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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [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: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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Teber R, Asakawa S. In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes. Int J Mol Sci 2024; 25:2566. [PMID: 38473813 DOI: 10.3390/ijms25052566] [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: 01/08/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.
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Affiliation(s)
- Rabeb Teber
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
- Signal Peptidome Research Laboratory, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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3
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Arbulu S, Kjos M. Revisiting the Multifaceted Roles of Bacteriocins : The Multifaceted Roles of Bacteriocins. MICROBIAL ECOLOGY 2024; 87:41. [PMID: 38351266 PMCID: PMC10864542 DOI: 10.1007/s00248-024-02357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Bacteriocins are gene-encoded antimicrobial peptides produced by bacteria. These peptides are heterogeneous in terms of structure, antimicrobial activities, biosynthetic clusters, and regulatory mechanisms. Bacteriocins are widespread in nature and may contribute to microbial diversity due to their capacity to target specific bacteria. Primarily studied as food preservatives and therapeutic agents, their function in natural settings is however less known. This review emphasizes the ecological significance of bacteriocins as multifunctional peptides by exploring bacteriocin distribution, mobility, and their impact on bacterial population dynamics and biofilms.
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Affiliation(s)
- Sara Arbulu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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4
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Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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5
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Chukamnerd A, Pomwised R, Jeenkeawpiam K, Sakunrang C, Chusri S, Surachat K. Genomic insights into bla NDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand. Microbiol Res 2022; 263:127136. [PMID: 35870342 DOI: 10.1016/j.micres.2022.127136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates is a serious threat to global health. Here, we elucidate the genetic features of blaNDM-carrying CRKP clinical isolates from a university hospital in Thailand. The entire genomes of 19 CRKP isolates were extracted and then sequenced using the MGISEQ200 platform. Using various bioinformatics tools, we analyzed the antimicrobial resistance (AMR), virulence factors, gene transfer, bacterial defense mechanisms, and genomic diversity of the CRKP isolates. The sequence type (ST) 16 was found in most of the isolates, along with carriages of the blaNDM-1, blaOXA-232, and blaCTX-M-15 genes. The IncFIB(pQil), Col440II, and ColKP3 plasmids were identified with high frequency. The CRKP isolates harbored genes encoding for virulence factors such as adherence, biofilm formation, immune evasion, and iron uptake. The CRISPR-Cas region in the CRKP9 isolate consisted of 28 distinct spacer sequences. The genomes of the CRKP isolates presented restriction-modification (R-M) sites (M.Kpn34618Dcm and M.Kpn928I) and integrated bacteriophage genomes (Klebsiella phage ST16-OXA48phi5.4 and Enterobacteria phage mEp390). Bottromycin and sactipeptides were also identified. The isolates could be separated into three clades according to STs and pairwise single nucleotide polymorphism (SNP) distance. Pairwise average nucleotide identity (ANI) values revealed intra-species. These findings support the importance of whole-genome sequencing (WGS) to the rapid and accurate genomic analysis of clinical isolates of CRKP.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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6
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Rebuffat S. Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions. Nat Prod Rep 2021; 39:273-310. [PMID: 34755755 DOI: 10.1039/d1np00052g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is currently well established that multicellular organisms live in tight association with complex communities of microorganisms including a large number of bacteria. These are immersed in complex interaction networks reflecting the relationships established between them and with host organisms; yet, little is known about the molecules and mechanisms involved in these mutual interactions. Ribosomally synthesized peptides, among which bacterial antimicrobial peptides called bacteriocins and microcins have been identified as contributing to host-microbe interplays, are either unmodified or post-translationally modified peptides. This review will unveil current knowledge on these ribosomal peptide-based natural products, their interplay with the host immune system, and their roles in microbial interactions and symbioses. It will include their major structural characteristics and post-translational modifications, the main rules of their maturation pathways, and the principal ecological functions they ensure (communication, signalization, competition), especially in symbiosis, taking select examples in various organisms. Finally, we address unanswered questions and provide a framework for deciphering big issues inspiring future directions in the field.
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Affiliation(s)
- Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), National Centre of Scientific Research (CNRS), CP 54, 57 rue Cuvier 75005, Paris, France.
