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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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2
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Lee AR, Carter RS, Imani AS, Dommaraju SR, Hudson GA, Mitchell DA, Freeman MF. Discovery of Borosin Catalytic Strategies and Function through Bioinformatic Profiling. ACS Chem Biol 2024; 19:1116-1124. [PMID: 38695893 DOI: 10.1021/acschembio.4c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) containing backbone α-N-methylations. These modifications confer favorable pharmacokinetic properties including increased membrane permeability and resistance to proteolytic degradation. Previous studies have biochemically and bioinformatically explored several borosins, revealing (1) numerous domain architectures and (2) diverse core regions lacking conserved sequence elements. Due to these characteristics, large-scale computational identification of borosin biosynthetic genes remains challenging and often requires additional, time-intensive manual inspection. This work builds upon previous findings and updates the genome-mining tool RODEO to automatically evaluate borosin biosynthetic gene clusters (BGCs) and identify putative precursor peptides. Using the new RODEO module, we provide an updated analysis of borosin BGCs identified in the NCBI database. From our data set, we bioinformatically predict and experimentally characterize a new fused borosin domain architecture, in which the modified natural product core is encoded N-terminal to the methyltransferase domain. Additionally, we demonstrate that a borosin precursor peptide is a native substrate of shewasin A, a reported aspartyl peptidase with no previously identified substrates. Shewasin A requires post-translational modification of the leader peptide for proteolytic maturation, a feature not previously observed in RiPPs. Overall, this work provides a user-friendly and open-access tool for the analysis of borosin BGCs and we demonstrate its utility to uncover additional biosynthetic strategies within the borosin class of RiPPs.
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Affiliation(s)
- Aileen R Lee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota 55108, United States
| | - Riley S Carter
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aman S Imani
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota 55108, United States
| | - Shravan R Dommaraju
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Michael F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota-Twin Cities, St. Paul, Minnesota 55108, United States
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota 55108, United States
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3
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Rukthanapitak P, Saito K, Kobayashi R, Kaweewan I, Kodani S. Heterologous production of a new lanthipeptide boletupeptin using a cryptic biosynthetic gene cluster of the myxobacterium Melittangium boletus. J Biosci Bioeng 2024; 137:354-359. [PMID: 38458885 DOI: 10.1016/j.jbiosc.2024.02.001] [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: 11/30/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 03/10/2024]
Abstract
Myxobacteria have comparatively large genomes that contain many biosynthetic genes with the potential to produce secondary metabolites. Based on genome mining, we discovered a new biosynthetic gene cluster of class III lanthipeptide in the genome of the myxobacterium Melittangium boletus. The biosynthetic gene cluster contained a precursor peptide-coding gene bolA, and a class III lanthipeptide synthetase-coding gene bolKC. The expression vector containing bolA and bolKC was constructed using synthetic DNA with codon-optimized sequences based on the commercially available vector pET29b. Co-expression of the two genes in the host Escherichia coli BL21(DE3) yielded a new class III lanthipeptide named boletupeptin. The structure of boletupeptin was proposed to have one unit of labionin, as determined by mass spectrometry experiments after reductive cleavage. This is the first report of a class III lanthipeptide from a myxobacterial origin.
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Affiliation(s)
- Pratchaya Rukthanapitak
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ryo Kobayashi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Medicine, Chiang Mai University, Inthawarorot Rd., Sri Phum, Muang, Chiang Mai 50200, Thailand
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan.
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4
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Harris LA, Saad H, Shelton KE, Zhu L, Guo X, Mitchell DA. Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications. Biochemistry 2024; 63:865-879. [PMID: 38498885 DOI: 10.1021/acs.biochem.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides. To uncover new ancillary modifications in a targeted manner, a bioinformatic strategy was developed to discover lasso peptides with modifications to tryptophan. This effort identified numerous putative lasso peptide biosynthetic gene clusters with core regions of the precursor peptides enriched in tryptophan. Parsing of these tryptophan (Trp)-rich biosynthetic gene clusters uncovered several putative ancillary modifying enzymes, including halogenases and dimethylallyltransferases expected to act upon Trp. Characterization of two gene products yielded a lasso peptide with two 5-Cl-Trp modifications (chlorolassin) and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications (wygwalassin). Bioinformatic analysis of the requisite halogenase and dimethylallyltransferase revealed numerous other putative Trp-modified lasso peptides that remain uncharacterized. We anticipate that the Trp-centric strategy reported herein may be useful in discovering ancillary modifications for other RiPP classes and, more generally, guide the functional prediction of enzymes that act on specific amino acids.
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Affiliation(s)
- Lonnie A Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hamada Saad
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kyle E Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xiaorui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Hourigan D, Stefanovic E, Hill C, Ross RP. Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy. BMC Microbiol 2024; 24:103. [PMID: 38539119 PMCID: PMC10976773 DOI: 10.1186/s12866-024-03243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/28/2024] [Indexed: 04/19/2024] Open
Abstract
Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
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Affiliation(s)
- David Hourigan
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - Ewelina Stefanovic
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, Biosciences Institute, Biosciences Research Institute, College Rd, University College, Cork, Ireland.
- School of Microbiology, University College Cork, College Rd, University College, Cork, Ireland.
- Teagasc Food Research Centre, Moorepark, Moorepark West, Fermoy, Co. Cork, Ireland.
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6
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Zhang ZJ, Wu C, Moreira R, Dorantes D, Pappas T, Sundararajan A, Lin H, Pamer EG, van der Donk WA. Activity of Gut-Derived Nisin-like Lantibiotics against Human Gut Pathogens and Commensals. ACS Chem Biol 2024; 19:357-369. [PMID: 38293740 PMCID: PMC10877564 DOI: 10.1021/acschembio.3c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/12/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024]
Abstract
Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However, the impact of nisin and nisin-like class I lantibiotics on commensal bacteria residing in the human gut remains unclear. Here, we report six gut-derived class I lantibiotics that are close homologues of nisin, four of which are novel. We applied an improved lantibiotic expression platform to produce and purify these lantibiotics for antimicrobial assays. We determined their minimal inhibitory concentration (MIC) against both Gram-positive human pathogens and gut commensals and profiled the lantibiotic resistance genes in these pathogens and commensals. Structure-activity relationship (SAR) studies with analogs revealed key regions and residues that impact their antimicrobial properties. Our characterization and SAR studies of nisin-like lantibiotics against both pathogens and human gut commensals could shed light on the future development of lantibiotic-based therapeutics and food preservatives.
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Affiliation(s)
- Zhenrun J. Zhang
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
- Department
of Microbiology, University of Chicago, Chicago, Illinois 60637, United States
| | - Chunyu Wu
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Ryan Moreira
- Department
of Chemistry, The Howard Hughes Medical
Institute, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Darian Dorantes
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Téa Pappas
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Anitha Sundararajan
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Huaiying Lin
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Eric G. Pamer
- Duchossois
Family Institute, University of Chicago, Chicago, Illinois 60637, United States
- Departments
of Medicine and Pathology, University of
Chicago, Chicago, Illinois 60637, United States
| | - Wilfred A. van der Donk
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, The Howard Hughes Medical
Institute, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
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7
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Li H, Ding W, Zhang Q. Discovery and engineering of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. RSC Chem Biol 2024; 5:90-108. [PMID: 38333193 PMCID: PMC10849128 DOI: 10.1039/d3cb00172e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/17/2023] [Indexed: 02/10/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a diverse superfamily of natural products with immense potential for drug development. This review provides a concise overview of the recent advances in the discovery of RiPP natural products, focusing on rational strategies such as bioactivity guided screening, enzyme or precursor-based genome mining, and biosynthetic engineering. The challenges associated with activating silent biosynthetic gene clusters and the development of elaborate catalytic systems are also discussed. The logical frameworks emerging from these research studies offer valuable insights into RiPP biosynthesis and engineering, paving the way for broader pharmaceutic applications of these peptide natural products.
