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Yin Y, Wang X, Zhang P, Wang P, Wen J. Strategies for improving fengycin production: a review. Microb Cell Fact 2024; 23:144. [PMID: 38773450 PMCID: PMC11110267 DOI: 10.1186/s12934-024-02425-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024] Open
Abstract
Fengycin is an important member of the lipopeptide family with a wide range of applications in the agricultural, food, medical and cosmetic industries. However, its commercial application is severely hindered by low productivity and high cost. Therefore, numerous studies have been devoted to improving the production of fengycin. We summarize these studies in this review with the aim of providing a reference and guidance for future researchers. This review begins with an overview of the synthesis mechanism of fengycin via the non-ribosomal peptide synthetases (NRPS), and then delves into the strategies for improving the fengycin production in recent years. These strategies mainly include fermentation optimization and metabolic engineering, and the metabolic engineering encompasses enhancement of precursor supply, application of regulatory factors, promoter engineering, and application of genome-engineering (genome shuffling and genome-scale metabolic network model). Finally, we conclude this review with a prospect of fengycin production.
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Affiliation(s)
- Ying Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Xin Wang
- Coll Biol & Pharmaceut Sci, China Three Gorges Univ, Yichang, 443002, P. R. China
| | - Pengsheng Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
| | - Pan Wang
- Department of Nuclear Medicine, The First Hospital of Shanxi Medical University, Collaborative Innovation Center of Molecular Imaging Precision Medical, Shanxi Medical University, Taiyuan, 030001, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China.
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Shu HY, Chen CC, Ku HT, Wang CL, Wu KM, Weng HY, Liu ST, Chen CL, Chiu CH. Complete genome sequence of Bacillus halotolerans F29-3, a fengycin-producing strain. Microbiol Resour Announc 2024; 13:e0124623. [PMID: 38451104 PMCID: PMC11008187 DOI: 10.1128/mra.01246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Bacillus halotolerans F29-3, a Gram-positive bacterium, is recognized for its synthesis of the antifungal substance fengycin. This announcement introduces the complete genome sequence and provides insights into the genetic products related to antibiotic secondary metabolites, including non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and NRPS/PKS combination.
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Affiliation(s)
- Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Hsin-Tzu Ku
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Keh-Ming Wu
- Bioinformatics Department, Welgene Biotech Co., Ltd., Taipei, Taiwan
| | - Hui-Ying Weng
- Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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Metabolic engineering of Bacillus subtilis 168 for the utilization of arabinose to synthesize the antifungal lipopeptide fengycin. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Li S, He P, Fan H, Liu L, Yin K, Yang B, Li Y, Huang SM, Li X, Zheng SJ. A Real-Time Fluorescent Reverse Transcription Quantitative PCR Assay for Rapid Detection of Genetic Markers' Expression Associated with Fusarium Wilt of Banana Biocontrol Activities in Bacillus. J Fungi (Basel) 2021; 7:353. [PMID: 33946404 PMCID: PMC8147159 DOI: 10.3390/jof7050353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023] Open
Abstract
Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), especially Tropical Race 4 (TR4), seriously threatens banana production worldwide. There is no single effective control measure, although certain Bacillus strains secrete antibiotics as promising disease-biocontrol agents. This study identified five Bacillus strains displaying strong antibiotic activity against TR4, using a systemic assessment for presence/absence of genetic markers at genome level, and expression profiles at transcriptome level. A conventional PCR with 13 specific primer pairs detected biocontrol-related genes. An accurate, quantitative real-time PCR protocol with novel designed specific primers was developed to characterise strain-specific gene expression, that optimises strain-culturing and RNA-isolation methodologies. Six genes responsible for synthesising non-ribosomal peptide synthetase biocontrol metabolites were detected in all five strains. Three genes were involved in synthesising three Polyketide synthetase metabolites in all five strains, but the macrolactin synthase gene mln was only detected in WBN06 and YN1282-2. All five Bacillus strains have the genes dhb and bioA, essential for synthesising bacillibactin and biotin. However, the gene sboA, involved in subtilisin synthesis, is absent in all five strains. These genes' expression patterns were significantly different among these strains, suggesting different mechanisms involved in TR4 biocontrol. Results will help elucidate functional genes' biocontrol mechanisms.
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Affiliation(s)
- Shu Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Ping He
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Ministry of Education Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Huacai Fan
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Lina Liu
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Kesuo Yin
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Baoming Yang
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Yongping Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Su-Mei Huang
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China;
| | - Xundong Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
| | - Si-Jun Zheng
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (S.L.); (P.H.); (H.F.); (L.L.); (K.Y.); (B.Y.); (Y.L.); (X.L.)
- Bioversity International, Kunming 650205, China
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Genome mining and UHPLC-QTOF-MS/MS to identify the potential antimicrobial compounds and determine the specificity of biosynthetic gene clusters in Bacillus subtilis NCD-2. BMC Genomics 2020; 21:767. [PMID: 33153447 PMCID: PMC7643408 DOI: 10.1186/s12864-020-07160-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/19/2020] [Indexed: 11/24/2022] Open
Abstract
Background Bacillus subtilis strain NCD-2 is an excellent biocontrol agent against plant soil-borne diseases and shows broad-spectrum antifungal activities. This study aimed to explore some secondary metabolite biosynthetic gene clusters and related antimicrobial compounds in strain NCD-2. An integrative approach combining genome mining and structural identification technologies using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry (UHPLC-MS/MS), was adopted to interpret the chemical origins of metabolites with significant biological activities. Results Genome mining revealed nine gene clusters encoding secondary metabolites with predicted functions, including fengycin, surfactin, bacillaene, subtilosin, bacillibactin, bacilysin and three unknown products. Fengycin, surfactin, bacillaene and bacillibactin were successfully detected from the fermentation broth of strain NCD-2 by UHPLC-QTOF-MS/MS. The biosynthetic gene clusters of bacillaene, subtilosin, bacillibactin, and bacilysin showed 100% amino acid sequence identities with those in B. velezensis strain FZB42, whereas the identities of the surfactin and fengycin gene clusters were only 83 and 92%, respectively. Further comparison revealed that strain NCD-2 had lost the fenC and fenD genes in the fengycin biosynthetic operon. The biosynthetic enzyme-related gene srfAB for surfactin was divided into two parts. Bioinformatics analysis suggested that FenE in strain NCD-2 had a similar function to FenE and FenC in strain FZB42, and that FenA in strain NCD-2 had a similar function to FenA and FenD in strain FZB42. Five different kinds of fengycins, with 26 homologs, and surfactin, with 4 homologs, were detected from strain NCD-2. To the best of our knowledge, this is the first report of a non-typical gene cluster related to fengycin synthesis. Conclusions Our study revealed a number of gene clusters encoding antimicrobial compounds in the genome of strain NCD-2, including a fengycin synthetic gene cluster that might be unique by using genome mining and UHPLC–QTOF–MS/MS. The production of fengycin, surfactin, bacillaene and bacillibactin might explain the biological activities of strain NCD-2. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07160-2.
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Key elements and regulation strategies of NRPSs for biosynthesis of lipopeptides by Bacillus. Appl Microbiol Biotechnol 2020; 104:8077-8087. [DOI: 10.1007/s00253-020-10801-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/08/2020] [Accepted: 07/27/2020] [Indexed: 10/23/2022]
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K R, Y V N, V P V. Acid soluble extracellular matrix confers structural stability to marine Bacillus haynesii pellicle biofilms. Colloids Surf B Biointerfaces 2020; 194:111160. [PMID: 32526635 DOI: 10.1016/j.colsurfb.2020.111160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/20/2020] [Accepted: 05/27/2020] [Indexed: 11/26/2022]
Abstract
In natural and engineered settings, bacteria predominantly thrive in biofilms, which are complex microbial communities embedded in a self-produced extracellular polymeric substances (EPSs) matrix. Pellicles are complex macroscopic biofilms floating at air-water interface. Though pellicle formation has been studied in detail in Bacillus subtilis, a soil bacterium, it is not reported in aquatic bacteria, which may use pellicle-growth as survival-strategy. This study shows that Bacillus haynesii isolated from a marine environment forms robust pellicle biofilms at air-water interface. B. haynesii pellicles showed complex architecture, involving dense cell-aggregates with interconnecting thread-like structures in an extracellular matrix. In situ staining by Alcian blue, Concanavalin A and ThioflavinT (ThT), respectively, localized acidic polymers, glycoconjugates and amyloid-like fibers in the pellicle. The pellicle was rigid and not disrupted by common EPS extraction protocols. Hence, a set of reagents and conditions were evaluated for solubilizing the EPS and pellicle. Acetic acid was able to effectively solubilize the structural EPS and pellicle structure. Acid soluble structural EPS contained chemical signatures for both proteins and carbohydrates, as revealed by elemental analysis, Fourier Transform Infrared Spectroscopy and Raman Spectroscopy. Ex situ staining of acid soluble EPS by ThT showed recovery of amyloid-forming proteins from pellicle. Results show that structural stability of the pellicle is mainly conferred by amyloid-like fibers of the EPS matrix. The robust pellicle-growth reported here may represent a survival-strategy in the aquatic bacterium. The findings reported here can support future research on biofilm structure, EPS matrix and its formation, which are critical for understanding how microbes thrive in natural and engineered settings.
