G, Errabalsells R, Audisio MC. Biological activity of the lipopeptide-producing Bacillus amyloliquefaciens PGPBacCA1 on common bean Phaseolus vulgaris L. pathogens. Biol Control. 2017;105:93–9.
CAS
Google Scholar
Agustín L-B, Raunel T-V, Gerardo C, Kohei K, Katsuhiro K, Enrique G, Leobardo S-C. Effects of bacillomycin D homologues produced by Bacillus amyloliquefaciens 83 on growth and viability of Colletotrichum gloeosporioides at different physiological stages. Biol Control. 2018;127:145–54.
Google Scholar
Stein T. Bacillus subtilis antibiotics: structures, syntheses and specific functions. Mol Microbiol. 2005;56(4):845–57.
CAS
Google Scholar
Kröber M, Wibberg D, Grosch R, Eikmeyer F, Verwaaijen B, Chowdhury SP, Hartmann A, Pühler A, Schlüter A. Effect of the strain Bacillus amyloliquefaciens FZB42 on the microbial community in the rhizosphere of lettuce under field conditions analyzed by whole metagenome sequencing. Front Microbiol. 2014;5:252.
Google Scholar
Beppu T. Secondary metabolites as chemical signals for cellular differentiation. Gene. 1992;115(1–2):159–65.
CAS
Google Scholar
Chaudhary AK, Dhakal D, Sohng JK. An insight into the “-omics” based engineering of streptomycetes for secondary metabolite overproduction. Biomed Res Int. 2013;2013:968518.
Google Scholar
Ichikawa N, Sasagawa M, Yamamoto M, Komaki H, Yoshida Y, Yamazaki S, Fujita N. DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters. Nucleic Acids Res. 2012;41(D1):D408–14.
Google Scholar
Chen XH, Koumoutsi A, Scholz R, Borriss R. More than anticipated - production of antibiotics and other secondary metabolites by Bacillus amyloliquefaciens FZB42. J Mol Microbiol Biotechnol. 2009;16(1–2):14–24.
CAS
Google Scholar
Stein T, Vater J, Kruft V, Otto A, Wittmannliebold B, Franke P, Panico M, Mcdowell RA, Morris HR. The multiple carrier model of nonribosomal peptide biosynthesis at modular multienzymatic templates. J Biol Chem. 1996;271(26):15428–35.
CAS
Google Scholar
Du L, Lou L. PKS and NRPS release mechanisms. Nat Prod Rep. 2010;27(2):255–78.
CAS
Google Scholar
Arguellesarias A, Ongena M, Halimi B, Lara Y, Brans A, Joris B, Fickers P. Bacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens. Microb Cell Factories. 2009;8(1):63.
Google Scholar
Tamehiro N, Okamotohosoya Y, Okamoto S, Ubukata M, Hamada M, Naganawa H, Ochi K. Bacilysocin, a novel phospholipid antibiotic produced by Bacillus subtilis 168. Antimicrob Agents Chemother. 2002;46(2):315–20.
CAS
Google Scholar
Carrillo C, Teruel JA, Aranda FJ, Ortiz A. Molecular mechanism of membrane permeabilization by the peptide antibiotic surfactin. Biochim Biophys Acta. 2003;1611(1–2):91–7.
CAS
Google Scholar
Yu GY, Sinclair JB, Hartman GL, Bertagnolli BL. Production of iturin a by Bacillus amyloliquefaciens suppressing Rhizoctonia solani. Soil Biol Biochem. 2002;34(7):955–63.
CAS
Google Scholar
Jacques P, Hbid C, Destain J, Razafindralambo H, Paquot M, De Pauw E, Thonart P. Optimization of biosurfactant lipopeptide production from Bacillus subtilis S499 by plackett-burman design. Appl Biochem Biotechnol. 1999;77–79:223–33.
Google Scholar
Moyne A, Cleveland TE, Tuzun S. Molecular characterization and analysis of the operon encoding the antifungal lipopeptide bacillomycin D. FEMS Microbiol Lett. 2004;234(1):43–9.
