1
|
Soualmia F, Cherrier MV, Chauviré T, Mauger M, Tatham P, Guillot A, Guinchard X, Martin L, Amara P, Mouesca JM, Daghmoum M, Benjdia A, Gambarelli S, Berteau O, Nicolet Y. Radical S-Adenosyl-l-Methionine Enzyme PylB: A C-Centered Radical to Convert l-Lysine into (3 R)-3-Methyl-d-Ornithine. J Am Chem Soc 2024; 146:6493-6505. [PMID: 38426440 DOI: 10.1021/jacs.3c03747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
PylB is a radical S-adenosyl-l-methionine (SAM) enzyme predicted to convert l-lysine into (3R)-3-methyl-d-ornithine, a precursor in the biosynthesis of the 22nd proteogenic amino acid pyrrolysine. This protein highly resembles that of the radical SAM tyrosine and tryptophan lyases, which activate their substrate by abstracting a H atom from the amino-nitrogen position. Here, combining in vitro assays, analytical methods, electron paramagnetic resonance spectroscopy, and theoretical methods, we demonstrated that instead, PylB activates its substrate by abstracting a H atom from the Cγ position of l-lysine to afford the radical-based β-scission. Strikingly, we also showed that PylB catalyzes the reverse reaction, converting (3R)-3-methyl-d-ornithine into l-lysine and using catalytic amounts of the 5'-deoxyadenosyl radical. Finally, we identified significant in vitro production of 5'-thioadenosine, an unexpected shunt product that we propose to result from the quenching of the 5'-deoxyadenosyl radical species by the nearby [Fe4S4] cluster.
Collapse
Affiliation(s)
- Feryel Soualmia
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Mickael V Cherrier
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Timothée Chauviré
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Mickaël Mauger
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Philip Tatham
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xavier Guinchard
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| | - Jean-Marie Mouesca
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Meriem Daghmoum
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | - Alhosna Benjdia
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, F-38000 Grenoble, France
| | - Olivier Berteau
- Université Paris-Saclay, Micalis Institute, ChemSyBio, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
| |
Collapse
|
2
|
Barreto JVDO, Casanova LM, Junior AN, Reis-Mansur MCPP, Vermelho AB. Microbial Pigments: Major Groups and Industrial Applications. Microorganisms 2023; 11:2920. [PMID: 38138065 PMCID: PMC10745774 DOI: 10.3390/microorganisms11122920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Microbial pigments have many structures and functions with excellent characteristics, such as being biodegradable, non-toxic, and ecologically friendly, constituting an important source of pigments. Industrial production presents a bottleneck in production cost that restricts large-scale commercialization. However, microbial pigments are progressively gaining popularity because of their health advantages. The development of metabolic engineering and cost reduction of the bioprocess using industry by-products opened possibilities for cost and quality improvements in all production phases. We are thus addressing several points related to microbial pigments, including the major classes and structures found, the advantages of use, the biotechnological applications in different industrial sectors, their characteristics, and their impacts on the environment and society.
Collapse
Affiliation(s)
| | | | | | | | - Alane Beatriz Vermelho
- Bioinovar Laboratory, Institute of Microbiology Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.V.d.O.B.); (L.M.C.); (A.N.J.); (M.C.P.P.R.-M.)
| |
Collapse
|
3
|
Benjdia A, Berteau O. B 12-dependent radical SAM enzymes: Ever expanding structural and mechanistic diversity. Curr Opin Struct Biol 2023; 83:102725. [PMID: 37931378 DOI: 10.1016/j.sbi.2023.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 11/08/2023]
Abstract
In the last decade, B12-dependent radical SAM enzymes have emerged as central biocatalysts in the biosynthesis of a myriad of natural products. Notably, these enzymes have been shown to catalyze carbon-carbon bond formation on unactivated carbon atoms leading to unusual methylations. Recently, structural studies have revealed unprecedented insights into the complex chemistry catalyzed by these enzymes. In this review, we cover recent advances in our understanding of B12-dependent radical SAM enzymes from a mechanistic and structural perspective. We discuss the unanticipated diversity of these enzymes which suggests evolutionary links between various biosynthetic and metabolic pathways from antibiotic to RiPP and methane biosynthesis.
