1
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Xian F, Yang L, Ye H, Xu J, Yue X, Wang X. Revealing the Mechanism of Aroma Production Driven by High Salt Stress in Trichomonascus ciferrii WLW. Foods 2024; 13:1593. [PMID: 38890822 PMCID: PMC11172348 DOI: 10.3390/foods13111593] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 06/20/2024] Open
Abstract
Douchi is a Chinese traditional fermented food with a unique flavor. Methyl anthranilate (MA) plays an important role in formation of this flavor. However, the complicated relationship between the MA formation and the metabolic mechanism of the key functional microorganisms remains unclear. Here, we elucidated the response mechanism of aroma production driven by high salt stress in Trichomonascus ciferrii WLW (T. ciferrii WLW), which originates from the douchi fermentation process. The highest production of MA was obtained in a 10% NaCl environment. The enhanced expression of the key enzyme genes of the pentose phosphate pathway and shikimic acid pathway directed carbon flow toward aromatic amino acid synthesis and helped sustain an increased expression of metK to synthesize a large amount of the methyl donor S-adenosylmethionine, which promoted methyl anthranilate yield. This provides a theoretical basis for in-depth research on the applications of the flavor formation mechanisms of fermented foods.
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Affiliation(s)
- Fangying Xian
- School of Life Science (Health), Jiangxi Normal University, Nanchang 330022, China; (F.X.); (L.Y.); (H.Y.); (J.X.)
| | - Lin Yang
- School of Life Science (Health), Jiangxi Normal University, Nanchang 330022, China; (F.X.); (L.Y.); (H.Y.); (J.X.)
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Huaqing Ye
- School of Life Science (Health), Jiangxi Normal University, Nanchang 330022, China; (F.X.); (L.Y.); (H.Y.); (J.X.)
| | - Jinlin Xu
- School of Life Science (Health), Jiangxi Normal University, Nanchang 330022, China; (F.X.); (L.Y.); (H.Y.); (J.X.)
| | - Xiaoping Yue
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Xiaolan Wang
- School of Life Science (Health), Jiangxi Normal University, Nanchang 330022, China; (F.X.); (L.Y.); (H.Y.); (J.X.)
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2
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Lee YH, Yeh YC, Fan PH, Zhong A, Ruszczycky MW, Liu HW. Changing Fates of the Substrate Radicals Generated in the Active Sites of the B 12-Dependent Radical SAM Enzymes OxsB and AlsB. J Am Chem Soc 2023; 145:3656-3664. [PMID: 36719327 PMCID: PMC9940012 DOI: 10.1021/jacs.2c12953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OxsB is a B12-dependent radical SAM enzyme that catalyzes the oxidative ring contraction of 2'-deoxyadenosine 5'-phosphate to the dehydrogenated, oxetane containing precursor of oxetanocin A phosphate. AlsB is a homologue of OxsB that participates in a similar reaction during the biosynthesis of albucidin. Herein, OxsB and AlsB are shown to also catalyze radical mediated, stereoselective C2'-methylation of 2'-deoxyadenosine monophosphate. This reaction proceeds with inversion of configuration such that the resulting product also possesses a C2' hydrogen atom available for abstraction. However, in contrast to methylation, subsequent rounds of catalysis result in C-C dehydrogenation of the newly added methyl group to yield a 2'-methylidene followed by radical addition of a 5'-deoxyadenosyl moiety to produce a heterodimer. These observations expand the scope of reactions catalyzed by B12-dependent radical SAM enzymes and emphasize the susceptibility of radical intermediates to bifurcation along different reaction pathways even within the highly organized active site of an enzyme.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Cheng Yeh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Po-Hsun Fan
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Aoshu Zhong
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Mark W. Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States; Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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3
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Nguyen TQ, Nicolet Y. Structure and Catalytic Mechanism of Radical SAM Methylases. Life (Basel) 2022; 12:1732. [PMID: 36362886 PMCID: PMC9692996 DOI: 10.3390/life12111732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/14/2023] Open
Abstract
Methyl transfer is essential in myriad biological pathways found across all domains of life. Unlike conventional methyltransferases that catalyze this reaction through nucleophilic substitution, many members of the radical S-adenosyl-L-methionine (SAM) enzyme superfamily use radical-based chemistry to methylate unreactive carbon centers. These radical SAM methylases reductively cleave SAM to generate a highly reactive 5'-deoxyadenosyl radical, which initiates a broad range of transformations. Recently, crystal structures of several radical SAM methylases have been determined, shedding light on the unprecedented catalytic mechanisms used by these enzymes to overcome the substantial activation energy barrier of weakly nucleophilic substrates. Here, we review some of the discoveries on this topic over the last decade, focusing on enzymes for which three-dimensional structures are available to identify the key players in the mechanisms, highlighting the dual function of SAM as a methyl donor and a 5'-deoxyadenosyl radical or deprotonating base source. We also describe the role of the protein matrix in orchestrating the reaction through different strategies to catalyze such challenging methylations.
