1
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Dong X, Zhang T, Wu W, Peng Y, Liu X, Han Y, Chen X, Gao Z, Xia J, Shao Z, Greening C. A vast repertoire of secondary metabolites potentially influences community dynamics and biogeochemical processes in cold seeps. SCIENCE ADVANCES 2024; 10:eadl2281. [PMID: 38669328 PMCID: PMC11051675 DOI: 10.1126/sciadv.adl2281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
In deep-sea cold seeps, microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds, differing from photosynthetically driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and 7 metabolomes derived from nine different cold seep areas to investigate their secondary metabolites. Cold seep microbiomes encode diverse and abundant biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling. The BGCs encode diverse antimicrobial compounds that potentially shape community dynamics and various metabolites predicted to influence biogeochemical cycling. BGCs from key players are widely distributed and highly expressed, with their abundance and expression levels varying with sediment depth. Sediment metabolomics reveals unique natural products, highlighting uncharted chemical potential and confirming BGC activity in these sediments. Overall, these results demonstrate that cold seep sediments serve as a reservoir of hidden natural products and sheds light on microbial adaptation in chemosynthetically driven ecosystems.
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Affiliation(s)
- Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Tianxueyu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310005, China
| | - Weichao Wu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yongyi Peng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Xinyue Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Yingchun Han
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Xiangwei Chen
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Jinmei Xia
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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2
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Gupta D, Chen K, Elliott SJ, Nayak DD. MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport in Methanosarcina acetivorans. Nat Commun 2024; 15:3300. [PMID: 38632227 PMCID: PMC11024163 DOI: 10.1038/s41467-024-47564-2] [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: 08/22/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Methanogens are a diverse group of Archaea that obligately couple energy conservation to the production of methane. Some methanogens encode alternate pathways for energy conservation, like anaerobic respiration, but the biochemical details of this process are unknown. We show that a multiheme c-type cytochrome called MmcA from Methanosarcina acetivorans is important for intracellular electron transport during methanogenesis and can also reduce extracellular electron acceptors like soluble Fe3+ and anthraquinone-2,6-disulfonate. Consistent with these observations, MmcA displays reversible redox features ranging from -100 to -450 mV versus SHE. Additionally, mutants lacking mmcA have significantly slower Fe3+ reduction rates. The mmcA locus is prevalent in members of the Order Methanosarcinales and is a part of a distinct clade of multiheme cytochromes that are closely related to octaheme tetrathionate reductases. Taken together, MmcA might act as an electron conduit that can potentially support a variety of energy conservation strategies that extend beyond methanogenesis.
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Affiliation(s)
- Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keying Chen
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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3
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Nguyen DT, Mitchell DA, van der Donk WA. Genome Mining for New Enzyme Chemistry. ACS Catal 2024; 14:4536-4553. [PMID: 38601780 PMCID: PMC11002830 DOI: 10.1021/acscatal.3c06322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/12/2024]
Abstract
A revolution in the field of biocatalysis has enabled scalable access to compounds of high societal values using enzymes. The construction of biocatalytic routes relies on the reservoir of available enzymatic transformations. A review of uncharacterized proteins predicted from genomic sequencing projects shows that a treasure trove of enzyme chemistry awaits to be uncovered. This Review highlights enzymatic transformations discovered through various genome mining methods and showcases their potential future applications in biocatalysis.
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Affiliation(s)
- Dinh T. Nguyen
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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5
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Nguyen NA, Vidya FNU, Yennawar NH, Wu H, McShan AC, Agarwal V. Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase. Nat Commun 2024; 15:1265. [PMID: 38341413 PMCID: PMC10858898 DOI: 10.1038/s41467-024-45593-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
To biosynthesize ribosomally synthesized and post-translationally modified peptides (RiPPs), enzymes recognize and bind to the N-terminal leader region of substrate peptides which enables catalytic modification of the C-terminal core. Our current understanding of RiPP leaders is that they are short and largely unstructured. Proteusins are RiPP precursor peptides that defy this characterization as they possess unusually long leaders. Proteusin peptides have not been structurally characterized, and we possess scant understanding of how these atypical leaders engage with modifying enzymes. Here, we determine the structure of a proteusin peptide which shows that unlike other RiPP leaders, proteusin leaders are preorganized into a rigidly structured region and a smaller intrinsically disordered region. With residue level resolution gained from NMR titration experiments, the intermolecular peptide-protein interactions between proteusin leaders and a flavin-dependent brominase are mapped onto the disordered region, leaving the rigidly structured region of the proteusin leader to be functionally dispensable. Spectroscopic observations are biochemically validated to identify a binding motif in proteusin peptides that is conserved among other RiPP leaders as well. This study provides a structural characterization of the proteusin peptides and extends the paradigm of RiPP modification enzymes using not only unstructured peptides, but also structured proteins as substrates.
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Affiliation(s)
- Nguyet A Nguyen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - F N U Vidya
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongwei Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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6
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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [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: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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7
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Zheng Y, Xu X, Fu X, Zhou X, Dou C, Yu Y, Yan W, Yang J, Xiao M, van der Donk WA, Zhu X, Cheng W. Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis. Structure 2023; 31:1220-1232.e5. [PMID: 37652001 PMCID: PMC10880893 DOI: 10.1016/j.str.2023.08.004] [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: 05/08/2023] [Revised: 07/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
Structural diverse natural products like ribosomally synthesized and posttranslationally modified peptides (RiPPs) display a wide range of biological activities. Currently, the mechanism of an uncommon reaction step during the biosynthesis of 3-thiaglutamate (3-thiaGlu) is poorly understood. The removal of the β-carbon from the Cys in the TglA-Cys peptide catalyzed by the TglHI holoenzyme remains elusive. Here, we present three crystal structures of TglHI complexes with and without bound iron, which reveal that the catalytic pocket is formed by the interaction of TglH-TglI and that its activation is conformation dependent. Biochemical assays suggest a minimum of two iron ions in the active cluster, and we identify the position of a third iron site. Collectively, our study offers insights into the activation and catalysis mechanisms of the non-heme dioxygen-dependent holoenzyme TglHI. Additionally, it highlights the evolutionary and structural conservation in the DUF692 family of biosynthetic enzymes that produce diverse RiPPs.
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Affiliation(s)
- Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoqing Xu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoli Fu
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xuerong Zhou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China; Department of Neurology, Affiliated Hospital of North Sichuan Medical College, Institute of Neurological Diseases, North Sichuan Medical College, Nanchong 637000, China
| | - Chao Dou
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yue Yu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Weizhu Yan
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Jingyuan Yang
- Core Facilities of West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minqin Xiao
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Wilfred A van der Donk
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Xiaofeng Zhu
- College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China.
