1
|
Dashti Y, Mohammadipanah F, Zhang Y, Cerqueira Diaz PM, Vocat A, Zabala D, Fage CD, Romero-Canelon I, Bunk B, Spröer C, Alkhalaf LM, Overmann J, Cole ST, Challis GL. Discovery and Biosynthesis of Persiathiacins: Unusual Polyglycosylated Thiopeptides Active Against Multidrug Resistant Tuberculosis. ACS Infect Dis 2024. [PMID: 39189814 DOI: 10.1021/acsinfecdis.4c00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Thiopeptides are ribosomally biosynthesized and post-translationally modified peptides (RiPPs) that potently inhibit the growth of Gram-positive bacteria by targeting multiple steps in protein biosynthesis. The poor pharmacological properties of thiopeptides, particularly their low aqueous solubility, has hindered their development into clinically useful antibiotics. Antimicrobial activity screens of a library of Actinomycetota extracts led to discovery of the novel polyglycosylated thiopeptides persiathiacins A and B from Actinokineospora sp. UTMC 2448. Persiathiacin A is active against methicillin-resistant Staphylococcus aureus and several Mycobacterium tuberculosis strains, including drug-resistant and multidrug-resistant clinical isolates, and does not significantly affect the growth of ovarian cancer cells at concentrations up to 400 μM. Polyglycosylated thiopeptides are extremely rare and nothing is known about their biosynthesis. Sequencing and analysis of the Actinokineospora sp. UTMC 2448 genome enabled identification of the putative persiathiacin biosynthetic gene cluster (BGC). A cytochrome P450 encoded by this gene cluster catalyzes the hydroxylation of nosiheptide in vitro and in vivo, consistent with the proposal that the cluster directs persiathiacin biosynthesis. Several genes in the cluster encode homologues of enzymes known to catalyze the assembly and attachment of deoxysugars during the biosynthesis of other classes of glycosylated natural products. One of these encodes a glycosyl transferase that was shown to catalyze attachment of a D-glucose residue to nosiheptide in vitro. The discovery of the persiathiacins and their BGC thus provides the basis for the development of biosynthetic engineering approaches to the creation of novel (poly)glycosylated thiopeptide derivatives with enhanced pharmacological properties.
Collapse
Affiliation(s)
- Yousef Dashti
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney NSW 2015, Australia
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455 Tehran, Iran
| | - Yu Zhang
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Daniel Zabala
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Isolda Romero-Canelon
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- School of Pharmacy, Institute of Clinical Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Boyke Bunk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- Technical University of Braunschweig, 38106 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- Technical University of Braunschweig, 38106 Braunschweig, Germany
| | - Lona M Alkhalaf
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
- Technical University of Braunschweig, 38106 Braunschweig, Germany
- German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
- Department of Biochemistry and Molecular Biology, Monash University, Clayton VIC 3168, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton VIC 3168, Australia
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Jäger C, Croft AK. If It Is Hard, It Is Worth Doing: Engineering Radical Enzymes from Anaerobes. Biochemistry 2022; 62:241-252. [PMID: 36121716 PMCID: PMC9850924 DOI: 10.1021/acs.biochem.2c00376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
With a pressing need for sustainable chemistries, radical enzymes from anaerobes offer a shortcut for many chemical transformations and deliver highly sought-after functionalizations such as late-stage C-H functionalization, C-C bond formation, and carbon-skeleton rearrangements, among others. The challenges in handling these oxygen-sensitive enzymes are reflected in their limited industrial exploitation, despite what they may deliver. With an influx of structures and mechanistic understanding, the scope for designed radical enzymes to deliver wanted processes becomes ever closer. Combined with new advances in computational methods and workflows for these complex systems, the outlook for an increased use of radical enzymes in future processes is exciting.
