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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Gao Y, Zhu Y, Awakawa T, Abe I. Unusual cysteine modifications in natural product biosynthesis. RSC Chem Biol 2024; 5:293-311. [PMID: 38576726 PMCID: PMC10989515 DOI: 10.1039/d4cb00020j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/08/2024] [Indexed: 04/06/2024] Open
Abstract
l-Cysteine is a highly reactive amino acid that is modified into a variety of chemical structures, including cysteine sulfinic acid in human metabolic pathways, and sulfur-containing scaffolds of amino acids, alkaloids, and peptides in natural product biosynthesis. Among the modification enzymes responsible for these cysteine-derived compounds, metalloenzymes constitute an important family of enzymes that catalyze a wide variety of reactions. Therefore, understanding their reaction mechanisms is important for the biosynthetic production of cysteine-derived natural products. This review mainly summarizes recent mechanistic investigations of metalloenzymes, with a particular focus on recently discovered mononuclear non-heme iron (NHI) enzymes, dinuclear NHI enzymes, and radical-SAM enzymes involved in unusual cysteine modifications in natural product biosynthesis.
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Affiliation(s)
- Yaojie Gao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yuhao Zhu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- RIKEN Center for Sustainable Resource Science Wako Saitama 351-0198 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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3
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Chioti VT, Clark KA, Ganley JG, Han EJ, Seyedsayamdost MR. N-Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster. J Am Chem Soc 2024; 146:7313-7323. [PMID: 38452252 PMCID: PMC11062405 DOI: 10.1021/jacs.3c11740] [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: 03/09/2024]
Abstract
DUF692 multinuclear iron oxygenases (MNIOs) are an emerging family of tailoring enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). Three members, MbnB, TglH, and ChrH, have been characterized to date and shown to catalyze unusual and complex transformations. Using a co-occurrence-based bioinformatic search strategy, we recently generated a sequence similarity network of MNIO-RiPP operons that encode one or more MNIOs adjacent to a transporter. The network revealed >1000 unique gene clusters, evidence of an unexplored biosynthetic landscape. Herein, we assess an MNIO-RiPP cluster from this network that is encoded in Proteobacteria and Actinobacteria. The cluster, which we have termed mov (for methanobactin-like operon in Vibrio), encodes a 23-residue precursor peptide, two MNIOs, a RiPP recognition element, and a transporter. Using both in vivo and in vitro methods, we show that one MNIO, homologous to MbnB, installs an oxazolone-thioamide at a Thr-Cys dyad in the precursor. Subsequently, the second MNIO catalyzes N-Cα bond cleavage of the penultimate Asn to generate a C-terminally amidated peptide. This transformation expands the reaction scope of the enzyme family, marks the first example of an MNIO-catalyzed modification that does not involve Cys, and sets the stage for future exploration of other MNIO-RiPPs.
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Affiliation(s)
- Vasiliki T Chioti
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Jack G Ganley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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4
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Johnson BA, Clark KA, Bushin LB, Spolar CN, Seyedsayamdost MR. Expanding the Landscape of Noncanonical Amino Acids in RiPP Biosynthesis. J Am Chem Soc 2024; 146:3805-3815. [PMID: 38316431 DOI: 10.1021/jacs.3c10824] [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: 02/07/2024]
Abstract
Advancements in DNA sequencing technologies and bioinformatics have enabled the discovery of new metabolic reactions from overlooked microbial species and metagenomic sequences. Using a bioinformatic co-occurrence strategy, we previously generated a network of ∼600 uncharacterized quorum-sensing-regulated biosynthetic gene clusters that code for ribosomally synthesized and post-translationally modified peptide (RiPP) natural products and are tailored by radical S-adenosylmethionine (RaS) enzymes in streptococci. The most complex of these is the GRC subfamily, named after a conserved motif in the precursor peptide and found exclusively in Streptococcus pneumoniae, the causative agent of bacterial pneumonia. In this study, using both in vivo and in vitro approaches, we have elucidated the modifications installed by the grc biosynthetic enzymes, including a ThiF-like adenylyltransferase/cyclase that generates a C-terminal Glu-to-Cys thiolactone macrocycle, and two RaS enzymes, which selectively epimerize the β-carbon of threonine and desaturate histidine to generate the first instances of l-allo-Thr and didehydrohistidine in RiPP biosynthesis. RaS-RiPPs that have been discovered thus far have stood out for their exotic macrocycles. The product of the grc cluster breaks this trend by generating two noncanonical residues rather than an unusual macrocycle in the peptide substrate. These modifications expand the landscape of nonproteinogenic amino acids in RiPP natural product biosynthesis and motivate downstream biocatalytic applications of the corresponding enzymes.
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Affiliation(s)
- Brooke A Johnson
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Calvin N Spolar
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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5
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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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Lee H, Park SH, Kim J, Lee J, Koh MS, Lee JH, Kim S. Evolutionary Spread of Distinct O-methyltransferases Guides the Discovery of Unique Isoaspartate-Containing Peptides, Pamtides. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305946. [PMID: 37987032 PMCID: PMC10787088 DOI: 10.1002/advs.202305946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/12/2023] [Indexed: 11/22/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural products with a distinct biosynthetic logic, the enzymatic modification of genetically encoded precursor peptides. Although their structural and biosynthetic diversity remains largely underexplored, the identification of novel subclasses with unique structural motifs and biosynthetic pathways is challenging. Here, it is reported that peptide/protein L-aspartyl O-methyltransferases (PAMTs) present in several RiPP subclasses are highly homologous. Importantly, it is discovered that the apparent evolutionary transmission of the PAMT gene to unrelated RiPP subclasses can serve as a basis to identify a novel RiPP subclass. Biochemical and structural analyses suggest that homologous PAMTs convert aspartate to isoaspartate via aspartyl-O-methyl ester and aspartimide intermediates, and often require cyclic or hairpin-like structures for modification. By conducting homology-based bioinformatic analysis of PAMTs, over 2,800 biosynthetic gene clusters (BGCs) are identified for known RiPP subclasses in which PAMTs install a secondary modification, and over 1,500 BGCs where PAMTs function as a primary modification enzyme, thereby defining a new RiPP subclass, named pamtides. The results suggest that the genome mining of proteins with secondary biosynthetic roles can be an effective strategy for discovering novel biosynthetic pathways of RiPPs through the principle of "guilt by association".
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Affiliation(s)
- Hyunbin Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sho Hee Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jiyoon Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jaehak Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Min Sun Koh
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jung Ho Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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7
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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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8
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Lang H, Liu Y, Duan H, Zhang W, Hu X, Zheng H. Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius. Nat Commun 2023; 14:7650. [PMID: 38001079 PMCID: PMC10673953 DOI: 10.1038/s41467-023-43352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Eusocial pollinators are crucial elements in global agriculture. The honeybees and bumblebees are associated with a simple yet host-restricted gut community, which protect the hosts against pathogen infections. Recent genome mining has led to the discovery of biosynthesis pathways of bioactive natural products mediating microbe-microbe interactions from the gut microbiota. Here, we investigate the diversity of biosynthetic gene clusters in the bee gut microbiota by analyzing 477 genomes from cultivated bacteria and metagenome-assembled genomes. We identify 744 biosynthetic gene clusters (BGCs) covering multiple chemical classes. While gene clusters for the post-translationally modified peptides are widely distributed in the bee guts, the distribution of the BGC classes varies significantly in different bee species among geographic locations, which is attributed to the strain-level variation of bee gut members in the chemical repertoire. Interestingly, we find that Gilliamella strains possessing a thiopeptide-like BGC show potent activity against the pathogenic Melissococcus plutonius. The spectrometry-guided genome mining reveals a RiPP-encoding BGC from Gilliamella with a 10 amino acid-long core peptide exhibiting antibacterial potentials. This study illustrates the widespread small-molecule-encoding BGCs in the bee gut symbionts and provides insights into the bacteria-derived natural products as potential antimicrobial agents against pathogenic infections.
