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Guez JS, Coucheney F, Guy J, Béchet M, Fontanille P, Chihib NE, Niehren J, Coutte F, Jacques P. Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Mycosubtilin Isoforms in Bacillus subtilis. Metabolites 2022; 12:metabo12020107. [PMID: 35208182 PMCID: PMC8877110 DOI: 10.3390/metabo12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.
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Affiliation(s)
- Jean-Sébastien Guez
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Françoise Coucheney
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Joany Guy
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Max Béchet
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Pierre Fontanille
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Nour-Eddine Chihib
- UMR 8207–UMET–Unité Matériaux et Transformations, Centrale Lille, INRAE, CNRS, Université de Lille, F-59000 Lille, France;
| | - Joachim Niehren
- Biocomputing Team, Centre de Recherche en Informatique, Signal et Automatique de Lille CRIStAL, UMR CNRS 9189, Université de Lille, F-59000 Lille, France;
- INRIA, Université de Lille, F-59000 Lille, France
| | - François Coutte
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
- Correspondence: ; Tel.: +33-(0)-328767497
| | - Philippe Jacques
- Équipe Métabolites Spécialisés d’Origine Microbienne, UMRt BioEcoAgro 1158-INRAE, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Université de Liège, B-5030 Gembloux, Belgium;
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Liu XY, Yang SZ, Mu BZ. Isolation and characterization of a C12-lipopeptide produced by Bacillus subtilis HSO 121. J Pept Sci 2008; 14:864-75. [PMID: 18265435 DOI: 10.1002/psc.1017] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A new lipopeptide with C12 fatty acid has been isolated from the cell broth of Bacillus subtilis HSO121 by chromatographic methods, which is believed to be the homologue of lipopeptides. The fatty acid portion was methylated and analyzed by GC/MS, ESI Q-TOF MS and 1H-NMR. The peptide portion, of which the amino acid composition was obtained by HPLC combined with a phenyl isothiocyanate (PITC) derivatization methods, was analyzed by ESI Q-TOF MS. Comparing the obtained results with surfactin C13 showed that the new lipopeptide has a peptide moiety similar to that of surfactin and the difference exists in the fatty acid portion, which is an iso-C12 beta-hydroxy fatty acid. The critical micelle concentration (CMC) of this new homologue is estimated to be 6.27 x 10(-5) mol/l in 10 mmol/l phosphate buffer solution (PBS, pH 8.0) at 30 degrees C, and the surface tension at CMC (gamma CMC) achieved is as little as 27.71 mN/m. The hemolytic activities of the C12-lipopeptide on 2% human erythrocytes showed a HC50 of 26.5 micromol/l.
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Affiliation(s)
- Xiang-Yang Liu
- Laboratory for Advanced Materials and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, China
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Affiliation(s)
- Annette F. Dexter
- Centre for Biomolecular Engineering, School of Engineering and The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia QLD 4072 Australia
| | - Anton P. J. Middelberg
- Centre for Biomolecular Engineering, School of Engineering and The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia QLD 4072 Australia