Collapse
Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, 78350, Jouy-en-Josas, France.
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
Collapse
Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| |
Collapse
|
6
|
Benjdia A, Berteau O. Radical SAM Enzymes and Ribosomally-Synthesized and Post-translationally Modified Peptides: A Growing Importance in the Microbiomes. Front Chem 2021; 9:678068. [PMID: 34350157 PMCID: PMC8326336 DOI: 10.3389/fchem.2021.678068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
To face the current antibiotic resistance crisis, novel strategies are urgently required. Indeed, in the last 30 years, despite considerable efforts involving notably high-throughput screening and combinatorial libraries, only few antibiotics have been launched to the market. Natural products have markedly contributed to the discovery of novel antibiotics, chemistry and drug leads, with more than half anti-infective and anticancer drugs approved by the FDA being of natural origin or inspired by natural products. Among them, thanks to their modular structure and simple biosynthetic logic, ribosomally synthesized and posttranslationally modified peptides (RiPPs) are promising scaffolds. In addition, recent studies have highlighted the pivotal role of RiPPs in the human microbiota which remains an untapped source of natural products. In this review, we report on recent developments in radical SAM enzymology and how these unique biocatalysts have been shown to install complex and sometimes unprecedented posttranslational modifications in RiPPs with a special focus on microbiome derived enzymes.
Collapse
Affiliation(s)
- Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| |
Collapse
|
7
|
Ye Y, Fu H, Hyster TK. Activation modes in biocatalytic radical cyclization reactions. J Ind Microbiol Biotechnol 2021; 48:6155068. [PMID: 33674826 PMCID: PMC8210684 DOI: 10.1093/jimb/kuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/17/2022]
Abstract
Radical cyclizations are essential reactions in the biosynthesis of secondary metabolites and the chemical synthesis of societally valuable molecules. In this review, we highlight the general mechanisms utilized in biocatalytic radical cyclizations. We specifically highlight cytochrome P450 monooxygenases (P450s) involved in the biosynthesis of mycocyclosin and vancomycin, nonheme iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGDs) used in the biosynthesis of kainic acid, scopolamine, and isopenicillin N, and radical S-adenosylmethionine (SAM) enzymes that facilitate the biosynthesis of oxetanocin A, menaquinone, and F420. Beyond natural mechanisms, we also examine repurposed flavin-dependent “ene”-reductases (ERED) for non-natural radical cyclization. Overall, these general mechanisms underscore the opportunity for enzymes to augment and enhance the synthesis of complex molecules using radical mechanisms.
Collapse
Affiliation(s)
- Yuxuan Ye
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
8
|
Yin Y, Ji X, Zhang Q. The Promiscuous Activity of the Radical
SAM
Enzyme
NosL
toward Two Unnatural Substrates. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100304] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yue Yin
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Xinjian Ji
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
| |
Collapse
|
9
|
Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea. Genes (Basel) 2021; 12:genes12070963. [PMID: 34202810 PMCID: PMC8305020 DOI: 10.3390/genes12070963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.
Collapse
|
10
|
Veerapen N, Hobrath J, Besra AK, Besra GS. Chemical insights into the search for MAIT cells activators. Mol Immunol 2020; 129:114-120. [PMID: 33293098 DOI: 10.1016/j.molimm.2020.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
Mucosal-associated invariant T cells (MAIT cells) represent a potential therapeutic target as they can tune or enhance immune responses. They recognise and become activated by antigens, presented by the monomorphic MHC-I related molecule, MR1. To assess the significance of MAIT cells in human diseases, a better understanding of the MAIT cell-MR1-antigen interaction is imperative. Easy access to MR1 ligands and MAIT cells activators can help achieve this. In this review, we summarise current literature that has identified the natural ligands and drug-like molecules that activate MAIT cells and provide insight into their key molecular interactions with MR1 and MAIT T cell receptors (TCRs). We focus on the progress made in synthesizing and isolating 5-amino-6-d-ribitylaminouracil (5-A-RU), a key precursor in the synthesis of the known natural ligands, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil(5-OP-RU) and 5-(2-oxoethylideneamino)-6-d-ribitylaminouracil (5-OE-RU), and also on the stabilisation and optimisation of the latter compounds.