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Affiliation(s)
- Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Yuwen Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Huijuan Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Wenhao Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Xiaosong Hu
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China.
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He BB, Liu J, Cheng Z, Liu R, Zhong Z, Gao Y, Liu H, Song ZM, Tian Y, Li YX. Bacterial Cytochrome P450 Catalyzed Post-translational Macrocyclization of Ribosomal Peptides. Angew Chem Int Ed Engl 2023; 62:e202311533. [PMID: 37767859 DOI: 10.1002/anie.202311533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 09/29/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a fascinating group of natural products that exhibit diverse structural features and bioactivities. P450-catalyzed RiPPs stand out as a unique but underexplored family. Herein, we introduce a rule-based genome mining strategy that harnesses the intrinsic biosynthetic principles of RiPPs, including the co-occurrence and co-conservation of precursors and P450s and interactions between them, successfully facilitating the identification of diverse P450-catalyzed RiPPs. Intensive BGC characterization revealed four new P450s, KstB, ScnB, MciB, and SgrB, that can catalyze the formation of Trp-Trp-Tyr (one C-C and two C-N bonds), Tyr-Trp (C-C bond), Trp-Trp (C-N bond), and His-His (ether bond) crosslinks, respectively, within three or four residues. KstB, ScnB, and MciB could accept non-native precursors, suggesting they could be promising starting templates for bioengineering to construct macrocycles. Our study highlights the potential of P450s to expand the chemical diversity of strained macrocyclic peptides and the range of biocatalytic tools available for peptide macrocyclization.
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Affiliation(s)
- Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jing Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Runze Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhi-Man Song
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongqi Tian
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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10
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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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11
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Cheng B, Huang J, Duan Y, Liu W. Association of Radical Chemistry with LanD Flavoprotein Activity for C-Terminal Macrocyclization of a Ribosomal Peptide by Formation of an Unsaturated Thioether Residue. Angew Chem Int Ed Engl 2023; 62:e202308733. [PMID: 37431841 DOI: 10.1002/anie.202308733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/12/2023]
Abstract
LanD flavoproteins catalyze oxidative decarboxylation of the C-terminal Cys residue of a peptide to produce an enethiol. This enethiol is highly reactive and can be coupled with an upstream dehydroamino acid through Michael addition to form S-[2-aminovinyl](3-methyl)cysteine, an unsaturated thioether residue known to be characteristic of an array of C-terminally macrocyclized, ribosomally synthesized and posttranslationally modified peptides (RiPPs). Based on a two-stage bioinformatics mining of posttranslational modifications (PTMs) related to C-terminal Cys processing, we report herein that LanD activity can couple with radical S-adenosylmethionine chemistry to provide a new unsaturated thioether residue, S-[2-aminovinyl]-3-carbamoylcysteine, by conjugating the resultant enethiol with Cβ of the Asn residue in the C-terminal NxxC motif of a peptide for macrocyclization. This study furthers our understanding of the variety of PTMs involved in creating the structure diversity of macrocyclic RiPPs.
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Affiliation(s)
- Botao Cheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jiwu Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yuting Duan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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12
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Hu X, Shi Y, Jiang B, Fu J, Li X, Li S, Sun G, Ren W, Hu X, You X, Liu Z, Han X, Zhang T, Hong B, Wu L. Iterative Methylation Leads to 3-Methylchuangxinmycin Production in Actinoplanes tsinanensis CPCC 200056. JOURNAL OF NATURAL PRODUCTS 2023; 86:1-7. [PMID: 36649560 DOI: 10.1021/acs.jnatprod.2c00360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A new congener of chuangxinmycin (CM) was identified from Actinoplanes tsinanensis CPCC 200056. Its structure was determined as 3-methylchuangxinmycin (MCM) by 1D and 2D NMR. MCM could be generated in vivo from CM by heterologous expression of the vitamin B12-dependent radical SAM enzyme CxnA/A1 responsible for methylation of 3-demethylchuangxinmycin (DCM) in CM biosynthesis, indicating that CxnA/A1 could perform iterative methylation for MCM production. In vitro assays revealed significant activities of CM, DCM, and MCM against Mycobacterium tuberculosis H37Rv and clinically isolated isoniazid/rifampin-resistant M. tuberculosis, suggesting that CM and its derivatives may have potential for antituberculosis drug development.
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Affiliation(s)
- Xiaomin Hu
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yuanyuan Shi
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Bingya Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jie Fu
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xingxing Li
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shufen Li
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Guizhi Sun
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Weicong Ren
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xinxin Hu
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xuefu You
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Xingli Han
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, People's Republic of China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Linzhuan Wu
- NHC Key Laboratory of Biotechnology of Antibiotics, and CAMS Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, People's Republic of China
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13
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Li X, Ma S, Zhang Q. Chemical Synthesis and Biosynthesis of Darobactin. Tetrahedron Lett 2023. [DOI: 10.1016/j.tetlet.2023.154337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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14
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Phan CS, Morinaka BI. A Prevalent Group of Actinobacterial Radical SAM/SPASM Maturases Involved in Triceptide Biosynthesis. ACS Chem Biol 2022; 17:3284-3289. [PMID: 36454686 DOI: 10.1021/acschembio.2c00621] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Triceptides are ribosomally synthesized and post-translationally modified peptides characterized by three-residue cyclophanes. The cyclophanes are installed by radical SAM/SPASM maturases referred to as 3-residue cyclophane forming enzymes (3-CyFEs) which catalyze C(sp2)-Cβ(sp3) bond formation on three residue motifs at the C-terminus of precursor peptides. Here, we bioinformatically map uncharacterized rSAM/SPASM enzymes, referred to as Actinobacterial multiple cyclophane maturases. The enzyme FwwB from Actinospira robinae was selected for in vivo functional studies in Escherichia coli, and was found to catalyze formation of multiple Phe- and Trp-derived 3-residue cyclophanes. FwwB was shown to accept a series of engineered substrates but showed specificity for the native 3-residue motif.
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Affiliation(s)
- Chin-Soon Phan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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15
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Ali A, Happel D, Habermann J, Schoenfeld K, Macarrón Palacios A, Bitsch S, Englert S, Schneider H, Avrutina O, Fabritz S, Kolmar H. Sactipeptide Engineering by Probing the Substrate Tolerance of a Thioether-Bond-Forming Sactisynthase. Angew Chem Int Ed Engl 2022; 61:e202210883. [PMID: 36049110 PMCID: PMC9828075 DOI: 10.1002/anie.202210883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Indexed: 01/12/2023]
Abstract
Sactipeptides are ribosomally synthesized peptides containing a unique sulfur to α-carbon crosslink. Catalyzed by sactisynthases, this thioether pattern endows sactipeptides with enhanced structural, thermal, and proteolytic stability, which makes them attractive scaffolds for the development of novel biotherapeutics. Herein, we report the in-depth study on the substrate tolerance of the sactisynthase AlbA to catalyze the formation of thioether bridges in sactipeptides. We identified a possible modification site within the sactipeptide subtilosin A allowing for peptide engineering without compromising formation of thioether bridges. A panel of natural and hybrid sactipeptides was produced to study the AlbA-mediated formation of thioether bridges, which were identified mass-spectrometrically. In a proof-of-principle study, we re-engineered subtilosin A to a thioether-bridged, specific streptavidin targeting peptide, opening the door for the functional engineering of sactipeptides.
