1
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Gao L, Ding Q, Lei X. Hunting for the Intermolecular Diels-Alderase. Acc Chem Res 2024. [PMID: 38994670 DOI: 10.1021/acs.accounts.4c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
ConspectusThe Diels-Alder reaction is well known as a concerted [4 + 2] cycloaddition governed by the Woodward-Hoffmann rules. Since Prof. Otto Diels and his student Kurt Alder initially reported the intermolecular [4 + 2] cycloaddition between cyclopentadiene and quinone in 1928, it has been recognized as one of the most powerful chemical transformations to build C-C bonds and construct cyclic structures. This named reaction has been widely used in synthesizing natural products and drug molecules. Driven by the synthetic importance of the Diels-Alder reaction, identifying the enzyme that stereoselectively catalyzes the Diels-Alder reaction has become an intriguing research area in natural product biosynthesis and biocatalysis. With significant progress in sequencing and bioinformatics, dozens of Diels-Alderases have been characterized in microbial natural product biosynthesis. However, few are evolutionally dedicated to catalyzing an intermolecular Diels-Alder reaction with a concerted mechanism.This Account summarizes our endeavors to hunt for the naturally occurring intermolecular Diels-Alderase from plants. Our research journey started from the biomimetic syntheses of D-A-type terpenoids and flavonoids, showing that plants use both nonenzymatic and enzymatic intermolecular [4 + 2] cycloadditions to create complex molecules. Inspired by the biomimetic syntheses, we identify an intermolecular Diels-Alderase hidden in the biosynthetic pathway of mulberry Diels-Alder-type cycloadducts using a biosynthetic intermediate probe-based target identification strategy. This enzyme, MaDA, is an endo-selective Diels-Alderase and is then functionally characterized as a standalone intermolecular Diels-Alderase with a concerted but asynchronous mechanism. We also discover the exo-selective intermolecular Diels-Alderases in Morus plants. Both the endo- and exo-selective Diels-Alderases feature a broad substrate scope, but their mechanisms for controlling the endo/exo pathway are different. These unique intermolecular Diels-Alderases phylogenetically form a subgroup of FAD-dependent enzymes that can be found only in moraceous plants, explaining why this type of [4 + 2] cycloadduct is unique to moraceous plants. Further studies of the evolutionary mechanism reveal that an FAD-dependent oxidocyclase could acquire the Diels-Alderase activity via four critical amino acid mutations and then gradually lose its original oxidative activity to become a standalone Diels-Alderase during the natural evolution. Based on these insights, we designed new Diels-Alderases and achieved the diversity-oriented chemoenzymatic synthesis of D-A products using either naturally occurring or engineered Diels-Alderases.Overall, this Account describes our decade-long efforts to discover the intermolecular Diels-Alderases in Morus plants, particularly highlighting the importance of biomimetic synthesis and chemical proteomics in discovering new intermolecular Diels-Alderases from plants. Meanwhile, this Account also covers the evolutionary and catalytic mechanism study of intermolecular Diels-Alderases that may provide new insights into how to discover and design new Diels-Alderases as powerful biocatalysts for organic synthesis.
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Affiliation(s)
- Lei Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Ding
- School of Life Science, Tsinghua University, Beijing 100084, China
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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2
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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3
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Ramos Figueroa J, Zhu L, van der Donk WA. Unexpected Transformations during Pyrroloiminoquinone Biosynthesis. J Am Chem Soc 2024; 146:14235-14245. [PMID: 38719200 PMCID: PMC11117183 DOI: 10.1021/jacs.4c03677] [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: 03/14/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/21/2024]
Abstract
Pyrroloiminoquinone-containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP- and tRNA-dependent manner catalyzed by a PEptide Aminoacyl-tRNA Ligase (PEARL). The indole of Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes from two gene clusters, which show that the previously proposed pathway is incorrect and that Nature's route toward pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, amino groups in pyrroloiminoquinones are derived from (at least) three different sources, glycine, asparagine, and leucine, all introduced in a tRNA-dependent manner. We also show that an FAD-dependent putative glycine oxidase (Amm14) is required for the process that incorporates the nitrogens from glycine and leucine and that a quinone reductase is required for the incorporation of asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes, such as the glutamyl-tRNA-dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry and
Howard Hughes Medical Institute, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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4
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Sugrue I, Ross RP, Hill C. Bacteriocin diversity, function, discovery and application as antimicrobials. Nat Rev Microbiol 2024:10.1038/s41579-024-01045-x. [PMID: 38730101 DOI: 10.1038/s41579-024-01045-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2024] [Indexed: 05/12/2024]
Abstract
Bacteriocins are potent antimicrobial peptides that are produced by bacteria. Since their discovery almost a century ago, diverse peptides have been discovered and described, and some are currently used as commercial food preservatives. Many bacteriocins exhibit extensively post-translationally modified structures encoded on complex gene clusters, whereas others have simple linear structures. The molecular structures, mechanisms of action and resistance have been determined for a number of bacteriocins, but most remain incompletely characterized. These gene-encoded peptides are amenable to bioengineering strategies and heterologous expression, enabling metagenomic mining and modification of novel antimicrobials. The ongoing global antimicrobial resistance crisis demands that novel therapeutics be developed to combat infectious pathogens. New compounds that are target-specific and compatible with the resident microbiota would be valuable alternatives to current antimicrobials. As bacteriocins can be broad or narrow spectrum in nature, they are promising tools for this purpose. However, few bacteriocins have gone beyond preclinical trials and none is currently used therapeutically in humans. In this Review, we explore the broad diversity in bacteriocin structure and function, describe identification and optimization methods and discuss the reasons behind the lack of translation beyond the laboratory of these potentially valuable antimicrobials.
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Affiliation(s)
- Ivan Sugrue
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
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5
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Guo C, Qi RY, Ren JY, Xu DD, Zhang Q, Gao JM, Tang JJ. Inubritantrimers A-D: Trimerized Sesquiterpenoid [4 + 2] Adducts Featuring a Distinctive Spiro-Polycyclic Scaffold from Inula britannica. J Org Chem 2024; 89:5029-5037. [PMID: 38531374 DOI: 10.1021/acs.joc.4c00248] [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: 03/28/2024]
Abstract
Inubritantrimer A (1), a trace trimerized sesquiterpenoid [4 + 2] adduct featuring an unusual exo-exo type spiro-polycyclic scaffold, together with three new endo-exo [4 + 2] adducts, inubritantrimers B-D (2-4), were discovered from the flowers of Inula britannica. Their structures were elucidated using 1D/2D NMR, X-ray diffraction, and ECD approaches. 1 is characterized as a novel exo-exo trimer, synthesized biogenetically from three sesquiterpenoid monomers, featuring a unique linkage of C-11/C-1', C-13/C-3' and C-13'/C-3″, C-11'/C-1″ through a two-step exo [4 + 2] cycloaddition process. Compounds 1-4 exhibited modest cytotoxicity against breast cancer cells with IC50 values in the range of 5.84-12.01 μM.
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Affiliation(s)
- Cong Guo
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Ruo-Yu Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Jie-Yi Ren
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Dan-Dan Xu
- School of Foundational Education, Xizang Agricultural and Animal Husbandry University, No. 100 Yucai West Road, Nyingchi, Xizang, 860000, China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
- Shenzhen Research Institute, Northwest A&F University, Shenzhen Virtual University Park Building, High-Tech Industrial Park, Shenzhen, Guangdong, 518000, China
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6
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Figueroa JR, Zhu L, van der Donk WA. Unexpected transformations during pyrroloiminoquinone biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584671. [PMID: 38559119 PMCID: PMC10979984 DOI: 10.1101/2024.03.12.584671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pyrroloiminoquinone containing natural products have long been known for their biological activities. They are derived from tryptophan, but their biosynthetic pathways have remained elusive. Studies on the biosynthetic gene cluster (BGC) that produces the ammosamides revealed that the first step is attachment of Trp to the C-terminus of a scaffold peptide in an ATP and tRNA dependent manner catalyzed by a PEptide Amino-acyl tRNA ligase (PEARL). The indole of the Trp is then oxidized to a hydroxyquinone. We previously proposed a chemically plausible and streamlined pathway for converting this intermediate to the ammosamides using additional enzymes encoded in the BGC. In this study, we report the activity of four additional enzymes that show that the proposed pathway is incorrect and that Nature's route towards pyrroloiminoquinones is much more complicated. We demonstrate that, surprisingly, the amino groups in pyrroloiminoquinones are derived from three different sources, glycine, asparagine, and leucine, all introduced in a tRNA dependent manner. We also show that an FAD-dependent putative glycine oxidase is required for the process that incorporates the nitrogens from glycine and leucine, and that a quinone reductase is required for the incorporation of the asparagine. Additionally, we provide the first insights into the evolutionary origin of the PEARLs as well as related enzymes such as the glutamyl-tRNA dependent dehydratases involved in the biosynthesis of lanthipeptides and thiopeptides. These enzymes appear to all have descended from the ATP-GRASP protein family.