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Affiliation(s)
| | - Yvain Nicolet
- Metalloproteins Unit, Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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4
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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5
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Bridwell-Rabb J, Li B, Drennan CL. Cobalamin-Dependent Radical S-Adenosylmethionine Enzymes: Capitalizing on Old Motifs for New Functions. ACS BIO & MED CHEM AU 2022; 2:173-186. [PMID: 35726326 PMCID: PMC9204698 DOI: 10.1021/acsbiomedchemau.1c00051] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 01/21/2023]
Abstract
The members of the radical S-adenosylmethionine (SAM) enzyme superfamily are responsible for catalyzing a diverse set of reactions in a multitude of biosynthetic pathways. Many members of this superfamily accomplish their transformations using the catalytic power of a 5'-deoxyadenosyl radical (5'-dAdo•), but there are also enzymes within this superfamily that bind auxiliary cofactors and extend the catalytic repertoire of SAM. In particular, the cobalamin (Cbl)-dependent class synergistically uses Cbl to facilitate challenging methylation and radical rearrangement reactions. Despite identification of this class by Sofia et al. 20 years ago, the low sequence identity between members has led to difficulty in predicting function of uncharacterized members, pinpointing catalytic residues, and elucidating reaction mechanisms. Here, we capitalize on the three recent structures of Cbl-dependent radical SAM enzymes that use common cofactors to facilitate ring contraction as well as radical-based and non-radical-based methylation reactions. With these three structures as a framework, we describe how the Cbl-dependent radical SAM enzymes repurpose the traditional SAM- and Cbl-binding motifs to form an active site where both Cbl and SAM can participate in catalysis. In addition, we describe how, in some cases, the classic SAM- and Cbl-binding motifs support the diverse functionality of this enzyme class, and finally, we define new motifs that are characteristic of Cbl-dependent radical SAM enzymes.
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Affiliation(s)
- Jennifer Bridwell-Rabb
- Department
of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109, United States,
| | - Bin Li
- Department
of Chemistry, University of Michigan, 930 N University Avenue, Ann Arbor, Michigan 48109, United States
| | - Catherine L. Drennan
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States,Howard
Hughes Medical Institute, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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6
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Dill Z, Li B, Bridwell-Rabb J. Purification and structural elucidation of a cobalamin-dependent radical SAM enzyme. Methods Enzymol 2022; 669:91-116. [PMID: 35644182 DOI: 10.1016/bs.mie.2021.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster, SAM, and Cbl to carry out remarkable catalytic feats in a large number of biosynthetic pathways. However, despite the abundance of annotated Cbl-dependent radical SAM enzymes, relatively few molecular details exist regarding how these enzymes function. Traditionally, challenges associated with purifying and reconstituting Cbl-dependent radical SAM enzymes have hindered biochemical studies aimed at elucidating the structures and mechanisms of these enzymes. Herein, we describe a bottom-up approach that was used to crystallize OxsB, learn about the overall architecture of a Cbl-dependent radical SAM enzyme, and facilitate mechanistic studies. We report lessons learned from the crystallization of different states of OxsB, including the apo-, selenomethionine (SeMet)-labeled, and fully reconstituted form of OxsB that has a [4Fe-4S] cluster, SAM, and Cbl bound. Further, we suggest that, when appropriate, this bottom-up method can be used to facilitate studies on enzymes in this class for which there are challenges associated with purifying and reconstituting the active enzyme.
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Affiliation(s)
- Zerick Dill
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States
| | - Bin Li
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI, United States.