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Affiliation(s)
- Ataurehman Ali
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Dominic Happel
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Jan Habermann
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Katrin Schoenfeld
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Arturo Macarrón Palacios
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Sebastian Bitsch
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Simon Englert
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Hendrik Schneider
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Olga Avrutina
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany
| | - Sebastian Fabritz
- Department of Chemical BiologyMax Planck Institute for Medical ResearchJahnstraße 2969120HeidelbergGermany
| | - Harald Kolmar
- Department for Organic Chemistry and BiochemistryTechnische Universität DarmstadtAlarich-Weiß-Straße 464287DarmstadtGermany,Centre for Synthetic BiologyTechnical University of Darmstadt64283DamstadtGermany
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16
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Mahanta N, PH K, KS S, Das S, G. D. Recent Advancements in Bottromycin Biosynthesis. Synlett 2022. [DOI: 10.1055/s-0042-1751373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractBottromycin is a structurally complex cyclic peptidic compound isolated from Streptomyces bottropensis and related organisms and belongs to the RiPP family of natural products (ribosomally synthesized and post-translationally modified peptides). It exhibits potent antibacterial properties against gram-positive pathogens (including drug resistant strains such as MRSA, MIC 1 μg/mL and VRE, MIC 0.5 μg/mL) and mycoplasma. Bottromycin blocks the binding of the aminoacyl-tRNA to the A-site on the 50S ribosome and hence inhibits protein synthesis. Bottromycins contain structurally diverse post-translational modifications (PTMs) on a small peptide (GPVVVFDC) including a unique macrocyclic amidine, rare β-methylation, terminal thiazole heterocycle, oxidative decarboxylation, and Asp epimerization, among others. It exhibits a precursor peptide organization with a C-terminal follower peptide and a N-terminal core peptide. There are several new studies reported recently which gave detailed insights into the bottromycin biosynthesis pathway. This Account highlights the current advancements in understanding the biosynthetic pathway of bottromycin focusing mainly on the biochemically and structurally characterized enzymes and intricate details of the peptide–protein biophysical interactions. These studies have provided a strong foundation for conducting combinatorial biosynthesis and synthetic biological studies to create novel bottromycin variants for therapeutic applications.1 Introduction2 Biosynthetic Pathway for Bottromycin3 Enzymology of Bottromycin Biosynthesis3.1 Cleavage of Methionine (BotP)3.2 Radical SAM Methyltransferases (BotRMT1, BotRMT2, BotRMT3)3.3 ATP-Dependent YcaO Enzymes3.3.1 Thiazoline Formation by BotC3.3.2 Macrolactamidine Formation by BotCD3.4 Follower Peptide Hydrolysis (BotAH)3.5 Aspartate Epimerization (BotH)3.6 Oxidative Decarboxylation (BotCYP)3.7 O-Methyltransferase (BotOMT)4 Heterologous Bottromycin Production and Analogue Preparation5 Summary and Outlook
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17
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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18
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Clark KA, Bushin LB, Seyedsayamdost MR. RaS-RiPPs in Streptococci and the Human Microbiome. ACS BIO & MED CHEM AU 2022; 2:328-339. [PMID: 35996476 PMCID: PMC9389541 DOI: 10.1021/acsbiomedchemau.2c00004] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Radical S-adenosylmethionine (RaS) enzymes have
quickly advanced to one of the most abundant and versatile enzyme
superfamilies known. Their chemistry is predicated upon reductive
homolytic cleavage of a carbon–sulfur bond in cofactor S-adenosylmethionine forming an oxidizing carbon-based radical,
which can initiate myriad radical transformations. An emerging role
for RaS enzymes is their involvement in the biosynthesis of ribosomally
synthesized and post-translationally modified peptides (RiPPs), a
natural product family that has become known as RaS-RiPPs. These metabolites
are especially prevalent in human and mammalian microbiomes because
the complex chemistry of RaS enzymes gives rise to correspondingly
complex natural products with minimal cellular energy and genomic
fingerprint, a feature that is advantageous in microbes with small,
host-adapted genomes in competitive environments. Herein, we review
the discovery and characterization of RaS-RiPPs from the human microbiome
with a focus on streptococcal bacteria. We discuss the varied chemical
modifications that RaS enzymes introduce onto their peptide substrates
and the diverse natural products that they give rise to. The majority
of RaS-RiPPs remain to be discovered, providing an intriguing avenue
for future investigations at the intersection of metalloenzymology,
chemical ecology, and the human microbiome.
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Affiliation(s)
- Kenzie A Clark
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Leah B Bushin
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States.,Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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19
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Sugiyama R, Suarez AFL, Morishita Y, Nguyen TQN, Tooh YW, Roslan MNHB, Lo Choy J, Su Q, Goh WY, Gunawan GA, Wong FT, Morinaka BI. The Biosynthetic Landscape of Triceptides Reveals Radical SAM Enzymes That Catalyze Cyclophane Formation on Tyr- and His-Containing Motifs. J Am Chem Soc 2022; 144:11580-11593. [PMID: 35729768 DOI: 10.1021/jacs.2c00521] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptide-derived cyclophanes inhabit a unique niche in the chemical space of macrocyclic peptides with several examples of pharmaceutical importance. Although both synthetic and biocatalytic methods are available for constructing these macrocycles, versatile (bio)catalysts able to incorporate a variety of amino acids that compose the macrocycle would be useful for the creation of diverse peptide cyclophanes. In this report, we synergized the use of bioinformatic tools to map the biosynthetic landscape of radical SAM enzymes (3-CyFEs) that catalyze three-residue cyclophane formation in the biosynthesis of a new family of RiPP natural products, the triceptides. This analysis revealed 3940 (3113 unique) putative precursor sequences predicted to be modified by 3-CyFEs. Several uncharacterized maturase systems were identified that encode unique precursor types. Functional studies were carried out in vivo in Escherichia coli to identify modified precursors containing His and Tyr residues. NMR analysis of the products revealed that Tyr and His can also be incorporated into cyclophane macrocycles by 3-CyFEs. Collectively, all aromatic amino acids can be incorporated by 3-CyFEs, and the cyclophane formation strictly occurs via a C(sp2)-C(sp3) cross-link between the (hetero)aromatic ring to Cβ. In addition to 3-CyFEs, we functionally validated an Fe(II)/α-ketoglutarate-dependent hydroxylase, resulting in β-hydroxylated residues within the cyclophane rings. This study reveals the potential breadth of triceptide precursors and a systematic approach for studying these enzymes to broaden the diversity of peptide macrocycles.
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Affiliation(s)
- Ryosuke Sugiyama
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Yohei Morishita
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Justin Lo Choy
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S 1A8, Canada
| | - Qi Su
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Wei Yang Goh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Gregory Adrian Gunawan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore.,Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Organic & Biomolecular Chemistry, Institute of Sustainability for Chemicals, Energy and Environment, A*STAR, Singapore 138665, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Singapore Institute of Food and Biotechnology Innovation, A*STAR, Singapore 138673, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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20
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Substrate specificity and reaction directionality of a three-residue cyclophane forming enzyme PauB. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Soualmia F, Guillot A, Sabat N, Brewee C, Kubiak X, Haumann M, Guinchard X, Benjdia A, Berteau O. Exploring the Biosynthetic Potential of TsrM, a B 12 -dependent Radical SAM Methyltransferase Catalyzing Non-radical Reactions. Chemistry 2022; 28:e202200627. [PMID: 35253932 DOI: 10.1002/chem.202200627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Indexed: 12/20/2022]
Abstract
B12 -dependent radical SAM enzymes are an emerging enzyme family with approximately 200,000 proteins. These enzymes have been shown to catalyze chemically challenging reactions such as methyl transfer to sp2- and sp3-hybridized carbon atoms. However, to date we have little information regarding their complex mechanisms and their biosynthetic potential. Here we show, using X-ray absorption spectroscopy, mutagenesis and synthetic probes that the vitamin B12 -dependent radical SAM enzyme TsrM catalyzes not only C- but also N-methyl transfer reactions further expanding its synthetic versatility. We also demonstrate that TsrM has the unique ability to directly transfer a methyl group to the benzyl core of tryptophan, including the least reactive position C4. Collectively, our study supports that TsrM catalyzes non-radical reactions and establishes the usefulness of radical SAM enzymes for novel biosynthetic schemes including serial alkylation reactions at particularly inert C-H bonds.