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Affiliation(s)
- He Li
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
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8
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Luo Y, Xu S, Frerk AM, van der Donk WA. Facile Method for Determining Lanthipeptide Stereochemistry. Anal Chem 2024; 96:1767-1773. [PMID: 38232355 PMCID: PMC10831782 DOI: 10.1021/acs.analchem.3c04958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/22/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Lanthipeptides make up a large group of natural products that belong to the ribosomally synthesized and post-translationally modified peptides (RiPPs). Lanthipeptides contain lanthionine and methyllanthionine bis-amino acids that have varying stereochemistry. The stereochemistry of new lanthipeptides is often not determined because current methods require equipment that is not standard in most laboratories. In this study, we developed a facile, efficient, and user-friendly method for detecting lanthipeptide stereochemistry, utilizing advanced Marfey's analysis with detection by liquid chromatography coupled with mass spectrometry (LC-MS). Under optimized conditions, 0.05 mg of peptide is sufficient to characterize the stereochemistry of five (methyl)lanthionines of different stereochemistry using a simple liquid chromatography setup, which is a much lower detection limit than current methods. In addition, we describe methods to readily access standards of the three different methyllanthionine stereoisomers and two different lanthionine stereoisomers that have been reported in known lanthipeptides. The developed workflow uses a commonly used nonchiral column system and offers a scalable platform to assist antimicrobial discovery. We illustrate its utility with an example of a lanthipeptide discovered by genome mining.
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Affiliation(s)
- Youran Luo
- Department
of Chemistry, University of Illinois at
Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Shuyun Xu
- Department
of Chemistry, University of Illinois at
Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Autumn M. Frerk
- Department
of Chemistry, University of Illinois at
Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana–Champaign, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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9
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Arias-Orozco P, Zhou L, Yi Y, Cebrián R, Kuipers OP. Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains. Microbiol Spectr 2024; 12:e0361123. [PMID: 38088546 PMCID: PMC10783134 DOI: 10.1128/spectrum.03611-23] [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: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Genome mining studies have revealed the remarkable combinatorial diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs) in marine bacteria, including prochlorosins. However, mining strategies also prove valuable in investigating the genomic landscape of associated genes within biosynthetic gene cluster (BGC) specific to targeted RiPPs of interest. Our study contributes to the enrichment of knowledge regarding prochlorosin diversity. It offers insights into potential mechanisms involved in their biosynthesis and modification, such as hyper-modification, which may give rise to active lantibiotics. Additionally, our study uncovers putative novel promiscuous post-translational enzymes, thereby expanding the chemical space explored within the Synechococcus genus. Moreover, this research extends the applications of mining techniques beyond the discovery of new RiPP-like clusters, allowing for a deeper understanding of genomics and diversity. Furthermore, it holds the potential to reveal previously unknown functions within the intriguing RiPP families, particularly in the case of prochlorosins.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Yunhai Yi
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
- Department of Clinical Microbiology, Instituto de Investigación Biosanitaria ibs.GRANADA, San Cecilio University Hospital, Granada, Spain
- CIBER de Enfermedades Infecciosas, CIBERINFEC, ISCIII, Madrid, Spain
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh, Groningen, The Netherlands
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10
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Lee AR, Carter RS, Imani AS, Dommaraju SR, Hudson GA, Mitchell DA, Freeman MF. Computationally guided exploration of borosin biosynthetic strategies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574750. [PMID: 38260703 PMCID: PMC10802470 DOI: 10.1101/2024.01.09.574750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides containing backbone α- N -methylations. Identification of borosin precursor peptides is difficult because (1) there are no conserved sequence elements among borosin precursor peptides and (2) the biosynthetic gene clusters contain numerous domain architectures and peptide fusions. To tackle this problem, we updated the genome mining tool RODEO to automatically evaluate putative borosin BGCs and identify precursor peptides. Enabled by the new borosin module, we analyzed all borosin BGCs found in available sequence data and assigned precursor peptides to previously orphan borosin methyltransferases. Additionally, we bioinformatically predict and experimentally characterize a new fused borosin domain architecture, in which the modified core is N-terminal to the methyltransferase domain. Finally, we demonstrate that a borosin precursor peptide is the native substrate of shewasin A, a previously characterized pepsin-like aspartic peptidase whose native biological function was unknown.
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11
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Haft DH, Badretdin A, Coulouris G, DiCuccio M, Durkin A, Jovenitti E, Li W, Mersha M, O’Neill K, Virothaisakun J, Thibaud-Nissen F. RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes. Nucleic Acids Res 2024; 52:D762-D769. [PMID: 37962425 PMCID: PMC10767926 DOI: 10.1093/nar/gkad988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million proteins with up-to-date and consistent annotation. In the past 3 years, we have expanded the diversity of the RefSeq collection by including the best quality metagenome-assembled genomes (MAGs) submitted to INSDC (DDBJ, ENA and GenBank), while maintaining its quality by adding validation checks. Assemblies are now more stringently evaluated for contamination and for completeness of annotation prior to acceptance into RefSeq. MAGs now account for over 17000 assemblies in RefSeq, split over 165 orders and 362 families. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP), which is used to annotate nearly all RefSeq assemblies include better detection of protein-coding genes. Nearly 83% of RefSeq proteins are now named by a curated Protein Family Model, a 4.7% increase in the past three years ago. In addition to literature citations, Enzyme Commission numbers, and gene symbols, Gene Ontology terms are now assigned to 48% of RefSeq proteins, allowing for easier multi-genome comparison. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/. PGAP is available as a stand-alone tool able to produce GenBank-ready files at https://github.com/ncbi/pgap.
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Affiliation(s)
- Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Azat Badretdin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - George Coulouris
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael DiCuccio
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - A Scott Durkin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eric Jovenitti
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Wenjun Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Megdelawit Mersha
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kathleen R O’Neill
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Joel Virothaisakun
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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12
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Mongia M, Yasaka TM, Liu Y, Guler M, Lu L, Bhagwat A, Behsaz B, Wang M, Dorrestein PC, Mohimani H. Fast mass spectrometry search and clustering of untargeted metabolomics data. Nat Biotechnol 2024:10.1038/s41587-023-01985-4. [PMID: 38168990 DOI: 10.1038/s41587-023-01985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/12/2023] [Indexed: 01/05/2024]
Abstract
The throughput of mass spectrometers and the amount of publicly available metabolomics data are growing rapidly, but analysis tools such as molecular networking and Mass Spectrometry Search Tool do not scale to searching and clustering billions of mass spectral data in metabolomics repositories. To address this limitation, we designed MASST+ and Networking+, which can process datasets that are up to three orders of magnitude larger than those processed by state-of-the-art tools.
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Affiliation(s)
- Mihir Mongia
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tyler M Yasaka
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yudong Liu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Mustafa Guler
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Liang Lu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Aditya Bhagwat
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bahar Behsaz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Chemia Biosciences Inc., Pittsburgh, PA, USA
| | - Mingxun Wang
- Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Department of Pharmacology and Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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13
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Lee H, Park SH, Kim J, Lee J, Koh MS, Lee JH, Kim S. Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305946. [PMID: 37987032 PMCID: PMC10787088 DOI: 10.1002/advs.202305946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiyoon Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehak Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min Sun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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14
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Wolden R, Ovchinnikov KV, Venter HJ, Oftedal TF, Diep DB, Cavanagh JP. The novel bacteriocin romsacin from Staphylococcus haemolyticus inhibits Gram-positive WHO priority pathogens. Microbiol Spectr 2023; 11:e0086923. [PMID: 37905822 PMCID: PMC10715183 DOI: 10.1128/spectrum.00869-23] [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: 03/03/2023] [Accepted: 09/24/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE Bacteria produce bacteriocins to inhibit growth of other bacterial species. We have studied the antimicrobial activity of a new bacteriocin produced by the skin bacterium S. haemolyticus. The bacteriocin is effective against several types of Gram-positive bacteria, including highly virulent and antibiotic-resistant strains such as Staphylococcus aureus and Enterococcus faecium. Effective antimicrobials are important for the treatment of infections and the success of major surgery and chemotherapy. Bacteriocins can be part of the solution to the global concern of antimicrobial resistance.
