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Kaweewan I, Mukai K, Rukthanapitak P, Nakagawa H, Hosaka T, Kodani S. Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins. Appl Microbiol Biotechnol 2024; 108:122. [PMID: 38229328 DOI: 10.1007/s00253-023-12834-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 01/18/2024]
Abstract
The myxobacteria are an attractive bioresource for bioactive compounds since the large size genome contains many biosynthetic gene clusters of secondary metabolites. The genome of the myxobacterium Melittangium boletus contains three biosynthetic gene clusters for lanthipeptide production. One of the gene clusters includes genes coding lanthipeptide precursor (melA), class II lanthipeptide synthetase (melM), and transporter (melT). The amino acid sequence of melA indicated similarity with that of known lanthipeptides mersacidin and lichenicidin A1 by the alignment. To perform heterologous production of new lanthipeptides, the expression vector containing the essential genes (melA and melM) was constructed by utilizing codon-optimized synthetic genes. The co-expression of two genes in the host bacterial cells of Escherichia coli BL21 (DE3) afforded new lanthipeptides named melittapeptins A-C. The structures of melittapeptins A-C including lanthionine/methyllanthionine bridge pattern were proposed based on protease digestion and MS/MS experiments. The native strain of M. boletus did not produce melittapeptins A-C, so heterologous production using the biosynthetic gene cluster was effective in obtaining the lanthipeptides. Melittapeptins A-C showed specific and potent antibacterial activity to the Gram-positive bacterium Micrococcus luteus. To the best of our knowledge, this is the first report of antibacterial lanthipeptides derived from myxobacterial origin. KEY POINTS: • New lanthipeptides melittapeptins were heterologously produced in Escherichia coli. • Melittapeptins showed specific antibacterial activity against Micrococcus luteus. • Melittapeptins were the first antibacterial lanthipeptides of myxobacterial origin.
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Affiliation(s)
- Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Keiichiro Mukai
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | | | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Takeshi Hosaka
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Shinya Kodani
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan.
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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Moreira R, Yang Y, Luo Y, Gilmore MS, van der Donk W. Bibacillin 1: A two-component lantibiotic from Bacillus thuringiensis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607848. [PMID: 39185197 PMCID: PMC11343131 DOI: 10.1101/2024.08.13.607848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Here we describe bibacillin 1 - a two-component lantibiotic from Bacillus thuringiensis. The peptides that comprise bibacillin 1 are modified by a class II lanthipeptide synthetase Bib1M producing two peptides with non-overlapping ring patterns that are reminiscent of cerecidin and the short component of the enterococcal cytolysin (CylLS"), a virulence factor associated with human disease. Stereochemical analysis demonstrated that each component contains LL-methyllanthionine and DL-lanthionine. The mature bibacillin 1 peptides showed cooperative bactericidal activity against Gram-positive bacteria, including members of ESKAPE pathogens, and weak hemolytic activity. Optimal ratio studies suggest that bibacillin 1 works best when the components are present in a 1:1 ratio, but near optimal activity was observed at ratios strongly favouring one component over the other, suggesting that the two peptides may have different but complementary targets. Mechanism of action studies suggest a lipid II-independent killing action distinguishing bibacillin 1 from two other two-component lantibiotics haloduracin and lacticin 3147. One of the two components of bibacillin 1 showed cross reactivity with the cytolysin regulatory system. These result support the involvement of bibacillin 1 in quorum sensing and raise questions about the impact of CylLS"-like natural products on lanthipeptide expression in diverse bacterial communities.
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Affiliation(s)
- Ryan Moreira
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA
| | - Yi Yang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA
| | - Youran Luo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA
| | - Michael S. Gilmore
- Departments of Ophthalmology and Microbiology, Harvard Medical School, Boston, MA 02144, USA
| | - Wilfred van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61822, USA
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3
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Mol M, de Maayer P. Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis. BMC Genomics 2024; 25:723. [PMID: 39054411 PMCID: PMC11270796 DOI: 10.1186/s12864-024-10635-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The genus Geobacillus and its associated taxa have been the focal point of numerous thermophilic biotechnological investigations, both at the whole cell and enzyme level. By contrast, comparatively little research has been done on its recently delineated sister genus, Parageobacillus. Here we performed pan-genomic analyses on a subset of publicly available Parageobacillus and Saccharococcus genomes to elucidate their biotechnological potential. RESULTS Phylogenomic analysis delineated the compared taxa into two distinct genera, Parageobacillus and Saccharococcus, with P. caldoxylosilyticus isolates clustering with S. thermophilus in the latter genus. Both genera present open pan-genomes, with the species P. toebii being characterized with the highest novel gene accrual. Diversification of the two genera is driven through the variable presence of plasmids, bacteriophages and transposable elements. Both genera present a range of potentially biotechnologically relevant features, including a source of novel antimicrobials, thermostable enzymes including DNA-active enzymes, carbohydrate active enzymes, proteases, lipases and carboxylesterases. Furthermore, they present a number of metabolic pathways pertinent to degradation of complex hydrocarbons and xenobiotics and for green energy production. CONCLUSIONS Comparative genomic analyses of Parageobacillus and Saccharococcus suggest that taxa in both of these genera can serve as a rich source of biotechnologically and industrially relevant secondary metabolites, thermostable enzymes and metabolic pathways that warrant further investigation.
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Affiliation(s)
- Michael Mol
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa
| | - Pieter de Maayer
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, 2000, South Africa.
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Maheshwari N, Jermiin LS, Cotroneo C, Gordon SV, Shields DC. Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240491. [PMID: 39021782 PMCID: PMC11251773 DOI: 10.1098/rsos.240491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
Lanthipeptides are a large group of ribosomally encoded peptides cyclized by thioether and methylene bridges, which include the lantibiotics, lanthipeptides with antimicrobial activity. There are over 100 experimentally characterized lanthipeptides, with at least 25 distinct cyclization bridging patterns. We set out to understand the evolutionary dynamics and diversity of lanthipeptides. We identified 977 peptides in 2785 bacterial genomes from short open-reading frames encoding lanthipeptide modifiable amino acids (C, S and T) that lay chromosomally adjacent to genes encoding proteins containing the cyclase domain. These appeared to be synthesized by both known and novel enzymatic combinations. Our predictor of bridging topology suggested 36 novel-predicted topologies, including a single-cysteine topology seen in 179 lanthionine or labionin containing peptides, which were enriched for histidine. Evidence that supported the relevance of the single-cysteine containing lanthipeptide precursors included the presence of the labionin motif among single cysteine peptides that clustered with labionin-associated synthetase domains, and the leader features of experimentally defined lanthipeptides that were shared with single cysteine predictions. Evolutionary rate variation among peptide subfamilies suggests that selection pressures for functional change differ among subfamilies. Lanthipeptides that have recently evolved specific novel features may represent a richer source of potential novel antimicrobials, since their target species may have had less time to evolve resistance.
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Affiliation(s)
- Nikunj Maheshwari
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lars S. Jermiin
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
| | - Chiara Cotroneo
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Denis C. Shields
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Gu Q, Yan J, Lou Y, Zhang Z, Li Y, Zhu Z, Liu M, Wu D, Liang Y, Pu J, Zhao X, Xiao H, Li P. Bacteriocins: Curial guardians of gastrointestinal tract. Compr Rev Food Sci Food Saf 2024; 23:e13292. [PMID: 38284593 DOI: 10.1111/1541-4337.13292] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
The human gastrointestinal (GI) tract microbiome secretes various metabolites that play pivotal roles in maintaining host physiological balance and influencing disease progression. Among these metabolites, bacteriocins-small, heat-stable peptides synthesized by ribosomes-are notably prevalent in the GI region. Their multifaceted benefits have garnered significant interest in the scientific community. This review comprehensively explores the methods for mining bacteriocins (traditional separation and purification, bioinformatics, and artificial intelligence), their effects on the stomach and intestines, and their complex bioactive mechanisms. These mechanisms include flora regulation, biological barrier restoration, and intervention in epithelial cell pathways. By detailing each well-documented bacteriocin, we reveal the diverse ways in which bacteriocins interact with the GI environment. Moreover, the future research direction is prospected. By further studying the function and interaction of intestinal bacteriocins, we can discover new pharmacological targets and develop drugs targeting intestinal bacteriocins to regulate and improve human health. It provides innovative ideas and infinite possibilities for further exploration, development, and utilization of bacteriocins. The inevitable fact is that the continuously exploration of bacteriocins is sure to bring the promising future for demic GI health understanding and interference strategy.
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Affiliation(s)
- Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Yan
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yeqing Lou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zihao Zhang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yonglu Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Zichun Zhu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Manman Liu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Danli Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Liang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiaqian Pu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Xiaodan Zhao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
| | - Hang Xiao
- Department of Food Science, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, People's Republic of China
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Kita K, Yoshida S, Masuo S, Nakamura A, Ishikawa S, Yoshida KI. Genes encoding a novel thermostable bacteriocin in the thermophilic bacterium Aeribacillus pallidus PI8. J Appl Microbiol 2023; 134:lxad293. [PMID: 38040658 DOI: 10.1093/jambio/lxad293] [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: 06/13/2023] [Revised: 11/10/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
AIM Aeribacillus pallidus PI8 is a Gram-positive thermophilic bacterium that produces thermostable antimicrobial substances against several bacterial species, including Geobacillus kaustophilus HTA426. In the present study, we sought to identify genes of PI8 with antibacterial activity. METHODS AND RESULTS We isolated, cloned, and characterized a thermostable bacteriocin from A. pallidus PI8 and named it pallidocyclin. Mass spectrometric analyses of pallidocyclin revealed that it had a circular peptide structure, and its precursor was encoded by pcynA in the PI8 genome. pcynA is the second gene within the pcynBACDEF operon. Expression of the full-length pcynBACDEF operon in Bacillus subtilis produced intact pallidocyclin, whereas expression of pcynF in G. kaustophilus HTA426 conferred resistance to pallidocyclin. CONCLUSION Aeribacillus pallidus PI8 possesses the pcynBACDEF operon to produce pallidocyclin. pcynA encodes the pallidocyclin precursor, and pcynF acts as an antagonist of pallidocyclin.
