Nonribosomal peptides synthetases and their applications in industry

Sustainable Chemical Processes - Tập 4 - Trang 1-8 - 2016
Mario Alberto Martínez-Núñez1,2, Víctor Eric López y López3
1Laboratorio de Ecogenómica, Facultad de Ciencias, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología de Yucatán, Mérida, Mexico
2Laboratorio Nacional de Resiliencia Costera, Laboratorios Nacionales CONACyT, Yucatán, Mexico
3Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Tepetitla de Lardizábal, Mexico

Tóm tắt

Nonribosomal peptides are products that fall into the class of secondary metabolites with a diverse properties as toxins, siderophores, pigments, or antibiotics, among others. Unlike other proteins, its biosynthesis is independent of ribosomal machinery. Nonribosomal peptides are synthesized on large nonribosomal peptide synthetase (NRPS) enzyme complexes. NRPSs are defined as multimodular enzymes, consisting of repeated modules. The NRPS enzymes are at operons and their regulation can be positive or negative at transcriptional or post-translational level. The presence of NRPS enzymes has been reported in the three domains of life, being prevalent in bacteria. Nonribosomal peptides are use in human medicine, crop protection, or environment restoration; and their use as commercial products has been approved by the U. S Food and Drug Administration (FDA) and the U. S. Environmental Protection Agency (EPA). The key features of nonribosomal peptides and NRPS enzymes, and some of their applications in industry are summarized.

Tài liệu tham khảo

Wang H, Fewer DP, Holm L, Rouhiainen L, Sivonen K (2014) Atlas of nonribosomal peptide and polyketide biosynthetic pathways reveals common occurrence of nonmodular enzymes. Proc Natl Acad Sci 111(25):9259–9264 Bushley KE, Turgeon BG (2010) Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships. BMC Evol Biol 10:26 Mootz HD, Schwarzer D, Marahiel MA (2002) Ways of assembling complex natural products on modular nonribosomal peptide synthetases. ChemBioChem 3(6):490–504 Singh RK, Singh P, Mohapatra TM (2012). Nonribosomal peptide synthesis in microbes. In Recent advances in microbiology. Nova Science Publishers, Inc, New York Crosa JH, Walsh CT (2002) Genetics and assembly line enzymology of siderophore biosynthesis in bacteria. Microbiol Mol Biol Rev 66(2):223–249 Du L, Shen B (1999) Identification and characterization of a type II peptidyl carrier protein from the bleomycin producer Streptomyces verticillus ATCC 15003. Chem Biol 6(8):507–517 Drake EJ, Miller BR, Shi C, Tarrasch JT, Sundlov JA, Allen CL, Skiniotis G, Aldrich CC, Gulick AM (2016) Structures of two distinct conformations of holo-non-ribosomal peptide synthetases. Nature 529(7585):235–238 Finking R, Marahiel MA (2004) Biosynthesis of nonribosomal peptides1. Annu Rev Microbiol 58:453–488 Hahn M, Stachelhaus T (2004) Selective interaction between nonribosomal peptide synthetases is facilitated by short communication-mediating domains. Proc Natl Acad Sci 101(44):15585–15590 Etchegaray A, Silva-Stenico ME, Moon DH, Tsai SM (2004) In silico analysis of nonribosomal peptide synthetases of Xanthomonas axonopodis pv. citri: identification of putative siderophore and lipopeptide biosynthetic genes. Microbiol Res 159(4):425–437 Miller BR, Sundlov JA, Drake EJ, Makin TA, Gulick AM (2014) Analysis of the linker region joining the adenylation and carrier protein domains of the modular nonribosomal peptide synthetases. Proteins 82(10):2691–2702 Tanovic A, Samel SA, Essen LO, Marahiel MA (2008) Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 321(5889):659–663 Tiburzi F, Visca P, Imperi F (2007) Do nonribosomal peptide synthetases occur in higher eukaryotes? IUBMB Life 59(11):730–733 Reimer JM, Aloise MN, Harrison PM, Schmeing TM (2016) Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Nature 