1
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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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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 2024:10.1038/s41557-024-01491-3. [PMID: 38528101 DOI: 10.1038/s41557-024-01491-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Eslami SM, van der Donk WA. Proteases Involved in Leader Peptide Removal during RiPP Biosynthesis. ACS BIO & MED CHEM AU 2024; 4:20-36. [PMID: 38404746 PMCID: PMC10885120 DOI: 10.1021/acsbiomedchemau.3c00059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/27/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) have received much attention in recent years because of their promising bioactivities and the portability of their biosynthetic pathways. Heterologous expression studies of RiPP biosynthetic enzymes identified by genome mining often leave a leader peptide on the final product to prevent toxicity to the host and to allow the attachment of a genetically encoded affinity purification tag. Removal of the leader peptide to produce the mature natural product is then carried out in vitro with either a commercial protease or a protease that fulfills this task in the producing organism. This review covers the advances in characterizing these latter cognate proteases from bacterial RiPPs and their utility as sequence-dependent proteases. The strategies employed for leader peptide removal have been shown to be remarkably diverse. They include one-step removal by a single protease, two-step removal by two dedicated proteases, and endoproteinase activity followed by aminopeptidase activity by the same protease. Similarly, the localization of the proteolytic step varies from cytoplasmic cleavage to leader peptide removal during secretion to extracellular leader peptide removal. Finally, substrate recognition ranges from highly sequence specific with respect to the leader and/or modified core peptide to nonsequence specific mechanisms.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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4
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Nguyen NA, Vidya FNU, Yennawar NH, Wu H, McShan AC, Agarwal V. Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase. Nat Commun 2024; 15:1265. [PMID: 38341413 PMCID: PMC10858898 DOI: 10.1038/s41467-024-45593-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
To biosynthesize ribosomally synthesized and post-translationally modified peptides (RiPPs), enzymes recognize and bind to the N-terminal leader region of substrate peptides which enables catalytic modification of the C-terminal core. Our current understanding of RiPP leaders is that they are short and largely unstructured. Proteusins are RiPP precursor peptides that defy this characterization as they possess unusually long leaders. Proteusin peptides have not been structurally characterized, and we possess scant understanding of how these atypical leaders engage with modifying enzymes. Here, we determine the structure of a proteusin peptide which shows that unlike other RiPP leaders, proteusin leaders are preorganized into a rigidly structured region and a smaller intrinsically disordered region. With residue level resolution gained from NMR titration experiments, the intermolecular peptide-protein interactions between proteusin leaders and a flavin-dependent brominase are mapped onto the disordered region, leaving the rigidly structured region of the proteusin leader to be functionally dispensable. Spectroscopic observations are biochemically validated to identify a binding motif in proteusin peptides that is conserved among other RiPP leaders as well. This study provides a structural characterization of the proteusin peptides and extends the paradigm of RiPP modification enzymes using not only unstructured peptides, but also structured proteins as substrates.
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Affiliation(s)
- Nguyet A Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - F N U Vidya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongwei Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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5
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Hu YL, Yin FZ, Shi J, Ma SY, Wang ZR, Tan RX, Jiao RH, Ge HM. P450-Modified Ribosomally Synthesized Peptides with Aromatic Cross-Links. J Am Chem Soc 2023; 145:27325-27335. [PMID: 38069901 DOI: 10.1021/jacs.3c07416] [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: 12/21/2023]
Abstract
Cyclization of linear peptides is an effective strategy to convert flexible molecules into rigid compounds, which is of great significance for enhancing the peptide stability and bioactivity. Despite significant advances in the past few decades, Nature and chemists' ability to macrocyclize linear peptides is still quite limited. P450 enzymes have been reported to catalyze macrocyclization of peptides through cross-linkers between aromatic amino acids with only three examples. Herein, we developed an efficient workflow for the identification of P450-modified RiPPs in bacterial genomes, resulting in the discovery of a large number of P450-modified RiPP gene clusters. Combined with subsequent expression and structural characterization of the products, we have identified 11 novel P450-modified RiPPs with different cross-linking patterns from four distinct classes. Our results greatly expand the structural diversity of P450-modified RiPPs and provide new insights and enzymatic tools for the production of cyclic peptides.