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Affiliation(s)
- Kyosuke Kita
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Sanako Yoshida
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
| | - Akira Nakamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8572 Ibaraki, Japan
| | - Shu Ishikawa
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ken-Ichi Yoshida
- Department of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [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] [Received: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Yu D, Pei Z, Chen Y, Wang H, Xiao Y, Zhang H, Chen W, Lu W. Bifidobacterium longum subsp. infantis as widespread bacteriocin gene clusters carrier stands out among the Bifidobacterium. Appl Environ Microbiol 2023; 89:e0097923. [PMID: 37681950 PMCID: PMC10537742 DOI: 10.1128/aem.00979-23] [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: 06/17/2023] [Accepted: 07/03/2023] [Indexed: 09/09/2023] Open
Abstract
Bifidobacterium is the dominant genus, particularly in the intestinal tract niche of healthy breast-fed infants, and many of these strains have been proven to elicit positive effects on infant development. In addition to its effective antimicrobial activity against detrimental microorganisms, it helps to improve the intestinal microbiota balance. The isolation and identification of bacteriocins from Bifidobacterium have been limited since the mid-1980s, leading to an underestimation of its ability for bacteriocin production. Here, we employed a silicon-based search strategy to mine 354 putative bacteriocin gene clusters (BGCs), most of which have never been reported, from the genomes of 759 Bifidobacterium strains distributed across 9 species. Consistent with previous reports, most Bifidobacterium strains did not carry or carry only a single BGC; however, Bifidobacterium longum subsp. infantis, in contrast to other Bifidobacterium species, carried numerous BGCs, including lanthipeptides, lasso peptides, thiopeptides, and class IId bacteriocins. The antimicrobial activity of the crude bacteriocins and transcription analysis confirmed its potential for bacteriocin biosynthesis. Additionally, we investigated the association of bacteriocins with the phylogenetic positions of their homologs from other genera and niches. In conclusion, this study re-examines a few Bifidobacterium species traditionally regarded as a poor source of bacteriocins. These bacteriocin genes impart a competitive advantage to Bifidobacterium in colonizing the infant intestinal tract. IMPORTANCE Development of the human gut microbiota commences from birth, with bifidobacteria being among the first colonizers of the newborn intestinal tract and dominating it for a considerable period. To date, the genetic basis for the successful adaptation of bifidobacteria to this particular niche remains unclear since studies have mainly focused on glycoside hydrolase and adhesion-related genes. Bacteriocins are competitive factors that help producers maintain colonization advantages without destroying the niche balance; however, they have rarely been reported in Bifidobacterium. The advancement in sequencing methods and bacteriocin databases enables the use of a silicon-based search strategy for the comprehensive and rapid re-evaluation of the bacteriocin distribution of Bifidobacterium. Our study revealed that B. infantis carries abundant bacteriocin biosynthetic gene clusters for the first time, presenting new evidence regarding the competitive interactions of Bifidobacterium in the infant intestinal tract.
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Affiliation(s)
- Di Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhangming Pei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yutao Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yue Xiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China
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Machado M, Silva S, Costa EM. Are Antimicrobial Peptides a 21st-Century Solution for Atopic Dermatitis? Int J Mol Sci 2023; 24:13460. [PMID: 37686269 PMCID: PMC10488019 DOI: 10.3390/ijms241713460] [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: 08/01/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Atopic dermatitis (AD) is a chronic inflammatory skin disorder that is the result of various environmental, bacterial and genetic stimuli, which culminate in the disruption of the skin's barrier function. Characterized by highly pruritic skin lesions, xerosis and an array of comorbidities among which skin infections are the most common, this condition results in both a significant loss of quality of life and in the need for life-long treatments (e.g., corticosteroids, monoclonal antibodies and regular antibiotic intake), all of which may have harmful secondary effects. This, in conjunction with AD's rising prevalence, made the development of alternative treatment strategies the focus of both the scientific community and the pharmaceutical industry. Given their potential to both manage the skin microbiome, fight infections and even modulate the local immune response, the use of antimicrobial peptides (AMPs) from more diverse origins has become one of the most promising alternative solutions for AD management, with some being already used with some success towards this end. However, their production and use also exhibit some limitations. The current work seeks to compile the available information and provide a better understanding of the state of the art in the understanding of AMPs' true potential in addressing AD.
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Affiliation(s)
| | - Sara Silva
- CBQF Centro de Biotecnologia e Química Fina Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
| | - Eduardo M. Costa
- CBQF Centro de Biotecnologia e Química Fina Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal;
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Li JY, Liu YF, Zhou L, Gang HZ, Liu JF, Sun GZ, Wang WD, Yang SZ, Mu BZ. Structural Diversity of the Lipopeptide Biosurfactant Produced by a Newly Isolated Strain, Geobacillus thermodenitrifcans ME63. ACS OMEGA 2023; 8:22150-22158. [PMID: 37360472 PMCID: PMC10286266 DOI: 10.1021/acsomega.3c02194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023]
Abstract
The genus Geobacillus is active in degradation of hydrocarbons in thermophilic and facultative environments since it was first reported in 1920. Here, we report a new strain, Geobacillus thermodenitrificans ME63, isolated from an oilfield with the ability of producing the biosurfactant. The composition, chemical structure, and surface activity of the biosurfactant produced by G. thermodenitrificans ME63 were investigated by using a combination of the high-performance liquid chromatography, time-of-flight ion mass spectrometry, and surface tensiometer. The biosurfactant produced by strain ME63 was identified as surfactin with six variants, which is one of the representative family of lipopeptide biosurfactants. The amino acid residue sequence in the peptide of this surfactin is N-Glu → Leu → Leu → Val → Leu → Asp → Leu-C. The critical micelle concentration (CMC) of the surfactin is 55 mg L-1, and the surface tension at CMC is 35.9 mN m-1, which is promising in bioremediation and oil recovery industries. The surface activity and emulsification properties of biosurfactants produced by G. thermodenitrificans ME63 showed excellent resistance to temperature changes, salinity changes, and pH changes.
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Affiliation(s)
- Jia-Yi Li
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
| | - Yi-Fan Liu
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Engineering
Research Center of MEOR, East China University
of Science and Technology, Shanghai 200237, China
| | - Lei Zhou
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Engineering
Research Center of MEOR, East China University
of Science and Technology, Shanghai 200237, China
| | - Hong-Ze Gang
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Engineering
Research Center of MEOR, East China University
of Science and Technology, Shanghai 200237, China
| | - Jin-Feng Liu
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Daqing
Huali Biotechnology Co., Ltd, Daqing, Heilongjiang 163511, China
| | - Gang-Zheng Sun
- Research
Institute of Petroleum Engineering and Technology, Shengli Oilfield Company, Sinopec, Dongying 257088, China
| | - Wei-Dong Wang
- Research
Institute of Petroleum Engineering and Technology, Shengli Oilfield Company, Sinopec, Dongying 257088, China
| | - Shi-Zhong Yang
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Engineering
Research Center of MEOR, East China University
of Science and Technology, Shanghai 200237, China
| | - Bo-Zhong Mu
- State
Key Laboratory of Bioreactor Engineering and School of Chemistry and
Molecular Engineering, East China University
of Science and Technology, Shanghai 200237, China
- Engineering
Research Center of MEOR, East China University
of Science and Technology, Shanghai 200237, China
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11
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Koniuchovaitė A, Petkevičiūtė A, Bernotaitė E, Gricajeva A, Gegeckas A, Kalėdienė L, Kaunietis A. Novel leaderless bacteriocin geobacillin 6 from thermophilic bacterium Parageobacillus thermoglucosidasius. Front Microbiol 2023; 14:1207367. [PMID: 37396380 PMCID: PMC10311245 DOI: 10.3389/fmicb.2023.1207367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/24/2023] [Indexed: 07/04/2023] Open
Abstract
Bacterial resistance to conventional antibiotics has urged us to develop alternative strategies against bacterial pathogens. Moreover, a demand for food products containing no chemical preservatives has led us to search for new alternative technologies for food preservation. Bacteriocins - ribosomally synthesized antimicrobial peptides - have been proposed as a new alternative to conventional antibiotics or chemicals for food preservation. This study describes biosynthesis and characterization of a novel leaderless bacteriocin, geobacillin 6, which was identified in the thermophilic bacterium Parageobacillus thermoglucosidasius. Its amino acid sequence shows low similarity to other bacteriocins and it is the first leaderless-type bacteriocin identified in thermophilic bacteria. Based on structure assessment, the bacteriocin forms a multi-helix bundle. Geobacillin 6 exhibits a relatively narrow antimicrobial spectrum, it is active in the μM range and against Gram-positive bacteria, mostly thermophilic species closely related to the producer strain. Bacteriocin demonstrates stability over pH 3-11 and is highly thermostable, retaining 100% of its activity after incubation at 95°C for 6 h. Geobacillin 6 has potential in the food industry and biotechnological processes where contamination with thermophilic bacteria is undesirable.
