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Rahman MS, Shimul MEK, Parvez MAK. Comprehensive analysis of genomic variation, pan-genome and biosynthetic potential of Corynebacterium glutamicum strains. PLoS One 2024; 19:e0299588. [PMID: 38718091 PMCID: PMC11078359 DOI: 10.1371/journal.pone.0299588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 02/13/2024] [Indexed: 05/12/2024] Open
Abstract
Corynebacterium glutamicum is a non-pathogenic species of the Corynebacteriaceae family. It has been broadly used in industrial biotechnology for the production of valuable products. Though it is widely accepted at the industrial level, knowledge about the genomic diversity of the strains is limited. Here, we investigated the comparative genomic features of the strains and pan-genomic characteristics. We also observed phylogenetic relationships among the strains based on average nucleotide identity (ANI). We found diversity between strains at the genomic and pan-genomic levels. Less than one-third of the C. glutamicum pan-genome consists of core genes and soft-core genes. Whereas, a large number of strain-specific genes covered about half of the total pan-genome. Besides, C. glutamicum pan-genome is open and expanding, which indicates the possible addition of new gene families to the pan-genome. We also investigated the distribution of biosynthetic gene clusters (BGCs) among the strains. We discovered slight variations of BGCs at the strain level. Several BGCs with the potential to express novel bioactive secondary metabolites have been identified. Therefore, by utilizing the characteristic advantages of C. glutamicum, different strains can be potential applicants for natural drug discovery.
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Affiliation(s)
- Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Ebrahim Khalil Shimul
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Genetic Engineering and Biotechnology, Bioinformatics and Microbial Biotechnology Laboratory, Jashore University of Science and Technology, Jashore, Bangladesh
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Abstract
Covering: 2008 to August 2020 Polyketides are a family of natural products constructed from simple building blocks to generate a diverse range of often complex chemical structures with biological activities of both pharmaceutical and agrochemical importance. Their biosynthesis is controlled by polyketide synthases (PKSs) which catalyse the condensation of thioesters to assemble a functionalised linear carbon chain. Alkyl-branches may be installed at the nucleophilic α- or electrophilic β-carbon of the growing chain. Polyketide β-branching is a fascinating biosynthetic modification that allows for the conversion of a β-ketone into a β-alkyl group or functionalised side-chain. The overall transformation is catalysed by a multi-protein 3-hydroxy-3-methylglutaryl synthase (HMGS) cassette and is reminiscent of the mevalonate pathway in terpene biosynthesis. The first step most commonly involves the aldol addition of acetate to the electrophilic carbon of the β-ketothioester catalysed by a 3-hydroxy-3-methylglutaryl synthase (HMGS). Subsequent dehydration and decarboxylation selectively generates either α,β- or β,γ-unsaturated β-alkyl branches which may be further modified. This review covers 2008 to August 2020 and summarises the diversity of β-branch incorporation and the mechanistic details of each catalytic step. This is extended to discussion of polyketides containing multiple β-branches and the selectivity exerted by the PKS to ensure β-branching fidelity. Finally, the application of HMGS in data mining, additional β-branching mechanisms and current knowledge of the role of β-branches in this important class of biologically active natural products is discussed.
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Affiliation(s)
- P D Walker
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - A N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - C L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - M P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Davies JA, Bull FM, Walker PD, Weir ANM, Lavigne R, Masschelein J, Simpson TJ, Race PR, Crump MP, Willis CL. Total Synthesis of Kalimantacin A. Org Lett 2020; 22:6349-6353. [PMID: 32806153 DOI: 10.1021/acs.orglett.0c02190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The kalimantacins make up a family of hybrid polyketide-nonribosomal peptide-derived natural products that display potent and selective antibiotic activity against multidrug resistant strains of Staphylococcus aureus. Herein, we report the first total synthesis of kalimantacin A, in which three fragments are prepared and then united via Sonogashira and amide couplings. The enantioselective synthetic approach is convergent, unlocking routes to further kalimantacins and analogues for structure-activity relationship studies and clinical evaluation.