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Peng F, Wang Y, Sun F, Liu Z, Lai Q, Shao Z. A novel lipopeptide produced by a Pacific Ocean deep-sea bacterium, Rhodococcus sp. TW53. J Appl Microbiol 2008; 105:698-705. [PMID: 18422956 DOI: 10.1111/j.1365-2672.2008.03816.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Our goal was to find a novel, biosurfactant-producing bacterium from Pacific Ocean deep-sea sediments. METHODS AND RESULTS An oil-degrading biosurfactant-producing bacterium TW53 was obtained from deep-sea sediment, and was identified through 16S rDNA analysis as belonging to the genus Rhodococcus. It lowered the surface tension of its culture to 34.4 mN m(-1). Thin layer chromatography (TLC) showed that the crude biosurfactants of TW53 were composed of lipopeptides and free fatty acids (FA). The lipopeptides were purified with column chromatography and then hydrolysed with 6 mol l(-1) HCl. Gas chromatography-mass spectrometry analysis showed that the hydrolyte in the hydrophobic fraction contained five kinds of FA with chain lengths of C(14)-C(19), and C(16)H(32)O(2) was a major component making up 59.18% of the total. However, 3-hydroxyl FA was not found, although it is usually found in lipopeptides. Silica gel TLC revealed that the hydrolyte in the hydrophilic fraction was composed of five kinds of amino acids; consistently, ESI-Q-TOF-MS analysis confirmed the composition results and provided their sequence tentatively as Ala-Ile-Asp-Met-Pro. Furthermore, the yield and CMC (critical micelle concentrations) of purified lipopeptides were examined. The purified product reduced the surface tension of water to 30.7 mN m(-1) with a CMC value of 23.7 mg l(-1). These results suggest that Rhodococcus sp. TW53 produces a novel lipopeptide that we have named rhodofactin. CONCLUSION The deep-sea isolate Rhodococcus sp. TW53 was the first reported lipopeptide-producing bacterium of this genus. The lipopeptides had novel chemical compositions. SIGNIFICANCE AND IMPACT OF THE STUDY Rhodococcus sp. TW53 has potential in the exploration of new biosurfactants and could be used in bioremediation of marine oil pollution.
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Affiliation(s)
- F Peng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China
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Youssef NH, Duncan KE, McInerney MJ. Importance of 3-hydroxy fatty acid composition of lipopeptides for biosurfactant activity. Appl Environ Microbiol 2006; 71:7690-5. [PMID: 16332741 PMCID: PMC1317328 DOI: 10.1128/aem.71.12.7690-7695.2005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Biosurfactant production may be an economic approach to improving oil recovery. To obtain candidates most suitable for oil recovery, 207 strains, mostly belonging to the genus Bacillus, were tested for growth and biosurfactant production in medium with 5% NaCl under aerobic and anaerobic conditions. All strains grew aerobically with 5% NaCl, and 147 strains produced a biosurfactant. Thirty-five strains grew anaerobically with 5% NaCl, and two produced a biosurfactant. In order to relate structural differences to activity, eight lipopeptide biosurfactants with different specific activities produced by various Bacillus species were purified by a new protocol. The amino acid compositions of the eight lipopeptides were the same (Glu/Gln:Asp/Asn:Val:Leu, 1:1:1:4), but the fatty acid compositions differed. Multiple regression analysis showed that the specific biosurfactant activity depended on the ratios of both iso to normal even-numbered fatty acids and anteiso to iso odd-numbered fatty acids. A multiple regression model accurately predicted the specific biosurfactant activities of four newly purified biosurfactants (r2= 0.91). The fatty acid composition of the biosurfactant produced by Bacillus subtilis subsp. subtilis strain T89-42 was altered by the addition of branched-chain amino acids to the growth medium. The specific activities of biosurfactants produced in cultures with different amino acid additions were accurately predicted by the multiple regression model derived from the fatty acid compositions (r2= 0.95). Our work shows that many strains of Bacillus mojavensis and Bacillus subtilis produce biosurfactants and that the fatty acid composition is important for biosurfactant activity.