Collapse
|
4
|
Guo S, Wang S, Ma S, Deng Z, Ding W, Zhang Q. Radical SAM-dependent ether crosslink in daropeptide biosynthesis. Nat Commun 2022; 13:2361. [PMID: 35487921 PMCID: PMC9055067 DOI: 10.1038/s41467-022-30084-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/14/2022] [Indexed: 12/15/2022] Open
Abstract
Darobactin is a ribosomally synthesized and post-translationally modified peptide (RiPP), which possesses potent activity against various Gram-negative bacteria. Darobactin features a highly unique bicyclic scaffold, consisting of an ether crosslink between two Trp residues and a C-C crosslink between a Lys and a Trp. Here we report in vivo and in vitro activity of darobactin synthase DarE. We show DarE is a radical S-adenosylmethionine (rSAM) enzyme and is solely responsible for forming the bicyclic scaffold of darobactin. DarE mainly produced the ether-crosslinked product in vitro, and when the assay was performed in H218O, apparent 18O incorporation was observed into the ether-crosslinked product. These observations suggested an rSAM-dependent process in darobactin biosynthesis, involving a highly unusual oxygen insertion step from a water molecule and subsequent O-H and C-H activations. Genome mining analysis demonstrates the diversity of darobactin-like biosynthetic gene clusters, a subclade of which likely encode monocyclic products with only an ether linkage. We propose the name daropeptide for this growing family of ether-containing RiPPs produced by DarE enzymes.
Collapse
Affiliation(s)
- Sijia Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Ding
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
5
|
Amara P, Saragaglia C, Mouesca JM, Martin L, Nicolet Y. L-tyrosine-bound ThiH structure reveals C-C bond break differences within radical SAM aromatic amino acid lyases. Nat Commun 2022; 13:2284. [PMID: 35477710 PMCID: PMC9046217 DOI: 10.1038/s41467-022-29980-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/05/2022] [Indexed: 11/08/2022] Open
Abstract
2-iminoacetate synthase ThiH is a radical S-adenosyl-L-methionine (SAM) L-tyrosine lyase and catalyzes the L-tyrosine Cα-Cβ bond break to produce dehydroglycine and p-cresol while the radical SAM L-tryptophan lyase NosL cleaves the L-tryptophan Cα-C bond to produce 3-methylindole-2-carboxylic acid. It has been difficult to understand the features that condition one C-C bond break over the other one because the two enzymes display significant primary structure similarities and presumably similar substrate-binding modes. Here, we report the crystal structure of L-tyrosine bound ThiH from Thermosinus carboxydivorans revealing an unusual protonation state of L-tyrosine upon binding. Structural comparison of ThiH with NosL and computational studies of the respective reactions they catalyze show that substrate activation is eased by tunneling effect and that subtle structural changes between the two enzymes affect, in particular, the hydrogen-atom abstraction by the 5´-deoxyadenosyl radical species, driving the difference in reaction specificity.
Collapse
Affiliation(s)
- Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000, Grenoble, France
| | - Claire Saragaglia
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000, Grenoble, France
| | - Jean-Marie Mouesca
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-DIESE-SyMMES-CAMPE, 38000, Grenoble, France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000, Grenoble, France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000, Grenoble, France.
| |
Collapse
|
6
|
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
|
7
|
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: 393] [Impact Index Per Article: 131.0] [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.
Collapse
|
8
|
|
9
|
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]
|
10
|
Sayler R, Stich TA, Joshi S, Cooper N, Shaw JT, Begley TP, Tantillo DJ, Britt RD. Trapping and Electron Paramagnetic Resonance Characterization of the 5'dAdo • Radical in a Radical S-Adenosyl Methionine Enzyme Reaction with a Non-Native Substrate. ACS CENTRAL SCIENCE 2019; 5:1777-1785. [PMID: 31807679 PMCID: PMC6891858 DOI: 10.1021/acscentsci.9b00706] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Indexed: 05/03/2023]
Abstract
