1
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Coe LJ, Zhao Y, Padva L, Keto A, Schittenhelm R, Tailhades J, Pierens G, Krenske EH, Crüsemann M, De Voss JJ, Cryle MJ. Reassignment of the Structure of a Tryptophan-Containing Cyclic Tripeptide Produced by the Biarylitide Crosslinking Cytochrome P450 blt. Chemistry 2024; 30:e202400988. [PMID: 38712638 DOI: 10.1002/chem.202400988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
The structure of the sidechain crosslinked Tyr-Leu-Trp peptide produced by the biarylitide crosslinking cytochrome P450Blt from Micromonospora sp. MW-13 has been reanalysed by a series of NMR, computational and isotope labelling experiments and shown to contain a C-N rather than a C-O bond. Additional in vivo experiments using such a modified peptide show there is a general tolerance of biarylitide crosslinking P450 enzymes for histidine to tryptophan mutations within their minimal peptide substrate sequences despite the lack of such residues noted in natural biarylitide gene clusters. This work further highlights the impressive ability of P450s from biarylitide biosynthesis pathways to act as biocatalysts for the formation of a range of sidechain crosslinked tripeptides.
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Affiliation(s)
- Laura J Coe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Leo Padva
- Institute of Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Angus Keto
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ralf Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Greg Pierens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
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2
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Wang CY, Hu JQ, Wang DG, Li YZ, Wu C. Recent advances in discovery and biosynthesis of natural products from myxobacteria: an overview from 2017 to 2023. Nat Prod Rep 2024; 41:905-934. [PMID: 38390645 DOI: 10.1039/d3np00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
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Affiliation(s)
- Chao-Yi Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Jia-Qi Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - De-Gao Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237 Qingdao, P.R. China.
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3
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Abstract
Covering: 2016 to 2023Ribosomally synthesized and posttranslationally modified peptides (RiPPs) continue to be a rich source of chemically diverse and bioactive peptide natural products. In recent years, cyclophane-containing RiPP natural products and their biosynthetic pathways have been more frequently encountered. This highlight will focus on bacterial monoaryl cyclophane-containing RiPPs. This class of RiPPs is produced by radical SAM/SPASM enzymes that form a crosslink between the aromatic ring and sidechain of two amino acid residues of the precursor peptide. Selected natural products from these pathways exhibit specific antibacterial activity against gram-negative pathogens. The approaches used to discover these pathways and products will be described and categorized as natural product-first or enzyme-first. The breadth of ring systems formed by the enzymes, enzyme mechanism, and recent reports of synthetic methods for constructing these ring systems will also be presented. Bacterial cyclophane-containing RiPPs and their biosynthetic enzymes represent an untapped source of scaffolds for drug discovery and tools for synthetic biology.
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Affiliation(s)
- Chin-Soon Phan
- Department of Pharmacy, National University of Singapore, 4 Science Dr 2, Singapore 117544, Singapore.
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, 4 Science Dr 2, Singapore 117544, Singapore.
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4
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of Macrocyclic Peptides with C-Terminal β-Amino-α-keto Acid Groups by Three Different Metalloenzymes. ACS CENTRAL SCIENCE 2024; 10:1022-1032. [PMID: 38799663 PMCID: PMC11117315 DOI: 10.1021/acscentsci.4c00088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new compound class involving modifications installed by a cytochrome P450, a multinuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-l-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C cross-link between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid, while the methyltransferase acted on the β-carbon of this α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configuration of the atropisomer formed upon biaryl cross-linking. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to isolate new macrocyclic RiPPs biosynthesized via previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Danielle L. Gray
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Toby J. Woods
- School
of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials
Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chandrashekhar Padhi
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kristen M. Flatt
- Materials
Research Laboratory, University of Illinois
at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Suarez AFL, Nguyen TQN, Chang L, Tooh YW, Yong RHS, Leow LC, Koh IYF, Chen H, Koh JWH, Selvanayagam A, Lim V, Tan YE, Agatha I, Winnerdy FR, Morinaka BI. Functional and Promiscuity Studies of Three-Residue Cyclophane Forming Enzymes Show Nonnative C-C Cross-Linked Products and Leader-Dependent Cyclization. ACS Chem Biol 2024; 19:774-783. [PMID: 38417140 DOI: 10.1021/acschembio.3c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Enzymes catalyzing peptide macrocyclization are important biochemical tools in drug discovery. The three-residue cyclophane-forming enzymes (3-CyFEs) are an emerging family of post-translational modifying enzymes that catalyze the formation of three-residue peptide cyclophanes. In this report, we introduce three additional 3-CyFEs, including ChlB, WnsB, and FnnB, that catalyze cyclophane formation on Tyr, Trp, and Phe, respectively. To understand the promiscuity of these enzymes and those previously reported (MscB, HaaB, and YxdB), we tested single amino acid substitutions at the three-residue motif of modification (Ω1X2X3, Ω1 = aromatic). Collectively, we observe that substrate promiscuity is observed at the Ω1 and X2 positions, but a greater specificity is observed for the X3 residue. Two nonnative cyclophane products were characterized showing a Phe-C3 to Arg-Cβ and His-C2 to Pro-Cβ cross-links, respectively. We also tested the leader dependence of selected 3-CyFEs and show that a predicted helix region is important for cyclophane formation. These results demonstrate the biocatalytic potential of these maturases and allow rational design of substrates to obtain a diverse array of genetically encoded 3-residue cyclophanes.