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Affiliation(s)
- Rajitha K
- Biofouling and Biofilm Processes, Water and Steam Chemistry Division, Chemistry Group, Bhabha Atomic Research Centre, Kalpakkam, 603102, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Nancharaiah Y V
- Biofouling and Biofilm Processes, Water and Steam Chemistry Division, Chemistry Group, Bhabha Atomic Research Centre, Kalpakkam, 603102, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Venugopalan V P
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Bioscience Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
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Kenawy A, Dailin DJ, Abo-Zaid GA, Malek RA, Ambehabati KK, Zakaria KHN, Sayyed RZ, El Enshasy HA. Biosynthesis of Antibiotics by PGPR and Their Roles in Biocontrol of Plant Diseases. PLANT GROWTH PROMOTING RHIZOBACTERIA FOR SUSTAINABLE STRESS MANAGEMENT 2019:1-35. [DOI: 10.1007/978-981-13-6986-5_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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10
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Fritz S, Rajaonison A, Chabrol O, Raoult D, Rolain JM, Merhej V. Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect. BMC Bioinformatics 2018; 19:463. [PMID: 30509188 PMCID: PMC6276269 DOI: 10.1186/s12859-018-2479-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
Background Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development of computational mining as an important tool in the discovery of natural products with antibiotic effect. Results NRPPUR (Non-Ribosomal Peptide and Polyketide Urmite) is a new bioinformatic tool that was created to detect polyketides and non-ribosomal peptide gene clusters (PKS and NRPS) in bacterial genomes using the rpsBlast program. The NRPPUR database was constructed locally by assembling all 3505 available sequences of NRPS-PKS that have been identified by in silico approaches to date, with 164 Biosynthetic Gene Clusters (BGCs) derived from the published literature that have demonstrated antimicrobial activity in vitro. The in silico analysis of 49 intestinal human bacterial genomes using the NRPPUR made it possible to identify 91 BGCs including 89 clusters that had never previously been described. On average, intestinal human bacterial genomes devote nearly 0.8% (±1.4% s.d.) of their genome to NRPS/PKS biosynthesis, with Bacillus vallismortis, Streptomyces massiliensis and Bacillus subtilis genomes apportioning 8.4, 3.6 and 3.15% of their genomes, respectively. When using the cross-streak method, S. massiliensis displayed antibacterial activity against many Gram-positive and negative bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Conclusions NRPPUR has proven to be a very useful tool for the primary in silico selection of species with potential antimicrobial activity and human microbiota could be the future source of new antimicrobial discoveries. Further exploration of this and other ecological niches, coupled with high-throughput antibacterial activity screening should be envisaged. Electronic supplementary material The online version of this article (10.1186/s12859-018-2479-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shirley Fritz
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France
| | | | - Olivier Chabrol
- CNRS, Centrale Marseille, Aix Marseille University, I2M, Marseille, France
| | - Didier Raoult
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Vicky Merhej
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, Marseille, France.
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Pramudito TE, Agustina D, Nguyen TKN, Suwanto A. A Novel Variant of Narrow-Spectrum Antifungal Bacterial Lipopeptides That Strongly Inhibit Ganoderma boninense. Probiotics Antimicrob Proteins 2018; 10:110-117. [PMID: 29101528 DOI: 10.1007/s12602-017-9334-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial antifungal cyclic lipopeptides (ACLs) have become a promising alternative to synthetic fungicide to control pathogenic fungi. Bacillus sp. is known to produce three families of ACL, namely iturin, surfactin, and fengycin. In this paper, we characterized the ACLs produced by B. methylotrophicus HC51 (referred as HC51) mainly regarding its composition and effectivity against fungal plant pathogen. HC51 culture was tested against various pathogenic fungi and the ACLs were extracted and analyzed using liquid chromatography-electrospray ionization mass spectrometry. HC51 showed strong antifungal activity against the plant pathogens Ganoderma sp. and Fusarium sp. Cell-free methanol extract of HC51 contains iturin A and various variants of fengycin. C16 fengycin A was present in four fractions which indicates it as a major component of ACL from HC51. Five variants of fengycin were detected, four of which had been previously reported. We found a novel C17 fengycin F that is characterized by a substitution of L-ornithine into lysine. Considering that L-ornithine is an important building block of fengycin, this substitution suggests the possibility of an alternative pathway for fengycin biosynthesis.
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Affiliation(s)
- Theodorus Eko Pramudito
- Biotechnology Research and Development, PT Wilmar Benih Indonesia, Bekasi, Jawa Barat, 17530, Indonesia
| | - Delia Agustina
- Biotechnology Research and Development, PT Wilmar Benih Indonesia, Bekasi, Jawa Barat, 17530, Indonesia
| | | | - Antonius Suwanto
- Biotechnology Research and Development, PT Wilmar Benih Indonesia, Bekasi, Jawa Barat, 17530, Indonesia.
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Chiang-Ni C, Tseng HC, Hung CH, Chiu CH. Acidic stress enhances CovR/S-dependent gene repression through activation of the covR/S promoter in emm1-type group A Streptococcus. Int J Med Microbiol 2017. [PMID: 28648357 DOI: 10.1016/j.ijmm.2017.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Streptococcus pyogenes (group A Streptococcus) is a clinically important gram-positive bacterium that causes severe diseases with high mortality. Spontaneous mutations in genes encoding the CovR/CovS two-component regulatory system have been shown to derepress expression of virulence factors and are significantly associated with invasiveness of infections. Sensor kinase CovS senses environmental signals and then regulates the levels of phosphorylated CovR. In addition, CovS is responsible for survival of group A Streptococcus under acidic stress. How this system regulates the expression of CovR-controlled genes under acidic stress is not clear. This study shows that the expression of CovR-controlled genes, including hasA, ska, and slo, is repressed under acidic conditions by a CovS-dependent mechanism. Inactivation of CovS kinase activity or CovR protein phosphorylation derepresses the transcription of these genes under acidic conditions, suggesting that the phosphorylation of CovR is required for the repression of the CovR-controlled genes. Furthermore, the promoter activity of the covR/covS operon (pcov) was upregulated after 15min of incubation under acidic conditions. Replacement of pcov with a constitutively activated promoter abrogated the acidic-stress-dependent repression of the genes, indicating that the pH-dependent pcov activity is directly involved in the repression of CovR-controlled genes. In summary, the present study shows that inactivation of CovS not only derepresses CovR-controlled genes but also abrogates the acidic-stress-dependent repression of the genes; these phenomena may significantly increase bacterial virulence during infection.
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Affiliation(s)
- Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Tao-yuan, Taiwan; Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Tao-yuan, Taiwan.
| | - Huei-Chuan Tseng
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Tao-yuan, Taiwan
| | - Chia-Hui Hung
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yuan, Taiwan
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yuan, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Tao-yuan, Taiwan; Department of Pediatrics, Chang Gung Children's Hospital, Tao-yuan, Taiwan
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13
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Zhang Z, Ding Z, Zhong J, Zhou J, Shu D, Luo D, Yang J, Tan H. Improvement of iturin A production inBacillus subtilisZK0 by overexpression of thecomAandsigAgenes. Lett Appl Microbiol 2017; 64:452-458. [DOI: 10.1111/lam.12739] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/26/2017] [Accepted: 03/27/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Z. Zhang
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- University of the Chinese Academy of Sciences; Beijing China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - Z.T. Ding
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- University of the Chinese Academy of Sciences; Beijing China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - J. Zhong
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- University of the Chinese Academy of Sciences; Beijing China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - J.Y. Zhou
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - D. Shu
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - D. Luo
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - J. Yang
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
| | - H. Tan
- Key Laboratory of Environmental and Applied Microbiology; Chengdu Institute of Biology; The Chinese Academy of Sciences; Chengdu China
- University of the Chinese Academy of Sciences; Beijing China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Sichuan China
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Calvo H, Marco P, Blanco D, Oria R, Venturini M. Potential of a new strain of Bacillus amyloliquefaciens BUZ-14 as a biocontrol agent of postharvest fruit diseases. Food Microbiol 2017; 63:101-110. [DOI: 10.1016/j.fm.2016.11.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 10/28/2016] [Accepted: 11/07/2016] [Indexed: 11/26/2022]
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Jasim B, Sreelakshmi S, Mathew J, Radhakrishnan EK. Identification of endophytic Bacillus mojavensis with highly specialized broad spectrum antibacterial activity. 3 Biotech 2016; 6:187. [PMID: 28330259 PMCID: PMC5009053 DOI: 10.1007/s13205-016-0508-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
Biosynthetic adaptation of endophytic bacteria to chemically support host plant is very remarkable. Hence these organisms from medicinal plants are considered as highly valuable sources for natural products with diverse bioactivity. Their metabolite diversity and biosynthetic versatility have been increasingly explored for drug discovery. In this study, an endophytic Bacillus mojavensis with broad spectrum antibacterial properties has been analyzed for the chemical basis of its activity. By LC-MS/MS the organism was identified to have the biosynthetic ability to produce lipopeptides surfactin and fengycin. The impressive antibacterial activity of B. mojavensis as reported in the study indicates its broad antimicrobial applications.