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Affiliation(s)
- Josseline Ramos Figueroa
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lingyang Zhu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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7
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Eslami SM, van der Donk WA. Proteases Involved in Leader Peptide Removal during RiPP Biosynthesis. ACS BIO & MED CHEM AU 2024; 4:20-36. [PMID: 38404746 PMCID: PMC10885120 DOI: 10.1021/acsbiomedchemau.3c00059] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/27/2024]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) have received much attention in recent years because of their promising bioactivities and the portability of their biosynthetic pathways. Heterologous expression studies of RiPP biosynthetic enzymes identified by genome mining often leave a leader peptide on the final product to prevent toxicity to the host and to allow the attachment of a genetically encoded affinity purification tag. Removal of the leader peptide to produce the mature natural product is then carried out in vitro with either a commercial protease or a protease that fulfills this task in the producing organism. This review covers the advances in characterizing these latter cognate proteases from bacterial RiPPs and their utility as sequence-dependent proteases. The strategies employed for leader peptide removal have been shown to be remarkably diverse. They include one-step removal by a single protease, two-step removal by two dedicated proteases, and endoproteinase activity followed by aminopeptidase activity by the same protease. Similarly, the localization of the proteolytic step varies from cytoplasmic cleavage to leader peptide removal during secretion to extracellular leader peptide removal. Finally, substrate recognition ranges from highly sequence specific with respect to the leader and/or modified core peptide to nonsequence specific mechanisms.
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Affiliation(s)
- Sara M. Eslami
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute, University of
Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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8
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Yu Y, van der Donk WA. PEARL-catalyzed peptide bond formation after chain reversal during the biosynthesis of non-ribosomal peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573212. [PMID: 38187666 PMCID: PMC10769383 DOI: 10.1101/2023.12.23.573212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic sequence towards these compounds. The putative lantibiotic dehydratase catalyzes peptide bond formation that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS catalyzes the formation of a ureido group, and bioinformatics analysis revealed distinct active site residues of ureido-generating condensation (UreaC) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and non-ribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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9
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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10
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Pei ZF, Zhu L, Nair SK. Core-dependent post-translational modifications guide the biosynthesis of a new class of hypermodified peptides. Nat Commun 2023; 14:7734. [PMID: 38007494 PMCID: PMC10676384 DOI: 10.1038/s41467-023-43604-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPPs) class of natural products has undergone significant expansion due to the rapid growth in genome sequencing data. Using a bioinformatics approach, we identify the dehydrazoles, a novel class of hypermodified RiPPs that contain both side chain dehydration of Ser residues, and backbone heterocyclization at Ser, Thr, and Cys residues to the corresponding azol(in)es. Structure elucidation of the hypermodified peptide carnazolamide, a representative class member, shows that 18 post-translational modifications are installed by just five enzymes. Complete biosynthetic reconstitution demonstrates that dehydration is carried out by an unusual DUF4135 dehydration domain fused to a zinc-independent cyclase domain (CcaM). We demonstrate that CcaM only modifies Ser residues that precede an azole in the core peptide. As heterocyclization removes the carbonyl following the Ser residue, CcaM likely catalyzes dehydration without generating an enolate intermediate. Additionally, CcaM does not require the leader peptide, and this core-dependence effectively sets the order for the biosynthetic reactions. Biophysical studies demonstrate direct binding of azoles to CcaM consistent with this azole moiety-dependent dehydration. Bioinformatic analysis reveals more than 50 related biosynthetic gene clusters that contain additional catalysts that may produce structurally diverse scaffolds.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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11
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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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12
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Yang Y, Kessler MGC, Marchán-Rivadeneira MR, Han Y. Combating Antimicrobial Resistance in the Post-Genomic Era: Rapid Antibiotic Discovery. Molecules 2023; 28:molecules28104183. [PMID: 37241928 DOI: 10.3390/molecules28104183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Constantly evolving drug-resistant "superbugs" have caused an urgent demand for novel antimicrobial agents. Natural products and their analogs have been a prolific source of antimicrobial agents, even though a high rediscovery rate and less targeted research has made the field challenging in the pre-genomic era. With recent advancements in technology, natural product research is gaining new life. Genome mining has allowed for more targeted excavation of biosynthetic potential from natural sources that was previously overlooked. Researchers use bioinformatic algorithms to rapidly identify and predict antimicrobial candidates by studying the genome before even entering the lab. In addition, synthetic biology and advanced analytical instruments enable the accelerated identification of novel antibiotics with distinct structures. Here, we reviewed the literature for noteworthy examples of novel antimicrobial agents discovered through various methodologies, highlighting the candidates with potent effectiveness against antimicrobial-resistant pathogens.
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Affiliation(s)
- Yuehan Yang
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - Mara Grace C Kessler
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Maria Raquel Marchán-Rivadeneira
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Center for Research on Health in Latinamerica (CISeAL)-Biological Science Department, Pontificia Universidad Católica del Ecuador (PUCE), Quito 170143, Ecuador
| | - Yong Han
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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13
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Liu C, Zhu A, Hou J, Wang L, Zhang R, Li J, Guo Y, Chu Y. Nonomuraea sediminis sp. nov., a novel actinobacterium with antimicrobial activity, isolated from sediment of Dianchi Lake. Arch Microbiol 2023; 205:91. [PMID: 36781487 DOI: 10.1007/s00203-023-03427-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/15/2023]
Abstract
A novel actinobacterium with antimicrobial activity, designated strain H16431T, was isolated from a sediment sample collected from Dianchi Lake, Yunnan Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain H16431T was most closely related to Nonomuraea rhizosphaerae CGMCC 4.7431T and Nonomuraea guangzhouensis CGMCC 4.7101T (98.1% similarity), but formed a monophyletic clade with Nonomuraea ceibae KCTC 39826T (98.0% similarity). Phylogenomic analysis based on whole-genome sequence showed that strain H16431T formed a separate clade within the genus Nonomuraea. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between strain H16431T and its closely related Nonomuraea species were 80.0-81.5%, 71.2-74.6%, and 23.2-25.0%, respectively, which were significantly lower than the widely accepted species-defined threshold. The DNA G + C content was 70.2% based on the whole-genome sequence. The menaquinones were identified as MK-9(H4), MK-9(H6), and MK-9(H2). The major fatty acids were iso-C16:0, 10 methyl-C17:0, and iso-C16:0 2OH. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, and phosphatidylinositol. These chemotaxonomic characteristics were corresponded to those of the genus Nonomuraea. On the basis of the taxonomic evidence, strain H16431T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea sediminis sp. nov. is proposed. The type strain is H16431T (=JCM 34852T=CICC 25119T).
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Affiliation(s)
- Chaolan Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Ao Zhu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jiabei Hou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Limei Wang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Ruilin Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jianghua Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yidong Guo
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, 610106, People's Republic of China
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14
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Sarksian R, Zhu L, van der Donk WA. syn-Elimination of glutamylated threonine in lanthipeptide biosynthesis. Chem Commun (Camb) 2023; 59:1165-1168. [PMID: 36625436 PMCID: PMC9890492 DOI: 10.1039/d2cc06345j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methyllanthionine (MeLan) containing macrocycles are key structural features of lanthipeptides. They are formed typically by anti-elimination of L-Thr residues followed by cyclization of L-Cys residues onto the (Z)-dehydrobutyrine (Dhb) intermediates. In this report we demonstrate that the biosynthesis of lanthipeptides containing the D-allo-L-MeLan macrocycle such as the morphogenetic lanthipeptide SapT proceeds through (E)-Dhb intermediates formed by net syn-elimination of L-Thr.