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Affiliation(s)
- Noha H Youssef
- Department of Botany and Microbiology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019, USA
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Pagadoy M, Peypoux F, Wallach J. Solid-Phase Synthesis of Surfactin, a Powerful Biosurfactant Produced by Bacillus subtilis, and of Four Analogues. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-6790-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kowall M, Vater J, Kluge B, Stein T, Franke P, Ziessow D. Separation and Characterization of Surfactin Isoforms Produced by Bacillus subtilis OKB 105. J Colloid Interface Sci 1998; 204:1-8. [PMID: 9665760 DOI: 10.1006/jcis.1998.5558] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Natural surfactin is a mixture of cyclic lipopeptides built from variants of a heptapeptide and a beta-hydroxy fatty acid with chain lengths of 13-15 carbon atoms. The lipopeptide biosurfactant was produced by Bacillus subtilis OKB 105 and part of the material subjected to esterification of its Glu and Asp residues. High-resolution preparative reversed phase HPLC on EnCaPharm 100 of surfactin and its monomethyl and dimethyl esters yielded 44 fractions which were characterized by NMR and MS methods. Among the separated isoforms are the known surfactin variants with l-Leu, l-Val, or l-Ile in position 7 of the peptide ring and three hitherto unknown variants showing replacements of the leucine residues in position 2 and/or 7 by l-Val and l-Ile. Our work makes available lipoheptapeptide compounds with modified structures and different hydrophobicities which promise to have potential for biotechnological and pharmaceutical applications. Copyright 1998 Academic Press.
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Affiliation(s)
- M Kowall
- Iwan N. Stranski Institut für Physikalische und Theoretische Chemie, Technische Universität Berlin, Strasse des 17. Juni 112, Berlin, D-10623, Germany
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Grangemard I, Peypoux F, Wallach J, Das BC, Labbé H, Caille A, Genest M, Maget-Dana R, Ptak M, Bonmatin JM. Lipopeptides with improved properties: structure by NMR, purification by HPLC and structure-activity relationships of new isoleucyl-rich surfactins. J Pept Sci 1997; 3:145-54. [PMID: 9230480 DOI: 10.1002/(sici)1099-1387(199703)3:2<145::aid-psc96>3.0.co;2-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The biosynthesis of bacterial isoleucyl-rich surfactins was controlled by supplementation of L-isoleucine to the culture medium. Two new variants, the [Ile4,7]- and [Ile2,4,7]surfactins, were thus produced by Bacillus subtilis and their separation was achieved by reverse-phase HPLC. Amino acids of the heptapeptide moiety were analysed by chemical methods, and the lipid moiety was identified by beta-hydroxy anteiso pentadecanoic acid by combined GC/MS. Sequences were established on the basis of two-dimensional NMR data. Because conformational parameters issuing from NMR spectra suggested that the cyclic backbone fold was globally conserved in the new variants, structure-activity relationships were discussed in details on the basis of the three-dimensional model of surfactin in solution. Indeed, both variants have increased surface properties compared with that of surfactin, and this improvement is assigned to an increase of the hydrophobicity of the apolar domain favouring micellization. Furthermore, the additional Leu-to-Ile substitution at position 2 in the [Ile2,4,7]surfactin leads to a substantial increase of its affinity for calcium, when compared with that of [Ile4,7]surfactin or surfactin. This effect is assigned, from the model, to an increase in the accessibility of the acidic side chains constituting the calcium binding site. Thus, the propensities of such active lipopeptides for both hydrophobic and electrostatic interactions were improved, further substantiating that they can be rationally designed.
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Affiliation(s)
- I Grangemard
- Laboratoire de Biochimie Analytique et Synthèse Bioorganique, Université Claude Bernard Lyon, France
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Feignier C, Besson F, Michel G. Characterization of iturin synthetase in the wild-type Bacillus subtilis strain producing iturin and in an iturin deficient mutant. FEMS Microbiol Lett 1996; 136:117-22. [PMID: 8869495 DOI: 10.1111/j.1574-6968.1996.tb08036.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The multi-enzyme system responsible for the biosynthesis of iturin, an antifungal lipopeptide of Bacillus subtilis, was partially purified by chromatography on different affigels. In the wild-type strain, two subunits of the iturin synthetase (ITs and ITagp) were characterized: ITs activated only L-Ser, one of the iturin amino acid components, and ITagp activated L-Asn, D-Asn, L-Gln and L-Pro, amino acids corresponding to a partial sequence of iturin. In an iturin deficient mutant, the activity of the ITagp subunit was modified.
