1
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Li Y, Shao K, Li Z, Zhu K, Gan BK, Shi J, Xiao Y, Luo M. Mechanistic insights into lanthipeptide modification by a distinct subclass of LanKC enzyme that forms dimers. Nat Commun 2024; 15:7090. [PMID: 39154050 PMCID: PMC11330476 DOI: 10.1038/s41467-024-51600-6] [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: 12/05/2023] [Accepted: 08/13/2024] [Indexed: 08/19/2024] Open
Abstract
Naturally occurring lanthipeptides, peptides post-translationally modified by various enzymes, hold significant promise as antibiotics. Despite extensive biochemical and structural studies, the events preceding peptide modification remain poorly understood. Here, we identify a distinct subclass of lanthionine synthetase KC (LanKC) enzymes with distinct structural and functional characteristics. We show that PneKC, a member of this subclass, forms a dimer and possesses GTPase activity. Through three cryo-EM structures of PneKC, we illustrate different stages of peptide PneA binding, from initial recognition to full binding. Our structures show the kinase domain complexed with the PneA core peptide and GTPγS, a phosphate-bound lyase domain, and an unconventional cyclase domain. The leader peptide of PneA interact with a gate loop, transitioning from an extended to a helical conformation. We identify a dimerization hot spot and propose a "negative cooperativity" mechanism toggling the enzyme between tense and relaxed conformation. Additionally, we identify an important salt bridge in the cyclase domain, differing from those in in conventional cyclase domains. These residues are highly conserved in the LanKC subclass and are part of two signature motifs. These results unveil potential differences in lanthipeptide modification enzymes assembly and deepen our understanding of allostery in these multifunctional enzymes.
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Affiliation(s)
- Yifan Li
- Department of Biological sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Kai Shao
- Department of Biological sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Zhaoxing Li
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Kongfu Zhu
- Department of Biological sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Bee Koon Gan
- Department of Biological sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jian Shi
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yibei Xiao
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Min Luo
- Department of Biological sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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2
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Ren H, Huang C, Pan Y, Dommaraju SR, Cui H, Li M, Gadgil MG, Mitchell DA, Zhao H. Non-modular fatty acid synthases yield distinct N-terminal acylation in ribosomal peptides. Nat Chem 2024; 16:1320-1329. [PMID: 38528101 PMCID: PMC11321927 DOI: 10.1038/s41557-024-01491-3] [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: 05/24/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries. However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machinery from other natural product families. Here we report lipoavitides, a class of RiPP/fatty-acid hybrid lipopeptides that display a unique, putatively membrane-targeting 4-hydroxy-2,4-dimethylpentanoyl (HMP)-modified N terminus. The HMP is formed via condensation of isobutyryl-coenzyme A (isobutyryl-CoA) and methylmalonyl-CoA catalysed by a 3-ketoacyl-(acyl carrier protein) synthase III enzyme, followed by successive tailoring reactions in the fatty acid biosynthetic pathway. The HMP and RiPP substructures are then connected by an acyltransferase exhibiting promiscuous activity towards the fatty acyl and RiPP substrates. Overall, the discovery of lipoavitides contributes a prototype of RiPP/fatty-acid hybrids and provides possible enzymatic tools for lipopeptide bioengineering.
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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
| | - Chunshuai Huang
- 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
| | - 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
| | - Haiyang Cui
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Maolin Li
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mayuresh G Gadgil
- 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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3
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Pfeiffer IPM, Schröder MP, Mordhorst S. Opportunities and challenges of RiPP-based therapeutics. Nat Prod Rep 2024; 41:990-1019. [PMID: 38411278 DOI: 10.1039/d3np00057e] [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: 02/28/2024]
Abstract
Covering: up to 2024Ribosomally synthesised and post-translationally modified peptides (RiPPs) comprise a substantial group of peptide natural products exhibiting noteworthy bioactivities ranging from antiinfective to anticancer and analgesic effects. Furthermore, RiPP biosynthetic pathways represent promising production routes for complex peptide drugs, and the RiPP technology is well-suited for peptide engineering to produce derivatives with specific functions. Thus, RiPP natural products possess features that render them potentially ideal candidates for drug discovery and development. Nonetheless, only a small number of RiPP-derived compounds have successfully reached the market thus far. This review initially outlines the therapeutic opportunities that RiPP-based compounds can offer, whilst subsequently discussing the limitations that require resolution in order to fully exploit the potential of RiPPs towards the development of innovative drugs.
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Affiliation(s)
- Isabel P-M Pfeiffer
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Maria-Paula Schröder
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
| | - Silja Mordhorst
- University of Tübingen, Pharmaceutical Institute, Department of Pharmaceutical Biology, Auf der Morgenstelle 8, 72076 Tübingen, Germany.
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4
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Botteon A, Fulvio B, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 20: Suitability of taxonomic units notified to EFSA until March 2024. EFSA J 2024; 22:e8882. [PMID: 39040570 PMCID: PMC11261301 DOI: 10.2903/j.efsa.2024.8882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024] Open
Abstract
The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. The TUs in the QPS list were updated based on a verification, against their respective authoritative databases, of the correctness of the names and completeness of synonyms. A new procedure has been established to ensure the TUs are kept up to date in relation to recent taxonomical insights. Of 83 microorganisms notified to EFSA between October 2023 and March 2024 (47 as feed additives, 25 as food enzymes or additives, 11 as novel foods), 75 were not evaluated because: 15 were filamentous fungi, 1 was Enterococcus faecium, 10 were Escherichia coli, 1 was a Streptomyces (all excluded from the QPS evaluation) and 48 were TUs that already have a QPS status. Two of the other eight notifications were already evaluated for a possible QPS status in the previous Panel Statement: Heyndrickxia faecalis (previously Weizmannia faecalis) and Serratia marcescens. One was notified at genus level so could not be assessed for QPS status. The other five notifications belonging to five TUs were assessed for possible QPS status. Akkermansia muciniphila and Actinomadura roseirufa were still not recommended for QPS status due to safety concerns. Rhizobium radiobacter can be recommended for QPS status with the qualification for production purposes. Microbacterium arborescens and Burkholderia stagnalis cannot be included in the QPS list due to a lack of body of knowledge for its use in the food and feed chain and for B. stagnalis also due to safety concerns. A. roseirufa and B. stagnalis have been excluded from further QPS assessment.
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5
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Maheshwari N, Jermiin LS, Cotroneo C, Gordon SV, Shields DC. Insights into the production and evolution of lantibiotics from a computational analysis of peptides associated with the lanthipeptide cyclase domain. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240491. [PMID: 39021782 PMCID: PMC11251773 DOI: 10.1098/rsos.240491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/20/2024]
Abstract
Lanthipeptides are a large group of ribosomally encoded peptides cyclized by thioether and methylene bridges, which include the lantibiotics, lanthipeptides with antimicrobial activity. There are over 100 experimentally characterized lanthipeptides, with at least 25 distinct cyclization bridging patterns. We set out to understand the evolutionary dynamics and diversity of lanthipeptides. We identified 977 peptides in 2785 bacterial genomes from short open-reading frames encoding lanthipeptide modifiable amino acids (C, S and T) that lay chromosomally adjacent to genes encoding proteins containing the cyclase domain. These appeared to be synthesized by both known and novel enzymatic combinations. Our predictor of bridging topology suggested 36 novel-predicted topologies, including a single-cysteine topology seen in 179 lanthionine or labionin containing peptides, which were enriched for histidine. Evidence that supported the relevance of the single-cysteine containing lanthipeptide precursors included the presence of the labionin motif among single cysteine peptides that clustered with labionin-associated synthetase domains, and the leader features of experimentally defined lanthipeptides that were shared with single cysteine predictions. Evolutionary rate variation among peptide subfamilies suggests that selection pressures for functional change differ among subfamilies. Lanthipeptides that have recently evolved specific novel features may represent a richer source of potential novel antimicrobials, since their target species may have had less time to evolve resistance.