529(7585):239–242 Walsh CT, Chen H, Keating TA, Hubbard BK, Losey HC, Luo L, Marshall CG, Miller DA, Patel HM (2001) Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines. Curr Opin Chem Biol 5(5):525–534 Losey HC, Peczuh MW, Chen Z, Eggert US, Dong SD, Pelczer I, Kahne D, Walsh CT (2001) Tandem action of glycosyltransferases in the maturation of vancomycin and teicoplanin aglycones: novel glycopeptides. Biochemistry 40(15):4745–4755 Weissman KJ (2015) The structural biology of biosynthetic megaenzymes. Nat Chem Biol 11(9):660–670 Wang X, Luo C, Liu Y, Nie Y, Liu Y, Zhang R, Chen Z (2010) Three non-aspartate amino acid mutations in the ComA response regulator receiver motif severely decrease surfactin production, competence development and spore formation in Bacillus subtilis. J Microbiol Biotechnol 20(2):301–310 Roongsawang N, Washio K, Morikawa M (2010) Diversity of nonribosomal peptide synthetases involved in the biosynthesis of lipopeptide biosurfactants. Int J Mol Sci 12(1):141–172 Mariappan A, Makarewicz O, Chen XH, Borriss R (2012) Two-component response regulator DegU controls the expression of bacilysin in plant-growth-promoting bacterium Bacillus amyloliquefaciens FZB42. J Mol Microbiol Biotechnol 22(2):114–125 Nakano MM, Zuber P (1993) Mutational analysis of the regulatory region of the srfA operon in Bacillus subtilis. J Bacteriol 175(10):3188–3191 Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M (2005) The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis. J Bacteriol 187(19):6659–6667 Koumoutsi A, Chen XH, Vater J, Borriss R (2007) DegU and YczE positively regulate the synthesis of bacillomycin D by Bacillus amyloliquefaciens strain FZB42. Appl Environ Microbiol 73(21):6953–6964 Inaoka T, Wang G, Ochi K (2009) ScoC regulates bacilysin production at the transcription level in Bacillus subtilis. J Bacteriol 191(23):7367–7371 Quadri LE, Weinreb PH, Lei M, Nakano MM, Zuber P, Walsh CT (1998) Characterization of Sfp, a Bacillus subtilis phosphopantetheinyl transferase for peptidyl carrier protein domains in peptide synthetases. Biochemistry 37(6):1585–1595 Chaudhary AK, Singh B, Maharjan S, Jha AK, Kim BG, Sohng JK (2014) Switching antibiotics production on and off in actinomycetes by an IclR family transcriptional regulator from Streptomyces peucetius ATCC 27952. J Microbiol Biotechnol 24(8):1065–1072 Urum K, Pekdemir T (2004) Evaluation of biosurfactants for crude oil contaminated soil washing. Chemosphere 57(9):1139–1150 Desai JD, Banat IM (1997) Microbial production of surfactants and their commercial potential. Microbiol Mol Biol Rev 61(1):47–64 Marchant R, Banat IM (2012) Biosurfactants: a sustainable replacement for chemical surfactants? Biotechnol Lett 34(9):1597–1605 Jackson SA, Borchert E, O’Gara F, Dobson ADW (2015) Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems. Curr Opin Biotechnol 33:176–182 Kuyukina MS, Ivshina IB, Makarov SO, Litvinenko LV, Cunningham CJ, Philp JC (2005) Effect of biosurfactants on crude oil desorption and mobilization in a soil system. Environ Int 31(2):155–161 Lai CC, Huang YC, Wei YH, Chang JS (2009) Biosurfactant-enhanced removal of total petroleum hydrocarbons from contaminated soil. J Hazard Mater 167(1–3):609–614 Harvey S, Elashvili I, Valdes JJ, Kamely D, Chakrabarty AM (1990) Enhanced removal of Exxon Valdez spilled oil from Alaskan gravel by a microbial surfactant. Biotechnology 8(3):228–230 Gong G, Zheng Z, Chen H, Yuan C, Wang P, Yao L, Yu Z (2009) Enhanced production of surfactin by Bacillus subtilis E8 mutant obtained by ion beam implantation. Food Technol Biotechnol. 