Collapse
Affiliation(s)
- Natacha Veerapen
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Judith Hobrath
- Drug Discovery Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Amareeta K Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
| |
Collapse
|
11
|
Balty C, Guillot A, Fradale L, Brewee C, Lefranc B, Herrero C, Sandström C, Leprince J, Berteau O, Benjdia A. Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes. J Biol Chem 2020; 295:16665-16677. [PMID: 32972973 PMCID: PMC8188230 DOI: 10.1074/jbc.ra120.015371] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and posttranslationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of nonnatural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element, present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the peptide recognition element and the core peptide for the installation of posttranslational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.
Collapse
Affiliation(s)
- Clémence Balty
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Alain Guillot
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Laura Fradale
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Brewee
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Benjamin Lefranc
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | | | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jérôme Leprince
- INSERM U1239, PRIMACEN, Université de Normandie-Rouen, Rouen, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
| |
Collapse
|
12
|
Redox Coenzyme F 420 Biosynthesis in Thermomicrobia Involves Reduction by Stand-Alone Nitroreductase Superfamily Enzymes. Appl Environ Microbiol 2020; 86:AEM.00457-20. [PMID: 32276981 DOI: 10.1128/aem.00457-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for a long time that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that phosphoenolpyruvate is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase (NTR) superfamily, converts dehydro-F420 into saturated F420 Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in vitro assays that stand-alone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in Escherichia coli in the future.IMPORTANCE Coenzyme F420 is a redox cofactor of Archaea and Actinobacteria, as well as some Gram-negative bacteria. Its involvement in processes such as the biosynthesis of antibiotics, the degradation of xenobiotics, and asymmetric enzymatic reductions renders F420 of great relevance for biotechnology. Recently, a new biosynthetic step during the formation of F420 in Actinobacteria was discovered, involving an enzyme domain belonging to the versatile nitroreductase (NTR) superfamily, while this process remained blurred in Gram-negative bacteria. Here, we show that a similar biosynthetic route exists in Thermomicrobia, although key biosynthetic enzymes show different domain architectures and are only distantly related. Our results shed light on the biosynthesis of F420 in Gram-negative bacteria and refine the knowledge about sequence-function relationships within the NTR superfamily of enzymes. Appreciably, these results offer an alternative route to produce F420 in Gram-negative model organisms and unveil yet another biochemical facet of this pathway to be explored by synthetic microbiologists.
Collapse
|
13
|
Adenosylation reactions catalyzed by the radical S-adenosylmethionine superfamily enzymes. Curr Opin Chem Biol 2020; 55:86-95. [DOI: 10.1016/j.cbpa.2020.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/22/2019] [Accepted: 01/15/2020] [Indexed: 01/23/2023]
|
14
|
Wu Y, Wu R, Mandalapu D, Ji X, Chen T, Ding W, Zhang Q. Radical SAM-dependent adenosylation catalyzed by l-tyrosine lyases. Org Biomol Chem 2019; 17:1809-1812. [DOI: 10.1039/c8ob02906g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tyrosine analogues containing an olefin moiety can be adenosylated by l-tyrosine lyases.