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Affiliation(s)
- Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-ChampaignUrbanaIL61822USA+1 217 244 5360
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-ChampaignUrbanaIL61822USA
| | - Wilfred A. van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-ChampaignUrbanaIL61822USA+1 217 244 5360,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-ChampaignUrbanaIL61822USA
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15
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Shelton KE, Mitchell DA. Bioinformatic prediction and experimental validation of RiPP recognition elements. Methods Enzymol 2022; 679:191-233. [PMID: 36682862 PMCID: PMC9871372 DOI: 10.1016/bs.mie.2022.08.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products for which discovery efforts have rapidly grown over the past decade. There are currently 38 known RiPP classes encoded by prokaryotes. Half of the prokaryotic RiPP classes include a protein domain called the RiPP Recognition Element (RRE) for successful installation of post-translational modifications on a RiPP precursor peptide. In most cases, the RRE domain binds to the N-terminal "leader" region of the precursor peptide, facilitating enzymatic modification of the C-terminal "core" region. The prevalence of the RRE domain renders it a theoretically useful bioinformatic handle for class-independent RiPP discovery; however, first-in-class RiPPs have yet to be isolated and experimentally characterized using an RRE-centric strategy. Moreover, with most known RRE domains engaging their cognate precursor peptide(s) with high specificity and nanomolar affinity, evaluation of the residue-specific interactions that govern RRE:substrate complexation is a necessary first step to leveraging the RRE domain for various bioengineering applications. This chapter details protocols for developing custom bioinformatic models to predict and annotate RRE domains in a class-specific manner. Next, we outline methods for experimental validation of precursor peptide binding using fluorescence polarization binding assays and in vitro enzyme activity assays. We anticipate the methods herein will guide and enhance future critical analyses of the RRE domain, eventually enabling its future use as a customizable tool for molecular biology.
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Affiliation(s)
- Kyle E Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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16
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Rice AJ, Pelton JM, Kramer NJ, Catlin DS, Nair SK, Pogorelov TV, Mitchell DA, Bowers AA. Enzymatic Pyridine Aromatization during Thiopeptide Biosynthesis. J Am Chem Soc 2022; 144:21116-21124. [PMID: 36351243 PMCID: PMC9955758 DOI: 10.1021/jacs.2c07377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thiazole-containing pyritides (thiopeptides) are ribosomally synthesized and post-translationally modified peptides (RiPPs) that have attracted interest owing to their potent biological activities and structural complexity. The class-defining feature of a thiopeptide is a six-membered, nitrogenous heterocycle formed by an enzymatic [4 + 2]-cycloaddition. In rare cases, piperidine or dehydropiperidine (DHP) is present; however, the aromatized pyridine is considerably more common. Despite significant effort, the mechanism by which the central pyridine is formed remains poorly understood. Building on our recent observation of the Bycroft-Gowland intermediate (i.e., the direct product of the [4 + 2]-cycloaddition), we interrogated thiopeptide pyridine synthases using a combination of targeted mutagenesis, kinetic assays, substrate analogs, enzyme-substrate cross-linking, and chemical rescue experiments. Collectively, our data delineate roles for several conserved residues in thiopeptide pyridine synthases. A critical tyrosine facilitates the final aromatization step of pyridine formation. This work provides a foundation for further exploration of the [4 + 2]-cycloaddition reaction and future customization of pyridine-containing macrocyclic peptides.
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Affiliation(s)
- Andrew J. Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA
| | - Jarrett M. Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
| | - Nicholas J. Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA
| | - Daniel S. Catlin
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Satish K. Nair
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801, USA
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, USA.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, 301 Pharmacy Lane, Chapel Hill, North Carolina 27599, USA,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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17
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Glassey E, King AM, Anderson DA, Zhang Z, Voigt CA. Functional expression of diverse post-translational peptide-modifying enzymes in Escherichia coli under uniform expression and purification conditions. PLoS One 2022; 17:e0266488. [PMID: 36121811 PMCID: PMC9484694 DOI: 10.1371/journal.pone.0266488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/22/2022] [Indexed: 11/18/2022] Open
Abstract
RiPPs (ribosomally-synthesized and post-translationally modified peptides) are a class of pharmaceutically-relevant natural products expressed as precursor peptides before being enzymatically processed into their final functional forms. Bioinformatic methods have illuminated hundreds of thousands of RiPP enzymes in sequence databases and the number of characterized chemical modifications is growing rapidly; however, it remains difficult to functionally express them in a heterologous host. One challenge is peptide stability, which we addressed by designing a RiPP stabilization tag (RST) based on a small ubiquitin-like modifier (SUMO) domain that can be fused to the N- or C-terminus of the precursor peptide and proteolytically removed after modification. This is demonstrated to stabilize expression of eight RiPPs representative of diverse phyla. Further, using Escherichia coli for heterologous expression, we identify a common set of media and growth conditions where 24 modifying enzymes, representative of diverse chemistries, are functional. The high success rate and broad applicability of this system facilitates: (i) RiPP discovery through high-throughput “mining” and (ii) artificial combination of enzymes from different pathways to create a desired peptide.
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Affiliation(s)
- Emerson Glassey
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Andrew M. King
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Daniel A. Anderson
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Zhengan Zhang
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Christopher A. Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
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18
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Mastachi-Loza S, Ramírez-Candelero TI, Benítez-Puebla LJ, Fuentes-Benítes A, González-Romero C, Vázquez MA. Chalcones, a Privileged Scaffold: Highly Versatile Molecules in [4+2] Cycloadditions. Chem Asian J 2022; 17:e202200706. [PMID: 35976743 DOI: 10.1002/asia.202200706] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/14/2022] [Indexed: 11/09/2022]
Abstract
Chalcones are aromatic ketones found in nature as the central core of many biological compounds. They have a wide range of biological activity and are biogenetic precursors of other important molecules such as flavonoids. Their pharmacological relevance makes them a privileged scaffold, advantageous for seeking alternative therapies in medicinal chemistry. Due to their structural diversity and ease of synthesis, they are often employed as building blocks for chemical transformations. Chalcones have a carbonyl conjugated system with two electrophilic centers that are commonly used for nucleophilic additions, as described in numerous articles. They can also participate in Diels-Alder reactions, which are [4+2] cycloadditions between a diene and a dienophile. This microreview presents a chronological survey of studies on chalcones as dienes and dienophiles in Diels-Alder cycloadditions. Although these reactions occur in nature, isolation of chalcones from plants yields very small quantities. Contrarily, synthesis leads to large quantities at a low cost. Hence, novel methodologies have been developed for [4+2] cycloadditions, with chalcones serving as a 2π or 4π electron system.
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Affiliation(s)
- Salvador Mastachi-Loza
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, Departamento de Química, MEXICO
| | - Tania I Ramírez-Candelero
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Luis J Benítez-Puebla
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, Departamento de Química, MEXICO
| | - Aydee Fuentes-Benítes
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Carlos González-Romero
- Universidad Autonoma del Estado de Mexico Facultad de Quimica, Departamento de Química Orgánica, MEXICO
| | - Miguel A Vázquez
- Universidad de Guanajuato Division de Ciencias Naturales y Exactas, CHEMISTRY, NORIA ALTA S/N, 36050, GUANAJUATO, MEXICO
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19
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Nguyen DT, Le TT, Rice AJ, Hudson GA, van der Donk WA, Mitchell DA. Accessing Diverse Pyridine-Based Macrocyclic Peptides by a Two-Site Recognition Pathway. J Am Chem Soc 2022; 144:11263-11269. [PMID: 35713415 PMCID: PMC9247985 DOI: 10.1021/jacs.2c02824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Macrocyclic peptides
are sought-after molecular scaffolds for drug
discovery, and new methods to access diverse libraries are of increasing
interest. Here, we report the enzymatic synthesis of pyridine-based
macrocyclic peptides (pyritides) from linear precursor peptides. Pyritides
are a recently described class of ribosomally synthesized and post-translationally
modified peptides (RiPPs) and are related to the long-known thiopeptide
natural products. RiPP precursors typically contain an N-terminal
leader region that is physically engaged by the biosynthetic proteins
that catalyze modification of the C-terminal core region of the precursor
peptide. We demonstrate that pyritide-forming enzymes recognize both
the leader region and a C-terminal tripeptide motif, with each contributing
to site-selective substrate modification. Substitutions in the core
region were well-tolerated and facilitated the generation of a wide
range of pyritide analogues, with variations in macrocycle sequence
and size. A combination of the pyritide biosynthetic pathway with
azole-forming enzymes was utilized to generate a thiazole-containing
pyritide (historically known as a thiopeptide) with no similarity
in sequence and macrocycle size to the naturally encoded pyritides.
The broad substrate scope of the pyritide biosynthetic enzymes serves
as a future platform for macrocyclic peptide lead discovery and optimization.