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7
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Wu R, Ding W, Zhang Q. Consecutive Methylation catalyzed by
TsrM
, an atypical Class B radical
SAM
methylase. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200174] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Runze Wu
- Department of Chemistry Fudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of Chemistry Fudan University Shanghai 200433 China
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8
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Ulrich EC, Drennan CL. The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. J Am Chem Soc 2022; 144:5673-5684. [PMID: 35344653 PMCID: PMC8992657 DOI: 10.1021/jacs.1c12064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cobalamin (Cbl)-dependent S-adenosyl-l-methionine (AdoMet) radical methylases are known for their use of a dual cofactor system to perform challenging radical methylation reactions at unactivated carbon and phosphorus centers. These enzymes are part of a larger subgroup of Cbl-dependent AdoMet radical enzymes that also perform difficult ring contractions and radical rearrangements. This subgroup is a largely untapped reservoir of diverse chemistry that requires steady efforts in biochemical and structural characterization to reveal its complexity. In this Perspective, we highlight the significant efforts over many years to elucidate the function, mechanism, and structure of TsrM, an unexpected nonradical methylase in this subgroup. We also discuss recent achievements in characterizing radical methylase subgroup members that exemplify how key tools in mechanistic enzymology are valuable time and again. Finally, we identify recent enzyme activity studies that have made use of bioinformatic analyses to expand our definition of the subgroup. Additional breakthroughs in radical (and nonradical) enzymatic chemistry and challenging transformations from the unexplored space of this subgroup are undoubtedly on the horizon.
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Affiliation(s)
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Structure of a B 12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 2022; 602:343-348. [PMID: 35110734 DOI: 10.1038/s41586-021-04392-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022]
Abstract
Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic1. The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of β-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the β-lactamase active site2. The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes3. These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.
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10
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Zhong A, Lee YH, Liu YN, Liu HW. Biosynthesis of Oxetanocin-A Includes a B 12-Dependent Radical SAM Enzyme That Can Catalyze both Oxidative Ring Contraction and the Demethylation of SAM. Biochemistry 2021; 60:537-546. [PMID: 33560833 DOI: 10.1021/acs.biochem.0c00915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxetanocin-A is an antitumor, antiviral, and antibacterial nucleoside. It is biosynthesized via the oxidative ring contraction of a purine nucleoside co-opted from primary metabolism. This reaction is catalyzed by a B12-dependent radical S-adenosyl-l-methionine (SAM) enzyme, OxsB, and a phosphohydrolase, OxsA. Previous experiments showed that the product of the OxsB/OxsA-catalyzed reaction is an oxetane aldehyde produced alongside an uncharacterized byproduct. Experiments reported herein reveal that OxsB/OxsA complex formation is crucial for the ring contraction reaction and that reduction of the aldehyde intermediate is catalyzed by a nonspecific dehydrogenase from the general cellular pool. In addition, the byproduct is identified as a 1,3-thiazinane adduct between the aldehyde and l-homocysteine. While homocysteine was never included in the OxsB/OxsA assays, the data suggest that it can be generated from SAM via S-adenosyl-l-homocysteine (SAH). Further study revealed that conversion of SAM to SAH is facilitated by OxsB; however, the subsequent conversion of SAH to homocysteine is due to protein contaminants that co-purify with OxsA. Nevertheless, the observed demethylation of SAM to SAH suggests possible methyltransferase activity of OxsB, and substrate methylation was indeed detected in the OxsB-catalyzed reaction. This work is significant because it not only completes the description of the oxetanocin-A biosynthetic pathway but also suggests that OxsB may be capable of methyltransferase activity.