Collapse
Affiliation(s)
- Yujie Wu
- State Key Laboratory of Cryospheric Sciences
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering
- Northwest Institute of Eco-environment and Resource
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Runze Wu
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | | | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering
- Northwest Institute of Eco-environment and Resource
- Chinese Academy of Sciences
- Lanzhou 730000
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai 200433
- China
| |
Collapse
|
15
|
Yokoyama K, Lilla EA. C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Nat Prod Rep 2018; 35:660-694. [PMID: 29633774 PMCID: PMC6051890 DOI: 10.1039/c8np00006a] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to the end of 2017 C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.
Collapse
Affiliation(s)
- Kenichi Yokoyama
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
| | | |
Collapse
|
16
|
Morinaka BI, Lakis E, Verest M, Helf MJ, Scalvenzi T, Vagstad AL, Sims J, Sunagawa S, Gugger M, Piel J. Natural noncanonical protein splicing yields products with diverse β-amino acid residues. Science 2018; 359:779-782. [DOI: 10.1126/science.aao0157] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 01/03/2018] [Indexed: 01/01/2023]
|
17
|
Identification of the Radical SAM Enzymes Involved in the Biosynthesis of Methanopterin and Coenzyme F 420 in Methanogens. Methods Enzymol 2018; 606:461-483. [DOI: 10.1016/bs.mie.2018.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
18
|
Bhandari DM, Fedoseyenko D, Begley TP. Mechanistic Studies on the Radical SAM Enzyme Tryptophan Lyase (NosL). Methods Enzymol 2018; 606:155-178. [DOI: 10.1016/bs.mie.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Qianzhu H, Ji W, Ji X, Chu L, Guo C, Lu W, Ding W, Gao J, Zhang Q. Reactivity of the nitrogen-centered tryptophanyl radical in the catalysis by the radical SAM enzyme NosL. Chem Commun (Camb) 2017; 53:344-347. [PMID: 27929146 DOI: 10.1039/c6cc08869d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The radical SAM tryptophan (Trp) lyase NosL involved in nosiheptide biosynthesis catalyzes two parallel reactions, converting l-Trp to 3-methyl-2-indolic acid (MIA) and to dehydroglycine and 3-methylindole, respectively. The two parallel reactions diverge from a nitrogen-centered tryptophanyl radical intermediate. Here we report an investigation on the intrinsic reactivity of the tryptophanyl radical using a chemical model study and DFT calculations. The kinetics of the formation and fragmentation of this nitrogen-centered radical in NosL catalysis were also studied in detail. Our analysis explains the intriguing catalytic promiscuity of NosL and highlights the remarkable role this enzyme plays in achieving an energetically highly unfavorable transformation.
Collapse
Affiliation(s)
- Haocheng Qianzhu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. and Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wenjuan Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Leixia Chu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Chuchu Guo
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wei Lu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wei Ding
- Department of Chemistry, Fudan University, Shanghai, 200433, China. and School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiangtao Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
20
|
Robbins JM, Souffrant MG, Hamelberg D, Gadda G, Bommarius AS. Enzyme-Mediated Conversion of Flavin Adenine Dinucleotide (FAD) to 8-Formyl FAD in Formate Oxidase Results in a Modified Cofactor with Enhanced Catalytic Properties. Biochemistry 2017. [PMID: 28640638 DOI: 10.1021/acs.biochem.7b00335] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavins, including flavin adenine dinucleotide (FAD), are fundamental catalytic cofactors that are responsible for the redox functionality of a diverse set of proteins. Alternatively, modified flavin analogues are rarely found in nature as their incorporation typically results in inactivation of flavoproteins, thus leading to the disruption of important cellular pathways. Here, we report that the fungal flavoenzyme formate oxidase (FOX) catalyzes the slow conversion of noncovalently bound FAD to 8-formyl FAD and that this conversion results in a nearly 10-fold increase in formate oxidase activity. Although the presence of an enzyme-bound 8-formyl FMN has been reported previously as a result of site-directed mutagenesis studies of lactate oxidase, FOX is the first reported case of 8-formyl FAD in a wild-type enzyme. Therefore, the formation of the 8-formyl FAD cofactor in formate oxidase was investigated using steady-state kinetics, site-directed mutagenesis, ultraviolet-visible, circular dichroism, and fluorescence spectroscopy, liquid chromatography with mass spectrometry, and computational analysis. Surprisingly, the results from these studies indicate not only that 8-formyl FAD forms spontaneously and results in the active form of FOX but also that its autocatalytic formation is dependent on a nearby arginine residue, R87. Thus, this work describes a new enzyme cofactor and provides insight into the little-understood mechanism of enzyme-mediated 8α-flavin modifications.