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Affiliation(s)
- Dinh T Nguyen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tung T Le
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew J Rice
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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20
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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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21
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Malit JJL, Leung HYC, Qian PY. Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery. Mar Drugs 2022; 20:md20060398. [PMID: 35736201 PMCID: PMC9231227 DOI: 10.3390/md20060398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.
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Affiliation(s)
- Jessie James Limlingan Malit
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hiu Yu Cherie Leung
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence:
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22
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Walker J, Hamlish N, Tytla A, Brauer DD, Francis MB, Schepartz A. Redirecting RiPP Biosynthetic Enzymes to Proteins and Backbone-Modified Substrates. ACS CENTRAL SCIENCE 2022; 8:473-482. [PMID: 35505866 PMCID: PMC9052802 DOI: 10.1021/acscentsci.1c01577] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Indexed: 05/04/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are peptide-derived natural products with potent antibiotic, antiviral, and anticancer properties. RiPP enzymes known as cyclodehydratases and dehydrogenases work together to catalyze intramolecular, inter-residue condensation and dehydrogenation reactions that install oxazoline/oxazole and thiazoline/thiazole heterocycles within ribosomally produced polypeptide chains. Here, we show that the previously reported enzymes MicD-F and ArtGox accept backbone-modified monomers-including aminobenzoic acid derivatives and beta-amino acids-within leader-free polypeptides, even at positions immediately preceding or following the site of cyclization/dehydrogenation. The products are sequence-defined chemical polymers with multiple, diverse non-α-amino acid subunits. We show further that MicD-F and ArtGox can install heterocyclic backbones within protein loops and linkers without disrupting the native tertiary fold. Calculations reveal the extent to which these heterocycles restrict conformational space; they also eliminate a peptide bond-both features could improve the stability or add function to linker sequences now commonplace in emerging biotherapeutics. This work represents a general strategy to expand the chemical diversity of the proteome beyond and in synergy with what can now be accomplished by expanding the genetic code.
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Affiliation(s)
- Joshua
A. Walker
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Center
for Genetically Encoded Materials, University
of California, Berkeley, California 94720, United States
| | - Noah Hamlish
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- Center
for Genetically Encoded Materials, University
of California, Berkeley, California 94720, United States
| | - Avery Tytla
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Daniel D. Brauer
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Center
for Genetically Encoded Materials, University
of California, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Center
for Genetically Encoded Materials, University
of California, Berkeley, California 94720, United States
- E-mail:
| | - Alanna Schepartz
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cellular Biology, University
of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Center
for Genetically Encoded Materials, University
of California, Berkeley, California 94720, United States
- E-mail:
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23
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Sarksian R, Hegemann JD, Simon MA, Acedo JZ, van der Donk WA. Unexpected Methyllanthionine Stereochemistry in the Morphogenetic Lanthipeptide SapT. J Am Chem Soc 2022; 144:6373-6382. [PMID: 35352944 PMCID: PMC9011353 DOI: 10.1021/jacs.2c00517] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
Lanthipeptides are
polycyclic peptides characterized by the presence
of lanthionine (Lan) and/or methyllanthionine (MeLan). They are members
of the ribosomally synthesized and post-translationally modified peptides (RiPPs). The stereochemical
configuration of (Me)Lan cross-links is important for the bioactivity
of lanthipeptides. To date, MeLan residues in characterized lanthipeptides
have either the 2S,3S or 2R,3R stereochemistry. Herein, we reconstituted
in Escherichia coli the biosynthetic pathway toward
SapT, a class I lanthipeptide that exhibits morphogenetic activity.
Through the synthesis of standards, the heterologously produced peptide
was shown to possess three MeLan residues with the 2S,3R stereochemistry (d-allo-l-MeLan), the first time such stereochemistry has been
observed in a lanthipeptide. Bioinformatic analysis of the biosynthetic
enzymes suggests this stereochemistry may also be present in other
lanthipeptides. Analysis of another gene cluster in Streptomyces
coelicolor that is widespread in actinobacteria confirmed
another example of d-allo-l-MeLan
and verified the bioinformatic prediction. We propose a mechanism
for the origin of the unexpected stereochemistry and provide support
using site-directed mutagenesis.
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Affiliation(s)
- Raymond Sarksian
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Max A Simon
- Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61822, United States
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24
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Thetsana C, Ijichi S, Kaweewan I, Nakagawa H, Kodani S. Heterologous expression of a cryptic gene cluster from a marine proteobacterium Thalassomonas actiniarum affords new lanthipeptides thalassomonasins A and B. J Appl Microbiol 2022; 132:3629-3639. [PMID: 35157343 DOI: 10.1111/jam.15491] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
AIMS The aim of this study was to utilize a cryptic biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum for production of new lanthipeptides by heterologous expression system. METHODS AND RESULTS Based on genome-mining, a new biosynthetic gene cluster of class I lanthipeptide was found in the genome sequence of a marine proteobacterium Thalassomonas actiniarum. Molecular cloning was performed to construct expression vector derived from commercial available plasmid pET-41a(+). Heterologous production of new lanthipeptides named thalassomonasins A and B was performed using the host Escherichia coli BL21(DE3) harboring the expression vector. The structure of thalassomonasin A was determined by interpretation of NMR and MS data. As a result, thalassomonasin A was determined to be a lanthipeptide with three units of lanthionine. The bridging pattern of the lanthionine rings in thalassomonasin A was determined by interpretation of NOESY data. The structure of thalassomonasin B was proposed by MS/MS experiment. CONCLUSIONS We succeeded in heterologous production of new class I lanthipeptides using a biosynthetic gene cluster of a marine proteobacterium Thalassomonas actiniarum. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report of heterologous production of lanthipeptides derived from proteobacterial origin. There are many cryptic biosynthetic gene clusters of this class of lanthipeptides in proteobacterial genomes. This study may lead to production of new lanthipeptides by utilizing the biosynthetic gene clusters.
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Affiliation(s)
- Chanaphat Thetsana
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Shinta Ijichi
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hiroyuki Nakagawa
- Research center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.,Faculty of Agriculture, Shizuoka University, Shizuoka, Japan.,Shizuoka Institute for the Study of Marine Biology and Chemistry, Shizuoka University, Shizuoka, Japan.,College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, Japan
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25
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Brimberry MA, Mathew L, Lanzilotta W. Making and breaking carbon-carbon bonds in class C radical SAM methyltransferases. J Inorg Biochem 2022; 226:111636. [PMID: 34717253 PMCID: PMC8667262 DOI: 10.1016/j.jinorgbio.2021.111636] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
Radical S-adenosylmethionine (SAM) enzymes utilize a [4Fe-4S]1+ cluster and S-(5'-adenosyl)-L-methionine, (SAM), to generate a highly reactive radical and catalyze what is arguably the most diverse set of chemical reactions for any known enzyme family. At the heart of radical SAM catalysis is a highly reactive 5'-deoxyadenosyl radical intermediate (5'-dAdo●) generated through reductive cleavage of SAM or nucleophilic attack of the unique iron of the [4Fe-4S]+ cluster on the 5' C atom of SAM. Spectroscopic studies reveal the 5'-dAdo● is transiently captured in an FeC bond (Ω species). In the presence of substrate, homolytic scission of this metal‑carbon bond regenerates the 5'-dAdo● for catalytic hydrogen atom abstraction. While reminiscent of the adenosylcobalamin mechanism, radical SAM enzymes appear to encompass greater catalytic diversity. In this review we discuss recent developments for radical SAM enzymes involved in unique chemical rearrangements, specifically regarding class C radical SAM methyltransferases. Illuminating this class of radical SAM enzymes is especially significant as many enzymes have been shown to play critical roles in pathogenesis and the synthesis of novel antimicrobial compounds.