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7
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Wu Z, Li Y, Zhang L, Ding Z, Shi G. Microbial production of small peptide: pathway engineering and synthetic biology. Microb Biotechnol 2021; 14:2257-2278. [PMID: 33459516 PMCID: PMC8601181 DOI: 10.1111/1751-7915.13743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 01/14/2023] Open
Abstract
Small peptides are a group of natural products with low molecular weights and complex structures. The diverse structures of small peptides endow them with broad bioactivities and suggest their potential therapeutic use in the medical field. The remaining challenge is methods to address the main limitations, namely (i) the low amount of available small peptides from natural sources, and (ii) complex processes required for traditional chemical synthesis. Therefore, harnessing microbial cells as workhorse appears to be a promising approach to synthesize these bioactive peptides. As an emerging engineering technology, synthetic biology aims to create standard, well-characterized and controllable synthetic systems for the biosynthesis of natural products. In this review, we describe the recent developments in the microbial production of small peptides. More importantly, synthetic biology approaches are considered for the production of small peptides, with an emphasis on chassis cells, the evolution of biosynthetic pathways, strain improvements and fermentation.
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Affiliation(s)
- Zhiyong Wu
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Youran Li
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Liang Zhang
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Zhongyang Ding
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
| | - Guiyang Shi
- Key Laboratory of Industrial BiotechnologyMinistry of EducationSchool of BiotechnologyJiangnan UniversityWuxiJiangsu Province214122China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
- Jiangsu Provisional Research Center for Bioactive Product Processing TechnologyJiangnan University1800 Lihu AvenueWuxiJiangsu Province214122China
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8
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Wang D, Li J, Zhu G, Zhao K, Jiang W, Li H, Wang W, Kumar V, Dong S, Zhu W, Tian X. Mechanism of the Potential Therapeutic Candidate Bacillus subtilis BSXE-1601 Against Shrimp Pathogenic Vibrios and Multifunctional Metabolites Biosynthetic Capability of the Strain as Predicted by Genome Analysis. Front Microbiol 2020; 11:581802. [PMID: 33193216 PMCID: PMC7649127 DOI: 10.3389/fmicb.2020.581802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/30/2020] [Indexed: 12/02/2022] Open
Abstract
The global shrimp industry has suffered bacterial diseases caused mainly by Vibrio species. The typical vibriosis, acute hepatopancreatic necrosis disease (AHPND), has resulted in mass mortality and devastating economic losses. Thus, therapeutic strategies are highly needed to decrease the risk of vibriosis outbreaks. Herein, we initially identified that the growth of the causative agent of AHPND, Vibrio parahaemolyticus (VP AHPND ) and other vibrios in Pacific white shrimp (Litopenaeus vannamei) was inhibited by a Bacillus subtilis strain BSXE-1601. The natural products amicoumacins A, B, and C were purified from the cell-free supernatant from the strain BSXE-1601, but only amicoumacin A was demonstrated to be responsible for this anti-Vibrio activity. Our discovery provided the first evidence that amicoumacin A was highly active against shrimp pathogens, including the representative strain VP AHPND . Furthermore, we elucidated the amicoumacin A biosynthetic gene cluster by whole genome sequencing of the B. subtilis strain BSXE-1601. In addition to amicoumacin A, the strain BSXE-1601 genome harbored other genes encoding bacillibactin, fengycin, surfactin, bacilysin, and subtilosin A, all of which have previously reported antagonistic activities against pathogenic strains. The whole-genome analysis provided unequivocal evidence in support of the huge potential of the strain BSXE-1601 to produce diverse biologically antagonistic natural products, which may facilitate further studies on the effective therapeutics for detrimental diseases in shrimp.
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Affiliation(s)
- Dongdong Wang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
- Lab of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiahui Li
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Kun Zhao
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Wenwen Jiang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Haidong Li
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Wenjun Wang
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Vikash Kumar
- Lab of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Shuanglin Dong
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangli Tian
- The Key Laboratory of Mariculture, Ocean University of China, Ministry of Education, Qingdao, China
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Vezina B, Rehm BHA, Smith AT. Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs. BMC Microbiol 2020; 20:77. [PMID: 32252629 PMCID: PMC7132975 DOI: 10.1186/s12866-020-01772-0] [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: 10/14/2019] [Accepted: 03/29/2020] [Indexed: 12/19/2022] Open
Abstract
Background Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence. Results Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes. Conclusions Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.
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Affiliation(s)
- Ben Vezina
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia
| | - Bernd H A Rehm
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia
| | - Andrew T Smith
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia.