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Affiliation(s)
- B Jasim
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, 686 560, Kerala, India
| | - S Sreelakshmi
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, 686 560, Kerala, India
| | - Jyothis Mathew
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, 686 560, Kerala, India
| | - E K Radhakrishnan
- School of Biosciences, Mahatma Gandhi University, PD Hills (PO), Kottayam, 686 560, Kerala, India.
- Inter University Instrumentation Centre, Mahatma Gandhi University, PD Hills (PO), Kottayam, 686 560, Kerala, India.
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16
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Modulation of Staphylococcus aureus spreading by water. Sci Rep 2016; 6:25233. [PMID: 27125382 PMCID: PMC4850448 DOI: 10.1038/srep25233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus is known to spread rapidly and form giant colonies on the surface of soft agar and animal tissues by a process called colony spreading. So far, the mechanisms underlying spreading remain poorly understood. This study investigated the spreading phenomenon by culturing S. aureus and its mutant derivatives on Tryptic Soy Agarose (TSA) medium. We found that S. aureus extracts water from the medium and floats on water at 2.5 h after inoculation, which could be observed using phase contrast microscopy. The floating of the bacteria on water could be verified by confocal microscopy using an S. aureus strain that constitutively expresses green fluorescence protein. This study also found that as the density of bacterial colony increases, a quorum sensing response is triggered, resulting in the synthesis of the biosurfactants, phenolic-soluble modulins (PSMs), which weakens water surface tension, causing water to flood the medium surface to allow the bacteria to spread rapidly. This study reveals a mechanism that explains how an organism lacking a flagellar motor is capable of spreading rapidly on a medium surface, which is important to the understanding of how S. aureus spreads in human tissues to cause infections.
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Cheng YC, Ke WJ, Liu ST. Regions involved in fengycin synthetases enzyme complex formation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 50:755-762. [PMID: 26857334 DOI: 10.1016/j.jmii.2015.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/14/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Fengycin is a lipopeptide antibiotic synthesized nonribosomally by five fengycin synthetases. These enzymes are linked in a specific order to form the complex. This study investigates how these enzymes interact in the complex and analyzes the regions in the enzymes that are critical to the interactions. METHODS Deletions were generated in the fengycin synthetases. The interaction of these mutant proteins with their partner enzymes in the complex was analyzed in vitro by a glutathione S-transferase (GST) or nickel pulldown assay. RESULTS The communication-mediating donor (COM-D) domains of the fengycin synthetases, when fused to GST, specifically pulled down their downstream partner enzymes in the GST-pulldown assays. The communication-mediating acceptor (COM-A) domains were required for binding between two partner enzymes, although the domains alone did not confer specificity of the binding to their upstream partner enzymes. This study found that the COM-A domain, the condensation domain, and a portion of the adenylation domain in fengycin synthetase B (FenB) were required for specific binding to fengycin synthetase A (FenA). CONCLUSION The interaction between the COM-D and COM-A domains in two partner enzymes is critical for nonribosomal peptide synthesis. The COM-A domain alone is insufficient for interacting with its upstream partner enzyme in the enzyme complex with specificity; a region that contains COM-A, condensation, and a portion of adenylation domains in the downstream partner enzyme is required.
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Affiliation(s)
- Yu-Chieh Cheng
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Ju Ke
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Microbiology and Immunology, Research Center for Bacterial Pathogenesis, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Medical Research and Development Chiayi Branch, Chang Gung Memorial Hospital, Chiayi, Taiwan.
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Leães FL, Velho RV, Caldas DGG, Ritter AC, Tsai SM, Brandelli A. Expression of essential genes for biosynthesis of antimicrobial peptides of Bacillus is modulated by inactivated cells of target microorganisms. Res Microbiol 2015; 167:83-9. [PMID: 26577655 DOI: 10.1016/j.resmic.2015.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 10/01/2015] [Accepted: 10/28/2015] [Indexed: 11/27/2022]
Abstract
Certain Bacillus strains are important producers of antimicrobial peptides with great potential for biological control. Antimicrobial peptide production by Bacillus amyloliquefaciens P11 was investigated in the presence of heat-inactivated cells of bacteria and fungi. B. amyloliquefaciens P11 exhibited higher antimicrobial activity in the presence of inactivated cells of Staphylococcus aureus and Aspergillus parasiticus compared to other conditions tested. Expression of essential genes related to biosynthesis of the antimicrobial peptides surfactin (sfp), iturin A (lpa-14 and ituD), subtilosin A (sboA) and fengycin (fenA) was investigated by quantitative real-time PCR (qRT-PCR). The genes lpa-14 and ituD were highly expressed in the presence of S. aureus (inactivated cells), indicating induction of iturin A production by B. amyloliquefaciens P11. The other inducing condition (inactivated cells of A. parasiticus) suppressed expression of lpa-14, but increased expression of ituD. A twofold increase in fenA expression was observed for both conditions, while strong suppression of sboA expression was observed in the presence of inactivated cells of S. aureus. An increase in antimicrobial activity was observed, indicating that synthesis of antimicrobial peptides may be induced by target microorganisms.
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Affiliation(s)
- Fernanda Leal Leães
- Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, ICTA, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
| | - Renata Voltolini Velho
- Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, ICTA, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
| | - Danielle Gregório Gomes Caldas
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, CENA, Universidade de São Paulo, USP, Piracicaba, SP, Brazil
| | - Ana Carolina Ritter
- Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, ICTA, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
| | - Siu Mui Tsai
- Laboratório de Biologia Celular e Molecular, Centro de Energia Nuclear na Agricultura, CENA, Universidade de São Paulo, USP, Piracicaba, SP, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Instituto de Ciência e Tecnologia de Alimentos, ICTA, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.
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Lin MH, Shu JC, Lin LP, Chong KY, Cheng YW, Du JF, Liu ST. Elucidating the crucial role of poly N-acetylglucosamine from Staphylococcus aureus in cellular adhesion and pathogenesis. PLoS One 2015; 10:e0124216. [PMID: 25876106 PMCID: PMC4398431 DOI: 10.1371/journal.pone.0124216] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 03/10/2015] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is an important pathogen that forms biofilms on the surfaces of medical implants. Biofilm formation by S. aureus is associated with the production of poly N-acetylglucosamine (PNAG), also referred to as polysaccharide intercellular adhesin (PIA), which mediates bacterial adhesion, leading to the accumulation of bacteria on solid surfaces. This study shows that the ability of S. aureus SA113 to adhere to nasal epithelial cells is reduced after the deletion of the ica operon, which contains genes encoding PIA/PNAG synthesis. However, this ability is restored after a plasmid carrying the entire ica operon is transformed into the mutant strain, S. aureus SA113Δica, showing that the synthesis of PIA/PNAG is important for adhesion to epithelial cells. Additionally, S. carnosus TM300, which does not produce PIA/PNAG, forms a biofilm and adheres to epithelial cells after the bacteria are transformed with a PIA/PNAG-expressing plasmid, pTXicaADBC. The adhesion of S. carnosus TM300 to epithelial cells is also demonstrated by adding purified exopolysaccharide (EPS), which contains PIA/PNAG, to the bacteria. In addition, using a mouse model, we find that the abscess lesions and bacterial burden in lung tissues is higher in mice infected with S. aureus SA113 than in those infected with the mutant strain, S. aureus SA113Δica. The results indicate that PIA/PNAG promotes the adhesion of S. aureus to human nasal epithelial cells and lung infections in a mouse model. This study elucidates a mechanism that is important to the pathogenesis of S. aureus infections.