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Affiliation(s)
- Marley A. Brimberry
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies,,Department of Chemistry University of Georgia, Athens GA 30602
| | - Liju Mathew
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies,,Department of Chemistry University of Georgia, Athens GA 30602
| | - William Lanzilotta
- Department of Biochemistry and Molecular Biology & Center for Metalloenzyme Studies,,Department of Chemistry University of Georgia, Athens GA 30602.,To whom correspondence should be addressed. Phone, (706) 542-1324; fax, (706) 542-1738;
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26
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A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nat Chem 2022; 14:71-77. [PMID: 34725492 PMCID: PMC8758506 DOI: 10.1038/s41557-021-00802-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/27/2021] [Indexed: 11/12/2022]
Abstract
Aromatic amines in nature are typically installed with Glu or Gln as the nitrogen donor. Here we report a pathway that features glycyl-tRNA instead. During the biosynthesis of pyrroloiminoquinone-type natural products such as ammosamides, peptide-aminoacyl tRNA ligases append amino acids to the C-terminus of a ribosomally synthesized peptide. First, [Formula: see text] adds Trp in a Trp-tRNA-dependent reaction and the flavoprotein AmmC1 then carries out three hydroxylations of the indole ring of Trp. After oxidation to the corresponding ortho-hydroxy para-quinone, [Formula: see text] attaches Gly to the indole ring in a Gly-tRNA dependent fashion. Subsequent decarboxylation and hydrolysis results in an amino-substituted indole. Similar transformations are catalysed by orthologous enzymes from Bacillus halodurans. This pathway features three previously unknown biochemical processes using a ribosomally synthesized peptide as scaffold for non-ribosomal peptide extension and chemical modification to generate an amino acid-derived natural product.
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27
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Isolation and Analysis of the Nisin Biosynthesis Complex NisBTC: further Insights into Their Cooperative Action. mBio 2021; 12:e0258521. [PMID: 34607454 PMCID: PMC8546558 DOI: 10.1128/mbio.02585-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Nisin is synthesized by a putative membrane-associated lantibiotic synthetase complex composed of the dehydratase NisB, the cyclase NisC, and the ABC transporter NisT in Lactococcus lactis. Earlier work has demonstrated that NisB and NisT are linked via NisC to form such a complex. Here, we conducted for the first time the isolation of the intact NisBTC complex and NisT-associated subcomplexes from the cytoplasmic membrane by affinity purification. A specific interaction of NisT, not only with NisC but also with NisB, was detected. The cellular presence of NisB and/or NisC in complex with precursor nisin (NisA) was determined, which shows a highly dynamic and transient assembly of the NisABC complex via an alternating binding mechanism during nisin dehydration and cyclization. Mutational analyses, with cysteine-to-alanine mutations in NisA, suggest a tendency for NisA to lose affinity to NisC concomitant with an increasing number of completed lanthionine rings. Split NisBs were able to catalyze glutamylation and elimination reactions in an alternating way as efficiently as full-length NisB, with no significant influence on the following cyclization and transport. Notably, the harvest of the leader peptide in complex with the independent elimination domain of NisB points to a second leader peptide binding motif that is located in the C-terminal region of NisB, giving rise to a model where the leader peptide binds to different sites in NisB for glutamylation and elimination. Overall, these combined studies provide new insights into the cooperative biosynthesis mechanism of nisin and thereby lay a foundation for further structural and functional characterization of the NisBTC complex.
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28
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The lanthipeptide biosynthetic clusters of the domain Archaea. Microbiol Res 2021; 253:126884. [PMID: 34628131 DOI: 10.1016/j.micres.2021.126884] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 09/27/2021] [Indexed: 11/21/2022]
Abstract
Research on Archaea's secondary metabolites is still lagging behind that of Bacteria and Eukarya. Our goal was to contribute to this knowledge gap by analyzing the lanthipeptide's clusters in Archaea. As previously proposed, Archaea encodes only class II synthetases (LanMs), which we found to be confined to the class Halobacteria (also known as haloarchaea). In total, we analyzed the phylogeny and the domains of 42 LanMs. Four types were identified, and the majority of them belong to the CCG group due to their cyclization domain, which includes LanMs of Cyanobacteria. Putative cognate peptides were predicted for most of LanMs and are a very diverse group of molecules that share a Kx(Y/F)(D/E)xx(F/Y) motif in their leader peptides. According to their homology, some of them were categorized into subfamilies, including Halolancins, Haladacins, Haloferaxcins and Halobiforcins. Many LanM genes were associated with mobile genetic elements, and their vicinities mainly encode ABC and MFS transporters, tailoring enzymes and uncharacterized proteins. Our results suggest that the biosynthesis of lanthipeptides in haloarchaea can entail distinct enzymology that must lead to the production of peptides with novel structures and unpredicted biological and ecological roles. Finally, an Haloferax mediterranei knockout, lacking its three lanM genes, was generated, and it was concluded that its antimicrobial activity is not primarily related to the production of lanthipeptides.
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29
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Thiocysteine lyases as polyketide synthase domains installing hydropersulfide into natural products and a hydropersulfide methyltransferase. Nat Commun 2021; 12:5672. [PMID: 34584078 PMCID: PMC8479088 DOI: 10.1038/s41467-021-25798-8] [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: 04/22/2021] [Accepted: 09/01/2021] [Indexed: 12/02/2022] Open
Abstract
Nature forms S-S bonds by oxidizing two sulfhydryl groups, and no enzyme installing an intact hydropersulfide (-SSH) group into a natural product has been identified to date. The leinamycin (LNM) family of natural products features intact S-S bonds, and previously we reported an SH domain (LnmJ-SH) within the LNM hybrid nonribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) assembly line as a cysteine lyase that plays a role in sulfur incorporation. Here we report the characterization of an S-adenosyl methionine (SAM)-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin (GNM) biosynthesis, discovery of hydropersulfides as the nascent products of the GNM and LNM hybrid NRPS-PKS assembly lines, and revelation of three SH domains (GnmT-SH, LnmJ-SH, and WsmR-SH) within the GNM, LNM, and weishanmycin (WSM) hybrid NRPS-PKS assembly lines as thiocysteine lyases. Based on these findings, we propose a biosynthetic model for the LNM family of natural products, featuring thiocysteine lyases as PKS domains that directly install a -SSH group into the GNM, LNM, or WSM polyketide scaffold. Genome mining reveals that SH domains are widespread in Nature, extending beyond the LNM family of natural products. The SH domains could also be leveraged as biocatalysts to install an -SSH group into other biologically relevant scaffolds. Enzymes installing an intact hydropersulfide (-SSH) group into natural products have so far not been identified. Here, the authors report the characterization of an S-adenosyl methionine-dependent hydropersulfide methyltransferase (GnmP) for guangnanmycin biosynthesis, and identification of three SH domains within several NRPS-PKS assembly lines as thiocysteine lyases.
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30
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Cheng B, Guo H, Wang H, Zhao Q, Liu W. Dissection of the Enzymatic Process for Forming a Central Imidazopiperidine Heterocycle in the Biosynthesis of a Series c Thiopeptide Antibiotic. J Am Chem Soc 2021; 143:13790-13797. [PMID: 34405994 DOI: 10.1021/jacs.1c05956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Thiopeptide antibiotics are a family of ribosomally synthesized and posttranslationally modified peptide natural products of significant interest in anti-infective agent development. These antibiotics are classified into five subfamilies according to differences in the central 6-membered heterocycle of the thiopeptide framework. The mechanism through which imidazopiperidine, the most heavily functionalized central domain characteristic of a series c thiopeptide, is formed remains unclear. Based on mining and characterization of the genes specifically involved in the biosynthesis of Sch40832, we here report an enzymatic process for transforming a series b thiopeptide into a series c product through a series a intermediate. This process starts with F420-dependent hydrogenation of the central dehydropiperidine unit to a saturated piperidine unit. With the activity of a cytochrome P450 monooxygenase, the piperidine-thiazole motif of the intermediate undergoes an unusual oxygenation-mediated rearrangement to provide an imidazopiperidine heterocycle subjected to further S-methylation and aldehyde reduction. This study represents the first biochemical reconstitution of the pathway forming a stable series c thiopeptide.
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Affiliation(s)
- Botao Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Heng Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Haoyang Wang
- Laboratory of Mass Spectrometry Analysis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.,Huzhou Center of Bio-Synthetic Innovation, 1366 Hongfeng Road, Huzhou 313000, China
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31
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Pei ZF, Yang MJ, Zhang K, Jian XH, Tang GL. Heterologous characterization of mechercharmycin A biosynthesis reveals alternative insights into post-translational modifications for RiPPs. Cell Chem Biol 2021; 29:650-659.e5. [PMID: 34474009 DOI: 10.1016/j.chembiol.2021.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/12/2021] [Accepted: 08/12/2021] [Indexed: 11/03/2022]
Abstract
Mechercharmycin A (MCM-A) is a marine natural product belonging to a family of polyazole cyclopeptides with remarkable bioactivities and unique structures. Identification, heterologous expression, and genetic characterizations of the MCM biosynthetic gene cluster in Bacillus subtilis revealed that it is a ribosomally synthesized and post-translationally modified peptide (RiPP) possessing complex with distinctive modifications. Based on this heterologous expression system, two MCM analogs with comparable antitumor activity are generated by engineering the biosynthetic pathway. Combinatorial co-production of a precursor peptide with different modifying enzymes in Escherichia coli identifies a different timing of modifications, showing that a tRNAGlu-dependent highly regioselective dehydration is the first modification step, followed by polyazole formation through heterocyclization and dehydrogenation in an N- to C-terminal direction. Therefore, a rational biosynthetic pathway of MCMs is proposed, which unveils a subfamily of azol(in)e-containing RiPPs and sets the stage for further investigations of the enzymatic mechanism and synthetic biology.