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Affiliation(s)
- Nikunj Maheshwari
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lars S. Jermiin
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Research School of Biology, Australian National University, Canberra, ACT, Australia
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
| | - Chiara Cotroneo
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Denis C. Shields
- School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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6
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Cheng Z, He BB, Lei K, Gao Y, Shi Y, Zhong Z, Liu H, Liu R, Zhang H, Wu S, Zhang W, Tang X, Li YX. Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates. Nat Commun 2024; 15:4901. [PMID: 38851779 PMCID: PMC11162475 DOI: 10.1038/s41467-024-49215-y] [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: 12/06/2023] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
Antimicrobial resistance remains a significant global threat, driving up mortality rates worldwide. Ribosomally synthesized and post-translationally modified peptides have emerged as a promising source of novel peptide antibiotics due to their diverse chemical structures. Here, we report the discovery of new aminovinyl-(methyl)cysteine (Avi(Me)Cys)-containing peptide antibiotics through a synergistic approach combining biosynthetic rule-based omics mining and heterologous expression. We first bioinformatically identify 1172 RiPP biosynthetic gene clusters (BGCs) responsible for Avi(Me)Cys-containing peptides formation from a vast pool of over 50,000 bacterial genomes. Subsequently, we successfully establish the connection between three identified BGCs and the biosynthesis of five peptide antibiotics via biosynthetic rule-guided metabolic analysis. Notably, we discover a class V lanthipeptide, massatide A, which displays excellent activity against gram-positive pathogens, including drug-resistant clinical isolates like linezolid-resistant S. aureus and methicillin-resistant S. aureus, with a minimum inhibitory concentration of 0.25 μg/mL. The remarkable performance of massatide A in an animal infection model, coupled with a relatively low risk of resistance and favorable safety profile, positions it as a promising candidate for antibiotic development. Our study highlights the potential of Avi(Me)Cys-containing peptides in expanding the arsenal of antibiotics against multi-drug-resistant bacteria, offering promising drug leads in the ongoing battle against infectious diseases.
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Affiliation(s)
- Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China
| | - Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kangfan Lei
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yuqi Shi
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Runze Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haili Zhang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenxuan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China.
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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7
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Cheng B, Xue Y, Duan Y, Liu W. Enzymatic Formation of an Aminovinyl Cysteine Residue in Ribosomal Peptide Natural Products. Chempluschem 2024; 89:e202400047. [PMID: 38517224 DOI: 10.1002/cplu.202400047] [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: 01/19/2024] [Revised: 02/25/2024] [Indexed: 03/23/2024]
Abstract
The carboxyl-terminal (C-terminal) S-[(Z)-2-aminovinyl]-cysteine (AviCys) analogs have been identified in four families of ribosomally synthesized and post-translationally modified peptides (RiPPs): lanthipeptides, linaridins, thioamitides, and lipolanthines. Within identified biosynthetic pathways, a highly reactive enethiol intermediate, formed through an oxidative decarboxylation catalyzed by a LanD-like flavoprotein, can undergo two types of cyclization: a Michael addition with a dehydroamino acid or a coupling reaction initiated by a radical species. The collaborative actions of LanD-like proteins with diverse enzymes involved in dehydration, dethiolation or cyclization lead to the construction of structurally distinct peptide natural products with analogous C-terminal macrocyclic moieties. This concept summarizes existing knowledge regarding biosynthetic pathways of AviCys analogs to emphasize the diversity of biosynthetic mechanisms that paves the way for future genome mining explorations into diverse peptide natural products.
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Affiliation(s)
- Botao Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yanqing Xue
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yuting Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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8
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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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9
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Yamaguchi A, Obiya N, Arichi N, Oishi S, Ohno H, Inuki S. Synthesis of labionin and avionin precursors via a nitrogen-centred-radical-triggered 1,5-HAT reaction of Tris derivatives. Org Biomol Chem 2024; 22:2049-2055. [PMID: 38362729 DOI: 10.1039/d3ob02037a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Labionin and avionin are non-proteinogenic amino acids containing 2,4-diamino-2-(mercaptomethyl)pentanedioic acid that forms the core structures of spirocyclic peptides including labyrinthopeptin A2 and microvionin, respectively. We have developed a diastereoselective synthetic route to labionin and avionin precursors. This route highlights the formation of the quaternary carbon stereocenter of an α,α-disubstituted amino acid via a regioselective 1,5-HAT reaction of a Tris derivative.
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Affiliation(s)
- Ayuta Yamaguchi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Naoki Obiya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Norihito Arichi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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10
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-guided discovery of biaryl-linked lasso peptides. Chem Sci 2023; 14:13176-13183. [PMID: 38023510 PMCID: PMC10664482 DOI: 10.1039/d3sc02380j] [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: 05/09/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Using mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectrometry, we report the structural characterization of two unique examples of (C-N) biaryl-linked lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with a Trp-Tyr crosslink, while longipepetin A, from Longimycelium tulufanense, features a Trp-Trp linkage. Besides the unusual bicyclic frame, a Met of longipepetin A undergoes S-methylation to yield a trivalent sulfonium, a heretofore unprecedented RiPP modification. A bioinformatic survey revealed additional lasso peptide BGCs containing P450 enzymes which await future characterization. Lastly, nocapeptin A bioactivity was assessed against a panel of human and bacterial cell lines with modest growth-suppression activity detected towards Micrococcus luteus.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Dinh T Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
| | - Douglas A Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
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11
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Ren H, Huang C, Pan Y, Cui H, Dommaraju SR, Mitchell DA, Zhao H. Non-modular Fatty Acid Synthases Yield Unique Acylation in Ribosomal Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564083. [PMID: 37961664 PMCID: PMC10634828 DOI: 10.1101/2023.10.25.564083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Recent efforts in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs) have expanded the diversity of post-translational modification chemistries 1, 2 . However, RiPPs are rarely reported as hybrid molecules incorporating biosynthetic machineries from other natural product families 3-8 . Here, we report lipoavitides, a class of RiPP/fatty acid hybrid lipopeptides that display a unique, membrane-targeting 4-hydroxy-2,4-dimethylpentanoyl (HMP)-modified N -terminus. The HMP is formed via condensation of isobutyryl-CoA and methylmalonyl-CoA catalyzed by a 3-ketoacyl-ACP synthase III enzyme, followed by successive tailoring reactions in the fatty acid biosynthetic pathway. The HMP and RiPP substructures are then connected by an acyltransferase exhibiting promiscuous activity towards the fatty acyl and RiPP substrates. Overall, the discovery of lipoavitides contributes a prototype of RiPP/fatty acid hybrids and provides possible enzymatic tools for lipopeptide bioengineering.