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Affiliation(s)
- Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Fang Zhou Yin
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Shi Ying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zi Ru Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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6
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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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7
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Hernandez Garcia A, Nair SK. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. ACS CENTRAL SCIENCE 2023; 9:1944-1956. [PMID: 37901177 PMCID: PMC10604976 DOI: 10.1021/acscentsci.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/31/2023]
Abstract
In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent β-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.
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Affiliation(s)
- Andrea Hernandez Garcia
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
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8
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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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9
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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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10
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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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11
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Zhong G, Wang ZJ, Yan F, Zhang Y, Huo L. Recent Advances in Discovery, Bioengineering, and Bioactivity-Evaluation of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:1-31. [PMID: 37101606 PMCID: PMC10125368 DOI: 10.1021/acsbiomedchemau.2c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 04/28/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are of increasing interest in natural products as well as drug discovery. This empowers not only the unique chemical structures and topologies in natural products but also the excellent bioactivities such as antibacteria, antifungi, antiviruses, and so on. Advances in genomics, bioinformatics, and chemical analytics have promoted the exponential increase of RiPPs as well as the evaluation of biological activities thereof. Furthermore, benefiting from their relatively simple and conserved biosynthetic logic, RiPPs are prone to be engineered to obtain diverse analogues that exhibit distinct physiological activities and are difficult to synthesize. This Review aims to systematically address the variety of biological activities and/or the mode of mechanisms of novel RiPPs discovered in the past decade, albeit the characteristics of selective structures and biosynthetic mechanisms are briefly covered as well. Almost one-half of the cases are involved in anti-Gram-positive bacteria. Meanwhile, an increasing number of RiPPs related to anti-Gram-negative bacteria, antitumor, antivirus, etc., are also discussed in detail. Last but not least, we sum up some disciplines of the RiPPs' biological activities to guide genome mining as well as drug discovery and optimization in the future.
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Affiliation(s)
- Guannan Zhong
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
| | - Zong-Jie Wang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fu Yan
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- CAS
Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty
of Synthetic Biology, Shenzhen Institute
of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liujie Huo
- Helmholtz
International Laboratory for Anti-Infectives, State Key Laboratory
of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute, Shandong University, Suzhou, Jiangsu 215123, P. R. China
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12
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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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13
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Chu L, Cheng J, Zhou C, Mo T, Ji X, Zhu T, Chen J, Ma S, Gao J, Zhang Q. Hijacking a Linaridin Biosynthetic Intermediate for Lanthipeptide Production. ACS Chem Biol 2022; 17:3198-3206. [PMID: 36288500 DOI: 10.1021/acschembio.2c00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Linaridins and lanthipeptides are two classes of natural products belonging to the ribosomally synthesized and posttranslationally modified peptide (RiPP) superfamily. Although these two RiPP classes share similar structural motifs such as dehydroamino acids and thioether-based cross-links, the biosynthesis of linaridins and lanthipeptides involved distinct sets of enzymes. Here, we report the identification of a novel lanthipeptide cypepeptin from a recombinant strain of Streptomyces lividans, which harbors most of the cypemycin (a prototypic linaridin) biosynthetic gene cluster but lacks the decarboxylase gene cypD. In contrast to the generally believed structure of cypemycin, multiple d-amino acids and Z-dehydrobutyrines were observed in both cypepeptin and cypemycin, and the stereochemistry of each amino acid was established by the extensive structural analysis in combination with genetic knockout and mutagenesis studies. Comparative analysis of cypemycin and cypepeptin showed that the aminovinyl-cysteine (AviCys) moiety of cypemycin plays an essential role in disrupting the cell integrity of M. luteus, which cannot be functionally substituted by the structurally similar lanthionine moiety.
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Affiliation(s)
- Leixia Chu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jinduo Cheng
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Chengzeng Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Taoting Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Jie Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Suze Ma
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jiangtao Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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14
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Huang S, Wang Y, Cai C, Xiao X, Liu S, Ma Y, Xie X, Liang Y, Chen H, Zhu J, Hegemann JD, Yao H, Wei W, Wang H. Discovery of a Unique Structural Motif in Lanthipeptide Synthetases for Substrate Binding and Interdomain Interactions. Angew Chem Int Ed Engl 2022; 61:e202211382. [PMID: 36102578 PMCID: PMC9828337 DOI: 10.1002/anie.202211382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Class III lanthipeptide synthetases catalyze the formation of lanthionine/methyllanthionine and labionin crosslinks. We present here the 2.40 Å resolution structure of the kinase domain of a class III lanthipeptide synthetase CurKC from the biosynthesis of curvopeptin. A unique structural subunit for leader binding, named leader recognition domain (LRD), was identified. The LRD of CurKC is responsible for the recognition of the leader peptide and for mediating interactions between the lyase and kinase domains. LRDs are highly conserved among the kinase domains of class III and class IV lanthipeptide synthetases. The discovery of LRDs provides insight into the substrate recognition and domain organization in multidomain lanthipeptide synthetases.
