1
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Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol 2024; 9:200-213. [PMID: 38110697 DOI: 10.1038/s41564-023-01544-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
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Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Daniela Janek
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Jan Bornikoel
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Berscheid
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sophia Krauss
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon J Jaag
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Norah Alqahtani
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José Manuel Beltrán-Beleña
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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2
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Meesil W, Muangpat P, Sitthisak S, Rattanarojpong T, Chantratita N, Machado RAR, Shi YM, Bode HB, Vitta A, Thanwisai A. Genome mining reveals novel biosynthetic gene clusters in entomopathogenic bacteria. Sci Rep 2023; 13:20764. [PMID: 38007490 PMCID: PMC10676414 DOI: 10.1038/s41598-023-47121-9] [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: 08/07/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
The discovery of novel bioactive compounds produced by microorganisms holds significant potential for the development of therapeutics and agrochemicals. In this study, we conducted genome mining to explore the biosynthetic potential of entomopathogenic bacteria belonging to the genera Xenorhabdus and Photorhabdus. By utilizing next-generation sequencing and bioinformatics tools, we identified novel biosynthetic gene clusters (BGCs) in the genomes of the bacteria, specifically plu00736 and plu00747. These clusters were identified as unidentified non-ribosomal peptide synthetase (NRPS) and unidentified type I polyketide synthase (T1PKS) clusters. These BGCs exhibited unique genetic architecture and encoded several putative enzymes and regulatory elements, suggesting its involvement in the synthesis of bioactive secondary metabolites. Furthermore, comparative genome analysis revealed that these BGCs were distinct from previously characterized gene clusters, indicating the potential for the production of novel compounds. Our findings highlighted the importance of genome mining as a powerful approach for the discovery of biosynthetic gene clusters and the identification of novel bioactive compounds. Further investigations involving expression studies and functional characterization of the identified BGCs will provide valuable insights into the biosynthesis and potential applications of these bioactive compounds.
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Affiliation(s)
- Wipanee Meesil
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Paramaporn Muangpat
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Triwit Rattanarojpong
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10400, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Yi-Ming Shi
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University, Frankfurt, 60438, Frankfurt am Main, Germany
- Chemical Biology, Department of Chemistry, Philipps University Marburg, 35032, Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- SYNMIKRO (Zentrum für Synthetische Mikrobiologie), 35032, Marburg, Germany
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
- Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok, 65000, Thailand.
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3
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post-Translational Formation of Aminomalonate by a Promiscuous Peptide-Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021; 60:19957-19964. [PMID: 34164914 DOI: 10.1002/anie.202107192] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/23/2021] [Indexed: 11/12/2022]
Abstract
Aminomalonate (Ama) is a widespread structural motif in Nature, whereas its biosynthetic route is only partially understood. In this study, we show that a radical S-adenosylmethionine (rSAM) enzyme involved in cyclophane biosynthesis exhibits remarkable catalytic promiscuity. This enzyme, named three-residue cyclophane forming enzyme (3-CyFE), mainly produces cyclophane in vivo, whereas it produces formylglycine (FGly) as a major product and barely produce cyclophane in vitro. Importantly, the enzyme can further oxidize FGly to produce Ama. Bioinformatic study revealed that 3-CyFEs have evolved from a common ancestor with anaerobic sulfatase maturases (anSMEs), and possess a similar set of catalytic residues with anSMEs. Remarkably, the enzyme does not need leader peptide for activity and is fully active on a truncated peptide containing only 5 amino acids of the core sequence. Our work discloses the first ribosomal path towards Ama formation, providing a possible hint for the rich occurrence of Ama in Nature.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Heng Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - He Li
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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4
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post‐Translational Formation of Aminomalonate by a Promiscuous Peptide‐Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Suze Ma
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Heng Chen
- Department of Chemistry Fudan University Shanghai 200433 China
| | - He Li
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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5
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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6
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Mo X, Gulder TAM. Biosynthetic strategies for tetramic acid formation. Nat Prod Rep 2021; 38:1555-1566. [PMID: 33710214 DOI: 10.1039/d0np00099j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Covering: up to the end of 2020Natural products bearing tetramic acid units as part of complex molecular architectures exhibit a broad range of potent biological activities. These compounds thus attract significant interest from both the biosynthetic and synthetic communities. Biosynthetically, most of the tetramic acids are derived from hybrid polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) machineries. To date, over 30 biosynthetic gene clusters (BGCs) involved in tetramate formation have been identified, from which different biosynthetic strategies evolved in Nature to assemble this intriguing structural unit were characterized. In this Highlight we focus on the biosynthetic concepts of tetramic acid formation and discuss the molecular mechanism towards selected representatives in detail, providing a systematic overview for the development of strategies for targeted tetramate genome mining and future applications of tetramate-forming biocatalysts for chemo-enzymatic synthesis.