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Affiliation(s)
- Mei Hui Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Jwu Ching Shu
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Li Ping Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Kowit yu Chong
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Ya Wen Cheng
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Jia Fu Du
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang-Gung University, Taoyuan, Taiwan, Republic of China
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Medical Research and Development, Chiayi Branch, Chang Gung Memorial Hospital, Chiayi, Taiwan, Republic of China
- * E-mail:
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20
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Hsieh YT, Chen KC, Cheng CM, Cheng TL, Tao MH, Roffler SR. Impediments to enhancement of CPT-11 anticancer activity by E. coli directed beta-glucuronidase therapy. PLoS One 2015; 10:e0118028. [PMID: 25688562 PMCID: PMC4331512 DOI: 10.1371/journal.pone.0118028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/05/2015] [Indexed: 12/17/2022] Open
Abstract
CPT-11 is a camptothecin analog used for the clinical treatment of colorectal adenocarcinoma. CPT-11 is converted into the therapeutic anti-cancer agent SN-38 by liver enzymes and can be further metabolized to a non-toxic glucuronide SN-38G, resulting in low SN-38 but high SN-38G concentrations in the circulation. We previously demonstrated that adenoviral expression of membrane-anchored beta-glucuronidase could promote conversion of SN-38G to SN-38 in tumors and increase the anticancer activity of CPT-11. Here, we identified impediments to effective tumor therapy with E. coli that were engineered to constitutively express highly active E. coli beta-glucuronidase intracellularly to enhance the anticancer activity of CPT-11. The engineered bacteria, E. coli (lux/βG), could hydrolyze SN-38G to SN-38, increased the sensitivity of cultured tumor cells to SN-38G by about 100 fold and selectively accumulated in tumors. However, E. coli (lux/βG) did not more effectively increase CPT-11 anticancer activity in human tumor xenografts as compared to non-engineered E. coli. SN-38G conversion to SN-38 by E. coli (lux/βG) appeared to be limited by slow uptake into bacteria as well as by segregation of E. coli in necrotic regions of tumors that may be relatively inaccessible to systemically-administered drug molecules. Studies using a fluorescent glucuronide probe showed that significantly greater glucuronide hydrolysis could be achieved in mice pretreated with E. coli (lux/βG) by direct intratumoral injection of the glucuronide probe or by intratumoral lysis of bacteria to release intracellular beta-glucuronidase. Our study suggests that the distribution of beta-glucuronidase, and possibly other therapeutic proteins, in the tumor microenvironment might be an important barrier for effective bacterial-based tumor therapy. Expression of secreted therapeutic proteins or induction of therapeutic protein release from bacteria might therefore be a promising strategy to enhance anti-tumor activity.
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Affiliation(s)
- Yuan-Ting Hsieh
- Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kai-Chuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chiu-Min Cheng
- Department of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mi-Hua Tao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Steve R. Roffler
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- * E-mail:
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21
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Promoter analysis and transcription regulation of fus gene cluster responsible for fusaricidin synthesis of Paenibacillus polymyxa SQR-21. Appl Microbiol Biotechnol 2013; 97:9479-89. [PMID: 24072159 DOI: 10.1007/s00253-013-5157-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 06/25/2013] [Accepted: 07/27/2013] [Indexed: 10/26/2022]
Abstract
Fusaricidins produced by Paenibacillus polymyxa are lipopeptide antibiotics with outstanding antifungal activity. In this study, the whole gene cluster responsible for fusaricidin biosynthesis (fusA) was isolated and identified from the cDNA library of one biocontrol agent P. polymyxa SQR-21 (SQR-21). MALDI-TOF MS analysis confirmed that SQR-21 could produce four kinds of fusaricidins: A, B, C, and D. A central promoter that drove the transcription of fusGFEDCBA was revealed by mapping of the fus promoter region by 5' deletions. The disruption of fusA in SQR-21 led to the abolishment of fusaricidin production and antifungal activity. The direct interaction between a potential regulator, AbrB, and the promoter region of fus gene cluster was confirmed by electrophoretic mobility shift assays. One abrB disruption mutant showed significantly higher antifungal activity compared with the wild type. These results revealed a pathway for the transcriptional regulation of the fus gene cluster in P. polymyxa.
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22
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Shishido TK, Kaasalainen U, Fewer DP, Rouhiainen L, Jokela J, Wahlsten M, Fiore MF, Yunes JS, Rikkinen J, Sivonen K. Convergent evolution of [D-Leucine(1)] microcystin-LR in taxonomically disparate cyanobacteria. BMC Evol Biol 2013; 13:86. [PMID: 23601305 PMCID: PMC3640908 DOI: 10.1186/1471-2148-13-86] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/09/2013] [Indexed: 11/24/2022] Open
Abstract
Background Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS secondary metabolic pathway. They are produced by a variety of cyanobacteria and are responsible for the poisoning of humans as well as the deaths of wild and domestic animals around the world. The chemical diversity of the microcystin family is attributed to a number of genetic events that have resulted in the diversification of the pathway for microcystin assembly. Results Here, we show that independent evolutionary events affecting the substrate specificity of the microcystin biosynthetic pathway have resulted in convergence on a rare [D-Leu1] microcystin-LR chemical variant. We detected this rare microcystin variant from strains of the distantly related genera Microcystis, Nostoc, and Phormidium. Phylogenetic analysis performed using sequences of the catalytic domains within the mcy gene cluster demonstrated a clear recombination pattern in the adenylation domain phylogenetic tree. We found evidence for conversion of the gene encoding the McyA2 adenylation domain in strains of the genera Nostoc and Phormidium. However, point mutations affecting the substrate-binding sequence motifs of the McyA2 adenylation domain were associated with the change in substrate specificity in two strains of Microcystis. In addition to the main [D-Leu1] microcystin-LR variant, these two strains produced a new microcystin that was identified as [Met1] microcystin-LR. Conclusions Phylogenetic analysis demonstrated that both point mutations and gene conversion result in functional mcy gene clusters that produce the same rare [D-Leu1] variant of microcystin in strains of the genera Microcystis, Nostoc, and Phormidium. Engineering pathways to produce recombinant non-ribosomal peptides could provide new natural products or increase the activity of known compounds. Our results suggest that the replacement of entire adenylation domains could be a more successful strategy to obtain higher specificity in the modification of the non-ribosomal peptides than point mutations.
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Affiliation(s)
- Tânia Keiko Shishido
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter (Viikinkaari 9), PO Box 56, Helsinki, FIN-00014, Finland
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Hsu CY, Lin MH, Chen CC, Chien SC, Cheng YH, Su IN, Shu JC. Vancomycin promotes the bacterial autolysis, release of extracellular DNA, and biofilm formation in vancomycin-non-susceptible Staphylococcus aureus. ACTA ACUST UNITED AC 2012; 63:236-47. [PMID: 22077227 DOI: 10.1111/j.1574-695x.2011.00846.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus, an important human pathogen, is particularly adept at producing biofilms on implanted medical devices. Although antibiotic treatment of nonsusceptible bacteria will not kill these strains, the consequences should be studied. The present study focuses on investigating the effect of vancomycin on biofilm formation by vancomycin-non-susceptible S. aureus. Biofilm adherence assays and scanning electron microscopy demonstrated that biofilm formation was significantly enhanced following vancomycin treatment. Bacterial autolysis of some subpopulations was observed and was confirmed by the live/dead staining and confocal laser scanning microscopy. A significant increase in polysaccharide intercellular adhesin (PIA) production was observed by measuring icaA transcript levels and in a semi-quantitative PIA assay in one resistant strain. We show that the release of extracellular DNA (eDNA) via cidA-mediated autolysis is a major contributor to vancomycin-enhanced biofilm formation. The addition of xenogeneic DNA could also significantly enhance biofilm formation by a PIA-overproducing S. aureus strain. The magnitude of the development of the biofilm depends on a balance between the amounts of eDNA and PIA. In conclusion, sublethal doses of cell wall-active antibiotics like vancomycin induce biofilm formation through an autolysis-dependent mechanism in vancomycin-non-susceptible S. aureus.