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11
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Knox HL, Chen PYT, Blaszczyk AJ, Mukherjee A, Grove TL, Schwalm EL, Wang B, Drennan CL, Booker SJ. Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat Chem Biol 2021; 17:485-491. [PMID: 33462497 PMCID: PMC7990684 DOI: 10.1038/s41589-020-00717-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
TsrM methylates C2 of the indole ring of L-tryptophan (Trp) during the biosynthesis of the quinaldic acid moiety of thiostrepton. It is annotated as a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase; however, TsrM does not reductively cleave SAM to the universal 5ʹ-deoxyadenosyl 5ʹ-radical intermediate, a hallmark of radical-SAM (RS) enzymes. Herein, we report structures of TsrM from Kitasatospora setae, the first of a cobalamin-dependent radical SAM methylase. Unexpectedly, the structures show an essential arginine residue that resides in the proximal coordination sphere of the cobalamin cofactor and a [4Fe–4S] cluster that is ligated by a glutamyl residue and three cysteines in a canonical CxxxCxxC RS motif. Structures in the presence of substrates suggest a substrate-assisted mechanism of catalysis, wherein the carboxylate group of SAM serves as a general base to deprotonate N1 of the tryptophan substrate, facilitating formation of a C2 carbanion. The first crystal structures of a cobalamin-dependent radical SAM methylase reveal an unexpected mode of methylation.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Catalent Pharma Solutions, Gaithersburg, MD, USA
| | - Arnab Mukherjee
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erica L Schwalm
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.,Merck & Co., Inc., Rahway, NJ, USA
| | - Bo Wang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA.
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12
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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: 384] [Impact Index Per Article: 128.0] [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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13
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Vinogradov AA, Suga H. Introduction to Thiopeptides: Biological Activity, Biosynthesis, and Strategies for Functional Reprogramming. Cell Chem Biol 2020; 27:1032-1051. [PMID: 32698017 DOI: 10.1016/j.chembiol.2020.07.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
Thiopeptides (also known as thiazolyl peptides) are structurally complex natural products with rich biological activities. Known for over 70 years for potent killing of Gram-positive bacteria, thiopeptides are experiencing a resurgence of interest in the last decade, primarily brought about by the genomic revolution of the 21st century. Every area of thiopeptide research-from elucidating their biological function and biosynthesis to expanding their structural diversity through genome mining-has made great strides in recent years. These advances lay the foundation for and inspire novel strategies for thiopeptide engineering. Accordingly, a number of diverse approaches are being actively pursued in the hope of developing the next generation of natural-product-inspired therapeutics. Here, we review the contemporary understanding of thiopeptide biological activities, biosynthetic pathways, and approaches to structural and functional reprogramming, with a special focus on the latter.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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14
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Wang Y, Begley TP. Mechanistic Studies on CysS - A Vitamin B 12-Dependent Radical SAM Methyltransferase Involved in the Biosynthesis of the tert-Butyl Group of Cystobactamid. J Am Chem Soc 2020; 142:9944-9954. [PMID: 32374991 DOI: 10.1021/jacs.9b06454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) methyltransferases catalyze methylation reactions at non-nucleophilic centers in a wide range of substrates. CysS is a Cbl-dependent radical SAM methyltransferase involved in cystobactamid biosynthesis. This enzyme catalyzes the sequential methylation of a methoxy group to form ethoxy, i-propoxy, s-butoxy, and t-butoxy groups on a p-aminobenzoate peptidyl carrier protein thioester intermediate. This biosynthetic strategy enables the host myxobacterium to biosynthesize a combinatorial antibiotic library of 25 cystobactamid analogues. In this Article, we describe three experiments to elucidate how CysS uses Cbl, SAM, and a [4Fe-4S] cluster to catalyze iterative methylation reactions: a cyclopropylcarbinyl rearrangement was used to trap the substrate radical and to estimate the rate of the radical substitution reaction involved in the methyl transfer; a bromoethoxy analogue was used to explore the active site topography; and deuterium isotope effects on the hydrogen atom abstraction by the adenosyl radical were used to investigate the kinetic significance of the hydrogen atom abstraction. On the basis of these experiments, a revised mechanism for CysS is proposed.
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Affiliation(s)
- Yuanyou Wang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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15
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Wang SC. Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis. Nat Prod Rep 2019; 35:707-720. [PMID: 30079906 DOI: 10.1039/c7np00059f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.
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Affiliation(s)
- Susan C Wang
- Case Western Reserve University School of Medicine, Department of Biochemistry, USA.