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Affiliation(s)
- Runa Wolden
- Department of Clinical Medicine, Faculty of Health Sciences, Research Group for Child and Adolescent Health, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Hermoine J. Venter
- Department of Clinical Medicine, Faculty of Health Sciences, Research Group for Child and Adolescent Health, UiT The Arctic University of Norway, Tromsø, Norway
| | - Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jorunn Pauline Cavanagh
- Department of Clinical Medicine, Faculty of Health Sciences, Research Group for Child and Adolescent Health, UiT The Arctic University of Norway, Tromsø, Norway
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15
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Ramírez-Rendón D, Guzmán-Chávez F, García-Ausencio C, Rodríguez-Sanoja R, Sánchez S. The untapped potential of actinobacterial lanthipeptides as therapeutic agents. Mol Biol Rep 2023; 50:10605-10616. [PMID: 37934370 PMCID: PMC10676316 DOI: 10.1007/s11033-023-08880-w] [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: 08/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
The increase in bacterial resistance generated by the indiscriminate use of antibiotics in medical practice set new challenges for discovering bioactive natural products as alternatives for therapeutics. Lanthipeptides are an attractive natural product group that has been only partially explored and shows engaging biological activities. These molecules are small peptides with potential application as therapeutic agents. Some members show antibiotic activity against problematic drug-resistant pathogens and against a wide variety of viruses. Nevertheless, their biological activities are not restricted to antimicrobials, as their contribution to the treatment of cystic fibrosis, cancer, pain symptoms, control of inflammation, and blood pressure has been demonstrated. The study of biosynthetic gene clusters through genome mining has contributed to accelerating the discovery, enlargement, and diversification of this group of natural products. In this review, we provide insight into the recent advances in the development and research of actinobacterial lanthipeptides that hold great potential as therapeutics.
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Affiliation(s)
- Dulce Ramírez-Rendón
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Fernando Guzmán-Chávez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Carlos García-Ausencio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico City, México.
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16
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King AM, Zhang Z, Glassey E, Siuti P, Clardy J, Voigt CA. Systematic mining of the human microbiome identifies antimicrobial peptides with diverse activity spectra. Nat Microbiol 2023; 8:2420-2434. [PMID: 37973865 DOI: 10.1038/s41564-023-01524-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Human-associated bacteria secrete modified peptides to control host physiology and remodel the microbiota species composition. Here we scanned 2,229 Human Microbiome Project genomes of species colonizing skin, gastrointestinal tract, urogenital tract, mouth and trachea for gene clusters encoding RiPPs (ribosomally synthesized and post-translationally modified peptides). We found 218 lanthipeptides and 25 lasso peptides, 70 of which were synthesized and expressed in E. coli and 23 could be purified and functionally characterized. They were tested for activity against bacteria associated with healthy human flora and pathogens. New antibiotics were identified against strains implicated in skin, nasal and vaginal dysbiosis as well as from oral strains selectively targeting those in the gut. Extended- and narrow-spectrum antibiotics were found against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococci. Mining natural products produced by human-associated microbes will enable the elucidation of ecological relationships and may be a rich resource for antimicrobial discovery.
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Affiliation(s)
- Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhengan Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emerson Glassey
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Piro Siuti
- Synthetic Biology Group, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Pei ZF, Zhu L, Nair SK. Core-dependent post-translational modifications guide the biosynthesis of a new class of hypermodified peptides. Nat Commun 2023; 14:7734. [PMID: 38007494 PMCID: PMC10676384 DOI: 10.1038/s41467-023-43604-5] [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: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPPs) class of natural products has undergone significant expansion due to the rapid growth in genome sequencing data. Using a bioinformatics approach, we identify the dehydrazoles, a novel class of hypermodified RiPPs that contain both side chain dehydration of Ser residues, and backbone heterocyclization at Ser, Thr, and Cys residues to the corresponding azol(in)es. Structure elucidation of the hypermodified peptide carnazolamide, a representative class member, shows that 18 post-translational modifications are installed by just five enzymes. Complete biosynthetic reconstitution demonstrates that dehydration is carried out by an unusual DUF4135 dehydration domain fused to a zinc-independent cyclase domain (CcaM). We demonstrate that CcaM only modifies Ser residues that precede an azole in the core peptide. As heterocyclization removes the carbonyl following the Ser residue, CcaM likely catalyzes dehydration without generating an enolate intermediate. Additionally, CcaM does not require the leader peptide, and this core-dependence effectively sets the order for the biosynthetic reactions. Biophysical studies demonstrate direct binding of azoles to CcaM consistent with this azole moiety-dependent dehydration. Bioinformatic analysis reveals more than 50 related biosynthetic gene clusters that contain additional catalysts that may produce structurally diverse scaffolds.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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18
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Vater J, Tam LTT, Jähne J, Herfort S, Blumenscheit C, Schneider A, Luong PT, Thao LTP, Blom J, Klee SR, Schweder T, Lasch P, Borriss R. Plant-Associated Representatives of the Bacillus cereus Group Are a Rich Source of Antimicrobial Compounds. Microorganisms 2023; 11:2677. [PMID: 38004689 PMCID: PMC10672896 DOI: 10.3390/microorganisms11112677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Seventeen bacterial strains able to suppress plant pathogens have been isolated from healthy Vietnamese crop plants and taxonomically assigned as members of the Bacillus cereus group. In order to prove their potential as biocontrol agents, we perform a comprehensive analysis that included the whole-genome sequencing of selected strains and the mining for genes and gene clusters involved in the synthesis of endo- and exotoxins and secondary metabolites, such as antimicrobial peptides (AMPs). Kurstakin, thumolycin, and other AMPs were detected and characterized by different mass spectrometric methods, such as MALDI-TOF-MS and LIFT-MALDI-TOF/TOF fragment analysis. Based on their whole-genome sequences, the plant-associated isolates were assigned to the following species and subspecies: B. cereus subsp. cereus (6), B. cereus subsp. bombysepticus (5), Bacillus tropicus (2), and Bacillus pacificus. These three isolates represent novel genomospecies. Genes encoding entomopathogenic crystal and vegetative proteins were detected in B. cereus subsp. bombysepticus TK1. The in vitro assays revealed that many plant-associated isolates enhanced plant growth and suppressed plant pathogens. Our findings indicate that the plant-associated representatives of the B. cereus group are a rich source of putative antimicrobial compounds with potential in sustainable agriculture. However, the presence of virulence genes might restrict their application as biologicals in agriculture.
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Affiliation(s)
- Joachim Vater
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Le Thi Thanh Tam
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Jennifer Jähne
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Stefanie Herfort
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Christian Blumenscheit
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Andy Schneider
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Pham Thi Luong
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Le Thi Phuong Thao
- Division of Pathology and Phyto-Immunology, Plant Protection Research Institute (PPRI), Duc Thang, Bac Tu Liem, Hanoi, Vietnam; (L.T.T.T.); (P.T.L.); (L.T.P.T.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig Universität Giessen, 35392 Giessen, Germany;
| | - Silke R. Klee
- Highly Pathogenic Microorganisms Unit (ZBS2), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany;
| | - Thomas Schweder
- Institute of Marine Biotechnology e.V. (IMaB), 17489 Greifswald, Germany;
- Pharmaceutical Biotechnology, University of Greifswald, 17489 Greifswald, Germany
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6), Center for Biological Threats and Special Pathogens, Robert Koch Institute, 13353 Berlin, Germany; (J.V.); (J.J.); (S.H.); (C.B.); (A.S.); (P.L.)
| | - Rainer Borriss
- Institute of Marine Biotechnology e.V. (IMaB), 17489 Greifswald, Germany;
- Institute of Biology, Humboldt University Berlin, 10115 Berlin, Germany
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19
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Saleem M, Yahya S, Razzak SA, Khawaja S, Ali A. Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation. Arch Microbiol 2023; 205:359. [PMID: 37884755 DOI: 10.1007/s00203-023-03701-x] [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: 09/07/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023]
Abstract
Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria, 23.9% were Firmicutes, 13% were Actinobacteria, and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas. Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.