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8
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Gupta D, Chen K, Elliott SJ, Nayak DD. MmcA is an electron conduit that facilitates both intracellular and extracellular electron transport in Methanosarcina acetivorans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537704. [PMID: 37131651 PMCID: PMC10153276 DOI: 10.1101/2023.04.20.537704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Methanogens are a diverse group of Archaea that couple energy conservation to the production of methane gas. While most methanogens have no alternate mode of energy conservation, strains like Methanosarcina acetivorans are known to also conserve energy by dissimilatory metal reduction (DSMR) in the presence of soluble ferric iron or iron-containing minerals. The ecological ramifications of energy conservation decoupled from methane production in methanogens are substantial, yet the molecular details are poorly understood. In this work, we conducted in vitro and in vivo studies with a multiheme c-type cytochrome (MHC), called MmcA, to establish its role during methanogenesis and DSMR in M. acetivorans. MmcA purified from M. acetivorans can donate electrons to methanophenazine, a membrane-bound electron carrier, to facilitate methanogenesis. In addition, MmcA can also reduce Fe(III) and the humic acid analog anthraquinone-2,6-disulfonate (AQDS) during DSMR. Furthermore, mutants lacking mmcA have slower Fe(III) reduction rates. The redox reactivities of MmcA are consistent with the electrochemical data where MmcA displays reversible redox features ranging from -100 to -450 mV versus SHE. MmcA is prevalent in members of the Order Methanosarcinales but does not belong to a known family of MHCs linked to extracellular electron transfer, bioinformatically, and instead forms a distinct clade that is closely related to octaheme tetrathionate reductases. Taken together, this study shows that MmcA is widespread in methanogens with cytochromes where it acts as an electron conduit to support a variety of energy conservation strategies that extend beyond methanogenesis.
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Affiliation(s)
- Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Keying Chen
- Department of Chemistry, Boston University, Boston, MA, USA
| | | | - Dipti D. Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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9
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Yu Z, Peng X, Liu L, Yang JR, Zhai X, Xue Y, Mo Y, Yang J. Microbial one‑carbon and nitrogen metabolisms are beneficial to the reservoir recovery after cyanobacterial bloom. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159004. [PMID: 36155037 DOI: 10.1016/j.scitotenv.2022.159004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacterial blooms have profound effects on the structure and function of plankton communities in inland waters, but few studies have focused on the effects of microbial-based processes in one‑carbon and nitrogen cycling on water quality improvement following the bloom. Here, we compared the structure and function of the bacterial community, focusing on microbial one‑carbon and nitrogen metabolisms during and after a cyanobacterial Microcystis bloom in a deep subtropical reservoir. Our data showed that microbial one‑carbon and nitrogen cycles were closely related to different periods of the bloom, and the changes of functional genes in microbial carbon and nitrogen cycling showed the same consistent trend as that of Methylomonas sp. With the receding of the bloom, the abundance of Methylomonas as well as the functional genes of microbial one‑carbon and nitrogen cycling reached the peak and then recovered. Our results indicate that microbial one‑carbon and nitrogen metabolisms were beneficial to the recovery of water quality from the cyanobacterial bloom. This study lays a foundation for a deep understanding of the cyanobacterial decomposition mediated by microbes in one‑carbon and nitrogen cycles in inland freshwaters.
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Affiliation(s)
- Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xuan Peng
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Lemian Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Jun R Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xingyu Zhai
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan 410083, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yuanyuan Mo
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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10
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YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Nat Chem Biol 2023; 19:111-119. [PMID: 36280794 DOI: 10.1038/s41589-022-01141-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022]
Abstract
YcaO enzymes catalyze ATP-dependent post-translation modifications on peptides, including the installation of (ox/thi)azoline, thioamide and/or amidine moieties. Here we demonstrate that, in the biosynthesis of the bis-methyloxazolic alkaloid muscoride A, the YcaO enzyme MusD carries out both ATP-dependent cyclodehydration and peptide bond cleavage, which is a mechanism unprecedented for such a reaction. YcaO-catalyzed modifications are proposed to occur through a backbone O-phosphorylated intermediate, but this mechanism remains speculative. We report, to our knowedge, the first characterization of an acyl-phosphate species consistent with the proposed mechanism for backbone amide activation. The 3.1-Å-resolution cryogenic electron microscopy structure of MusD along with biochemical analysis allow identification of residues that enable peptide cleavage reaction. Bioinformatics analysis identifies other cyanobactin pathways that may deploy bifunctional YcaO enzymes. Our structural, mutational and mechanistic studies expand the scope of modifications catalyzed by YcaO proteins to include peptide hydrolysis and provide evidence for a unifying mechanism for the catalytically diverse outcomes.
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11
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Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling. SCIENCE ADVANCES 2022; 8:eabm9651. [PMID: 36332026 PMCID: PMC9635834 DOI: 10.1126/sciadv.abm9651] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/19/2022] [Indexed: 05/19/2023]
Abstract
Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.
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Affiliation(s)
- Panagiotis S. Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Corresponding author.
| | - George E. Kolyfetis
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15784 Athens, Greece
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
- Research Center One Health Ruhr, Research Alliance Ruhr, Environmental Metagenomics, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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12
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Chatterjee S, Hausinger RP. Sulfur incorporation into biomolecules: recent advances. Crit Rev Biochem Mol Biol 2022; 57:461-476. [PMID: 36403141 PMCID: PMC10192010 DOI: 10.1080/10409238.2022.2141678] [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: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022]
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
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13
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Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea. J Bacteriol 2022; 204:e0019722. [PMID: 35880875 PMCID: PMC9380564 DOI: 10.1128/jb.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.
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14
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Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin-Dependent Radical SAM Enzyme Catalyzes the Unique C α -Methylation of Glutamine in Methyl-Coenzyme M Reductase. Angew Chem Int Ed Engl 2022; 61:e202204198. [PMID: 35638156 PMCID: PMC9401015 DOI: 10.1002/anie.202204198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/22/2022]
Abstract
Methyl‐coenzyme M reductase, which is responsible for the production of the greenhouse gas methane during biological methane formation, carries several unique posttranslational amino acid modifications, including a 2‐(S)‐methylglutamine. The enzyme responsible for the Cα‐methylation of this glutamine is not known. Herein, we identify and characterize a cobalamin‐dependent radical SAM enzyme as the glutamine C‐methyltransferase. The recombinant protein from Methanoculleus thermophilus binds cobalamin in a base‐off, His‐off conformation and contains a single [4Fe‐4S] cluster. The cobalamin cofactor cycles between the methyl‐cob(III)alamin, cob(II)alamin and cob(I)alamin states during catalysis and produces methylated substrate, 5′‐deoxyadenosine and S‐adenosyl‐l‐homocysteine in a 1 : 1 : 1 ratio. The newly identified glutamine C‐methyltransferase belongs to the class B radical SAM methyltransferases known to catalyze challenging methylation reactions of sp3‐hybridized carbon atoms.