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Affiliation(s)
- Feryel Soualmia
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Nazarii Sabat
- UPR 2301, Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Xavier Guinchard
- UPR 2301, Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
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22
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Guo S, Wang S, Ma S, Deng Z, Ding W, Zhang Q. Radical SAM-dependent ether crosslink in daropeptide biosynthesis. Nat Commun 2022; 13:2361. [PMID: 35487921 PMCID: PMC9055067 DOI: 10.1038/s41467-022-30084-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/14/2022] [Indexed: 12/15/2022] Open
Abstract
Darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP), which possesses potent activity against various Gram-negative bacteria. Darobactin features a highly unique bicyclic scaffold, consisting of an ether crosslink between two Trp residues and a C-C crosslink between a Lys and a Trp. Here we report in vivo and in vitro activity of darobactin synthase DarE. We show DarE is a radical S-adenosylmethionine (rSAM) enzyme and is solely responsible for forming the bicyclic scaffold of darobactin. DarE mainly produced the ether-crosslinked product in vitro, and when the assay was performed in H218O, apparent 18O incorporation was observed into the ether-crosslinked product. These observations suggested an rSAM-dependent process in darobactin biosynthesis, involving a highly unusual oxygen insertion step from a water molecule and subsequent O-H and C-H activations. Genome mining analysis demonstrates the diversity of darobactin-like biosynthetic gene clusters, a subclade of which likely encode monocyclic products with only an ether linkage. We propose the name daropeptide for this growing family of ether-containing RiPPs produced by DarE enzymes.
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Affiliation(s)
- Sijia Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Suze Ma
- 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
| | - 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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23
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Imani AS, Lee AR, Vishwanathan N, de Waal F, Freeman MF. Diverse Protein Architectures and α- N-Methylation Patterns Define Split Borosin RiPP Biosynthetic Gene Clusters. ACS Chem Biol 2022; 17:908-917. [PMID: 35297605 PMCID: PMC9019853 DOI: 10.1021/acschembio.1c01002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Borosins are ribosomally synthesized and post-translationally modified peptides (RiPPs) with α-N-methylations installed on the peptide backbone that impart unique properties like proteolytic stability to these natural products. The borosin RiPP family was initially reported only in fungi until our recent discovery and characterization of a Type IV split borosin system in the metal-respiring bacterium Shewanella oneidensis. Here, we used hidden Markov models and sequence similarity networks to identify over 1600 putative pathways that show split borosin biosynthetic gene clusters are widespread in bacteria. Noteworthy differences in precursor and α-N-methyltransferase open reading frame sizes, architectures, and core peptide properties allow further subdivision of the borosin family into six additional discrete structural types, of which five have been validated in this study.
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Affiliation(s)
| | | | | | - Floris de Waal
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
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24
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D'Angelo F, Fernández-Fueyo E, Garcia PS, Shomar H, Pelosse M, Manuel RR, Büke F, Liu S, van den Broek N, Duraffourg N, de Ram C, Pabst M, Bouveret E, Gribaldo S, Py B, Ollagnier de Choudens S, Barras F, Bokinsky G. Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host. eLife 2022; 11:70936. [PMID: 35244541 PMCID: PMC8896826 DOI: 10.7554/elife.70936] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and enzymes are often inactive outside their native host species. We sought to systematically investigate the compatibility of Fe-S networks with non-native Fe-S enzymes. By using collections of Fe-S enzyme orthologs representative of the entire range of prokaryotic diversity, we uncovered a striking correlation between phylogenetic distance and probability of functional expression. Moreover, coexpression of a heterologous Fe-S biogenesis pathway increases the phylogenetic range of orthologs that can be supported by the foreign host. We also find that Fe-S enzymes that require specific electron carrier proteins are rarely functionally expressed unless their taxon-specific reducing partners are identified and co-expressed. We demonstrate how these principles can be applied to improve the activity of a radical S-adenosyl methionine(rSAM) enzyme from a Streptomyces antibiotic biosynthesis pathway in Escherichia coli. Our results clarify how oxygen sensitivity and incompatibilities with foreign Fe-S and electron transfer networks each impede heterologous activity. In particular, identifying compatible electron transfer proteins and heterologous Fe-S biogenesis pathways may prove essential for engineering functional Fe-S enzyme-dependent pathways.
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Affiliation(s)
- Francesca D'Angelo
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Elena Fernández-Fueyo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Pierre Simon Garcia
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France.,Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Helena Shomar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Martin Pelosse
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Rita Rebelo Manuel
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Ferhat Büke
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Siyi Liu
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | - Niels van den Broek
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Nicolas Duraffourg
- Univ. Grenoble Alpes, CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux, Grenoble, France
| | - Carol de Ram
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Emmanuelle Bouveret
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris, CNRS UMR6047, Evolutionary Biology of the Microbial Cell, Department of Microbiology, Paris, France
| | - Béatrice Py
- Aix-Marseille Université-CNRS, Laboratoire de Chimie Bactérienne UMR 7283, Institut de Microbiologie de la Méditerranée, Institut Microbiologie Bioénergies Biotechnologie, Marseille, France
| | | | - Frédéric Barras
- Unit Stress Adaptation and Metabolism of Enterobacteria, Department of Microbiology, Université de Paris, UMR CNRS 2001, Institut Pasteur, Paris, France
| | - Gregory Bokinsky
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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25
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Crystallographic snapshots of a B 12-dependent radical SAM methyltransferase. Nature 2022; 602:336-342. [PMID: 35110733 PMCID: PMC8828468 DOI: 10.1038/s41586-021-04355-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/15/2021] [Indexed: 01/01/2023]
Abstract
By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas1,2. The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications3–6, such as a unique C-methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S-adenosyl-l-methionine (SAM) enzyme7,8. Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans, a unique B12 (cobalamin)-dependent radical SAM enzyme9. The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme–substrate complex offers a glimpse into a B12-dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B12-dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry. Structural and spectroscopic studies show how a B12-dependent radical SAM enzyme catalyses unique and challenging alkylation chemistry, including protein post-translational modification required for methane biosynthesis.
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26
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Ramesh S, Guo X, DiCaprio AJ, De Lio AM, Harris LA, Kille BL, Pogorelov TV, Mitchell DA. Bioinformatics-Guided Expansion and Discovery of Graspetides. ACS Chem Biol 2021; 16:2787-2797. [PMID: 34766760 DOI: 10.1021/acschembio.1c00672] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, or lysine donor residues linked to aspartate or glutamate acceptor residues. Characterized graspetides include serine protease inhibitors such as the microviridins and plesiocin. Here, we report an update to Rapid ORF Description and Evaluation Online (RODEO) for the automated detection of graspetides, which identified 3,923 high-confidence graspetide biosynthetic gene clusters. Sequence and co-occurrence analyses doubled the number of graspetide groups from 12 to 24, defined based on core consensus sequence and putative secondary modification. Bioinformatic analyses of the ATP-grasp ligase superfamily suggest that extant graspetide synthetases diverged once from an ancestral ATP-grasp ligase and later evolved to introduce a variety of ring connectivities. Furthermore, we characterized thatisin and iso-thatisin, two graspetides related by conformational stereoisomerism from Lysobacter antibioticus. Derived from a newly identified graspetide group, thatisin and iso-thatisin feature two interlocking macrolactones with identical ring connectivity, as determined by a combination of tandem mass spectrometry (MS/MS), methanolytic, and mutational analyses. NMR spectroscopy of thatisin revealed a cis conformation for a key proline residue, while molecular dynamics simulations, solvent-accessible surface area calculations, and partial methanolytic analysis coupled with MS/MS support a trans conformation for iso-thatisin at the same position. Overall, this work provides a comprehensive overview of the graspetide landscape, and the improved RODEO algorithm will accelerate future graspetide discoveries by enabling open-access analysis of existing and emerging genomes.