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Affiliation(s)
- Chi-Yu Hsu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
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Chen HY, Chen CC, Fang CS, Hsieh YT, Lin MH, Shu JC. Vancomycin activates σ(B) in vancomycin-resistant Staphylococcus aureus resulting in the enhancement of cytotoxicity. PLoS One 2011; 6:e24472. [PMID: 21912698 PMCID: PMC3166330 DOI: 10.1371/journal.pone.0024472] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/11/2011] [Indexed: 12/16/2022] Open
Abstract
The alternative transcription factor σB is responsible for transcription in Staphylococcus aureus during the stress response. Many virulence-associated genes are directly or indirectly regulated by σB. We hypothesized that treatment with antibiotics may act as an environmental stressor that induces σB activity in antibiotic-resistant strains. Several antibiotics with distinct modes of action, including ampicillin (12 µg/ml), vancomycin (16 or 32 µg/ml), chloramphenicol (15 µg/ml), ciprofloxacin (0.25 µg/ml), and sulfamethoxazole/trimethoprim (SXT, 0.8 µg/ml), were investigated for their ability to activate this transcription factor. We were especially interested in the stress response in vancomycin-resistant S. aureus (VRSA) strains treated with vancomycin. The transcription levels of selected genes associated with virulence were also measured. Real-time quantitative reverse transcription PCR was employed to evaluate gene transcription levels. Contact hemolytic and cytotoxicity assays were used to evaluate cell damage following antibiotic treatment. Antibiotics that target the cell wall (vancomycin and ampicillin) and SXT induced σB activity in VRSA strains. Expression of σB-regulated virulence genes, including hla and fnbA, was associated with the vancomycin-induced σB activity in VRSA strains and the increase in cytotoxicity upon vancomycin treatment. These effects were not observed in the sigB-deficient strain but were observed in the complemented strain. We demonstrate that sub-minimum inhibitory concentration (sub-MIC) levels of antibiotics act as environmental stressors and activate the stress response sigma factor, σB. The improper use of antibiotics may alter the expression of virulence factors through the activation of σB in drug-resistant strains of S. aureus and lead to worse clinical outcomes.
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Affiliation(s)
- Hong-Yi Chen
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Chun-Sheng Fang
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Ting Hsieh
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Mei-Hui Lin
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
- Research Center for Pathogenic Bacteria, Chang Gung University, Taoyuan, Taiwan
| | - Jwu-Ching Shu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
- Research Center for Pathogenic Bacteria, Chang Gung University, Taoyuan, Taiwan
- * E-mail:
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Marvasi M, Visscher PT, Casillas Martinez L. Exopolymeric substances (EPS) from Bacillus subtilis: polymers and genes encoding their synthesis. FEMS Microbiol Lett 2011; 313:1-9. [PMID: 20735481 DOI: 10.1111/j.1574-6968.2010.02085.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bacterial exopolymeric substances (EPS) are molecules released in response to the physiological stress encountered in the natural environment. EPS are structural components of the extracellular matrix in which cells are embedded during biofilm development. The chemical nature and functions of these EPS are dependent on the genetic expression of the cells within each biofilm. Although some bacterial matrices have been characterized, understanding of the function of the EPS is relatively limited, particularly within the Bacillus genus. Similar gaps of knowledge exist with respect to the chemical composition and specific roles of the macromolecules secreted by Bacillus subtilis in its natural environment. In this review, the different EPS from B. subtilis were classified into four main functional categories: structural (neutral polymers), sorptive (charged polymers), surface-active and active polymers. In addition, current information regarding the genetic expression, production and function of the main polymers secreted by B. subtilis strains, particularly those related to biofilm formation and its architecture, has been compiled. Further characterization of these EPS from B. subtilis remains a challenge.
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Affiliation(s)
- Massimiliano Marvasi
- Biology Department, Pontifical Catholic University of Puerto Rico, Ponce, PR, USA
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Activation of the promoter of the fengycin synthetase operon by the UP element. J Bacteriol 2009; 191:4615-23. [PMID: 19447911 DOI: 10.1128/jb.00255-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis F29-3 produces an antifungal peptidic antibiotic that is synthesized nonribosomally by fengycin synthetases. Our previous work established that the promoter of the fengycin synthetase operon is located 86 nucleotides upstream of the translational initiation codon of fenC. This investigation involved transcriptional fusions with a DNA fragment that contains the region between positions -105 and +80 and determined that deleting the region between positions -55 and -42 reduces the promoter activity by 64.5%. Transcriptional fusions in the B. subtilis DB2 chromosome also indicated that mutating the sequence markedly reduces the promoter activity. An in vitro transcription analysis confirmed that the transcription is inefficient when the sequence in this region is mutated. Electrophoretic mobility shift and footprinting analyses demonstrated that the C-terminal domain of the RNA polymerase alpha subunit binds to the region between positions -55 and -39. These results indicated that the sequence is an UP element. Finally, this UP element is critical for the production of fengycin, since mutating the UP sequence in the chromosome of B. subtilis F29-3 reduces the transcription of the fen operon by 85% and prevents the cells from producing enough fengycin to suppress the germination of Paecilomyces variotii spores on agar plates.
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Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens. J Biotechnol 2009; 140:27-37. [DOI: 10.1016/j.jbiotec.2008.10.011] [Citation(s) in RCA: 301] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2008] [Revised: 09/23/2008] [Accepted: 10/21/2008] [Indexed: 11/18/2022]
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Rounge TB, Rohrlack T, Kristensen T, Jakobsen KS. Recombination and selectional forces in cyanopeptolin NRPS operons from highly similar, but geographically remote Planktothrix strains. BMC Microbiol 2008; 8:141. [PMID: 18727817 PMCID: PMC2533009 DOI: 10.1186/1471-2180-8-141] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2007] [Accepted: 08/26/2008] [Indexed: 11/20/2022] Open
Abstract
Background Cyanopeptolins are nonribosomally produced heptapetides showing a highly variable composition. The cyanopeptolin synthetase operon has previously been investigated in three strains from the genera Microcystis, Planktothrix and Anabaena. Cyanopeptolins are displaying protease inhibitor activity, but the biological function(s) is (are) unknown. Cyanopeptolin gene cluster variability and biological functions of the peptide variants are likely to be interconnected. Results We have investigated two cyanopeptolin gene clusters from highly similar, but geographically remote strains of the same genus. Sequencing of a nonribosomal peptide synthetase (NRPS) cyanopeptolin gene cluster from the Japanese strain Planktothrix NIES 205 (205-oci), showed the 30 kb gene cluster to be highly similar to the oci gene cluster previously described in Planktothrix NIVA CYA 116, isolated in Norway. Both operons contained seven NRPS modules, a sulfotransferase (S) and a glyceric acid loading (GA)-domain. Sequence analyses showed a high degree of conservation, except for the presence of an epimerase domain in NIES 205 and the regions around the epimerase, showing high substitution rates and Ka/Ks values above 1. The two strains produce almost identical cyanopeptolins, cyanopeptolin-1138 and oscillapeptin E respectively, but with slight differences regarding the production of minor cyanopeptolin variants. These variants may be the result of relaxed adenylation (A)-domain specificity in the nonribosomal enzyme complex. Other genetic markers (16S rRNA, ntcA and the phycocyanin cpcBA spacer) were identical, supporting that these geographically separated Planktothrix strains are closely related. Conclusion A horizontal gene transfer event resulting in exchange of a whole module-encoding region was observed. Nucleotide statistics indicate that both purifying selection and positive selection forces are operating on the gene cluster. The positive selection forces are acting within and around the epimerase insertion while purifying selection conserves the remaining (major) part of the gene cluster. The presence of an epimerase in the gene cluster is in line with the D-configuration of Htyr, determined experimentally in oscillapeptin E in a previous study.
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Affiliation(s)
- Trine B Rounge
- University of Oslo, Department of Biology, Centre for Ecological and Evolutionary Synthesis, 0316 Oslo,
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Nonribosomal biosynthesis of fusaricidins by Paenibacillus polymyxa PKB1 involves direct activation of a D-amino acid. ACTA ACUST UNITED AC 2008; 15:118-27. [PMID: 18291316 DOI: 10.1016/j.chembiol.2007.12.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/24/2007] [Accepted: 12/04/2007] [Indexed: 11/23/2022]
Abstract
Paenibacillus polymyxa PKB1 produces fusaricidins, a family of lipopeptide antibiotics that strongly inhibits the growth of many plant pathogenic fungi. The fusaricidin biosynthetic gene cluster was cloned and sequenced, and it spans 32.4 kb, including an open reading frame (fusA) encoding a six-module nonribosomal peptide synthetase. The second, fourth, and fifth modules of fusaricidin synthetase each contain an epimerization domain, consistent with the structure of fusaricidins. However, no epimerization domain is found in the sixth module, corresponding to D-Ala. This sixth adenylation domain was produced at a high level in Escherichia coli and is shown to activate D-Ala specifically, providing evidence for direct activation of a D-amino acid by a prokaryotic peptide synthetase. The fusaricidin gene cluster also includes genes involved in the biosynthesis of the lipid moiety, but no genes for resistance, regulation, or transport functions were encountered.