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Affiliation(s)
- Mahnoor Saleem
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto University of Science and Technology, Karachi, 75600, Sindh, Pakistan.
| | - Saira Yahya
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto University of Science and Technology, Karachi, 75600, Sindh, Pakistan.
| | - Safina Abdul Razzak
- Department of Bioscience, Muhammad Ali Jinnah University, Karachi, 75600, Pakistan
| | - Shariqa Khawaja
- International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Akhtar Ali
- School of Agriculture, Food and Ecosystem Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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20
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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [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: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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21
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Bunyat-Zada AR, Ross AC. Highlights of bioinformatic tools and methods for validating bioinformatics derived hypotheses for microbial natural products research. Curr Opin Chem Biol 2023; 76:102367. [PMID: 37453164 DOI: 10.1016/j.cbpa.2023.102367] [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: 12/20/2022] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Historically, bacterial natural products have served as an excellent source of drug leads, however, in recent decades the rate of discovery has slowed due to multiple challenges. Rapid advances in genome sequencing science in recent years have revealed the vast untapped encoded potential of bacteria to make natural products. To access these molecules, researchers can employ the ever-growing array of bioinformatic tools at their disposal and leverage newly developed experimental approaches to validate these bioinformatic-driven hypotheses. When used together effectively, bioinformatic and experimental tools enable researchers to deeply examine the full diversity of bacterial natural products. This review briefly outlines recent bioinformatic tools that can facilitate natural product research in bacteria including the use of CRISPR, co-occurrence network analysis, and combinatorial generation of microbial natural products to test bioinformatic hypotheses in the lab.
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Affiliation(s)
- Amir R Bunyat-Zada
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, ON, K7L 3N6, Canada.
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22
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Yuan Y, Shi C, Zhao H. Machine Learning-Enabled Genome Mining and Bioactivity Prediction of Natural Products. ACS Synth Biol 2023; 12:2650-2662. [PMID: 37607352 PMCID: PMC10615616 DOI: 10.1021/acssynbio.3c00234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Natural products (NPs) produced by microorganisms and plants are a major source of drugs, herbicides, and fungicides. Thanks to recent advances in DNA sequencing, bioinformatics, and genome mining tools, a vast amount of data on NP biosynthesis has been generated over the years, which has been increasingly exploited to develop machine learning (ML) tools for NP discovery. In this review, we discuss the latest advances in developing and applying ML tools for exploring the potential NPs that can be encoded by genomic language and predicting the types of bioactivities of NPs. We also examine the technical challenges associated with the development and application of ML tools for NP research.
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Affiliation(s)
- Yujie Yuan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chengyou Shi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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23
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Van Zyl WF, Van Staden AD, Dicks LMT, Trindade M. Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli. Microb Cell Fact 2023; 22:149. [PMID: 37559122 PMCID: PMC10413542 DOI: 10.1186/s12934-023-02162-7] [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: 03/24/2023] [Accepted: 07/29/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Lanthipeptides are a rapidly expanding family of ribosomally synthesized and post-translationally modified natural compounds with diverse biological functions. Lanthipeptide structural and biosynthetic genes can readily be identified in genomic datasets, which provides a substantial repository for unique peptides with a wide range of potentially novel bioactivities. To realize this potential efficiently optimized heterologous production systems are required. However, only a few class I lanthipeptides have been successfully expressed using Escherichia coli as heterologous producer. This may be attributed to difficulties experienced in the co-expression of structural genes and multiple processing genes as well as complex optimization experiments. RESULTS Here, an optimized modular plasmid system is presented for the complete biosynthesis for each of the class I lanthipeptides nisin and clausin, in E. coli. Genes encoding precursor lanthipeptides were fused to the gene encoding the mCherry red fluorescent protein and co-expressed along with the required synthetases from the respective operons. Antimicrobially active nisin and clausin were proteolytically liberated from the expressed mCherry fusions. The mCherry-NisA expression system combined with in vivo fluorescence monitoring was used to elucidate the effect of culture media composition, promoter arrangement, and culture conditions including choice of growth media and inducer agents on the heterologous expression of the class I lanthipeptides. To evaluate the promiscuity of the clausin biosynthetic enzymes, the optimized clausin expression system was used for the heterologous expression of epidermin. CONCLUSION We succeeded in developing novel mCherry-fusion based plug and play heterologous expression systems to produce two different subgroups of class I lanthipeptides. Fully modified Pre-NisA, Pre-ClausA and Pre-EpiA fused to the mCherry fluorescence gene was purified from the Gram-negative host E. coli BL21 (DE3). Our study demonstrates the potential of using in vivo fluorescence as a platform to evaluate the expression of mCherry-fused lanthipeptides in E. coli. This allowed a substantial reduction in optimization time, since expression could be monitored in real-time, without the need for extensive and laborious purification steps or the use of in vitro activity assays. The optimized heterologous expression systems developed in this study may be employed in future studies for the scalable expression of novel NisA derivatives, or novel genome mined derivatives of ClausA and other class I lanthipeptides in E. coli.
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Affiliation(s)
- Winschau F Van Zyl
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa.
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa.
| | - Anton D Van Staden
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
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24
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Thibodeaux CJ. The conformationally dynamic structural biology of lanthipeptide biosynthesis. Curr Opin Struct Biol 2023; 81:102644. [PMID: 37352604 DOI: 10.1016/j.sbi.2023.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/25/2023]
Abstract
Lanthipeptide synthetases are fascinating biosynthetic enzymes that install intramolecular thioether bridges into genetically encoded peptides, typically endowing the peptide with therapeutic properties. The factors that control the macrocyclic topology of lanthipeptides are numerous and remain difficult to predict and manipulate. The key challenge in this endeavor derives from the vast conformational space accessible to the disordered precursor lanthipeptide, which can be manipulated in subtle ways by interaction with the cognate synthetase. This review explores the unique strategies employed by each of the five phylogenetically divergent classes of lanthipeptide synthetase to manipulate and exploit the dynamic lanthipeptide conformational ensemble, collectively enabling these biosynthetic enzymes to guide peptide maturation along specific trajectories to products with distinct macrocyclic topology and biological activity.
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Affiliation(s)
- Christopher J Thibodeaux
- McGill University, Department of Chemistry, 801Sherbooke St. West, Montréal, Québec, H3A 0B8, Canada.
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25
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Lee YY, Guler M, Chigumba DN, Wang S, Mittal N, Miller C, Krummenacher B, Liu H, Cao L, Kannan A, Narayan K, Slocum ST, Roth BL, Gurevich A, Behsaz B, Kersten RD, Mohimani H. HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search. Nat Commun 2023; 14:4219. [PMID: 37452020 PMCID: PMC10349150 DOI: 10.1038/s41467-023-39905-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Recent analyses of public microbial genomes have found over a million biosynthetic gene clusters, the natural products of the majority of which remain unknown. Additionally, GNPS harbors billions of mass spectra of natural products without known structures and biosynthetic genes. We bridge the gap between large-scale genome mining and mass spectral datasets for natural product discovery by developing HypoRiPPAtlas, an Atlas of hypothetical natural product structures, which is ready-to-use for in silico database search of tandem mass spectra. HypoRiPPAtlas is constructed by mining genomes using seq2ripp, a machine-learning tool for the prediction of ribosomally synthesized and post-translationally modified peptides (RiPPs). In HypoRiPPAtlas, we identify RiPPs in microbes and plants. HypoRiPPAtlas could be extended to other natural product classes in the future by implementing corresponding biosynthetic logic. This study paves the way for large-scale explorations of biosynthetic pathways and chemical structures of microbial and plant RiPP classes.
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Affiliation(s)
- Yi-Yuan Lee
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Cornell University, Ithaca, NY, 14850, USA
| | - Mustafa Guler
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Shen Wang
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Neel Mittal
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | | | | | - Haodong Liu
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Liu Cao
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Aditya Kannan
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | | | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarbrücken, Germany
- Department of Computer Science, Saarland University, Saarbrücken, Germany
| | - Bahar Behsaz
- Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
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26
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Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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27
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Mi X, Desormeaux EK, Le TT, van der Donk WA, Shukla D. Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chem Sci 2023; 14:6904-6914. [PMID: 37389248 PMCID: PMC10306099 DOI: 10.1039/d2sc06546k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/08/2023] [Indexed: 07/01/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that are generated from precursor peptides through a dehydration and cyclization process. ProcM, a class II lanthipeptide synthetase, demonstrates high substrate tolerance. It is enigmatic that a single enzyme can catalyze the cyclization process of many substrates with high fidelity. Previous studies suggested that the site-selectivity of lanthionine formation is determined by substrate sequence rather than by the enzyme. However, exactly how substrate sequence contributes to site-selective lanthipeptide biosynthesis is not clear. In this study, we performed molecular dynamic simulations for ProcA3.3 variants to explore how the predicted solution structure of the substrate without enzyme correlates to the final product formation. Our simulation results support a model in which the secondary structure of the core peptide is important for the final product's ring pattern for the substrates investigated. We also demonstrate that the dehydration step in the biosynthesis pathway does not influence the site-selectivity of ring formation. In addition, we performed simulation for ProcA1.1 and 2.8, which are well-suited candidates to investigate the connection between order of ring formation and solution structure. Simulation results indicate that in both cases, C-terminal ring formation is more likely which was supported by experimental results. Our findings indicate that the substrate sequence and its solution structure can be used to predict the site-selectivity and order of ring formation, and that secondary structure is a crucial factor influencing the site-selectivity. Taken together, these findings will facilitate our understanding of the lanthipeptide biosynthetic mechanism and accelerate bioengineering efforts for lanthipeptide-derived products.
