Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics

The reduction of epoxyqueuosine (oQ)
is the last step in the synthesis
of the tRNA modification queuosine (Q). While the epoxyqueuosine reductase
(EC 1.17.99.6) enzymatic activity was first described 30 years ago,
the encoding gene queG was only identified in Escherichia coli in 2011. Interestingly, queG is absent from a large number of sequenced genomes that harbor Q
synthesis or salvage genes, suggesting the existence of an alternative
epoxyqueuosine reductase in these organisms. By analyzing phylogenetic
distributions, physical gene clustering, and fusions, members of the
Domain of Unknown Function 208 (DUF208) family were predicted to encode
for an alternative epoxyqueuosine reductase. This prediction was validated
with genetic methods. The Q modification is present in Lactobacillus
salivarius, an organism missing queG but
harboring the duf208 gene. Acinetobacter
baylyi ADP1 is one of the few organisms that harbor both
QueG and DUF208, and deletion of both corresponding genes was required
to observe the absence of Q and the accumulation of oQ in tRNA. Finally,
the conversion oQ to Q was restored in an E. coli queG mutant by complementation with plasmids harboring duf208 genes from different bacteria. Members of the DUF208 family are
not homologous to QueG enzymes, and thus, duf208 is
a non-orthologous replacement of queG. We propose
to name DUF208 encoding genes as queH. While QueH
contains conserved cysteines that could be involved in the coordination
of a Fe/S center in a similar fashion to what has been identified
in QueG, no cobalamin was identified associated with recombinant QueH
protein.