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16
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Blaszczyk AJ, Knox HL, Booker SJ. Understanding the role of electron donors in the reaction catalyzed by Tsrm, a cobalamin-dependent radical S-adenosylmethionine methylase. J Biol Inorg Chem 2019; 24:831-839. [PMID: 31350635 DOI: 10.1007/s00775-019-01689-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
The cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme TsrM catalyzes the methylation of C2 of L-tryptophan to form 2-methyltryptophan during the biosynthesis of thiostrepton A. Although TsrM is a member of the radical SAM superfamily, unlike all other annotated members, it does not catalyze a reductive cleavage of SAM to a 5'-deoxyadenosyl 5'-radical intermediate. In fact, it has been proposed that TsrM catalyzes its reaction through two polar nucleophilic displacements, with its cobalamin cofactor cycling directly between methylcobalamin (MeCbl) and cob(I)alamin. Nevertheless, the enzyme has been stated to require the action of a reductant, which can be satisfied by dithiothreitol. By contrast, all other annotated RS enzymes require a reductant that exhibits a much lower reduction potential, which is necessary for the reductive cleavage of SAM. Herein, we show that TsrM can catalyze multiple turnovers in the absence of any reducing agent, but only when it is pre-loaded with MeCbl. When hydroxocobalamin (OHCbl) or cob(II)alamin is bound to TsrM, a reductant is required to convert it to cob(I)alamin, which can acquire a methyl group directly from SAM. Our studies suggest that TsrM uses an external reductant to prime its reaction by converting bound OHCbl or cob(II)alamin to MeCbl, and to regenerate the MeCbl form of the cofactor upon adventitious oxidation of the cob(I)alamin intermediate to cob(II)alamin.
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Affiliation(s)
- Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hayley L Knox
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, 16802, USA.
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17
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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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18
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Ruszczycky MW, Zhong A, Liu HW. Following the electrons: peculiarities in the catalytic cycles of radical SAM enzymes. Nat Prod Rep 2019; 35:615-621. [PMID: 29485151 DOI: 10.1039/c7np00058h] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radical SAM enzymes use S-adenosyl-l-methionine as an oxidant to initiate radical-mediated transformations that would otherwise not be possible with Lewis acid/base chemistry alone. These reactions are either redox neutral or oxidative leading to certain expectations regarding the role of SAM as either a reusable cofactor or the ultimate electron acceptor during each turnover. However, these expectations are frequently not realized resulting in fundamental questions regarding the redox handling and movement of electrons associated with these biological catalysts. Herein we provide a focused perspective on several of these questions and associated hypotheses with an emphasis on recently discovered radical SAM enzymes.
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Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, USA.
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19
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Schnepel C, Kemker I, Sewald N. One-Pot Synthesis of d-Halotryptophans by Dynamic Stereoinversion Using a Specific l-Amino Acid Oxidase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b04944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian Schnepel
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Isabell Kemker
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
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20
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Wang B, Blaszczyk A, Knox HL, Zhou S, Blaesi EJ, Krebs C, Wang RX, Booker SJ. Stereochemical and Mechanistic Investigation of the Reaction Catalyzed by Fom3 from Streptomyces fradiae, a Cobalamin-Dependent Radical S-Adenosylmethionine Methylase. Biochemistry 2018; 57:4972-4984. [PMID: 30036047 PMCID: PMC6554712 DOI: 10.1021/acs.biochem.8b00693] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fom3, a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase, has recently been shown to catalyze the methylation of carbon 2″ of cytidylyl-2-hydroxyethylphosphonate (HEP-CMP) to form cytidylyl-2-hydroxypropylphosphonate (HPP-CMP) during the biosynthesis of fosfomycin, a broad-spectrum antibiotic. It has been hypothesized that a 5'-deoxyadenosyl 5'-radical (5'-dA•) generated from the reductive cleavage of SAM abstracts