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Bommisetti P, Bandarian V. Insights into the Mechanism of Installation of 5-Carboxymethylaminomethyl Uridine Hypermodification by tRNA-Modifying Enzymes MnmE and MnmG. J Am Chem Soc 2023; 145:26947-26961. [PMID: 38050996 PMCID: PMC10723064 DOI: 10.1021/jacs.3c10182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023]
Abstract
The evolutionarily conserved bacterial proteins MnmE and MnmG (and their homologues in Eukarya) install a 5-carboxymethylaminomethyl (cmnm5) or a 5-taurinomethyl (τm5) group onto wobble uridines of several tRNA species. The Escherichia coli MnmE binds guanosine-5'-triphosphate (GTP) and methylenetetrahydrofolate (CH2THF), while MnmG binds flavin adenine dinucleotide (FAD) and a reduced nicotinamide adenine dinucleotide (NADH). Together with glycine, MnmEG catalyzes the installation of cmnm5 in a reaction that also requires hydrolysis of GTP. In this letter, we investigated key steps of the MnmEG reaction using a combination of biochemical techniques. We show multiple lines of evidence supporting flavin-iminium FADH[N5═CH2]+ as a central intermediate in the MnmEG reaction. Using a synthetic FADH[N5═CD2]+ analogue, the intermediacy of the FAD in the transfer of the methylene group from CH2THF to the C5 position of U34 was unambiguously demonstrated. Further, MnmEG reactions containing the deuterated flavin-iminium intermediate and alternate nucleophiles such as taurine and ammonia also led to the formation of the anticipated U34-modified tRNAs, showing FAD[N5═CH2]+ as the universal intermediate for all MnmEG homologues. Additionally, an RNA-protein complex stable to urea-denaturing polyacrylamide gel electrophoresis was identified. Studies involving a series of nuclease (RNase T1) and protease (trypsin) digestions along with reverse transcription experiments suggest that the complex may be noncovalent. While the conserved MnmG cysteine C47 and C277 mutant variants were shown to reduce FAD, they were unable to promote the modified tRNA formation. Overall, this study provides critical insights into the biochemical mechanism underlying tRNA modification by the MnmEG.
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Affiliation(s)
- Praneeth Bommisetti
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake
City, Utah 84112, United States
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2
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Brimberry M, Corrigan P, Silakov A, Lanzilotta WN. Evidence for Porphyrin-Mediated Electron Transfer in the Radical SAM Enzyme HutW. Biochemistry 2023; 62:1191-1196. [PMID: 36877586 PMCID: PMC10035031 DOI: 10.1021/acs.biochem.2c00474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/16/2023] [Indexed: 03/07/2023]
Abstract
Bacteria that infect the human gut must compete for essential nutrients, including iron, under a variety of different metabolic conditions. Several enteric pathogens, including Vibrio cholerae and Escherichia coli O157:H7, have evolved mechanisms to obtain iron from heme in an anaerobic environment. Our laboratory has demonstrated that a radical S-adenosylmethionine (SAM) methyltransferase is responsible for the opening of the heme porphyrin ring and release of iron under anaerobic conditions. Furthermore, the enzyme in V. cholerae, HutW, has recently been shown to accept electrons from NADPH directly when SAM is utilized to initiate the reaction. However, how NADPH, a hydride donor, catalyzes the single electron reduction of a [4Fe-4S] cluster, and/or subsequent electron/proton transfer reactions, was not addressed. In this work, we provide evidence that the substrate, in this case, heme, facilitates electron transfer from NADPH to the [4Fe-4S] cluster. This study uncovers a new electron transfer pathway adopted by radical SAM enzymes and further expands our understanding of these enzymes in bacterial pathogens.
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Affiliation(s)
- Marley Brimberry
- Department
of Biochemistry and Molecular Biology & Center for Metalloenzyme
Studies, University of Georgia, Athens, Georgia 30602, United States
| | - Patrick Corrigan
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - William N. Lanzilotta
- Department
of Biochemistry and Molecular Biology & Center for Metalloenzyme
Studies, University of Georgia, Athens, Georgia 30602, United States
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3
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Booker SJ, Lloyd CT. Twenty Years of Radical SAM! The Genesis of the Superfamily. ACS BIO & MED CHEM AU 2022; 2:538-547. [PMID: 37101427 PMCID: PMC10114671 DOI: 10.1021/acsbiomedchemau.2c00078] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Indexed: 12/10/2022]
Affiliation(s)
- Squire J Booker
- Departments of Chemistry, and of Biochemistry and Molecular Biology, and the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Cody T Lloyd
- Departments of Chemistry, and of Biochemistry and Molecular Biology, and the Howard Hughes Medical Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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4
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Young AP, Bandarian V. Insertion of 4-Demethylwyosine in tRNA Phe Catalyzed by the Radical S-Adenosyl-l-methionine Enzyme TYW1 Entails Oxidative Cleavage of Pyruvate to Form CO 2. Biochemistry 2022; 61:2643-2647. [PMID: 36326713 PMCID: PMC10874244 DOI: 10.1021/acs.biochem.2c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The radical S-adenosyl-l-methionine (SAM) enzyme TYW1 catalyzes the condensation of C-2 and C-3 atoms of pyruvate with N-methylguanosine containing tRNAPhe to form 4-demethylwyosine (imG-14) modified tRNAPhe. The fate of C-1 is not known, and either formate or carbon dioxide (CO2) has been proposed. In this study, a coupled assay that transforms either CO2 or formate to oxaloacetate (OAA) was used to determine the fate of C-1. In the presence of [1-13C1]-pyruvate, 13C-enriched OAA was observed in a process that is concomitant with the formation of imG-14, under conditions that preferentially transform CO2 and not formate to OAA. These findings are discussed in the context of the cofactor content of TYW1 and a new role for the auxiliary cluster in catalyzing the oxidative cleavage of C-1-C-2 bond of pyruvate in the catalytic cycle of TYW1.