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Affiliation(s)
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Litao Chang
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Rubin How Sheng Yong
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Li Chuan Leow
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Ivan Yu Fan Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Huiyi Chen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Jeffery Wei Heng Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Vernon Lim
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi En Tan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Irene Agatha
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Fernaldo R Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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7
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Treisman M, Coe L, Zhao Y, Sasi VM, Gullick J, Hansen MH, Ly A, Leichthammer V, Hess C, Machell DL, Schittenhelm RB, Hooper J, Jackson CJ, Tailhades J, De Voss JJ, Cryle MJ. An Engineered Biarylitide Cross-Linking P450 from RiPP Biosynthesis Generates Alternative Cyclic Peptides. Org Lett 2024; 26:1828-1833. [PMID: 38417822 DOI: 10.1021/acs.orglett.3c04366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Cytochrome-P450-mediated cross-linking of ribosomally encoded peptides (RiPPs) is rapidly expanding and displays great potential for biocatalysis. Here, we demonstrate that active site engineering of the biarylitide cross-linking enzyme P450Blt enables the formation of His-X-Tyr and Tyr-X-Tyr cross-linked peptides, thus showing how such P450s can be further exploited to produce alternate cyclic tripeptides with controlled cross-linking states.
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Affiliation(s)
- Maxine Treisman
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Laura Coe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Vishnu Mini Sasi
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Jemma Gullick
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Mathias H Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Aviva Ly
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Victor Leichthammer
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Caroline Hess
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Daniel L Machell
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Joel Hooper
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Colin J Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Acton, ACT 2601, Australia
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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8
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Liu CL, Wang ZJ, Shi J, Yan ZY, Zhang GD, Jiao RH, Tan RX, Ge HM. P450-Modified Multicyclic Cyclophane-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides. Angew Chem Int Ed Engl 2024; 63:e202314046. [PMID: 38072825 DOI: 10.1002/anie.202314046] [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: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Cyclic peptides with cyclophane linkers are an attractive compound type owing to the fine-tuned rigid three-dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C-C and C-O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450-modified multicyclic RiPPs, we set out to find cryptic and unknown P450-modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450-modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450-modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450-modified multicyclic RiPPs with different cyclophane linkers through heterologous expression. Further mutation of the key ring-forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane-containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.
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Affiliation(s)
- Cheng Li Liu
- 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 Jie 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
| | - 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
| | - Zhang Yuan Yan
- 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
| | - Guo Dong Zhang
- 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
| | - 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
| | - 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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9
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Pattanayakanahalli Henjarappa K, Das S, Mahanta N. A new class of macrocyclic peptides. Nat Chem Biol 2024; 20:136-139. [PMID: 38191943 DOI: 10.1038/s41589-023-01507-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Affiliation(s)
| | - Simita Das
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Nilkamal Mahanta
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India.
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10
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Nguyen DT, Zhu L, Gray DL, Woods TJ, Padhi C, Flatt KM, Mitchell DA, van der Donk WA. Biosynthesis of macrocyclic peptides with C-terminal β-amino-α-keto acid groups by three different metalloenzymes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564719. [PMID: 37965205 PMCID: PMC10635010 DOI: 10.1101/2023.10.30.564719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Advances in genome sequencing and bioinformatics methods have identified a myriad of biosynthetic gene clusters (BGCs) encoding uncharacterized molecules. By mining genomes for BGCs containing a prevalent peptide-binding domain used for the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), we uncovered a new class involving modifications installed by a cytochrome P450, a multi-nuclear iron-dependent non-heme oxidative enzyme (MNIO, formerly DUF692), a cobalamin- and radical S-adenosyl-L-methionine-dependent enzyme (B12-rSAM), and a methyltransferase. All enzymes encoded by the BGC were functionally expressed in Burkholderia sp. FERM BP-3421. Structural characterization with 2D-NMR and Marfey's method on the resulting RiPP demonstrated that the P450 enzyme catalyzed the formation of a biaryl C-C crosslink between two Tyr residues with the B12-rSAM generating β-methyltyrosine. The MNIO transformed a C-terminal Asp residue into aminopyruvic acid while the methyltransferase acted on the β-carbon of the α-keto acid. Exciton-coupled circular dichroism spectroscopy and microcrystal electron diffraction (MicroED) were used to elucidate the stereochemical configurations of the atropisomer that formed upon biaryl crosslinking. The conserved Cys residue in the precursor peptide was not modified as in all other characterized MNIO-containing BGCs; However, mutational analyses demonstrated that it was essential for the MNIO activity on the C-terminal Asp. To the best of our knowledge, the MNIO featured in this pathway is the first to modify a residue other than Cys. This study underscores the utility of genome mining to discover new macrocyclic RiPPs and that RiPPs remain a significant source of previously undiscovered enzyme chemistry.