CAS
Google Scholar
Tulp M, Bohlin L. Rediscovery of known natural compounds: nuisance or goldmine? Bioorg Med Chem. 2005;13(17):5274–82.
CAS
Google Scholar
Oman TJ, van der Donk WA. Follow the leader: the use of leader peptides to guide natural product biosynthesis. Nat Chem Biol. 2010;6(1):9–18.
CAS
Google Scholar
Lane AL, Moore BS. A sea of biosynthesis: marine natural products meet the molecular age. Nat Prod Rep. 2011;28(2):411–28.
CAS
Google Scholar
Rutledge PJ, Challis GL. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol. 2015;13(8):509–23.
CAS
Google Scholar
van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014;30(9):418–26.
Google Scholar
Guo Q, Li S, Lu X, Li B, Ma P. PhoR/PhoP two component regulatory system affects biocontrol capability of Bacillus subtilis NCD-2. Genet Mol Biol. 2010;33(2):333–40.
CAS
Google Scholar
Guo Q, Dong W, Li S, Lu X, Wang P, Zhang X, Wang Y, Ma P. Fengycin produced by Bacillus subtilis NCD-2 plays a major role in biocontrol of cotton seedling damping-off disease. Microbiol Res. 2014;169(7–8):533–40.
CAS
Google Scholar
Zerbino D, Birney E. Velvet : algorithms for de novo short read assembly using de bruijn graphs. Genome Res. 2008;18(5):821–9.
CAS
Google Scholar
Dunlap CA, Bowman MJ, Zeigler DR. Promotion of Bacillus subtilis subsp. inaquosorum, Bacillus subtilis subsp. spizizenii and Bacillus subtilis subsp. stercoris to species status. Anton Leeuw Int J Gen Mol Microbiol. 2020;113(1):1–12.
CAS
Google Scholar
Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R, Takano E, Weber T. antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers. Nucleic Acids Res. 2013;41(W1):W204–12.
Google Scholar
Sansinenea E, Ortiz A. Secondary metabolites of soil Bacillus spp. Biotechnol Lett. 2011;33(8):1523–38.
CAS
Google Scholar
Yu D, Fang Y, Tang C, Klosterman SJ, Tian C, Wang Y. Genomewide transcriptome profiles reveal how Bacillus subtilis lipopeptides inhibit microsclerotia formation in Verticillium dahliae. Mol Plant-Microbe Interact. 2019;32(5):622–34.
CAS
Google Scholar
Xiao X, Chen H, Chen H, Wang J, Ren C, Wu L. Impact of Bacillus subtilis JA, a biocontrol strain of fungal plant pathogens, on arbuscular mycorrhiza formation in Zea mays. World J Microbiol Biotechnol. 2008;24(7):1133–7.
Google Scholar
Challis GL, Ravel J. Coelichelin, a new peptide siderophore encoded by the Streptomyces coelicolor genome: structure prediction from the sequence of its non-ribosomal peptide synthetase. FEMS Microbiol Lett. 2000;187(2):111–4.
CAS
Google Scholar
Basichipalu S, Dischinger J, Josten M, Szekat C, Zweynert A, Sahl H, Bierbaum G. Pseudomycoicidin, a class II lantibiotic from Bacillus pseudomycoides. Appl Environ Microbiol. 2015;81(10):3419–29.
CAS
Google Scholar
Seydlová G, Svobodová J. Review of surfactin chemical properties and the potential biomedical applications. Central Eur J Med. 2008;3(2):123–33.
Google Scholar
Patel PS, Huang S, Fisher S, Pirnik D, Aklonis C, Dean L, Meyers E, Fernandes P, Mayerl F. Bacillaene, a novel inhibitor of procaryotic protein synthesis produced by Bacillus subtilis. J Antibiot. 2006;48(9):997.
Article
Google Scholar
Ramarathnam R, Bo S, Chen Y, Fernando WG, Xuewen G, de Kievit T. Molecular and biochemical detection of fengycin- and bacillomycin D-producing Bacillus spp., antagonistic to fungal pathogens of canola and wheat. Can J Microbiol. 2007;53(7):901–11.
