The Genetic Basis for Bacterial Mercury Methylation

Mercury Methylating Microbes Mercury (Hg) most commonly becomes bioavailable and enters the food web as the organic form methylmercury, where it induces acute toxicity effects that can be magnified up the food chain. But most natural and anthropogenic Hg exists as inorganic Hg2+ and is only transformed into methylmercury by anaerobic microorganisms—typically sulfur-reducing bacteria. Using comparative genomics, Parks et al. (p. 1332, published online 7 February; see the Perspective by Poulain and Barkay) identified two genes that encode a corrinoid and iron-sulfur proteins in six known Hg-methylating bacteria but were absent in nonmethylating bacteria. In two distantly related model Hg-methylating bacteria, deletion of either gene—or both genes simultaneously—reduced the ability for the bacteria to produce methylmercury but did not impair cellular growth. The presence of this two-gene cluster in several other bacterial and lineages for which genome sequences are available suggests the ability to produce methylmercury may be more broadly distributed in the microbial world than previously recognized. A two-gene cluster encodes proteins required for the production of the neurotoxin methylmercury in bacteria. [Also see Perspective by Poulain and Barkay] Methylmercury is a potent neurotoxin produced in natural environments from inorganic mercury by anaerobic bacteria. However, until now the genes and proteins involved have remained unidentified. Here, we report a two-gene cluster, hgcA and hgcB, required for mercury methylation by Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA. In either bacterium, deletion of hgcA, hgcB, or both genes abolishes mercury methylation. The genes encode a putative corrinoid protein, HgcA, and a 2[4Fe-4S] ferredoxin, HgcB, consistent with roles as a methyl carrier and an electron donor required for corrinoid cofactor reduction, respectively. Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in nonmethylators, suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date.

[1]  E. Kremmer,et al.  The C9orf72 GGGGCC Repeat Is Translated into Aggregating Dipeptide-Repeat Proteins in FTLD/ALS , 2013, Science.

[2]  E. Bonch‐Osmolovskaya,et al.  Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria. , 2012, International journal of systematic and evolutionary microbiology.

[3]  C. Gilmour,et al.  Detailed Assessment of the Kinetics of Hg-Cell Association, Hg Methylation, and Methylmercury Degradation in Several Desulfovibrio Species , 2012, Applied and Environmental Microbiology.

[4]  B. Dridi,et al.  Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. , 2012, International journal of systematic and evolutionary microbiology.

[5]  Ralph Turner,et al.  Contribution of coexisting sulfate and iron reducing bacteria to methylmercury production in freshwater river sediments. , 2012, Environmental science & technology.

[6]  S. Ragsdale,et al.  Visualising molecular juggling within a B12-dependent methyltransferase complex , 2012, Nature.

[7]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[8]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[9]  S. Sammartano,et al.  Sequestration of Hg2+ by Some Biologically Important Thiols , 2011 .

[10]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[11]  Yanping Wang,et al.  Methanogens: principal methylators of mercury in lake periphyton. , 2011, Environmental science & technology.

[12]  T. Brunold,et al.  Spectroscopic and computational studies of glutathionylcobalamin: nature of Co-S bonding and comparison to Co-C bonding in coenzyme B12. , 2011, Inorganic chemistry.

[13]  H. Dobbek,et al.  Structural basis for electron and methyl-group transfer in a methyltransferase system operating in the reductive acetyl-CoA pathway. , 2011, Journal of molecular biology.

[14]  Swapnil Chhabra,et al.  Methods for engineering sulfate reducing bacteria of the genus Desulfovibrio. , 2011, Methods in enzymology.

[15]  F. Morel,et al.  Active transport, substrate specificity, and methylation of Hg(II) in anaerobic bacteria , 2011, Proceedings of the National Academy of Sciences.

[16]  C. Schadt,et al.  Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury Methylation , 2011, Applied and Environmental Microbiology.

[17]  Natalia N. Ivanova,et al.  Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132 , 2011, Journal of bacteriology.

[18]  R. Guyoneaud,et al.  Simultaneous determination of mercury methylation and demethylation capacities of various sulfate‐reducing bacteria using species‐specific isotopic tracers , 2011, Environmental toxicology and chemistry.

[19]  Judy D. Wall,et al.  Effect of the Deletion of qmoABC and the Promoter-Distal Gene Encoding a Hypothetical Protein on Sulfate Reduction in Desulfovibrio vulgaris Hildenborough , 2010, Applied and Environmental Microbiology.

[20]  H. Hintelmann 11:Organomercurials. Their Formation and Pathways in the Environment , 2010 .

[21]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[22]  Geoffrey J. Barton,et al.  Jalview Version 2—a multiple sequence alignment editor and analysis workbench , 2009, Bioinform..

[23]  R. Duran,et al.  Overview of Mercury Methylation Capacities among Anaerobic Bacteria Including Representatives of the Sulphate-Reducers: Implications for Environmental Studies , 2009 .

[24]  Guishan Zhang,et al.  Methanogenesis from Methanol at Low Temperatures by a Novel Psychrophilic Methanogen, “Methanolobus psychrophilus” sp. nov., Prevalent in Zoige Wetland of the Tibetan Plateau , 2008, Applied and Environmental Microbiology.

[25]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[26]  Adam P. Arkin,et al.  Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris , 2010 .