Collapse
Affiliation(s)
- John M Robbins
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States
| | - Michael G Souffrant
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Molecular Basis of Disease Program, Georgia State University , Atlanta, Georgia 30303, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Diagnostics and Therapeutics, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Center for Biotechnology and Drug Design, Georgia State University , Atlanta, Georgia 30302-3965, United States.,Department of Biology, Georgia State University , Atlanta, Georgia 30302-3965, United States
| | - Andreas S Bommarius
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0100, United States.,Engineered Biosystems Building (EBB), Georgia Institute of Technology , Atlanta, Georgia 30332-2000, United States.,School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
21
|
Liu L, Ji X, Li Y, Ji W, Mo T, Ding W, Zhang Q. A mechanistic study of the non-oxidative decarboxylation catalyzed by the radical S-adenosyl-l-methionine enzyme BlsE involved in blasticidin S biosynthesis. Chem Commun (Camb) 2017; 53:8952-8955. [DOI: 10.1039/c7cc04286h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BlsE-catalyzed non-oxidative decarboxylation is initiated by a hydrogen abstraction from a sugar carbon of the substrate cytosylglucuronic acid (CGA).
Collapse
Affiliation(s)
- Lei Liu
- College of Life Science & Biotechnology
- Mianyang Normal University
- Mianyang 621000
- P. R. China
- Department of Chemistry
| | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Yongzhen Li
- Department of Chemistry
- Fudan University
- Shanghai
- China
- Medical College of Qinghai University
| | - Wenjuan Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Tianlu Mo
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
| |
Collapse
|
22
|
Sulfatases and radical SAM enzymes: emerging themes in glycosaminoglycan metabolism and the human microbiota. Biochem Soc Trans 2016; 44:109-15. [PMID: 26862195 DOI: 10.1042/bst20150191] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Humans live in a permanent association with bacterial populations collectively called the microbiota. In the last 10 years, major advances in our knowledge of the microbiota have shed light on its critical roles in human physiology. The microbiota has also been shown to be a major factor in numerous pathologies including obesity or inflammatory disorders. Despite tremendous progresses, our understanding of the key functions of the human microbiota and the molecular basis of its interactions with the host remain still poorly understood. Among the factors involved in host colonization, two enzymes families, sulfatases and radical S-adenosyl-L-methionine enzymes, have recently emerged as key enzymes.
Collapse
|
23
|
Ney B, Ahmed FH, Carere CR, Biswas A, Warden AC, Morales SE, Pandey G, Watt SJ, Oakeshott JG, Taylor MC, Stott MB, Jackson CJ, Greening C. The methanogenic redox cofactor F 420 is widely synthesized by aerobic soil bacteria. ISME JOURNAL 2016; 11:125-137. [PMID: 27505347 DOI: 10.1038/ismej.2016.100] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 02/07/2023]
Abstract
F420 is a low-potential redox cofactor that mediates the transformations of a wide range of complex organic compounds. Considered one of the rarest cofactors in biology, F420 is best known for its role in methanogenesis and has only been chemically identified in two phyla to date, the Euryarchaeota and Actinobacteria. In this work, we show that this cofactor is more widely distributed than previously reported. We detected the genes encoding all five known F420 biosynthesis enzymes (cofC, cofD, cofE, cofG and cofH) in at least 653 bacterial and 173 archaeal species, including members of the dominant soil phyla Proteobacteria, Chloroflexi and Firmicutes. Metagenome datamining validated that these genes were disproportionately abundant in aerated soils compared with other ecosystems. We confirmed through high-performance liquid chromatography analysis that aerobically grown stationary-phase cultures of three bacterial species, Paracoccus denitrificans, Oligotropha carboxidovorans and Thermomicrobium roseum, synthesized F420, with oligoglutamate sidechains of different lengths. To understand the evolution of F420 biosynthesis, we also analyzed the distribution, phylogeny and genetic organization of the cof genes. Our data suggest that although the Fo precursor to F420 originated in methanogens, F420 itself was first synthesized in an ancestral actinobacterium. F420 biosynthesis genes were then disseminated horizontally to archaea and other bacteria. Together, our findings suggest that the cofactor is more significant in aerobic bacterial metabolism and soil ecosystem composition than previously thought. The cofactor may confer several competitive advantages for aerobic soil bacteria by mediating their central metabolic processes and broadening the range of organic compounds they can synthesize, detoxify and mineralize.