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Affiliation(s)
- Shanqing Huang
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Ying Wang
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Chuangxu Cai
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Xiuyun Xiao
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Shulei Liu
- Institute of Molecular EnzymologySchool of Biology and Basic Medical SciencesSoochow UniversitySuzhou215123China
| | - Yeying Ma
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Xiangqian Xie
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Yong Liang
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Hao Chen
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
| | - Jiapeng Zhu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)Helmholtz Centre for Infection Research (HZI)Saarland University Campus66123SaarbrückenGermany
| | - Julian D. Hegemann
- School of Medicine and Life SciencesState Key Laboratory Cultivation Base for TCM Quality and EfficacyJiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia MedicaNanjing University of Chinese MedicineNanjing210023China
| | - Hongwei Yao
- Institute of Molecular EnzymologySchool of Biology and Basic Medical SciencesSoochow UniversitySuzhou215123China
| | - Wanqing Wei
- State Key Laboratory of Food Science and TechnologyJiangnan UniversityWuxi214122P. R. China
| | - Huan Wang
- State Key Laboratory of Coordination ChemistryChemistry and Biomedicine Innovation Center of Nanjing UniversityJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing UniversityNo. 163 Xianlin AveNanjing210093China
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15
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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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16
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LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates. Nat Catal 2022. [DOI: 10.1038/s41929-022-00822-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Wang H, Li C, Wu Q, Wen H, Sun T, Xie Z. A cationic BODIPY photosensitizer decorated with quaternary ammonium for high-efficiency photodynamic inhibition of bacterial growth. J Mater Chem B 2022; 10:4967-4973. [PMID: 35734874 DOI: 10.1039/d2tb00778a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
On account of the constant evolution of antibiotic-resistant bacteria, the effects of existing antibacterial materials are being gradually weakened, and the difficulty in curing infectious diseases is increasing. Therefore, more novel antibacterial materials or methods are eagerly required to combat microbial infections. Recently, the advantages of photodynamic therapy in the antibacterial field have gradually been validated. Herein, a trimethylamine (TMA) salt-modified 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) photosensitizer (BODIPY-TMA) was synthesized for antibacterial applications. Due to the positive charge of the TMA group, enhanced interactions were observed between the prepared BODIPY-TMA nanoparticles (BODIPY-TMA NPs) and negatively-charged bacterial membranes. The BODIPY-TMA NPs showed much better antibacterial effect toward both S. aureus and E. coli compared with their BODIPY-Br NPs counterpart without a positive charge. Moreover, the BODIPY-TMA NPs efficiently prevented the formation of biofilms and destroyed pre-established biofilms. Thus, such positively-charged photosensitizers may pave the way for the exploration of highly effective antibacterial agents.
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Affiliation(s)
- Hongyu Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering University of Science and Technology of China, Hefei 230026, P. R. China
| | - Chaonan Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering University of Science and Technology of China, Hefei 230026, P. R. China
| | - Qihang Wu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering University of Science and Technology of China, Hefei 230026, P. R. China
| | - Hui Wen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering University of Science and Technology of China, Hefei 230026, P. R. China
| | - Tingting Sun
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.
| | - Zhigang Xie
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China. .,School of Applied Chemistry and Engineering University of Science and Technology of China, Hefei 230026, P. R. China
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18
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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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19
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Xue D, Older EA, Zhong Z, Shang Z, Chen N, Dittenhauser N, Hou L, Cai P, Walla MD, Dong SH, Tang X, Chen H, Nagarkatti P, Nagarkatti M, Li YX, Li J. Correlational networking guides the discovery of unclustered lanthipeptide protease-encoding genes. Nat Commun 2022; 13:1647. [PMID: 35347143 PMCID: PMC8960859 DOI: 10.1038/s41467-022-29325-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/21/2022] [Indexed: 11/09/2022] Open
Abstract
Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on hidden enzymes encoded elsewhere in the genome for completion of biosynthesis. The study and application of lanthipeptides are frequently hindered by unclustered protease genes required for final maturation. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and hidden proteases. Applying our analysis to 161,954 bacterial genomes, we establish 5209 correlations between precursors and hidden proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of previously unreported class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of hidden lanthipeptide proteases and potentially other missing enzymes for natural products biosynthesis.