a hydrogen atom from HEP-CMP to prime the substrate for addition of a methyl group from methylcobalamin (MeCbl); however, the mechanistic details of this reaction remain elusive. Moreover, it has been reported that Fom3 catalyzes the methylation of HEP-CMP to give a mixture of the ( S)-HPP and ( R)-HPP stereoisomers, which is rare for an enzyme-catalyzed reaction. Herein, we describe a detailed biochemical investigation of a Fom3 that is purified with 1 equiv of its cobalamin cofactor bound, which is almost exclusively in the form of MeCbl. Electron paramagnetic resonance and Mössbauer spectroscopies confirm that Fom3 contains one [4Fe-4S] cluster. Using deuterated enantiomers of HEP-CMP, we demonstrate that the 5'-dA• generated by Fom3 abstracts the C2″- pro-R hydrogen of HEP-CMP and that methyl addition takes place with inversion of configuration to yield solely ( S)-HPP-CMP. Fom3 also sluggishly converts cytidylyl-ethylphosphonate to the corresponding methylated product but more readily acts on cytidylyl-2-fluoroethylphosphonate, which exhibits a lower C2″ homolytic bond-dissociation energy. Our studies suggest a mechanism in which the substrate C2″ radical, generated upon hydrogen atom abstraction by the 5'-dA•, directly attacks MeCbl to transfer a methyl radical (CH3•) rather than a methyl cation (CH3+), directly forming cob(II)alamin in the process.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Anthony Blaszczyk
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hayley L. Knox
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shengbin Zhou
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth J. Blaesi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Roy X. Wang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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21
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Kincannon WM, Bruender NA, Bandarian V. A Radical Clock Probe Uncouples H Atom Abstraction from Thioether Cross-Link Formation by the Radical S-Adenosyl-l-methionine Enzyme SkfB. Biochemistry 2018; 57:4816-4823. [PMID: 29965747 PMCID: PMC6094349 DOI: 10.1021/acs.biochem.8b00537] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Sporulation
killing factor (SKF) is a ribosomally synthesized and
post-translationally modified peptide (RiPP) produced by Bacillus. SKF contains a thioether cross-link between the α-carbon
at position 40 and the thiol of Cys32, introduced by a member of the
radical S-adenosyl-l-methionine (SAM) superfamily,
SkfB. Radical SAM enzymes employ a 4Fe–4S cluster to bind and
reductively cleave SAM to generate a 5′-deoxyadenosyl radical.
SkfB utilizes this radical intermediate to abstract the α-H
atom at Met40 to initiate cross-linking. In addition to the cluster
that binds SAM, SkfB also has an auxiliary cluster, the function of
which is not known. We demonstrate that a substrate analogue with
a cyclopropylglycine (CPG) moiety replacing the wild-type Met40 side
chain forgoes thioether cross-linking for an alternative radical ring
opening of the CPG side chain. The ring opening reaction also takes
place with a catalytically inactive SkfB variant in which the auxiliary
Fe–S cluster is absent. Therefore, the CPG-containing peptide
uncouples H atom abstraction from thioether bond formation, limiting
the role of the auxiliary cluster to promoting thioether cross-link
formation. CPG proves to be a valuable tool for uncoupling H atom
abstraction from peptide modification in RiPP maturases and demonstrates
potential to leverage RS enzyme reactivity to create noncanonical
amino acids.
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Affiliation(s)
- William M Kincannon
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Nathan A Bruender
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - Vahe Bandarian
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
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22
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Iterative Methylations Resulting in the Biosynthesis of the t-Butyl Group Catalyzed by a B 12-Dependent Radical SAM Enzyme in Cystobactamid Biosynthesis. Methods Enzymol 2018; 606:199-216. [PMID: 30097093 DOI: 10.1016/bs.mie.2018.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
B12-dependent radical SAM enzymes that can perform methylations on sp3 carbon centers are important for functional diversity and regulation of biological activity in several nonribosomal peptides. Detailed studies on these enzymes are hindered by the complexity of the substrates and low levels of expression of active enzymes. CysS can catalyze iterative methylations of a methoxybenzene moiety during the biosynthesis of the cystobactamids. Here, we describe the overexpression, purification, substrate identification, and mechanism of this enzyme.