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Affiliation(s)
- Jonathan A Davies
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Freya M Bull
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Paul D Walker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Angus N M Weir
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, P.O. Box 2462, 3001 Leuven, Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery and Engineering, KU Leuven, Kasteel Park, Ardenberg 31, P.O. Box 2438, 3001 Leuven, Belgium.,VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Paul R Race
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
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Adeniji AA, Aremu OS, Babalola OO. Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5. Microbiologyopen 2018; 8:e00742. [PMID: 30358165 PMCID: PMC6562122 DOI: 10.1002/mbo3.742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/03/2018] [Accepted: 09/10/2018] [Indexed: 12/29/2022] Open
Abstract
The results of this study indicate that the maize rhizosphere remains a reservoir for microbial strains with unique beneficial properties. The study sought to provide an indigenous Bacillus strain with a bioprotective potential to alleviate maize fusariosis in South Africa. We selected seven Bacillus isolates (MORWBS1.1, MARBS2.7, VERBS5.5, MOREBS6.3, MOLBS8.5, MOLBS8.6, and NWUMFkBS10.5) with biosuppressive effects against two maize fungal pathogens (Fusarium graminearum and Fusarium culmorum) based on 16S rDNA gene characterization and lipopeptide gene analysis. The PCR analysis revealed that lipopeptide genes encoding the synthesis of iturin, surfactin, and fengycin might be responsible for their antifungal activities. Few of the isolates also showed possible biosurfactant capability, and their susceptibility to known antibiotics is indicative of their eco‐friendly attributes. In addition, in silico genomic analysis of our best isolate (Bacillus velezensis NWUMFkBS10.5) and characterization of its active metabolite with FTIR, NMR, and ESI‐Micro‐Tof MS confirmed the presence of valuable genes clusters and metabolic pathways. The versatile genomic potential of our Bacillus isolate emphasizes the continued relevance of Bacillus spp. in biological management of plant diseases.
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Affiliation(s)
- Adetomiwa Ayodele Adeniji
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Oluwole Samuel Aremu
- Department of Chemistry, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Department of Biological Sciences, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa.,Food Security and Safety Niche Area, Faculty of Natural and Agriculture Science, North-West University, Mmabatho, South Africa
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de Frias UA, Pereira GKB, Guazzaroni ME, Silva-Rocha R. Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors. Biomed Res Int 2018; 2018:7021826. [PMID: 30079350 PMCID: PMC6069586 DOI: 10.1155/2018/7021826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/11/2018] [Indexed: 01/05/2023]
Abstract
Bacteria are a source of a large number of secondary metabolites with several biomedical and biotechnological applications. In recent years, there has been tremendous progress in the development of novel synthetic biology approaches both to increase the production rate of secondary metabolites of interest in native producers and to mine and reconstruct novel biosynthetic gene clusters in heterologous hosts. Here, we present the recent advances toward the engineering of novel microbial biosensors to detect the synthesis of secondary metabolites in bacteria and in the development of synthetic promoters and expression systems aiming at the construction of microbial cell factories for the production of these compounds. We place special focus on the potential of Gram-negative bacteria as a source of biosynthetic gene clusters and hosts for pathway assembly, on the construction and characterization of novel promoters for native hosts, and on the use of computer-aided design of novel pathways and expression systems for secondary metabolite production. Finally, we discuss some of the potentials and limitations of the approaches that are currently being developed and we highlight new directions that could be addressed in the field.
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Affiliation(s)
| | | | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Medical School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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Thistlethwaite IRG, Bull FM, Cui C, Walker PD, Gao SS, Wang L, Song Z, Masschelein J, Lavigne R, Crump MP, Race PR, Simpson TJ, Willis CL. Elucidation of the relative and absolute stereochemistry of the kalimantacin/batumin antibiotics. Chem Sci 2017; 8:6196-6201. [PMID: 28989652 PMCID: PMC5628338 DOI: 10.1039/c7sc01670k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/02/2017] [Indexed: 12/18/2022] Open
Abstract
A multidisciplinary approach combining natural product degradation, fragment synthesis, bioinformatics and NMR spectroscopy was used.
Kalimantacin A and batumin exhibit potent and selective antibiotic activity against Staphylococcus species including MRSA. Both compounds are formed via a hybrid polyketide synthase/non-ribosomal peptide synthetase (PKS-NRPS) biosynthetic pathway and from comparison of the gene clusters it is apparent that batumin from Pseudomonas batumici and kalimantacin from P. fluorescens are the same compound. The linear structure of this unsaturated acid was assigned by spectroscopic methods, but the relative and absolute stereochemistry of the five stereocentres remained unknown. Herein we describe isolation of kalimantacin A and two further metabolites 17,19-diol 2 and 27-descarbomyl hydroxyketone 3 from cultures of P. fluorescens. Their absolute and relative stereochemistries are rigorously determined using a multidisciplinary approach combining natural product degradation and fragment synthesis with bioinformatics and NMR spectroscopy. Diol 2 has the 5R, 15S, 17S, 19R, 26R, 27R configuration and is the immediate biosynthetic precursor of the bioactive kalimantacin A formed by oxidation of the 17-alcohol to the ketone.