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Affiliation(s)
- Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhuo Shang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Nanzhu Chen
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Nolan Dittenhauser
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Lukuan Hou
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Peiyan Cai
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Michael D Walla
- The Mass Spectrometry Center, Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Hexin Chen
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, USA.
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20
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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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21
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Thetsana C, Ijichi S, Kaweewan I, Nakagawa H, Kodani S. Heterologous expression of a cryptic gene cluster from a marine proteobacterium Thalassomonas actiniarum affords new lanthipeptides thalassomonasins A and B. J Appl Microbiol 2022; 132:3629-3639. [PMID: 35157343 DOI: 10.1111/jam.15491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
AIMS The aim of this study was to utilize a cryptic biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum for production of new lanthipeptides by heterologous expression system. METHODS AND RESULTS Based on genome-mining, a new biosynthetic gene cluster of class I lanthipeptide was found in the genome sequence of a marine proteobacterium Thalassomonas actiniarum. Molecular cloning was performed to construct expression vector derived from commercial available plasmid pET-41a(+). Heterologous production of new lanthipeptides named thalassomonasins A and B was performed using the host Escherichia coli BL21(DE3) harboring the expression vector. The structure of thalassomonasin A was determined by interpretation of NMR and MS data. As a result, thalassomonasin A was determined to be a lanthipeptide with three units of lanthionine. The bridging pattern of the lanthionine rings in thalassomonasin A was determined by interpretation of NOESY data. The structure of thalassomonasin B was proposed by MS/MS experiment. CONCLUSIONS We succeeded in heterologous production of new class I lanthipeptides using a biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report of heterologous production of lanthipeptides derived from proteobacterial origin. There are many cryptic biosynthetic gene clusters of this class of lanthipeptides in proteobacterial genomes. This study may lead to production of new lanthipeptides by utilizing the biosynthetic gene clusters.
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Affiliation(s)
- Chanaphat Thetsana
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Shinta Ijichi
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakagawa
- Research center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Faculty of Agriculture, Shizuoka University, Shizuoka, Japan.,Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka University, Shizuoka, Japan.,College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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22
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Zhang Y, Hong Z, Zhou L, Zhang Z, Tang T, Guo E, Zheng J, Wang C, Dai L, Si T, Wang H. Biosynthesis of Gut‐Microbiota‐Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Liang Zhou
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhenkun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Ting Tang
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 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 No. 163 Xianlin Ave Nanjing 210093 China
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23
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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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24
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Zhang Y, Hong Z, Zhou L, Zhang Z, Tang T, Guo E, Zheng J, Wang C, Dai L, Si T, Wang H. Biosynthesis of Gut-Microbiota-Derived Lantibiotics Reveals a Subgroup of S8 Family Proteases for Class III Leader Removal. Angew Chem Int Ed Engl 2021; 61:e202114414. [PMID: 34889011 DOI: 10.1002/anie.202114414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Indexed: 11/08/2022]
Abstract
Lanthipeptides are a group of ribosomally synthesized and post-translationally modified peptides with diverse structural features and bioactivities. Gut-microbiota-derived lanthipeptides play important roles in gut homeostasis of the host. Herein, we report the discovery and biosynthesis of class III lantibiotics named amylopeptins, which are derived from the gut microbiota of Sprague-Dawley rats and display a narrow antimicrobial spectrum. In contrast to known class III lanthipeptides, the biosynthesis of amylopeptins employs AmyP, which belongs to a subgroup of S8 family serine proteases, to remove the leader of corresponding precursor peptides in a site-specific manner during the last step of their maturation. Overall, this study shows for the first time that S8 family proteases participate in the biosynthesis of class III lanthipeptides.