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12
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Barbour A, Smith L, Oveisi M, Williams M, Huang RC, Marks C, Fine N, Sun C, Younesi F, Zargaran S, Orugunty R, Horvath TD, Haidacher SJ, Haag AM, Sabharwal A, Hinz B, Glogauer M. Discovery of phosphorylated lantibiotics with proimmune activity that regulate the oral microbiome. Proc Natl Acad Sci U S A 2023; 120:e2219392120. [PMID: 37216534 PMCID: PMC10235938 DOI: 10.1073/pnas.2219392120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/15/2023] [Indexed: 05/24/2023] Open
Abstract
Lantibiotics are ribosomally synthesized and posttranslationally modified peptides (RiPPs) that are produced by bacteria. Interest in this group of natural products is increasing rapidly as alternatives to conventional antibiotics. Some human microbiome-derived commensals produce lantibiotics to impair pathogens' colonization and promote healthy microbiomes. Streptococcus salivarius is one of the first commensal microbes to colonize the human oral cavity and gastrointestinal tract, and its biosynthesis of RiPPs, called salivaricins, has been shown to inhibit the growth of oral pathogens. Herein, we report on a phosphorylated class of three related RiPPs, collectively referred to as salivaricin 10, that exhibit proimmune activity and targeted antimicrobial properties against known oral pathogens and multispecies biofilms. Strikingly, the immunomodulatory activities observed include upregulation of neutrophil-mediated phagocytosis, promotion of antiinflammatory M2 macrophage polarization, and stimulation of neutrophil chemotaxis-these activities have been attributed to the phosphorylation site identified on the N-terminal region of the peptides. Salivaricin 10 peptides were determined to be produced by S. salivarius strains found in healthy human subjects, and their dual bactericidal/antibiofilm and immunoregulatory activity may provide new means to effectively target infectious pathogens while maintaining important oral microbiota.
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Affiliation(s)
- Abdelahhad Barbour
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Leif Smith
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Morvarid Oveisi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - McKinley Williams
- Department of Biology, College of Science, Texas A&M University, College Station, TX 77843
| | - Ruo Chen Huang
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Cara Marks
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Noah Fine
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Chunxiang Sun
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Fereshteh Younesi
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Sina Zargaran
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | | | - Thomas D Horvath
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Sigmund J Haidacher
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Anthony M Haag
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX 77030
| | - Amarpreet Sabharwal
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Boris Hinz
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's Hospital, Toronto, ON M5B 1T8, Canada
| | - Michael Glogauer
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
- Department of Dental Oncology, Maxillofacial and Ocular Prosthetics, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
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13
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Chaudhary S, Kishen S, Singh M, Jassal S, Pathania R, Bisht K, Sareen D. Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin. AMB Express 2023; 13:34. [PMID: 36940043 PMCID: PMC10027976 DOI: 10.1186/s13568-023-01536-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/21/2023] Open
Abstract
Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.
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Affiliation(s)
- Sandeep Chaudhary
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Shweta Kishen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Sunanda Jassal
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Reeva Pathania
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Kalpana Bisht
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India
| | - Dipti Sareen
- Department of Biochemistry, Panjab University, Chandigarh, 160014, India.
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14
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Lee H, Wu C, Desormeaux EK, Sarksian R, van der Donk WA. Improved production of class I lanthipeptides in Escherichia coli. Chem Sci 2023; 14:2537-2546. [PMID: 36908960 PMCID: PMC9993889 DOI: 10.1039/d2sc06597e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Lanthipeptides are ribosomally synthesised and post-translationally modified peptides containing lanthionine (Lan) and methyllanthionine (MeLan) residues that are formed by dehydration of Ser/Thr residues followed by conjugate addition of Cys to the resulting dehydroamino acids. Class I lanthipeptide dehydratases utilize glutamyl-tRNAGlu as a co-substrate to glutamylate Ser/Thr followed by glutamate elimination. Here we report a new system to heterologously express class I lanthipeptides in Escherichia coli through co-expression of the producing organism's glutamyl-tRNA synthetase (GluRS) and tRNAGlu pair in the vector pEVOL. In contrast to the results in the absence of the pEVOL system, we observed the production of fully-dehydrated peptides, including epilancin 15X, and peptides from the Bacteroidota Chryseobacterium and Runella. A second common obstacle to production of lanthipeptides in E. coli is the formation of glutathione adducts. LanC-like (LanCL) enzymes were previously reported to add glutathione to dehydroamino-acid-containing proteins in Eukarya. Herein, we demonstrate that the LanCL enzymes can remove GSH adducts from C-glutathionylated peptides with dl- or ll-lanthionine stereochemistry. These two advances will aid synthetic biology-driven genome mining efforts to discover new lanthipeptides.
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Affiliation(s)
- Hyunji Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign 1206 W Gregory Drive Urbana Illinois 61801 USA
- College of Pharmacy, Kyungsung University Busan 48434 Republic of Korea
| | - Chunyu Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA
| | - Emily K Desormeaux
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA
| | - Raymond Sarksian
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA
| | - Wilfred A van der Donk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign 1206 W Gregory Drive Urbana Illinois 61801 USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA
- Department of Chemistry, The Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign 600 South Mathews Avenue Urbana Illinois 61801 USA
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15
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Knospe CV, Kamel M, Spitz O, Hoeppner A, Galle S, Reiners J, Kedrov A, Smits SHJ, Schmitt L. The structure of MadC from Clostridium maddingley reveals new insights into class I lanthipeptide cyclases. Front Microbiol 2023; 13:1057217. [PMID: 36741885 PMCID: PMC9889658 DOI: 10.3389/fmicb.2022.1057217] [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] [Received: 09/29/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
The rapid emergence of microbial multi-resistance against antibiotics has led to intense search for alternatives. One of these alternatives are ribosomally synthesized and post-translationally modified peptides (RiPPs), especially lantibiotics. They are active in a low nanomolar range and their high stability is due to the presence of characteristic (methyl-) lanthionine rings, which makes them promising candidates as bacteriocides. However, innate resistance against lantibiotics exists in nature, emphasizing the need for artificial or tailor-made lantibiotics. Obviously, such an approach requires an in-depth mechanistic understanding of the modification enzymes, which catalyze the formation of (methyl-)lanthionine rings. Here, we determined the structure of a class I cyclase (MadC), involved in the modification of maddinglicin (MadA) via X-ray crystallography at a resolution of 1.7 Å, revealing new insights about the structural composition of the catalytical site. These structural features and substrate binding were analyzed by mutational analyses of the leader peptide as well as of the cyclase, shedding light into the mode of action of MadC.
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Affiliation(s)
- C. Vivien Knospe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Kamel
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Olivia Spitz
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefanie Galle
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Reiners
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexej Kedrov
- Synthetic Membrane Systems, Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany,Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany,*Correspondence: Lutz Schmitt, ✉
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16
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Janssen K, Krasenbrink J, Strangfeld S, Kroheck S, Josten M, Engeser M, Bierbaum G. Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin. Chembiochem 2023; 24:e202200540. [PMID: 36399337 PMCID: PMC10107895 DOI: 10.1002/cbic.202200540] [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: 09/15/2022] [Revised: 11/18/2022] [Indexed: 11/19/2022]
Abstract
Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.
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Affiliation(s)
- Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany
| | - Julia Krasenbrink
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany.,Present address: Centre for Microbiology and Environmental Systems Science, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Sarina Strangfeld
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany
| | - Sarah Kroheck
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany
| | - Michaele Josten
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany
| | - Marianne Engeser
- Kekulé Institute of Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127, Bonn, Germany
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17
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Escámez PSF, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 17: suitability of taxonomic units notified to EFSA until September 2022. EFSA J 2023; 21:e07746. [PMID: 36704192 PMCID: PMC9875162 DOI: 10.2903/j.efsa.2023.7746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, new information was found leading to the withdrawal of the qualification 'absence of aminoglycoside production ability' for Bacillus velezensis. The qualification for Bacillus paralicheniformis was changed to 'absence of bacitracin production ability'. For the other TUs, no new information was found that would change the status of previously recommended QPS TUs. Of 52 microorganisms notified to EFSA between April and September 2022 (inclusive), 48 were not evaluated because: 7 were filamentous fungi, 3 were Enterococcus faecium, 2 were Escherichia coli, 1 was Streptomyces spp., and 35 were taxonomic units (TUs) that already have a QPS status. The other four TUs notified within this period, and one notified previously as a different species, which was recently reclassified, were evaluated for the first time for a possible QPS status: Xanthobacter spp. could not be assessed because it was not identified to the species level; Geobacillus thermodenitrificans is recommended for QPS status with the qualification 'absence of toxigenic activity'. Streptoccus oralis is not recommended for QPS status. Ogataea polymorpha is proposed for QPS status with the qualification 'for production purposes only'. Lactiplantibacillus argentoratensis (new species) is included in the QPS list.