Collapse
Affiliation(s)
- Blair Ney
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory, Australia.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| | - F Hafna Ahmed
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory, Australia
| | - Carlo R Carere
- GNS Science, Wairakei Research Centre, Taupō, New Zealand
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Andrew C Warden
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gunjan Pandey
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| | - Stephen J Watt
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory, Australia
| | - John G Oakeshott
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| | - Matthew C Taylor
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| | | | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, Australian Capital Territory, Australia
| | - Chris Greening
- The Commonwealth Scientific and Industrial Research Organisation, Land and Water, Acton, Australian Capital Territory, Australia
| |
Collapse
|
24
|
Ding W, Ji X, Li Y, Zhang Q. Catalytic Promiscuity of the Radical S-adenosyl-L-methionine Enzyme NosL. Front Chem 2016; 4:27. [PMID: 27446906 PMCID: PMC4916742 DOI: 10.3389/fchem.2016.00027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Catalytic promiscuity plays a key role in enzyme evolution and the acquisition of novel biological functions. Because of the high reactivity of radical species, in our view enzymes involving radical-mediated mechanisms could intrinsically be more prone to catalytic promiscuity. This mini-review summarizes the recent advances in the study of NosL, a radical S-adenosyl-L-methionine (SAM)-dependent L-tryptophan (L-Trp) lyase. We demonstrate here the interesting chemistry and remarkable catalytic promiscuity of NosL, and attempt to highlight the high evolvability of radical SAM enzymes and the potential to engineer these enzymes for novel and improved activities.
Collapse
Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University Shanghai, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University Shanghai, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University Shanghai, China
| | - Qi Zhang
- Department of Chemistry, Fudan University Shanghai, China
| |
Collapse
|
25
|
Physiology, Biochemistry, and Applications of F420- and Fo-Dependent Redox Reactions. Microbiol Mol Biol Rev 2016; 80:451-93. [PMID: 27122598 DOI: 10.1128/mmbr.00070-15] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
5-Deazaflavin cofactors enhance the metabolic flexibility of microorganisms by catalyzing a wide range of challenging enzymatic redox reactions. While structurally similar to riboflavin, 5-deazaflavins have distinctive and biologically useful electrochemical and photochemical properties as a result of the substitution of N-5 of the isoalloxazine ring for a carbon. 8-Hydroxy-5-deazaflavin (Fo) appears to be used for a single function: as a light-harvesting chromophore for DNA photolyases across the three domains of life. In contrast, its oligoglutamyl derivative F420 is a taxonomically restricted but functionally versatile cofactor that facilitates many low-potential two-electron redox reactions. It serves as an essential catabolic cofactor in methanogenic, sulfate-reducing, and likely methanotrophic archaea. It also transforms a wide range of exogenous substrates and endogenous metabolites in aerobic actinobacteria, for example mycobacteria and streptomycetes. In this review, we discuss the physiological roles of F420 in microorganisms and the biochemistry of the various oxidoreductases that mediate these roles. Particular focus is placed on the central roles of F420 in methanogenic archaea in processes such as substrate oxidation, C1 pathways, respiration, and oxygen detoxification. We also describe how two F420-dependent oxidoreductase superfamilies mediate many environmentally and medically important reactions in bacteria, including biosynthesis of tetracycline and pyrrolobenzodiazepine antibiotics by streptomycetes, activation of the prodrugs pretomanid and delamanid by Mycobacterium tuberculosis, and degradation of environmental contaminants such as picrate, aflatoxin, and malachite green. The biosynthesis pathways of Fo and F420 are also detailed. We conclude by considering opportunities to exploit deazaflavin-dependent processes in tuberculosis treatment, methane mitigation, bioremediation, and industrial biocatalysis.