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Affiliation(s)
- Jana Gagsteiger
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
| | - Sören Jahn
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Lorenz Heidinger
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Lukas Gericke
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Jennifer N Andexer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Thorsten Friedrich
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Christoph Loenarz
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104, Freiburg, Germany
| | - Gunhild Layer
- Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 19, 79104, Freiburg, Germany
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15
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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16
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Abstract
The past decade has seen impressive advances in understanding the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs). One of the most common modifications found in these natural products is macrocyclization, a strategy also used by medicinal chemists to improve metabolic stability and target affinity and specificity. Another tool of the peptide chemist, modification of the amides in a peptide backbone, has also been observed in RiPPs. This review discusses the molecular mechanisms of biosynthesis of a subset of macrocyclic RiPP families, chosen because of the unusual biochemistry involved: the five classes of lanthipeptides (thioether cyclization by Michael-type addition), sactipeptides and ranthipeptides (thioether cyclization by radical chemistry), thiopeptides (cyclization by [4+2] cycloaddition), and streptide (cyclization by radical C-C bond formation). In addition, the mechanisms of backbone amide methylation, backbone epimerization, and backbone thioamide formation are discussed, as well as an unusual route to small molecules by posttranslational modification.
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Affiliation(s)
- Hyunji Lee
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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17
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Malit JJL, Leung HYC, Qian PY. Targeted Large-Scale Genome Mining and Candidate Prioritization for Natural Product Discovery. Mar Drugs 2022; 20:md20060398. [PMID: 35736201 PMCID: PMC9231227 DOI: 10.3390/md20060398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022] Open
Abstract
Large-scale genome-mining analyses have identified an enormous number of cryptic biosynthetic gene clusters (BGCs) as a great source of novel bioactive natural products. Given the sheer number of natural product (NP) candidates, effective strategies and computational methods are keys to choosing appropriate BGCs for further NP characterization and production. This review discusses genomics-based approaches for prioritizing candidate BGCs extracted from large-scale genomic data, by highlighting studies that have successfully produced compounds with high chemical novelty, novel biosynthesis pathway, and potent bioactivities. We group these studies based on their BGC-prioritization logics: detecting presence of resistance genes, use of phylogenomics analysis as a guide, and targeting for specific chemical structures. We also briefly comment on the different bioinformatics tools used in the field and examine practical considerations when employing a large-scale genome mining study.
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Affiliation(s)
- Jessie James Limlingan Malit
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hiu Yu Cherie Leung
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; (J.J.L.M.); (H.Y.C.L.)
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence:
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18
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Gagsteiger J, Jahn S, Heidinger L, Gericke L, Andexer JN, Friedrich T, Loenarz C, Layer G. A Cobalamin‐Dependent Radical SAM Enzyme Catalyzes the Unique Cα‐Methylation of Glutamine in Methyl‐Coenzyme M Reductase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jana Gagsteiger
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie GERMANY
| | - Sören Jahn
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Lorenz Heidinger
- Albert-Ludwigs-Universität Freiburg Institut für Biochemie GERMANY
| | - Lukas Gericke
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Jennifer N. Andexer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Biochemie GERMANY
| | - Christoph Loenarz
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische und Medizinische Chemie GERMANY
| | - Gunhild Layer
- Albert-Ludwigs-Universität Freiburg, Fakultät für Chemie und Pharmazie Institut für Pharmazeutische Wissenschaften, Pharmazeutische Biologie Stefan-Meier-Str. 19 79104 Freiburg GERMANY
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19
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Gendron A, Allen KD. Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression. Front Microbiol 2022; 13:867342. [PMID: 35547147 PMCID: PMC9081873 DOI: 10.3389/fmicb.2022.867342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/01/2022] [Indexed: 12/02/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F430. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.
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Affiliation(s)
- Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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20
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Fiore KE, Patist MJ, Giannakoulias S, Huang CH, Verma H, Khatri B, Cheng RP, Chatterjee J, Petersson EJ. Structural impact of thioamide incorporation into a β-hairpin. RSC Chem Biol 2022; 3:582-591. [PMID: 35656485 PMCID: PMC9092430 DOI: 10.1039/d1cb00229e] [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: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Martijn J Patist
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Cheng-Hsin Huang
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
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21
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Lemaire ON, Wagner T. A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea. Biochemistry 2022; 61:805-821. [PMID: 35500274 PMCID: PMC9118554 DOI: 10.1021/acs.biochem.2c00135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Microbial anaerobic
oxidation of alkanes intrigues the scientific
community by way of its impact on the global carbon cycle, and its
biotechnological applications. Archaea are proposed to degrade short-
and long-chain alkanes to CO2 by reversing methanogenesis,
a theoretically reversible process. The pathway would start with alkane
activation, an endergonic step catalyzed by methyl-coenzyme M reductase
(MCR) homologues that would generate alkyl-thiols carried by coenzyme
M. While the methane-generating MCR found in methanogens has been
well characterized, the enzymatic activity of the putative alkane-fixing
counterparts has not been validated so far. Such an absence of biochemical
investigations contrasts with the current explosion of metagenomics
data, which draws new potential alkane-oxidizing pathways in various
archaeal phyla. Therefore, validating the physiological function of
these putative alkane-fixing machines and investigating how their
structures, catalytic mechanisms, and cofactors vary depending on
the targeted alkane have become urgent needs. The first structural
insights into the methane- and ethane-capturing MCRs highlighted unsuspected
differences and proposed some explanations for their substrate specificity.
This Perspective reviews the current physiological, biochemical, and
structural knowledge of alkyl-CoM reductases and offers fresh ideas
about the expected mechanistic and chemical differences among members
of this broad family. We conclude with the challenges of the investigation
of these particular enzymes, which might one day generate biofuels
for our modern society.