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12
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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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13
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Cheng B, Huang J, Duan Y, Liu W. Association of Radical Chemistry with LanD Flavoprotein Activity for C-Terminal Macrocyclization of a Ribosomal Peptide by Formation of an Unsaturated Thioether Residue. Angew Chem Int Ed Engl 2023; 62:e202308733. [PMID: 37431841 DOI: 10.1002/anie.202308733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/12/2023]
Abstract
LanD flavoproteins catalyze oxidative decarboxylation of the C-terminal Cys residue of a peptide to produce an enethiol. This enethiol is highly reactive and can be coupled with an upstream dehydroamino acid through Michael addition to form S-[2-aminovinyl](3-methyl)cysteine, an unsaturated thioether residue known to be characteristic of an array of C-terminally macrocyclized, ribosomally synthesized and posttranslationally modified peptides (RiPPs). Based on a two-stage bioinformatics mining of posttranslational modifications (PTMs) related to C-terminal Cys processing, we report herein that LanD activity can couple with radical S-adenosylmethionine chemistry to provide a new unsaturated thioether residue, S-[2-aminovinyl]-3-carbamoylcysteine, by conjugating the resultant enethiol with Cβ of the Asn residue in the C-terminal NxxC motif of a peptide for macrocyclization. This study furthers our understanding of the variety of PTMs involved in creating the structure diversity of macrocyclic RiPPs.
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Affiliation(s)
- Botao Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jiwu Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yuting Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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14
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Xia Y, Yi Y, Shi Y, Long T, Wang H. Enzymatic Generation of Thioaldehyde Motifs by Flavin-Dependent Cysteine Decarboxylases for Peptide Bioconjugation and Macrocyclization. Org Lett 2023; 25:6035-6039. [PMID: 37548910 DOI: 10.1021/acs.orglett.3c02184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Thioaldehyde is a highly electrophilic group under aqueous conditions and can be generated via oxidative enzymatic modifications of cysteine residues in peptides and proteins. Herein, we report the installation of thioaldehyde and aldehyde groups at the C-terminus of peptides by flavin-dependent cysteine decarboxylases from the biosynthesis of ribosomally synthesized and post-translationally modified peptides. The in situ generated (thio)aldehyde is utilized as a reactive handle for peptide bioconjugation and macrocyclization.
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Affiliation(s)
- Yinzheng Xia
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuchen Yi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tengfang Long
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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15
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Chang S, Luo Y, He N, Huang X, Chen M, Yuan L, Xie Y. Nocaviogua A and B: two lipolanthines from root-nodule-associated Nocardia sp. Front Chem 2023; 11:1233938. [PMID: 37601909 PMCID: PMC10435860 DOI: 10.3389/fchem.2023.1233938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Nocaviogua A (1) and B (2), two lipolanthines featuring a non-canonical avionin (Avi)-containing macrocycle and a long acyl chain, were identified from the mutualistic actinomycete Nocardia sp. XZ19_369, which was isolated from the nodules of sea buckthorn collected in Tibet. Their planar structures were elucidated via extensive analyses of 1D and 2D NMR, as well as HRMS data. The absolute configurations were fully elucidated by advanced Marfey's analysis and GIAO NMR calculations, representing the first time that the configurations of this family of lipolanthines have been determined. Nocaviogua A (1) exhibited weak cytotoxicity against human chronic uveal melanoma cells (UM92-1), non-small cell lung cancer (NCI-H2170), and breast cancer (MDA-MB-231). Our work provides valuable information on this burgeoning class of lipolanthines for further investigations.
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Affiliation(s)
- Shanshan Chang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yajun Luo
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Ning He
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyue Huang
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingxu Chen
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lijie Yuan
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yunying Xie
- CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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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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17
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Li Y, Ma Y, Xia Y, Zhang T, Sun S, Gao J, Yao H, Wang H. Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks. Nat Commun 2023; 14:2944. [PMID: 37221219 DOI: 10.1038/s41467-023-38517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Cyclic peptide natural products represent an important class of bioactive compounds and clinical drugs. Enzymatic side-chain macrocyclization of ribosomal peptides is a major strategy developed by nature to generate these chemotypes, as exemplified by the superfamily of ribosomally synthesized and post-translational modified peptides. Despite the diverse types of side-chain crosslinks in this superfamily, the participation of histidine residues is rare. Herein, we report the discovery and biosynthesis of bacteria-derived tricyclic lanthipeptide noursin, which is constrained by a tri amino acid labionin crosslink and an unprecedented histidine-to-butyrine crosslink, named histidinobutyrine. Noursin displays copper-binding ability that requires the histidinobutyrine crosslink and represents the first copper-binding lanthipeptide. A subgroup of lanthipeptide synthetases, named LanKCHbt, were identified to catalyze the formation of both the labionin and the histidinobutyrine crosslinks in precursor peptides and produce noursin-like compounds. The discovery of the histidinobutyrine-containing lanthipeptides expands the scope of post-translational modifications, structural diversity and bioactivity of ribosomally synthesized and post-translational modified peptides.
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Affiliation(s)
- Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yeying Ma
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Yinzheng Xia
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China
| | - Tao Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Shuaishuai Sun
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, 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.
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, China.
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18
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Ortiz-López FJ, Oves-Costales D, Carretero-Molina D, Martín J, Díaz C, de la Cruz M, Román-Hurtado F, Álvarez-Arévalo M, Jørgensen TS, Reyes F, Weber T, Genilloud O. Crossiellidines A-F, Unprecedented Pyrazine-Alkylguanidine Metabolites with Broad-Spectrum Antibacterial Activity from Crossiella sp. Org Lett 2023; 25:3502-3507. [PMID: 37162500 DOI: 10.1021/acs.orglett.3c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Crosiellidines are intriguing pyrazine-alkylguanidine metabolites isolated from the minor actinomycete genus Crossiella. Their structures present an unprecedented 2-methoxy-3,5,6-trialkyl pyrazine scaffold and uncommon guanidine prenylations, including an exotic O-prenylated N-hydroxyguanidine moiety. The novel substitution pattern of the 2-methoxypyrazine core inaugurates a new class of naturally occurring pyrazine compounds, the biosynthetic implications of which are discussed herein. Isotopic feeding and genome analysis allowed us to propose a biosynthetic pathway from arginine. The crossiellidines exhibited remarkable, broad-spectrum antibacterial activity.
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Affiliation(s)
- Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - María Álvarez-Arévalo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
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19
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Ijichi S, Hoshino S, Asamizu S, Onaka H. SolS-catalyzed sulfoxidation of labionin to solabionin drives antibacterial activity of solabiomycins. Bioorg Med Chem Lett 2023; 89:129323. [PMID: 37169227 DOI: 10.1016/j.bmcl.2023.129323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/13/2023]
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) with polar-functionalized fatty acyl groups are newly found lipopeptide-class natural products. We recently employed a combined approach of genome mining and stable isotope labeling and discovered solabiomycins as one of the polar-functionalized fatty-acylated RiPPs (PFARs) from Streptomyces lydicus NBRC13058. The solabiomycins contained a characteristic sulfoxide group in the labionin moiety referred to as the 'solabionin' structure for the RiPP moiety. A previous gene knockout experiment indicated that solS, which encodes a putative flavin adenine dinucleotide (FAD)-nicotinamide adenine dinucleotide (phosphate) (NAD(P))-binding protein, is involved in the sulfoxidation of an alkyl sulfide in the solabionin. In this study, we isolated deoxysolabiomycins A and B from ΔsolS mutant and fully determined the chemical structures using a series of NMR experiments. We also tested the bioactivity of deoxysolabiomycins against Gram-positive bacteria, including Mycolicibacterium smegmatis, and notably found that the sulfoxide is critical for the antibacterial activity. To characterize the catalytic activity of SolS, the recombinant protein was incubated with a putative substrate, deoxysolabiomycins, and the cofactors FAD and NADPH. In vitro reactions demonstrated that SolS catalyzes the sulfoxidation, converting deoxysolabiomycins to solabiomycins.