Collapse
|
26
|
Sicoli G, Mouesca JM, Zeppieri L, Amara P, Martin L, Barra AL, Fontecilla-Camps JC, Gambarelli S, Nicolet Y. Fine-tuning of a radical-based reaction by radical S-adenosyl-L-methionine tryptophan lyase. Science 2016; 351:1320-3. [DOI: 10.1126/science.aad8995] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
27
|
Ji X, Li Y, Jia Y, Ding W, Zhang Q. Mechanistic Insights into the RadicalS-adenosyl-l-methionine Enzyme NosL From a Substrate Analogue and the Shunt Products. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509900] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xinjian Ji
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Youli Jia
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Wei Ding
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
28
|
Ji X, Li Y, Jia Y, Ding W, Zhang Q. Mechanistic Insights into the RadicalS-adenosyl-l-methionine Enzyme NosL From a Substrate Analogue and the Shunt Products. Angew Chem Int Ed Engl 2016; 55:3334-7. [DOI: 10.1002/anie.201509900] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Xinjian Ji
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Youli Jia
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Wei Ding
- Department of Chemistry; Fudan University; Shanghai 200433 China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering; Gansu Province Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
29
|
Benjdia A, Guillot A, Lefranc B, Vaudry H, Leprince J, Berteau O. Thioether bond formation by SPASM domain radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis. Chem Commun (Camb) 2016; 52:6249-6252. [DOI: 10.1039/c6cc01317a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radical SAM enzyme AlbA has been reported to catalyze the formation of a thioether bond in the antibiotic subtilosin A. By modeling, biochemical and synthetic approaches, we propose novel mechanistic perspectives on this emerging group of enzymes.
Collapse
Affiliation(s)
- Alhosna Benjdia
- Micalis Institute, ChemSyBio
- INRA
- AgroParisTech
- Université Paris-Saclay
- 78350 Jouy-en-Josas
| | - Alain Guillot
- Micalis Institute, ChemSyBio
- INRA
- AgroParisTech
- Université Paris-Saclay
- 78350 Jouy-en-Josas
| | - Benjamin Lefranc
- INSERM U982
- F-76821 Mont-Saint-Aignan
- France
- Institute for Research and Innovation in Biomedicine (IRIB)
- Regional Platform for Cell Imaging
| | - Hubert Vaudry
- INSERM U982
- F-76821 Mont-Saint-Aignan
- France
- Institute for Research and Innovation in Biomedicine (IRIB)
- Regional Platform for Cell Imaging
| | - Jérôme Leprince
- INSERM U982
- F-76821 Mont-Saint-Aignan
- France
- Institute for Research and Innovation in Biomedicine (IRIB)
- Regional Platform for Cell Imaging
| | - Olivier Berteau
- Micalis Institute, ChemSyBio
- INRA
- AgroParisTech
- Université Paris-Saclay
- 78350 Jouy-en-Josas
| |
Collapse
|
30
|
Ji X, Liu WQ, Yuan S, Yin Y, Ding W, Zhang Q. Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions. Chem Commun (Camb) 2016; 52:10555-8. [DOI: 10.1039/c6cc05661j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Radical SAM-dependent amine dehydrogenation of tryptophan andl–tyrosine has resulted from the 5′-deoxyadenosyl radical-mediated hydrogen abstraction from the Cα of the substrates.