47(1):27–31 Ponte Rocha MV, Gomes Barreto RV, Melo VMM, Barros Goncalves LR (2009) Evaluation of cashew apple juice for surfactin production by Bacillus subtilis LAMI008. Appl Biochem Biotechnol 155(1–3):366–378 Raza ZA, Khan MS, Khalid ZM (2007) Physicochemical and surface-active properties of biosurfactant produced using molasses by a Pseudomonas aeruginosa mutant. J Environ Sci Health A Tox Hazard Subst Environ Eng. 42(1):73–80 Silva SN, Farias CB, Rufino RD, Luna JM, Sarubbo LA (2010) Glycerol as substrate for the production of biosurfactant by Pseudomonas aeruginosa UCP0992. Colloids Surf B Biointerfaces. 79(1):174–183 Wu JY, Yeh KL, Lu WB, Lin CL, Chang JS (2008) Rhamnolipid production with indigenous Pseudomonas aeruginosa EM1 isolated from oil-contaminated site. Bioresour Technol 99(5):1157–1164 Wittgens A, Tiso T, Arndt TT, Wenk P, Hemmerich J, Müller C, Wichmann R, Küpper B, Zwick M, Wilhelm S, Hausmann R, Syldatk C, Rosenau F, Blank LM (2011) Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440. Microb Cell Fact 10:80 Ochsner UA, Reiser J, Fiechter A, Witholt B (1995) Production of Pseudomonas aeruginosa rhamnolipid biosurfactants in heterologous hosts. Appl Environ Microbiol 61(9):3503–3506 Wang Q, Fang X, Bai B, Liang X, Shuler PJ, Goddard WA 3rd, Tang Y (2007) Engineering bacteria for production of rhamnolipid as an agent for enhanced oil recovery. Biotechnol Bioeng 98(4):842–853 Goldrick S, Ştefan A, Lovett D, Montague G, Barry Lennox (2015) The development of an industrial-scale fed-batch fermentation simulation. J Biotechnol 193:70–82 PrauBe MTE, Schäuble S, Guthke R, Schuster S (2016) Computing the various pathways of penicillin synthesis and their molar yields. Biotechnol Bioeng 113:173–181 Gidijal L, Kiel JAKW, Douma RD, Seifar RM, van Gulik WM, Bovenberg RAL, Veenhuis M, Van der Klei IJ (2009) An engineered yeast efficiently secreting penicillin. PLoS ONE 4(12):e8317 Jørgensen H, Nielsen J, Villadsen J, Møllgaard H (1995) Meatbolic flux distributions in Penicillum chrysogenum during fed-batch cultivations. Biotechnol Bioeng 46:117–131 Lawen A, Zocher R (1990) Cyclosporin Synthetase J Biol Chem 265:11355–11360 Survase SA, Kagliwal LD, Annapure US, Singhal RS (2011) Cyclosporin A—a review on fermentative production, downstream processing and pharmacological applications. Biotechnol Adv 29:418–435 Survase S, Bankar SB, Annapure AS, Singhal RS (2015) The effect of agitation and aeration on production of cylcosporinA n batch cultures of Tolypocladium inflatum. Indian J Biotechnol 14(394):401 Emri T, Majoros L, Tóth V, Pócsi I (2013) Echinocandins: production and applications. Appl Microbiol Biotechnol 97:3267–3284 Zou SP, Liu M, Wang QL, Xiong Y, Niu K, Zheng YG, Shen YC (2015) Preparative separation of echinocandin B from Aspergillus nidulans broth using macroporous resin adsorption chromatography. J Chromatography B 978–979:111–117 Balkovec JM, Hughes DL, Masurekar PS, Sable CA, Shwartz RE, Singh SB (2014) Discovery and development of first in class antifungal caspofungin (CANCIDAS®)-A case of study. Nat Prod Rep 31:15–34 Kanda M, Tsuboi M, Sakamoto K, Shimizu S, Yamashita M, Honda H (2009) Improvement of FR901379 production by mutant selection and medium optimization. J Biosc Bioeng 107:530–534 Bérdy J (2012) Thoughts and facts about antibiotics: where are now and where are heading. J Antib 65(385):395 Gu J, Codd R (2012) Copper(II)-based metal affinity chromatography for the isolation of the anticancer agent bleomycin from Streptomyces verticillus culture. J Inorg Biochem 115:198–203 Gu J, Codd R (2015) The resolution of two clinical agents, bleomycin and desferrioxamine B, from a Streptomyces verticillus fermentation mixture using multidimensional immobilised metal ion affinity chromatography. RSC Adv 5:3443 Arthur LB, Peter CF, Steven DB (2001) In vitro activities of daptomycin against 2,789 clinical isolates from 11 North American medical centers. Antimicrob gents Chemother 45:1919–1922 Ng IS, Chimimg Ye, Zhang Z, Lu Y, Jing K (2014) Daptomycin antibiotic production processes in fed-batch fermentation