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Affiliation(s)
- Xuhua Mo
- Shandong Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 266109 Qingdao, China. and Chair of Technical Biochemistry, Technische Universität Dresden, Bergstraße 66, 01069 Dresden, Germany.
| | - Tobias A M Gulder
- Chair of Technical Biochemistry, Technische Universität Dresden, Bergstraße 66, 01069 Dresden, Germany.
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7
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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8
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Majumder MAA, Rahman S, Cohall D, Bharatha A, Singh K, Haque M, Gittens-St Hilaire M. Antimicrobial Stewardship: Fighting Antimicrobial Resistance and Protecting Global Public Health. Infect Drug Resist 2020; 13:4713-4738. [PMID: 33402841 PMCID: PMC7778387 DOI: 10.2147/idr.s290835] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health. It increases morbidity and mortality, and is associated with high economic costs due to its health care burden. Infections with multidrug-resistant (MDR) bacteria also have substantial implications on clinical and economic outcomes. Moreover, increased indiscriminate use of antibiotics during the COVID-19 pandemic will heighten bacterial resistance and ultimately lead to more deaths. This review highlights AMR's scale and consequences, the importance, and implications of an antimicrobial stewardship program (ASP) to fight resistance and protect global health. Antimicrobial stewardship (AMS), an organizational or system-wide health-care strategy, is designed to promote, improve, monitor, and evaluate the rational use of antimicrobials to preserve their future effectiveness, along with the promotion and protection of public health. ASP has been very successful in promoting antimicrobials' appropriate use by implementing evidence-based interventions. The "One Health" approach, a holistic and multisectoral approach, is also needed to address AMR's rising threat. AMS practices, principles, and interventions are critical steps towards containing and mitigating AMR. Evidence-based policies must guide the "One Health" approach, vaccination protocols, health professionals' education, and the public's awareness about AMR.
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Affiliation(s)
- Md Anwarul Azim Majumder
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Sayeeda Rahman
- School of Medicine, American University of Integrative Sciences, Bridgetown, Barbados
| | - Damian Cohall
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Ambadasu Bharatha
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Keerti Singh
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
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9
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Zhao F, Liu Z, Yang S, Ding N, Gao X. Quinolactacin Biosynthesis Involves Non‐Ribosomal‐Peptide‐Synthetase‐Catalyzed Dieckmann Condensation to Form the Quinolone‐γ‐lactam Hybrid. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fanglong Zhao
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Zhiwen Liu
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Ning Ding
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering Rice University Houston TX 77005 USA
- Department of Bioengineering Rice University Houston TX 77005 USA
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10
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Zhao F, Liu Z, Yang S, Ding N, Gao X. Quinolactacin Biosynthesis Involves Non-Ribosomal-Peptide-Synthetase-Catalyzed Dieckmann Condensation to Form the Quinolone-γ-lactam Hybrid. Angew Chem Int Ed Engl 2020; 59:19108-19114. [PMID: 32663343 PMCID: PMC10165850 DOI: 10.1002/anie.202005770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/16/2020] [Indexed: 12/15/2022]
Abstract
Quinolactacins are novel fungal alkaloids that feature a quinolone-γ-lactam hybrid, which is a potential pharmacophore for the treatment of cancer and Alzheimer's disease. Herein, we report the identification of the quinolactacin A2 biosynthetic gene cluster and elucidate the enzymatic basis for the formation of the quinolone-γ-lactam structure. We reveal an unusual β-keto acid (N-methyl-2-aminobenzoylacetate) precursor that is derived from the primary metabolite l-kynurenine via methylation, oxidative decarboxylation, and amide hydrolysis reactions. In vitro assays reveal two single-module non-ribosomal peptide synthetases (NRPs) that incorporate the β-keto acid and l-isoleucine, followed by Dieckmann condensation, to form the quinolone-γ-lactam. Notably, the bioconversion from l-kynurenine to the β-keto acid is a unique strategy employed by nature to decouple R*-domain-containing NRPS from the polyketide synthase (PKS) machinery, expanding the paradigm for the biosynthesis of quinolone-γ-lactam natural products via Dieckmann condensation.
