S-adenosyl-L-methionine is the unexpected methyl donor for the methylation of mercury by the membrane-associated HgcAB complex

Zheng, Kaiyuan; Rush, Katherine W.; Date, Swapneeta S.; Johs, Alexander; Parks, Jerry M.; Fleischhacker, Angela S.; Abernathy, Macon J.; Sarangi, Ritimukta; Ragsdale, Stephen W.

doi:10.1073/pnas.2408086121

Title: S-adenosyl-L-methionine is the unexpected methyl donor for the methylation of mercury by the membrane-associated HgcAB complex

Journal Article · 14 November 2024 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2408086121 · OSTI ID:2479042

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Univ. of Michigan, Ann Arbor, MI (United States); Univ. of Virginia, Charlottesville, VA (United States)
Univ. of Michigan, Ann Arbor, MI (United States); Auburn Univ., AL (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Vanderbilt Univ., Nashville, TN (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Univ. of Michigan, Ann Arbor, MI (United States)
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Mercury (Hg) is a heavy metal that exhibits high biological toxicity. Monomethylmercury and dimethylmercury are neurotoxins and a significant environmental concern as they bioaccumulate and biomagnify within the aquatic food web. Microbial Hg methylation involves two proteins, HgcA and HgcB. Here, we show that HgcA and HgcB can be heterologously coexpressed, and the HgcAB complex can be purified. We demonstrated that HgcA is a membrane-associated cobalamin-dependent methyltransferase and HgcB is a ferredoxin-like protein containing two [4Fe-4S] clusters. Further, spectroscopic and kinetic results demonstrate that S-adenosyl-L-methionine (SAM) donates the methyl group to Hg in a two-step reaction involving a methylcob(III)alamin intermediate including Co-thiolate ligation from a conserved Cys residue. Our findings uncover a biological role for SAM in microbial Hg methylation.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)

Contributing Organization:: Oak Ridge National Laboratory (ORNL)