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Affiliation(s)
- Dinh T. Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Danielle L. Gray
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Toby J. Woods
- School of Chemical Sciences George L. Clark X-Ray Facility and 3M Materials Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chandrashekhar Padhi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
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11
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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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12
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-guided discovery of biaryl-linked lasso peptides. Chem Sci 2023; 14:13176-13183. [PMID: 38023510 PMCID: PMC10664482 DOI: 10.1039/d3sc02380j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Using mass spectrometry, stable isotope incorporation, and extensive 2D-NMR spectrometry, we report the structural characterization of two unique examples of (C-N) biaryl-linked lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with a Trp-Tyr crosslink, while longipepetin A, from Longimycelium tulufanense, features a Trp-Trp linkage. Besides the unusual bicyclic frame, a Met of longipepetin A undergoes S-methylation to yield a trivalent sulfonium, a heretofore unprecedented RiPP modification. A bioinformatic survey revealed additional lasso peptide BGCs containing P450 enzymes which await future characterization. Lastly, nocapeptin A bioactivity was assessed against a panel of human and bacterial cell lines with modest growth-suppression activity detected towards Micrococcus luteus.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Dinh T Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
| | - Douglas A Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen Tübingen Germany
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13
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He BB, Liu J, Cheng Z, Liu R, Zhong Z, Gao Y, Liu H, Song ZM, Tian Y, Li YX. Bacterial Cytochrome P450 Catalyzed Post-translational Macrocyclization of Ribosomal Peptides. Angew Chem Int Ed Engl 2023; 62:e202311533. [PMID: 37767859 DOI: 10.1002/anie.202311533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 09/29/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a fascinating group of natural products that exhibit diverse structural features and bioactivities. P450-catalyzed RiPPs stand out as a unique but underexplored family. Herein, we introduce a rule-based genome mining strategy that harnesses the intrinsic biosynthetic principles of RiPPs, including the co-occurrence and co-conservation of precursors and P450s and interactions between them, successfully facilitating the identification of diverse P450-catalyzed RiPPs. Intensive BGC characterization revealed four new P450s, KstB, ScnB, MciB, and SgrB, that can catalyze the formation of Trp-Trp-Tyr (one C-C and two C-N bonds), Tyr-Trp (C-C bond), Trp-Trp (C-N bond), and His-His (ether bond) crosslinks, respectively, within three or four residues. KstB, ScnB, and MciB could accept non-native precursors, suggesting they could be promising starting templates for bioengineering to construct macrocycles. Our study highlights the potential of P450s to expand the chemical diversity of strained macrocyclic peptides and the range of biocatalytic tools available for peptide macrocyclization.
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Affiliation(s)
- Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jing Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Runze Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongqi Tian
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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14
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Zhong G. Cytochromes P450 Associated with the Biosyntheses of Ribosomally Synthesized and Post-translationally Modified Peptides. ACS BIO & MED CHEM AU 2023; 3:371-388. [PMID: 37876494 PMCID: PMC10591300 DOI: 10.1021/acsbiomedchemau.3c00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 10/26/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of exponentially increased natural products with characteristic chemical structures, topologies, and biosynthetic mechanisms as well as exceptional bioactivities including antibacteria, antitumors, and antiviruses. The biosynthesis of RiPP proceeds via a ribosomally assembled precursor peptide that undergoes varied post-translational modifications to generate a mature peptide. Cytochrome P450 (CYP or P450) monooxygenases are a superfamily of heme-containing enzymes that span a wide range of secondary metabolite biosynthetic pathways due to their broad substrate scopes and excellent catalytic versatility. In contrast to the enormous quantities of RiPPs and P450s, the P450 associated RiPP biosynthesis is comparatively limited, with most of their functions and timings remaining mysterious. Herein, this Review aims to provide an overview on the striking roles of P450s in RiPP biosyntheses uncovered to date and to illustrate their remarkable functions, mechanisms, as well as remaining challenges. This will shed light on novel P450 discovery and characterizations in RiPP biosyntheses.