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Affiliation(s)
- Olivier N Lemaire
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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22
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Gupta D, Shalvarjian KE, Nayak DD. An archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans. eLife 2022; 11:76970. [PMID: 35380107 PMCID: PMC9084895 DOI: 10.7554/elife.76970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
c-Type cytochromes (cyt c) are proteins that undergo post-translational modification to covalently bind heme, which allows them to facilitate redox reactions in electron transport chains across all domains of life. Genomic evidence suggests that cyt c are involved in electron transfer processes among the Archaea, especially in members that produce or consume the potent greenhouse gas methane. However, neither the maturation machinery for cyt c in Archaea nor their role in methane metabolism has ever been functionally characterized. Here, we have used CRISPR-Cas9 genome editing tools to map a distinct pathway for cyt c biogenesis in the model methanogenic archaeon Methanosarcina acetivorans, and have also identified substrate-specific functional roles for cyt c during methanogenesis. Although the cyt c maturation machinery from M. acetivorans is universally conserved in the Archaea, our evolutionary analyses indicate that different clades of Archaea acquired this machinery through multiple independent horizontal gene transfer events from different groups of Bacteria. Overall, we demonstrate the convergent evolution of a novel Archaea-specific cyt c maturation machinery and its physiological role during methanogenesis, a process which contributes substantially to global methane emissions. Archaea are single-celled organisms that were discovered over half a century ago. Recently, there has been a renewed interest in these microbes because theyplay a key role in climate change by controlling greenhouse gas emissions, like methane. Indeed, methane-producing Archaea generate nearly 70% of the methane gas released into the atmosphere. A group of proteins called c-type cytochromes are essential to energy generation in several methane-producing archaea. However, it is a mystery how Archaea assemble their c-type cytochromes. In fact, genomic studies suggest that Archaea are missing some of the c-type cytochrome assembly machinery that bacteria use. This has led scientists to suspect that Archaea have an alternate mechanism for building these essential components. To solve this mystery, Gupta, Shalvarjian, and Nayak used CRISPR-Cas9 gene-editing tools to characterize which proteins are essential for c-type cytochrome production in Methanosarcina acetivorans, a species of Archaea that produces methane. These experiments showed that M. acetivorans discarded a few parts of the process used by bacteria to generate c-type cytochromes, streamlining the assembly of these proteins. By comparing the genes of different Archaeal species, Gupta, Shalvarjian and Nayak were able to determine that Archaea acquired the genes for producing c-type cytochromes from bacteria via horizontal gene transfer, a process in which genes move directly from one organism into another. The streamlining of the process took place later, as different Archaeal species evolved independently, but losing the same parts of the process. Gupta Shalvajiran and Nayak’s experiments also showed that c-type cytochromes are essential for the growth and fitness of methane-producing Archaea like M. acetivorans. The role of c-type cytochromes in methane production varies in different species of Archaea depending on their growth substrate or where they live. These results provide vital information about how Archaea produce methane, and the tools and techniques developed will aid further investigation of the role of Archaea in climate change.
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Affiliation(s)
- Dinesh Gupta
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Katie E Shalvarjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Dipti D Nayak
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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23
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Sikandar A, Lopatniuk M, Luzhetskyy A, Müller R, Koehnke J. Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway. J Am Chem Soc 2022; 144:5136-5144. [PMID: 35263083 DOI: 10.1021/jacs.2c00402] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Thioholgamides are ribosomally synthesized and posttranslationally modified peptides (RiPPs), with potent activity against cancerous cell lines and an unprecedented structure. Despite being one of the most structurally and chemically complex RiPPs, very few biosynthetic steps have been elucidated. Here, we report the complete in vitro reconstitution of the biosynthetic pathway. We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing. Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes─ThoH/I and ThoC/D. Harnessing the power of AlphaFold, we deduce that ThoD acts as a lyase and also proposes putative catalytic residues. ThoF catalyzes the oxidative decarboxylation of the terminal Cys, and the subsequent macrocyclization is facilitated by ThoE. This is followed by Ser dehydration, which is also carried out by ThoC/D. ThoG is responsible for histidine bis-N-methylation, which is a prerequisite for His β-hydroxylation─a modification carried out by ThoJ. The last step of the pathway is the removal of the leader peptide by ThoK to afford mature thioholgamide.
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Affiliation(s)
- Asfandyar Sikandar
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany
| | - Maria Lopatniuk
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Andriy Luzhetskyy
- Department of Pharmacy, Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) and Department of Pharmacy at Saarland University (UdS), Campus E8.1, 66123 Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Jesko Koehnke
- Workgroup Structural Biology of Biosynthetic Enzymes, HIPS, HZI, UdS, 66123 Saarbrücken, Germany.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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24
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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25
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XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase. J Inorg Biochem 2022; 230:111768. [DOI: 10.1016/j.jinorgbio.2022.111768] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 01/08/2023]
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26
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Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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Russell AH, Vior NM, Hems ES, Lacret R, Truman AW. Discovery and characterisation of an amidine-containing ribosomally-synthesised peptide that is widely distributed in nature. Chem Sci 2021; 12:11769-11778. [PMID: 34659714 PMCID: PMC8442711 DOI: 10.1039/d1sc01456k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/31/2021] [Indexed: 12/30/2022] Open
Abstract
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a structurally diverse class of natural product with a wide range of bioactivities. Genome mining for RiPP biosynthetic gene clusters (BGCs) is often hampered by poor annotation of the short precursor peptides that are ultimately modified into the final molecule. Here, we utilise a previously described genome mining tool, RiPPER, to identify novel RiPP precursor peptides near YcaO-domain proteins, enzymes that catalyse various RiPP post-translational modifications including heterocyclisation and thioamidation. Using this dataset, we identified a novel and diverse family of RiPP BGCs spanning over 230 species of Actinobacteria and Firmicutes. A representative BGC from Streptomyces albidoflavus J1074 (formerly known as Streptomyces albus) was characterised, leading to the discovery of streptamidine, a novel amidine-containing RiPP. This new BGC family highlights the breadth of unexplored natural products with structurally rare features, even in model organisms.
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Affiliation(s)
- Alicia H Russell
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Edward S Hems
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre Norwich NR4 7UH UK
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28
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Khatri B, Raj N, Chatterjee J. Opportunities and challenges in the synthesis of thioamidated peptides. Methods Enzymol 2021; 656:27-57. [PMID: 34325789 DOI: 10.1016/bs.mie.2021.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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29
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Liu A, Krushnamurthy PH, Subramanya KS, Mitchell DA, Mahanta N. Enzymatic thioamidation of peptide backbones. Methods Enzymol 2021; 656:459-494. [PMID: 34325795 DOI: 10.1016/bs.mie.2021.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Thioamides are found in a few natural products and two known protein assemblies: the Escherichia coli ribosome and methyl-coenzyme M reductase (MCR) from methane-metabolizing archaea. Compared to an amide, thioamides alter the physical and chemical properties of peptide backbones, including the conformation dynamics, proteolytic stability, hydrogen-bonding capabilities, and possibly reactivity of a protein when installed. Recently, there has been significant progress in elucidating enzymatic post-translational thioamide installation, with most work leveraging the archaeal MCR-modifying enzymes. This chapter describes the protocols used for the in vitro enzymatic thioamidation of MCR-derived peptides, including polypeptide overexpression, purification, reaction reconstitution, and mass spectrometry-based product analysis. In addition, we highlight the protocols used for the biochemical, kinetics, and binding studies using recombinant enzymes obtained heterologously from E. coli. We anticipate that these methods will serve to guide future studies on peptide post-translational thioamidation, as well as other peptide backbone modifications using a parallel workflow.