by Streptomyces roseosporus NRRL11379 with precursor effect and medium optimization. Bioprocess Biosyst Eng 37:415–423 Konz D, Klens A, Schörgendorfer K, Marahiel MA (1997) The bacitracin biosynthesis operon of Bacillus licheniformis ATCC 10716: molecular characterization of three multi-modular peptide synthetases. Chem Biol 4:927–937 Murphy T, Roy I, Harrop A, Dixon K, Keshavarz T (2007) Effect of oligosaccharide elicitors on bacitracin A production and evidence of transcriptional level control. J Biotechnol 131:397–403 Shaheen M, Li J, Ross AC, Vederas JC, Jensen SE (2011) Paenibacillus polymyxa PKB1 Produces Variants of polymyxin B-Type antibiotics. Chem Biol 18:1640–1648 Li J, Nation RL, Turnidge JD, Milne RW, Coulthard K, Rayner CR, Paterson DL (2006) Colistin: the re-emerging antibiotic for multidrug-resistant gram-negative bacterial infections. Lancet Infect Dis 6:589–601 Michalopoulos A, Falagas ME (2008) Colistin and polymyxin B in critical care. Crit Care Clin 24:377–391 Rabanal F, Grau-Campistany A, Vila-Farrés X, Gonzalez-Linares J, Borràs M, Vila J, Manresa A, Cajal Y (2015) A bioinspired peptide scaffold with high antibiotic activity and low in vivo toxicity. Scientific Rep 5:10558 Roberts KD, Azad MAK, Wang J, Horne AS, Thomposon PE, Nation RL, Velkov T, Li J (2016) Antimicrobial activity and toxicity of the major lipopeptide components of polymyxin B and colistin: last-line antibiotics. ACS Infect Dis 1:568–575 Schneditz G, Rentner J, Roier S, Pletz J, Herzog KA, Bücker R, Troeger H, Schild S, Weber H, Breinbauer R, Gorkiewicz G, Högenauer C, Zechner EL (2014) Enterotoxicity of a nonribosomal peptide causes antibiotic-associated colitis. Proc Natl Acad Sci USA 111(36):13181–13186 Jiang J, Gao L, Bie X, Lu Z, Liu H, Zhang C, Lu F, Zhao H (2016) Identification of novel surfactin derivatives from NRPS modification of Bacillus subtilis and its antifungal activity against Fusarium moniliforme. BMC Microbiol 16:31 Robbel L, Marahiel MA (2010) Daptomycin, a bacterial lipopeptide synthesized by a nonribosomal machinery. J Biol Chem 285(36):27501–27508 Cochrane SA, Vederas JC (2016) Lipopeptides from Bacillus and Paenibacillus spp.: a gold mine of antibiotic candidates. Med Res Rev 36(1):4–31. doi:10.1002/med.21321 Rodrigues L, Banat IM, Teixeira J, Oliveira R (2006) Biosurfactants: potential applications in medicine. J Antimicrob Chemother 57:609–618 Cameotra SS, Makkar RS (2004) Recent applications of biosurfactants as biological and immunological molecules. Curr Opin Microbiol 7:262–266 Reis RS, Pacheco GJ, Pereira AG and Freire DMG (2013) Biosurfactants: production and applications. In: Chamy R (ed) Biodegradation—life of science. InTech Campos JM, Stamford TLM, Sarubbo LA, Luna JM, Rufino RD, Banat IM (2013) Microbial biosurfactants as additives for food industries. Biotechnol Prog 29:1097–1108 Mukherjee S, Das P, Sen R (2006) Towards commercial production of microbial surfactants. Trends Biotechnol 24(11):509–515 Makkar RS, Cameotra SS, Banat IM (2011) Advances in utilization of renewable substrates for biosurfactant production. AMB Express. 1:5 Van Bogaert INA, Saerens K, De Muynck C, Develter D, Soetaert W, Vandamme EJ (2007) Microbial production and application of sophorolipids. Appl Microbiol Biotechnol 76(1):23–34 Van Bogaert INA, Soetaert W (2011) Sophorolipids. In: Soberón-Chávez G (ed) Biosurfactants: From genes to applications. Springer, Heidelberg Müller MM, Kügler JH, Henkel M, Gerlitzki M, Hörmann B, Pöhnlein M, Syldatk C, Hausmann R (2012) Rhamnolipids–next generation surfactants? J Biotechnol 162(4):366–380 Marchant R, Banat IM (2012) Microbial biosurfactants: challenges and opportunities for future exploitation. Trends Biotechnol 30(11):558–565 Schwarzer D, Finking R, Marahiel MA (2003) Nonribosomal peptides: from genes to products. Nat Prod Rep 20:275–287