Grant/Contract Number:: AC02-76SF00515; AC05-00OR22725

OSTI ID:: 2479042

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 47 Vol. 121; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Human toxicology of Mercury Clarkson, Thomas W. The Journal of Trace Elements in Experimental Medicine, Vol. 11, Issue 2-3 https://doi.org/10.1002/(SICI)1520-670X(1998)11:2/3<303::AID-JTRA18>3.0.CO;2-V	journal	January 1998
Mercury Methylation by Cobalt Corrinoids: Relativistic Effects Dictate the Reaction Mechanism Demissie, Taye B.; Garabato, Brady D.; Ruud, Kenneth Angewandte Chemie International Edition, Vol. 55, Issue 38 https://doi.org/10.1002/anie.201606001	journal	August 2016
Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes Qian, Chen; Chen, Hongmei; Johs, Alexander PROTEOMICS, Vol. 18, Issue 17 https://doi.org/10.1002/pmic.201700479	journal	August 2018
An improved staining procedure for the detection of the peroxidase activity of cytochrome P-450 on sodium dodecyl sulfate polyacrylamide gels Thomas, Paul E.; Ryan, Dene; Levin, Wayne Analytical Biochemistry, Vol. 75, Issue 1 https://doi.org/10.1016/0003-2697(76)90067-1	journal	September 1976
On the Nature of the Spin Coupling between the Iron-Sulfur Clusters in the Eight-Iron Ferredoxins Mathews, Robert; Charlton, Steven; Sands, Richard H. Journal of Biological Chemistry, Vol. 249, Issue 13 https://doi.org/10.1016/S0021-9258(19)42521-0	journal	July 1974
Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase Doukov, Tzanko; Seravalli, Javier; Stezowski, John J. Structure, Vol. 8, Issue 8 https://doi.org/10.1016/S0969-2126(00)00172-6	journal	August 2000
Initial characterization of Fom3 from Streptomyces wedmorensis: The methyltransferase in fosfomycin biosynthesis Allen, Kylie D.; Wang, Susan C. Archives of Biochemistry and Biophysics, Vol. 543 https://doi.org/10.1016/j.abb.2013.12.004	journal	February 2014
Tuning the redox properties of a [4Fe-4S] center to modulate the activity of Mo-bisPGD periplasmic nitrate reductase Zeamari, Kamal; Gerbaud, Guillaume; Grosse, Sandrine Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1860, Issue 5 https://doi.org/10.1016/j.bbabio.2019.01.003	journal	May 2019
Auxiliary iron–sulfur cofactors in radical SAM enzymes Lanz, Nicholas D.; Booker, Squire J. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6 https://doi.org/10.1016/j.bbamcr.2015.01.002	journal	June 2015
Structural Basis for Electron and Methyl-Group Transfer in a Methyltransferase System Operating in the Reductive Acetyl-CoA Pathway Goetzl, Sebastian; Jeoung, Jae-Hun; Hennig, Sandra Elisabeth Journal of Molecular Biology, Vol. 411, Issue 1, p. 96-109 https://doi.org/10.1016/j.jmb.2011.05.025	journal	August 2011
Enhanced Solubilization of Class B Radical S -Adenosylmethionine Methylases by Improved Cobalamin Uptake in Escherichia coli Lanz, Nicholas D.; Blaszczyk, Anthony J.; McCarthy, Erin L. Biochemistry, Vol. 57, Issue 9 https://doi.org/10.1021/acs.biochem.7b01205	journal	January 2018
A (Re)Discovery of the Fom3 Substrate Blaszczyk, Anthony J.; Booker, Squire J. Biochemistry, Vol. 57, Issue 6 https://doi.org/10.1021/acs.biochem.7b01281	journal	January 2018
Stereochemical and Mechanistic Investigation of the Reaction Catalyzed by Fom3 from Streptomyces fradiae , a Cobalamin-Dependent Radical S -Adenosylmethionine Methylase Wang, Bo; Blaszczyk, Anthony J.; Knox, Hayley L. Biochemistry, Vol. 57, Issue 33 https://doi.org/10.1021/acs.biochem.8b00693	journal	July 2018
Twenty Years of Radical SAM! The Genesis of the Superfamily Booker, Squire J.; Lloyd, Cody T. ACS Bio & Med Chem Au, Vol. 2, Issue 6 https://doi.org/10.1021/acsbiomedchemau.2c00078	journal	December 2022
Spectroelectrochemical studies of the corrinoid/iron-sulfur protein involved in acetyl coenzyme A synthesis by Clostridium thermoaceticum Harder, Scott R.; Lu, Wei Ping; Feinberg, Benjamin A. Biochemistry, Vol. 28, Issue 23 https://doi.org/10.1021/bi00449a019	journal	November 1989
Mechanism of reductive activation of cobalamin-dependent methionine synthase: an electron paramagnetic resonance spectroelectrochemical study Banerjee, Ruma V.; Harder, Scott R.; Ragsdale, Stephen W. Biochemistry, Vol. 29, Issue 5 https://doi.org/10.1021/bi00457a005	journal	February 1990
In Vitro Phosphinate Methylation by PhpK from Kitasatospora phosalacinea Werner, Williard J.; Allen, Kylie D.; Hu, Kaifeng Biochemistry, Vol. 50, Issue 42 https://doi.org/10.1021/bi201220r	journal	October 2011
Mercury as a Global Pollutant: Sources, Pathways, and Effects Driscoll, Charles T.; Mason, Robert P.; Chan, Hing Man Environmental Science & Technology, Vol. 47, Issue 10 https://doi.org/10.1021/es305071v	journal	May 2013
Mercury Methylation by Novel Microorganisms from New Environments Gilmour, Cynthia C.; Podar, Mircea; Bullock, Allyson L. Environmental Science & Technology, Vol. 47, Issue 20 https://doi.org/10.1021/es403075t	journal	September 2013