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Cho KM, Hong SY, Lee SM, Kim YH, Kahng GG, Lim YP, Kim H, Yun HD. Endophytic bacterial communities in ginseng and their antifungal activity against pathogens. MICROBIAL ECOLOGY 2007; 54:341-51. [PMID: 17492474 DOI: 10.1007/s00248-007-9208-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 01/03/2007] [Accepted: 01/04/2007] [Indexed: 05/13/2023]
Abstract
Plant roots are associated with diverse communities of endophytic bacteria which do not exert adverse effects. The diversity of bacterial endophytes associated with ginseng roots cultivated in three different areas in Korea was investigated. Sixty-three colonies were isolated from the interior of ginseng roots. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates belonged to three major phylogenetic groups: the high G+C Gram-positive bacteria (HGCGPB), low G+C Gram-positive bacteria (LGCGPB), and the Proteobacteria. The dominant species at the three different ginseng growing areas were: HGCGPB at Ganghwa (55.0%), LGCGPB at Geumsan (45.5%), and Proteobacteria at Jinan (61.9%). Most cellulase-, xylanase-, and pectinase-producing colonies among the isolates belong to the LGCGPB group, except for Pectobacterium carotovora which belonged to the Proteobacteria. The 13 isolates belonging to LGCGPB and Proteobacteria were assessed for their antifungal activity against phytopathogenic fungi such as Rhizoctonia solani. Among them, Paenibacillus polymyxa GS01, Bacillus sp. GS07, and Pseudomonas poae JA01 show potential activity as biocontrol agents against phytopathogenic fungi. Finally, most of the low G+C Gram-positive bacteria with antifungal activity against phytopathogenic microorganisms showed cellulolytic enzyme activity while some Proteobacteria with the antifungal activity and the high G+C Gram-positive bacteria did not show any cellulolytic activity.
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Affiliation(s)
- Kye Man Cho
- Division of Applied Life Science, Gyeongsang National University, Chinju, Republic of Korea
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Ramarathnam R, Bo S, Chen Y, Fernando WGD, 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; 53:901-11. [PMID: 17898845 DOI: 10.1139/w07-049] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacillus species are well known for their ability to control plant diseases through various mechanisms, including the production of secondary metabolites. Bacillus subtilis DFH08, an antagonist of Fusarium graminearum , and other Bacillus spp. that are antagonists of common fungal pathogens of canola were screened for peptide synthetase biosynthetic genes of fengycin and bacillomycin D. Specific polymerase chain reaction (PCR) primers identified B. subtilis strains DFH08 and 49 for the presence of the fenD gene of the fengycin operon. Bacillus cereus DFE4, Bacillus amyloliquefaciens strains DFE16 and BS6, and B. subtilis 49 were identified for the presence of the bamC gene of the bacillomycin D synthetase biosynthetic operon. Both fengycin and bacillomycin D were detected in the culture extract of strain Bs49, characterized through MALDI–TOF–MS (matrix-assisted laser desorption ionization – time of flight – mass spectrometry), and their antifungal activities demonstrated against F. graminearum and Sclerotinia sclerotiorum . This study designed and used specific PCR primers for the detection of potential fengycin- and bacillomycin D-producing bacterial antagonists and confirmed the molecular detection with the biochemical detection of the corresponding antibiotic produced. This is also the first report of a B. cereus strain (DFE4) to have bacillomycin D biosynthetic genes. Bacteria that synthesize these lipopeptides could act as natural genetic sources for genetic engineering of the peptide synthetases for production of novel peptides.
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Affiliation(s)
- Rajesh Ramarathnam
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Wu CY, Chen CL, Lee YH, Cheng YC, Wu YC, Shu HY, Götz F, Liu ST. Nonribosomal Synthesis of Fengycin on an Enzyme Complex Formed by Fengycin Synthetases. J Biol Chem 2007; 282:5608-16. [PMID: 17182617 DOI: 10.1074/jbc.m609726200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fengycin, a lipopeptidic antibiotic, is synthesized nonribosomally by five fengycin synthetases (FenC, FenD, FenE, FenA, and FenB) in Bacillus subtilis F29-3. This work demonstrates that these fengycin synthetases interlock to form a chain, which coils into a 14.5-nm structure. In this chain, fengycin synthetases are linked in the order FenC-FenD-FenE-FenA-FenB by interactions between the C-terminal region of an upstream enzyme and the N-terminal region of its downstream partner enzyme, with their amino acid activation modules arranged colinearly with the amino acids in fengycin. This work also reveals that fengycin is synthesized on this fengycin synthetase chain, explaining how fengycin is synthesized efficiently and accurately. The results from this investigation demonstrate that forming a peptide synthetase complex is crucial to nonribosomal peptide synthesis.
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Affiliation(s)
- Cheng-Yeu Wu
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan 333, Taiwan
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Samel SA, Wagner B, Marahiel MA, Essen LO. The Thioesterase Domain of the Fengycin Biosynthesis Cluster: A Structural Base for the Macrocyclization of a Non-ribosomal Lipopeptide. J Mol Biol 2006; 359:876-89. [PMID: 16697411 DOI: 10.1016/j.jmb.2006.03.062] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Revised: 03/28/2006] [Accepted: 03/29/2006] [Indexed: 12/01/2022]
Abstract
Many secondary metabolic peptides from bacteria and fungi are produced by non-ribosomal peptide synthetases (NRPS) where the final step of biosynthesis is often catalysed by designated thioesterase domains. Here, we report the 1.8A crystal structure of the fengycin thioesterase (FenTE) from Bacillus subtilis F29-3, which catalyses the regio- and stereoselective release and macrocyclization of the antibiotic fengycin from the NRPS template. A structure of the PMSF-inactivated FenTE domain suggests the location of the oxyanion hole and the binding site of the C-terminal residue l-Ile11 of the lipopeptide. Using a combination of docking, molecular dynamics simulations and in vitro activity assays, a model of the FenTE-fengycin complex was derived in which peptide cyclization requires strategic interactions with residues lining the active site canyon.
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Affiliation(s)
- Stefan A Samel
- Department of Chemistry, Philipps-Universität, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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35
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Roongsawang N, Lim SP, Washio K, Takano K, Kanaya S, Morikawa M. Phylogenetic analysis of condensation domains in the nonribosomal peptide synthetases. FEMS Microbiol Lett 2005; 252:143-51. [PMID: 16182472 DOI: 10.1016/j.femsle.2005.08.041] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 10/25/2022] Open
Abstract
Condensation (C) domains in the nonribosomal peptide synthetases are capable of catalyzing peptide bond formation between two consecutively bound various amino acids. C-domains coincide in frequency with the number of peptide bonds in the product peptide. In this study, a phylogenetic approach was used to investigate structural diversity of bacterial C-domains. Phylogenetic trees show that the C-domains are clustered into three functional groups according to the types of substrate donor molecules. They are l-peptidyl donors, d-peptidyl donors, and N-acyl donors. The fact that C-domain structure is not subject to optical configuration of amino acid acceptor molecules supports an idea that the conversion from l to d-form of incorporating amino acid acceptor occurs during or after peptide bond formation. l-peptidyl donors and d-peptidyl donors are suggested to separate before separating the lineage of Gram-positive and Gram-negative bacteria in the evolution process.
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Affiliation(s)
- Niran Roongsawang
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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36
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Stein DB, Linne U, Marahiel MA. Utility of epimerization domains for the redesign of nonribosomal peptide synthetases. FEBS J 2005; 272:4506-20. [PMID: 16128819 DOI: 10.1111/j.1742-4658.2005.04871.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Many pharmacologically important agents are assembled on multimodular nonribosomal peptide synthetases (NRPSs) whose modules comprise a set of core domains with all essential catalytic functions necessary for the incorporation and modification of one building block. Very often, d-amino acids are found in such products which, with few exceptions, are generated by the action of NRPS integrated epimerization (E) domains that alter the stereochemistry of the corresponding peptidyl carrier protein (PCP) bound l-intermediate. In this study we present a quantitative investigation of substrate specificity of four different E domains (two 'peptidyl-' and two 'aminoacyl-'E domains) derived from different NRPSs towards PCP bound peptides. The respective PCP-E bidomain apo-proteins (TycB(3)-, FenD(2)-, TycA- and GrsA-PCP-E) were primed with various peptidyl-CoA precursors by utilizing the promiscuous phosphopantetheinyl transferase Sfp. PCP bound peptidyl-S-Ppant epimerization products were chemically cleaved and analyzed for their l/d-ratios by LCMS. We were able to show that all four E domains tolerate a broad variety of peptidyl-S-Ppant-substrates as evaluated by k(obs) values and final l/d-product equilibria determined for each reaction. The two C-terminal amino acids of the substrate seem to be recognized by 'peptidyl-'E domains. Interestingly, the 'aminoacyl-'E domains GrsA- and TycA-E were also able to convert the elongated intermediates. All four E domains accepted an N-methylated precursor as well and epimerized this substrate with high efficiency. Finally, we could demonstrate that the condensation (C) domain of TycB(1) is also able to process peptidyl substrates transferred by TycA. In conclusion, these findings are of great impact on future engineering attempts.