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Affiliation(s)
- Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily K Desormeaux
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Tung T Le
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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28
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Saito K, Mukai K, Kaweewan I, Nakagawa H, Hosaka T, Kodani S. Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense. J Microbiol 2023; 61:641-648. [PMID: 37306831 DOI: 10.1007/s12275-023-00059-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023]
Abstract
Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.
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Affiliation(s)
- Keita Saito
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Keiichiro Mukai
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO), Ibaraki, 305-8642, Japan
| | - Takeshi Hosaka
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, 399-4598, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, 399-4598, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
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29
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Wang X, Wang Z, Dong Z, Yan Y, Zhang Y, Huo L. Deciphering the Biosynthesis of Novel Class I Lanthipeptides from Marine Pseudoalteromonas Reveals a Dehydratase PsfB with Dethiolation Activity. ACS Chem Biol 2023; 18:1218-1227. [PMID: 37162177 DOI: 10.1021/acschembio.3c00135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Lanthipeptides are a representative class of RiPPs that possess characteristic lanthionine and/or methyllanthionine thioether cross-links. The biosynthetic potentials of marine-derived lanthipeptides remain largely unexplored. In this study, we characterized three novel lanthipeptides pseudorosin A-C by heterologous expression of a class I lanthipeptide biosynthetic gene cluster from marine Pseudoalteromonas flavipulchra S16. Interestingly, pseudorosin C contains a large loop spanning 18 amino acid residues, which is rare in lanthipeptides. Unexpectedly, the dehydratase PsfB could catalyze the dethiolation of specific Cys residues in all three core peptides, thereby generating dehydroalanines in the absence of LanC cyclase. To the best of our knowledge, we identified the first member of the LanB dehydratase family to perform glutamylation and subsequent elimination on Cys thiol groups, which likely represents a new bypass for class I lanthipeptide biosynthesis. Furthermore, we employed mutagenesis to determine the important motif of the core peptide for dethiolation activity. Moreover, sequence analysis revealed that PsfB exhibited a distinct phylogenetic distance from the characterized LanBs from Gram-positive bacteria. Our findings, therefore, pave the way for further genome mining of lanthipeptides, novel post-translational modification enzymes from marine Gram-negative bacteria, and bioengineering applications.
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Affiliation(s)
- Xiaotong Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Zongjie Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Zhiqi Dong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Yihai Yan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
| | - Liujie Huo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China
- Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao 266237, P. R. China
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30
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Liang H, Song ZM, Zhong Z, Zhang D, Yang W, Zhou L, Older EA, Li J, Wang H, Zeng Z, Li YX. Genomic and metabolic analyses reveal antagonistic lanthipeptides in archaea. MICROBIOME 2023; 11:74. [PMID: 37060102 PMCID: PMC10105419 DOI: 10.1186/s40168-023-01521-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/16/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Microbes produce diverse secondary metabolites (SMs) such as signaling molecules and antimicrobials that mediate microbe-microbe interaction. Archaea, the third domain of life, are a large and diverse group of microbes that not only exist in extreme environments but are abundantly distributed throughout nature. However, our understanding of archaeal SMs lags far behind our knowledge of those in bacteria and eukarya. RESULTS Guided by genomic and metabolic analysis of archaeal SMs, we discovered two new lanthipeptides with distinct ring topologies from a halophilic archaeon of class Haloarchaea. Of these two lanthipeptides, archalan α exhibited anti-archaeal activities against halophilic archaea, potentially mediating the archaeal antagonistic interactions in the halophilic niche. To our best knowledge, archalan α represents the first lantibiotic and the first anti-archaeal SM from the archaea domain. CONCLUSIONS Our study investigates the biosynthetic potential of lanthipeptides in archaea, linking lanthipeptides to antagonistic interaction via genomic and metabolic analyses and bioassay. The discovery of these archaeal lanthipeptides is expected to stimulate the experimental study of poorly characterized archaeal chemical biology and highlight the potential of archaea as a new source of bioactive SMs. Video Abstract.
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Affiliation(s)
- Haoyu Liang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou, 515031, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Dengwei Zhang
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Le Zhou
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. Nat Commun 2023; 14:1624. [PMID: 36959188 PMCID: PMC10036551 DOI: 10.1038/s41467-023-37287-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/09/2023] [Indexed: 03/25/2023] Open
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual (S)-N2,N2-dimethyl-1,2-propanediamine (Dmp)-modified C-terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C-terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C-terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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Affiliation(s)
- Hengqian Ren
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shravan R Dommaraju
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chunshuai Huang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yuwei Pan
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marko Nesic
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - David Sarlah
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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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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Xue D, Shang Z, Older EA, Zhong Z, Pulliam C, Peter K, Nagarkatti M, Nagarkatti P, Li YX, Li J. Refactoring and Heterologous Expression of Class III Lanthipeptide Biosynthetic Gene Clusters Lead to the Discovery of N, N-Dimethylated Lantibiotics from Firmicutes. ACS Chem Biol 2023; 18:508-517. [PMID: 36926816 PMCID: PMC10069475 DOI: 10.1021/acschembio.2c00849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Class III lanthipeptides are an emerging subclass of lanthipeptides, representing an underexplored trove of new natural products with potentially broad chemical diversity and important biological activity. Bioinformatic analysis of class III lanthipeptide biosynthetic gene cluster (BGC) distribution has revealed their high abundance in the phylum Firmicutes. Many of these clusters also feature methyltransferase (MT) genes, which likely encode uncommon class III lanthipeptides. However, two hurdles, silent BGCs and low-yielding pathways, have hindered the discovery of class III lanthipeptides from Firmicutes. Here, we report the design and construction of a biosynthetic pathway refactoring and heterologous overexpression strategy which seeks to overcome these hurdles, simultaneously activating and increasing the production of these Firmicutes class III lanthipeptides. Applying our strategy to MT-containing BGCs, we report the discovery of new class III lanthipeptides from Firmicutes bearing rare N,N-dimethylations. We reveal the importance of the first two amino acids in the N-terminus of the core peptide in controlling the MT dimethylation activity. Leveraging this feature, we engineer class III lanthipeptides to enable N,N-dimethylation, resulting in significantly increased antibacterial activity. Furthermore, the refactoring and heterologous overexpression strategy showcased in this study is potentially applicable to other ribosomally synthesized and post-translationally modified peptide BGCs from Firmicutes, unlocking the genetic potential of Firmicutes for producing peptide natural products.
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Affiliation(s)
- Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zhuo Shang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zheng Zhong
- Department of Chemistry and the Swire Institute of Marine Science, The University of Hong Kong, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 519000, China
| | - Conor Pulliam
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Kyle Peter
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Yong-Xin Li
- Department of Chemistry and the Swire Institute of Marine Science, The University of Hong Kong, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 519000, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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Ren H, Dommaraju SR, Huang C, Cui H, Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell DA, Zhao H. Genome mining unveils a class of ribosomal peptides with two amino termini. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531785. [PMID: 36945508 PMCID: PMC10028931 DOI: 10.1101/2023.03.08.531785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
The era of inexpensive genome sequencing and improved bioinformatics tools has reenergized the study of natural products, including the ribosomally synthesized and post-translationally modified peptides (RiPPs). In recent years, RiPP discovery has challenged preconceptions about the scope of post-translational modification chemistry, but genome mining of new RiPP classes remains an unsolved challenge. Here, we report a RiPP class defined by an unusual ( S )- N 2 , N 2 -dimethyl-1,2-propanediamine (Dmp)-modified C -terminus, which we term the daptides. Nearly 500 daptide biosynthetic gene clusters (BGCs) were identified by analyzing the RiPP Recognition Element (RRE), a common substrate-binding domain found in half of prokaryotic RiPP classes. A representative daptide BGC from Microbacterium paraoxydans DSM 15019 was selected for experimental characterization. Derived from a C -terminal threonine residue, the class-defining Dmp is installed over three steps by an oxidative decarboxylase, aminotransferase, and methyltransferase. Daptides uniquely harbor two positively charged termini, and thus we suspect this modification could aid in membrane targeting, as corroborated by hemolysis assays. Our studies further show that the oxidative decarboxylation step requires a functionally unannotated accessory protein. Fused to the C -terminus of the accessory protein is an RRE domain, which delivers the unmodified substrate peptide to the oxidative decarboxylase. This discovery of a class-defining post-translational modification in RiPPs may serve as a prototype for unveiling additional RiPP classes through genome mining.