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Affiliation(s)
- Zeng-Fei Pei
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Min-Jie Yang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Kai Zhang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xiao-Hong Jian
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong 643000, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China; School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China.
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32
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Vinogradov AA, Nagano M, Goto Y, Suga H. Site-Specific Nonenzymatic Peptide S/O-Glutamylation Reveals the Extent of Substrate Promiscuity in Glutamate Elimination Domains. J Am Chem Soc 2021; 143:13358-13369. [PMID: 34392675 DOI: 10.1021/jacs.1c06470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Formation of dehydroalanine and dehydrobutyrine residues via tRNA-dependent dehydration of serine and threonine is a key post-translational modification in the biosynthesis of lanthipeptide and thiopeptide RiPPs. The dehydration process involves two reactions, wherein the O-glutamyl Ser/Thr intermediate, accessed by a dedicated enzyme utilizing Glu-tRNAGlu as the acyl donor, is recognized by the second enzyme, referred to as the glutamate elimination domain (ED), which catalyzes the eponymous reaction yielding a dehydroamino acid. Many details of ED catalysis remain unexplored because the scope of available substrates for testing is limited to those that the upstream enzymes can furnish. Here, we report two complementary strategies for direct, nonenzymatic access to diverse ED substrates. We establish that a thiol-thioester exchange reaction between a Cys-containing peptide and an α thioester of glutamic acid leads an S-glutamylated intermediate which can act as a substrate for EDs. Furthermore, we show that the native O-glutamylated substrates can be accessible from S-glutamylated peptides upon a site-specific S-to-O acyl transfer reaction. Combined with flexible in vitro translation utilized for rapid peptide production, these chemistries enabled us to dissect the substrate recognition requirements of three known EDs. Our results establish that EDs are uniquely promiscuous enzymes capable of acting on substrates with arbitrary amino acid sequences and performing retro-Michael reaction beyond the canonical glutamate elimination. To facilitate substrate recruitment, EDs apparently engage in nonspecific hydrophobic interactions with their substrates. Altogether, our results establish the substrate scope of EDs and provide clues to their catalysis.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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33
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Bothwell IR, Caetano T, Sarksian R, Mendo S, van der Donk WA. Structural Analysis of Class I Lanthipeptides from Pedobacter lusitanus NL19 Reveals an Unusual Ring Pattern. ACS Chem Biol 2021; 16:1019-1029. [PMID: 34085816 PMCID: PMC9845027 DOI: 10.1021/acschembio.1c00106] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lanthipeptides are ribosomally synthesized and post-translationally modified peptide natural products characterized by the presence of lanthionine and methyllanthionine cross-linked amino acids formed by dehydration of Ser/Thr residues followed by conjugate addition of Cys to the resulting dehydroamino acids. Class I lanthipeptide dehydratases utilize glutamyl-tRNAGlu as a cosubstrate to glutamylate Ser/Thr followed by glutamate elimination. A vast majority of lanthipeptides identified from class I synthase systems have been from Gram-positive bacteria. Herein, we report the heterologous expression and modification in Escherichia coli of two lanthipeptides from the Gram-negative Bacteroidetes Pedobacter lusitanus NL19. These peptides are representative of a group of compounds frequently encoded in Pedobacter genomes. Structural characterization of the lanthipeptides revealed a novel ring pattern as well as an unusual ll-lanthionine stereochemical configuration and a cyclase that lacks the canonical zinc ligands found in most LanC enzymes.
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Affiliation(s)
- Ian R. Bothwell
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Tânia Caetano
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Raymond Sarksian
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
| | - Sónia Mendo
- Molecular Biotechnology Laboratory, CESAM & Departamento de Biologia
- Campus de Santiago, University of Aveiro, 3810-189 Aveiro, Portugal
| | - Wilfred A. van der Donk
- Howard Hughes Medical Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, IL 61822
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34
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Abstract
Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products characterized by the presence of lanthionine and methyllanthionine. During the maturation of select lanthipeptides, five different alterations have been observed to the chemical structure of the peptide backbone. First, dehydratases generate dehydroalanine and dehydrobutyrine from Ser or Thr residues, respectively. A second example of introduction of unsaturation is the oxidative decarboxylation of C-terminal Cys residues catalyzed by the decarboxylase LanD. Both modifications result in loss of chirality at the α-carbon of the amino acid residues. Attack of a cysteine thiol onto a dehydrated amino acid results in thioether crosslink formation with either inversion or retention of the l-stereochemical configuration at the α-carbon of former Ser and Thr residues. A fourth modification of the protein backbone is the hydrogenation of dehydroamino acids to afford d-amino acids catalyzed by NAD(P)H-dependent reductases. A fifth modification is the conversion of Asp to isoAsp. Herein, the methods used to produce and characterize the lanthipeptide bicereucin will be described in detail along with a brief overview of other lanthipeptides.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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35
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Xu G, Yang S. Diverse evolutionary origins of microbial [4 + 2]-cyclases in natural product biosynthesis. Int J Biol Macromol 2021; 182:154-161. [PMID: 33836196 DOI: 10.1016/j.ijbiomac.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Natural [4 + 2]-cyclases catalyze concerted cycloaddition during biosynthesis of over 400 natural products reported. Microbial [4 + 2]-cyclases are structurally diverse with a broad range of substrates. Thus far, about 52 putative microbial [4 + 2]-cyclases of 13 different types have been characterized, with over 20 crystal structures. However, how these cyclases have evolved during natural product biosynthesis remains elusive. Structural and phylogenetic analyses suggest that these different types of [4 + 2]-cyclases might have diverse evolutionary origins, such as reductases, dehydratases, methyltransferases, oxidases, etc. Divergent evolution of enzyme function might have occurred in these different families. Understanding the independent evolutionary history of these cyclases would provide new insights into their catalysis mechanisms and the biocatalyst design.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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36
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Franz L, Kazmaier U, Truman AW, Koehnke J. Bottromycins - biosynthesis, synthesis and activity. Nat Prod Rep 2021; 38:1659-1683. [PMID: 33621290 DOI: 10.1039/d0np00097c] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 1950s up to the end of 2020Bottromycins are a class of macrocyclic peptide natural products that are produced by several Streptomyces species and possess promising antibacterial activity against clinically relevant multidrug-resistant pathogens. They belong to the ribosomally synthesised and post-translationally modified peptide (RiPP) superfamily of natural products. The structure contains a unique four-amino acid macrocycle formed via a rare amidine linkage, C-methylation and a d-amino acid. This review covers all aspects of bottromycin research with a focus on recent years (2009-2020), in which major advances in total synthesis and understanding of bottromycin biosynthesis were achieved.
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Affiliation(s)
- Laura Franz
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Uli Kazmaier
- Saarland University, Organic Chemistry, Campus Geb. C4.2, 66123 Saarbrücken, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Jesko Koehnke
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany and School of Chemistry, University of Glasgow, Glasgow, UK.
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37
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Lu J, Li Y, Bai Z, Lv H, Wang H. Enzymatic macrocyclization of ribosomally synthesized and posttranslational modified peptides via C-S and C-C bond formation. Nat Prod Rep 2021; 38:981-992. [PMID: 33185226 DOI: 10.1039/d0np00044b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2000 to 2020 Ribosomally synthesized and posttranslational modified peptides (RiPPs) are a rapidly growing class of bioactive natural products. Many members of RiPPs contain macrocyclic structural units constructed by modification enzymes through macrocyclization of linear precursor peptides. In this study, we summarize recent progress in the macrocyclization of RiPPs by C-S and C-C bond formation with a focus on the current understanding of the enzymatic mechanisms.