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18
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Kaweewan I, Ijichi S, Nakagawa H, Kodani S. Heterologous production of new lanthipeptides hazakensins A and B using a cryptic gene cluster of the thermophilic bacterium Thermosporothrix hazakensis. World J Microbiol Biotechnol 2022; 39:30. [PMID: 36445498 DOI: 10.1007/s11274-022-03463-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
Abstract
The thermophilic bacterium Thermosporothrix hazakensis belongs to a class of Ktedonobacteria in the phylum Chloroflexota. Lanthipeptides are a naturally occurring peptide group that contains antibacterial compounds such as nisin. To find a new lanthipeptide that is a possible candidate for an antibacterial reagent, we performed genome-mining of T. hazakensis and heterologous expression experiments. Based on genome-mining, the presence of a total of ten putative biosynthetic gene clusters for class I and class II lanthipeptides was indicated from the genome sequence of T. hazakensis. New lanthipeptides named hazakensins A and B were produced by heterologous expression of a class I lanthipeptide biosynthetic gene cluster in the expression host Escherichia coli. Co-expression of the biosynthetic gene cluster with tRNA-Glu and glutamyl-tRNA synthetase coding genes derived from T. hazakensis increased the production yield of both lanthipeptides by about 4-6 times. The chemical structures of hazakensins A and B including the bridging pattern of lanthionine/methyllanthionine rings were determined by NMR and MS experiments. Since production of hazakensins A and B was not observed in the native strain T. hazakensis, heterologous production was an effective method to obtain the lanthipeptides derived from the biosynthetic gene cluster. This is the first report of heterologous production of class I lanthipeptides originating from the filamentous green non-sulfur bacteria, to the best of our knowledge. The success of heterologous production of hazakensins may lead to the discovery and development of new lanthipeptides derived from the origins of bacteria in the phylum Chloroflexota.
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Affiliation(s)
- Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Shinta Ijichi
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, 305-8642, Japan
| | - Shinya Kodani
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan. .,Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka University, Shizuoka, 422-8529, Japan. .,College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
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19
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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In pursuit of next-generation therapeutics: Antimicrobial peptides against superbugs, their sources, mechanism of action, nanotechnology-based delivery, and clinical applications. Int J Biol Macromol 2022; 218:135-156. [PMID: 35868409 DOI: 10.1016/j.ijbiomac.2022.07.103] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 12/12/2022]
Abstract
Antimicrobial peptides (AMPs) attracted attention as potential source of novel antimicrobials. Multi-drug resistant (MDR) infections have emerged as a global threat to public health in recent years. Furthermore, due to rapid emergence of new diseases, there is pressing need for development of efficient antimicrobials. AMPs are essential part of the innate immunity in most living organisms, acting as the primary line of defense against foreign invasions. AMPs kill a wide range of microorganisms by primarily targeting cell membranes or intracellular components through a variety of ways. AMPs can be broadly categorized based on their physico-chemical properties, structure, function, target and source of origin. The synthetic analogues produced either with suitable chemical modifications or with the use of suitable delivery systems are projected to eliminate the constraints of toxicity and poor stability commonly linked with natural AMPs. The concept of peptidomimetics is gaining ground around the world nowadays. Among the delivery systems, nanoparticles are emerging as potential delivery tools for AMPs, amplifying their utility against a variety of pathogens. In the present review, the broad classification of various AMPs, their mechanism of action (MOA), challenges associated with AMPs, current applications, and novel strategies to overcome the limitations have been discussed.
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21
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Johnston CW, Badran AH. Natural and engineered precision antibiotics in the context of resistance. Curr Opin Chem Biol 2022; 69:102160. [PMID: 35660248 DOI: 10.1016/j.cbpa.2022.102160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Antibiotics are essential weapons in our fight against infectious disease, yet the consequences of broad-spectrum antibiotic use on microbiome stability and pathogen resistance are prompting investigations into more selective alternatives. Echoing the advent of precision medicine in oncology, precision antibiotics with focused activities are emerging as a means of addressing infections without damaging microbiomes or incentivizing resistance. Historically, antibiotic design principles have been gleaned from Nature, and reinvestigation of overlooked antibacterials is now providing scaffolds and targets for the design of pathogen-specific drugs. In this perspective, we summarize the biosynthetic and antibacterial mechanisms used to access these activities, and discuss how such strategies may be co-opted through engineering approaches to afford precision antibiotics.
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Affiliation(s)
- Chad W Johnston
- Department of Pharmacology & Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ahmed H Badran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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22
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Tenea GN, Ascanta P. Bioprospecting of Ribosomally Synthesized and Post-translationally Modified Peptides Through Genome Characterization of a Novel Probiotic Lactiplantibacillus plantarum UTNGt21A Strain: A Promising Natural Antimicrobials Factory. Front Microbiol 2022; 13:868025. [PMID: 35464932 PMCID: PMC9020862 DOI: 10.3389/fmicb.2022.868025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
The present work describes the genome sequencing and characterization of a novel Lactiplantibacillus plantarum strain assigned UTNGt21A isolated from wild Solanum quitoense (L.) fruits. In silico analysis has led to identifying a wide range of biosynthetic gene clusters (BGCs) and metabolic compounds. The genome had a total of 3,558,611 bp with GC of 43.96%, harboring 3,449 protein-coding genes, among which 3,209 were assigned by the EggNOG database, and 240 hypothetical proteins have no match in the BLASTN database. It also contains 68 tRNAs, 1 23S rRNA, 1 16S rRNA, 6 5S rRNA, and 1 tmRNA. In addition, no acquired resistance genes nor virulence and pathogenic factors were predicted, indicating that UTNGt21A is a safe strain. Three areas of interest (AOI) consisting of multiple genes encoding for bacteriocins and ABC transporters were predicted with BAGEL4, while eight secondary metabolite regions were predicted with the antiSMASH web tool. GutSMASH analysis predicted one metabolic gene cluster (MGC) type pyruvate to acetate-formate, a primary metabolite region essential for anaerobe growth. Several lanthipeptides and non-ribosomal peptide synthetase (NRPS) clusters were detected in the UTNGt21A but not the reference genomes, suggesting that their genome diversity might be linked to its niche-specific lineage and adaptation to a specific environment. Moreover, the application of a targeted genome mining tool (RiPPMiner) uncovered a diverse arsenal of important antimicrobial molecules such as lanthipeptides. Furthermore, in vitro analysis indicated that the crude extract (CE) of UTNGt21A exerted a wide spectrum of inhibition against several pathogens. The results indicated that the possible peptide-protein extract (PC) from UTNGt21A induces morphological and ultrastructural changes of Salmonella enterica subsp. enterica ATCC51741, compatible with its inhibitory potential. Genome characterization is the basis for further in vitro and in vivo studies to explore their use as antimicrobial producers or probiotic strains.
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Affiliation(s)
- Gabriela N Tenea
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
| | - Pamela Ascanta
- Biofood and Nutraceutics Research and Development Group, Faculty of Engineering in Agricultural and Environmental Sciences, Technical University of the North, Ibarra, Ecuador
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23
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Thetsana C, Ijichi S, Kaweewan I, Nakagawa H, Kodani S. Heterologous expression of a cryptic gene cluster from a marine proteobacterium Thalassomonas actiniarum affords new lanthipeptides thalassomonasins A and B. J Appl Microbiol 2022; 132:3629-3639. [PMID: 35157343 DOI: 10.1111/jam.15491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
AIMS The aim of this study was to utilize a cryptic biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum for production of new lanthipeptides by heterologous expression system. METHODS AND RESULTS Based on genome-mining, a new biosynthetic gene cluster of class I lanthipeptide was found in the genome sequence of a marine proteobacterium Thalassomonas actiniarum. Molecular cloning was performed to construct expression vector derived from commercial available plasmid pET-41a(+). Heterologous production of new lanthipeptides named thalassomonasins A and B was performed using the host Escherichia coli BL21(DE3) harboring the expression vector. The structure of thalassomonasin A was determined by interpretation of NMR and MS data. As a result, thalassomonasin A was determined to be a lanthipeptide with three units of lanthionine. The bridging pattern of the lanthionine rings in thalassomonasin A was determined by interpretation of NOESY data. The structure of thalassomonasin B was proposed by MS/MS experiment. CONCLUSIONS We succeeded in heterologous production of new class I lanthipeptides using a biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report of heterologous production of lanthipeptides derived from proteobacterial origin. There are many cryptic biosynthetic gene clusters of this class of lanthipeptides in proteobacterial genomes. This study may lead to production of new lanthipeptides by utilizing the biosynthetic gene clusters.
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Affiliation(s)
- Chanaphat Thetsana
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Shinta Ijichi
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakagawa
- Research center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Faculty of Agriculture, Shizuoka University, Shizuoka, Japan.,Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka University, Shizuoka, Japan.,College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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24
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Antimicrobial Potential of the Genera Geobacillus and Parageobacillus, as Well as Endolysins Biosynthesized by Their Bacteriophages. Antibiotics (Basel) 2022; 11:antibiotics11020242. [PMID: 35203843 PMCID: PMC8868475 DOI: 10.3390/antibiotics11020242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 02/05/2023] Open
Abstract
In the recent decades, antibiotic resistance has emerged and spread rapidly among clinically relevant pathogens. The natural ability of bacteria to transmit resistance determinants through horizontal gene transfer poses constant challenges to drug development. Natural molecules produced by soil microorganisms continue to be a key source of new antimicrobial agents. In this context, bacteria from the Geobacillus and Parageobacillus genera deserve special attention. Although there is commercial and industrial interest in these microorganisms, the full range of antibacterial compounds biosynthesized by the Geobacillus and Parageobacillus species remains largely unexplored. The aim of this review is to present the strong antimicrobial potential of these bacteria and endolysins produced by their bacteriophages.