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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: 4] [Impact Index Per Article: 4.0] [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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37
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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38
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Morio KA, Sternowski RH, Brogden KA. Induction of Endogenous Antimicrobial Peptides to Prevent or Treat Oral Infection and Inflammation. Antibiotics (Basel) 2023; 12:antibiotics12020361. [PMID: 36830272 PMCID: PMC9952314 DOI: 10.3390/antibiotics12020361] [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: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Antibiotics are often used to treat oral infections. Unfortunately, excessive antibiotic use can adversely alter oral microbiomes and promote the development of antibiotic-resistant microorganisms, which can be difficult to treat. An alternate approach could be to induce the local transcription and expression of endogenous oral antimicrobial peptides (AMPs). To assess the feasibility and benefits of this approach, we conducted literature searches to identify (i) the AMPs expressed in the oral cavity; (ii) the methods used to induce endogenous AMP expression; and (iii) the roles that expressed AMPs may have in regulating oral inflammation, immunity, healing, and pain. Search results identified human neutrophil peptides (HNP), human beta defensins (HBD), and cathelicidin AMP (CAMP) gene product LL-37 as prominent AMPs expressed by oral cells and tissues. HNP, HBD, and LL-37 expression can be induced by micronutrients (trace elements, elements, and vitamins), nutrients, macronutrients (mono-, di-, and polysaccharides, amino acids, pyropeptides, proteins, and fatty acids), proinflammatory agonists, thyroid hormones, and exposure to ultraviolet (UV) irradiation, red light, or near infrared radiation (NIR). Localized AMP expression can help reduce infection, inflammation, and pain and help oral tissues heal. The use of a specific inducer depends upon the overall objective. Inducing the expression of AMPs through beneficial foods would be suitable for long-term health protection. Additionally, the specialized metabolites or concentrated extracts that are utilized as dosage forms would maintain the oral and intestinal microbiome composition and control oral and intestinal infections. Inducing AMP expression using irradiation methodologies would be applicable to a specific oral treatment area in addition to controlling local infections while regulating inflammatory and healing processes.
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Affiliation(s)
| | | | - Kim A. Brogden
- College of Dentistry, The University of Iowa, Iowa City, IA 52242, USA
- Correspondence:
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39
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Dijamentiuk A, Mangavel C, Elfassy A, Michaux F, Burgain J, Rondags E, Delaunay S, Ferrigno S, Revol-Junelles AM, Borges F. Invert emulsions alleviate biotic interactions in bacterial mixed culture. Microb Cell Fact 2023; 22:16. [PMID: 36670385 PMCID: PMC9854087 DOI: 10.1186/s12934-022-02014-w] [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: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
The large application potential of microbiomes has led to a great need for mixed culture methods. However, microbial interactions can compromise the maintenance of biodiversity during cultivation in a reactor. In particular, competition among species can lead to a strong disequilibrium in favor of the fittest microorganism. In this study, an invert emulsion system was designed by dispersing culture medium in a mixture of sunflower oil and the surfactant PGPR. Confocal laser scanning microscopy revealed that this system allowed to segregate microorganisms in independent droplets. Granulomorphometric analysis showed that the invert emulsion remains stable during at least 24 h, and that the introduction of bacteria did not have a significant impact on the structure of the invert emulsion. A two-strain antagonistic model demonstrated that this invert emulsion system allows the propagation of two strains without the exclusion of the less-fit bacterium. The monitoring of single-strain cultures of bacteria representative of a cheese microbiota revealed that all but Brevibacterium linens were able to grow. A consortium consisting of Lactococcus lactis subsp. lactis biovar diacetylactis, Streptococcus thermophilus, Leuconostoc mesenteroides, Staphylococcus xylosus, Lactiplantibacillus plantarum and Carnobacterium maltaromaticum was successfully cultivated without detectable biotic interactions. Metabarcoding analysis revealed that the system allowed a better maintenance of alpha diversity and produced a propagated bacterial consortium characterized by a structure closer to the initial state compared to non-emulsified medium. This culture system could be an important tool in the field of microbial community engineering.
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Affiliation(s)
- Alexis Dijamentiuk
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Cécile Mangavel
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Annelore Elfassy
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Florentin Michaux
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Jennifer Burgain
- grid.29172.3f0000 0001 2194 6418LIBio, Université de Lorraine, Nancy, France
| | - Emmanuel Rondags
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Stéphane Delaunay
- grid.29172.3f0000 0001 2194 6418LRGP, Université de Lorraine, Nancy, France
| | - Sandie Ferrigno
- grid.29172.3f0000 0001 2194 6418IECL, Equipe BIGS, INRIA Nancy, Université de Lorraine, Nancy, France
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40
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He Y, Fan A, Han M, Li H, Li M, Fan H, An X, Song L, Zhu S, Tong Y. Mammalian Commensal Streptococci Utilize a Rare Family of Class VI Lanthipeptide Synthetases to Synthesize Miniature Lanthipeptide-type Ribosomal Peptide Natural Products. Biochemistry 2023; 62:462-475. [PMID: 36577516 DOI: 10.1021/acs.biochem.2c00534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are natural products with remarkable chemical and functional diversities. These peptides are often synthesized as signals or antibiotics and frequently associated with quorum sensing (QS) systems. With the increasing number of available genomes, many hitherto unseen RiPP biosynthetic pathways have been mined, providing new resources for novel bioactive compounds. Herein, we investigated the underexplored biosynthetic potential of Streptococci, prevalent bacteria in mammal-microbiomes that include pathogenic, mutualistic, and commensal members. Using the transcription factor-centric genome mining strategy, we discovered a new family of lanthipeptide biosynthetic loci under the control of potential QS. By in vitro studies, we investigated the reaction of one of these lanthipeptide synthetases and found that it installs only one lanthionine moiety onto its short precursor peptide by connecting a conserved TxxC region. Bioinformatics and in vitro studies revealed that these lanthipeptide synthetases (class VI) are novel lanthipeptide synthetases with a truncated lyase, a kinase, and a truncated cyclase domain. Our data provide important insights into the processing and evolution of lanthipeptide synthetase to tailor smaller substrates. The data are important for obtaining a mechanistic understanding of the post-translational biosynthesis machinery of the growing variety of lanthipeptides.
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Affiliation(s)
- Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People's Republic of China
| | - Meng Han
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Hongwei Li
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
| | - Shaozhou Zhu
- National Institutes for Food and Drug Control, Beijing 102629, People's Republic of China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China
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41
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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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42
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Shelton KE, Mitchell DA. Bioinformatic prediction and experimental validation of RiPP recognition elements. Methods Enzymol 2022; 679:191-233. [PMID: 36682862 PMCID: PMC9871372 DOI: 10.1016/bs.mie.2022.08.050] [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] [Indexed: 11/25/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products for which discovery efforts have rapidly grown over the past decade. There are currently 38 known RiPP classes encoded by prokaryotes. Half of the prokaryotic RiPP classes include a protein domain called the RiPP Recognition Element (RRE) for successful installation of post-translational modifications on a RiPP precursor peptide. In most cases, the RRE domain binds to the N-terminal "leader" region of the precursor peptide, facilitating enzymatic modification of the C-terminal "core" region. The prevalence of the RRE domain renders it a theoretically useful bioinformatic handle for class-independent RiPP discovery; however, first-in-class RiPPs have yet to be isolated and experimentally characterized using an RRE-centric strategy. Moreover, with most known RRE domains engaging their cognate precursor peptide(s) with high specificity and nanomolar affinity, evaluation of the residue-specific interactions that govern RRE:substrate complexation is a necessary first step to leveraging the RRE domain for various bioengineering applications. This chapter details protocols for developing custom bioinformatic models to predict and annotate RRE domains in a class-specific manner. Next, we outline methods for experimental validation of precursor peptide binding using fluorescence polarization binding assays and in vitro enzyme activity assays. We anticipate the methods herein will guide and enhance future critical analyses of the RRE domain, eventually enabling its future use as a customizable tool for molecular biology.
