1
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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation. J Am Chem Soc 2024; 146:14328-14340. [PMID: 38728535 PMCID: PMC11225102 DOI: 10.1021/jacs.4c03994] [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] [Indexed: 05/12/2024]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique targeting of the outer membrane protein BamA. Darobactin, a ribosomally synthesized and post-translationally modified peptide (RiPP), is produced by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) and contains one ether and one C-C cross-link. Herein, we analyze the substrate tolerance of DarE and describe an underlying catalytic principle of the enzyme. These efforts produced 51 enzymatically modified darobactin variants, revealing that DarE can install the ether and C-C cross-links independently and in different locations on the substrate. Notable variants with fused bicyclic structures were characterized, including darobactin W3Y, with a non-Trp residue at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. While lacking antibiotic activity, quantum mechanical modeling of darobactins W3Y and K5F aided in the elucidation of the requisite features for high-affinity BamA engagement. We also provide experimental evidence for β-oxo modification, which adds support for a proposed DarE mechanism. Based on these results, ether and C-C cross-link formation was investigated computationally, and it was determined that more stable and longer-lived aromatic Cβ radicals correlated with ether formation. Further, molecular docking and transition state structures based on high-level quantum mechanical calculations support the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) cross-links. Finally, mutational analysis and protein structural predictions identified substrate residues that govern engagement to DarE. Our work informs on darobactin scaffold engineering and further unveils the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M Woodard
- 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
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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2
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Li H, Ding W, Zhang Q. Discovery and engineering of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. RSC Chem Biol 2024; 5:90-108. [PMID: 38333193 PMCID: PMC10849128 DOI: 10.1039/d3cb00172e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/17/2023] [Indexed: 02/10/2024] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a diverse superfamily of natural products with immense potential for drug development. This review provides a concise overview of the recent advances in the discovery of RiPP natural products, focusing on rational strategies such as bioactivity guided screening, enzyme or precursor-based genome mining, and biosynthetic engineering. The challenges associated with activating silent biosynthetic gene clusters and the development of elaborate catalytic systems are also discussed. The logical frameworks emerging from these research studies offer valuable insights into RiPP biosynthesis and engineering, paving the way for broader pharmaceutic applications of these peptide natural products.
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Affiliation(s)
- He Li
- Department of Chemistry, Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai 200433 China
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3
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Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Benzylic Radical Stabilization Permits Ether Formation During Darobactin Biosynthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569256. [PMID: 38076856 PMCID: PMC10705402 DOI: 10.1101/2023.11.29.569256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique mode of action. Biosynthetic studies have revealed that darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP). During maturation, the darobactin precursor peptide (DarA) is modified by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) to contain ether and C-C crosslinks. In this work, we describe the enzymatic tolerance of DarE using a panel of DarA variants, revealing that DarE can install the ether and C-C crosslinks independently and in different locations on DarA. These efforts produced 57 darobactin variants, 50 of which were enzymatically modified. Several new variants with fused bicyclic structures were characterized, including darobactin W3Y, which replaces tryptophan with tyrosine at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. Three additional darobactin variants contained fused diether macrocycles, leading us to investigate the origin of ether versus C-C crosslink formation. Computational analyses found that more stable and long-lived Cβ radicals found on aromatic amino acids correlated with ether formation. Further, molecular docking and calculated transition state structures provide support for the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) crosslink formation. We also provide experimental evidence for a β-oxotryptophan modification, a proposed intermediate during ether crosslink formation. Finally, mutational analysis of the DarA leader region and protein structural predictions identified which residues were dispensable for processing and others that govern substrate engagement by DarE. Our work informs on darobactin scaffold engineering and sheds additional light on the underlying principles of rSAM catalysis.