Mercury Methylation by HgcA: Theory Supports Carbanion Transfer to Hg(II) Zhou, Jing; Riccardi, Demian; Beste, Ariana Inorganic Chemistry, Vol. 53, Issue 2 https://doi.org/10.1021/ic401992y	journal	December 2013
GenK-Catalyzed C-6′ Methylation in the Biosynthesis of Gentamicin: Isolation and Characterization of a Cobalamin-Dependent Radical SAM Enzyme Kim, Hak Joong; McCarty, Reid M.; Ogasawara, Yasushi Journal of the American Chemical Society, Vol. 135, Issue 22 https://doi.org/10.1021/ja312641f	journal	May 2013
An Interprotein Co–S Coordination Complex in the B₁₂-Trafficking Pathway Li, Zhu; Mascarenhas, Romila; Twahir, Umar T. Journal of the American Chemical Society, Vol. 142, Issue 38 https://doi.org/10.1021/jacs.0c06590	journal	September 2020
Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S -Adenosyl- l -methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration Kim, Hak Joong; Liu, Yung-nan; McCarty, Reid M. Journal of the American Chemical Society, Vol. 139, Issue 45 https://doi.org/10.1021/jacs.7b09890	journal	November 2017
Molecular Mechanism of ISC Iron–Sulfur Cluster Biogenesis Revealed by High-Resolution Native Mass Spectrometry Lin, Cheng-Wei; McCabe, Jacob W.; Russell, David H. Journal of the American Chemical Society, Vol. 142, Issue 13 https://doi.org/10.1021/jacs.9b11454	journal	March 2020
Visualizing molecular juggling within a B₁₂-dependent methyltransferase complex Kung, Yan; Ando, Nozomi; Doukov, Tzanko I. Nature, Vol. 484, Issue 7393, p. 265-269 https://doi.org/10.1038/nature10916	journal	March 2012
Crystallographic snapshots of a B12-dependent radical SAM methyltransferase Fyfe, Cameron D.; Bernardo-García, Noelia; Fradale, Laura Nature, Vol. 602, Issue 7896 https://doi.org/10.1038/s41586-021-04355-9	journal	February 2022
Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis Knox, Hayley L.; Sinner, Erica K.; Townsend, Craig A. Nature, Vol. 602, Issue 7896 https://doi.org/10.1038/s41586-021-04392-4	journal	February 2022
Structural basis for non-radical catalysis by TsrM, a radical SAM methylase Knox, Hayley L.; Chen, Percival Yang-Ting; Blaszczyk, Anthony J. Nature Chemical Biology, Vol. 17, Issue 4 https://doi.org/10.1038/s41589-020-00717-y	journal	January 2021
Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation Cooper, Connor J.; Zheng, Kaiyuan; Rush, Katherine W. Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-1047-5	journal	June 2020
The chemistry of vitamin B12. Part IX. Evidence for five-co-ordinate cobalt(III) complexes Firth, R. A.; Hill, H. A. O.; Mann, B. E. Journal of the Chemical Society A: Inorganic, Physical, Theoretical https://doi.org/10.1039/j19680002419	journal	January 1968
Delayed Cerebellar Disease and Death after Accidental Exposure to Dimethylmercury Nierenberg, David W.; Nordgren, Richard E.; Chang, Morris B. New England Journal of Medicine, Vol. 338, Issue 23 https://doi.org/10.1056/NEJM199806043382305	journal	June 1998
Structural insights into methyltransfer reactions of a corrinoid iron-sulfur protein involved in acetyl-CoA synthesis Svetlitchnaia, T.; Svetlitchnyi, V.; Meyer, O. Proceedings of the National Academy of Sciences, Vol. 103, Issue 39, p. 14331-14336 https://doi.org/10.1073/pnas.0601420103	journal	September 2006
One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Chung, C. T.; Niemela, S. L.; Miller, R. H. Proceedings of the National Academy of Sciences, Vol. 86, Issue 7 https://doi.org/10.1073/pnas.86.7.2172	journal	April 1989
Activation Mechanism of Methanol:5-Hydroxybenzimidazolylcobamide Methyltransferase from Daas, Piet J. H.; Hagen, Wilfred R.; Keltjens, Jan T. Journal of Biological Chemistry, Vol. 271, Issue 37 https://doi.org/10.1074/jbc.271.37.22346	journal	September 1996
Structural and Kinetic Evidence for an Extended Hydrogen-bonding Network in Catalysis of Methyl Group Transfer Doukov, Tzanko I.; Hemmi, Hisashi; Drennan, Catherine L. Journal of Biological Chemistry, Vol. 282, Issue 9 https://doi.org/10.1074/jbc.M609828200	journal	December 2006
Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S -adenosylmethionine methylase that unexpectedly requires cobalamin Radle, Matthew I.; Miller, Danielle V.; Laremore, Tatiana N. Journal of Biological Chemistry, Vol. 294, Issue 31 https://doi.org/10.1074/jbc.RA119.007609	journal	May 2019
Hyperproduction of Recombinant Ferredoxins in Escherichia coli by Coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 Gene Cluster Nakamura, M.; Saeki, K.; Takahashi, Y. Journal of Biochemistry, Vol. 126, Issue 1 https://doi.org/10.1093/oxfordjournals.jbchem.a022409	journal	July 1999
Cobalamin‐dependent methionine synthase Banerjee, Ruma V.; Matthews, Rowena G. The FASEB Journal, Vol. 4, Issue 5 https://doi.org/10.1096/fasebj.4.5.2407589	journal	March 1990