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25
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Nunes LGP, Reichert T, Machini MT. His-Rich Peptides, Gly- and His-Rich Peptides: Functionally Versatile Compounds with Potential Multi-Purpose Applications. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10302-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Gerst MM, Somogyi Á, Yang X, Yousef AE. Detection and characterization of a rare two-component lantibiotic, amyloliquecidin GF610 produced by Bacillus velezensis, using a combination of culture, molecular and bioinformatic analyses. J Appl Microbiol 2021; 132:994-1007. [PMID: 34487591 DOI: 10.1111/jam.15290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/24/2021] [Accepted: 08/30/2021] [Indexed: 01/26/2023]
Abstract
AIM To detect and characterize novel lantibiotics from a collection of Bacillus spp. using a multifaceted analytical approach. METHODS AND RESULTS A previously completed microassay identified 45 Bacillus isolates with anti-Listeria activity. The isolates were PCR screened using degenerate primers targeting conserved sequences in lanM-type lantibiotics. B. velezensis GF610 produced a PCR product whose sequence, along with genome mining and bioinformatics, guided the liquid chromatographic analysis of strain's cell-free extracts and the mass spectrometry of purified fractions. Results revealed a new amyloliquecidin variant (designated GF610) produced by the strain. Amyloliquecidin GF610 is a two-component lantibiotic with α and β peptides having monoisotopic masses of 3026 and 2451 Da, and molecular formulae C130 H191 N35 O39 S5 and C110 H158 N26 O30 S4 , respectively. Amyloliquecidin GF610 is active against Listeria monocytogenes, Clostridium sporogenes, Clostridioides difficile, Staphylococcus aureus and Alicyclobacillus acidoterrestris with minimum inhibitory concentrations (MICs) in the range of 0.5-7.0 µmol l-1 . CONCLUSIONS The proposed multifaceted analytical approach was valuable to provide a deep and proper characterization of a novel bacteriocin, amyloliquecidin GF610, with high antimicrobial activity against Gram-positive bacteria. SIGNIFICANCE AND IMPACT The discovered Amyloliquecidin GF610 is potentially useful in food, agricultural or medical applications. The analytical approach followed may facilitate future discoveries of two-component lantibiotics, which are challenging compounds to detect and characterize.
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Affiliation(s)
- Michelle M Gerst
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Árpád Somogyi
- Mass Spectrometry and Proteomics Facility, Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, USA
| | - Xu Yang
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
| | - Ahmed E Yousef
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA.,Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
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27
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Dang X, Wang G. Spotlight on the Selected New Antimicrobial Innate Immune Peptides Discovered During 2015-2019. Curr Top Med Chem 2021; 20:2984-2998. [PMID: 33092508 DOI: 10.2174/1568026620666201022143625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Antibiotic resistance is a global issue and new anti-microbials are required. INTRODUCTION Anti-microbial peptides are important players of host innate immune systems that prevent infections. Due to their ability to eliminate drug-resistant pathogens, AMPs are promising candidates for developing the next generation of anti-microbials. METHODS The anti-microbial peptide database provides a useful tool for searching, predicting, and designing new AMPs. In the period from 2015-2019, ~500 new natural peptides have been registered. RESULTS This article highlights a selected set of new AMP members with interesting properties. Teixobactin is a cell wall inhibiting peptide antibiotic, while darobactin inhibits a chaperone and translocator for outer membrane proteins. Remarkably, cOB1, a sex pheromone from commensal enterococci, restricts the growth of multidrug-resistant Enterococcus faecalis in the gut at a picomolar concentration. A novel proline-rich AMP has been found in the plant Brassica napus. A shrimp peptide MjPen- II comprises three different sequence domains: serine-rich, proline-rich, and cysteine-rich regions. Surprisingly, an amphibian peptide urumin specifically inhibits H1 hemagglutinin-bearing influenza A virus. Defensins are abundant and typically consist of three pairs of intramolecular disulfide bonds. However, rat rattusin dimerizes via forming five pairs of intermolecular disulfide bonds. While human LL-37 can be induced by vitamin D, vitamin A induces the expression of resistin-like molecule alpha (RELMα) in mice. The isolation and characterization of an alternative human cathelicidin peptide, TLN-58, substantiates the concept of one gene multiple peptides. The involvement of a fly AMP nemuri in sleep induction may promote the research on the relationship between sleep and infection control. CONCLUSION The functional roles of AMPs continue to grow and the general term "innate immune peptides" becomes useful. These discoveries widen our view on the anti-microbial peptides and may open new opportunities for developing novel peptide therapeutics for different applications.
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Affiliation(s)
- Xiangli Dang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5900, United States
| | - Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5900, United States
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28
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Bothwell IR, Caetano T, Sarksian R, Mendo S, van der Donk WA. Structural Analysis of Class I Lanthipeptides from Pedobacter lusitanus NL19 Reveals an Unusual Ring Pattern. ACS Chem Biol 2021; 16:1019-1029. [PMID: 34085816 PMCID: PMC9845027 DOI: 10.1021/acschembio.1c00106] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide natural products characterized by the presence of lanthionine and methyllanthionine cross-linked amino acids formed by dehydration of Ser/Thr residues followed by conjugate addition of Cys to the resulting dehydroamino acids. Class I lanthipeptide dehydratases utilize glutamyl-tRNAGlu as a cosubstrate to glutamylate Ser/Thr followed by glutamate elimination. A vast majority of lanthipeptides identified from class I synthase systems have been from Gram-positive bacteria. Herein, we report the heterologous expression and modification in Escherichia coli of two lanthipeptides from the Gram-negative Bacteroidetes Pedobacter lusitanus NL19. These peptides are representative of a group of compounds frequently encoded in Pedobacter genomes. Structural characterization of the lanthipeptides revealed a novel ring pattern as well as an unusual ll-lanthionine stereochemical configuration and a cyclase that lacks the canonical zinc ligands found in most LanC enzymes.
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Affiliation(s)
- Ian R. Bothwell
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Tânia Caetano
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Raymond Sarksian
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Sónia Mendo
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
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29
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Exploring structural signatures of the lanthipeptide prochlorosin 2.8 using tandem mass spectrometry and trapped ion mobility-mass spectrometry. Anal Bioanal Chem 2021; 413:4815-4824. [PMID: 34105020 DOI: 10.1007/s00216-021-03437-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 10/21/2022]
Abstract
Lanthipeptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by intramolecular thioether cross-links formed between a dehydrated serine/threonine (dSer/dThr) and a cysteine residue. Prochlorosin 2.8 (Pcn2.8) is a class II lanthipeptide that exhibits a non-overlapping thioether ring pattern, for which no biological activity has been reported yet. The variant Pcn2.8[16RGD] has been shown to bind tightly to the αvβ3 integrin receptor. In the present work, tandem mass spectrometry, using collision-induced dissociation (CID) and electron capture dissociation (ECD), and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) were used to investigate structural signatures for the non-overlapping thioether ring pattern of Pcn2.8. CID experiments on Pcn2.8 yielded bi and yj fragments between the thioether cross-links, evidencing the presence of a non-overlapping thioether ring pattern. ECD experiments of Pcn2.8 showed a significant increase of hydrogen migration events near the residues involved in the thioether rings with a more pronounced effect at the dehydrated residues as compared to the cysteine residues. The high-resolution mobility analysis, aided by site-directed mutagenesis ([P8A], [P11A], [P12A], [P8A/P11A], [P8A/P12A], [P11A/P12A], and [P8A/P11A/P12A] variants), demonstrated that Pcn2.8 adopts cis/trans-conformations at Pro8, Pro11, and Pro12 residues. These observations were complementary to recent NMR findings, for which only the Pro8 residue was evidenced to adopt cis/trans-orientations. This study highlights the analytical power of the TIMS-MS/MS workflow for the structural characterization of lanthipeptides and could be a useful tool in our understanding of the biologically important structural elements that drive the thioether cyclization process.
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30
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Aftab Uddin M, Akter S, Ferdous M, Haidar B, Amin A, Shofiul Islam Molla AHM, Khan H, Islam MR. A plant endophyte Staphylococcus hominis strain MBL_AB63 produces a novel lantibiotic, homicorcin and a position one variant. Sci Rep 2021; 11:11211. [PMID: 34045548 PMCID: PMC8159966 DOI: 10.1038/s41598-021-90613-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Here we report a jute endophyte Staphylococcus hominis strain MBL_AB63 isolated from jute seeds which showed promising antimicrobial activity against Staphylococcus aureus SG511 when screening for antimicrobial substances. The whole genome sequence of this strain, annotated using BAGEL4 and antiSMASH 5.0 to predict the gene clusters for antimicrobial substances identified a novel antimicrobial peptide cluster that belongs to the class I lantibiotic group. The predicted lantibiotic (homicorcin) was found to be 82% similar to a reported peptide epicidin 280 having a difference of seven amino acids at several positions of the core peptide. Two distinct peaks obtained at close retention times from a RP-HPLC purified fraction have comparable antimicrobial activities and LC-MS revealed the molecular mass of these peaks to be 3046.5 and 3043.2 Da. The presence of an oxidoreductase (homO) similar to that of epicidin 280- associated eciO or epilancin 15X- associated elxO in the homicorcin gene cluster is predicted to be responsible for the reduction of the first dehydrated residue dehydroalanine (Dha) to 2-hydroxypropionate that causes an increase of 3 Da mass of homicorcin 1. Trypsin digestion of the core peptide and its variant followed by ESI-MS analysis suggests the presence of three ring structures, one in the N-terminal and other two interlocking rings at the C-terminal region that remain undigested. Homicorcin exerts bactericidal activity against susceptible cells by disrupting the integrity of the cytoplasmic membrane through pore formation as observed under FE-SEM.