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Affiliation(s)
- Austin M. Woodard
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D. Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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4
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Ma S, Xi W, Wang S, Chen H, Guo S, Mo T, Chen W, Deng Z, Chen F, Ding W, Zhang Q. Substrate-Controlled Catalysis in the Ether Cross-Link-Forming Radical SAM Enzymes. J Am Chem Soc 2023; 145:22945-22953. [PMID: 37769281 DOI: 10.1021/jacs.3c04355] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Darobactin is a heptapeptide antibiotic featuring an ether cross-link and a C-C cross-link, and both cross-links are installed by a radical S-adenosylmethionine (rSAM) enzyme DarE. How a single DarE enzyme affords the two chemically distinct cross-links remains largely obscure. Herein, by mapping the biosynthetic landscape for darobactin-like RiPP (daropeptide), we identified and characterized two novel daropeptides that lack the C-C cross-link present in darobactin and instead are solely composed of ether cross-links. Phylogenetic and mutagenesis analyses reveal that the daropeptide maturases possess intrinsic multifunctionality, catalyzing not only the formation of ether cross-link but also C-C cross-linking and Ser oxidation. Intriguingly, the different chemical outcomes are controlled by the exact substrate motifs. Our work not only provides a roadmap for the discovery of new daropeptide natural products but also offers insights into the regulatory mechanisms that govern these remarkably versatile ether cross-link-forming rSAM enzymes.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Wenhui Xi
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Heng Chen
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Sijia Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wenxue Chen
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fener Chen
- Department of Chemistry, Fudan University, Shanghai 200433, China
- National Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
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5
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Pei ZF, Zhu L, Sarksian R, van der Donk WA, Nair SK. Class V Lanthipeptide Cyclase Directs the Biosynthesis of a Stapled Peptide Natural Product. J Am Chem Soc 2022; 144:17549-17557. [PMID: 36107785 PMCID: PMC9621591 DOI: 10.1021/jacs.2c06808] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lanthipeptides are a class of cyclic peptides characterized by the presence of one or more lanthionine (Lan) or methyllanthionine (MeLan) thioether rings. These cross-links are produced by α,β-unsaturation of Ser or Thr residues in peptide substrates by dehydration, followed by a Michael-type conjugate addition of Cys residues onto the dehydroamino acids. Lanthipeptides may be broadly classified into at least five different classes, and the biosynthesis of classes I-IV lanthipeptides requires catalysis by LanC cyclases that control both the site-specificity and the stereochemistry of the conjugate addition. In contrast, there are no current examples of LanCs that occur in class V biosynthetic clusters, despite the presence of lanthionine rings in these compounds. In this work, bioinformatics-guided co-occurrence analysis identifies more than 240 putative class V lanthipeptide clusters that contain a LanC cyclase. Reconstitution studies demonstrate that the cyclase-catalyzed product is notably distinct from the product formed spontaneously. Stereochemical analysis shows that the cyclase diverts the final product to a configuration that is distinct from one that is energetically favored. Structural characterization of the final product by multi-dimensional NMR spectroscopy reveals that it forms a helical stapled peptide. Mutational analysis identified a plausible order for cyclization and suggests that enzymatic rerouting to the final structure is largely directed by the construction of the first lanthionine ring. These studies show that lanthipeptide cyclases are needed for the biosynthesis of some constrained peptides, the formations of which would otherwise be energetically unfavored.
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Affiliation(s)
- Zeng-Fei Pei
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Raymond Sarksian
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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6
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Takino J, Kotani A, Ozaki T, Peng W, Yu J, Guo Y, Mochizuki S, Akimitsu K, Hashimoto M, Ye T, Minami A, Oikawa H. Biochemistry-Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides. Angew Chem Int Ed Engl 2021; 60:23403-23411. [PMID: 34448341 DOI: 10.1002/anie.202110658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Indexed: 11/08/2022]
Abstract
Highly reducing polyketide synthases (HR-PKSs) produce structurally diverse polyketides (PKs). The PK diversity is constructed by a variety of factors, including the β-keto processing, chain length, methylation pattern, and relative and absolute configurations of the substituents. We examined the stereochemical course of the PK processing for the synthesis of polyhydroxy PKs such as phialotides, phomenoic acid, and ACR-toxin. Heterologous expression of a HR-PKS gene, a trans-acting enoylreductase gene, and a truncated non-ribosomal peptide synthetase gene resulted in the formation of a linear PK with multiple stereogenic centers. The absolute configurations of the stereogenic centers were determined by chemical degradation followed by comparison of the degradation products with synthetic standards. A stereochemical rule was proposed to explain the absolute configurations of other reduced PKs and highlights an error in the absolute configurations of a reported structure. The present work demonstrates that focused functional analysis of functionally related HR-PKSs leads to a better understanding of the stereochemical course.