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Affiliation(s)
- Guannan Zhong
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Suzhou
Research Institute of Shandong University, Suzhou 215123, China
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15
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Nam H, An JS, Lee J, Yun Y, Lee H, Park H, Jung Y, Oh KB, Oh DC, Kim S. Exploring the Diverse Landscape of Biaryl-Containing Peptides Generated by Cytochrome P450 Macrocyclases. J Am Chem Soc 2023; 145:22047-22057. [PMID: 37756205 DOI: 10.1021/jacs.3c07140] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Cytochrome P450 enzymes (P450s) catalyze diverse oxidative cross-coupling reactions between aromatic substrates in the natural product biosynthesis. Specifically, P450s install distinct biaryl macrocyclic linkages in three families of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, the chemical diversity of biaryl-containing macrocyclic RiPPs remains largely unexplored. Here, we demonstrate that P450s have the capability to generate diverse biaryl linkages on RiPPs, collectively named "cyptides". Homology-based genome mining for P450 macrocyclases revealed 19 novel groups of homologous biosynthetic gene clusters (BGCs) with distinct aromatic residue patterns in the precursor peptides. Using the P450-modified precursor peptides heterologously coexpressed with corresponding P450s in Escherichia coli, we determined the NMR structures of three novel biaryl-containing peptides─the enzymatic products, roseovertin (1), rubrin (2), and lapparbin (3)─and confirmed the formation of three unprecedented or rare biaryl linkages: Trp C-7'-to-His N-τ in 1, Trp C-7'-to-Tyr C-6 in 2, and Tyr C-6-to-Trp N-1' in 3. Biochemical characterization indicated that certain P450s in these pathways have a relaxed substrate specificity. Overall, our studies suggest that P450 macrocyclases have evolved to create diverse biaryl linkages in RiPPs, promoting the exploration of a broader chemical space for biaryl-containing peptides encoded in bacterial genomes.
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16
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Zdouc MM, van der Hooft JJJ, Medema MH. Metabolome-guided genome mining of RiPP natural products. Trends Pharmacol Sci 2023; 44:532-541. [PMID: 37391295 DOI: 10.1016/j.tips.2023.06.004] [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: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a chemically diverse class of metabolites. Many RiPPs show potent biological activities that make them attractive starting points for drug development. A promising approach for the discovery of new classes of RiPPs is genome mining. However, the accuracy of genome mining is hampered by the lack of signature genes shared across different RiPP classes. One way to reduce false-positive predictions is by complementing genomic information with metabolomics data. In recent years, several new approaches addressing such integrative genomics and metabolomics analyses have been developed. In this review, we provide a detailed discussion of RiPP-compatible software tools that integrate paired genomics and metabolomics data. We highlight current challenges in data integration and identify opportunities for further developments targeting new classes of bioactive RiPPs.
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Affiliation(s)
- Mitja M Zdouc
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands; Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands.
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17
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An JS, Lee H, Kim H, Woo S, Nam H, Lee J, Lee JY, Nam SJ, Lee SK, Oh KB, Kim S, Oh DC. Discovery and Biosynthesis of Cihunamides, Macrocyclic Antibacterial RiPPs with a Unique C-N Linkage Formed by CYP450 Catalysis. Angew Chem Int Ed Engl 2023; 62:e202300998. [PMID: 37114290 DOI: 10.1002/anie.202300998] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
Cihunamides A-D (1-4), novel antibacterial RiPPs, were isolated from volcanic-island-derived Streptomyces sp. The structures of 1-4 were elucidated by 1 H, 13 C, and 15 N NMR, MS, and chemical derivatization; they contain a tetrapeptide core composed of WNIW, cyclized by a unique C-N linkage between two Trp units. Genome mining of the producer strain revealed two biosynthetic genes encoding a cytochrome P450 enzyme and a precursor peptide. Heterologous co-expression of the core genes demonstrated the biosynthesis of cihunamides through P450-mediated oxidative Trp-Trp cross-linking. Further bioinformatic analysis uncovered 252 homologous gene clusters, including that of tryptorubins, which possess a distinct Trp-Trp linkage. Cihunamides do not display the non-canonical atropisomerism shown in tryptorubins, which are the founding members of the "atropitide" family. Therefore, we propose to use a new RiPP family name, "bitryptides", for cihunamides, tryptorubins, and their congeners, wherein the Trp-Trp linkages define the structural class rather than non-canonical atropisomerism.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyunbin Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyungyu Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Seungyeon Woo
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Hyunsung Nam
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Jayho Lee
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Ji Yun Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, College of Natural Sciences, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760 (Republic of, Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Ki-Bong Oh
- Department of Agriculture Biotechnology, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Seokhee Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 (Republic of, Korea
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18
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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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19
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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20
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Saad H, Majer T, Bhattarai K, Lampe S, Nguyen DT, Kramer M, Straetener J, Brötz-Oesterhelt H, Mitchell DA, Gross H. Bioinformatics-Guided Discovery of Biaryl-Tailored Lasso Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531328. [PMID: 36945544 PMCID: PMC10028836 DOI: 10.1101/2023.03.06.531328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that feature an isopeptide bond and a distinct lariat fold. A growing number of secondary modifications have been described that further decorate lasso peptide scaffolds. Using genome mining, we have discovered a pair of lasso peptide biosynthetic gene clusters (BGCs) that include cytochrome P450 genes. Here, we report the structural characterization of two unique examples of (C-N) biaryl-containing lasso peptides. Nocapeptin A, from Nocardia terpenica, is tailored with Trp-Tyr crosslink while longipepetin A, from Longimycelium tulufanense, features Trp-Trp linkage. Besides the unusual bicyclic frame, longipepetin A receives an S-methylation by a new Met methyltransferase resulting in unprecedented sulfonium-bearing RiPP. Our bioinformatic survey revealed P450(s) and further maturating enzyme(s)-containing lasso BGCs awaiting future characterization.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Thomas Majer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Keshab Bhattarai