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Affiliation(s)
- Daniel B Stein
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Germany
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Lin TP, Chen CL, Fu HC, Wu CY, Lin GH, Huang SH, Chang LK, Liu ST. Functional analysis of fengycin synthetase FenD. ACTA ACUST UNITED AC 2005; 1730:159-64. [PMID: 16102594 DOI: 10.1016/j.bbaexp.2005.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Revised: 11/27/2004] [Accepted: 02/15/2005] [Indexed: 10/25/2022]
Abstract
Fengycin is a cyclic lipopeptidic antibiotic produced nonribosomally by Bacillus subtilis. A fengycin synthetase mutant of B. subtilis F29-3 was generated with Tn917lux, which contains a transposon inserted in a 7716-bp gene, fenD. The mutation can be genetically complemented by transforming a plasmid carrying a wild-type fenD, confirming the participation of the gene in fengycin synthesis. Sequencing and biochemical analysis reveal that this gene encodes an enzyme that includes two amino acid-activating modules, FenD1 and FenD2, which activate l-Tyr and l-Thr, the third and the fourth amino acids in fengycin, respectively.
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Affiliation(s)
- Tsuey-Pin Lin
- Department of Health and Nutrition, Chia Nan University of Pharmacy and Science, Tainan 701, Taiwan
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38
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Hofemeister J, Conrad B, Adler B, Hofemeister B, Feesche J, Kucheryava N, Steinborn G, Franke P, Grammel N, Zwintscher A, Leenders F, Hitzeroth G, Vater J. Genetic analysis of the biosynthesis of non-ribosomal peptide- and polyketide-like antibiotics, iron uptake and biofilm formation by Bacillus subtilis A1/3. Mol Genet Genomics 2004; 272:363-78. [PMID: 15480790 DOI: 10.1007/s00438-004-1056-y] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Accepted: 08/10/2004] [Indexed: 10/26/2022]
Abstract
The Bacillus subtilis strain A1/3 shows exceptionally diverse antibiotic capacities compared to other B. subtilis strains. To analyze this phenomenon, mutants for the putative pantotheinyltransferase gene (pptS), and for several genes involved in non-ribosomal peptide synthesis and polyketide synthesis were constructed and characterized, using bioassays with blood cells, bacterial and fungal cells, and mass spectrometry. Among at least nine distinct bioactive compounds, five antibiotics and one siderophore activity were identified. The anti-fungal and hemolytic activities of strain A1/3 could be eliminated by mutation of the fen and srf genes essential for the synthesis of fengycins and surfactins. Both pptS- and dhb -type mutants were defective in iron uptake, indicating an inability to produce a 2,3-dihydroxybenzoate-type iron siderophore. Transposon mutants in the malonyl CoA transacylase gene resulted in the loss of hemolytic and anti-fungal activities due to the inhibition of bacillomycin L synthesis, and this led to the discovery of bmyLD-LA-LB* genes. In mutants bearing disruption mutations in polyketide (pksM- and/or pksR -like) genes, the biosynthesis of bacillaene and difficidins, respectively, was inactivated and was accompanied by the loss of discrete antibacterial activities. The formation of biofilms (pellicles) was shown to require the production of surfactins, but no other lipopeptides, indicating that surfactins serve specific developmental functions.
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Affiliation(s)
- J Hofemeister
- Department of Molecular Genetics, Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse 3, 06466 Gatersleben, Germany.
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Lee S, Flores-Encarnación M, Contreras-Zentella M, Garcia-Flores L, Escamilla JE, Kennedy C. Indole-3-acetic acid biosynthesis is deficient in Gluconacetobacter diazotrophicus strains with mutations in cytochrome c biogenesis genes. J Bacteriol 2004; 186:5384-91. [PMID: 15292139 PMCID: PMC490937 DOI: 10.1128/jb.186.16.5384-5391.2004] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Accepted: 05/17/2004] [Indexed: 11/20/2022] Open
Abstract
Gluconacetobacter diazotrophicus is an endophyte of sugarcane frequently found in plants grown in agricultural areas where nitrogen fertilizer input is low. Recent results from this laboratory, using mutant strains of G. diazotrophicus unable to fix nitrogen, suggested that there are two beneficial effects of G. diazotrophicus on sugarcane growth: one dependent and one not dependent on nitrogen fixation. A plant growth-promoting substance, such as indole-3-acetic acid (IAA), known to be produced by G. diazotrophicus, could be a nitrogen fixation-independent factor. One strain, MAd10, isolated by screening a library of Tn5 mutants, released only approximately 6% of the amount of IAA excreted by the parent strain in liquid culture. The mutation causing the IAA(-) phenotype was not linked to Tn5. A pLAFR3 cosmid clone that complemented the IAA deficiency was isolated. Sequence analysis of a complementing subclone indicated the presence of genes involved in cytochrome c biogenesis (ccm, for cytochrome c maturation). The G. diazotrophicus ccm operon was sequenced; the individual ccm gene products were 37 to 52% identical to ccm gene products of Escherichia coli and equivalent cyc genes of Bradyrhizobium japonicum. Although several ccm mutant phenotypes have been described in the literature, there are no reports of ccm gene products being involved in IAA production. Spectral analysis, heme-associated peroxidase activities, and respiratory activities of the cell membranes revealed that the ccm genes of G. diazotrophicus are involved in cytochrome c biogenesis.
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Affiliation(s)
- Sunhee Lee
- Division of Plant Pathology and Microbiology, Department of Plant Sciences, University of Arizona, Tucson, 85721, USA
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Touré Y, Ongena M, Jacques P, Guiro A, Thonart P. Role of lipopeptides produced by Bacillus subtilis GA1 in the reduction of grey mould disease caused by Botrytis cinerea on apple. J Appl Microbiol 2004; 96:1151-60. [PMID: 15078533 DOI: 10.1111/j.1365-2672.2004.02252.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIM Test of Bacillus subtilis strain GA1 for its potential to control grey mould disease of apple caused by Botrytis cinerea. METHODS AND RESULTS GA1 was first tested for its ability to antagonize in vitro the growth of a wide variety of plant pathogenic fungi responsible for diseases of economical importance. The potential of strain GA1 to reduce post-harvest infection caused by B. cinerea was tested on apples by treating artificially wounded fruits with endospore suspensions. Strain GA1 was very effective at reducing disease incidence during the first 5 days following pathogen inoculation and a 80% protection level was maintained over the next 10 days. Treatment of fruits with an extract of GA1 culture supernatant also exerted a strong preventive effect on the development of grey mould. Further analysis of this extract revealed that strain GA1 produces a wide variety of antifungal lipopeptide isomers from the iturin, fengycin and surfactin families. A strong evidence for the involvement of such compounds in disease reduction arose from the recovery of fengycins from protected fruit sites colonized by bacterial cells. CONCLUSIONS The results presented here demonstrate that, despite unfavourable pH, B. subtilis endospores inoculated on apple pulp can readily germinate allowing significant cell populations to establish and efficient in vivo synthesis of lipopeptides which could be related to grey mould reduction. SIGNIFICANCE AND IMPACT OF THE STUDY This work enables for the first time to correlate the strong protective effect of a particular B. subtilis strain against grey mould with in situ production of fengycins in infected sites of apple fruits.
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Affiliation(s)
- Y Touré
- Service de Technologie Microbienne, CWBI, Université de Liège, Liège, Belgium
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Roongsawang N, Hase KI, Haruki M, Imanaka T, Morikawa M, Kanaya S. Cloning and Characterization of the Gene Cluster Encoding Arthrofactin Synthetase from Pseudomonas sp. MIS38. ACTA ACUST UNITED AC 2003; 10:869-80. [PMID: 14522057 DOI: 10.1016/j.chembiol.2003.09.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Arthrofactin is a potent cyclic lipopeptide-type biosurfactant produced by Pseudomonas sp. MIS38. In this work, an arthrofactin synthetase gene cluster (arf) spanning 38.7 kb was cloned and characterized. Three genes termed arfA, arfB, and arfC encode ArfA, ArfB, and ArfC, containing two, four, and five functional modules, respectively. Each module bears condensation, adenylation, and thiolation domains, like other nonribosomal peptide synthetases. However, unlike most of them, none of the 11 modules possess the epimerization domain responsible for the conversion of amino acid residues from L to D form. Possible L- and D-Leu adenylation domains specifically recognized only L-Leu. Moreover, two thioesterase domains are tandemly located at the C-terminal end of ArfC. These results suggest that ArfA, ArfB, and ArfC assemble to form a unique structure. Gene disruption of arfB impaired arthrofactin production, reduced swarming activity, and enhanced biofilm formation.