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Affiliation(s)
- 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, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liang Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhenkun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ting Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, 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, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - 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, No. 163 Xianlin Ave, Nanjing, 210093, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, 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, No. 163 Xianlin Ave, Nanjing, 210093, China
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25
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Hegemann JD, Süssmuth RD. Identification of the Catalytic Residues in the Cyclase Domain of the Class IV Lanthipeptide Synthetase SgbL. Chembiochem 2021; 22:3169-3172. [PMID: 34490957 PMCID: PMC9292228 DOI: 10.1002/cbic.202100391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/06/2021] [Indexed: 11/08/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into different classes based on their processing enzymes. The three-domain class IV lanthipeptide synthetases (LanL enzymes) consist of N-terminal lyase, central kinase, and C-terminal cyclase domains. While the catalytic residues of the kinase domains (mediating ATP-dependent Ser/Thr phosphorylations) and the lyase domains (carrying out subsequent phosphoserine/phosphothreonine (pSer/pThr) eliminations to yield dehydroalanine/dehydrobutyrine (Dha/Dhb) residues) have been characterized previously, such studies are missing for LanL cyclase domains. To close this gap of knowledge, this study reports on the identification and validation of the catalytic residues in the cyclase domain of the class IV lanthipeptide synthetase SgbL, which facilitate the nucleophilic attacks by Cys thiols on Dha/Dhb residues for the formation of β-thioether crosslinks.
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Affiliation(s)
- Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Strasse des 17. Juni 124, 10623, Berlin, Germany
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26
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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: 4] [Impact Index Per Article: 1.3] [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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27
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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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28
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Wu C, van der Donk WA. Engineering of new-to-nature ribosomally synthesized and post-translationally modified peptide natural products. Curr Opin Biotechnol 2021; 69:221-231. [PMID: 33556835 DOI: 10.1016/j.copbio.2020.12.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/11/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022]
Abstract
Natural products have historically been important lead sources for drug development, particularly to combat infectious diseases. Increasingly, their structurally complex scaffolds are also envisioned as leads for applications for which they did not evolve, an approach aided by engineering of new-to-nature analogs. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are promising candidates for bioengineering because they are genetically encoded and their biosynthetic enzymes display significant substrate tolerance. This review highlights recent advances in the discovery of highly unusual new reactions by genome mining and the application of engineering approaches to generate and screen novel RiPP variants. Furthermore, through the use of synthetic biology approaches, hybrid molecules with enhanced or completely new activities have been identified, which opens the door for future advancement of RiPPs as potential next-generation therapeutics.
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Affiliation(s)
- Chunyu Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, United States
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, United States; Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL 61801, United States.
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29
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Lu J, Wu Y, Li Y, Wang H. The Utilization of Lanthipeptide Synthetases Is a General Strategy for the Biosynthesis of 2‐Aminovinyl‐Cysteine Motifs in Thioamitides**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuan Wu
- 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - 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 No. 163 Xianlin Ave Nanjing 210093 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 No. 163 Xianlin Ave Nanjing 210093 China
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30
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Qiu Y, Liu J, Li Y, Xue Y, Liu W. Formation of an aminovinyl-cysteine residue in thioviridamides occurs through a path independent of known lanthionine synthetase activity. Cell Chem Biol 2021; 28:675-685.e5. [PMID: 33476565 DOI: 10.1016/j.chembiol.2020.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022]
Abstract
2-Aminovinyl-cysteine (AviCys) is a thioether amino acid shared by a variety of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Based on investigations into the biosynthesis of thioviridamide RiPPs in Streptomyces sp. NRRL S-87, we here report a path for the formation of this unusual thioether residue. This path relies on four dedicated proteins: phosphotransferase TvaCS-87, Lyase TvaDS-87, kinase homolog TvaES-87, and LanD-like flavoprotein TvaFS-87. TvaES-87 plays a critical role in effective AviCys formation. During the posttranslational modifications of the precursor peptide, it works with TvaFS-87 to form a minimum AviCys synthetase complex, which follows the combined activity of TvaCDS-87 for Thr dehydration and catalyzes Cys oxidative decarboxylation and subsequent Michael addition of the resulting enethiol nucleophile onto the newly formed dehydroamino acid residue for cyclization. With TvaES-87, TvaFS-87 activity for Cys processing can be coordinated with TvaCDS-87 activity for minimizing competitive or unexpected spontaneous reactions and forming AviCys effectively.
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Affiliation(s)
- Yanping Qiu
- 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
| | - Jingyu 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
| | - Yuqing Li
- 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
| | - 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; Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China.