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Affiliation(s)
- Jingxia Lu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Yuqing Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Zengbing Bai
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Hongmei Lv
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center of Nanjing University, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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38
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 388] [Impact Index Per Article: 129.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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39
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Chan DCK, Burrows LL. Thiopeptides: antibiotics with unique chemical structures and diverse biological activities. J Antibiot (Tokyo) 2020; 74:161-175. [PMID: 33349675 DOI: 10.1038/s41429-020-00387-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022]
Abstract
Thiopeptides are a class of natural product antibiotics with diverse structures and functions. Their complex structures and biosynthesis have intrigued researchers since their discovery in 1948, but not a single thiopeptide has been approved for human use. This is mainly due to their poor solubility, challenging synthesis, and low bioavailability. This review summarizes the current research on the biosynthesis and biological activity of thiopeptide antibiotics since 2015. The focus of research since 2015 has been on uncovering biosynthetic routes, developing methods for total synthesis, and understanding the biological activity of thiopeptides. Overall, there is still much to learn about this family of molecules.
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Affiliation(s)
- Derek C K Chan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada. .,Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada.
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40
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Adam S, Franz L, Milhim M, Bernhardt R, Kalinina OV, Koehnke J. Characterization of the Stereoselective P450 Enzyme BotCYP Enables the In Vitro Biosynthesis of the Bottromycin Core Scaffold. J Am Chem Soc 2020; 142:20560-20565. [PMID: 33249843 DOI: 10.1021/jacs.0c10361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bottromycins are ribosomally synthesized and post-translationally modified peptide natural product antibiotics that are effective against high-priority human pathogens such as methicillin-resistant Staphylococcus aureus. The total synthesis of bottromycins involves at least 17 steps, with a poor overall yield. Here, we report the characterization of the cytochrome P450 enzyme BotCYP from a bottromycin biosynthetic gene cluster. We determined the structure of a close BotCYP homolog and used our data to conduct the first large-scale survey of P450 enzymes associated with RiPP biosynthetic gene clusters. We demonstrate that BotCYP converts a C-terminal thiazoline to a thiazole via an oxidative decarboxylation reaction and provides stereochemical resolution for the pathway. Our data enable the two-pot in vitro production of the bottromycin core scaffold and may allow the rapid generation of bottromycin analogues for compound development.
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Affiliation(s)
- Sebastian Adam
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Laura Franz
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany
| | - Mohammed Milhim
- Department of Biochemistry, Saarland University, Campus Geb. B2.2, 66123 Saarbrücken, Germany
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus Geb. B2.2, 66123 Saarbrücken, Germany
| | - Olga V Kalinina
- Research Group Drug Bioinformatics, HIPS, HZI, 66123 Saarbrücken, Germany.,Faculty of Medicine, Saarland University, 66424 Homburg, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus Geb. E8.1, 66123 Saarbrücken, Germany.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, U.K
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41
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Liu R, Zhang Y, Zhai G, Fu S, Xia Y, Hu B, Cai X, Zhang Y, Li Y, Deng Z, Liu T. A Cell-Free Platform Based on Nisin Biosynthesis for Discovering Novel Lanthipeptides and Guiding their Overproduction In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001616. [PMID: 32995136 PMCID: PMC7507342 DOI: 10.1002/advs.202001616] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/10/2020] [Indexed: 05/12/2023]
Abstract
Lanthipeptides have extensive therapeutic and industrial applications. However, because many are bactericidal, traditional in vivo platforms are limited in their capacity to discover and mass produce novel lanthipeptides as bacterial organisms are often critical components in these systems. Herein, the development of a cell-free protein synthesis (CFPS) platform that enables rapid genome mining, screening, and guided overproduction of lanthipeptides in vivo is described. For proof-of-concept studies, a type I lanthipeptide, nisin, is selected. Four novel lanthipeptides with antibacterial activity are identified among all nisin analogs in the National Center for Biotechnology Information (NCBI) database in a single day. Further, the CFPS platform is coupled with a screening assay for anti-gram-negative bacteria growth, resulting in the identification of a potent nisin mutant, M5. The titers of nisin and the nisin analog are found to be improved with CFPS platform guidance. Owing to the similarities in biosynthesis, the CFPS platform is broadly applicable to other lanthipeptides, thereby providing a universal method for lanthipeptide discovery and overproduction.
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Affiliation(s)
- Ran Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Guoqing Zhai
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Shuai Fu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Yao Xia
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Ben Hu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
| | - Xuan Cai
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Zhang
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Yan Li
- Department of Clinical Laboratory Renmin Hospital of Wuhan University Wuhan 430060 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education and Wuhan University School of Pharmaceutical Sciences Wuhan 430071 China
- Hubei Engineering Laboratory for Synthetic Microbiology Wuhan Institute of Biotechnology Wuhan 430075 China
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42
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Hudson GA, Hooper AR, DiCaprio AJ, Sarlah D, Mitchell DA. Structure Prediction and Synthesis of Pyridine-Based Macrocyclic Peptide Natural Products. Org Lett 2020; 23:253-256. [PMID: 32845158 DOI: 10.1021/acs.orglett.0c02699] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural and functional characterization of natural products is vastly outpaced by the bioinformatic identification of biosynthetic gene clusters (BGCs) that encode such molecules. Uniting our knowledge of bioinformatics and enzymology to predict and synthetically access natural products is an effective platform for investigating cryptic/silent BGCs. We report the identification, biosynthesis, and total synthesis of a minimalistic class of ribosomally synthesized and post-translationally modified peptides (RiPPs) with the responsible BGCs encoding a subset of enzymes known from thiopeptide biosynthesis. On the basis of the BGC content, these RiPPs were predicted to undergo enzymatic dehydration of serine followed by [4+2]-cycloaddition to produce a trisubstituted, pyridine-based macrocycle. These RiPPs, termed "pyritides", thus contain the same six-membered, nitrogenous heterocycle that defines the thiopeptide RiPP class but lack the ubiquitous thiazole/thiazoline heterocycles, suggesting that thiopeptides should be reclassified as a more elaborate subclass of the pyritides. One pyritide product was obtained using an 11-step synthesis, and the structure verified by an orthogonal chemoenzymatic route using the precursor peptide and cognate pyridine synthase. This work exemplifies complementary bioinformatics, enzymology, and synthesis to characterize a minimalistic yet structurally intriguing scaffold that, unlike most thiopeptides, lacks growth-suppressive activity toward Gram-positive bacteria.
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Affiliation(s)
- Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Annie R Hooper
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - David Sarlah
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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43
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Li Q, Ding W, Tu J, Chi C, Huang H, Ji X, Yao Z, Ma M, Ju J. Nonspecific Heme-Binding Cyclase, AbmU, Catalyzes [4 + 2] Cycloaddition during Neoabyssomicin Biosynthesis. ACS OMEGA 2020; 5:20548-20557. [PMID: 32832808 PMCID: PMC7439702 DOI: 10.1021/acsomega.0c02776] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/27/2020] [Indexed: 05/05/2023]
Abstract
Diels-Alder (DA) [4 + 2]-cycloaddition reactions rank among the most powerful transformations in synthetic organic chemistry; biosynthetic examples, however, are few and far between. We report here a heme-binding cyclase, AbmU, that catalyzes an essential [4 + 2] cycloaddition during neoabyssomicin scaffold assembly. In vivo genetic and in vitro biochemical analyses strongly suggest that AbmU catalyzes an intramolecular and stereoselective [4 + 2] cycloaddition to form a spirotetronate skeleton from an acyclic substrate featuring both a terminal 1,3-diene and an exo-methylene group. Biochemical assays and X-ray diffraction analyses reveal that AbmU binds nonspecifically to a heme b cofactor and that this association does not play a catalytic role in AbmU catalysis. A detailed study of the AbmU crystal structure reveals a unique mode of substrate binding and reaction catalysis; His160 forms a H-bond with the C-1 carbonyl O-atom of the acyclic substrate, and the imidazole of the same amino acid directs the tetronate moiety of acyclic substrate toward the terminal Δ10,11, Δ12,13-diene moiety, thereby facilitating intramolecular DA chemistry. Our findings expand upon what is known about mechanistic diversities available to biosynthetic [4 + 2] cyclases and help to lay the foundation for the use of AbmU in possible industrial applications.