Article
CAS
Google Scholar
Miethke M, Klotz O, Linne U, May JJ, Beckering CL, Marahiel MA. Ferri-bacillibactin uptake and hydrolysis in Bacillus subtilis. Mol Microbiol. 2006;61(6):1413–27.
CAS
Google Scholar
Thennarasu S, Lee DK, Poon A, Kawulka KE, Vederas JC, Ramamoorthy A. Membrane permeabilization, orientation, and antimicrobial mechanism of subtilosin a. Chem Phys Lipids. 2005;137(1–2):38–51.
CAS
Google Scholar
Kenig M, Abraham EP. Antimicrobial activities and antagonists of bacilysin and anticapsin. Microbiology. 1976;94(1):37–45.
CAS
Google Scholar
Fan B, Wang C, Song X, Ding X, Wu L, Wu H, Gao X, Borriss R. Bacillus velezensis FZB42 in 2018: the gram-positive model strain for plant growth promotion and biocontrol. Front Microbiol. 2018;9:2491.
Google Scholar
Jin P, Wang H, Liu W, Miao W. Characterization of lpaH2 gene corresponding to lipopeptide synthesis in Bacillus amyloliquefaciens HAB-2. BMC Microbiol. 2017;17(1):227.
Google Scholar
Chen X, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess W, Reva O, et al. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol. 2007;25(9):1007–14.
CAS
Google Scholar
Koumoutsi A, Chen X, Henne A, Liesegang H, Hitzeroth G, Franke P, Vater J, Borriss R. Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J Bacteriol. 2004;186(4):1084–96.
CAS
Google Scholar
Chen C, Chang L, Chang Y, Liu S, Tschen JS. Transposon mutagenesis and cloning of the genes encoding the enzymes of fengycin biosynthesis in Bacillus subtilis. Mol Gen Genomics. 1995;248(2):121–5.
CAS
Google Scholar
Lin G, Chen C, Tschen JS, Tsay S, Chang Y, Liu S. Molecular cloning and characterization of fengycin synthetase gene fenB from Bacillus subtilis. J Bacteriol. 1998;180(5):1338–41.
CAS
Google Scholar
Lin TP, Chen CL, Chang LK, Tschen JS, Liu ST. Functional and transcriptional analyses of a fengycin synthetase gene, fenC, from Bacillus subtilis. J Bacteriol. 1999;181(16):5060–7.
CAS
Google Scholar
Lautru S, Deeth RJ, Bailey LM, Challis GL. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat Chem Biol. 2005;1(5):265–9.
CAS
Google Scholar
Bie XM, Lü FX, Lu ZX, Huang XQ, Shen J. Isolation and identification of lipopeptides produced by Bacillus subtilis fmbJ. Sheng wu gong cheng xue bao. 2006;22(4):644–9.
Google Scholar
Tripathi L, Irorere VU, Marchant R, Banat IM. Marine derived biosurfactants: a vast potential future resource. Biotechnol Lett. 2018;40(11–12):1441–57.
CAS
Google Scholar
Sivapathasekaran C, Mukherjee S, Samanta R, Sen R. High-performance liquid chromatography purification of biosurfactant isoforms produced by a marine bacterium. Anal Bioanal Chem. 2009;395(3):845–54.
CAS
Google Scholar
Pan H, Tian X, Shao M, Xie Y, Huang H, Hu J, Ju J. Genome mining and metabolic profiling illuminate the chemistry driving diverse biological activities of Bacillus siamensis SCSIO 05746. Appl Microbiol Biotechnol. 2019;103(10):4153–65.
CAS
Google Scholar
Ongena M, Jacques P. Bacillus lipopeptides: versatile weapons for plant disease biocontrol. Trends Microbiol. 2008;16(3):115–25.
CAS
Google Scholar
Bhat A, Chakraborty R, Adlakha K, Agam G, Chakraborty K, Sengupta S. Ncl1-mediated metabolic rewiring critical during metabolic stress. Life Sci Alliance. 2019;2(4):e201900360. https://doi.org/10.26508/lsa.201900360.