Collapse
Affiliation(s)
- Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wan-Qiu Liu
- Department of Chemistry
- Fudan University
- Shanghai
- China
- School of Life Sciences
| | - Shuguang Yuan
- Institute of Chemical Sciences and Engineering
- Ecole Polytechnique Fédérale de Lausanne (EPFL)
- Lausanne
- Switzerland
| | - Yue Yin
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Wei Ding
- Department of Chemistry
- Fudan University
- Shanghai
- China
- School of Life Sciences
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
| |
Collapse
|
31
|
Benjdia A, Pierre S, Gherasim C, Guillot A, Carmona M, Amara P, Banerjee R, Berteau O. The thiostrepton A tryptophan methyltransferase TsrM catalyses a cob(II)alamin-dependent methyl transfer reaction. Nat Commun 2015; 6:8377. [PMID: 26456915 PMCID: PMC4632189 DOI: 10.1038/ncomms9377] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 08/17/2015] [Indexed: 11/09/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a novel class of natural products including several antibiotics and bacterial toxins. In countless RiPP biosynthetic pathways, cobalamin-dependent radical SAM (B12/rSAM) enzymes play a pivotal role. In the biosynthetic pathway of the antibiotic and anti-cancer agent thiostrepton A, TsrM, a B12/rSAM enzyme, catalyses the transfer of a methyl group to an electrophilic carbon atom of tryptophan. Here we show that methylcob(III)alamin is the probable physiological enzyme cofactor, and cob(II)alamin rather than cob(I)alamin is a key reaction intermediate. Furthermore, we establish that TsrM and a triple-alanine mutant alkylate cob(II)alamin efficiently leading to the synthesis of MeCbl. Exploiting TsrM substrate ambiguity, we demonstrate that TsrM does not catalyse substrate H-atom abstraction like most radical SAM enzymes. Based on these data, we propose an unprecedented radical-based C-methylation mechanism, which further expands the chemical versatility of rSAM enzymes.
Collapse
Affiliation(s)
- Alhosna Benjdia
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Stéphane Pierre
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Carmen Gherasim
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Alain Guillot
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Manon Carmona
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| | - Patricia Amara
- Metalloproteins Unit, Institut de Biologie Structurale, UMR5075, CEA, CNRS, Univ. Grenoble-Alpes. 71, Avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
| | - Olivier Berteau
- INRA, ChemSyBio, UMR 1319 Micalis, F-78350 Jouy-en-Josas, France.,AgroParisTech, ChemSyBio, UMR Micalis, F-78350 Jouy-en-Josas, France
| |
Collapse
|
32
|
Bhandari DM, Xu H, Nicolet Y, Fontecilla-Camps JC, Begley TP. Tryptophan Lyase (NosL): Mechanistic Insights from Substrate Analogues and Mutagenesis. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00764] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dhananjay M. Bhandari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Hui Xu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yvain Nicolet
- Metalloproteins
Unit, Institut de Biologie Structurale UMR5075, CEA, CNRS, Université Grenoble-Alpes 71, Avenue des Martyrs, CS 10090, 38044 Grenoble cedex 9, France
| | - Juan C. Fontecilla-Camps
- Metalloproteins
Unit, Institut de Biologie Structurale UMR5075, CEA, CNRS, Université Grenoble-Alpes 71, Avenue des Martyrs, CS 10090, 38044 Grenoble cedex 9, France
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
33
|
Ji X, Li Y, Ding W, Zhang Q. Substrate-Tuned Catalysis of the RadicalS-Adenosyl-L-Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis. Angew Chem Int Ed Engl 2015; 54:9021-4. [DOI: 10.1002/anie.201503976] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/23/2022]
|
34
|
Ji X, Li Y, Ding W, Zhang Q. Substrate-Tuned Catalysis of the RadicalS-Adenosyl-L-Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|