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Affiliation(s)
- Andi Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States; Department of Microbiology, University of Illinois, Urbana, IL, United States
| | - P H Krushnamurthy
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - K S Subramanya
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Douglas A Mitchell
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States; Department of Microbiology, University of Illinois, Urbana, IL, United States; Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Nilkamal Mahanta
- Department of Chemistry, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India.
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30
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Liu A, Si Y, Dong SH, Mahanta N, Penkala HN, Nair SK, Mitchell DA. Functional elucidation of TfuA in peptide backbone thioamidation. Nat Chem Biol 2021; 17:585-592. [PMID: 33707784 PMCID: PMC8084935 DOI: 10.1038/s41589-021-00771-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023]
Abstract
YcaO enzymes catalyze several post-translational modifications on peptide substrates, including thioamidation, which substitutes an amide oxygen with sulfur. Most predicted thioamide-forming YcaO enzymes are encoded adjacent to TfuA, which when present, is required for thioamidation. While activation of the peptide amide backbone is well established for YcaO enzymes, the function of TfuA has remained enigmatic. Here we characterize the TfuA protein involved in methyl-coenzyme M reductase thioamidation and demonstrate that TfuA catalyzes the hydrolysis of thiocarboxylated ThiS (ThiS-COSH), a proteinaceous sulfur donor, and enhances the affinity of YcaO toward the thioamidation substrate. We also report a crystal structure of a TfuA, which displays a new protein fold. Our structural and mutational analyses of TfuA have uncovered conserved binding interfaces with YcaO and ThiS in addition to revealing a hydrolase-like active site featuring a Ser-Lys catalytic pair.
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Affiliation(s)
- Andi Liu
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA;,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Yuanyuan Si
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA;,Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA;,current address: State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, P.R. China
| | - Nilkamal Mahanta
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA;,Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA;,current address: Department of Chemistry, Indian Institute of Technology Dharwad, Karnataka, 580011, India
| | - Haley N. Penkala
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA;,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Satish K. Nair
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA;,Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA;,Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
| | - Douglas A. Mitchell
- Department of Microbiology, University of Illinois, Urbana, IL, 61801, USA;,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA;,Department of Chemistry, University of Illinois, Urbana, IL, 61801, USA;,To whom correspondence should be addressed: Phone: 1-217-333-1345; Fax: 1-217-333-0508;
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31
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Eyles TH, Vior NM, Lacret R, Truman AW. Understanding thioamitide biosynthesis using pathway engineering and untargeted metabolomics. Chem Sci 2021; 12:7138-7150. [PMID: 34123341 PMCID: PMC8153245 DOI: 10.1039/d0sc06835g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/19/2021] [Indexed: 11/21/2022] Open
Abstract
Thiostreptamide S4 is a thioamitide, a family of promising antitumour ribosomally synthesised and post-translationally modified peptides (RiPPs). The thioamitides are one of the most structurally complex RiPP families, yet very few thioamitide biosynthetic steps have been elucidated, even though the biosynthetic gene clusters (BGCs) of multiple thioamitides have been identified. We hypothesised that engineering the thiostreptamide S4 BGC in a heterologous host could provide insights into its biosynthesis when coupled with untargeted metabolomics and targeted mutations of the precursor peptide. Modified BGCs were constructed, and in-depth metabolomics enabled a detailed understanding of the biosynthetic pathway to thiostreptamide S4, including the identification of a protein critical for amino acid dehydration that has homology to HopA1, an effector protein used by a plant pathogen to aid infection. We use this biosynthetic understanding to bioinformatically identify diverse RiPP-like BGCs, paving the way for future RiPP discovery and engineering.
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Affiliation(s)
- Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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32
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Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications. Microorganisms 2021; 9:microorganisms9040837. [PMID: 33919946 PMCID: PMC8070964 DOI: 10.3390/microorganisms9040837] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/24/2021] [Accepted: 04/10/2021] [Indexed: 11/24/2022] Open
Abstract
Methanogenic archaea operate an ancient, if not primordial, metabolic pathway that releases methane as an end-product. This last step is orchestrated by the methyl-coenzyme M reductase (MCR), which uses a nickel-containing F430-cofactor as the catalyst. MCR astounds the scientific world by its unique reaction chemistry, its numerous post-translational modifications, and its importance in biotechnology not only for production but also for capturing the greenhouse gas methane. In this report, we investigated MCR natively isolated from Methermicoccus shengliensis. This methanogen was isolated from a high-temperature oil reservoir and has recently been shown to convert lignin and coal derivatives into methane through a process called methoxydotrophic methanogenesis. A methoxydotrophic culture was obtained by growing M. shengliensis with 3,4,5-trimethoxybenzoate as the main carbon and energy source. Under these conditions, MCR represents more than 12% of the total protein content. The native MCR structure refined at a resolution of 1.6-Å precisely depicts the organization of a dimer of heterotrimers. Despite subtle surface remodeling and complete conservation of its active site with other homologues, MCR from the thermophile M. shengliensis contains the most limited number of post-translational modifications reported so far, questioning their physiological relevance in other relatives.
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33
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 362] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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34
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Chen H, Gan Q, Fan C. Methyl-Coenzyme M Reductase and Its Post-translational Modifications. Front Microbiol 2020; 11:578356. [PMID: 33162960 PMCID: PMC7581889 DOI: 10.3389/fmicb.2020.578356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/11/2020] [Indexed: 11/13/2022] Open
Abstract
The methyl-coenzyme M reductase (MCR) is a central enzyme in anaerobic microbial methane metabolism, which consists of methanogenesis and anaerobic oxidation of methane (AOM). MCR catalyzes the final step of methanogenesis and the first step of AOM to achieve the production and oxidation of methane, respectively. Besides a unique nickel tetrahydrocorphinoid (coenzyme F430), MCR also features several unusual post-translational modifications (PTMs), which are assumed to play important roles in regulating MCR functions. However, only few studies have been implemented on MCR PTMs. Therefore, to recapitulate current knowledge and prospect future studies, this review summarizes and discusses studies on MCR and its PTMs.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States.,Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, United States
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35
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Shima S, Huang G, Wagner T, Ermler U. Structural Basis of Hydrogenotrophic Methanogenesis. Annu Rev Microbiol 2020; 74:713-733. [DOI: 10.1146/annurev-micro-011720-122807] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea use the rudimentary hydrogenotrophic pathway—from CO2and H2to methane—as the terminal step of microbial biomass degradation in anoxic habitats. The barely exergonic process that just conserves sufficient energy for a modest lifestyle involves chemically challenging reactions catalyzed by complex enzyme machineries with unique metal-containing cofactors. The basic strategy of the methanogenic energy metabolism is to covalently bind C1species to the C1carriers methanofuran, tetrahydromethanopterin, and coenzyme M at different oxidation states. The four reduction reactions from CO2to methane involve one molybdopterin-based two-electron reduction, two coenzyme F420–based hydride transfers, and one coenzyme F430–based radical process. For energy conservation, one ion-gradient-forming methyl transfer reaction is sufficient, albeit supported by a sophisticated energy-coupling process termed flavin-based electron bifurcation for driving the endergonic CO2reduction and fixation. Here, we review the knowledge about the structure-based catalytic mechanism of each enzyme of hydrogenotrophic methanogenesis.