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Affiliation(s)
- Sangeetha Ramesh
- Department of Microbiology, 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
| | - Xiaorui Guo
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Adam J. DiCaprio
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ashley M. De Lio
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
| | - Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Bryce L. Kille
- Department of Computer Science, University of Illinois at Urbana-Champaign, 201 North Goodwin Avenue, Urbana, Illinois 61801, United States
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 1205 West Clark Street, Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department of Microbiology, 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
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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27
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Lewis JK, Jochimsen AS, Lefave SJ, Young AP, Kincannon WM, Roberts AG, Kieber-Emmons MT, Bandarian V. New Role for Radical SAM Enzymes in the Biosynthesis of Thio(seleno)oxazole RiPP Natural Products. Biochemistry 2021; 60:3347-3361. [PMID: 34730336 DOI: 10.1021/acs.biochem.1c00469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ribosomally synthesized post-translationally modified peptides (RiPPs) are ubiquitous and represent a structurally diverse class of natural products. The ribosomally encoded precursor polypeptides are often extensively modified post-translationally by enzymes that are encoded by coclustered genes. Radical S-adenosyl-l-methionine (SAM) enzymes catalyze numerous chemically challenging transformations. In RiPP biosynthetic pathways, these transformations include the formation of C-H, C-C, C-S, and C-O linkages. In this paper, we show that the Geobacter lovleyi sbtM gene encodes a radical SAM protein, SbtM, which catalyzes the cyclization of a Cys/SeCys residue in a minimal peptide substrate. Biochemical studies of this transformation support a mechanism involving H-atom abstraction at the C-3 of the substrate Cys to initiate the chemistry. Several possible cyclization products were considered. The collective biochemical, spectroscopic, mass spectral, and computational observations point to a thiooxazole as the product of the SbtM-catalyzed modification. To our knowledge, this is the first example of a radical SAM enzyme that catalyzes a transformation involving a SeCys-containing peptide and represents a new paradigm for formation of oxazole-containing RiPP natural products.
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Affiliation(s)
- Julia K Lewis
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew S Jochimsen
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Sarah J Lefave
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Anthony P Young
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - William M Kincannon
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Andrew G Roberts
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Matthew T Kieber-Emmons
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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28
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Rebuffat S. Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions. Nat Prod Rep 2021; 39:273-310. [PMID: 34755755 DOI: 10.1039/d1np00052g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is currently well established that multicellular organisms live in tight association with complex communities of microorganisms including a large number of bacteria. These are immersed in complex interaction networks reflecting the relationships established between them and with host organisms; yet, little is known about the molecules and mechanisms involved in these mutual interactions. Ribosomally synthesized peptides, among which bacterial antimicrobial peptides called bacteriocins and microcins have been identified as contributing to host-microbe interplays, are either unmodified or post-translationally modified peptides. This review will unveil current knowledge on these ribosomal peptide-based natural products, their interplay with the host immune system, and their roles in microbial interactions and symbioses. It will include their major structural characteristics and post-translational modifications, the main rules of their maturation pathways, and the principal ecological functions they ensure (communication, signalization, competition), especially in symbiosis, taking select examples in various organisms. Finally, we address unanswered questions and provide a framework for deciphering big issues inspiring future directions in the field.
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Affiliation(s)
- Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), National Centre of Scientific Research (CNRS), CP 54, 57 rue Cuvier 75005, Paris, France.
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29
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Lee YJ, Dai N, Müller SI, Guan C, Parker MJ, Fraser ME, Walsh SE, Sridar J, Mulholland A, Nayak K, Sun Z, Lin YC, Comb DG, Marks K, Gonzalez R, Dowling DP, Bandarian V, Saleh L, Corrêa IR, Weigele PR. Pathways of thymidine hypermodification. Nucleic Acids Res 2021; 50:3001-3017. [PMID: 34522950 PMCID: PMC8989533 DOI: 10.1093/nar/gkab781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/12/2021] [Indexed: 11/15/2022] Open
Abstract
The DNAs of bacterial viruses are known to contain diverse, chemically complex modifications to thymidine that protect them from the endonuclease-based defenses of their cellular hosts, but whose biosynthetic origins are enigmatic. Up to half of thymidines in the Pseudomonas phage M6, the Salmonella phage ViI, and others, contain exotic chemical moieties synthesized through the post-replicative modification of 5-hydroxymethyluridine (5-hmdU). We have determined that these thymidine hypermodifications are derived from free amino acids enzymatically installed on 5-hmdU. These appended amino acids are further sculpted by various enzyme classes such as radical SAM isomerases, PLP-dependent decarboxylases, flavin-dependent lyases and acetyltransferases. The combinatorial permutations of thymidine hypermodification genes found in viral metagenomes from geographically widespread sources suggests an untapped reservoir of chemical diversity in DNA hypermodifications.
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Affiliation(s)
- Yan-Jiun Lee
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Nan Dai
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Stephanie I Müller
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Chudi Guan
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Mackenzie J Parker
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Morgan E Fraser
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Shannon E Walsh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Janani Sridar
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Andrew Mulholland
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Krutika Nayak
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Zhiyi Sun
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Yu-Cheng Lin
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Donald G Comb
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Katherine Marks
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Reyaz Gonzalez
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Daniel P Dowling
- Chemistry Department, University of Massachusetts Boston, 100 William T. Morrissey Blvd. Boston, MA02125, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 South 1400 East Salt Lake City, UT 84112, USA
| | - Lana Saleh
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Ivan R Corrêa
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Inc., 240 County Road, Ipswich, MA01938, USA
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30
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post-Translational Formation of Aminomalonate by a Promiscuous Peptide-Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021; 60:19957-19964. [PMID: 34164914 DOI: 10.1002/anie.202107192] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/23/2021] [Indexed: 11/12/2022]
Abstract
Aminomalonate (Ama) is a widespread structural motif in Nature, whereas its biosynthetic route is only partially understood. In this study, we show that a radical S-adenosylmethionine (rSAM) enzyme involved in cyclophane biosynthesis exhibits remarkable catalytic promiscuity. This enzyme, named three-residue cyclophane forming enzyme (3-CyFE), mainly produces cyclophane in vivo, whereas it produces formylglycine (FGly) as a major product and barely produce cyclophane in vitro. Importantly, the enzyme can further oxidize FGly to produce Ama. Bioinformatic study revealed that 3-CyFEs have evolved from a common ancestor with anaerobic sulfatase maturases (anSMEs), and possess a similar set of catalytic residues with anSMEs. Remarkably, the enzyme does not need leader peptide for activity and is fully active on a truncated peptide containing only 5 amino acids of the core sequence. Our work discloses the first ribosomal path towards Ama formation, providing a possible hint for the rich occurrence of Ama in Nature.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Heng Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - He Li
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xinjian Ji
- 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
| | - 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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31
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Ma S, Chen H, Li H, Ji X, Deng Z, Ding W, Zhang Q. Post‐Translational Formation of Aminomalonate by a Promiscuous Peptide‐Modifying Radical SAM Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Suze Ma
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Heng Chen
- Department of Chemistry Fudan University Shanghai 200433 China
| | - He Li
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- 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
| | - 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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Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz‐Oesterhelt H, Gross H. Nocathioamides, Uncovered by a Tunable Metabologenomic Approach, Define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Department of Phytochemistry and Plant Systematics Division of Pharmaceutical Industries National Research Centre Dokki Cairo Egypt
| | - Saefuddin Aziz
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Microbiology Department Biology Faculty Jenderal Soedirman University Purwokerto Indonesia
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
| | - Markus Kramer
- Institute of Organic Chemistry University of Tübingen Auf der Morgenstelle 18 72076 Tübingen Germany
| | - Jan Straetener
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Heike Brötz‐Oesterhelt
- Department of Microbial Bioactive Compounds Interfaculty Institute of Microbiology and Infection Medicine University of Tübingen Auf der Morgenstelle 28 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection University of Tübingen Tübingen Germany
| | - Harald Gross
- Department of Pharmaceutical Biology Institute of Pharmaceutical Sciences University of Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection University of Tübingen Tübingen Germany
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33
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Saad H, Aziz S, Gehringer M, Kramer M, Straetener J, Berscheid A, Brötz‐Oesterhelt H, Gross H. Nocathioamides, Uncovered by a Tunable Metabologenomic Approach, Define a Novel Class of Chimeric Lanthipeptides. Angew Chem Int Ed Engl 2021; 60:16472-16479. [PMID: 33991039 PMCID: PMC8362196 DOI: 10.1002/anie.202102571] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/09/2021] [Indexed: 12/16/2022]
Abstract
The increasing number of available genomes, in combination with advanced genome mining techniques, unveiled a plethora of biosynthetic gene clusters (BGCs) coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). The products of these BGCs often represent an enormous resource for new and bioactive compounds, but frequently, they cannot be readily isolated and remain cryptic. Here, we describe a tunable metabologenomic approach that recruits a synergism of bioinformatics in tandem with isotope- and NMR-guided platform to identify the product of an orphan RiPP gene cluster in the genomes of Nocardia terpenica IFM 0406 and 0706T . The application of this tactic resulted in the discovery of nocathioamides family as a founder of a new class of chimeric lanthipeptides I.