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Affiliation(s)
- Junya Takino
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Akari Kotani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Wenquan Peng
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China
| | - Jie Yu
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Yian Guo
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Susumu Mochizuki
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture, Kagawa University, Kagawa, 761-0795, Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, 036-8561, Japan
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen, 518055, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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7
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Takino J, Kotani A, Ozaki T, Peng W, Yu J, Guo Y, Mochizuki S, Akimitsu K, Hashimoto M, Ye T, Minami A, Oikawa H. Biochemistry‐Guided Prediction of the Absolute Configuration of Fungal Reduced Polyketides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Junya Takino
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Akari Kotani
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Taro Ozaki
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Wenquan Peng
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
| | - Jie Yu
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 China
| | - Yian Guo
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 China
| | - Susumu Mochizuki
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture Kagawa University Kagawa 761-0795 Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education & Faculty of Agriculture Kagawa University Kagawa 761-0795 Japan
| | - Masaru Hashimoto
- Faculty of Agriculture and Life Science Hirosaki University Hirosaki 036-8561 Japan
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics Peking University Shenzhen Graduate School Xili, Nanshan District Shenzhen 518055 China
| | - Atsushi Minami
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Hideaki Oikawa
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
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8
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Lee H, Choi M, Park JU, Roh H, Kim S. Genome Mining Reveals High Topological Diversity of ω-Ester-Containing Peptides and Divergent Evolution of ATP-Grasp Macrocyclases. J Am Chem Soc 2020; 142:3013-3023. [PMID: 31961152 DOI: 10.1021/jacs.9b12076] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ω-Ester-containing peptides (OEPs) are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) containing intramolecular ω-ester or ω-amide bonds. Although their distinct side-to-side connections may create considerable topological diversity of multicyclic peptides, it is largely unknown how diverse ring patterns have been developed in nature. Here, using genome mining of biosynthetic enzymes of OEPs, we identified genes encoding nine new groups of putative OEPs with novel core consensus sequences, disclosing a total of ∼1500 candidate OEPs in 12 groups. Connectivity analysis revealed that OEPs from three different groups contain novel tricyclic structures, one of which has a distinct biosynthetic pathway where a single ATP-grasp enzyme produces both ω-ester and ω-amide linkages. Analysis of the enzyme cross-reactivity showed that, while enzymes are promiscuous to nonconserved regions of the core peptide, they have high specificity to the cognate core consensus sequence, suggesting that the enzyme-core pair has coevolved to create a unique ring topology within the same group and has sufficiently diversified across different groups. Collectively, our results demonstrate that the diverse ring topologies, in addition to diverse sequences, have been developed in nature with multiple ω-ester or ω-amide linkages in the OEP family of RiPPs.
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Mingyu Choi
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Jung-Un Park
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Heejin Roh
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
| | - Seokhee Kim
- Department of Chemistry , Seoul National University , 1 Gwanak-ro , Gwanak-gu, Seoul 08826 , South Korea
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9
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Liu B, Fu S, Zhou C. Naturally occurring [4 + 2] type terpenoid dimers: sources, bioactivities and total syntheses. Nat Prod Rep 2020; 37:1627-1660. [DOI: 10.1039/c9np00037b] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This review article highlights recent progress on their sources, bioactivities, biosynthetic hypotheses and total chemical syntheses of naturally occurring [4 + 2] type terpenoid dimers.
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Affiliation(s)
- Bo Liu
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Shaomin Fu
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu
- China
| | - Chengying Zhou
- Key Laboratory of Green Chemistry & Technology of the Ministry of Education
- College of Chemistry
- Sichuan University
- Chengdu
- China
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10
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Mo T, Ji X, Yuan W, Mandalapu D, Wang F, Zhong Y, Li F, Chen Q, Ding W, Deng Z, Yu S, Zhang Q. Thuricin Z: A Narrow‐Spectrum Sactibiotic that Targets the Cell Membrane. Angew Chem Int Ed Engl 2019; 58:18793-18797. [DOI: 10.1002/anie.201908490] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/19/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Tianlu Mo
- Department of ChemistryFudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of ChemistryFudan University Shanghai 200433 China
| | - Wei Yuan
- Department of ChemistryFudan University Shanghai 200433 China
| | - Dhanaraju Mandalapu
- Department of ChemistryFudan University Shanghai 200433 China
- Institute of Mass SpectrometrySchool of Material Science and Chemical EngineeringNingbo University Ningbo Zhejiang 315211 China
| | - Fangting Wang
- Department of ChemistryFudan University Shanghai 200433 China
| | - Yuting Zhong
- Department of ChemistryFudan University Shanghai 200433 China
| | - Fuyou Li
- Department of ChemistryFudan University Shanghai 200433 China
| | - Qin Chen
- Department of ChemistryFudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 China
| | - Shaoning Yu
- Institute of Mass SpectrometrySchool of Material Science and Chemical EngineeringNingbo University Ningbo Zhejiang 315211 China
| | - Qi Zhang
- Department of ChemistryFudan University Shanghai 200433 China
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11