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23
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Yan F, Auerbach D, Chai Y, Keller L, Tu Q, Hüttel S, Glemser A, Grab HA, Bach T, Zhang Y, Müller R. Biosynthesis and Heterologous Production of Vioprolides: Rational Biosynthetic Engineering and Unprecedented 4‐Methylazetidinecarboxylic Acid Formation. Angew Chem Int Ed Engl 2018; 57:8754-8759. [DOI: 10.1002/anie.201802479] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/08/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Fu Yan
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - David Auerbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Yi Chai
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Lena Keller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Qiang Tu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Stephan Hüttel
- Helmholtz Centre for Infection Research Department of Microbial Drugs Braunschweig Germany
| | - Amelie Glemser
- Helmholtz Centre for Infection Research Department of Microbial Drugs Braunschweig Germany
| | - Hanusch A. Grab
- Lehrstuhl für Organische Chemie I Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Thorsten Bach
- Lehrstuhl für Organische Chemie I Technische Universität München Lichtenbergstrasse 4 85747 Garching Germany
| | - Youming Zhang
- Shandong University-Helmholtz Joint Institute of Biotechnology State Key Laboratory of Microbial Technology School of Life Science Shandong University Qingdao P. R. China
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Center for Infection Research, and Department of Pharmacy Saarland University Campus Building E8.1 66123 Saarbrücken Germany
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24
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Yan F, Auerbach D, Chai Y, Keller L, Tu Q, Hüttel S, Glemser A, Grab HA, Bach T, Zhang Y, Müller R. Biosynthese und heterologe Expression der Vioprolide: rationale gentechnische Eingriffe in die Biosynthese und 4‐Methylazetidincarbonsäure‐Bildung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Fu Yan
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - David Auerbach
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Yi Chai
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Lena Keller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Qiang Tu
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
| | - Stephan Hüttel
- Helmholtz-Zentrum für Infektionsforschung (HZI) Abteilung Mikrobielle Wirkstoffe Braunschweig Deutschland
| | - Amelie Glemser
- Helmholtz-Zentrum für Infektionsforschung (HZI) Abteilung Mikrobielle Wirkstoffe Braunschweig Deutschland
| | - Hanusch A. Grab
- Lehrstuhl für Organische Chemie I Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Thorsten Bach
- Lehrstuhl für Organische Chemie I Technische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Youming Zhang
- Shandong University-Helmholtz Joint Institute of Biotechnology State Key Laboratory of Microbial Technology School of Life Science Shandong University Qingdao VR China
| | - Rolf Müller
- Helmholtz-Institut für Pharmazeutische Forschung Saarland (HIPS) Helmholtz-Zentrum für Infektionsforschung und Pharmazeutische Biotechnologie Universität des Saarlands Campus Gebäude E8.1 66123 Saarbrücken Deutschland
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25
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Lanz ND, Blaszczyk AJ, McCarthy EL, Wang B, Wang RX, Jones BS, Booker SJ. Enhanced Solubilization of Class B Radical S-Adenosylmethionine Methylases by Improved Cobalamin Uptake in Escherichia coli. Biochemistry 2018; 57:1475-1490. [PMID: 29298049 DOI: 10.1021/acs.biochem.7b01205] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The methylation of unactivated carbon and phosphorus centers is a burgeoning area of biological chemistry, especially given that such reactions constitute key steps in the biosynthesis of numerous enzyme cofactors, antibiotics, and other natural products of clinical value. These kinetically challenging reactions are catalyzed exclusively by enzymes in the radical S-adenosylmethionine (SAM) superfamily and have been grouped into four classes (A-D). Class B radical SAM (RS) methylases require a cobalamin cofactor in addition to the [4Fe-4S] cluster that is characteristic of RS enzymes. However, their poor solubility upon overexpression and their generally poor turnover has hampered detailed in vitro studies of these enzymes. It has been suggested that improper folding, possibly caused by insufficient cobalamin during their overproduction in Escherichia coli, leads to formation of inclusion bodies. Herein, we report our efforts to improve the overproduction of class B RS methylases in a soluble form by engineering a strain of E. coli to take in more cobalamin. We cloned five genes ( btuC, btuE, btuD, btuF, and btuB) that encode proteins that are responsible for cobalamin uptake and transport in E. coli and co-expressed these genes with those that encode TsrM, Fom3, PhpK, and ThnK, four class B RS methylases that suffer from poor solubility during overproduction. This strategy markedly enhances the uptake of cobalamin into the cytoplasm and improves the solubility of the target enzymes significantly.