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Affiliation(s)
- Qinglian Li
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Wenjuan Ding
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Jiajia Tu
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Changbiao Chi
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Hongbo Huang
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Xiaoqi Ji
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Ziwei Yao
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
| | - Ming Ma
- State
Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical
Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Jianhua Ju
- CAS
Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong
Key Laboratory of Marine Materia
Medica, RNAM Center for Marine Microbiology, South China Sea Institute
of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- College
of Oceanology, University of Chinese Academy
of Sciences, 19 Yuquan
Road, Beijing 100049, China
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44
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Vinogradov AA, Shimomura M, Kano N, Goto Y, Onaka H, Suga H. Promiscuous Enzymes Cooperate at the Substrate Level En Route to Lactazole A. J Am Chem Soc 2020; 142:13886-13897. [PMID: 32664727 DOI: 10.1021/jacs.0c05541] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs) often have relaxed specificity profiles and are able to modify diverse substrates. When several such enzymes act together during precursor peptide maturation, a multitude of products can form, yet usually the biosynthesis converges on a single natural product. For the most part, the mechanisms controlling the integrity of RiPP assembly remain elusive. Here, we investigate the biosynthesis of lactazole A, a model thiopeptide produced by five promiscuous enzymes from a ribosomal precursor peptide. Using our in vitro thiopeptide production (FIT-Laz) system, we determine the order of biosynthetic events at the individual modification level and supplement this study with substrate scope analysis for participating enzymes. Our results reveal an unusual but well-defined assembly process where cyclodehydration, dehydroalanine formation, and azoline dehydrogenation events are intertwined due to minimal substrate recognition requirements characteristic of every lactazole enzyme. Additionally, each enzyme plays a role in directing LazBF-mediated dehydroalanine formation, which emerges as the central theme of the assembly process. Cyclodehydratase LazDE discriminates a single serine residue for azoline formation, leaving the remaining five as potential dehydratase substrates. Pyridine synthase LazC exerts kinetic control over LazBF to prevent the formation of overdehydrated thiopeptides, whereas the coupling of dehydrogenation to dehydroalanine installation impedes generation of underdehydrated products. Altogether, our results indicate that substrate-level cooperation between the biosynthetic enzymes maintains the integrity of lactazole assembly. This work advances our understanding of RiPP biosynthesis processes and facilitates thiopeptide bioengineering.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Naokazu Kano
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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45
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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46
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Bogart JW, Kramer NJ, Turlik A, Bleich RM, Catlin DS, Schroeder FC, Nair SK, Williamson RT, Houk KN, Bowers AA. Interception of the Bycroft-Gowland Intermediate in the Enzymatic Macrocyclization of Thiopeptides. J Am Chem Soc 2020; 142:13170-13179. [PMID: 32609512 DOI: 10.1021/jacs.0c05639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thiopeptides are a broad class of macrocyclic, heavily modified peptide natural products that are unified by the presence of a substituted, nitrogen-containing heterocycle core. Early work indicated that this core might be fashioned from two dehydroalanines by an enzyme-catalyzed aza-[4 + 2] cycloaddition to give a cyclic-hemiaminal intermediate. This common intermediate could then follow a reductive path toward a dehydropiperidine, as in the thiopeptide thiostrepton, or an aromatization path to yield the pyridine groups observed in many other thiopeptides. Although several of the enzymes proposed to perform this cycloaddition have been reconstituted, only pyridine products have been isolated and any hemiaminal intermediates have yet to be observed. Here, we identify the conditions and substrates that decouple the cycloaddition from subsequent steps and allow interception and characterization of this long hypothesized intermediate. Transition state modeling indicates that the key amide-iminol tautomerization is the major hurdle in an otherwise energetically favorable cycloaddition. An anionic model suggests that deprotonation and polarization of this amide bond by TbtD removes this barrier and provides a sufficient driving force for facile (stepwise) cycloaddition. This work provides evidence for a mechanistic link between disparate cyclases in thiopeptide biosynthesis.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nicholas J Kramer
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Rachel M Bleich
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel S Catlin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Ithaca, New York 14853, United States
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - R Thomas Williamson
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, North Carolina 28403, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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47
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Yan Y, Liu N, Tang Y. Recent developments in self-resistance gene directed natural product discovery. Nat Prod Rep 2020; 37:879-892. [PMID: 31912842 PMCID: PMC7340575 DOI: 10.1039/c9np00050j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2019Natural products (NPs) are important sources of human therapeutic agents and pesticides. To prevent self-harm from bioactive NPs, some microbial producers employ self-resistance genes to protect themselves. One effective strategy is to employ a self-resistance enzyme (SRE), which is a slightly mutated version of the original metabolic enzyme, and is resistant to the toxic NP but is still functional. The presence of a SRE in a gene cluster can serve as a predictive window to the biological activity of the NPs synthesized by the pathway. In this highlight, we summarize representative examples of NP biosynthetic pathways that utilize self-resistance genes for protection. Recent discoveries based on self-resistance gene identification have helped in bridging the gap between activity-guided and genome-driven approaches for NP discovery and functional assignment.
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Affiliation(s)
- Yan Yan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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48
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Lagedroste M, Reiners J, Knospe CV, Smits SHJ, Schmitt L. A Structural View on the Maturation of Lanthipeptides. Front Microbiol 2020; 11:1183. [PMID: 32582108 PMCID: PMC7296275 DOI: 10.3389/fmicb.2020.01183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/08/2020] [Indexed: 01/16/2023] Open
Abstract
Lanthipeptides are ribosomally synthesized and posttranslationally modified peptides, which display diverse bioactivities (e.g., antifungal, antimicrobial, and antiviral). One characteristic of these lanthipeptides is the presence of thioether bonds, which are termed (methyl-) lanthionine rings. These modifications are installed by corresponding modification enzymes in a two-step modality. First, serine and threonine residues are dehydrated followed by a subsequent catalyzed cyclization reaction, in which the dehydrated serine and threonine residues are undergoing a Michael-type addition with cysteine residues. The dedicated enzymes are encoded by one or two genes and the classification of lanthipeptides is pending on this. The modification steps form the basis of distinguishing the different classes of lanthipeptides and furthermore reflect also important mechanistic differences. Here, we will summarize recent insights into the mechanisms and the structures of the participating enzymes, focusing on the two core modification steps - dehydration and cyclization.
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Affiliation(s)
- Marcel Lagedroste
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - C Vivien Knospe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Walker MC, Eslami SM, Hetrick KJ, Ackenhusen SE, Mitchell DA, van der Donk WA. Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family. BMC Genomics 2020; 21:387. [PMID: 32493223 PMCID: PMC7268733 DOI: 10.1186/s12864-020-06785-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Background Lanthipeptides belong to the ribosomally synthesized and post-translationally modified peptide group of natural products and have a variety of biological activities ranging from antibiotics to antinociceptives. These peptides are cyclized through thioether crosslinks and can bear other secondary post-translational modifications. While lanthipeptide biosynthetic gene clusters can be identified by the presence of genes encoding characteristic enzymes involved in the post-translational modification process, locating the precursor peptides encoded within these clusters is challenging due to their short length and high sequence variability, which limits the high-throughput exploration of lanthipeptide biosynthesis. To address this challenge, we enhanced the predictive capabilities of Rapid ORF Description & Evaluation Online (RODEO) to identify members of all four known classes of lanthipeptides. Results Using RODEO, we mined over 100,000 bacterial and archaeal genomes in the RefSeq database. We identified nearly 8500 lanthipeptide precursor peptides. These precursor peptides were identified in a broad range of bacterial phyla as well as the Euryarchaeota phylum of archaea. Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. A number of these precursor peptides are similar to those of previously characterized lanthipeptides, but even more were not, including potential antibiotics. One such new antimicrobial lanthipeptide was purified and characterized. Additionally, examination of the biosynthetic gene clusters revealed that enzymes installing secondary post-translational modifications are more widespread than initially thought. Conclusion Lanthipeptide biosynthetic gene clusters are more widely distributed and the precursor peptides encoded within these clusters are more diverse than previously appreciated, demonstrating that the lanthipeptide sequence-function space remains largely underexplored.
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Affiliation(s)
- Mark C Walker
- Department of Chemistry and Chemical Biology, University of New Mexico, 346 Clark Hall, 300 Terrace St. NE, Albuquerque, NM, 87131, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.
| | - Sara M Eslami
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Kenton J Hetrick
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Sarah E Ackenhusen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory, 600 S. Mathews Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL, 61801, USA
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Gao L, Su C, Du X, Wang R, Chen S, Zhou Y, Liu C, Liu X, Tian R, Zhang L, Xie K, Chen S, Guo Q, Guo L, Hano Y, Shimazaki M, Minami A, Oikawa H, Huang N, Houk KN, Huang L, Dai J, Lei X. FAD-dependent enzyme-catalysed intermolecular [4+2] cycloaddition in natural product biosynthesis. Nat Chem 2020; 12:620-628. [DOI: 10.1038/s41557-020-0467-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/14/2020] [Indexed: 01/21/2023]
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