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Mo T, Ji X, Yuan W, Mandalapu D, Wang F, Zhong Y, Li F, Chen Q, Ding W, Deng Z, Yu S, Zhang Q. Thuricin Z: A Narrow‐Spectrum Sactibiotic that Targets the Cell Membrane. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tianlu Mo
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Wei Yuan
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Dhanaraju Mandalapu
- Department of Chemistry Fudan University Shanghai 200433 China
- Institute of Mass Spectrometry School of Material Science and Chemical Engineering Ningbo University Ningbo Zhejiang 315211 China
| | - Fangting Wang
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Yuting Zhong
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Fuyou Li
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Qin Chen
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism School of Life Sciences & Biotechnology Shanghai Jiao Tong University Shanghai 200240 China
| | - Shaoning Yu
- Institute of Mass Spectrometry School of Material Science and Chemical Engineering Ningbo University Ningbo Zhejiang 315211 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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12
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Mo T, Liu WQ, Ji W, Zhao J, Chen T, Ding W, Yu S, Zhang Q. Biosynthetic Insights into Linaridin Natural Products from Genome Mining and Precursor Peptide Mutagenesis. ACS Chem Biol 2017; 12:1484-1488. [PMID: 28452467 DOI: 10.1021/acschembio.7b00262] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Linaridin is a small class of peptide natural products belonging to the ribosomally synthesized and post-translationally modified peptides (RiPPs) superfamily. By an extensive genome-wide survey of linaridin biosynthetic genes, we show that this class of natural products is widespread in nature and possesses vast structural diversity. The linaridin precursor peptides are relatively conserved in the N-termini but have diverse sequences in the core region, which appear to have coevolved with the biosynthetic enzymes. Using the prototypic linaridin cypemycin as a model, we have explored the structure-activity relationships involved in precursor peptide maturation and generated a diverse set of novel cypemycin variants, among which the T2S variant exhibits enhanced activity against Micrococcus luteus. Our results reveal valuable insights into linaridin biosynthesis and highlight the potential to explore this class of natural products by genome mining and by biosynthetic engineering studies.
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Affiliation(s)
- Tianlu Mo
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Wan-Qiu Liu
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Wenjuan Ji
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Junfeng Zhao
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Tuo Chen
- Key
Laboratory of Extreme Environmental Microbial Resources and Engineering,
Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
| | - Wei Ding
- Department
of Chemistry, Fudan University, Shanghai 200433, China
- Key
Laboratory of Extreme Environmental Microbial Resources and Engineering,
Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, Gansu 730000, China
| | - Shaoning Yu
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
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Dunbar KL, Scharf DH, Litomska A, Hertweck C. Enzymatic Carbon-Sulfur Bond Formation in Natural Product Biosynthesis. Chem Rev 2017; 117:5521-5577. [PMID: 28418240 DOI: 10.1021/acs.chemrev.6b00697] [Citation(s) in RCA: 348] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sulfur plays a critical role for the development and maintenance of life on earth, which is reflected by the wealth of primary metabolites, macromolecules, and cofactors bearing this element. Whereas a large body of knowledge has existed for sulfur trafficking in primary metabolism, the secondary metabolism involving sulfur has long been neglected. Yet, diverse sulfur functionalities have a major impact on the biological activities of natural products. Recent research at the genetic, biochemical, and chemical levels has unearthed a broad range of enzymes, sulfur shuttles, and chemical mechanisms for generating carbon-sulfur bonds. This Review will give the first systematic overview on enzymes catalyzing the formation of organosulfur natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel H Scharf
- Life Sciences Institute, University of Michigan , 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Agnieszka Litomska
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI) , Beutenbergstrasse 11a, 07745 Jena, Germany.,Friedrich Schiller University , 07743 Jena, Germany
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14
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Ding W, Ji X, Li Y, Zhang Q. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL. Front Chem 2016; 4:27. [PMID: 27446906 PMCID: PMC4916742 DOI: 10.3389/fchem.2016.00027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities.
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Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University Shanghai, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University Shanghai, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University Shanghai, China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai, China
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15
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Ding W, Li Q, Jia Y, Ji X, Qianzhu H, Zhang Q. Emerging Diversity of the Cobalamin-Dependent Methyltransferases Involving Radical-Based Mechanisms. Chembiochem 2016; 17:1191-7. [PMID: 27028019 DOI: 10.1002/cbic.201600107] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Indexed: 11/10/2022]
Abstract
Cobalamins comprise a group of cobalt-containing organometallic cofactors that play important roles in cellular metabolism. Although many cobalamin-dependent methyltransferases (e.g., methionine synthase MetH) have been extensively studied, a new group of methyltransferases that are cobalamin-dependent and utilize radical chemistry in catalysis is just beginning to be appreciated. In this Concept article, we summarize recent advances in the understanding of the radical-based and cobalamin-dependent methyltransferases and discuss the functional and mechanistic diversity of this emerging class of enzymes.
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Affiliation(s)
- Wei Ding
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qien Li
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Youli Jia
- Key Laboratory of Cell Activities and Stress Adaptations, (Ministry of Education), School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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