mer Genes Broadens Mercury

Overview

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Key numbers

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identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in
were identified in a number of genomes (∼50% of all MerB-encoding genomes) that
dihydrolipoamide dehydrogenase from Magnetospirillum and bacterial genomes (Table 1; Supplementary Table 1),
HB27 (YP_005669), Pseudomonas fluorescens Pf0-1 homologs (Table 2). The 7544 MerA homologs were derived from
trimmed from the alignment block as previously described (13.8%) encoded MerA homologs and these were distributed
(Barkay et al., 2010; Boyd and Barkay, 2012). The aligned among 12 phyla (Table 1). The 307 archaeal MerA protein
optimal substitution model and parameters for the phylogenetic (Table 1; Boyd and Barkay, 2012), and include homologs from
are available in fasta format in Supplementary Dataset 2. Nearly all (99.6% of total) MerA encoding archaeal genomes
Compiled MerB protein homologs were aligned with Clustal coded for a single copy (Table 2) with the exception of
included in IQ-TREE version 1.6.12 as mentioned above. The MerA encoded in C. divulgatum are highly similar (89.2%
6274 (7.75%) encoded MerA homologs (Table 1). An additional
(Table 1), out of the 1148 plasmid genomes queried. The 7207
Giovannonibacteria, among others (Table 1). Further, homologs
Table 1) and these were distributed among 6574 archaeal strains are frequently isolated from environments impacted
TABLE 1 | Number of genomes that encode MerA or MerB protein homologs and their distribution at the Phylum level in the database constructed in 2012 (Boyd and
TABLE 1 | Continued
TABLE 2 | Abundance of archaeal, bacterial, and plasmid genomes that encode one or more MerA or MerB protein homologs.
genome are identical (100% sequence identities) suggesting phenylalanine in archaeal homologs (Supplementary Figure 1).
from characterized sequences, in particular, at position 605 phenylalanine in this same position (Supplementary Table 2).
Euryarchaeota (Supplementary Table 2). All but two of these et al., 2015). These 8 homologs probably originated from 2
with a MerA homolog with the typical residue at that position groups that each comprise 4 identical (100% sequence identities)
(canonical MerA) (Supplementary Table 1). To date, no MerA homologs; the 100% similarity within each group suggests
with 94 genomes encoding multiple homologs (up to 8; Table 2). cereus strain #17 broadens the range of organomercurials that
Among the 1959 archaeal genomes examined, 11 (0.6%) organomercurials, leading to selection for a strain that encoded
(Table 1). Demethylation of MeHg has not yet been described environmental organomercurials that selected for this high level
(Table 2). Interestingly, MerB homologs were not identified cysteines at position 159 and 117. Apart from the MerB homologs
(2.4%) encoded MerB protein homologs and these were acid signatures, these homologs were designated as MerB-like
divisions (Table 1), including 11 new phyla and candidate like variant 99Ser, serine is found at position 99 instead of aspartic
the Nitrospirae, Spirochetes, and Chloroflexi along with the Figure 1; Supplementary Table 3). The 13 MerB-like 99Ser
and Acidithiobacillia, among others (Table 1). Additionally, 7 MerB with the aforementioned canonical sequence signatures;
with 1 plasmid containing 2 homologs (Table 2). Studies on Firmicutes. Previous structural and biochemical characterization
been focused on proteobacterial (Pitts and Summers, 2002) and 2016) has shown that they have expanded range of affinities
strain #17 (Supplementary Table 3; Table 2). This strain an affinity for other divalent metals is thus not well understood
detoxification enzymes than canonical MerB. If so, strains MerA homolog, 732 (81.3%) belong to the genera Clostridioides,
clear. Pitts and Summers (2002), who initially identified it as Table 1). These genera include aerobic, facultatively anaerobic,
to Actinobacteria and Firmicutes (Supplementary Table 3). to reveal a pattern in the distribution of organismal genomes
and Spirochetes (Supplementary Table 3). Crystallographic, and Barkay, 2012; Grégoire and Poulain, 2018). Organomercury
of our knowledge, the activity and/or substrate range of variants et al., 2004) raising questions about how MerB catalysis can
of 906 genomes, slightly higher than 50% of all merB-carrying reduction in cells are examined with the goal of identifying
Table 1). These included 10 draft genomes and 896 finished The suggested mechanisms could be tested for their role in
in the case of MAGs, it is possible that a MerA-encoding plasmid detoxification (Table 3). Constitutive Hg(II) reduction was
TABLE 3 | Possible Hg(II) detoxification mechanisms independent of the mer system1 .

Methods (brief)

was isolated from a mouse gut microbiome sample (Böhm especially when a native MerB 99Ser, in B. megaterium MerB2,
environmental samples. 2003; Taubner et al., 2006; Kaur and Subramanian, 2014),
collected from the Juan de Fuca ridge (Jungbluth et al., 2017). reconstructions of MerB (Supplementary Figure 2). Other
branching lineages of crenarchaeal and thaumarchaeal MerA 2015), these mats were collected from a low-temperature
Volodin, A. A., et al. (1998). Horizontal spread of mer operons among Gram- Mercury as a global pollutant: sources, pathways, and effects. Environ. Sci.
isolated from activated sludge. Stand. Genomic Sci. 13:32. doi: 10.1186/s40793- Acidulodesulfobacterales by metagenomics and metatranscriptomics. ISME J.

Implications

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Update history

The five most recent substantive edits to this page, classified major (evidence or structure moved), correction (a published value or statement was wrong and has been fixed), or minor (narrative rewritten without changing the underlying evidence). Each description is derived from what the edit did to this page; the linked commit is the authoritative record, routine regeneration passes are excluded, and the full version history lives in git. When DOI minting comes online (see schema docs), each entry below will also link to a version-pinned DataCite DOI.

Commit	Date	Change	Description
b01ec52c	2026-08-04	major	2 sections added
d49e450f	2026-08-03	major	5 sections added; narrative text revised