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Affiliation(s)
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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5
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Boswinkle K, McKinney J, Allen KD. Highlighting the Unique Roles of Radical S-Adenosylmethionine Enzymes in Methanogenic Archaea. J Bacteriol 2022; 204:e0019722. [PMID: 35880875 PMCID: PMC9380564 DOI: 10.1128/jb.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes catalyze an impressive variety of difficult biochemical reactions in various pathways across all domains of life. These metalloenzymes employ a reduced [4Fe-4S] cluster and SAM to generate a highly reactive 5'-deoxyadenosyl radical that is capable of initiating catalysis on otherwise unreactive substrates. Interestingly, the genomes of methanogenic archaea encode many unique radical SAM enzymes with underexplored or completely unknown functions. These organisms are responsible for the yearly production of nearly 1 billion tons of methane, a potent greenhouse gas as well as a valuable energy source. Thus, understanding the details of methanogenic metabolism and elucidating the functions of essential enzymes in these organisms can provide insights into strategies to decrease greenhouse gas emissions as well as inform advances in bioenergy production processes. This minireview provides an overview of the current state of the field regarding the functions of radical SAM enzymes in methanogens and discusses gaps in knowledge that should be addressed.
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Affiliation(s)
- Kaleb Boswinkle
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Justin McKinney
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kylie D. Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
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6
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Bandarian V. Journey on the Radical SAM Road as an Accidental Pilgrim. ACS BIO & MED CHEM AU 2022; 2:187-195. [PMID: 35726327 PMCID: PMC9204691 DOI: 10.1021/acsbiomedchemau.1c00059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022]
Abstract
![]()
Radical S-adenosyl-l-methionine (SAM)
enzymes catalyze a diverse group of complex transformations in all
aspects of cellular physiology. These metalloenzymes bind SAM to a
4Fe–4S cluster and reductively cleave SAM to generate a 5′-deoxyadenosyl
radical, which generally initiates the catalytic cycle by catalyzing
a H atom to activate the substrate for subsequent chemistry. This
perspective will focus on our discovery of several members of this
superfamily of enzymes, with a particular emphasis on the current
state of the field, challenges, and outlook.
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Affiliation(s)
- Vahe Bandarian
- Department of Chemistry, University of Utah, 315 S 1400 E, Salt Lake City, Utah 84112, United States
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7
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Sjekloća L, Ferré-D’Amaré AR. Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA Phe 4-demethylwyosine synthase Tyw1 in complex with FMN. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000570. [PMID: 35693892 PMCID: PMC9186531 DOI: 10.17912/micropub.biology.000570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022]
Abstract
The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from Schizosaccharomyces japonicus in complex with flavin mononucleotide (FMN), exploiting an unexpected anomalous scatterer present in the recombinant protein. Our results show how eukaryotic TYW1 enzymes bind the coenzyme FMN and will help further elucidation of the structural enzymology of 4-demethylwyosine synthesis.
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Affiliation(s)
- Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, Bethesda, Maryland, 20892-8012, United States
,
Current affiliation: Molecular Pathology, International Centre for Genetic Engineering and Biotechnology, Padriciano 99, Trieste 34149, Italy
,
Correspondence to: Ljiljana Sjekloća (
)
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, Bethesda, Maryland, 20892-8012, United States
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8
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Tunçkanat T, Gendron A, Sadler Z, Neitz A, Byquist S, Lie TJ, Allen KD. Lysine 2,3-Aminomutase and a Newly Discovered Glutamate 2,3-Aminomutase Produce β-Amino Acids Involved in Salt Tolerance in Methanogenic Archaea. Biochemistry 2022; 61:1077-1090. [PMID: 35544775 DOI: 10.1021/acs.biochem.2c00014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many methanogenic archaea synthesize β-amino acids as osmolytes that allow survival in high salinity environments. Here, we investigated the radical S-adenosylmethionine (SAM) aminomutases involved in the biosynthesis of Nε-acetyl-β-lysine and β-glutamate in Methanococcus maripaludis C7. Lysine 2,3-aminomutase (KAM), encoded by MmarC7_0106, was overexpressed and purified from Escherichia coli, followed by biochemical characterization. In the presence of l-lysine, SAM, and dithionite, this archaeal KAM had a kcat = 14.3 s-1 and a Km = 19.2 mM. The product was shown to be 3(S)-β-lysine, which is like the well-characterized Clostridium KAM as opposed to the E. coli KAM that produces 3(R)-β-lysine. We further describe the function of MmarC7_1783, a putative radical SAM aminomutase with a ∼160 amino acid extension at its N-terminus. Bioinformatic analysis of the possible substrate-binding residues suggested a function as glutamate 2,3-aminomutase, which was confirmed here through heterologous expression in a methanogen followed by detection of β-glutamate in cell extracts. β-Glutamate has been known to serve as an osmolyte in select methanogens for a long time, but its biosynthetic origin remained unknown until now. Thus, this study defines the biosynthetic routes for β-lysine and β-glutamate in M. maripaludis and expands the importance and diversity of radical SAM enzymes in all domains of life.
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Affiliation(s)
- Taylan Tunçkanat
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Aleksei Gendron
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Zoie Sadler
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alex Neitz
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, United States
| | - Sarah Byquist
- Department of Chemistry and Biochemistry, Gonzaga University, Spokane, Washington 99258, United States
| | - Thomas J Lie
- Department of Microbiology, University of Washington, Seattle, Washington 98195, United States
| | - Kylie D Allen
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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