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Affiliation(s)
- Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gangfeng Huang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Ulrich Ermler
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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36
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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: 32] [Impact Index Per Article: 8.0] [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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37
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Khatri B, Majumder P, Nagesh J, Penmatsa A, Chatterjee J. Increasing protein stability by engineering the n → π* interaction at the β-turn. Chem Sci 2020; 11:9480-9487. [PMID: 34094214 PMCID: PMC8161691 DOI: 10.1039/d0sc03060k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction. Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.![]()
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
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38
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Catalytic activity regulation through post-translational modification: the expanding universe of protein diversity. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:97-125. [PMID: 32951817 PMCID: PMC7320668 DOI: 10.1016/bs.apcsb.2020.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein composition is restricted by the genetic code to a relatively small number of natural amino acids. Similarly, the known three-dimensional structures adopt a limited number of protein folds. However, proteins exert a large variety of functions and show a remarkable ability for regulation and immediate response to intracellular and extracellular stimuli. To some degree, the wide variability of protein function can be attributed to the post-translational modifications. Post-translational modifications have been observed in all kingdoms of life and give to proteins a significant degree of chemical and consequently functional and structural diversity. Their importance is partly reflected in the large number of genes dedicated to their regulation. So far, hundreds of post-translational modifications have been observed while it is believed that many more are to be discovered along with the technological advances in sequencing, proteomics, mass spectrometry and structural biology. Indeed, the number of studies which report novel post translational modifications is getting larger supporting the notion that their space is still largely unexplored. In this review we explore the impact of post-translational modifications on protein structure and function with emphasis on catalytic activity regulation. We present examples of proteins and protein families whose catalytic activity is substantially affected by the presence of post translational modifications and we describe the molecular basis which underlies the regulation of the protein function through these modifications. When available, we also summarize the current state of knowledge on the mechanisms which introduce these modifications to protein sites.
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39
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Nayak DD, Liu A, Agrawal N, Rodriguez-Carerro R, Dong SH, Mitchell DA, Nair SK, Metcalf WW. Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans. PLoS Biol 2020; 18:e3000507. [PMID: 32092071 PMCID: PMC7058361 DOI: 10.1371/journal.pbio.3000507] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/05/2020] [Accepted: 02/04/2020] [Indexed: 01/27/2023] Open
Abstract
The enzyme methyl-coenzyme M reductase (MCR) plays an important role in mediating global levels of methane by catalyzing a reversible reaction that leads to the production or consumption of this potent greenhouse gas in methanogenic and methanotrophic archaea. In methanogenic archaea, the alpha subunit of MCR (McrA) typically contains four to six posttranslationally modified amino acids near the active site. Recent studies have identified enzymes performing two of these modifications (thioglycine and 5-[S]-methylarginine), yet little is known about the formation and function of the remaining posttranslationally modified residues. Here, we provide in vivo evidence that a dedicated S-adenosylmethionine-dependent methyltransferase encoded by a gene we designated methylcysteine modification (mcmA) is responsible for formation of S-methylcysteine in Methanosarcina acetivorans McrA. Phenotypic analysis of mutants incapable of cysteine methylation suggests that the S-methylcysteine residue might play a role in adaption to mesophilic conditions. To examine the interactions between the S-methylcysteine residue and the previously characterized thioglycine, 5-(S)-methylarginine modifications, we generated M. acetivorans mutants lacking the three known modification genes in all possible combinations. Phenotypic analyses revealed complex, physiologically relevant interactions between the modified residues, which alter the thermal stability of MCR in a combinatorial fashion that is not readily predictable from the phenotypes of single mutants. High-resolution crystal structures of inactive MCR lacking the modified amino acids were indistinguishable from the fully modified enzyme, suggesting that interactions between the posttranslationally modified residues do not exert a major influence on the static structure of the enzyme but rather serve to fine-tune the activity and efficiency of MCR.
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Affiliation(s)
- Dipti D. Nayak
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Andi Liu
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Neha Agrawal
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Roy Rodriguez-Carerro
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
| | - Shi-Hui Dong
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Douglas A. Mitchell
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
- Center for Biophysics & Quantitative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - William W. Metcalf
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Microbiology, University of Illinois, Urbana, Illinois, United States of America
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40
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Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis. J Bacteriol 2020; 202:JB.00654-19. [PMID: 31740491 DOI: 10.1128/jb.00654-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 11/09/2019] [Indexed: 02/05/2023] Open
Abstract
Catalyzing the key step for anaerobic production and/or oxidation of methane and likely other short-chain alkanes, methyl coenzyme M reductase (Mcr) and its homologs play a key role in the global carbon cycle. The McrA subunit possesses up to five conserved posttranslational modifications (PTMs) at its active site. It was previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To systematically examine its physiological role, mmpX (locus tag MMP1554), the gene encoding Mmp10 in Methanococcus maripaludis, was deleted with a new genetic tool, resulting in the complete loss of the 5-C-(S)-methylarginine PTM of residue 275 in the McrA subunit. When the ΔmmpX mutant was complemented with the wild-type gene expressed by either a strong or a weak promoter, methylation was fully restored. Compared to the parental strain, maximal rates of methane formation by whole cells were reduced by 40 to 60% in the ΔmmpX mutant. The reduction in activity was fully reversed by the complement with the strong promoter. Site-directed mutagenesis of mmpX resulted in a differential loss of arginine methylation among the mutants in vivo, suggesting that activities of Mmp10 directly modulated methylation. R275 was present in a highly conserved PXRR275(A/S)R(G/A) signature sequence in McrAs. The only other protein in M. maripaludis containing a similar sequence was not methylated, suggesting that Mmp10 is specific for McrA. In conclusion, Mmp10 modulates the methyl-Arg PTM on McrA in a highly specific manner, which has a profound impact on Mcr activity.IMPORTANCE Mcr is the key enzyme in methanogenesis and a promising candidate for bioengineering the conversion of methane to liquid fuel. Our knowledge of Mcr is still limited. In terms of complexity, uniqueness, and environmental importance, Mcr is more comparable to photosynthetic reaction centers than conventional enzymes. PTMs have long been hypothesized to play key roles in modulating Mcr activity. Here, we directly link the mmpX gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights into its substrate specificity and putative cofactor binding sites. This is also the first time that a PTM of McrA has been shown to have a substantial impact on both methanogenesis and growth in the absence of additional stressors.