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Affiliation(s)
| | - Freya M Bull
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Chengsen Cui
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Paul D Walker
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Shu-Shan Gao
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Luoyi Wang
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Zhongshu Song
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | | | - Rob Lavigne
- Laboratory of Gene Technology , KULeuven , Leuven B-3001 , Belgium
| | - Matthew P Crump
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Paul R Race
- School of Biochemistry , University of Bristol , Bristol BS8 1TD , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Christine L Willis
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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Abstract
Covering: up to 2017The overwhelming majority of antibiotics in clinical use originate from Gram-positive Actinobacteria. In recent years, however, Gram-negative bacteria have become increasingly recognised as a rich yet underexplored source of novel antimicrobials, with the potential to combat the looming health threat posed by antibiotic resistance. In this article, we have compiled a comprehensive list of natural products with antimicrobial activity from Gram-negative bacteria, including information on their biosynthetic origin(s) and molecular target(s), where known. We also provide a detailed discussion of several unusual pathways for antibiotic biosynthesis in Gram-negative bacteria, serving to highlight the exceptional biocatalytic repertoire of this group of microorganisms.
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Affiliation(s)
- J Masschelein
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - M Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
| | - G L Challis
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, UK.
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Klochko VV, Zelena LB, Kim JY, Avdeeva LV, Reva ON. Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321. Int J Antimicrob Agents 2016; 47:56-61. [DOI: 10.1016/j.ijantimicag.2015.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/25/2015] [Accepted: 10/02/2015] [Indexed: 11/16/2022]
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Abstract
This review discusses the biosynthesis of natural products that are generated bytrans-AT polyketide synthases, a family of catalytically versatile enzymes that represents one of the major group of proteins involved in the production of bioactive polyketides.
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Affiliation(s)
- Eric J. N. Helfrich
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
| | - Jörn Piel
- Institute of Microbiology
- Eidgenössische Technische Hochschule (ETH) Zurich
- 8093 Zurich
- Switzerland
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Kapley A, Sagarkar S, Tanksale H, Sharma N, Qureshi A, Khardenavis A, Purohit HJ. Genome Sequence of Alcaligenes sp. Strain HPC1271. Genome Announc 2013; 1:e00235-12. [PMID: 23469352 DOI: 10.1128/genomeA.00235-12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 12/31/2012] [Indexed: 11/20/2022]
Abstract
We report a draft genome sequence of Alcaligenes sp. strain HPC1271, which demonstrates antimicrobial activity against multidrug-resistant bacteria. Antibiotic production by Alcaligenes has not been frequently reported, and hence, the availability of the genome sequence should enable us to explore new antibiotic-producing gene clusters.
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Mattheus W, Masschelein J, Gao LJ, Herdewijn P, Landuyt B, Volckaert G, Lavigne R. The kalimantacin/batumin biosynthesis operon encodes a self-resistance isoform of the FabI bacterial target. ACTA ACUST UNITED AC 2011; 17:1067-71. [PMID: 21035728 DOI: 10.1016/j.chembiol.2010.07.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 06/20/2010] [Accepted: 07/13/2010] [Indexed: 10/18/2022]
Abstract
BatG is a trans-2-enoyl-ACP reductase, encoded in the kalimantacin/batumin (kal/bat) biosynthesis operon. It is not essential for the production of the kal/bat secondary metabolite. Instead, BatG is an isoform of FabI, conferring full resistance to target bacteria. It also complements FabI in its role in fatty acid biosynthesis. The identification of FabI as the antibacterial target is important to assess clinical potential of the kalimantacin/batumin antibiotics against Staphylococcus aureus.
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Affiliation(s)
- Wesley Mattheus
- Laboratory of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21 Box 2462, Leuven B-3001, Belgium
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Mattheus W, Gao L, Herdewijn P, Landuyt B, Verhaegen J, Masschelein J, Volckaert G, Lavigne R. Isolation and Purification of a New Kalimantacin/Batumin-Related Polyketide Antibiotic and Elucidation of Its Biosynthesis Gene Cluster. ACTA ACUST UNITED AC 2010; 17:149-59. [DOI: 10.1016/j.chembiol.2010.01.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/06/2010] [Accepted: 01/14/2010] [Indexed: 11/24/2022]
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Doboszewski B, Herdewijn P. Carbohydrate chiral-pool approach to four enantiomerically pure 2-naphthylmethyl 3-hydroxy-2-methylbutanoates. Tetrahedron 2008; 64:5551-62. [DOI: 10.1016/j.tet.2008.03.088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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