S-Adenosyl methionine (SAM) is employed as a [4Fe-4S]-bound cofactor in the superfamily of radical SAM (rSAM) enzymes, in which one-electron reduction of the [4Fe-4S]-SAM moiety leads to homolytic cleavage of the S-adenosyl methionine to generate the 5'-deoxyadenosyl radical (5'dAdo•), a potent H-atom abstractor. HydG, a member of this rSAM family, uses the 5'dAdo• radical to lyse its substrate, tyrosine, producing CO and CN that bind to a unique Fe site of a second HydG Fe-S cluster, ultimately producing a mononuclear organometallic Fe-l-cysteine-(CO)2CN complex as an intermediate in the bioassembly of the catalytic H-cluster of [Fe-Fe] hydrogenase. Here we report the use of non-native tyrosine substrate analogues to further probe the initial radical chemistry of HydG. One such non-native substrate is 4-hydroxy phenyl propanoic acid (HPPA) which lacks the amino group of tyrosine, replacing the CαH-NH2 with a CH2 at the C2 position. Electron paramagnetic resonance (EPR) studies show the generation of a strong and relatively stable radical in the HydG reaction with natural abundance and 13C2-HPPA, with appreciable spin density localized at C2. These results led us to try parallel experiments with the more oxidized non-native substrate coumaric acid, which has a C2=C3 alkene substitution relative to HPPA's single bond. Interestingly, the HydG reaction with the cis-p-coumaric acid isomer led to the trapping of a new radical EPR signal, and EPR studies using cis-p-coumaric acid along with isotopically labeled SAM reveal that we have for the first time trapped and characterized the 5'dAdo• radical in an actual rSAM enzyme reaction, here by using this specific non-native substrate cis-p-coumaric acid. Density functional theory energetics calculations show that the cis-p-coumaric acid has approximately the same C-H bond dissociation free energy as 5'dAdo•, providing a possible explanation for our ability to trap an appreciable fraction of 5'dAdo• in this specific rSAM reaction. The radical's EPR line shape and its changes with SAM isotopic substitution are nearly identical to those of a 5'dAdo• radical recently generated by cryophotolysis of a prereduced [4Fe-4S]-SAM center in another rSAM enzyme, pyruvate formate-lyase activating enzyme, further supporting our assignment that we have indeed trapped and characterized the 5'dAdo• radical in a radical SAM enzymatic reaction by appropriate tuning of the relative radical free energies via the judicious selection of a non-native substrate.
Collapse
Affiliation(s)
- Richard
I. Sayler
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Troy A. Stich
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Sumedh Joshi
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Nicole Cooper
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Jared T. Shaw
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - Tadhg P. Begley
- Department
of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
| | - R. David Britt
- Department
of Chemistry, University of California,
Davis, Davis, California 95616, United States
- E-mail: . Phone: (530) 752
6377
| |
Collapse
|
11
|
Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN. Angew Chem Int Ed Engl 2019; 58:6235-6238. [DOI: 10.1002/anie.201814708] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 03/13/2019] [Indexed: 12/26/2022]
|
12
|
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.
Collapse
Affiliation(s)
- Mark W Ruszczycky
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, USA.
| | | | | |
Collapse
|
13
|
Ji X, Mo T, Liu W, Ding W, Deng Z, Zhang Q. Revisiting the Mechanism of the Anaerobic Coproporphyrinogen III Oxidase HemN. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xinjian Ji
- Department of ChemistryFudan University Shanghai 200433 China
| | - Tianlu Mo
- Department of ChemistryFudan University Shanghai 200433 China
| | - Wan‐Qiu Liu
- Department of ChemistryFudan University Shanghai 200433 China
| | - Wei Ding
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 China
| | - Zixin Deng
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong University Shanghai 200240 China
| | - Qi Zhang
- Department of ChemistryFudan University Shanghai 200433 China
| |
Collapse
|
14
|
Amara P, Mouesca JM, Bella M, Martin L, Saragaglia C, Gambarelli S, Nicolet Y. Radical S-Adenosyl-l-methionine Tryptophan Lyase (NosL): How the Protein Controls the Carboxyl Radical •CO 2- Migration. J Am Chem Soc 2018; 140:16661-16668. [PMID: 30418774 DOI: 10.1021/jacs.8b09142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The radical S-adenosyl-l-methionine tryptophan lyase uses radical-based chemistry to convert l-tryptophan into 3-methyl-2-indolic acid, a fragment in the biosynthesis of the thiopeptide antibiotic nosiheptide. This complex reaction involves several successive steps corresponding to (i) the activation by a specific hydrogen-atom abstraction, (ii) an unprecedented •CO2- radical migration, (iii) a cyanide fragment release, and (iv) the termination of the radical-based reaction. In vitro study of this reaction is made more difficult because the enzyme produces a significant amount of a shunt product instead of the natural product. Here, using a combination of X-ray crystallography, electron paramagnetic resonance spectroscopy, and quantum and hybrid quantum mechanical/molecular mechanical calculations, we have deciphered the fine mechanism of the key •CO2- radical migration, highlighting how the preorganized active site of the protein tightly controls this reaction.