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Affiliation(s)
- Niran Roongsawang
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
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Christiansen G, Fastner J, Erhard M, Börner T, Dittmann E. Microcystin biosynthesis in planktothrix: genes, evolution, and manipulation. J Bacteriol 2003; 185:564-72. [PMID: 12511503 PMCID: PMC145317 DOI: 10.1128/jb.185.2.564-572.2003] [Citation(s) in RCA: 228] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2002] [Accepted: 10/16/2002] [Indexed: 11/20/2022] Open
Abstract
Microcystins represent an extraordinarily large family of cyclic heptapeptide toxins that are nonribosomally synthesized by various cyanobacteria. Microcystins specifically inhibit the eukaryotic protein phosphatases 1 and 2A. Their outstanding variability makes them particularly useful for studies on the evolution of structure-function relationships in peptide synthetases and their genes. Analyses of microcystin synthetase genes provide valuable clues for the potential and limits of combinatorial biosynthesis. We have sequenced and analyzed 55.6 kb of the potential microcystin synthetase gene (mcy) cluster from the filamentous cyanobacterium Planktothrix agardhii CYA 126. The cluster contains genes for peptide synthetases (mcyABC), polyketide synthases (PKSs; mcyD), chimeric enzymes composed of peptide synthetase and PKS modules (mcyEG), a putative thioesterase (mcyT), a putative ABC transporter (mcyH), and a putative peptide-modifying enzyme (mcyJ). The gene content and arrangement and the sequence of specific domains in the gene products differ from those of the mcy cluster in Microcystis, a unicellular cyanobacterium. The data suggest an evolution of mcy clusters from, rather than to, genes for nodularin (a related pentapeptide) biosynthesis. Our data do not support the idea of horizontal gene transfer of complete mcy gene clusters between the genera. We have established a protocol for stable genetic transformation of Planktothrix, a genus that is characterized by multicellular filaments exhibiting continuous motility. Targeted mutation of mcyJ revealed its function as a gene coding for a O-methyltransferase. The mutant cells produce a novel microcystin variant exhibiting reduced inhibitory activity toward protein phosphatases.
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Shu HY, Lin GH, Wu YC, Tschen JSM, Liu ST. Amino acids activated by fengycin synthetase FenE. Biochem Biophys Res Commun 2002; 292:789-93. [PMID: 11944882 DOI: 10.1006/bbrc.2002.6729] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fengycin is a lipopeptidic antibiotic produced nonribosomally by Bacillus subtilis F29-3. Synthesis of this antibiotic requires five fengycin synthetases encoded by fenC, fenD, fenE, fenA, and fenB. In this study, we analyze the functions of the enzyme encoded by fenE, which contains two amino acid activation modules, FenE1 and FenE2. ATP-PP(i) exchange assay revealed that FenE1 activates l-Glu and FenE2 activates l-Ala, l-Val, and l-2-aminobutyric acid, indicating that FenE activates the fifth and the sixth amino acids in fengycin. Furthermore, l-Val is a better substrate than l-Ala for FenE2 in vitro, explaining why B. subtilis F29-3 normally produces twice as much of fengycin B than fengycin A, which contains d-Val and d-Ala at the sixth amino acid position, respectively. Results presented herein suggest that fengycin synthetase genes and amino acids in fengycin are colinear.
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Affiliation(s)
- Hung-Yu Shu
- Graduate Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei, 112, Taiwan
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Abstract
Bacillus subtilis RB14 is a producer of the antifungal lipopeptide iturin A. Using a transposon, we identified and cloned the iturin A synthetase operon of RB14, and the sequence of this operon was also determined. The iturin A operon spans a region that is more than 38 kb long and is composed of four open reading frames, ituD, ituA, ituB, and ituC. The ituD gene encodes a putative malonyl coenzyme A transacylase, whose disruption results in a specific deficiency in iturin A production. The second gene, ituA, encodes a 449-kDa protein that has three functional modules homologous to fatty acid synthetase, amino acid transferase, and peptide synthetase. The third gene, ituB, and the fourth gene, ituC, encode 609- and 297-kDa peptide synthetases that harbor four and two amino acid modules, respectively. Mycosubtilin, which is produced by B. subtilis ATCC 6633, has almost the same structure as iturin A, but the amino acids at positions 6 and 7 in the mycosubtilin sequence are D-Ser-->L-Asn, while in iturin A these amino acids are inverted (i.e., D-Asn-->L-Ser). Comparison of the amino acid sequences encoded by the iturin A operon and the mycosubtilin operon revealed that ituD, ituA, and ituB have high levels of homology to the counterpart genes fenF (79%), mycA (79%), and mycB (79%), respectively. Although the overall level of homology of the amino acid sequences encoded by ituC and mycC, the counterpart of ituC, is relatively low (64%), which indicates that there is a difference in the amino acid sequences of the two lipopeptides, the levels of homology between the putative serine adenylation domains and between the asparagine adenylation domains in the two synthetases are high (79 and 80%, respectively), implying that there is an intragenic domain change in the synthetases. The fact that the flanking sequence of the iturin A synthetase coding region was highly homologous to the flanking sequence that of xynD of B. subtilis 168 and the fact that the promoter of the iturin A operon which we identified was also conserved in an upstream sequence of xynD imply that horizontal transfer of this operon occurred. When the promoter was replaced by the repU promoter of the plasmid pUB110 replication protein, production of iturin A increased threefold.
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Affiliation(s)
- K Tsuge
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
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45
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Wu CY, Fu JF, Liu ST. The replicon of pSW800 from Pantoea stewartii. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2757-2767. [PMID: 11577155 DOI: 10.1099/00221287-147-10-2757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A 2019 bp DNA fragment containing the replicon of pSW800 from Pantoea stewartii SW2 was cloned and characterized. This replicon contains two genes--repA and repB, which encode a 36.5 kDa replication initiation protein (RepA) and a peptide of 18 aa, respectively. These two genes overlap by 8 bases with repB situated upstream. The replicon also transcribes an antisense RNA (RNAI) that inhibits the expression of repA and repB. The ribosome-binding sequence (RBS) of repA is likely to be hidden in a stem-loop structure, inhibiting the translation of repA. Furthermore, translation of repB is likely to disrupt the stem-loop structure, which is one of the criteria allowing the translation of repA to begin. A mutagenesis study revealed that a sequence (5'-GCACGGG-3') located 111 nt upstream from repA is crucial; mutation of this sequence prevented the translation of repA. Additionally, this region and the stem-loop structure containing the RBS of repA may form an RNA pseudoknot. Results in this study demonstrate that a mechanism similar to that regulating plasmid replication in the IncB, IncIalpha and IncL/M groups also regulates pSW800 replication.
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Affiliation(s)
- Cheng-Yeu Wu
- Department of Microbiology and Immunology, Chang-Gung University, Kwei-Shan, 333, Taiwan2
- Graduate Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei, 112, Taiwan1
| | - Jen-Fen Fu
- Department of Microbiology and Immunology, Chang-Gung University, Kwei-Shan, 333, Taiwan2
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, Chang-Gung University, Kwei-Shan, 333, Taiwan2
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Schwarzer D, Mootz HD, Marahiel MA. Exploring the impact of different thioesterase domains for the design of hybrid peptide synthetases. CHEMISTRY & BIOLOGY 2001; 8:997-1010. [PMID: 11590023 DOI: 10.1016/s1074-5521(01)00068-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND A large number of pharmacologically important peptides are synthesized by multifunctional enzymes, the nonribosomal peptide synthetases (NRPSs). The thioesterase (Te) domain at the C-terminus of the last NRPS catalyzes product cleavage by hydrolysis or complex macrocyclization. Recent studies with excised Te domains and peptidyl-S-N-acetyl cysteamine substrate substitutes led to substantial insights in terms of cyclization activity and substrate tolerance of these enzymes. Their use in engineered hybrid NRPSs is an interesting but yet only little explored target for approaches to achieve new structural diversity and designed products. RESULTS To study the capability of various Te domains to function in hybrid NRPSs, six different Te domains that catalyze different modes of termination in their natural systems were fused to a bimodular model NRPS system, consisting of the first two modules of tyrocidine NRPS, TycA and ProCAT. All Te domains were active in hydrolyzing the enzymatically generated dipeptide substrate D-Phe-Abu from the NRPS template with, however, greatly varying turnover rates. Two Te domains were also capable of hydrolyzing the substrate D-Phe-Pro and partially cyclized the D-Phe-Abu dipeptide, indicating that in an artificial context Te domains may display hydrolytic and cyclization activities that are not easily predictable. CONCLUSIONS Te domains from heterologous NRPSs can be utilized for the construction of hybrid NRPSs. This is the first comparative study to explore their influence on the product pattern. The inherent specificity and regioselectivity of Te domains should allow control of the desired product cleavage, but can also lead to other modes of termination potentially useful for generating structural diversity. Our results provide the first data for choosing the proper Te domain for a particular termination reaction.
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Affiliation(s)
- D Schwarzer
- Philipps-Universität Marburg, Fachbereich Chemie/Biochemie, Hans-Meerwein-Str., D-35032 Marburg, Germany
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