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Affiliation(s)
- Shinta Ijichi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan
| | - Shotaro Hoshino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo, 113-8657, Japan.
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20
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. NATURE REVIEWS. METHODS PRIMERS 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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21
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Zhao X, Zhu D, Tan J, Wang R, Qi G. Cooperative Action of Fulvic Acid and Bacillus paralicheniformis Ferment in Regulating Soil Microbiota and Improving Soil Fertility and Plant Resistance to Bacterial Wilt Disease. Microbiol Spectr 2023; 11:e0407922. [PMID: 36861975 PMCID: PMC10100657 DOI: 10.1128/spectrum.04079-22] [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: 10/06/2022] [Accepted: 01/28/2023] [Indexed: 03/03/2023] Open
Abstract
Excessive continuous cropping and soil degradation, such as acidification, hardening, fertility decline, and the degradation of microbial community, lead to the epidemic of soilborne diseases and cause great loss in agriculture production. Application of fulvic acid can improve the growth and yield of various crops and effectively suppress soilborne plant diseases. Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid is used to remove the organic acid that can cause soil acidification and increase the fertilizer effect of fulvic acid and the effect of improving soil quality and inhibiting soilborne disease. In field experiments, the application of fulvic acid and Bacillus paralicheniformis ferment effectively reduced the incidence of bacterial wilt disease and improved soil fertility. Both fulvic acid powder and B. paralicheniformis ferment improved soil microbial diversity and increased the complexity and stability of the microbial network. For B. paralicheniformis ferment, the molecular weight of poly-gamma-glutamic acid became smaller after heating, which could better improve the soil microbial community and network structure. In fulvic acid and B. paralicheniformis ferment-treated soils, the synergistic interaction between microorganisms increased and the number of keystone microorganisms increased, which included antagonistic bacteria and plant growth-promoting bacteria. Changes in the microbial community and network structure were the main reason for the reduced incidence of bacterial wilt disease. Application of fulvic acid and Bacillus paralicheniformis ferment improved soil physicochemical properties and effectively controlled bacterial wilt disease by changing microbial community and network structure and enriching antagonistic and beneficial bacteria. IMPORTANCE Continuous cropping tobacco has led to soil degradation and caused soilborne bacterial wilt disease. Fulvic acid as a biostimulator was applied to restore soil and control bacterial wilt disease. For improving its effect, fulvic acid was fermented with Bacillus paralicheniformis strain 285-3 producing poly-gamma-glutamic acid. Fulvic acid and B. paralicheniformis ferment inhibited bacterial wilt disease, improved soil quality, enriched beneficial bacteria, and increased microbial diversity and microbial network complexity. Some keystone microorganisms in fulvic acid and B. paralicheniformis ferment-treated soils had potential antimicrobial activity and plant growth-promoting attributes. Fulvic acid and B. paralicheniformis 285-3 ferment could be used to restore soil quality and microbiota and control bacterial wilt disease. This study found new biomaterial to control soilborne bacterial disease by combining fulvic acid and poly-gamma-glutamic acid application.
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Affiliation(s)
- Xiuyun Zhao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Di Zhu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Tan
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Rui Wang
- Enshi Tobacco Company of Hubei Province, Enshi, China
| | - Gaofu Qi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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22
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Sreedharan SM, Rishi N, Singh R. Microbial Lipopeptides: Properties, Mechanics and Engineering for Novel Lipopeptides. Microbiol Res 2023; 271:127363. [PMID: 36989760 DOI: 10.1016/j.micres.2023.127363] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/04/2022] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Microorganisms produce active surface agents called lipopeptides (LPs) which are amphiphilic in nature. They are cyclic or linear compounds and are predominantly isolated from Bacillus and Pseudomonas species. LPs show antimicrobial activity towards various plant pathogens and act by inhibiting the growth of these organisms. Several mechanisms are exhibited by LPs, such as cell membrane disruption, biofilm production, induced systematic resistance, improving plant growth, inhibition of spores, etc., making them suitable as biocontrol agents and highly advantageous for industrial utilization. The biosynthesis of lipopeptides involves large multimodular enzymes referred to as non-ribosomal peptide synthases. These enzymes unveil a broad range of engineering approaches through which lipopeptides can be overproduced and new LPs can be generated asserting high efficacy. Such approaches involve several synthetic biology systems and metabolic engineering techniques such as promotor engineering, enhanced precursor availability, condensation domain engineering, and adenylation domain engineering. Finally, this review provides an update of the applications of lipopeptides in various fields.
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23
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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: 10] [Impact Index Per Article: 10.0] [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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24
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [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: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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25
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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: 7] [Impact Index Per Article: 3.5] [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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26
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Laws D, Plouch EV, Blakey SB. Synthesis of Ribosomally Synthesized and Post-Translationally Modified Peptides Containing C-C Cross-Links. JOURNAL OF NATURAL PRODUCTS 2022; 85:2519-2539. [PMID: 36136399 PMCID: PMC9617794 DOI: 10.1021/acs.jnatprod.2c00508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are known for their macrocyclic structures, which impart unique biological activity. One rapidly emerging subclass of RiPP natural products contains macrocyclic C-C cross-links between two amino acid side chains. These linkages, often biosynthetically formed by a single rSAM or P450 enzyme, introduce significant structural and synthetic complexity to the molecules. While nature utilizes elegant mechanisms to produce C-C cross-linked RiPPs, synthetic tools are only able to access a portion of these biologically relevant natural products. This review provides an overview of the structures in this subclass as well as a discussion on their chemical syntheses.