[27]  S. Ragsdale,et al.  Structural and Kinetic Evidence for an Extended Hydrogen-bonding Network in Catalysis of Methyl Group Transfer , 2007, Journal of Biological Chemistry.

[28]  S. Elledge,et al.  Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC , 2007, Nature Methods.

[29]  A. Sali,et al.  Statistical potential for assessment and prediction of protein structures , 2006, Protein science : a publication of the Protein Society.

[30]  A. Heyes,et al.  Mercury methylation in estuaries: Insights from using measuring rates using stable mercury isotopes , 2006 .

[31]  C. Gilmour,et al.  Mercury Methylation by Dissimilatory Iron-Reducing Bacteria , 2006, Applied and Environmental Microbiology.

[32]  H. Dobbek,et al.  Structural insights into methyltransfer reactions of a corrinoid iron–sulfur protein involved in acetyl-CoA synthesis , 2006, Proceedings of the National Academy of Sciences.

[33]  Fabrice Armougom,et al.  Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee , 2006, Nucleic Acids Res..

[34]  D. Nelson,et al.  Mercury Methylation from Unexpected Sources: Molybdate-Inhibited Freshwater Sediments and an Iron-Reducing Bacterium , 2006, Applied and Environmental Microbiology.

[35]  Aleksey A. Porollo,et al.  Combining prediction of secondary structure and solvent accessibility in proteins , 2005, Proteins.

[36]  S. Stürup,et al.  Isotope dilution quantification of 200Hg2+ and CH3201Hg+ enriched species-specific tracers in aquatic systems by cold vapor ICPMS and algebraic de-convoluting , 2005 .

[37]  Cédric Notredame,et al.  3DCoffee: combining protein sequences and structures within multiple sequence alignments. , 2004, Journal of molecular biology.

[38]  J A Eisen,et al.  Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments , 2003, Science.

[39]  F. Morel,et al.  Mercury Methylation Independent of the Acetyl-Coenzyme A Pathway in Sulfate-Reducing Bacteria , 2003, Applied and Environmental Microbiology.

[40]  Catherine L Drennan,et al.  A Ni-Fe-Cu Center in a Bifunctional Carbon Monoxide Dehydrogenase/ Acetyl-CoA Synthase , 2002, Science.

[41]  Amos Bairoch,et al.  PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors , 2002, Briefings Bioinform..

[42]  C. Leang,et al.  Development of a Genetic System forGeobacter sulfurreducens , 2001, Applied and Environmental Microbiology.

[43]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[44]  S. Ragsdale,et al.  Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. , 2000, Structure.

[45]  M. Frischer,et al.  Sulfate-Reducing Bacteria Methylate Mercury at Variable Rates in Pure Culture and in Marine Sediments , 2000, Applied and Environmental Microbiology.

[46]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[47]  R. Matthews,et al.  How a protein binds B12: A 3.0 A X-ray structure of B12-binding domains of methionine synthase. , 1994, Science.

[48]  R. Bartha,et al.  Metabolic Pathways Leading to Mercury Methylation in Desulfovibrio desulfuricans LS , 1994, Applied and environmental microbiology.

[49]  R. Bartha,et al.  Enzymatic catalysis of mercury methylation by Desulfovibrio desulfuricans LS , 1994, Applied and environmental microbiology.

[50]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[51]  Ralph Mitchell,et al.  Sulfate stimulation of mercury methylation in freshwater sediments , 1992 .

[52]  S. Ragsdale,et al.  Mössbauer, EPR, and optical studies of the corrinoid/iron-sulfur protein involved in the synthesis of acetyl coenzyme A by Clostridium thermoaceticum. , 1987, The Journal of biological chemistry.

[53]  R. Bartha,et al.  Sulfate-Reducing Bacteria: Principal Methylators of Mercury in Anoxic Estuarine Sediment , 1985, Applied and environmental microbiology.

[54]  N. Pfennig,et al.  Growth yield increase linked to caffeate reduction in Acetobacterium woodii , 1984, Archives of Microbiology.

[55]  H. Wood,et al.  Purification of five components from Clostridium thermoaceticum which catalyze synthesis of acetate from pyruvate and methyltetrahydrofolate. Properties of phosphotransacetylase. , 1981, The Journal of biological chemistry.

[56]  R. Thauer,et al.  Growth of Desulfovibrio species on Hydrogen and Sulphate as Sole Energy Source , 1981 .

[57]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[58]  J. Wood Biological cycles for toxic elements in the environment. , 1974, Science.

[59]  J. M. Pratt,et al.  The kinetics and mechanism of cobalamin-dependent methyl and ethyl transfer to mercuric ion. , 1973, Biochimica et biophysica acta.

[60]  G. Schrauzer,et al.  Acetate synthesis from carbon dioxide and methylcorrinoids. Simulation of the microbial carbon dioxide fixation reaction in a model system , 1970 .

[61]  J. Wood,et al.  Synthesis of Methyl-mercury Compounds by Extracts of a Methanogenic Bacterium , 1968, Nature.

[62]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[63]  N. Kyrpides,et al.  Comparative genome analysis in the integrated microbial genomes (IMG) system. , 2007, Methods in molecular biology.

[64]  H. Hintelmann,et al.  Determination of stable mercury isotopes by ICP/MS and their application in environmental studies. , 2002 .

[65]  F. Nome,et al.  Interaction of cysteine with vitamin B12a: kinetic and thermodynamic investigations , 1976 .