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Affiliation(s)
- Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Shuyuan Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Ning Ding
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, 77005, USA.,Department of Bioengineering, Rice University, Houston, TX, 77005, USA
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11
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Aslam B, Rasool M, Idris A, Muzammil S, Alvi RF, Khurshid M, Rasool MH, Zhang D, Ma Z, Baloch Z. CRISPR-Cas system: a potential alternative tool to cope antibiotic resistance. Antimicrob Resist Infect Control 2020; 9:131. [PMID: 32778162 PMCID: PMC7418376 DOI: 10.1186/s13756-020-00795-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 08/02/2020] [Indexed: 12/20/2022] Open
Abstract
Antibiotic exposure leads to massive selective pressures that initiate the emergence and spread of antibiotic resistance in commensal and pathogenic bacteria. The slow process of developing new antibiotics makes this approach counterintuitive for combatting the rapid emergence of new antibiotic resistant pathogens. Therefore, alternative approaches such as, the development of nucleic acid-based anti-bacterial treatments, anti-bacterial peptides, bacteriocins, anti-virulence compounds and bacteriophage therapies should be exploited to cope infections caused by resistant superbugs. In this editorial, we discuss how the newly popular CRISPR-Cas system has been applied to combat antibiotic resistance.
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Affiliation(s)
- Bilal Aslam
- Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, P. R. China.,Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Maria Rasool
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Adi Idris
- Menzies Health Institute Queensland and School of Medical Science, Griffith University, Southport, QLD, Australia
| | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Roman Farooq Alvi
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, P. R. China
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, P. R. China
| | - Zulqarnain Baloch
- Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, P. R. China.
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12
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Microbial production of vitamin K2: current status and future prospects. Biotechnol Adv 2019; 39:107453. [PMID: 31629792 DOI: 10.1016/j.biotechadv.2019.107453] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/24/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022]
Abstract
Vitamin K2, also called menaquinone, is an essential lipid-soluble vitamin that plays a critical role in blood clotting and prevention of osteoporosis. It has become a focus of research in recent years and has been widely used in the food and pharmaceutical industries. This review will briefly introduce the functions and applications of vitamin K2 first, after which the biosynthesis pathways and enzymes will be analyzed in-depth to highlight the bottlenecks facing the microbial vitamin K2 production on the industrial scale. Then, various strategies, including strain mutagenesis and genetic modification, different cultivation modes, fermentation and separation processes, will be summarized and discussed. The future prospects and perspectives of microbial menaquinone production will also be discussed finally.
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13
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Kaniusaite M, Tailhades J, Marschall EA, Goode RJA, Schittenhelm RB, Cryle MJ. A proof-reading mechanism for non-proteinogenic amino acid incorporation into glycopeptide antibiotics. Chem Sci 2019; 10:9466-9482. [PMID: 32055321 PMCID: PMC6993612 DOI: 10.1039/c9sc03678d] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/29/2019] [Indexed: 01/09/2023] Open
Abstract
A complex interplay of non-ribosomal peptide synthetase domains works together with trans-acting enzymes to ensure effective GPA biosynthesis.
Non-ribosomal peptide biosynthesis produces highly diverse natural products through a complex cascade of enzymatic reactions that together function with high selectivity to produce bioactive peptides. The modification of non-ribosomal peptide synthetase (NRPS)-bound amino acids can introduce significant structural diversity into these peptides and has exciting potential for biosynthetic redesign. However, the control mechanisms ensuring selective modification of specific residues during NRPS biosynthesis have previously been unclear. Here, we have characterised the incorporation of the non-proteinogenic amino acid 3-chloro-β-hydroxytyrosine during glycopeptide antibiotic (GPA) biosynthesis. Our results demonstrate that the modification of this residue by trans-acting enzymes is controlled by the selectivity of the upstream condensation domain responsible for peptide synthesis. A proofreading thioesterase works together with this process to ensure that effective peptide biosynthesis proceeds even when the selectivity of key amino acid activation domains within the NRPS is low. Furthermore, the exchange of condensation domains with altered amino acid specificities allows the modification of such residues within NRPS biosynthesis to be controlled, which will doubtless prove important for reengineering of these assembly lines. Taken together, our results indicate the importance of the complex interplay of NRPS domains and trans-acting enzymes to ensure effective GPA biosynthesis, and in doing so reveals a process that is mechanistically comparable to the hydrolytic proofreading function of tRNA synthetases in ribosomal protein synthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Edward A Marschall
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
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