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Affiliation(s)
- David Laws
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Eleda V Plouch
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Simon B Blakey
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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27
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Asamizu S, Ijichi S, Hoshino S, Jo H, Takahashi H, Itoh Y, Matsumoto S, Onaka H. Stable Isotope-Guided Metabolomics Reveals Polar-Functionalized Fatty-Acylated RiPPs from Streptomyces. ACS Chem Biol 2022; 17:2936-2944. [PMID: 36112882 DOI: 10.1021/acschembio.2c00601] [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
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) with polar-functionalized fatty acyl groups are a rarely found untapped class of natural products. Although polar-functionalized fatty-acylated RiPPs (PFARs) have potential as antimicrobial agents, the repertoire is still limited. Therefore, expanding the chemical space is expected to contribute to the development of pharmaceutical agents. In this study, we performed genome mining and stable isotope-guided comparative metabolomics to discover new PFAR natural products. We focused on the feature that PFARs incorporate l-arginine or l-lysine as the starter unit of the fatty acyl group and fed 13C6,15N4-l-arginine or 13C6,15N2-l-lysine to bacterial cultures. Metabolites were extracted and compared with those extracted from nonlabeled l-arginine or l-lysine fed cultures. We identified putative PFARs and successfully isolated solabiomycin A and B from Streptomyces lydicus NBRC 13 058 and albopeptin B from Streptomyces nigrescens HEK616, which contained a sulfoxide group in the labionin moiety. The gene disruption experiment indicated that solS, which encodes a putative flavin adenine dinucleotide (FAD)-nicotinamide adenine dinucleotide (phosphate) (NAD(P))-binding protein, is involved in the sulfoxidation of aryl sulfides. The solabiomycins showed antibacterial activity against Gram-positive bacteria, including Mycobacterium tuberculosis H37Rv with a minimum 95% inhibitory concentration (MIC95) of 3.125 μg/mL, suggesting their potential as antituberculosis agents.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan
| | - Shinta Ijichi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan
| | - Shotaro Hoshino
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan
| | - Hansaem Jo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan
| | - Hidenori Takahashi
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Yuko Itoh
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-9510, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University School of Medicine, 1-757 Asahimachi-Dori, Chuo-ku, Niigata 951-9510, Japan.,Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl., Mulyorejo, Surabaya 60115, Indonesia
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan
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28
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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29
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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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30
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Wang S, Lin S, Fang Q, Gyampoh R, Lu Z, Gao Y, Clarke DJ, Wu K, Trembleau L, Yu Y, Kyeremeh K, Milne BF, Tabudravu J, Deng H. A ribosomally synthesised and post-translationally modified peptide containing a β-enamino acid and a macrocyclic motif. Nat Commun 2022; 13:5044. [PMID: 36028509 PMCID: PMC9415263 DOI: 10.1038/s41467-022-32774-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are structurally complex natural products with diverse bioactivities. Here we report discovery of a RiPP, kintamdin, for which the structure is determined through spectroscopy, spectrometry and genomic analysis to feature a bis-thioether macrocyclic ring and a β-enamino acid residue. Biosynthetic investigation demonstrated that its pathway relies on four dedicated proteins: phosphotransferase KinD, Lyase KinC, kinase homolog KinH and flavoprotein KinI, which share low homologues to enzymes known in other RiPP biosynthesis. During the posttranslational modifications, KinCD is responsible for the formation of the characteristic dehydroamino acid residues including the β-enamino acid residue, followed by oxidative decarboxylation on the C-terminal Cys and subsequent cyclization to provide the bis-thioether ring moiety mediated by coordinated action of KinH and KinI. Finally, conserved genomic investigation allows further identification of two kintamdin-like peptides among the kin-like BGCs, suggesting the occurrence of RiPPs from actinobacteria. The chemical diversity of peptides from ribosomal origin is a growing field of research. Here, the authors report the discovery, genomic and biosynthetic investigations of kintamdin, a ribosomally synthesized and post-translationally modified peptides featuring a beta-enamino acid and a bis-thioether macrocyclic motif.
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Affiliation(s)
- Shan Wang
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Sixing Lin
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Qing Fang
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Roland Gyampoh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana
| | - Zhou Lu
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Yingli Gao
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK.,College of Marine Life and Fisheries, Jiangsu Ocean University, Lianyungang, Jiangsu Province, China
| | - David J Clarke
- EastChem, School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Kewen Wu
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Laurent Trembleau
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Yi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Centre for Fluorinated Pharmaceuticals, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra, Ghana.
| | - Bruce F Milne
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK. .,CFisUC, Department of Physics, University of Coimbra, Rua Larga, 3004-516, Coimbra, Portugal.
| | - Jioji Tabudravu
- School of Natural Sciences, University of Central Lancashire, PR1 2HE, Preston, England, United Kingdom.
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, UK.
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31
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Sukmarini L. Marine Bacterial Ribosomal Peptides: Recent Genomics- and Synthetic Biology-Based Discoveries and Biosynthetic Studies. Mar Drugs 2022; 20:md20090544. [PMID: 36135733 PMCID: PMC9505594 DOI: 10.3390/md20090544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/27/2022] Open
Abstract
Marine biodiversity is represented by an exceptional and ample array of intriguing natural product chemistries. Due to their extensive post-translational modifications, ribosomal peptides—also known as ribosomally synthesized and post-translationally modified peptides (RiPPs)—exemplify a widely diverse class of natural products, endowing a broad range of pharmaceutically and biotechnologically relevant properties for therapeutic or industrial applications. Most RiPPs are of bacterial origin, yet their marine derivatives have been quite rarely investigated. Given the rapid advancement engaged in a more powerful genomics approach, more biosynthetic gene clusters and pathways for these ribosomal peptides continue to be increasingly characterized. Moreover, the genome-mining approach in integration with synthetic biology techniques has markedly led to a revolution of RiPP natural product discovery. Therefore, this present short review article focuses on the recent discovery of RiPPs from marine bacteria based on genome mining and synthetic biology approaches during the past decade. Their biosynthetic studies are discussed herein, particularly the organization of targeted biosynthetic gene clusters linked to the encoded RiPPs with potential bioactivities.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor, Km. 46, Cibinong 16911, West Java, Indonesia
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32
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Srain BM, Pantoja-Gutiérrez S. Microbial production of toluene in oxygen minimum zone waters in the Humboldt Current System off Chile. Sci Rep 2022; 12:10669. [PMID: 35739129 PMCID: PMC9226047 DOI: 10.1038/s41598-022-14103-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022] Open
Abstract
Expansion of oxygen minimum zones in the world's oceans is likely to enhance the production of anaerobic metabolites by marine microorganisms. Here we show that toluene is present throughout the year in shelf waters of the upwelling ecosystem off Concepción (36° S), Chile, and it is a product of microbial anaerobic metabolism. The intra-annual variability in toluene concentrations is consistent with seasonal variability in the strengths of suboxic equatorial and oxygenated subantarctic water masses. Laboratory incubations of oxygen minimum zone water showed microbial production of toluene in the absence of O2. Toluene concentrations were elevated (up to 96 nM) in deeper O2-depleted waters and followed a seasonal pattern in oceanographic conditions. There is evidence to hypothesize that microbial production of toluene could be a homeostatic biochemical mechanism to thrive in the more acidic oxygen minimum zone waters. On the other hand, evidence indicates that microbial anaerobic degradation of toluene may be a source of NO2− by partial denitrification, as shown for aquifer sediments. Since toluene production was not detected in incubations under aerobic conditions, we hypothesize that oxygen minimum zone waters export toluene to surrounding oxygenated waters. Expansion of hypoxia in the ocean will certainly enhance the production and export of anaerobic metabolites by marine microorganisms.
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Affiliation(s)
- Benjamín M Srain
- Departamento de Oceanografía and Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile. .,Programa de Estudios Ecosistémicos del Golfo de Arauco (PREGA), Universidad de Concepción, Concepción, Chile.
| | - Silvio Pantoja-Gutiérrez
- Departamento de Oceanografía and Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile. .,Centro de Investigación Oceanográfica COPAS Coastal, Universidad de Concepción, Concepción, Chile.