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Huo L, Zhao X, Acedo JZ, Estrada P, Nair SK, van der Donk WA. Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae. Chembiochem 2020; 21:190-199. [PMID: 31532570 PMCID: PMC6980331 DOI: 10.1002/cbic.201900483] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Indexed: 12/15/2022]
Abstract
As a result of the exponential increase in genomic data, discovery of novel ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has progressed rapidly in the past decade. The lanthipeptides are a major subset of RiPPs. Through genome mining we identified a novel lanthipeptide biosynthetic gene cluster (lah) from Lachnospiraceae bacterium C6A11, an anaerobic bacterium that is a member of the human microbiota and which is implicated in the development of host disease states such as type 2 diabetes and resistance to Clostridium difficile colonization. The lah cluster encodes at least seven putative precursor peptides and multiple post-translational modification (PTM) enzymes. Two unusual class II lanthipeptide synthetases LahM1/M2 and a substrate-tolerant S-adenosyl-l-methionine (SAM)-dependent methyltransferase LahSB are biochemically characterized in this study. We also present the crystal structure of LahSB in complex with product S-adenosylhomocysteine. This study sets the stage for further exploration of the final products of the lah pathway as well as their potential physiological functions in human/animal gut microbiota.
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Affiliation(s)
- Liujie Huo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- State Key Laboratory for Microbial Technology (SKLMT), Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University, Qingdao, 266237, P. R. China
| | - Xiling Zhao
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Paola Estrada
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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42
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Maini R, Kimura H, Takatsuji R, Katoh T, Goto Y, Suga H. Ribosomal Formation of Thioamide Bonds in Polypeptide Synthesis. J Am Chem Soc 2019; 141:20004-20008. [DOI: 10.1021/jacs.9b11097] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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43
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Santos-Aberturas J, Chandra G, Frattaruolo L, Lacret R, Pham TH, Vior NM, Eyles TH, Truman AW. Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool. Nucleic Acids Res 2019; 47:4624-4637. [PMID: 30916321 PMCID: PMC6511847 DOI: 10.1093/nar/gkz192] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 01/26/2023] Open
Abstract
The rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, which are proposed to be introduced by YcaO-TfuA proteins. Using RiPPER, we show that previously undescribed RiPP gene clusters encoding YcaO and TfuA proteins are widespread in Actinobacteria and encode a highly diverse landscape of precursor peptides that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new structural class of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.
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Affiliation(s)
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Luca Frattaruolo
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Rodney Lacret
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Thu H Pham
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Natalia M Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Tom H Eyles
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
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44
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Dunbar KL, Dell M, Molloy EM, Kloss F, Hertweck C. Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Florian Kloss
- Transfer Group Antiinfectives Leibniz Institute for Natural Product Research and Infection Biology HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology, HKI Beutenbergstrasse 11a 07745 Jena Germany
- Chair of Natural Product Chemistry Friedrich Schiller University Jena 07743 Jena Germany
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45
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Farley KR, Metcalf WW. The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea. FEMS Microbiol Lett 2019; 366:5586563. [PMID: 31605529 DOI: 10.1093/femsle/fnz216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/10/2019] [Indexed: 11/14/2022] Open
Abstract
A repertoire of sophisticated genetic tools has significantly enhanced studies of Methanosarcina genera, yet the lack of multiple positive selectable markers has limited the types of genetic experiments that can be performed. In this study, we report the development of an additional positive selection system for Methanosarcina that utilizes the antibiotic nourseothricin and the Streptomyces rochei streptothricin acetyltransferase (sat) gene, which may be broadly applicable to other groups of methanogenic archaea. Nourseothricin was found to inhibit growth of four different methanogen species at concentrations ≤300 μg/ml in liquid or on solid media. Selection of nourseothricin resistant transformants was possible in two genetically tractable Methanosarcina species, M. acetivorans and M. barkeri, using the sat gene as a positive selectable marker. Additionally, the sat marker was useful for constructing a gene deletion mutant strain of M. acetivorans, emphasizing its utility as a second positive selectable marker for genetic analyses of Methanosarcina genera. Interestingly, two human gut-associated methanogens Methanobrevibacter smithii and Methanomassillicoccus luminyensis were more sensitive to nourseothricin than either Methanosarcina species, suggesting the nourseothricin-sat gene pair may provide a robust positive selection system for development of genetic tools in these and other methanogens.
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Affiliation(s)
- Kristen R Farley
- Department of Microbiology, B103 Chemical and Life Sciences Laboratory, University of Illinois Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, Illinois 61801
| | - William W Metcalf
- Department of Microbiology, B103 Chemical and Life Sciences Laboratory, University of Illinois Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, Illinois 61801
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46
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Dunbar KL, Dell M, Molloy EM, Kloss F, Hertweck C. Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones. Angew Chem Int Ed Engl 2019; 58:13014-13018. [PMID: 31276268 PMCID: PMC6772006 DOI: 10.1002/anie.201905992] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 12/31/2022]
Abstract
Thioamide‐containing nonribosomal peptides (NRPs) are exceedingly rare. Recently the biosynthetic gene cluster for the thioamidated NRP antibiotic closthioamide (CTA) was reported, however, the enzyme responsible for and the timing of thioamide formation remained enigmatic. Here, genome editing, biochemical assays, and mutational studies are used to demonstrate that an Fe‐S cluster containing member of the adenine nucleotide α‐hydrolase protein superfamily (CtaC) is responsible for sulfur incorporation during CTA biosynthesis. However, unlike all previously characterized members, CtaC functions in a thiotemplated manner. In addition to prompting a revision of the CTA biosynthetic pathway, the reconstitution of CtaC provides the first example of a NRP thioamide synthetase. Finally, CtaC is used as a bioinformatic handle to demonstrate that thioamidated NRP biosynthetic gene clusters are more widespread than previously appreciated.