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Affiliation(s)
- Hamada Saad
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Department of Phytochemistry and Plant SystematicsDivision of Pharmaceutical IndustriesNational Research CentreDokkiCairoEgypt
| | - Saefuddin Aziz
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Microbiology DepartmentBiology FacultyJenderal Soedirman UniversityPurwokertoIndonesia
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry Institute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Markus Kramer
- Institute of Organic ChemistryUniversity of TübingenAuf der Morgenstelle 1872076TübingenGermany
| | - Jan Straetener
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Anne Berscheid
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
| | - Heike Brötz‐Oesterhelt
- Department of Microbial Bioactive CompoundsInterfaculty Institute of Microbiology and Infection MedicineUniversity of TübingenAuf der Morgenstelle 2872076TübingenGermany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight InfectionUniversity of TübingenTübingenGermany
| | - Harald Gross
- Department of Pharmaceutical BiologyInstitute of Pharmaceutical SciencesUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight InfectionUniversity of TübingenTübingenGermany
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Chen Y, Wang J, Li G, Yang Y, Ding W. Current Advancements in Sactipeptide Natural Products. Front Chem 2021; 9:595991. [PMID: 34095082 PMCID: PMC8172795 DOI: 10.3389/fchem.2021.595991] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products that benefited from genome sequencing technology in the past two decades. RiPPs are widely distributed in nature and show diverse chemical structures and rich biological activities. Despite the various structural characteristic of RiPPs, they follow a common biosynthetic logic: a precursor peptide containing an N-terminal leader peptide and a C-terminal core peptide; in some cases,a follower peptide is after the core peptide. The precursor peptide undergoes a series of modification, transport, and cleavage steps to form a mature natural product with specific activities. Sactipeptides (Sulfur-to-alpha carbon thioether cross-linked peptides) belong to RiPPs that show various biological activities such as antibacterial, spermicidal and hemolytic properties. Their common hallmark is an intramolecular thioether bond that crosslinks the sulfur atom of a cysteine residue to the α-carbon of an acceptor amino acid, which is catalyzed by a rSAM enzyme. This review summarizes recent achievements concerning the discovery, distribution, structural elucidation, biosynthesis and application prospects of sactipeptides.
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Affiliation(s)
- Yunliang Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Jinxiu Wang
- Northwest Institute of Eco-Environmental and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guoquan Li
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang, China
| | - Yunpeng Yang
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Malit JJL, Wu C, Liu LL, Qian PY. Global Genome Mining Reveals the Distribution of Diverse Thioamidated RiPP Biosynthesis Gene Clusters. Front Microbiol 2021; 12:635389. [PMID: 33995295 PMCID: PMC8120280 DOI: 10.3389/fmicb.2021.635389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Thioamidated ribosomally synthesized and post-translationally modified peptides (RiPPs) are recently characterized natural products with wide range of potent bioactivities, such as antibiotic, antiproliferative, and cytotoxic activities. These peptides are distinguished by the presence of thioamide bonds in the peptide backbone catalyzed by the YcaO-TfuA protein pair with its genes adjacent to each other. Genome mining has facilitated an in silico approach to identify biosynthesis gene clusters (BGCs) responsible for thioamidated RiPP production. In this work, publicly available genomic data was used to detect and illustrate the diversity of putative BGCs encoding for thioamidated RiPPs. AntiSMASH and RiPPER analysis identified 613 unique TfuA-related gene cluster families (GCFs) and 797 precursor peptide families, even on phyla where the presence of these clusters have not been previously described. Several additional biosynthesis genes are colocalized with the detected BGCs, suggesting an array of possible chemical modifications. This study shows that thioamidated RiPPs occupy a widely unexplored chemical landscape.
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Affiliation(s)
- Jessie James Limlingan Malit
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Chuanhai Wu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ling-Li Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China.,Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, Yangling, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
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Quorum Sensing in Streptococcus mutans Regulates Production of Tryglysin, a Novel RaS-RiPP Antimicrobial Compound. mBio 2021; 12:mBio.02688-20. [PMID: 33727351 PMCID: PMC8092268 DOI: 10.1128/mbio.02688-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria interact and compete with a large community of organisms in their natural environment. Streptococcus mutans is one such organism, and it is an important member of the oral microbiota. We found that S. mutans uses a quorum-sensing system to regulate production of a novel posttranslationally modified peptide capable of inhibiting growth of several streptococcal species. The genus Streptococcus encompasses a large bacterial taxon that commonly colonizes mucosal surfaces of vertebrates and is capable of disease etiologies originating from diverse body sites, including the respiratory, digestive, and reproductive tracts. Identifying new modes of treating infections is of increasing importance, as antibiotic resistance has escalated. Streptococcus mutans is an important opportunistic pathogen that is an agent of dental caries and is capable of systemic diseases such as endocarditis. As such, understanding how it regulates virulence and competes in the oral niche is a priority in developing strategies to defend from these pathogens. We determined that S. mutans UA159 possesses a bona fide short hydrophobic peptide (SHP)/Rgg quorum-sensing system that regulates a specialized biosynthetic operon featuring a radical-SAM (S-adenosyl-l-methionine) (RaS) enzyme and produces a ribosomally synthesized and posttranslationally modified peptide (RiPP). The pairing of SHP/Rgg regulatory systems with RaS biosynthetic operons is conserved across streptococci, and a locus similar to that in S. mutans is found in Streptococcus ferus, an oral streptococcus isolated from wild rats. We identified the RaS-RiPP product from this operon and solved its structure using a combination of analytical methods; we term these RiPPs tryglysin A and B for the unusual Trp-Gly-Lys linkage. We report that tryglysins specifically inhibit the growth of other streptococci, but not other Gram-positive bacteria such as Enterococcus faecalis or Lactococcus lactis. We predict that tryglysin is produced by S. mutans in its oral niche, thus inhibiting the growth of competing species, including several medically relevant streptococci.