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Affiliation(s)
- Kyle E Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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43
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Chu L, Cheng J, Zhou C, Mo T, Ji X, Zhu T, Chen J, Ma S, Gao J, Zhang Q. Hijacking a Linaridin Biosynthetic Intermediate for Lanthipeptide Production. ACS Chem Biol 2022; 17:3198-3206. [PMID: 36288500 DOI: 10.1021/acschembio.2c00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Linaridins and lanthipeptides are two classes of natural products belonging to the ribosomally synthesized and posttranslationally modified peptide (RiPP) superfamily. Although these two RiPP classes share similar structural motifs such as dehydroamino acids and thioether-based cross-links, the biosynthesis of linaridins and lanthipeptides involved distinct sets of enzymes. Here, we report the identification of a novel lanthipeptide cypepeptin from a recombinant strain of Streptomyces lividans, which harbors most of the cypemycin (a prototypic linaridin) biosynthetic gene cluster but lacks the decarboxylase gene cypD. In contrast to the generally believed structure of cypemycin, multiple d-amino acids and Z-dehydrobutyrines were observed in both cypepeptin and cypemycin, and the stereochemistry of each amino acid was established by the extensive structural analysis in combination with genetic knockout and mutagenesis studies. Comparative analysis of cypemycin and cypepeptin showed that the aminovinyl-cysteine (AviCys) moiety of cypemycin plays an essential role in disrupting the cell integrity of M. luteus, which cannot be functionally substituted by the structurally similar lanthionine moiety.
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Affiliation(s)
- Leixia Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jinduo Cheng
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Chengzeng Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Taoting Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jie Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Suze Ma
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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44
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Zhang H, Yang MF, Zhang Q, Yan B, Jiang YL. Screening for broad-spectrum antimicrobial endophytes from Rosa roxburghii and multi-omic analyses of biosynthetic capacity. FRONTIERS IN PLANT SCIENCE 2022; 13:1060478. [PMID: 36466255 PMCID: PMC9709285 DOI: 10.3389/fpls.2022.1060478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Plants with certain medicinal values are a good source for isolating function-specific endophytes. Rosa roxburghii Tratt. has been reported to be a botanical source of antimicrobial compounds, which may represent a promising candidate for screening endophytic fungi with antimicrobial potential. In this study, 54 endophytes were isolated and molecularly identified from R. roxburghii. The preliminary screening using the plate confrontation method resulted in 15 different endophytic strains showing at least one strong inhibition or three or more moderate inhibition against the 12 tested strains. Further re-screening experiments based on the disc diffusion method demonstrated that Epicoccum latusicollum HGUP191049 and Setophoma terrestris HGUP190028 had excellent antagonistic activity. The minimum inhibitory concentration (MIC) test for extracellular metabolites finally indicated that HGUP191049 had lower MIC values and a broader antimicrobial spectrum, compared to HGUP190028. Genomic, non-target metabolomic, and comparative genomic studies were performed to understand the biosynthetic capacity of the screened-out endophytic fungus. Genome sequencing and annotation of HGUP191049 revealed a size of 33.24 megabase pairs (Mbp), with 24 biosynthetic gene clusters (BGCs), where the putative antimicrobial compounds, oxyjavanicin, patulin and squalestatin S1 were encoded by three different BGCs, respectively. In addition, the non-targeted metabolic results demonstrated that the strain contained approximately 120 antimicrobial secondary metabolites and was structurally diverse. Finally, comparative genomics revealed differences in pathogenicity, virulence, and carbohydrate-active enzymes in the genome of Epicoccum spp. Moreover, the results of the comparative analyses presumed that Epicoccum is a promising source of antimicrobial terpenes, while oxyjavanicin and squalestatin S1 are antimicrobial compounds shared by the genus. In conclusion, R. roxburghii and the endophytic HGUP191049 isolated from it are promising sources of broad-spectrum antimicrobial agents.
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Affiliation(s)
- Hong Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Academy of Testing and Analysis, Guiyang, China
| | - Mao-Fa Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Qian Zhang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Bin Yan
- Institute of Entomology, Guizhou University, Guiyang, China
| | - Yu-Lan Jiang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
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45
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Ayikpoe RS, Shi C, Battiste AJ, Eslami SM, Ramesh S, Simon MA, Bothwell IR, Lee H, Rice AJ, Ren H, Tian Q, Harris LA, Sarksian R, Zhu L, Frerk AM, Precord TW, van der Donk WA, Mitchell DA, Zhao H. A scalable platform to discover antimicrobials of ribosomal origin. Nat Commun 2022; 13:6135. [PMID: 36253467 PMCID: PMC9576775 DOI: 10.1038/s41467-022-33890-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 10/06/2022] [Indexed: 12/24/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a promising source of new antimicrobials in the face of rising antibiotic resistance. Here, we report a scalable platform that combines high-throughput bioinformatics with automated biosynthetic gene cluster refactoring for rapid evaluation of uncharacterized gene clusters. As a proof of concept, 96 RiPP gene clusters that originate from diverse bacterial phyla involving 383 biosynthetic genes are refactored in a high-throughput manner using a biological foundry with a success rate of 86%. Heterologous expression of all successfully refactored gene clusters in Escherichia coli enables the discovery of 30 compounds covering six RiPP classes: lanthipeptides, lasso peptides, graspetides, glycocins, linear azol(in)e-containing peptides, and thioamitides. A subset of the discovered lanthipeptides exhibit antibiotic activity, with one class II lanthipeptide showing low µM activity against Klebsiella pneumoniae, an ESKAPE pathogen. Overall, this work provides a robust platform for rapidly discovering RiPPs.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chengyou Shi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Alexander J Battiste
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Sara M Eslami
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Sangeetha Ramesh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Max A Simon
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Ian R Bothwell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Hyunji Lee
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Andrew J Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Hengqian Ren
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Qiqi Tian
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Lonnie A Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Raymond Sarksian
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Autumn M Frerk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Timothy W Precord
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, 20815, MD, USA.
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
| | - Huimin Zhao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA.
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Liang H, Lopez IJ, Sánchez-Hidalgo M, Genilloud O, van der Donk WA. Mechanistic Studies on Dehydration in Class V Lanthipeptides. ACS Chem Biol 2022; 17:2519-2527. [PMID: 36044589 PMCID: PMC9486802 DOI: 10.1021/acschembio.2c00458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptides characterized by lanthionine (Lan) and/or methyllanthionine (MeLan) residues. Four classes of enzymes have been identified to install these structures in a substrate peptide. Recently, a novel class of lanthipeptides was discovered that lack genes for known class I-IV lanthionine synthases in their biosynthetic gene cluster (BGC). In this study, the dehydration of Ser/Thr during the biosynthesis of the class V lanthipeptide cacaoidin was reconstituted in vitro. The aminoglycoside phosphotransferase-like enzyme CaoK iteratively phosphorylates Ser/Thr residues on the precursor peptide CaoA, followed by phosphate elimination catalyzed by the HopA1 effector-like protein CaoY to achieve eight successive dehydrations. CaoY shows sequence similarity to the OspF family proteins and the lyase domains of class III/IV lanthionine synthetases, and mutagenesis studies identified residues that are critical for catalysis. An AlphaFold prediction of the structure of the dehydration enzyme complex engaged with its substrate suggests the importance of hydrophobic interactions between the CaoA leader peptide and CaoK in enzyme-substrate recognition. This model is supported by site-directed mutagenesis studies.