Collapse
Affiliation(s)
- Patricia Amara
- Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France
| | | | - Maxime Bella
- Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France
| | - Lydie Martin
- Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France
| | - Claire Saragaglia
- Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France
| | - Serge Gambarelli
- Univ. Grenoble Alpes, CNRS, CEA , INAC-SyMMES , 38000 Grenoble , France
| | - Yvain Nicolet
- Univ. Grenoble Alpes, CEA, CNRS, IBS , Metalloproteins Unit , F-38000 Grenoble , France
| |
Collapse
|
15
|
Mandalapu D, Ji X, Zhang Q. Reductive Cleavage of Sulfoxide and Sulfone by Two Radical S-Adenosyl-l-methionine Enzymes. Biochemistry 2018; 58:36-39. [DOI: 10.1021/acs.biochem.8b00844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| |
Collapse
|
16
|
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
|
17
|
Bhandari DM, Fedoseyenko D, Begley TP. Mechanistic Studies on Tryptophan Lyase (NosL): Identification of Cyanide as a Reaction Product. J Am Chem Soc 2018; 140:542-545. [PMID: 29232124 PMCID: PMC6078386 DOI: 10.1021/jacs.7b09000] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tryptophan lyase (NosL) catalyzes the formation of 3-methylindole-2-carboxylic acid and 3-methylindole from l-tryptophan. In this paper, we provide evidence supporting a formate radical intermediate and demonstrate that cyanide is a byproduct of the NosL-catalyzed reaction with l-tryptophan. These experiments require a major revision of the NosL mechanism and uncover an unanticipated connection between NosL and HydG, the radical SAM enzyme that forms cyanide and carbon monoxide from tyrosine during the biosynthesis of the metallo-cluster of the [Fe-Fe] hydrogenase.
Collapse
Affiliation(s)
- Dhananjay M. Bhandari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dmytro Fedoseyenko
- 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
| |
Collapse
|
18
|
Aminofutalosine Synthase (MqnE): A New Catalytic Motif in Radical SAM Enzymology. Methods Enzymol 2018; 606:179-198. [DOI: 10.1016/bs.mie.2018.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
19
|
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]
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Blaszczyk AJ, Wang B, Silakov A, Ho JV, Booker SJ. Efficient methylation of C2 in l-tryptophan by the cobalamin-dependent radical S-adenosylmethionine methylase TsrM requires an unmodified N1 amine. J Biol Chem 2017; 292:15456-15467. [PMID: 28747433 PMCID: PMC5602403 DOI: 10.1074/jbc.m117.778548] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 07/20/2017] [Indexed: 11/06/2022] Open
Abstract
TsrM catalyzes the methylation of C2 in l-tryptophan (Trp). This reaction is the first step in the biosynthesis of the quinaldic acid moiety of the thiopeptide antibiotic thiostrepton, which exhibits potent activity against Gram-positive pathogens. TsrM is a member of the radical S-adenosylmethionine (SAM) superfamily of enzymes, but it does not catalyze the formation of 5'-deoxyadenosin-5'-yl or any other SAM-derived radical. In addition to a [4Fe-4S] cluster, TsrM contains a cobalamin cofactor that serves as an intermediate methyl carrier in its reaction. However, how this cofactor donates a methyl moiety to the Trp substrate is unknown. Here, we showed that the unmodified N1 position of Trp is important for turnover and that 1-thia-Trp and 1-oxa-Trp serve as competitive inhibitors. We also showed that β-cyclopropyl-Trp undergoes C2 methylation in the absence of cyclopropyl ring opening, disfavoring mechanisms that involve unpaired electron density at C3 of the indole ring. Moreover, we showed that all other indole-substituted analogs of Trp undergo methylation at varying but measurable rates and that the analog 7-aza-Trp, which is expected to temper the nucleophilicity of C2 in Trp, is a very poor substrate. Last, no formation of cob(II)alamin or substrate radicals was observed during the reaction with Trp or any molecule within a tested panel of Trp analogs. In summary, our results are most consistent with a mechanism that involves two polar nucleophilic displacements, the second of which requires deprotonation of the indole nitrogen in Trp during its attack on methylcobalamin.