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Affiliation(s)
- M Aftab Uddin
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shammi Akter
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Mahbuba Ferdous
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
- Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashuliya, Savar, Dhaka, 1349, Bangladesh
| | - Badrul Haidar
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
- Divisional DNA Screening Laboratory, Sylhet MAG Osmani Medical College Hospital, Sylhet, 3100, Bangladesh
| | - Al Amin
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A H M Shofiul Islam Molla
- Institute of National Analytical Research and Service, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Haseena Khan
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Mohammad Riazul Islam
- Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh.
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Toyoncin, a Novel Leaderless Bacteriocin That Is Produced by Bacillus toyonensis XIN-YC13 and Specifically Targets B. cereus and Listeria monocytogenes. Appl Environ Microbiol 2021; 87:e0018521. [PMID: 33811023 PMCID: PMC8174769 DOI: 10.1128/aem.00185-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteriocins have attracted increasing interest because of their potential as natural preservatives. Recent studies showed that the Bacillus cereus group is a prominent producer of bacteriocins. Using a laboratory-based screening strategy, we identified a strain in the B. cereus group, Bacillus toyonensis XIN-YC13, with antimicrobial activity against B. cereus. A novel, 70-amino-acid-long leaderless bacteriocin, toyoncin, was purified from the culture supernatant of strain XIN-YC13, and its molecular mass was found to be 7,817.1012 Da. Toyoncin shares no similarity with any other known bacteriocins, and its N-terminal amino acid is formylmethionine rather than methionine. Toyoncin shows good pH and heat stability and exhibits specific antimicrobial activity against two important foodborne pathogens, B. cereus and Listeria monocytogenes. Additionally, toyoncin exerts bactericidal activity and induces cell membrane damage. Toyoncin can also inhibit the outgrowth of B. cereus spores. Preservation assays showed that toyoncin effectively suppressed or eradicated B. cereus and L. monocytogenes in pasteurized skim milk. These results suggest that toyoncin can be used as a new biopreservative against B. cereus and L. monocytogenes in the food industry. IMPORTANCE We identified a novel leaderless bacteriocin, toyoncin, produced by B. toyonensis XIN-YC13. Toyoncin shows good pH and heat stability, and it has specific antimicrobial activity against B. cereus and L. monocytogenes (two important foodborne pathogens), likely by destroying their cell membrane integrity. Toyoncin inhibited the outgrowth of B. cereus spores and effectively inhibited or eliminated B. cereus and L. monocytogenes in a milk model system. These results indicate the potential of toyoncin as a food preservative.
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32
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Identification and characterization of a novel circular bacteriocin, bacicyclicin XIN-1, from Bacillus sp. Xin1. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107696] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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33
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Genome-Driven Discovery of Enzymes with Industrial Implications from the Genus Aneurinibacillus. Microorganisms 2021; 9:microorganisms9030499. [PMID: 33652876 PMCID: PMC7996765 DOI: 10.3390/microorganisms9030499] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 01/27/2023] Open
Abstract
Bacteria belonging to the genus Aneurinibacillus within the family Paenibacillaceae are Gram-positive, endospore-forming, and rod-shaped bacteria inhabiting diverse environments. Currently, there are eight validly described species of Aneurinibacillus; however, several unclassified species have also been reported. Aneurinibacillus spp. have shown the potential for producing secondary metabolites (SMs) and demonstrated diverse types of enzyme activities. These features make them promising candidates with industrial implications. At present, genomes of 9 unique species from the genus Aneurinibacillus are available, which can be utilized to decipher invaluable information on their biosynthetic potential as well as enzyme activities. In this work, we performed the comparative genome analyses of nine Aneurinibacillus species representing the first such comprehensive study of this genus at the genome level. We focused on discovering the biosynthetic, biodegradation, and heavy metal resistance potential of this under-investigated genus. The results indicate that the genomes of Aneurinibacillus contain SM-producing regions with diverse bioactivities, including antimicrobial and antiviral activities. Several carbohydrate-active enzymes (CAZymes) and genes involved in heavy metal resistance were also identified. Additionally, a broad range of enzyme classes were also identified in the Aneurinibacillus pan-genomes, making this group of bacteria potential candidates for future investigations with industrial applications.
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Karbalaei-Heidari HR, Budisa N. Combating Antimicrobial Resistance With New-To-Nature Lanthipeptides Created by Genetic Code Expansion. Front Microbiol 2020; 11:590522. [PMID: 33250877 PMCID: PMC7674664 DOI: 10.3389/fmicb.2020.590522] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/13/2020] [Indexed: 01/10/2023] Open
Abstract
Due to the rapid emergence of multi-resistant bacterial strains in recent decades, the commercially available effective antibiotics are becoming increasingly limited. On the other hand, widespread antimicrobial peptides (AMPs) such as the lantibiotic nisin has been used worldwide for more than 40 years without the appearance of significant bacterial resistance. Lantibiotics are ribosomally synthesized antimicrobials generated by posttranslational modifications. Their biotechnological production is of particular interest to redesign natural scaffolds improving their pharmaceutical properties, which has great potential for therapeutic use in human medicine and other areas. However, conventional protein engineering methods are limited to 20 canonical amino acids prescribed by the genetic code. Therefore, the expansion of the genetic code as the most advanced approach in Synthetic Biology allows the addition of new amino acid building blocks (non-canonical amino acids, ncAAs) during protein translation. We now have solid proof-of-principle evidence that bioexpression with these novel building blocks enabled lantibiotics with chemical properties transcending those produced by natural evolution. The unique scaffolds with novel structural and functional properties are the result of this bioengineering. Here we will critically examine and evaluate the use of the expanded genetic code and its alternatives in lantibiotics research over the last 7 years. We anticipate that Synthetic Biology, using engineered lantibiotics and even more complex scaffolds will be a promising tool to address an urgent problem of antibiotic resistance, especially in a class of multi-drug resistant microbes known as superbugs.
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Affiliation(s)
- Hamid Reza Karbalaei-Heidari
- Department of Biology, Faculty of Sciences, Shiraz University, Shiraz, Iran
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- Institute of Chemistry, Technical University of Berlin, Berlin, Germany
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In Silico Analysis Highlights the Diversity and Novelty of Circular Bacteriocins in Sequenced Microbial Genomes. mSystems 2020; 5:5/3/e00047-20. [PMID: 32487738 PMCID: PMC8534725 DOI: 10.1128/msystems.00047-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Consumer demand for “fresh food” with no chemical preservatives has prompted researchers to pay more attention to natural antimicrobial peptides such as bacteriocins. Nisin is currently the most widely used food biopreservative among the bacteriocins; however, its applications are restricted due to its low stability at neutral and alkaline pH values. Circular bacteriocins have potent antimicrobial activity against foodborne pathogens, show exceptional stability, and have great potential to be developed as biopreservatives. Here, we take advantage of the precursor peptides of 15 reported circular bacteriocins to devise an in silico approach to identify potential circular bacteriocins in sequenced microbial genomes. A total of nearly 7,000 putative precursor peptides were identified from 86 species of bacteria and further classified into 28 groups based on their amino acid similarity. Among the groups, 19 showed low similarity (less than 50%) to any known precursor peptide of circular bacteriocins. One novel circular bacteriocin in group 11, cerecyclin, showed the highest identity (34%) to the known circular bacteriocin enterocin NKR-5-3B and was selected for verification. Cerecyclin showed antimicrobial activity against several Gram-positive bacteria, inhibited the outgrowth of Bacillus cereus spores, and did not exhibit hemolysis activity. Moreover, it showed 4-fold- to 8-fold-higher antimicrobial activity against B. cereus and Listeria monocytogenes than nisin A. Cerecyclin also had increased stability compared to nisin A under neutral or alkaline conditions. This work not only identified a promising food biopreservative but also provided a rich source for novel circular bacteriocins. IMPORTANCE Circular bacteriocins are promising biopreservatives, and it is important to identify more novel circular bacteriocins to enhance the current arsenal of antimicrobials. In this study, we used an in silico approach to identify a large number of novel circular bacteriocins and classified these bacteriocins into 28 groups rather than the 2 groups that were described in previous studies. Nineteen groups were novel and had low similarity (less than 50%) to any known precursor peptides of circular bacteriocins; this finding greatly expands the awareness of the novelty and diversity of circular bacteriocins. A novel circular bacteriocin which we named cerecyclin was identified in the B. cereus group; this circular bacteriocin had great antimicrobial activity against some foodborne pathogens and showed extreme stability. This study not only identified a promising food biopreservative but also provided a rich source for the identification of novel circular bacteriocins and the development of new biopreservatives.