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Sarah Lampe
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
| | - Dinh T. Nguyen
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Markus Kramer
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen (Germany)
| | - Jan Straetener
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen (Germany)
| | - Douglas A. Mitchell
- Department of Chemistry and the Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 (United States)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen (Germany)
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21
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Biermann F, Wenski SL, Helfrich EJN. Navigating and expanding the roadmap of natural product genome mining tools. Beilstein J Org Chem 2022; 18:1656-1671. [PMID: 36570563 PMCID: PMC9749553 DOI: 10.3762/bjoc.18.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
Natural products are structurally highly diverse and exhibit a wide array of biological activities. As a result, they serve as an important source of new drug leads. Traditionally, natural products have been discovered by bioactivity-guided fractionation. The advent of genome sequencing technology has resulted in the introduction of an alternative approach towards novel natural product scaffolds: Genome mining. Genome mining is an in-silico natural product discovery strategy in which sequenced genomes are analyzed for the potential of the associated organism to produce natural products. Seemingly universal biosynthetic principles have been deciphered for most natural product classes that are used to detect natural product biosynthetic gene clusters using pathway-encoded conserved key enzymes, domains, or motifs as bait. Several generations of highly sophisticated tools have been developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that lack genes with conserved signature sequences. In this perspective, we take a closer look at state-of-the-art genome mining tools that are based on either hard-coded rules or machine learning algorithms, with an emphasis on the confidence of their predictions and potential to identify non-canonical natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The combination of all genome mining approaches will pave the way towards a more comprehensive understanding of the full biosynthetic repertoire encoded in microbial genome sequences.
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Affiliation(s)
- Friederike Biermann
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Sebastian L Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Eric J N Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt am Main, Germany,LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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22
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He B, Cheng Z, Zhong Z, Gao Y, Liu H, Li Y. Expanded Sequence Space of Radical S‐Adenosylmethionine‐Dependent Enzymes Involved in Post‐translational Macrocyclization**. Angew Chem Int Ed Engl 2022; 61:e202212447. [DOI: 10.1002/anie.202212447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Bei‐Bei He
- 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 Cheng
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
| | - Ying Gao
- 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
| | - Hongyan Liu
- 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
| | - Yong‐Xin Li
- Department of Chemistry and The Swire Institute of Marine Science The University of Hong Kong Pokfulam Road Hong Kong China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China
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23
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022; 61:e202208361. [PMID: 35939298 PMCID: PMC9826248 DOI: 10.1002/anie.202208361] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 01/11/2023]
Abstract
Biomacromolecules are known to feature complex three-dimensional shapes that are essential for their function. Among natural products, ambiguous molecular shapes are a rare phenomenon. The hexapeptide tryptorubin A can adopt one of two unusual atropisomeric configurations. Initially hypothesized to be a non-ribosomal peptide, we show that tryptorubin A is the first characterized member of a new family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) that we named atropopeptides. The sole modifying enzyme encoded in the gene cluster, a cytochrome P450 monooxygenase, is responsible for the atropospecific formation of one carbon-carbon and two carbon-nitrogen bonds. The characterization of two additional atropopeptide biosynthetic pathways revealed a two-step maturation process. Atropopeptides promote pro-angiogenic cell functions as indicated by an increase in endothelial cell proliferation and undirected migration. Our study expands the biochemical space of RiPP-modifying enzymes and paves the way towards the chemoenzymatic utilization of atropopeptide-modifying P450s.
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Affiliation(s)
- Pakjira Nanudorn
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Friederike Biermann
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Pelin Erkoc
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Sabrina D. Dirnberger
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Thao N. Phan
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Robert Fürst
- LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany,Institute of Pharmaceutical BiologyGoethe University FrankfurtMax-von-Laue Strasse 960438FrankfurtGermany
| | - Reiko Ueoka
- School of Marine BiosciencesKitasato University1-15-1 Kitasato, Minami-kuSagamiharaKanagawa, 252-0373Japan
| | - Eric J. N. Helfrich
- Institute for Molecular Bio ScienceGoethe University FrankfurtMax-von-Laue Strasse 960438Frankfurt am MainGermany,LOEWE Center for Translational Biodiversity Genomics (TBG)Senckenberganlage 2560325Frankfurt am MainGermany
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24
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450 Blt Enables Versatile Peptide Cyclisation to Generate Histidine- and Tyrosine-Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202204957. [PMID: 35851739 PMCID: PMC9542247 DOI: 10.1002/anie.202204957] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 12/05/2022]
Abstract
We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.
