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Arias-Orozco P, Yi Y, Ruijne F, Cebrián R, Kuipers OP. Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synth Biol 2022; 12:164-177. [PMID: 36520855 PMCID: PMC9872173 DOI: 10.1021/acssynbio.2c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform for engineering lanthipeptides. Most remarkably, SyncM can modify up to 79 SyncA substrates in a single strain. Six SyncAs were previously characterized from this pool of substrates. They showed particular characteristics, such as the presence of one or two lanthionine rings, different flanking residues influencing ring formation, and different ring directions, demonstrating the relaxed specificity of SyncM toward its precursor peptides. To gain a deeper understanding of the potential of SyncM as a biosynthetic tool, we further explored the enzyme's capabilities and limits in dehydration and ring formation. We used different SyncA scaffolds for peptide engineering, including changes in the ring's directionality (relative position of Ser/Thr to Cys in the peptide) and size. We further aimed to rationally design mimetics of cyclic antimicrobials and introduce macrocycles in prochlorosin-related and nonrelated substrates. This study highlights the largest lanthionine ring with 15 amino acids (ring-forming residues included) described to date. Taking advantage of the amino acid substrate tolerance of SyncM, we designed the first single-SyncA-based antimicrobial. The insights gained from this work will aid future bioengineering studies. Additionally, it broadens SyncM's application scope for introducing macrocycles in other bioactive molecules.
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Affiliation(s)
- Patricia Arias-Orozco
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Yunhai Yi
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Fleur Ruijne
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Rubén Cebrián
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,Department
of Clinical Microbiology, Instituto de Investigación Biosanitaria,
ibs. GRANADA, San Cecilio University Hospital, Av. De la Innovación s/n, 18016 Granada, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,
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Sharma BR, Halami PM, Tamang JP. Novel pathways in bacteriocin synthesis by lactic acid bacteria with special reference to ethnic fermented foods. Food Sci Biotechnol 2022; 31:1-16. [PMID: 35059226 PMCID: PMC8733103 DOI: 10.1007/s10068-021-00986-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/28/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022] Open
Abstract
Ethnic fermented foods are known for their unique aroma, flavour, taste, texture and other sensory properties preferred by every ethnic community in this world culturally as parts of their eatables. Some beneficial microorganisms associated with fermented foods have several functional properties and health-promoting benefits. Bacteriocins are the secondary metabolites produced by the microorganisms mostly lactic acid bacteria present in the fermented foods which can act as lantibiotics against the pathogen bacteria. Several studies have been conducted regarding the isolation and characterization of potent strains as well as their association with different types of bacteriocins. Collective information regarding the gene organizations responsible for the potent effect of bacteriocins as lantibiotics, mode of action on pathogen bacterial cells is not yet available. This review focuses on the gene organizations, pathways include for bacteriocin and their mode of action for various classes of bacteriocins produced by lactic acid bacteria in some ethnic fermented foods.
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Affiliation(s)
- Basista Rabina Sharma
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Prakash M. Halami
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysore, Karnataka 570020 India
| | - Jyoti Prakash Tamang
- DAICENTER, Department of Microbiology, Sikkim University, Science Building, Tadong, Gangtok, Sikkim 737102 India
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Arias-Orozco P, Inklaar M, Lanooij J, Cebrián R, Kuipers OP. Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies. ACS Synth Biol 2021; 10:2579-2591. [PMID: 34554737 PMCID: PMC8524650 DOI: 10.1021/acssynbio.1c00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Lanthipeptides are
ribosomally synthesized and post-translationally
modified peptides characterized by the presence of lanthionine rings
that provide stability and functionality. Genome mining techniques
have shown their huge diversity and potential for the discovery of
novel active molecules. However, in many cases, they are not easily
produced under laboratory conditions. The heterologous expression
of these molecules using well-characterized lanthipeptide biosynthetic
enzymes is rising as an alternative system for the design and production
of new lanthipeptides with biotechnological or clinical properties.
Nevertheless, the substrate-enzyme specificity limits the complete
modification of the desired peptides and hence, their full stability
and/or biological activity. New low substrate-selective biosynthetic
enzymes are therefore necessary for the heterologous production of
new-to-nature peptides. Here, we have identified, cloned, and heterologously
expressed in Lactococcus lactis the
most promiscuous lanthipeptide synthetase described to date, i.e.,
SyncM from the marine cyanobacteria Synechococcus MITS9509. We have characterized the functionality of SyncM by the
successful expression of 15 out of 18 different SyncA substrates,
subsequently determining the dehydration and cyclization processes
in six representatives of them. This characterization highlights the
very relaxed substrate specificity of SyncM toward its precursors
and the ability to catalyze the formation of exceptionally large rings
in a variety of topologies. Our results suggest that SyncM could be
an attractive enzyme to design and produce a wide variety of new-to-nature
lanthipeptides with a broad range of ring topologies.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Maartje Inklaar
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Judith Lanooij
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
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Li C, Alam K, Zhao Y, Hao J, Yang Q, Zhang Y, Li R, Li A. Mining and Biosynthesis of Bioactive Lanthipeptides From Microorganisms. Front Bioeng Biotechnol 2021; 9:692466. [PMID: 34395400 PMCID: PMC8358304 DOI: 10.3389/fbioe.2021.692466] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance is one of the most serious public health issues in the worldwide and only a few new antimicrobial drugs have been discovered in recent decades. To overcome the ever-increasing emergence of multidrug-resistant (MDR) pathogens, discovery of new natural products (NPs) against MDR pathogens with new technologies is in great demands. Lanthipeptides which are ribosomally synthesized and post-translationally modified peptides (RiPPs) display high diversity in their chemical structures and mechanisms of action. Genome mining and biosynthetic engineering have also yielded new lanthipeptides, which are a valuable source of drug candidates. In this review we cover the recent advances in the field of microbial derived lanthipeptide discovery and development.
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Affiliation(s)
- Caiyun Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Khorshed Alam
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yiming Zhao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qing Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruijuan Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Sandiford SK. An overview of lantibiotic biosynthetic machinery promiscuity and its impact on antimicrobial discovery. Expert Opin Drug Discov 2020; 15:373-382. [PMID: 31941374 DOI: 10.1080/17460441.2020.1699530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The continued emergence of drug resistant bacteria within the nosocomial and community environment recalcitrant to conventional antimicrobial therapies has enforced the requirement for novel therapeutics. This has led to a renewed interest in peptide antimicrobials, including ribosomally synthesized peptides termed lantibiotics. Lantibiotics represent a novel class of agents that many studies have highlighted as effective against a range of pathogenic bacteria.Areas covered: In this review, the modular nature of lantibiotic synthesis is discussed and how this can be exploited not only to improve known lantibiotics but also for the creation of new to nature lantibiotics exhibiting improved pharmacological properties, antimicrobial activity and ability to bypass bacterial resistance mechanisms.Expert opinion: The use of combinatorial biosynthetic systems to combine different modules or ring structures of known lantibiotics have also been utilized to create new to nature lantibiotics. To fully exploit the available information and its application to lantibiotic engineering, additional structure activity relationship (SAR) analysis is required to fully understand the impact of certain post-translational modifications and the impact they have upon the activity, stability and pharmacological properties.
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