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Barbour A, Wescombe P, Smith L. Evolution of Lantibiotic Salivaricins: New Weapons to Fight Infectious Diseases. Trends Microbiol 2020; 28:578-593. [PMID: 32544444 DOI: 10.1016/j.tim.2020.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
Lantibiotic salivaricins are polycyclic peptides containing lanthionine and/or β-methyllanthionine residues produced by certain strains of Streptococcus salivarius, which almost exclusively reside in the human oral cavity. The importance of these molecules stems from their antimicrobial activity towards relevant oral pathogens which has so far been applied through the development of salivaricin-producing probiotic strains. However, salivaricins may also prove to be of great value in the development of new and novel antibacterial therapies in this era of emerging antibiotic resistance. In this review, we describe the biosynthesis, antimicrobial activity, structure, and mode of action of the lantibiotic salivaricins characterized to date. Moreover, we also provide an expert opinion and suggestions for future development of this important field of microbiology.
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Affiliation(s)
| | - Philip Wescombe
- Yili Innovation Center Oceania, Lincoln University, Christchurch, New Zealand
| | - Leif Smith
- Department of Biology, College of Science, Texas A&M University, College Station, TX, USA
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11
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Vior NM, Cea-Torrescassana E, Eyles TH, Chandra G, Truman AW. Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator. Front Microbiol 2020; 11:495. [PMID: 32273872 PMCID: PMC7113386 DOI: 10.3389/fmicb.2020.00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/06/2020] [Indexed: 01/18/2023] Open
Abstract
Bottromycin is a ribosomally synthesized and post-translationally modified peptide (RiPP) produced by several streptomycetes, including the plant pathogen Streptomyces scabies. There is significant interest in this molecule as it possesses strong antibacterial activity against clinically relevant multidrug resistant pathogens and is structurally distinct from all other antibiotics. However, studies into its efficacy are hampered by poor yields. An understanding of how bottromycin biosynthesis is regulated could aid the development of strategies to increase titres. Here, we use 5′-tag-RNA-seq to identify the transcriptional organization of the gene cluster, which includes an internal transcriptional start site that precedes btmD, the gene that encodes the bottromycin precursor peptide. We show that the gene cluster does not encode a master regulator that controls pathway expression and instead encodes a regulatory gene, btmL, which functions as a modulator that specifically affects the expression of btmD but not genes up- or downstream of btmD. In order to identify non-cluster associated proteins involved in regulation, proteins were identified that bind to the main promoter of the pathway, which precedes btmC. This study provides insights into how this deceptively complex pathway is regulated in the absence of a pathway specific master regulator, and how it might coordinate with the central metabolism of the cell.
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Affiliation(s)
- Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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12
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Severi E, Thomas GH. Antibiotic export: transporters involved in the final step of natural product production. Microbiology (Reading) 2019; 165:805-818. [DOI: 10.1099/mic.0.000794] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, Wentworth Way, York, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
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Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria. Antonie van Leeuwenhoek 2019; 112:1477-1499. [DOI: 10.1007/s10482-019-01276-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/14/2019] [Indexed: 01/22/2023]
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14
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Liu L, Chan S, Mo T, Ding W, Yu S, Zhang Q, Yuan S. Movements of the Substrate-Binding Clamp of Cypemycin Decarboxylase CypD. J Chem Inf Model 2019; 59:2924-2929. [DOI: 10.1021/acs.jcim.9b00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Lei Liu
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Shaoning Yu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, Lausanne CH-1015, Switzerland
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van der Heul HU, Bilyk BL, McDowall KJ, Seipke RF, van Wezel GP. Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era. Nat Prod Rep 2019; 35:575-604. [PMID: 29721572 DOI: 10.1039/c8np00012c] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2000 to 2018 The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described.