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26
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Benjdia A, Balty C, Berteau O. Radical SAM Enzymes in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides (RiPPs). Front Chem 2017; 5:87. [PMID: 29167789 PMCID: PMC5682303 DOI: 10.3389/fchem.2017.00087] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/11/2017] [Indexed: 11/13/2022] Open
Abstract
Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large and diverse family of natural products. They possess interesting biological properties such as antibiotic or anticancer activities, making them attractive for therapeutic applications. In contrast to polyketides and non-ribosomal peptides, RiPPs derive from ribosomal peptides and are post-translationally modified by diverse enzyme families. Among them, the emerging superfamily of radical SAM enzymes has been shown to play a major role. These enzymes catalyze the formation of a wide range of post-translational modifications some of them having no counterparts in living systems or synthetic chemistry. The investigation of radical SAM enzymes has not only illuminated unprecedented strategies used by living systems to tailor peptides into complex natural products but has also allowed to uncover novel RiPP families. In this review, we summarize the current knowledge on radical SAM enzymes catalyzing RiPP post-translational modifications and discuss their mechanisms and growing importance notably in the context of the human microbiota.
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Affiliation(s)
- Alhosna Benjdia
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémence Balty
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Berteau
- Micalis Institute, ChemSyBio, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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27
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Kim HJ, Liu YN, McCarty RM, Liu HW. Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J Am Chem Soc 2017; 139:16084-16087. [PMID: 29091410 DOI: 10.1021/jacs.7b09890] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Many cobalamin (Cbl)-dependent radical S-adenosyl-l-methionine (SAM) methyltransferases have been identified through sequence alignment and/or genetic analysis; however, few have been studied in vitro. GenK is one such enzyme that catalyzes methylation of the 6'-carbon of gentamicin X2 (GenX2) to produce G418 during the biosynthesis of gentamicins. Reported herein, several alternative substrates and fluorinated substrate analogs were prepared to investigate the mechanism of methyl transfer from Cbl to the substrate as well as the substrate specificity of GenK. Experiments with deuterated substrates are also shown here to demonstrate that the 6'-pro-R-hydrogen atom of GenX2 is stereoselectively abstracted by the 5'-dAdo· radical and that methylation occurs with retention of configuration at C6'. Based on these observations, a model of GenK catalysis is proposed wherein free rotation of the radical-bearing carbon is prevented and the radical SAM machinery sits adjacent rather than opposite to the Me-Cbl cofactor with respect to the substrate in the enzyme active site.
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Affiliation(s)
- Hak Joong Kim
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yung-Nan Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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28
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Mahanta N, Hudson GA, Mitchell DA. Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis. Biochemistry 2017; 56:5229-5244. [PMID: 28895719 DOI: 10.1021/acs.biochem.7b00771] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) display a diverse range of structures and continue to expand as a natural product class. Accordingly, RiPPs exhibit a wide array of bioactivities, acting as broad and narrow spectrum growth suppressors, antidiabetics, and antinociception and anticancer agents. Because of these properties, and the complex repertoire of post-translational modifications (PTMs) that give rise to these molecules, RiPP biosynthesis has been intensely studied. RiPP biosynthesis often involves enzymes that perform unique chemistry with intriguing reaction mechanisms, which attract chemists and biochemists alike to study and re-engineer these pathways. One particular type of RiPP biosynthetic enzyme is the so-called radical S-adenosylmethionine (rSAM) enzyme, which utilizes radical-based chemistry to install several distinct PTMs. Here, we describe the rSAM enzymes characterized over the past decade that catalyze six reaction types from several RiPP biosynthetic pathways. We present the current state of mechanistic understanding and conclude with possible directions for future characterization of this enzyme family.
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Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Graham A Hudson
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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29
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TsrM as a Model for Purifying and Characterizing Cobalamin-Dependent Radical S-Adenosylmethionine Methylases. Methods Enzymol 2017; 595:303-329. [PMID: 28882204 DOI: 10.1016/bs.mie.2017.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases play vital roles in the de novo biosynthesis of many antibiotics, cofactors, and other important natural products, yet remain an understudied subclass of radical SAM enzymes. In addition to a [4Fe-4S] cluster that is ligated by three cysteine residues, these enzymes also contain an N-terminal cobalamin-binding domain. In vitro studies of these enzymes have been severely limited because many are insoluble or sparingly soluble upon their overproduction in Escherichia coli. This solubility issue has led a number of groups either to purify the protein from inclusion bodies or to purify soluble protein that often lacks proper cofactor incorporation. Herein, we use TsrM as a model to describe methods that we have used to generate soluble protein that is purified in an active form with both cobalamin and [4Fe-4S] cluster cofactors bound. Additionally, we highlight the methods that we developed to characterize the enzyme following purification.
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