Collapse
Affiliation(s)
| | - Bo Wang
- the Department of Chemistry, and
| | | | | | - Squire J Booker
- From the Department of Biochemistry and Molecular Biology,
- the Department of Chemistry, and
- the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
23
|
Ding W, Ji W, Wu Y, Wu R, Liu WQ, Mo T, Zhao J, Ma X, Zhang W, Xu P, Deng Z, Tang B, Yu Y, Zhang Q. Biosynthesis of the nosiheptide indole side ring centers on a cryptic carrier protein NosJ. Nat Commun 2017; 8:437. [PMID: 28874663 PMCID: PMC5585349 DOI: 10.1038/s41467-017-00439-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/28/2017] [Indexed: 01/10/2023] Open
Abstract
Nosiheptide is a prototypal thiopeptide antibiotic, containing an indole side ring in addition to its thiopeptide-characteristic macrocylic scaffold. This indole ring is derived from 3-methyl-2-indolic acid (MIA), a product of the radical S-adenosylmethionine enzyme NosL, but how MIA is incorporated into nosiheptide biosynthesis remains to be investigated. Here we report functional dissection of a series of enzymes involved in nosiheptide biosynthesis. We show NosI activates MIA and transfers it to the phosphopantetheinyl arm of a carrier protein NosJ. NosN then acts on the NosJ-bound MIA and installs a methyl group on the indole C4, and the resulting dimethylindolyl moiety is released from NosJ by a hydrolase-like enzyme NosK. Surface plasmon resonance analysis show that the molecular complex of NosJ with NosN is much more stable than those with other enzymes, revealing an elegant biosynthetic strategy in which the reaction flux is controlled by protein-protein interactions with different binding affinities.Thiopeptides such as nosiheptide are clinically-interesting antimicrobial natural products. Here the authors show the functional dissection of a series of enzymes involved in nosiheptide biosynthesis, revealing a unique biosynthetic pathway that centers on a previously-unknown carrier protein.
Collapse
Affiliation(s)
- Wei Ding
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng, 224002, China.,Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Wenjuan Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yujie Wu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Runze Wu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Wan-Qiu Liu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Junfeng Zhao
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaoyan Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resource, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, 102206, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bioagriculture, Yancheng Teachers University, Yancheng, 224002, China.
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| |
Collapse
|
24
|
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
|
25
|
Bruender NA, Grell TAJ, Dowling DP, McCarty RM, Drennan CL, Bandarian V. 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies. J Am Chem Soc 2017; 139:1912-1920. [PMID: 28045519 PMCID: PMC5301278 DOI: 10.1021/jacs.6b11381] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Radical S-adenosyl-l-methionine (SAM)
enzymes are widely distributed and catalyze diverse reactions. SAM
binds to the unique iron atom of a site-differentiated [4Fe-4S] cluster
and is reductively cleaved to generate a 5′-deoxyadenosyl radical,
which initiates turnover. 7-Carboxy-7-deazaguanine (CDG) synthase
(QueE) catalyzes a key step in the biosynthesis of 7-deazapurine containing
natural products. 6-Carboxypterin (6-CP), an oxidized analogue of
the natural substrate 6-carboxy-5,6,7,8-tetrahydropterin (CPH4), is shown to be an alternate substrate for CDG synthase.
Under reducing conditions that would promote the reductive cleavage
of SAM, 6-CP is turned over to 6-deoxyadenosylpterin (6-dAP), presumably
by radical addition of the 5′-deoxyadenosine followed by oxidative
decarboxylation to the product. By contrast, in the absence of the
strong reductant, dithionite, the carboxylate of 6-CP is esterified
to generate 6-carboxypterin-5′-deoxyadenosyl ester (6-CP-dAdo
ester). Structural studies with 6-CP and SAM also reveal electron
density consistent with the ester product being formed in crystallo.
The differential reactivity of 6-CP under reducing and nonreducing
conditions highlights the ability of radical SAM enzymes to carry
out both polar and radical transformations in the same active site.
Collapse
Affiliation(s)
- Nathan A Bruender
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | | | | | - Reid M McCarty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| |
Collapse
|
26
|
The Catalytic Mechanism of the Class C Radical S
-Adenosylmethionine Methyltransferase NosN. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609948] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
27
|
Ding W, Li Y, Zhao J, Ji X, Mo T, Qianzhu H, Tu T, Deng Z, Yu Y, Chen F, Zhang Q. The Catalytic Mechanism of the Class C Radical S-Adenosylmethionine Methyltransferase NosN. Angew Chem Int Ed Engl 2017; 56:3857-3861. [PMID: 28112859 DOI: 10.1002/anie.201609948] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/15/2016] [Indexed: 12/23/2022]
Abstract
S-Adenosylmethionine (SAM) is one of the most common co-substrates in enzyme-catalyzed methylation reactions. Most SAM-dependent reactions proceed through an SN 2 mechanism, whereas a subset of them involves radical intermediates for methylating non-nucleophilic substrates. Herein, we report the characterization and mechanistic investigation of NosN, a class C radical SAM methyltransferase involved in the biosynthesis of the thiopeptide antibiotic nosiheptide. We show that, in contrast to all known SAM-dependent methyltransferases, NosN does not produce S-adenosylhomocysteine (SAH) as a co-product. Instead, NosN converts SAM into 5'-methylthioadenosine as a direct methyl donor, employing a radical-based mechanism for methylation and releasing 5'-thioadenosine as a co-product. A series of biochemical and computational studies allowed us to propose a comprehensive mechanism for NosN catalysis, which represents a new paradigm for enzyme-catalyzed methylation reactions.