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31
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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32
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Lu J, Li Y, Bai Z, Lv H, Wang H. Enzymatic macrocyclization of ribosomally synthesized and posttranslational modified peptides via C-S and C-C bond formation. Nat Prod Rep 2021; 38:981-992. [PMID: 33185226 DOI: 10.1039/d0np00044b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2000 to 2020 Ribosomally synthesized and posttranslational modified peptides (RiPPs) are a rapidly growing class of bioactive natural products. Many members of RiPPs contain macrocyclic structural units constructed by modification enzymes through macrocyclization of linear precursor peptides. In this study, we summarize recent progress in the macrocyclization of RiPPs by C-S and C-C bond formation with a focus on the current understanding of the enzymatic mechanisms.
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Affiliation(s)
- 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 210093, China.
| | - 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.
| | - Zengbing Bai
- 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.
| | - Hongmei Lv
- 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.
| | - 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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33
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 362] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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34
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Lu J, Wu Y, Li Y, Wang H. The Utilization of Lanthipeptide Synthetases Is a General Strategy for the Biosynthesis of 2‐Aminovinyl‐Cysteine Motifs in Thioamitides**. Angew Chem Int Ed Engl 2020; 60:1951-1958. [DOI: 10.1002/anie.202012871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Indexed: 01/04/2023]
Affiliation(s)
- 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - Yuan Wu
- 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 No. 163 Xianlin Ave Nanjing 210093 China
| | - 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 No. 163 Xianlin Ave Nanjing 210093 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 No. 163 Xianlin Ave Nanjing 210093 China
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35
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Hegemann JD, Süssmuth RD. Matters of class: coming of age of class III and IV lanthipeptides. RSC Chem Biol 2020; 1:110-127. [PMID: 34458752 PMCID: PMC8341899 DOI: 10.1039/d0cb00073f] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
Lanthipeptides belong to the superfamily of ribosomally-synthesized and posttranslationally-modified peptides (RiPPs). Despite the fact that they represent one of the longest known RiPP subfamilies, their youngest members, classes III and IV, have only been described more recently. Since then, a plethora of studies furthered the understanding of their biosynthesis. While there are commonalities between classes III and IV due to the similar domain architectures of their processing enzymes, there are also striking differences that allow their discrimination. In this concise review article, we summarize what is known about the underlying biosynthetic principles of these lanthipeptides and discuss open questions for future research.
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Affiliation(s)
- Julian D Hegemann
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
| | - Roderich D Süssmuth
- Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124 10623 Berlin Germany
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36
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Wiebach V, Mainz A, Schnegotzki R, Siegert MAJ, Hügelland M, Pliszka N, Süssmuth RD. An Amphipathic Alpha-Helix Guides Maturation of the Ribosomally-Synthesized Lipolanthines. Angew Chem Int Ed Engl 2020; 59:16777-16785. [PMID: 32533616 PMCID: PMC7540663 DOI: 10.1002/anie.202003804] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/15/2020] [Indexed: 12/19/2022]
Abstract
The recently discovered strongly anti‐Gram‐positive lipolanthines represent a new group of lipidated, ribosomally synthesized and post‐translationally modified peptides (RiPPs). They are bicyclic octapeptides with a central quaternary carbon atom (avionin), which is installed through the cooperative action of the class‐III lanthipeptide synthetase MicKC and the cysteine decarboxylase MicD. Genome mining efforts indicate a widespread distribution and unprecedented biosynthetic diversity of lipolanthine gene clusters, combining elements of RiPPs, polyketide and non‐ribosomal peptide biosynthesis. Utilizing NMR spectroscopy, we show that a (θxx)θxxθxxθ (θ=L, I, V, M or T) motif, which is conserved in the leader peptides of all class‐III and ‐IV lanthipeptides, forms an amphipathic α‐helix in MicA that destines the peptide substrate for enzymatic processing. Our results provide general rules of substrate recruitment and enzymatic regulation during lipolanthine maturation. These insights will facilitate future efforts to rationally design new lanthipeptide scaffolds with antibacterial potency.
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Affiliation(s)
- Vincent Wiebach
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Romina Schnegotzki
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Mary-Ann J Siegert
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Manuela Hügelland
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Nicole Pliszka
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
| | - Roderich D Süssmuth
- Institut für Chemie/ Biologische Chemie, Technische Universität Berlin, Straße des 17. Juni 124, 10623, Berlin, Germany
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