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33
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Oikawa H, Mizunoue Y, Nakamura T, Fukushi E, Yulu J, Ozaki T, Minami A. Structure and biosynthesis of the ribosomal lipopeptide antibiotic albopeptins. Biosci Biotechnol Biochem 2022; 86:717-723. [PMID: 35285875 DOI: 10.1093/bbb/zbac039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 01/21/2023]
Abstract
Albopeptins produced by Streptomyces albofaciens JC-82-120 were isolated as effective antibiotics for plant pathogenetic disease in 1986. However, their unusual physicochemical properties hampered the determination of their chemical structures. In this report, we describe our efforts to elucidate their structures. Initially, the structure of an unusual C13-fatty acid with an N-hydroxyguanidyl group was determined using degradation and chemical synthesis. After the linear portion of the octapeptide core was constructed based on the 2D-NMR data, the final assembly of the unusual structure, including the sulfoxide bridge, was achieved through the analysis of detailed NMR data. The proposed structure of albopeptin B was supported by MS/MS data, which also enabled us to determine the structure of 5 albopeptin family members. Bioinformatics analysis of the genomic data of the producer strain further led us to propose that their biosynthetic pathway is similar to the ribosomally derived lanthipeptides possessing a long-chain fatty acid.
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Affiliation(s)
- Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Yusuke Mizunoue
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Takemichi Nakamura
- Molecular Structure Characterization Unit, Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Eri Fukushi
- GC-MS & NMR Lab, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jiang Yulu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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34
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Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases. Nat Chem Biol 2022; 18:724-732. [PMID: 35513512 DOI: 10.1038/s41589-022-01018-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/23/2022] [Indexed: 02/05/2023]
Abstract
Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanPM1 enzymes, a subgroup of M1 zinc-metallopeptidases, have been recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanPM1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states, and identified a unique interdomain Ca2+ binding site as a regulatory element that modulates its domain dynamics and proteolytic activity. Inspired by this regulatory Ca2+ binding, we developed a strategy to engineer LanPM1 enzymes for enhanced catalytic activities by strengthening interdomain associations and driving the conformational equilibrium toward their closed forms.
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35
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Zheng Y, Cong Y, Schmidt EW, Nair SK. Catalysts for the Enzymatic Lipidation of Peptides. Acc Chem Res 2022; 55:1313-1323. [PMID: 35442036 DOI: 10.1021/acs.accounts.2c00108] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biologically active peptides are a major growing class of drugs, but their therapeutic potential is constrained by several limitations including bioavailability and poor pharmacokinetics. The attachment of functional groups like lipids has proven to be a robust and effective strategy for improving their therapeutic potential. Biochemical and bioactivity-guided screening efforts have identified the cyanobactins as a large class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that are modified with lipids. These lipids are attached by the F superfamily of peptide prenyltransferase enzymes that utilize 5-carbon (prenylation) or 10-carbon (geranylation) donors. The chemical structures of various cyanobactins initially showed isoprenoid attachments on Ser, Thr, or Tyr. Biochemical characterization of the F prenyltransferases from the corresponding clusters shows that the different enzymes have different acceptor residue specificities but are otherwise remarkably sequence tolerant. Hence, these enzymes are well suited for biotechnological applications. The crystal structure of the Tyr O-prenyltransferase PagF reveals that the F enzyme shares a domain architecture reminiscent of a canonical ABBA prenyltransferase fold but lacks secondary structural elements necessary to form an enclosed active site. Binding of either cyclic or linear peptides is sufficient to close the active site to allow for productive catalysis, explaining why these enzymes cannot use isolated amino acids as substrates.Almost all characterized isoprenylated cyanobactins are modified with 5-carbon isoprenoids. However, chemical characterization demonstrates that the piricyclamides are modified with a 10-carbon geranyl moiety, and in vitro reconstitution of the corresponding PirF shows that the enzyme is a geranyltransferase. Structural analysis of PirF shows an active site nearly identical with that of the PagF prenyltransferase but with a single amino acid substitution. Of note, mutation at this residue in PagF or PirF can completely switch the isoprenoid donor specificity of these enzymes. Recent efforts have resulted in significant expansion of the F family with enzymes identified that can carry out C-prenylations of Trp, N-prenylations of Trp, and bis-N-prenylations of Arg. Additional genome-guided efforts based on the sequence of F enzymes identify linear cyanobactins that are α-N-prenylated and α-C-methylated by a bifunctional prenyltransferase/methyltransferase fusion and a bis-α-N- and α-C-prenylated linear peptide. The discovery of these different classes of prenyltransferases with diverse acceptor residue specificities expands the biosynthetic toolkit for enzymatic prenylation of peptide substrates.In this Account, we review the current knowledge scope of the F family of peptide prenyltransferases, focusing on the biochemical, structure-function, and chemical characterization studies that have been carried out in our laboratories. These enzymes are easily amenable for diversity-oriented synthetic efforts as they can accommodate substrate peptides of diverse sequences and are thus attractive catalysts for use in synthetic biology approaches to generate high-value peptidic therapeutics.
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Affiliation(s)
- Yiwu Zheng
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Computational Biology, 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
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36
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Imani AS, Lee AR, Vishwanathan N, de Waal F, Freeman MF. Diverse Protein Architectures and α- N-Methylation Patterns Define Split Borosin RiPP Biosynthetic Gene Clusters. ACS Chem Biol 2022; 17:908-917. [PMID: 35297605 PMCID: PMC9019853 DOI: 10.1021/acschembio.1c01002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylations installed on the peptide backbone that impart unique properties like proteolytic stability to these natural products. The borosin RiPP family was initially reported only in fungi until our recent discovery and characterization of a Type IV split borosin system in the metal-respiring bacterium Shewanella oneidensis. Here, we used hidden Markov models and sequence similarity networks to identify over 1600 putative pathways that show split borosin biosynthetic gene clusters are widespread in bacteria. Noteworthy differences in precursor and α-N-methyltransferase open reading frame sizes, architectures, and core peptide properties allow further subdivision of the borosin family into six additional discrete structural types, of which five have been validated in this study.
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Affiliation(s)
| | | | | | - Floris de Waal
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
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37
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Sikandar A, Lopatniuk M, Luzhetskyy A, Müller R, Koehnke J. Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway. J Am Chem Soc 2022; 144:5136-5144. [PMID: 35263083 DOI: 10.1021/jacs.2c00402] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thioholgamides are ribosomally synthesized and posttranslationally modified peptides (RiPPs), with potent activity against cancerous cell lines and an unprecedented structure. Despite being one of the most structurally and chemically complex RiPPs, very few biosynthetic steps have been elucidated. Here, we report the complete in vitro reconstitution of the biosynthetic pathway. We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing. Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes─ThoH/I and ThoC/D. Harnessing the power of AlphaFold, we deduce that ThoD acts as a lyase and also proposes putative catalytic residues. ThoF catalyzes the oxidative decarboxylation of the terminal Cys, and the subsequent macrocyclization is facilitated by ThoE. This is followed by Ser dehydration, which is also carried out by ThoC/D. ThoG is responsible for histidine bis-N-methylation, which is a prerequisite for His β-hydroxylation─a modification carried out by ThoJ. The last step of the pathway is the removal of the leader peptide by ThoK to afford mature thioholgamide.