Collapse
Affiliation(s)
- Wei Ding
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongzhen Li
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Junfeng Zhao
- Department of Chemistry, Fudan University, Shanghai, 200433, China.,Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Haocheng Qianzhu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tao Tu
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fener Chen
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| |
Collapse
|
28
|
Wang X, Zhu W, Liu Y. Tryptophan lyase (NosL): mechanistic insights into amine dehydrogenation and carboxyl fragment migration by QM/MM calculations. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00573c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM calculations suggest two feasible pathways for the breaking of the C–C bond of the substrate. The breaking of the Cα–Cβ bond leads to the final product, whereas the cleavage of the Cα–C bond will terminate in the EPR-trapped radical intermediate.
Collapse
Affiliation(s)
- Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering
- Xuzhou Institute of Technology
- Xuzhou
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| |
Collapse
|
29
|
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
|
30
|
Ding W, Wu Y, Ji X, Qianzhu H, Chen F, Deng Z, Yu Y, Zhang Q. Nucleoside-linked shunt products in the reaction catalyzed by the class C radical S-adenosylmethionine methyltransferase NosN. Chem Commun (Camb) 2017; 53:5235-5238. [DOI: 10.1039/c7cc02162c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A series of nucleoside-linked shunt products have been identified in reactions catalyzed by NosN, a class C radical S-adenosylmethionine (SAM) methyltransferase, providing strong evidence supporting that 5′-methylthioadenosine (MTA) is a direct methyl donor in this reaction.
Collapse
Affiliation(s)
- Wei Ding
- School of Life Sciences
- Lanzhou University
- Lanzhou
- China
- Department of Chemistry
| | - Yujie Wu
- School of Life Sciences
- Lanzhou University
- Lanzhou
- China
- Department of Chemistry
| | - Xinjian Ji
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | | | - Fener Chen
- Department of Chemistry
- Fudan University
- Shanghai
- China
| | - Zixin Deng
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan
- China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education)
- School of Pharmaceutical Sciences
- Wuhan University
- Wuhan
- China
| | - Qi Zhang
- Department of Chemistry
- Fudan University
- Shanghai
- China
| |
Collapse
|
31
|
Bhandari DM, Fedoseyenko D, Begley TP. Tryptophan Lyase (NosL): A Cornucopia of 5′-Deoxyadenosyl Radical Mediated Transformations. J Am Chem Soc 2016; 138:16184-16187. [DOI: 10.1021/jacs.6b06139] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dhananjay M. Bhandari
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dmytro Fedoseyenko
- 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
| |
Collapse
|
32
|
Ortega MA, van der Donk WA. New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products. Cell Chem Biol 2016; 23:31-44. [PMID: 26933734 DOI: 10.1016/j.chembiol.2015.11.012] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 10/24/2022]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large group of structurally diverse natural products. Their biological activities and unique biosynthetic pathways have sparked a growing interest in RiPPs. Furthermore, the relatively low genetic complexity associated with RiPP biosynthesis makes them excellent candidates for synthetic biology applications. This Review highlights recent developments in the understanding of the biosynthesis of several bacterial RiPP family members, the use of the RiPP biosynthetic machinery for generating novel macrocyclic peptides, and the implementation of tools designed to guide the discovery and characterization of novel RiPPs.
Collapse
Affiliation(s)
- Manuel A Ortega
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| |
Collapse
|
33
|
Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016; 55:11845-8. [DOI: 10.1002/anie.201605917] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
34
|
Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
35
|
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: 31] [Impact Index Per Article: 3.9] [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
|
36
|
Affiliation(s)
- Jennifer Bridwell-Rabb
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
37
|
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]
|
38
|
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
|
39
|
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
|
40
|
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
|