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16
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Zhang R, Li C, Wang J, Yang Y, Yan Y. Microbial production of small medicinal molecules and biologics: From nature to synthetic pathways. Biotechnol Adv 2018; 36:2219-2231. [DOI: 10.1016/j.biotechadv.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 01/07/2023]
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17
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Listeria monocytogenes and Salmonella enterica affect the expression of nisin gene and its production by Lactococcus lactis. Microb Pathog 2018; 123:28-35. [DOI: 10.1016/j.micpath.2018.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 01/09/2023]
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18
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Perez RH, Zendo T, Sonomoto K. Circular and Leaderless Bacteriocins: Biosynthesis, Mode of Action, Applications, and Prospects. Front Microbiol 2018; 9:2085. [PMID: 30233551 PMCID: PMC6131525 DOI: 10.3389/fmicb.2018.02085] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/15/2018] [Indexed: 01/02/2023] Open
Abstract
Bacteriocins are a huge family of ribosomally synthesized peptides known to exhibit a range of bioactivities, most predominantly antibacterial activities. Bacteriocins from lactic acid bacteria are of particular interest due to the latter's association to food fermentation and the general notion of them to be safe. Among the family of bacteriocins, the groups known as circular bacteriocins and leaderless bacteriocins are gaining more attention due to their enormous potential for industrial application. Circular bacteriocins and leaderless bacteriocins, arguably the least understood groups of bacteriocins, possess distinctively peculiar characteristics in their structures and biosynthetic mechanisms. Circular bacteriocins have N-to-C- terminal covalent linkage forming a structurally distinct circular peptide backbone. The circular nature of their structures provides them superior stability against various stresses compared to most linear bacteriocins. The molecular mechanism of their biosynthesis, albeit has remained poorly understood, is believed to possesses huge application prospect as it can serve as scaffold in bioengineering other biologically important peptides. On the other hand, while most bacteriocins are synthesized as inactive precursor peptides, which possess an N-terminal leader peptide attached to a C-terminal propeptide, leaderless bacteriocins are atypical as they do not have an N-terminal leader peptide, hence the name. Leaderless bacteriocins are active right after translation as they do not undergo any post-translational processing common to other groups of bacteriocins. This "simplicity" in the biosynthesis of leaderless bacteriocins offers a huge commercial potential as scale-up production systems are considerably easier to assemble. In this review, we summarize the current studies of both circular and leaderless bacteriocins, highlighting the progress in understanding their biosynthesis, mode of action, application and their prospects.
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Affiliation(s)
- Rodney H Perez
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan.,National Institute of Molecular Biology and Biotechnology, University of the Philippines Los Baños, Los Baños, Philippines
| | - Takeshi Zendo
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Kenji Sonomoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
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19
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Ding W, Mo T, Mandalapu D, Zhang Q. Substrate specificity of the cypemycin decarboxylase CypD. Synth Syst Biotechnol 2018; 3:159-162. [PMID: 30345401 PMCID: PMC6190514 DOI: 10.1016/j.synbio.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
The linaridin antibiotic cypemycin is a ribosomal synthesized and post-translationally modified peptide (RiPP) that possesses potent activity against mouse leukemia cells. This peptide natural product contains an S-[(Z)-2-aminovinyl]-d-cysteine (AviCys) moiety in the C-terminus. Formation of AviCys moiety requires an oxidative decarboxylation of the C-terminal Cys of the precursor peptide CypA, and this process is catalyzed by a flavin-containing protein CypD. In this work, we tested CypD substrate specificity with a series of synthetic oligopeptides. We show that most of the N-terminal sequence of CypA is not required for CypD activity, and the C-terminal three residues serve as the minimal structural element for enzyme recognition. We also show that CypD tolerates various substrates with modified C-termini, allowing for the generation of four novel cypemycin variants with modified AviCys moiety by site direct mutagenesis of the precursor peptide CypA. Our study demonstrates the relaxed substrate specificity of CypD and lays a foundation for future bioengineering of AviCys-containing natural products.
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Affiliation(s)
| | | | | | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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20
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Zhang Y, Chen M, Bruner SD, Ding Y. Heterologous Production of Microbial Ribosomally Synthesized and Post-translationally Modified Peptides. Front Microbiol 2018; 9:1801. [PMID: 30135682 PMCID: PMC6092494 DOI: 10.3389/fmicb.2018.01801] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides, or RiPPs, which have mainly isolated from microbes as well as plants and animals, are an ever-expanding group of peptidic natural products with diverse chemical structures and biological activities. They have emerged as a major category of secondary metabolites partly due to a myriad of microbial genome sequencing endeavors and the availability of genome mining software in the past two decades. Heterologous expression of RiPP gene clusters mined from microbial genomes, which are often silent in native producers, in surrogate hosts such as Escherichia coli and Streptomyces strains can be an effective way to elucidate encoded peptides and produce novel derivatives. Emerging strategies have been developed to facilitate the success of the heterologous expression by targeting multiple synthetic biology levels, including individual proteins, pathways, metabolic flux and hosts. This review describes recent advances in heterologous production of RiPPs, mainly from microbes, with a focus on E. coli and Streptomyces strains as the surrogate hosts.
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Affiliation(s)
- Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
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Rigali S, Anderssen S, Naômé A, van Wezel GP. Cracking the regulatory code of biosynthetic gene clusters as a strategy for natural product discovery. Biochem Pharmacol 2018; 153:24-34. [DOI: 10.1016/j.bcp.2018.01.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/03/2018] [Indexed: 12/19/2022]
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