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Affiliation(s)
- Yongwei Zhao
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Maxine Treisman
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Alasdair McKay
- Department of ChemistryMonash UniversityClaytonVIC 3800Australia
| | - Leo Padva
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of TennesseeMemphisTN 38163USA
| | - David L. Steer
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
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25
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Nanudorn P, Thiengmag S, Biermann F, Erkoc P, Dirnberger SD, Phan TN, Fürst R, Ueoka R, Helfrich EJN. Atropopeptides are a Novel Family of Ribosomally Synthesized and Posttranslationally Modified Peptides with a Complex Molecular Shape. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pakjira Nanudorn
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sirinthra Thiengmag
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Friederike Biermann
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Pelin Erkoc
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Sabrina Doris Dirnberger
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Thao Ngoc Phan
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute for Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Robert Fürst
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Institute of Pharmaceutical Biology Biozentrum Building 230Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
| | - Reiko Ueoka
- Kitasato University: Kitasato Daigaku School of Marine Biosciences 1-15-1 KitasatoMinami-kuSagamihara 252-0373 Kanagawa JAPAN
| | - Eric Jan Nikolaus Helfrich
- Goethe University Frankfurt: Goethe-Universitat Frankfurt am Main Molecular Bio Science Biozentrum Building 250Max-von-Laue-Strasse 9 60438 Frankfurt GERMANY
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26
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450Blt Enables Versatile Peptide Cyclisation to Generate Histidine and Tyrosine Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | - Leo Padva
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Pharmaceutical Biology GERMANY
| | - Max Crüsemann
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Biology GERMANY
| | - David R Nelson
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Microbiology UNITED STATES
| | - David L Steer
- Monash University Biochemistry and Molecular Biology AUSTRALIA
| | | | | | - Max J. Cryle
- Monash University Department of Biochemistry and Molecular Biology 15 Innovation WalkMonash University 3800 Melbourne AUSTRALIA
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27
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Abstract
The past decade has seen impressive advances in understanding the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). One of the most common modifications found in these natural products is macrocyclization, a strategy also used by medicinal chemists to improve metabolic stability and target affinity and specificity. Another tool of the peptide chemist, modification of the amides in a peptide backbone, has also been observed in RiPPs. This review discusses the molecular mechanisms of biosynthesis of a subset of macrocyclic RiPP families, chosen because of the unusual biochemistry involved: the five classes of lanthipeptides (thioether cyclization by Michael-type addition), sactipeptides and ranthipeptides (thioether cyclization by radical chemistry), thiopeptides (cyclization by [4+2] cycloaddition), and streptide (cyclization by radical C-C bond formation). In addition, the mechanisms of backbone amide methylation, backbone epimerization, and backbone thioamide formation are discussed, as well as an unusual route to small molecules by posttranslational modification.
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Affiliation(s)
- Hyunji Lee
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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28
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Sugawara K, Kanki D, Watanabe R, Matsushima R, Ise Y, Yokose H, Morii Y, Yamawaki N, Ninomiya A, Okada S, Matsunaga S. Aciculitin D, a cytotoxic heterodetic cyclic peptide from a Poecillastra sp. marine sponge. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Vind K, Maffioli S, Fernandez Ciruelos B, Waschulin V, Brunati C, Simone M, Sosio M, Donadio S. N-Acetyl-Cysteinylated Streptophenazines from Streptomyces. JOURNAL OF NATURAL PRODUCTS 2022; 85:1239-1247. [PMID: 35422124 PMCID: PMC9150181 DOI: 10.1021/acs.jnatprod.1c01123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Indexed: 05/29/2023]
Abstract
Here, we describe two N-acetyl-cysteinylated streptophenazines (1 and 2) produced by the soil-derived Streptomyces sp. ID63040 and identified through a metabolomic approach. These metabolites attracted our interest due to their low occurrence frequency in a large library of fermentation broth extracts and their consistent presence in biological replicates of the producer strain. The compounds were found to possess broad-spectrum antibacterial activity while exhibiting low cytotoxicity. The biosynthetic gene cluster from Streptomyces sp. ID63040 was found to be highly similar to the streptophenazine reference cluster in the MIBiG database, which originates from the marine Streptomyces sp. CNB-091. Compounds 1 and 2 were the main streptophenazine products from Streptomyces sp. ID63040 at all cultivation times but were not detected in Streptomyces sp. CNB-091. The lack of obvious candidates for cysteinylation in the Streptomyces sp. ID63040 biosynthetic gene cluster suggests that the N-acetyl-cysteine moiety derives from cellular functions, most likely from mycothiol. Overall, our data represent an interesting example of how to leverage metabolomics for the discovery of new natural products and point out the often-neglected contribution of house-keeping cellular functions to natural product diversification.