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Lajis AFB. Biomanufacturing process for the production of bacteriocins from Bacillaceae family. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-0295-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
AbstractMembers of Bacillaceae family are of major interest in medical industry due to vast antimicrobial peptides they produce as therapeutic agents. For decades, synthetic and natural occurring antibiotics have been used to treat infectious diseases, but heavy dependence on these drugs has led to significant drawbacks which propel continuous development of new antibiotics generation. Recent findings have shown several bacteriocins of Bacillaceae as promising alternatives to the conventional drugs to combat the emergence of new drug-resistant pathogens. In this present review, Bacillaceae bacteriocins’ classification such as lantibiotics and thiazole/oxazole-modified microcins as well as their biochemical characterization such as sensitivity to enzymes, temperature, pH and chemicals are described. This article enlightens on the medical application of several Bacillaceae bacteriocins emphasizing those that underwent and on-going preclinical trials. This review also discusses the development of Bacillaceae bacteriocins production, focusing strains selection and fermentation factors such as inocula size, medium (carbon, nitrogen, minerals sources), temperature, pH, agitation and aeration rate, dissolved oxygen tension (DOT), fermentation time, inducers and mode of operation via various statistical methods for their optimization. It also highlights recent advance in the production of bioengineered and recombinant bacteriocins in bioreactors system which are rarely disclosed in literature.
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Huo L, Zhao X, Acedo JZ, Estrada P, Nair SK, van der Donk WA. Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae. Chembiochem 2020; 21:190-199. [PMID: 31532570 PMCID: PMC6980331 DOI: 10.1002/cbic.201900483] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 12/15/2022]
Abstract
As a result of the exponential increase in genomic data, discovery of novel ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has progressed rapidly in the past decade. The lanthipeptides are a major subset of RiPPs. Through genome mining we identified a novel lanthipeptide biosynthetic gene cluster (lah) from Lachnospiraceae bacterium C6A11, an anaerobic bacterium that is a member of the human microbiota and which is implicated in the development of host disease states such as type 2 diabetes and resistance to Clostridium difficile colonization. The lah cluster encodes at least seven putative precursor peptides and multiple post-translational modification (PTM) enzymes. Two unusual class II lanthipeptide synthetases LahM1/M2 and a substrate-tolerant S-adenosyl-l-methionine (SAM)-dependent methyltransferase LahSB are biochemically characterized in this study. We also present the crystal structure of LahSB in complex with product S-adenosylhomocysteine. This study sets the stage for further exploration of the final products of the lah pathway as well as their potential physiological functions in human/animal gut microbiota.
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Affiliation(s)
- Liujie Huo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- State Key Laboratory for Microbial Technology (SKLMT), Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao, 266237, P. R. China
| | - Xiling Zhao
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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38
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Wang G. The antimicrobial peptide database provides a platform for decoding the design principles of naturally occurring antimicrobial peptides. Protein Sci 2020; 29:8-18. [PMID: 31361941 PMCID: PMC6933855 DOI: 10.1002/pro.3702] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
This article is written for the 2020 tool issue of Protein Science. It briefly introduces the widely used antimicrobial peptide database, initially online in 2003. After a description of the main features of each database version and some recent additions, the focus is on the peptide design parameters for each of the four unified classes of natural antimicrobial peptides (AMPs). The amino acid signature in AMPs varies substantially, leading to a variety of structures for functional and mechanistic diversity. Also, Nature is a master of combinatorial chemistry by deploying different amino acids onto the same structural scaffold to tune peptide functions. In addition, the single-domain AMPs may be posttranslationally modified, self-assembled, or combined with other AMPs for function. Elucidation of the design principles of natural AMPs will facilitate future development of novel molecules for various applications.
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Affiliation(s)
- Guangshun Wang
- Department of Pathology and Microbiology, College of MedicineUniversity of Nebraska Medical CenterOmahaNebraska
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39
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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40
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Vaičikauskaitė M, Ger M, Valius M, Maneikis A, Lastauskienė E, Kalėdienė L, Kaunietis A. Geobacillin 26 - high molecular weight bacteriocin from a thermophilic bacterium. Int J Biol Macromol 2019; 141:333-344. [DOI: 10.1016/j.ijbiomac.2019.09.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/12/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023]
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41
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Singh M, Chaudhary S, Sareen D. Roseocin, a novel two‐component lantibiotic from an actinomycete. Mol Microbiol 2019; 113:326-337. [DOI: 10.1111/mmi.14419] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Mangal Singh
- Department of Biochemistry Basic Medical Sciences Block‐II Panjab University Chandigarh India
| | - Sandeep Chaudhary
- Department of Biochemistry Basic Medical Sciences Block‐II Panjab University Chandigarh India
| | - Dipti Sareen
- Department of Biochemistry Basic Medical Sciences Block‐II Panjab University Chandigarh India
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42
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Baindara P, Nallabelli N, Korpole S. Whole genome mining reveals a diverse repertoire of lanthionine synthetases and lanthipeptides among the genus
Paenibacillus. J Appl Microbiol 2019; 128:473-490. [DOI: 10.1111/jam.14495] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022]
Affiliation(s)
- P Baindara
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
| | - N Nallabelli
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
| | - S Korpole
- CSIR‐Institute of Microbial Technology Microbial Type Culture Collection and Gene Bank Chandigarh India
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43
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Van Staden ADP, Faure LM, Vermeulen RR, Dicks LMT, Smith C. Functional Expression of GFP-Fused Class I Lanthipeptides in Escherichia coli. ACS Synth Biol 2019; 8:2220-2227. [PMID: 31553571 DOI: 10.1021/acssynbio.9b00167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides, with several having antimicrobial activity. The biosynthetic machinery responsible for modification of the class I lanthipeptide nisin provides a means for modification of a diverse range of lanthipeptides. However, literature regarding expression of class I lanthipeptides in a malleable Gram-negative host such as Escherichia coli is limited. Here, we coexpressed precursor class I lanthipeptides fused to green fluorescent protein (GFP) along with the dehydratase and cyclase from the nisin operon. Fusion to GFP did not interfere with post-translational modifications as antimicrobially active nisin could be proteolytically liberated from the expressed GFP fusion. Additionally, we used this system to express two other class I lanthipeptides precursors fused to GFP (Pep5 and epilancin 15X), although only Pep5 exhibited consistent antimicrobial activity. This is the first report of a GFP-based fusion expression system for the expression of class I lanthipeptides in E. coli. The GFP-based fusion expression system is a robust system with the advantage of directly visualizing expression and purification through GFP fluorescence.
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Affiliation(s)
- Anton Du Preez Van Staden
- Department of Physiological Sciences, Stellenbosch University, Matieland 7602, South Africa
- Department of Microbiology, Stellenbosch University, Matieland 7602, South Africa
| | - Lindsay M. Faure
- Department of Microbiology, Stellenbosch University, Matieland 7602, South Africa
| | - Ross R. Vermeulen
- Department of Microbiology, Stellenbosch University, Matieland 7602, South Africa
| | - Leon M. T. Dicks
- Department of Microbiology, Stellenbosch University, Matieland 7602, South Africa
| | - Carine Smith
- Department of Physiological Sciences, Stellenbosch University, Matieland 7602, South Africa
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44
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Lin JH, Zhang KC, Tao WY, Wang D, Li S. Geobacillus strains that have potential value in microbial enhanced oil recovery. Appl Microbiol Biotechnol 2019; 103:8339-8350. [PMID: 31501940 DOI: 10.1007/s00253-019-10115-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 12/31/2022]
Abstract
Bacteria from the genus Geobacillus are generally obligately thermophilic, with a unique bioenergy production capacity and unique enzymes. Geobacillus species were isolated primarily from hot springs, oilfields, and associated soils. They often exhibit unique survival patterns in these extreme oligotrophic environments. With the development of the microbial resources found in oilfields, Geobacillus spp. have been proven as valuable bacteria in many reports related to oilfields. After the isolation of Geobacillus by culture methods, more evidence was found that they possess the abilities of hydrocarbon utilization and bioemulsifier production. This paper mainly summarizes some characteristics of the Geobacillus species found in the oilfield environment, focusing on the inference and analysis of hydrocarbon degradation and bioemulsifier synthesis based on existing research, which may reveal their potential value in microbial enhanced oil recovery. It also provides references for understanding microbes in extreme environments.
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Affiliation(s)
- Jia-Hui Lin
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Kun-Cheng Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Wei-Yi Tao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Dan Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China
| | - Shuang Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu Road, Nanjing, 211800, China.
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45
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Kaunietis A, Buivydas A, Čitavičius DJ, Kuipers OP. Heterologous biosynthesis and characterization of a glycocin from a thermophilic bacterium. Nat Commun 2019; 10:1115. [PMID: 30846700 PMCID: PMC6405829 DOI: 10.1038/s41467-019-09065-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 02/18/2019] [Indexed: 11/18/2022] Open
Abstract
The genome of the thermophilic bacterium, Aeribacillus pallidus 8, encodes the bacteriocin pallidocin. It belongs to the small class of glycocins and is posttranslationally modified, containing an S-linked glucose on a specific Cys residue. In this study, the pallidocin biosynthetic machinery is cloned and expressed in Escherichia coli to achieve its full biosynthesis and modification. It targets other thermophilic bacteria with potent activity, demonstrated by a low minimum inhibitory concentration (MIC) value. Moreover, the characterized biosynthetic machinery is employed to produce two other glycopeptides Hyp1 and Hyp2. Pallidocin and Hyp1 exhibit antibacterial activity against closely related thermophilic bacteria and some Bacillus sp. strains. Thus, heterologous expression of a glycocin biosynthetic gene cluster including an S-glycosyltransferase provides a good tool for production of hypothetical glycocins encoded by various bacterial genomes and allows rapid in vivo screening. Heterologous production of the glycocins, posttranslationally modified peptide bacteriocins containing a sugar moiety, has not been achieved. Here, the authors express a thermophilic bacterium glycocin biosynthetic gene cluster and S-glycosyltransferase for the production of antibacterial glycocins in E. coli.