Bae J, Park J, Hahn M, Kim M, Roe J. Redox-dependent changes in RsrA, an anti-sigma factor in Streptomyces coelicolor: zinc release and disulfide bond formation. J Mol Biol. 2004;335(2):425–35.
CAS
Google Scholar
Landy M, Warren GH. Bacillomycin; an antibiotic from Bacillus subtilis active against pathogenic fungi. Proc Soc Exp Biol Med Soc Exp Biol Med (New York). 1948;67(4):539–41.
CAS
Google Scholar
Wu L, Wu H, Chen L, Xie S, Zang H, Borriss R, Gao X. Bacilysin from Bacillus amyloliquefaciens FZB42 has specific bactericidal activity against harmful algal bloom species. Appl Environ Microbiol. 2014;80(24):7512–20.
Google Scholar
Li Y, Jiang W, Gao R, Cai Y, Guan Z, Liao X. Fe (III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from CD36. 3 Biotech. 2018;8(9):392.
Google Scholar
Shelburne C, An F, Dholpe V, Ramamoorthy A, Lopatin D, Lantz M. The spectrum of antimicrobial activity of the bacteriocin subtilosin a. J Antimicrob Chemother. 2007;59(2):297–300.
CAS
Google Scholar
Karim A, Poirot O, Khatoon A, Aurongzeb M. Draft genome sequence of a novel Bacillus glycinifermentans strain having antifungal and antibacterial properties. J Glob Antimicrob Resist. 2019;19:308–10.
CAS
Google Scholar
Andrews S. FastQC A quality control tool for high throughput sequence data; 2010.
Google Scholar
Alexey G, Vladislav S, Nikolay V, Glenn T: QUAST: quality assessment tool for genome assemblies. In: 2013; 2013: 1072–1075.
Torsten S. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–9.
Google Scholar
Disz T, Akhter S, Cuevas DA, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards R. Accessing the SEED genome databases via web services API: tools for programmers. BMC Bioinformatics. 2010;11(1):319.
Google Scholar
Aziz RK, Bartels D, Best AA, Dejongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass EM, Kubal M. The rast server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Google Scholar
Haubold B, Klotzl F, Pfaffelhuber P. Andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics. 2015;31(8):1169–75.
Google Scholar
Tamura K, Peterson DS, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9.
CAS
Google Scholar
Xu X, Reid N. On the robustness of maximum composite likelihood estimate. J Stat Plan Inference. 2011;141(9):3047–54.
Google Scholar
Armenteros JJA, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, Nielsen H. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37(4):420–3.
Google Scholar
Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018;46(W1):W246–51.
CAS
Google Scholar
Medema MH, Blin K, Cimermancic P, De Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 2011;39(2):W339–46.
CAS
Google Scholar
Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster ALH, Wyatt MA, Magarvey NA. Genomes to natural products PRediction informatics for secondary Metabolomes (PRISM). Nucleic Acids Res. 2015;43(20):9645–62.
CAS
Google Scholar
Bachmann BO, Ravel J. Methods for in silico prediction of microbial polyketide and nonribosomal peptide biosynthetic pathways from DNA sequence data. Methods Enzymol. 2009;458:181–217.
CAS
Google Scholar
Byers H, Stackebrandt E, Hayward C, Blackall LL. Molecular investigation of a microbial mat associated with the great Artesian Basin. FEMS Microbiol Ecol. 1998;25(4):391–403.
CAS
Google Scholar
Li B, Lu X, Guo Q, Qian C, Li S, Ma P. Isolation and identification of lipopeptides and volatile compounds produced by Bacillus subtilis strain BAB-1, vol. 43; 2010.
Google Scholar
Reddick J, Antolak S, Raner G. PksS from Bacillus subtilis is a cytochrome P450 involved in bacillaene metabolism. Biochem Biophys Res Commun. 2007;358(1):363–7.
CAS
Google Scholar