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Affiliation(s)
- Kristiina Vind
- NAICONS
Srl, 20139 Milan, Italy
- Host-Microbe
Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | | | | | - Valentin Waschulin
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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30
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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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31
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Iorio M, Gentile A, Brunati C, Tocchetti A, Landini P, Maffioli SI, Donadio S, Sosio M. Allopeptimicins: unique antibacterial metabolites generated by hybrid PKS-NRPS, with original self-defense mechanism in Actinoallomurus. RSC Adv 2022; 12:16640-16655. [PMID: 35754877 PMCID: PMC9169493 DOI: 10.1039/d2ra02094g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
In the search for structurally novel metabolites with antibacterial activity, innovative approaches must be implemented to increase the probability of discovering novel chemistry from microbial sources. Here we report on the application of metabolomic tools to the genus Actinoallomurus, a poorly explored member of the Actinobacteria. From examining extracts derived from 88 isolates belonging to this genus, we identified a family of cyclodepsipeptides acylated with a C20 polyketide chain, which we named allopeptimicins. These molecules possess unusual structural features, including several double bonds in the amino-polyketide chain and four non-proteinogenic amino acids in the octapeptide. Remarkably, allopeptimicins are produced as a complex of active and inactive congeners, the latter carrying a sulfate group on the polyketide amine. This modification is also a mechanism of self-protection in the producer strain. The structural uniqueness of allopeptimicins is reflected in a biosynthetic gene cluster showing a mosaic structure, with dedicated gene cassettes devoted to formation of specialized precursors and modular assembly lines related to those from different pathways. Untargeted metabolomic analysis of Actinoallomurus spp. unveiled an unprecedented acylated cyclodepsipeptide with unusual features and potent antibacterial activity.![]()
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Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C-N Biaryl Crosslinking in RiPP Biosynthesis. Molecules 2021; 26:molecules26247483. [PMID: 34946566 PMCID: PMC8708641 DOI: 10.3390/molecules26247483] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing post-translational modifications, as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl linkage between two aromatic amino acids. Recent genomic analyses revealed that the minimal biosynthetic prerequisite of biarylitide biosynthesis consists of only one ribosomally synthesized pentapeptide precursor as the substrate and a modifying cytochrome-P450-dependent enzyme. In silico analyses revealed that minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders, including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH, termed Myxarylin, from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide that surprisingly exhibits a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides that feature a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by the heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide-type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.
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33
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Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021; 38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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34
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Tocchetti A, Iorio M, Hamid Z, Armirotti A, Reggiani A, Donadio S. Understanding the Mechanism of Action of NAI-112, a Lanthipeptide with Potent Antinociceptive Activity. Molecules 2021; 26:molecules26226764. [PMID: 34833857 PMCID: PMC8624038 DOI: 10.3390/molecules26226764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
NAI-112, a glycosylated, labionine-containing lanthipeptide with weak antibacterial activity, has demonstrated analgesic activity in relevant mouse models of nociceptive and neuropathic pain. However, the mechanism(s) through which NAI-112 exerts its analgesic and antibacterial activities is not known. In this study, we analyzed changes in the spinal cord lipidome resulting from treatment with NAI-112 of naive and in-pain mice. Notably, NAI-112 led to an increase in phosphatidic acid levels in both no-pain and pain models and to a decrease in lysophosphatidic acid levels in the pain model only. We also showed that NAI-112 can form complexes with dipalmitoyl-phosphatidic acid and that Staphylococcus aureus can become resistant to NAI-112 through serial passages at sub-inhibitory concentrations of the compound. The resulting resistant mutants were phenotypically and genotypically related to vancomycin-insensitive S. aureus strains, suggesting that NAI-112 binds to the peptidoglycan intermediate lipid II. Altogether, our results suggest that NAI-112 binds to phosphate-containing lipids and blocks pain sensation by decreasing levels of lysophosphatidic acid in the TRPV1 pathway.
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Affiliation(s)
| | - Marianna Iorio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; (A.T.); (S.D.)
- Correspondence:
| | - Zeeshan Hamid
- D3 Validation, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy; (Z.H.); (A.R.)
| | - Andrea Armirotti
- Analytical Chemistry Lab, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy;
| | - Angelo Reggiani
- D3 Validation, Fondazione Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy; (Z.H.); (A.R.)
| | - Stefano Donadio
- Naicons Srl, Viale Ortles 22/4, 20139 Milan, Italy; (A.T.); (S.D.)
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35
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Russell AH, Vior NM, Hems ES, Lacret R, Truman AW. Discovery and characterisation of an amidine-containing ribosomally-synthesised peptide that is widely distributed in nature. Chem Sci 2021; 12:11769-11778. [PMID: 34659714 PMCID: PMC8442711 DOI: 10.1039/d1sc01456k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/31/2021] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural product with a wide range of bioactivities. Genome mining for RiPP biosynthetic gene clusters (BGCs) is often hampered by poor annotation of the short precursor peptides that are ultimately modified into the final molecule. Here, we utilise a previously described genome mining tool, RiPPER, to identify novel RiPP precursor peptides near YcaO-domain proteins, enzymes that catalyse various RiPP post-translational modifications including heterocyclisation and thioamidation. Using this dataset, we identified a novel and diverse family of RiPP BGCs spanning over 230 species of Actinobacteria and Firmicutes. A representative BGC from Streptomyces albidoflavus J1074 (formerly known as Streptomyces albus) was characterised, leading to the discovery of streptamidine, a novel amidine-containing RiPP. This new BGC family highlights the breadth of unexplored natural products with structurally rare features, even in model organisms.