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Affiliation(s)
- C Feignier
- Laboratoire de Biochimie Microbienne, Université Claude Bernard-Lyon, Villeurbanne, France
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Feignier C, Besson F, Michel G. Studies on lipopeptide biosynthesis by Bacillus subtilis: isolation and characterization of iturin-, surfactin+ mutants. FEMS Microbiol Lett 1995; 127:11-5. [PMID: 7737471 DOI: 10.1111/j.1574-6968.1995.tb07442.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Two mutant strains, M35 and M89, were obtained by UV irradiation from a wild-type Bacillus subtilis producing iturin and surfactin. Sporulation and surfactin production were similar in both mutants and in the parent strain, while the iturin production of M35 was 300-fold less than that of the wild-type strain; M89 did not produce any iturin. The analysis of the incorporation of sodium [1-14C]acetate into cellular lipids and lipopeptides showed that M89 still synthesized beta-amino fatty acids, the lipid moiety of iturin.
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Affiliation(s)
- C Feignier
- Laboratoire de Biochimie Microbienne, Université Claude Bernard, Lyon I, Villeurbanne, France
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Abstract
If we include beta-lactam antibiotics on the grounds that they have the same biosynthetic origin, peptides remain commercially the most important group of pharmaceuticals. However, our increasing knowledge of the genetic and enzymic background to biosynthesis, and of the regulation of metabolite production, will eventually bring a more unified approach to bioactive compounds. Mixing of structural types will become important, and we will be able to use our knowledge of biosynthetic genes and their regulatory networks. We will also benefit from an appreciation of the modular organization of catalytic functions, substrate transfer mechanisms and signalling between interacting enzymes. Since all of this is, in fact, the basis for enzymic synthesis of complex natural products in vivo, the exploitation of living cells requires mastery of a formidable network of cellular controls and compartments. For the present we are able to see fascinating connections emerging between genes in a variety of reaction sequences, not only in biosynthetic but also in degradative pathways. Peptide synthetases show surprising similarities to acylcoenzyme A synthetases, which are key enzymes in forming polyketides as well as in generating the CoA-derivatives that serve as substrates in degradative pathways. 4'-Phosphopantetheine, the functional half of CoA, plays a key role as the intrinsic transfer cofactor in various multienzyme systems. The comparatively small catalogue of reactions modifying natural products, notably epimerization, methylation, hydroxylation, decarboxylation (of peptides) and reduction/dehydration (of polyketides) can be found within or amongst biosynthetic proteins, generally as modules and organized in a specified order. The biochemist is coming close to the synthetic chemist's recipes, and may soon be recruiting proteins to carry them out.
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Affiliation(s)
- H von Döhren
- Institut für Biochemie und Molekulare Biologie Technische Universitt Berlin, Germany
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Biosynthesis of iturin and surfactin byBacillus subtilis: Evidence for amino acid activating enzymes. Biotechnol Lett 1992. [DOI: 10.1007/bf01021050] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Besson F, Michel G. Biosynthesis of bacillomycin D by Bacillus subtilis. Evidence for amino acid-activating enzymes by the use of affinity chromatography. FEBS Lett 1992; 308:18-21. [PMID: 1644198 DOI: 10.1016/0014-5793(92)81040-s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacillomycin D is an antifungal lipopeptide produced by B. subtilis. The formation of the peptidyl bonds of bacillomycin D occurs non-ribosomally, as demonstrated by the use of chloramphenicol, an inhibitor of protein biosynthesis. Amino acid-activating enzymes were found in B. subtilis cell lysates purified by affinity chromatography on a gel containing L-Pro, an amino acid of bacillomycin D. Presence of ATP during this purification increases the binding of enzymatic proteins and their activity. An enzyme, with an apparent molecular weight of 230 kDa, catalyzed ATP-PPi exchange reactions, which were mediated by specific amino acids, corresponding to a partial sequence of bacillomycin D.
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Affiliation(s)
- F Besson
- Laboratoire de Biochimie Microbienne (CNRS UMR 24), Université Claude-Bernard Lyon I, Villeurbanne, France
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