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Affiliation(s)
- Haoqian Liang
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Isaiah J. Lopez
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States
| | - Marina Sánchez-Hidalgo
- Fundación
MEDINA Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico
de Ciencias de la Salud, Armilla, 18016 Granada, Spain
| | - Olga Genilloud
- Fundación
MEDINA Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico
de Ciencias de la Salud, Armilla, 18016 Granada, Spain
| | - Wilfred A. van der Donk
- Department
of Biochemistry, University of Illinois
at Urbana—Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States,Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana—Champaign, 600 S. Mathews Avenue, Urbana, Illinois 61801, United States,
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47
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Abstract
The three-dimensional structure of natural products is critical for their biological activities and, as such, enzymes have evolved that specifically generate active stereoisomers. Lanthipeptides are post-translationally modified peptidic natural products that contain macrocyclic thioethers featuring lanthionine (Lan) and/or methyllanthionine (MeLan) residues with defined stereochemistry. In this report, we compare two class I lanthipeptide biosynthetic gene clusters (BGCs), coi and olv, that represent two families of lanthipeptide gene clusters found in Actinobacteria. The precursor peptides and BGCs are quite similar with genes encoding a dehydratase, cyclase, and methyltransferase (MT). We illustrate that the precursor peptide CoiA1 is converted by these enzymes into a polymacrocyclic product, mCoiA1, that contains an analogous ring pattern to the previously characterized post-translationally modified OlvA peptide (mOlvA). However, a clear distinction between the two BGCs is an additional Thr-glutamyl lyase (GL) domain that is fused to the MT, CoiSA, which results in divergence of the product stereochemistry for the coi BGC. Two out of three MeLan rings of mCoiA1 contain different stereochemistry than the corresponding residues in mOlvA, with the most notable difference being a rare d-allo-l-MeLan residue, the formation of which is guided by CoiSA. This study illustrates how nature utilizes a distinct GL to control natural product stereochemistry in lanthipeptide biosynthesis.
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Affiliation(s)
- Raymond Sarksian
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States,Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States,. Tel: 217 244 5360
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48
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Pei ZF, Zhu L, Sarksian R, van der Donk WA, Nair SK. Class V Lanthipeptide Cyclase Directs the Biosynthesis of a Stapled Peptide Natural Product. J Am Chem Soc 2022; 144:17549-17557. [PMID: 36107785 PMCID: PMC9621591 DOI: 10.1021/jacs.2c06808] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lanthipeptides are a class of cyclic peptides characterized by the presence of one or more lanthionine (Lan) or methyllanthionine (MeLan) thioether rings. These cross-links are produced by α,β-unsaturation of Ser or Thr residues in peptide substrates by dehydration, followed by a Michael-type conjugate addition of Cys residues onto the dehydroamino acids. Lanthipeptides may be broadly classified into at least five different classes, and the biosynthesis of classes I-IV lanthipeptides requires catalysis by LanC cyclases that control both the site-specificity and the stereochemistry of the conjugate addition. In contrast, there are no current examples of LanCs that occur in class V biosynthetic clusters, despite the presence of lanthionine rings in these compounds. In this work, bioinformatics-guided co-occurrence analysis identifies more than 240 putative class V lanthipeptide clusters that contain a LanC cyclase. Reconstitution studies demonstrate that the cyclase-catalyzed product is notably distinct from the product formed spontaneously. Stereochemical analysis shows that the cyclase diverts the final product to a configuration that is distinct from one that is energetically favored. Structural characterization of the final product by multi-dimensional NMR spectroscopy reveals that it forms a helical stapled peptide. Mutational analysis identified a plausible order for cyclization and suggests that enzymatic rerouting to the final structure is largely directed by the construction of the first lanthionine ring. These studies show that lanthipeptide cyclases are needed for the biosynthesis of some constrained peptides, the formations of which would otherwise be energetically unfavored.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Raymond Sarksian
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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49
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Uggowitzer KA, Shao ARQ, Habibi Y, Zhang QE, Thibodeaux CJ. Exploring the Heterogeneous Structural Dynamics of Class II Lanthipeptide Synthetases with Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Biochemistry 2022; 61:2118-2130. [PMID: 36094889 DOI: 10.1021/acs.biochem.2c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Class II lanthipeptide synthetases (LanM enzymes) catalyze the installation of multiple thioether bridges into genetically encoded peptides to produce macrocyclic lanthipeptides, a class of biologically active natural products. Collectively, LanM enzymes install thioether rings of different sizes, topologies, and stereochemistry into a vast array of different LanA precursor peptide sequences. The factors that govern the outcome of the LanM-catalyzed reaction cascade are not fully characterized but are thought to involve both intermolecular interactions and intramolecular conformational changes in the [LanM:LanA] Michaelis complex. To test this hypothesis, we have combined AlphaFold modeling with hydrogen-deuterium exchange mass spectrometry (HDX-MS) analysis of a small collection of divergent LanM/LanA systems to investigate the similarities and differences in their conformational dynamic properties. Our data indicate that LanA precursor peptide binding triggers relatively conserved changes in the structural dynamics of the LanM dehydratase domain, supporting the existence of a similar leader peptide binding mode across the LanM family. In contrast, changes induced in the dynamics of the LanM cyclase domain were more highly variable between enzymes, perhaps reflecting different peptide-cyclase interactions and/or different modes of allosteric activation in class II lanthipeptide biosynthesis. Our analysis highlights the ability of the emerging AlphaFold platform to predict protein-peptide interactions that are supported by other lines of experimental evidence. The combination of AlphaFold modeling with HDX-MS analysis should emerge as a useful approach for investigating other conformationally dynamic enzymes involved in peptide natural product biosynthesis.
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Affiliation(s)
- Kevin A Uggowitzer
- Department of Chemistry, McGill University, 801 Sherbrooke St., Montreal, Quebec H3A0B8, Canada
| | - Annie R Q Shao
- Department of Chemistry, McGill University, 801 Sherbrooke St., Montreal, Quebec H3A0B8, Canada
| | - Yeganeh Habibi
- Department of Chemistry, McGill University, 801 Sherbrooke St., Montreal, Quebec H3A0B8, Canada
| | - Qianyi E Zhang
- Department of Chemistry, McGill University, 801 Sherbrooke St., Montreal, Quebec H3A0B8, Canada
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50
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Helfrich M, Entian KD, Stein T. Antibiotic profiling of wild-type bacilli led to the discovery of new lanthipeptide subtilin-producing Bacillus spizizenii strains whose 16S rDNA sequences differ from the B. spizizenii typing strain. INTERNATIONAL MICROBIOLOGY : THE OFFICIAL JOURNAL OF THE SPANISH SOCIETY FOR MICROBIOLOGY 2022; 25:839-850. [PMID: 35902452 PMCID: PMC9526687 DOI: 10.1007/s10123-022-00266-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/12/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022]
Abstract
Two dozen field-collected Bacillus and a dozen Bacillus spizizenii wild-type strains from strain collections were selected on the basis of their antagonistic properties against the Gram-positive strain Micrococcus luteus. Based on their genetic and antibiotic profiles, they were characterized (subtilin encoding spaS gene sequences, mass spectrometric, and quantitative-reversed phase liquid chromatographic analyses, as well as the presence of the lanthionine cyclase protein SpaC by western blotting), seven novel producers of the lanthipeptide subtilin. Phylogenetic analyses of the subtilin-producing wild-type strains based on their 16S rRNA sequences showed that all seven strains could be classified as B. spizizenii: The field-collected strains HS and N5, as well as strains DSM 618, 1087, 6395, 6405, and 8439 from the German Collection of Microorganisms and Cell Cultures. To the best of our knowledge, all B. spizizenii strains described so far are characterized by the fact that they can produce a lanthipeptide of the subtilin family. Both the lanthipeptide structures and the organization and sequences of the 16S rRNA-encoding genes suggest a subdivision of B. spizizenii into subspecies: The subtilin-producing B. spizizenii strains are distinctly different from the entianin-producing B. spizizenii typing strain TU-B-10 T (DSM 15029 T).
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Affiliation(s)
- Markus Helfrich
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, 53619, Rheinbreitbach, Germany
| | - Karl-Dieter Entian
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany
| | - Torsten Stein
- Life Sciences, Johann Wolfgang-Goethe-University, Max v. Laue Str. 9, 60439, Frankfurt/Main, Germany.
- Chemistry & Molecular Biotechnology, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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