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Affiliation(s)
- Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Edward S Hems
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
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Undabarrena A, Pereira CF, Kruasuwan W, Parra J, Sélem-Mojica N, Vind K, Schniete JK. Integrating perspectives in actinomycete research: an ActinoBase review of 2020-21. MICROBIOLOGY (READING, ENGLAND) 2021; 167:001084. [PMID: 34515628 PMCID: PMC8549240 DOI: 10.1099/mic.0.001084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Last year ActinoBase, a Wiki-style initiative supported by the UK Microbiology Society, published a review highlighting the research of particular interest to the actinomycete community. Here, we present the second ActinoBase review showcasing selected reports published in 2020 and early 2021, integrating perspectives in the actinomycete field. Actinomycetes are well-known for their unsurpassed ability to produce specialised metabolites, of which many are used as therapeutic agents with antibacterial, antifungal, or immunosuppressive activities. Much research is carried out to understand the purpose of these metabolites in the environment, either within communities or in host interactions. Moreover, many efforts have been placed in developing computational tools to handle big data, simplify experimental design, and find new biosynthetic gene cluster prioritisation strategies. Alongside, synthetic biology has provided advances in tools to elucidate the biosynthesis of these metabolites. Additionally, there are still mysteries to be uncovered in understanding the fundamentals of filamentous actinomycetes' developmental cycle and regulation of their metabolism. This review focuses on research using integrative methodologies and approaches to understand the bigger picture of actinomycete biology, covering four research areas: i) technology and methodology; ii) specialised metabolites; iii) development and regulation; and iv) ecology and host interactions.
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Affiliation(s)
- Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile
| | - Camila F Pereira
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Worarat Kruasuwan
- Microbial Cell Factory Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Jonathan Parra
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Nelly Sélem-Mojica
- Centro de Ciencias Matemáticas, Antigua Carretera a Pátzcuaro # 8701, Col. Ex Hacienda San José de la Huerta, Morelia C.P. 58089, Michoacán, México
| | - Kristiina Vind
- NAICONS Srl, Viale Ortles 22/4, 20139 Milan (MI), Italy
- Host-Microbe Interactomics Group, Wageningen University, De Elst 1 6708 WD, Wageningen, Netherlands
| | - Jana K. Schniete
- Biology, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
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Crüsemann M. Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows. Mar Drugs 2021; 19:142. [PMID: 33807702 PMCID: PMC7998270 DOI: 10.3390/md19030142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/18/2022] Open
Abstract
Bacterial natural products possess potent bioactivities and high structural diversity and are typically encoded in biosynthetic gene clusters. Traditional natural product discovery approaches rely on UV- and bioassay-guided fractionation and are limited in terms of dereplication. Recent advances in mass spectrometry, sequencing and bioinformatics have led to large-scale accumulation of genomic and mass spectral data that is increasingly used for signature-based or correlation-based mass spectrometry genome mining approaches that enable rapid linking of metabolomic and genomic information to accelerate and rationalize natural product discovery. In this mini-review, these approaches are presented, and discovery examples provided. Finally, future opportunities and challenges for paired omics-based natural products discovery workflows are discussed.
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Affiliation(s)
- Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
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Zdouc MM, Iorio M, Maffioli SI, Crüsemann M, Donadio S, Sosio M. Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus. JOURNAL OF NATURAL PRODUCTS 2021; 84:204-219. [PMID: 33496580 PMCID: PMC7922807 DOI: 10.1021/acs.jnatprod.0c00807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 06/12/2023]
Abstract
Despite an excellent track record, microbial drug discovery suffers from high rates of rediscovery. Better workflows for the rapid investigation of complex extracts are needed to increase throughput and to allow early prioritization of samples. In addition, systematic characterization of poorly explored strains is seldomly performed. Here, we report a metabolomic study of 72 isolates belonging to the rare actinomycete genus Planomonospora, using a workflow of commonly used open access tools to investigate its secondary metabolites. The results reveal a correlation of chemical diversity and strain phylogeny, with classes of metabolites exclusive to certain phylogroups. We were able to identify previously reported Planomonospora metabolites, including the ureylene-containing oligopeptide antipain, the thiopeptide siomycin including new congeners, and the ribosomally synthesized peptides sphaericin and lantibiotic 97518. In addition, we found that Planomonospora strains can produce the siderophore desferrioxamine or a salinichelin-like peptide. Analysis of the genomes of three newly sequenced strains led to the detection of 59 gene cluster families, of which three were connected to products found by LC-MS/MS profiling. This study demonstrates the value of metabolomic studies to investigate poorly explored taxa and provides a first picture of the biosynthetic capabilities of the genus Planomonospora.
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Affiliation(s)
- Mitja M. Zdouc
- Naicons
Srl., Viale Ortles 22/4, 20139 Milano, Italy
- Swammerdam
Institute for Life Sciences, University
of Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | | | | | - Max Crüsemann
- Institut
für Pharmazeutische Biologie, Rheinische
Friedrich-Wilhelms-Universität, Nußallee 6, 53115 Bonn, Germany
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