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Affiliation(s)
- Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Florian Kloss
- Transfer Group Antiinfectives, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745, Jena, Germany.,Chair of Natural Product Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
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47
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Kudo K, Koiwai H, Kagaya N, Nishiyama M, Kuzuyama T, Shin-ya K, Ikeda H. Comprehensive Derivatization of Thioviridamides by Heterologous Expression. ACS Chem Biol 2019; 14:1135-1140. [PMID: 31184470 DOI: 10.1021/acschembio.9b00330] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New technology for the derivatization of peptide natural products is required for drug development. Despite the recent advances in the genome sequencing technique enabling us to search for the biosynthetic genes for wide variety of natural products, the technical methods to get access to them are limited. A class of RiPPs, a recently emerged natural product family such as thioviridamide, is one of those possessing such unexplored chemical space. In this paper, we report a streamlined method to generate new thioviridamide derivatives and to assess their biological activities. Heterologous expression of 42 constructs in an engineered Streptomyces avermitilis host gave 35 designed thioviridamide derivatives, along with several unprecedented analogues. Moreover, cytotoxicity assay revealed that several derivatives showed more potent activities than those of prethioviridamide. These results indicate that this strategy can become one of the potential ways to produce supreme unnatural products.
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Affiliation(s)
- Kei Kudo
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Hanae Koiwai
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Noritaka Kagaya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomohisa Kuzuyama
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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48
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Dong SH, Liu A, Mahanta N, Mitchell DA, Nair SK. Mechanistic Basis for Ribosomal Peptide Backbone Modifications. ACS CENTRAL SCIENCE 2019; 5:842-851. [PMID: 31139720 PMCID: PMC6535971 DOI: 10.1021/acscentsci.9b00124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/16/2023]
Abstract
YcaO enzymes are known to catalyze the ATP-dependent formation of azoline heterocycles, thioamides, and (macro)lactamidines on peptide substrates. These enzymes are found in multiple biosynthetic pathways, including those for several different classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, there are major knowledge gaps in the mechanistic and structural underpinnings that govern each of the known YcaO-mediated modifications. Here, we present the first structure of any YcaO enzyme bound to its peptide substrate in the active site, specifically that from Methanocaldococcus jannaschii which is involved in the thioamidation of the α-subunit of methyl-coenzyme M reductase (McrA). The structural data are leveraged to identify and test the residues involved in substrate binding and catalysis by site-directed mutagenesis. We also show that thioamide-forming YcaOs can carry out the cyclodehydration of a related peptide substrate, which underscores the mechanistic conservation across the YcaO family and allows for the extrapolation of mechanistic details to azoline-forming YcaOs involved in RiPP biosynthesis. A bioinformatic survey of all YcaOs highlights the diverse sequence space in azoline-forming YcaOs and suggests their early divergence from a common ancestor. The data presented within provide a detailed molecular framework for understanding this family of enzymes, which reconcile several decades of prior data on RiPP cyclodehydratases. These studies also provide the foundational knowledge to impact our mechanistic understanding of additional RiPP biosynthetic classes.
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Affiliation(s)
- Shi-Hui Dong
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Andi Liu
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Nilkamal Mahanta
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Douglas A. Mitchell
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Satish K. Nair
- Department
of Biochemistry, Carl R. Woese Institute for Genomic Biology, Department of Microbiology, Department of Chemistry, and Center for Biophysics
and Quantitative Biology, University of
Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
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49
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Radle MI, Miller DV, Laremore TN, Booker SJ. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J Biol Chem 2019; 294:11712-11725. [PMID: 31113866 DOI: 10.1074/jbc.ra119.007609] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/10/2019] [Indexed: 11/06/2022] Open
Abstract
Methyl coenzyme M reductase (MCR) catalyzes the last step in the biological production of methane by methanogenic archaea, as well as the first step in the anaerobic oxidation of methane to methanol by methanotrophic archaea. MCR contains a number of unique post-translational modifications in its α subunit, including thioglycine, 1-N-methylhistidine, S-methylcysteine, 5-C-(S)-methylarginine, and 2-C-(S)-methylglutamine. Recently, genes responsible for the thioglycine and methylarginine modifications have been identified in bioinformatics studies and in vivo complementation of select mutants; however, none of these reactions has been verified in vitro Herein, we purified and biochemically characterized the radical S-adenosylmethionine (SAM) protein MaMmp10, the product of the methanogenesis marker protein 10 gene in the methane-producing archaea Methanosarcina acetivorans Using an array of approaches, including kinetic assays, LC-MS-based quantification, and MALDI TOF-TOF MS analyses, we found that MaMmp10 catalyzes the methylation of the equivalent of Arg285 in a peptide substrate surrogate, but only in the presence of cobalamin. We noted that the methyl group derives from SAM, with cobalamin acting as an intermediate carrier, and that MaMmp10 contains a C-terminal cobalamin-binding domain. Given that Mmp10 has not been annotated as a cobalamin-binding protein, these findings suggest that cobalamin-dependent radical SAM proteins are more prevalent than previously thought.
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Affiliation(s)
- Matthew I Radle
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Danielle V Miller
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Tatiana N Laremore
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802.,Howard Hughes Medical Institute, Pennsylvania State University, University Park, Pennsylvania 16802
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50
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Thauer RK. Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes. Biochemistry 2019; 58:5198-5220. [PMID: 30951290 PMCID: PMC6941323 DOI: 10.1021/acs.biochem.9b00164] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Methyl-coenzyme
M reductase (MCR) catalyzes the methane-forming
step in methanogenic archaea. The active enzyme harbors the nickel(I)
hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the
reversible reduction of methyl-coenzyme M (CH3–S-CoM)
with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is
also involved in anaerobic methane oxidation in reverse of methanogenesis
and most probably in the anaerobic oxidation of ethane, propane, and
butane. The challenging question is how the unreactive CH3–S thioether bond in methyl-coenzyme M and the even more unreactive
C–H bond in methane and the other hydrocarbons are anaerobically
cleaved. A key to the answer is the negative redox potential (Eo′) of the Ni(II)F-430/Ni(I)F-430 couple
below −600 mV and the radical nature of Ni(I)F-430. However,
the negative one-electron redox potential is also the Achilles heel
of MCR; it makes the nickel enzyme one of the most O2-sensitive
enzymes known to date. Even under physiological conditions, the Ni(I)
in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in
the cells the redox potential (E′) of the
CoM-S–S-CoB/HS-CoM and HS-CoB couple (Eo′ = −140 mV) gets too high. Methanogens therefore
harbor an enzyme system for the reactivation of inactivated MCR in
an ATP-dependent reduction reaction. Purification of active MCR in
the Ni(I) oxidation state is very challenging and has been achieved
in only a few laboratories. This perspective reviews the function,
structure, and properties of MCR, what is known and not known about
the catalytic mechanism, how the inactive enzyme is reactivated, and
what remains to be discovered.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology , Karl-von-Frisch-Strasse 10 , Marburg 35043 , Germany
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