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Balty C, Guillot A, Fradale L, Brewee C, Lefranc B, Herrero C, Sandström C, Leprince J, Berteau O, Benjdia A. Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes. J Biol Chem 2020; 295:16665-16677. [PMID: 32972973 PMCID: PMC8188230 DOI: 10.1074/jbc.ra120.015371] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | | | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
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Zhong Z, He B, Li J, Li YX. Challenges and advances in genome mining of ribosomally synthesized and post-translationally modified peptides (RiPPs). Synth Syst Biotechnol 2020; 5:155-172. [PMID: 32637669 PMCID: PMC7327761 DOI: 10.1016/j.synbio.2020.06.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 01/05/2023] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a class of cyclic or linear peptidic natural products with remarkable structural and functional diversity. Recent advances in genomics and synthetic biology, are facilitating us to discover a large number of new ribosomal natural products, including lanthipeptides, lasso peptides, sactipeptides, thiopeptides, microviridins, cyanobactins, linear thiazole/oxazole-containing peptides and so on. In this review, we summarize bioinformatic strategies that have been developed to identify and prioritize biosynthetic gene clusters (BGCs) encoding RiPPs, and the genome mining-guided discovery of novel RiPPs. We also prospectively provide a vision of what genomics-guided discovery of RiPPs may look like in the future, especially the discovery of RiPPs from dominant but uncultivated microbes, which will be promoted by the combinational use of synthetic biology and metagenome mining strategies.
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Affiliation(s)
- Zheng Zhong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Beibei He
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, USA
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
- The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
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Nguyen TQN, Tooh YW, Sugiyama R, Nguyen TPD, Purushothaman M, Leow LC, Hanif K, Yong RHS, Agatha I, Winnerdy FR, Gugger M, Phan AT, Morinaka BI. Post-translational formation of strained cyclophanes in bacteria. Nat Chem 2020; 12:1042-1053. [DOI: 10.1038/s41557-020-0519-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/04/2020] [Indexed: 11/09/2022]
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Roblin C, Chiumento S, Bornet O, Nouailler M, Müller CS, Jeannot K, Basset C, Kieffer-Jaquinod S, Couté Y, Torelli S, Le Pape L, Schünemann V, Olleik H, De La Villeon B, Sockeel P, Di Pasquale E, Nicoletti C, Vidal N, Poljak L, Iranzo O, Giardina T, Fons M, Devillard E, Polard P, Maresca M, Perrier J, Atta M, Guerlesquin F, Lafond M, Duarte V. The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties. Proc Natl Acad Sci U S A 2020; 117:19168-19177. [PMID: 32719135 PMCID: PMC7431081 DOI: 10.1073/pnas.2004045117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here we report its unique compact structure on the basis of four intramolecular thioether bridges with reversed stereochemistry introduced posttranslationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.
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Affiliation(s)
- Clarisse Roblin
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
- ADISSEO France SAS, Centre d'Expertise et de Recherche en Nutrition, 03600 Commentry, France
| | - Steve Chiumento
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Olivier Bornet
- NMR Platform, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France;
| | - Matthieu Nouailler
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Christina S Müller
- Fachbereich Physik, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Katy Jeannot
- Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, 25030 Besançon, France
- UMR 6249 Chrono-Environnement, Unité de Formation et de Recherche (UFR) Santé, Université de Bourgogne-Franche-Comté, 25030 Besançon, France
| | - Christian Basset
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Sylvie Kieffer-Jaquinod
- Université Grenoble Alpes, CEA, INSERM, IRIG, Biologie à Grande Echelle (BGE), 38054 Grenoble, France
| | - Yohann Couté
- Université Grenoble Alpes, CEA, INSERM, IRIG, Biologie à Grande Echelle (BGE), 38054 Grenoble, France
| | - Stéphane Torelli
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Laurent Le Pape
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Volker Schünemann
- Fachbereich Physik, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Hamza Olleik
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Bruno De La Villeon
- Department of Digestive, Endocrine and Metabolic Surgery, Hôpital Laveran, Military Health Service, 13013 Marseille, France
| | - Philippe Sockeel
- Department of Digestive, Endocrine and Metabolic Surgery, Hôpital Laveran, Military Health Service, 13013 Marseille, France
| | - Eric Di Pasquale
- Institut de NeuroPhysioPathologie, Faculté de Médecine, Aix Marseille Université, 13397 Marseille, France
| | - Cendrine Nicoletti
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Nicolas Vidal
- Yelen Analytics, Institut de Chimie Radicalaire, Aix-Marseille Université, 13013 Marseille, France
| | - Leonora Poljak
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier (UPS), 31400 Toulouse, France
| | - Olga Iranzo
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Thierry Giardina
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Michel Fons
- Laboratoire de Bioénergétique et Ingénierie des Protéines, UMR 7281, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Estelle Devillard
- ADISSEO France SAS, Centre d'Expertise et de Recherche en Nutrition, 03600 Commentry, France
| | - Patrice Polard
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier (UPS), 31400 Toulouse, France
| | - Marc Maresca
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Josette Perrier
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France
| | - Mohamed Atta
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France
| | - Françoise Guerlesquin
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Institut de Microbiologie de la Méditerranée, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Mickael Lafond
- Aix-Marseille Université, CNRS, Centrale Marseille, Institut des Sciences Moléculaires de Marseille (iSm2), 13013 Marseille, France;
| | - Victor Duarte
- Université Grenoble Alpes, Commissariat à l'Energie Atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Chimie et Biologie des Métaux (CBM), CNRS UMR 5249, 38054 Grenoble, France;
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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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Precord TW, Mahanta N, Mitchell DA. Reconstitution and Substrate Specificity of the Thioether-Forming Radical S-Adenosylmethionine Enzyme in Freyrasin Biosynthesis. ACS Chem Biol 2019; 14:1981-1989. [PMID: 31449382 DOI: 10.1021/acschembio.9b00457] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The radical non-α-carbon thioether peptides (ranthipeptides) are a newly described class of ribosomally synthesized and post-translationally modified peptide (RiPP). Ranthipeptide biosynthetic gene clusters are characterized by a Cys-rich precursor peptide and a radical S-adenosylmethionine (rSAM)-dependent enzyme that forms a thioether linkage between a Cys donor and an acceptor residue. Unlike the sulfur-to-α-carbon linked thioether peptides (sactipeptides), known ranthipeptides contain thioethers to either the β- or γ-carbon (i.e., non-α-carbon) of an acceptor residue. Recently, we reported the discovery of freyrasin, a ranthipeptide from Paenibacillus polymyxa, which contains six thioethers from Cys-X3-Asp motifs present in the precursor peptide (PapA). The linkages are exclusively to the β-carbon of Asp (S-Cβ). In this report, we performed mutational analysis of PapA and the cognate thioether-forming rSAM enzyme (PapB) to define the substrate scope. Using a mass spectrometry-based activity assay, our data show that PapB is intolerant toward Ala and Asn in the acceptor position but tolerates Glu-containing variants. NMR spectroscopic data of a Glu variant demonstrated that the thioether linkage was to the 4-position of Glu (S-Cγ). Furthermore, we demonstrate that PapB is intolerant to expansion and contraction of the thioether motifs (Cys-Xn-Asp, n = 2 or 4), although a minimal substrate featuring only one Cys-X3-Asp motif was competent for thioether formation. Akin to the sactipeptides, PapB was dependent on a RiPP recognition element (RRE) to bind the cognate precursor peptide, with deletion resulting in loss-of-function in vivo. The activity of PapB could be restored in vivo by supplying the excised RRE in trans. Finally, we reconstituted the activity of PapB in vitro, which led to modification of all six Cys residues in PapA. These studies provide insights into ranthipeptide biosynthesis and expand our understanding of rSAM enzyme chemistry in natural product biosynthesis.
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Affiliation(s)
| | - Nilkamal Mahanta
- Department of Chemistry, Indian Institute of Technology, Dharwad, Karnataka 580011, India
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43
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Wang SC. Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep 2019; 35:707-720. [PMID: 30079906 DOI: 10.1039/c7np00059f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.
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Affiliation(s)
- Susan C Wang
- Case Western Reserve University School of Medicine, Department of Biochemistry, USA.