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Affiliation(s)
- Arnoldas Kaunietis
- Molecular Genetics Dept., Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands.,Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223, Vilnius, Lithuania
| | - Andrius Buivydas
- Molecular Genetics Dept., Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands
| | - Donaldas J Čitavičius
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223, Vilnius, Lithuania
| | - Oscar P Kuipers
- Molecular Genetics Dept., Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, Netherlands.
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46
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Lagedroste M, Reiners J, Smits SHJ, Schmitt L. Systematic characterization of position one variants within the lantibiotic nisin. Sci Rep 2019; 9:935. [PMID: 30700815 PMCID: PMC6353901 DOI: 10.1038/s41598-018-37532-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 11/09/2022] Open
Abstract
Lantibiotics are a growing class of natural compounds, which possess antimicrobial activity against a broad range of Gram-positive bacteria. Their high potency against human pathogenic strains such as MRSA and VRE makes them excellent candidates as substitutes for classic antibiotics in times of increasing multidrug resistance of bacterial strains. New lantibiotics are detected in genomes and can be heterologously expressed. The functionality of these novel lantibiotics requires a systematic purification and characterization to benchmark them against for example the well-known lantibiotic nisin. Here, we used a standardized workflow to characterize lantibiotics consisting of six individual steps. The expression and secretion of the lantibiotic was performed employing the promiscuous nisin modification machinery. We mutated the first amino acid of nisin into all proteinaceous amino acids and compared their bactericidal potency against sensitive strains as well as strains expressing nisin resistance proteins. Interestingly, we can highlight four distinct groups based on the residual activity of nisin against sensitive as well as resistant L. lactis strains.
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Affiliation(s)
- Marcel Lagedroste
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
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47
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Tang W, Bobeica SC, Wang L, van der Donk WA. CylA is a sequence-specific protease involved in toxin biosynthesis. J Ind Microbiol Biotechnol 2018; 46:537-549. [PMID: 30484123 DOI: 10.1007/s10295-018-2110-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/13/2018] [Indexed: 12/27/2022]
Abstract
CylA is a subtilisin-like protein belonging to a recently expanded serine protease family related to class II lanthipeptide biosynthesis. As a leader peptidase, CylA is responsible for maturation of the enterococcal cytolysin, a lantibiotic important for Enterococcus faecalis virulence. In vitro reconstitution of CylA reveals that it accepts both linear and modified cytolysin peptides with a preference for cyclized peptides. Further characterization indicates that CylA activates itself by removing its N-terminal 95 amino acids. CylA achieves sequence-specific traceless cleavage of non-cognate peptides even if they are post-translationally modified, which makes the peptidase a powerful tool for mining novel lanthipeptides by providing a general strategy for leader peptide removal. Knowledge about the substrate specificity of CylA may also facilitate the development of protease inhibitors targeting cytolysin biosynthesis as a potential therapeutic approach for enterococcal infections.
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Affiliation(s)
- Weixin Tang
- Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL, 61801, USA
| | - Silvia C Bobeica
- Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL, 61801, USA
| | - Li Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Wilfred A van der Donk
- Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL, 61801, USA.
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48
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Egan K, Field D, Ross RP, Cotter PD, Hill C. In silico Prediction and Exploration of Potential Bacteriocin Gene Clusters Within the Bacterial Genus Geobacillus. Front Microbiol 2018; 9:2116. [PMID: 30298056 PMCID: PMC6160750 DOI: 10.3389/fmicb.2018.02116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022] Open
Abstract
The thermophilic, endospore-forming genus of Geobacillus has historically been associated with spoilage of canned food. However, in recent years it has become the subject of much attention due its biotechnological potential in areas such as enzyme and biofuel applications. One aspect of this genus that has not been fully explored or realized is its use as a source of novel forms of the ribosomally synthesized antimicrobial peptides known as bacteriocins. To date only two bacteriocins have been fully characterized within this genus, i.e., Geobacillin I and II, with only a small number of others partially characterized. Here we bioinformatically investigate the potential of this genus as a source of novel bacteriocins through the use of the in silico screening software BAGEL3, which scans publically available genomes for potential bacteriocin gene clusters. In this study we examined the association of bacteriocin gene presence with niche and phylogenetic position within the genus. We also identified a number of candidates from multiple bacteriocin classes which may be promising antimicrobial candidates when investigated in vitro in future studies.
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Affiliation(s)
- Kevin Egan
- School of Microbiology, University College, Cork, Ireland
| | - Des Field
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Institute, Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
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Alkhalili RN, Canbäck B. Identification of Putative Novel Class-I Lanthipeptides in Firmicutes: A Combinatorial In Silico Analysis Approach Performed on Genome Sequenced Bacteria and a Close Inspection of Z-Geobacillin Lanthipeptide Biosynthesis Gene Cluster of the Thermophilic Geobacillus sp. Strain ZGt-1. Int J Mol Sci 2018; 19:E2650. [PMID: 30200662 PMCID: PMC6165006 DOI: 10.3390/ijms19092650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Accepted: 09/04/2018] [Indexed: 01/03/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified polycyclic peptides. Lanthipeptides that have antimicrobial activity are known as lantibiotics. Accordingly, the discovery of novel lantibiotics constitutes a possible solution for the problem of antibiotic resistance. We utilized the publicly available genome sequences and the bioinformatic tools tailored for the detection of lanthipeptides. We designed our strategy for screening of 252 firmicute genomes and detecting class-I lanthipeptide-coding gene clusters. The designed strategy resulted in identifying 69 class-I lanthipeptide sequences, of which more than 10% were putative novel. The identified putative novel lanthipeptides have not been annotated on the original or the RefSeq genomes, or have been annotated merely as coding for hypothetical proteins. Additionally, we identified bacterial strains that have not been previously recognized as lanthipeptide-producers. Moreover, we suggest corrections for certain firmicute genome annotations, and recommend lanthipeptide records for enriching the bacteriocin genome mining tool (BAGEL) databases. Furthermore, we propose Z-geobacillin, a putative class-I lanthipeptide coded on the genome of the thermophilic strain Geobacillus sp. ZGt-1. We provide lists of putative novel lanthipeptide sequences and of the previously unrecognized lanthipeptide-producing bacterial strains, so they can be prioritized for experimental investigation. Our results are expected to benefit researchers interested in the in vitro production of lanthipeptides.
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Affiliation(s)
- Rawana N Alkhalili
- Biotechnology, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden.
| | - Björn Canbäck
- Department of Biology, Lund University, SE-221 00 Lund, Sweden.
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Xu B, Aitken EJ, Baker BP, Turner CA, Harvey JE, Stott MB, Power JF, Harris PWR, Keyzers RA, Brimble MA. Genome mining, isolation, chemical synthesis and biological evaluation of a novel lanthipeptide, tikitericin, from the extremophilic microorganism Thermogemmatispora strain T81. Chem Sci 2018; 9:7311-7317. [PMID: 30294420 PMCID: PMC6167946 DOI: 10.1039/c8sc02170h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/19/2018] [Indexed: 01/31/2023] Open
Abstract
Tikitericin, a novel lanthipeptide was isolated and characterised together with its first total synthesis.
Genome mining of the New Zealand extremophilic microorganism Thermogemmatispora strain T81 indicated the presence of biosynthetic machinery to produce several different peptidic natural products. Solid-phase culture of T81 led to the isolation of tikitericin 1, a new lanthipeptide characterised by four (methyl)lanthionine bridges. The mass-guided isolation and structural elucidation of tikitericin 1 is described together with its total synthesis via Fmoc-solid-phase peptide synthesis (SPPS). The key non-canonical (methyl)lanthionine residues were synthesised in solution phase via an improved synthetic route and subsequently assembled to construct the peptide backbone using Fmoc-SPPS. N-Terminal truncated analogues of tikitericin (2–5) were also prepared in order to evaluate the contribution of each sequential ring of the polycyclic lanthipeptide to the antibacterial activity.
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Affiliation(s)
- Buzhe Xu
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117
| | - Emma J Aitken
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Benjamin P Baker
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Claire A Turner
- School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Joanne E Harvey
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Matthew B Stott
- School of Biological Sciences , University of Canterbury , Private Bag 4800 , Christchurch 8140 , New Zealand.,GNS Science , Private Bag 2000 , Taupō 3352 , New Zealand
| | - Jean F Power
- GNS Science , Private Bag 2000 , Taupō 3352 , New Zealand
| | - Paul W R Harris
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Biological Sciences , 23 Symonds Street , Auckland 1010 , New Zealand
| | - Robert A Keyzers
- Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Chemical & Physical Sciences , The Centre for Biodiscovery , Victoria University of Wellington , PO Box 600 , Wellington 6140 , New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences , 23 Symonds Street , Auckland 1010 , New Zealand . ; Tel: +64 9 9238259.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand . ; Tel: +64 4 4635117.,School of Biological Sciences , 23 Symonds Street , Auckland 1010 , New Zealand
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