A consensus protocol for the recovery of mercury methylation genes from metagenomes Capo, Eric; Peterson, Benjamin D.; Kim, Minjae Molecular Ecology Resources, Vol. 23, Issue 1 https://doi.org/10.1111/1755-0998.13687	journal	August 2022
Global prevalence and distribution of genes and microorganisms involved in mercury methylation Podar, Mircea; Gilmour, Cynthia C.; Brandt, Craig C. Science Advances, Vol. 1, Issue 9 https://doi.org/10.1126/sciadv.1500675	journal	October 2015
The Genetic Basis for Bacterial Mercury Methylation Parks, J. M.; Johs, A.; Podar, M. Science, Vol. 339, Issue 6125, p. 1332-1335 https://doi.org/10.1126/science.1230667	journal	February 2013
Synergistic Effects of a Chalkophore, Methanobactin, on Microbial Methylation of Mercury Yin, Xixiang; Wang, Lihong; Zhang, Lijie Applied and Environmental Microbiology, Vol. 86, Issue 11 https://doi.org/10.1128/AEM.00122-20	journal	May 2020
Site-Directed Mutagenesis of HgcA and HgcB Reveals Amino Acid Residues Important for Mercury Methylation Smith, Steven D.; Bridou, Romain; Johs, Alexander Applied and Environmental Microbiology, Vol. 81, Issue 9 https://doi.org/10.1128/AEM.00217-15	journal	February 2015
Kinetics of Enzymatic Mercury Methylation at Nanomolar Concentrations Catalyzed by HgcAB Date, Swapneeta S.; Parks, Jerry M.; Rush, Katherine W. Applied and Environmental Microbiology, Vol. 85, Issue 13 https://doi.org/10.1128/AEM.00438-19	journal	April 2019
Characterization of the Corrinoid Iron-Sulfur Protein Tetrachloroethene Reductive Dehalogenase of Dehalobacter restrictus Maillard, J.; Schumacher, W.; Vazquez, F. Applied and Environmental Microbiology, Vol. 69, Issue 8 https://doi.org/10.1128/AEM.69.8.4628-4638.2003	journal	August 2003
Mercury Methylation Independent of the Acetyl-Coenzyme A Pathway in Sulfate-Reducing Bacteria Ekstrom, E. B.; Morel, F. M. M.; Benoit, J. M. Applied and Environmental Microbiology, Vol. 69, Issue 9, p. 5414-5422 https://doi.org/10.1128/AEM.69.9.5414-5422.2003	journal	September 2003
Carbon Flow in Mercury Biomethylation by Desulfovibrio desulfuricans† Berman, Mitchell; Chase, Theodore; Bartha, Richard Applied and Environmental Microbiology, Vol. 56, Issue 1 https://doi.org/10.1128/aem.56.1.298-300.1990	journal	January 1990
Metabolic Pathways Leading to Mercury Methylation in Desulfovibrio desulfuricans LS † Choi, Sung-Chan; Chase, Theodore; Bartha, Richard Applied and Environmental Microbiology, Vol. 60, Issue 11 https://doi.org/10.1128/aem.60.11.4072-4077.1994	journal	January 1994
Enzymatic catalysis of mercury methylation by Desulfovibrio desulfuricans LS. Choi, S. C.; Chase, T.; Bartha, R. Applied and Environmental Microbiology, Vol. 60, Issue 4 https://doi.org/10.1128/aem.60.4.1342-1346.1994	journal	January 1994
Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis Haft, Daniel H.; Gwadz, Marc Journal of Bacteriology, Vol. 205, Issue 1 https://doi.org/10.1128/jb.00259-22	journal	January 2023
The reductive acetyl coenzyme A pathway: sequence and heterologous expression of active methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase from Clostridium thermoaceticum Roberts, D. L.; Zhao, S.; Doukov, T. Journal of Bacteriology, Vol. 176, Issue 19, p. 6127-6130 https://doi.org/10.1128/jb.176.19.6127-6130.1994	journal	October 1994
Robust Mercury Methylation across Diverse Methanogenic Archaea Gilmour, Cynthia C.; Bullock, Allyson L.; McBurney, Alyssa mBio, Vol. 9, Issue 2 https://doi.org/10.1128/mBio.02403-17	journal	April 2018
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms McDaniel, Elizabeth A.; Peterson, Benjamin D.; Stevens, Sarah L. R. mSystems, Vol. 5, Issue 4 https://doi.org/10.1128/mSystems.00299-20	journal	August 2020
Structure, Function, and Formation of Biological Iron-Sulfur Clusters Johnson, Deborah C.; Dean, Dennis R.; Smith, Archer D. Annual Review of Biochemistry, Vol. 74, Issue 1 https://doi.org/10.1146/annurev.biochem.74.082803.133518	journal	June 2005
Axial Ligation and Redox Changes at the Cobalt Ion in Cobalamin Bound to Corrinoid Iron-Sulfur Protein (CoFeSP) or in Solution Characterized by XAS and DFT Schrapers, Peer; Mebs, Stefan; Goetzl, Sebastian PLOS ONE, Vol. 11, Issue 7 https://doi.org/10.1371/journal.pone.0158681	journal	July 2016
Minamata Disease: Methylmercury Poisoning in Japan Caused by Environmental Pollution Harada, Masazumi Critical Reviews in Toxicology, Vol. 25, Issue 1 https://doi.org/10.3109/10408449509089885	journal	January 1995

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Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
S-adenosyl-L-methionine
cobalamin
iron-sulfur
methyl mercury
methyltransferase

Title: S-adenosyl-L-methionine is the unexpected methyl donor for the methylation of mercury by the membrane-associated HgcAB complex

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