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44
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Balty C, Guillot A, Fradale L, Brewee C, Boulay M, Kubiak X, Benjdia A, Berteau O. Ruminococcin C, an anti-clostridial sactipeptide produced by a prominent member of the human microbiota Ruminococcus gnavus. J Biol Chem 2019; 294:14512-14525. [PMID: 31337708 PMCID: PMC6779426 DOI: 10.1074/jbc.ra119.009416] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Indexed: 11/06/2022] Open
Abstract
The human microbiota plays a central role in human physiology. This complex ecosystem is a promising but untapped source of bioactive compounds and antibiotics that are critical for its homeostasis. However, we still have a very limited knowledge of its metabolic and biosynthetic capabilities. Here we investigated an enigmatic biosynthetic gene cluster identified previously in the human gut symbiont Ruminococcus gnavus. This gene cluster which encodes notably for peptide precursors and putative radical SAM enzymes, has been proposed to be responsible for the biosynthesis of ruminococcin C (RumC), a ribosomally synthesized and posttranslationally modified peptide (RiPP) with potent activity against the human pathogen Clostridium perfringens. By combining in vivo and in vitro approaches, including recombinant expression and purification of the respective peptides and proteins, enzymatic assays, and LC-MS analyses, we determined that RumC is a sulfur-to–α-carbon thioether-containing peptide (sactipeptide) with an unusual architecture. Moreover, our results support that formation of the thioether bridges follows a processive order, providing mechanistic insights into how radical SAM (AdoMet) enzymes install posttranslational modifications in RiPPs. We also found that the presence of thioether bridges and removal of the leader peptide are required for RumC's antimicrobial activity. In summary, our findings provide evidence that production of the anti-Clostridium peptide RumC depends on an R. gnavus operon encoding five potential RumC precursor peptides and two radical SAM enzymes, uncover key RumC structural features, and delineate the sequence of posttranslational modifications leading to its formation and antimicrobial activity.
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Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Mylène Boulay
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Xavier Kubiak
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Abstract
Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similarity-based bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed.
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Hudson GA, Burkhart BJ, DiCaprio AJ, Schwalen CJ, Kille B, Pogorelov TV, Mitchell DA. Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides. J Am Chem Soc 2019; 141:8228-8238. [PMID: 31059252 DOI: 10.1021/jacs.9b01519] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently developed bioinformatic tools have bolstered the discovery of ribosomally synthesized and post-translationally modified peptides (RiPPs). Using an improved version of Rapid ORF Description and Evaluation Online (RODEO 2.0), a biosynthetic gene cluster mining algorithm, we bioinformatically mapped the sactipeptide RiPP class via the radical S-adenosylmethionine (SAM) enzymes that form the characteristic sactionine (sulfur-to-α carbon) cross-links between cysteine and acceptor residues. Hundreds of new sactipeptide biosynthetic gene clusters were uncovered, and a novel sactipeptide "huazacin" with growth-suppressive activity against Listeria monocytogenes was characterized. Bioinformatic analysis further suggested that a group of sactipeptide-like peptides heretofore referred to as six cysteines in forty-five residues (SCIFFs) might not be sactipeptides as previously thought. Indeed, the bioinformatically identified SCIFF peptide "freyrasin" was demonstrated to contain six thioethers linking the β carbons of six aspartate residues. Another SCIFF, thermocellin, was shown to contain a thioether cross-linked to the γ carbon of threonine. SCIFFs feature a different paradigm of non-α carbon thioether linkages, and they are exclusively formed by radical SAM enzymes, as opposed to the polar chemistry employed during lanthipeptide biosynthesis. Therefore, we propose the renaming of the SCIFF family as radical non-α thioether peptides (ranthipeptides) to better distinguish them from the sactipeptide and lanthipeptide RiPP classes.
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Liu L, Chan S, Mo T, Ding W, Yu S, Zhang Q, Yuan S. Movements of the Substrate-Binding Clamp of Cypemycin Decarboxylase CypD. J Chem Inf Model 2019; 59:2924-2929. [DOI: 10.1021/acs.jcim.9b00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Lei Liu
- College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Stephen Chan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianlu Mo
- 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 200030, China
| | - Shaoning Yu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Shuguang Yuan
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, Lausanne CH-1015, Switzerland
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48
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Biocatalytic hydrogen atom transfer: an invigorating approach to free-radical reactions. Curr Opin Chem Biol 2018; 49:16-24. [PMID: 30269010 DOI: 10.1016/j.cbpa.2018.09.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/02/2018] [Indexed: 10/28/2022]
Abstract
Initiating and terminating free-radical reactionis via hydrogen atom transfer (HAT) is an attractive means of avoiding substrate prefunctionalization. Small molecule catalysts and reagents, however, struggle to execute this fundamental step with useful levels of diastereoselectivity and enantioselectivity. In contrast, nature often carries out HAT with exquisite levels of selectivity for even electronically unactivated carbon-hydrogen bonds. By understanding how enzymes exploit and control this fundamental step, new strategies can be developed to address several long-standing challenges in free-radical reactions. This review will cover recent discoveries in biocatalysis that exploit a HAT mechanism to either initiate or terminate novel one-electron reactions.
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Ding W, Mo T, Mandalapu D, Zhang Q. Substrate specificity of the cypemycin decarboxylase CypD. Synth Syst Biotechnol 2018; 3:159-162. [PMID: 30345401 PMCID: PMC6190514 DOI: 10.1016/j.synbio.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
The linaridin antibiotic cypemycin is a ribosomal synthesized and post-translationally modified peptide (RiPP) that possesses potent activity against mouse leukemia cells. This peptide natural product contains an S-[(Z)-2-aminovinyl]-d-cysteine (AviCys) moiety in the C-terminus. Formation of AviCys moiety requires an oxidative decarboxylation of the C-terminal Cys of the precursor peptide CypA, and this process is catalyzed by a flavin-containing protein CypD. In this work, we tested CypD substrate specificity with a series of synthetic oligopeptides. We show that most of the N-terminal sequence of CypA is not required for CypD activity, and the C-terminal three residues serve as the minimal structural element for enzyme recognition. We also show that CypD tolerates various substrates with modified C-termini, allowing for the generation of four novel cypemycin variants with modified AviCys moiety by site direct mutagenesis of the precursor peptide CypA. Our study demonstrates the relaxed substrate specificity of CypD and lays a foundation for future bioengineering of AviCys-containing natural products.
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Affiliation(s)
| | | | | | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
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50
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Schwalen CJ, Hudson GA, Kille B, Mitchell DA. Bioinformatic Expansion and Discovery of Thiopeptide Antibiotics. J Am Chem Soc 2018; 140:9494-9501. [PMID: 29983054 PMCID: PMC6070396 DOI: 10.1021/jacs.8b03896] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Thiopeptides are members of the ribosomally synthesized and post-translationally modified peptide family of natural products. Most characterized thiopeptides display nanomolar potency toward Gram-positive bacteria by blocking protein translation with several being produced at the industrial scale for veterinary and livestock applications. Employing our custom bioinformatics program, RODEO, we expand the thiopeptide family of natural products by a factor of four. This effort revealed many new thiopeptide biosynthetic gene clusters with products predicted to be distinct from characterized thiopeptides and identified gene clusters for previously characterized molecules of unknown biosynthetic origin. To further validate our data set of predicted thiopeptide biosynthetic gene clusters, we isolated and characterized a structurally unique thiopeptide featuring a central piperidine and rare thioamide moiety. Termed saalfelduracin, this thiopeptide displayed potent antibiotic activity toward several drug-resistant Gram-positive pathogens. A combination of whole-genome sequencing, comparative genomics, and heterologous expression experiments confirmed that the thioamide moiety of saalfelduracin is installed post-translationally by the joint action of two proteins, TfuA and YcaO. These results reconcile the previously unknown origin of the thioamide in two long-known thiopeptides, thiopeptin and Sch 18640. Armed with these new insights into thiopeptide chemical-genomic space, we provide a roadmap for the discovery of additional members of this natural product family.
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Affiliation(s)
- Christopher J. Schwalen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Graham A. Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Bryce Kille
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South 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
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