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Affiliation(s)
- Asfandyar Sikandar
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany
| | - Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, HIPS, HZI, UdS, 66123 Saarbrücken, Germany.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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38
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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39
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Ribosomally derived lipopeptides containing distinct fatty acyl moieties. Proc Natl Acad Sci U S A 2022; 119:2113120119. [PMID: 35027450 PMCID: PMC8784127 DOI: 10.1073/pnas.2113120119] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
Lipopeptides represent a large group of microbial natural products that include important antibacterial and antifungal drugs and some of the most-powerful known biosurfactants. The vast majority of lipopeptides comprise cyclic peptide backbones N-terminally equipped with various fatty acyl moieties. The known compounds of this type are biosynthesized by nonribosomal peptide synthetases, giant enzyme complexes that assemble their products in a non-gene-encoded manner. Here, we report the genome-guided discovery of ribosomally derived, fatty-acylated lipopeptides, termed selidamides. Heterologous reconstitution of three pathways, two from cyanobacteria and one from an arctic, ocean-derived alphaproteobacterium, allowed structural characterization of the probable natural products and suggest that selidamides are widespread over various bacterial phyla. The identified representatives feature cyclic peptide moieties and fatty acyl units attached to (hydroxy)ornithine or lysine side chains by maturases of the GCN5-related N-acetyltransferase superfamily. In contrast to nonribosomal lipopeptides that are usually produced as congener mixtures, the three selidamides are selectively fatty acylated with C10, C12, or C16 fatty acids, respectively. These results highlight the ability of ribosomal pathways to emulate products with diverse, nonribosomal-like features and add to the biocatalytic toolbox for peptide drug improvement and targeted discovery.
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40
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Shi J, Ma JQ, Wang YC, Xu ZF, Zhang B, Jiao RH, Tan RX, Ge HM. Discovery of daspyromycins A and B, 2-aminovinyl-cysteine containing lanthipeptides, through a genomics-based approach. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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Wang C, Lu J, Zhang Y, Zheng J, Sun S, Huang S, Wang H. Substrate plasticity of dehydratase SpaKC from the biosynthesis of thiosparsoamide. J Pept Sci 2021; 28:e3388. [PMID: 34931400 DOI: 10.1002/psc.3388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 11/23/2021] [Indexed: 11/08/2022]
Abstract
Thioamitides are a group of ribosomally synthesized and post-translationally modified peptides that possess diverse bioactivities and are usually featured by thioamide and 2-aminovinyl-cysteine (AviCys) motifs. In natural product thiosparsoamide, the AviCys motif is formed by an enzyme cascade formed by the flavin-dependent decarboxylase SpaD and dehydratase SpaKC. SpaKC is a lanthipeptide synthetase homolog located outside the thiosparsoamide biosynthetic gene cluster. In this study, we show that SpaKC does not strictly require the N-terminal leader peptide of precursor peptide SpaA for substrate recognition and dehydration. The C-terminal seven residues serve as a minimal structural element for enzyme recognition. Through a systematic mutagenesis experiments, our study demonstrates the relaxed substrate specificity of SpaKC as a dehydratase and potentially as an enzymatic tool to install dehydroalanine or dehydrobutyrine motifs in peptides.
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Affiliation(s)
- Ciji Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Jingxia Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Yingying Zhang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Jie Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Shuaishuai Sun
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Shanqing Huang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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42
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Grant-Mackie E, Williams ET, Harris PWR, Brimble MA. Aminovinyl Cysteine Containing Peptides: A Unique Motif That Imparts Key Biological Activity. JACS AU 2021; 1:1527-1540. [PMID: 34723257 PMCID: PMC8549060 DOI: 10.1021/jacsau.1c00308] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Natural products that contain distinctive chemical functionality can serve as useful starting points to develop Nature's compounds into viable therapeutics. Peptide natural products, an under-represented class of medicines, such as ribosomally synthesized and post-translationally modified peptides (RiPPs), often contain noncanonical amino acids and structural motifs that give rise to potent biological activity. However, these motifs can be difficult to obtain synthetically, thereby limiting the transition of RiPPs to the clinic. Aminovinyl cysteine containing peptides, which display potent antimicrobial or anticancer activity, possess an intricate C-terminal ring that is critical for bioactivity. To date, successful methods for the total chemical synthesis of such peptides are yet to be realized, although several advancements have been achieved. In this perspective, we review this burgeoning class of aminovinyl cysteine peptides and critically evaluate the chemical strategies to install the distinct aminovinyl cysteine motif.
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Affiliation(s)
- Emily
S. Grant-Mackie
- School
of Chemical Sciences, The University of
Auckland, 23 Symonds Street, Auckland 1132, New Zealand
| | - Elyse T. Williams
- School
of Chemical Sciences, The University of
Auckland, 23 Symonds Street, Auckland 1132, New Zealand
| | - Paul W. R. Harris
- School
of Chemical Sciences, The University of
Auckland, 23 Symonds Street, Auckland 1132, New Zealand
- School
of Biological Sciences, The University of
Auckland, 3b Symonds
Street, Auckland 1132, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1132, New Zealand
| | - Margaret A. Brimble
- School
of Chemical Sciences, The University of
Auckland, 23 Symonds Street, Auckland 1132, New Zealand
- School
of Biological Sciences, The University of
Auckland, 3b Symonds
Street, Auckland 1132, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1132, New Zealand
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43
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Yao G, Knittel CH, Kosol S, Wenz MT, Keller BG, Gruß H, Braun AC, Lutz C, Hechler T, Pahl A, Süssmuth RD. Iodine-Mediated Tryptathionine Formation Facilitates the Synthesis of Amanitins. J Am Chem Soc 2021; 143:14322-14331. [PMID: 34459587 DOI: 10.1021/jacs.1c06565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthetic methods on the macrocyclization of peptides are of high interest since they facilitate the synthesis of various types of potentially bioactive compounds, e.g. addressing targets like protein-protein-interactions. Herein, we report on an efficient method to construct tryptathionine-cross-links in peptides between the amino acids Trp and Cys. This reaction not only is the basis for the total synthesis of the death cap toxin α-amanitin but also provides rapid access to various new amanitin analogues. This study for the first time presents a systematic compilation of structure-activity relations (SAR) of amatoxins with regard to RNA polymerase II inhibition and cytotoxicity with one amanitin derivative of superior RNAP II inhibition. The present approach paves the way for the synthesis of structurally diverse amatoxins as future payloads for antibody-toxin conjugates in cancer therapy.
