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Comparative Genomics Reveal Genes Used by Mercury-Methylating Microbes

NEW YORK (GenomeWeb) – Orthologs of the same gene pair seem to spur mercury methylation across a range of bacterial and archaeal species, according to a study published online today in Science.

"Among bacteria and archaea with sequenced genomes, gene orthologs are present in confirmed methylators but absent in non-methylators," the study's authors explained, "suggesting a common mercury methylation pathway in all methylating bacteria and archaea sequenced to date."

A team led by researchers at Oak Ridge National Laboratory and the University of Tennessee tracked down the two genes — a corrinoid protein-coding gene called hgcA and a corrinoid-associated ferredoxin gene, hgcB — by comparing genome sequences from six mercury-methylating bacterial species and eight related species that don't methylate the inorganic element.

The team saw the same two-gene cluster within certain bacteria from both the Proteobacteria and Firmicutes phyla and in some members of an archaeal phylum called Euryarchaeota, though the reason for the genes' presence or absence still needs to be worked out.

"The sparse phylogenetic gene distribution of the hgcAB system may be due to gene loss, lateral gene transfer, or both, across distant taxa" ORNL's Liyuan Liang and Dwayne Elias with ORNL and the University of Tennessee, and their co-authors explained, "and may be linked to environmental and community structure factors."

Several microbes — including the anaerobic bacteria Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA — are known for turning inorganic mercury into a methylated compound called methylmercury that can subsequently enter the food chain.

The genes and pathways behind that feat are of interest from both basic biological and health perspectives, authors of the new study explained, since methylmercury acts as a neurotoxin in humans and some other animals.

For its part, the team brought together data for 14 sequenced bacterial species, specifically comparing the genomic features found in half a dozen species known for methylating mercury with those present in eight related, but non-mercury-methylating, bugs.

As part of this comparison, the group considered whether the methylating and non-methylating species might show differences related to a so-called corrinoid pathway, since a corrinoid iron-sulfur protein has been linked to other types of methyl transfer in bacteria.

With that in mind, researchers narrowed in on two genes, hgcA and hcgB, that are believed to code for methyl carrier and electron donor proteins during corrinoid cofactor-mediated mercury methylation.

In the absence of either gene (or their orthologs), neither D. desulfuricans ND132 nor G. sulfurreducens could carry out mercury methylation, they found, supporting the notion that both members of the gene cluster are vital to this process.

Orthologs of the mercury-methylating hgcAB gene pair showed up in other mercury-methylating microbes, too, suggesting the sequences could be a universal feature of bacteria and archaea prone to producing methylmercury.

The study authors noted that this explanation is "in agreement with all currently available sequence information for methylating bacteria and archaea," but they also cautioned that "[i]n the absence of genome sequences for all [mercury]-methylating organisms, the generality of the present findings cannot yet be ascertained."

More research is also needed to get a complete mechanistic view of mercury methylation, the team added, and to understand why this pathway is present in certain microbes and not others.

"The sporadic distribution of these genes and the lack of an obvious selective advantage related to mercury toxicity raise important questions regarding their physiological roles," they wrote, while the "[i]dentification of these genes is a critical step linking specific microorganisms and environmental factors that influence microbial [mercury] methylation in aquatic ecosystems."

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