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Affiliation(s)
- Guiyang Yao
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Caroline H Knittel
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Simone Kosol
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
| | - Marius T Wenz
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hendrik Gruß
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Alexandra C Braun
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Christian Lutz
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Torsten Hechler
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Andreas Pahl
- Heidelberg Pharma Research GmbH, Gregor-Mendel-Straße 22, 68526 Ladenburg, Germany
| | - Roderich D Süssmuth
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany
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44
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Vinogradov AA, Nagano M, Goto Y, Suga H. Site-Specific Nonenzymatic Peptide S/O-Glutamylation Reveals the Extent of Substrate Promiscuity in Glutamate Elimination Domains. J Am Chem Soc 2021; 143:13358-13369. [PMID: 34392675 DOI: 10.1021/jacs.1c06470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Formation of dehydroalanine and dehydrobutyrine residues via tRNA-dependent dehydration of serine and threonine is a key post-translational modification in the biosynthesis of lanthipeptide and thiopeptide RiPPs. The dehydration process involves two reactions, wherein the O-glutamyl Ser/Thr intermediate, accessed by a dedicated enzyme utilizing Glu-tRNAGlu as the acyl donor, is recognized by the second enzyme, referred to as the glutamate elimination domain (ED), which catalyzes the eponymous reaction yielding a dehydroamino acid. Many details of ED catalysis remain unexplored because the scope of available substrates for testing is limited to those that the upstream enzymes can furnish. Here, we report two complementary strategies for direct, nonenzymatic access to diverse ED substrates. We establish that a thiol-thioester exchange reaction between a Cys-containing peptide and an α thioester of glutamic acid leads an S-glutamylated intermediate which can act as a substrate for EDs. Furthermore, we show that the native O-glutamylated substrates can be accessible from S-glutamylated peptides upon a site-specific S-to-O acyl transfer reaction. Combined with flexible in vitro translation utilized for rapid peptide production, these chemistries enabled us to dissect the substrate recognition requirements of three known EDs. Our results establish that EDs are uniquely promiscuous enzymes capable of acting on substrates with arbitrary amino acid sequences and performing retro-Michael reaction beyond the canonical glutamate elimination. To facilitate substrate recruitment, EDs apparently engage in nonspecific hydrophobic interactions with their substrates. Altogether, our results establish the substrate scope of EDs and provide clues to their catalysis.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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45
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Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz‐Oesterhelt H, Gross H. Nocathioamides, Uncovered by a Tunable Metabologenomic Approach, Define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Phytochemistry and Plant Systematics Division of Pharmaceutical Industries National Research Centre Dokki Cairo Egypt
| | - Saefuddin Aziz
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Microbiology Department Biology Faculty Jenderal Soedirman University Purwokerto Indonesia
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Markus Kramer
- Institute of Organic Chemistry University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz‐Oesterhelt
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection University of Tübingen Tübingen Germany
| | - Harald Gross
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection University of Tübingen Tübingen Germany
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46
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Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz‐Oesterhelt H, Gross H. Nocathioamides, Uncovered by a Tunable Metabologenomic Approach, Define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl 2021; 60:16472-16479. [PMID: 33991039 PMCID: PMC8362196 DOI: 10.1002/anie.202102571] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/09/2021] [Indexed: 12/16/2022]
Abstract
The increasing number of available genomes, in combination with advanced genome mining techniques, unveiled a plethora of biosynthetic gene clusters (BGCs) coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). The products of these BGCs often represent an enormous resource for new and bioactive compounds, but frequently, they cannot be readily isolated and remain cryptic. Here, we describe a tunable metabologenomic approach that recruits a synergism of bioinformatics in tandem with isotope- and NMR-guided platform to identify the product of an orphan RiPP gene cluster in the genomes of Nocardia terpenica IFM 0406 and 0706T . The application of this tactic resulted in the discovery of nocathioamides family as a founder of a new class of chimeric lanthipeptides I.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Department of Phytochemistry and Plant SystematicsDivision of Pharmaceutical IndustriesNational Research CentreDokkiCairoEgypt
| | - Saefuddin Aziz
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Microbiology DepartmentBiology FacultyJenderal Soedirman UniversityPurwokertoIndonesia
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry Institute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Markus Kramer
- Institute of Organic ChemistryUniversity of TübingenAuf der Morgenstelle 1872076TübingenGermany
| | - Jan Straetener
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Anne Berscheid
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Heike Brötz‐Oesterhelt
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight InfectionUniversity of TübingenTübingenGermany
| | - Harald Gross
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight InfectionUniversity of TübingenTübingenGermany
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47
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Engelbrecht A, Saad H, Gross H, Kaysser L. Natural Products from Nocardia and Their Role in Pathogenicity. Microb Physiol 2021; 31:217-232. [PMID: 34139700 DOI: 10.1159/000516864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.
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Affiliation(s)
- Alicia Engelbrecht
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Hamada Saad
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Harald Gross
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
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48
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Grigoreva A, Andreeva J, Bikmetov D, Rusanova A, Serebryakova M, Garcia AH, Slonova D, Nair SK, Lippens G, Severinov K, Dubiley S. Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis. iScience 2021; 24:102480. [PMID: 34113822 PMCID: PMC8169954 DOI: 10.1016/j.isci.2021.102480] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/21/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Lanthipeptides, ribosomally synthesized and post-translationally modified peptides (RiPPs), can be divided into five classes based on their structures and biosynthetic pathways. Class I and II lanthipeptides have been well characterized, whereas less is known about members of the other three classes. Here, we describe a new family of class III lanthipeptides from Firmicutes. Members of the family are distinguished by the presence of a single carboxy-terminal labionin. We identified and characterized andalusicin, a representative of this family. Andalusicin bears two methyl groups at the α-amino terminus, a post-translational modification that has not previously been identified in class III lanthipeptides. Mature andalusicin A shows bioactivity against various Gram-positive bacteria, an activity that is highly dependent on the α-N dimethylation.
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Affiliation(s)
- Anastasiia Grigoreva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Julia Andreeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Dmitry Bikmetov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Anastasiia Rusanova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Marina Serebryakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrea Hernandez Garcia
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801 USA
| | - Darya Slonova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801 USA
| | - Guy Lippens
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse 31077, France
| | - Konstantin Severinov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
- Waksman Institute for Microbiology, Piscataway, NJ 08854-8020, USA
| | - Svetlana Dubiley
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
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49
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Abstract
Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products characterized by the presence of lanthionine and methyllanthionine. During the maturation of select lanthipeptides, five different alterations have been observed to the chemical structure of the peptide backbone. First, dehydratases generate dehydroalanine and dehydrobutyrine from Ser or Thr residues, respectively. A second example of introduction of unsaturation is the oxidative decarboxylation of C-terminal Cys residues catalyzed by the decarboxylase LanD. Both modifications result in loss of chirality at the α-carbon of the amino acid residues. Attack of a cysteine thiol onto a dehydrated amino acid results in thioether crosslink formation with either inversion or retention of the l-stereochemical configuration at the α-carbon of former Ser and Thr residues. A fourth modification of the protein backbone is the hydrogenation of dehydroamino acids to afford d-amino acids catalyzed by NAD(P)H-dependent reductases. A fifth modification is the conversion of Asp to isoAsp. Herein, the methods used to produce and characterize the lanthipeptide bicereucin will be described in detail along with a brief overview of other lanthipeptides.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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50
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Eyles TH, Vior NM, Lacret R, Truman AW. Understanding thioamitide biosynthesis using pathway engineering and untargeted metabolomics. Chem Sci 2021; 12:7138-7150. [PMID: 34123341 PMCID: PMC8153245 DOI: 10.1039/d0sc06835g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Thiostreptamide S4 is a thioamitide, a family of promising antitumour ribosomally synthesised and post-translationally modified peptides (RiPPs). The thioamitides are one of the most structurally complex RiPP families, yet very few thioamitide biosynthetic steps have been elucidated, even though the biosynthetic gene clusters (BGCs) of multiple thioamitides have been identified. We hypothesised that engineering the thiostreptamide S4 BGC in a heterologous host could provide insights into its biosynthesis when coupled with untargeted metabolomics and targeted mutations of the precursor peptide. Modified BGCs were constructed, and in-depth metabolomics enabled a detailed understanding of the biosynthetic pathway to thiostreptamide S4, including the identification of a protein critical for amino acid dehydration that has homology to HopA1, an effector protein used by a plant pathogen to aid infection. We use this biosynthetic understanding to bioinformatically identify diverse RiPP-like BGCs, paving the way for future RiPP discovery and engineering.
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Affiliation(s)
- Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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