Database of curated H8-L-H9 motif sequences from
bacterial GluRS
Is the unique D-helix interacting H8-L -H9 motif in GluRS a
“protein” signature of tRNAGlx-discrimination that
complements the GluRS-discriminatory D-helix signature on
“tRNAGln” ? To address this question, we first
classified the H8-L -H9 motif of bacterial GluRSs. Subsequently,
we sought a correlation between different classes of H8-L -H9
motif and the intrinsic tRNAGln-discrminatory
character of GluRSs they belong to. In order to analyze GluRS sequences
with a focus on the H8-L -H9 motif, a comprehensive and curated
bacterial GluRS sequence database is required. We had earlier curated
such a database (4), based on the presence/absence of a second copy of
GluRS, the presence of GlnRS and the presence of gatCAB in each
bacterial genome.
The presence of GlnRS in the genome signifies that the corresponding
GluRS in the genome is tRNAGln-discriminatory
(D-GluRS). Further, the GluRS is designated as D(-) if the genome lacks
gatCAB (for which GluRS must strictly be
tRNAGln-discriminatory since misacylated
Glu-tRNAGln cannot be transformed to
Gln-tRNAGln) or D(+) if the genome contains gatCAB
(the GluRS may not be strictly tRNAGln-discriminatory,
since misacylated Glu-tRNAGln can still be transformed
to Gln-tRNAGln by gatCAB). The absence of GlnRS in the
genome (in this case the genome always contains gatCAB), and the
presence of a single copy of GluRS in the genome signifies that the
genomic GluRS is tRNAGln-non-discriminatory
(ND-GluRS). When the genome lacked GlnRS but contained twin copies of
GluRS, the GluRSs are designated as T1-GluRS and T2-GluRS. To summarize,
D(-)-GluRS glutamylates only tRNAGlu and is strictly
discriminatory against tRNAGln, D(+)-GluRS
glutamylates tRNAGlu and possibly discriminates
against tRNAGln, ND-GluRS glutamylates both
tRNAGlu and tRNAGln. Experiments
performed on a few twin GluRSs (10,11) suggest that T1-GluRS
glutamylates tRNAGlu and discriminates against
tRNAGln, while T2-GluRS possibly glutamylates
tRNAGln and not tRNAGlu.
Following this nomenclature scheme, complete genomic sequences of 433
bacterial species were analyzed from the KEGG database
(www.genome.jp/kegg) and annotated as D(-)-GluRS, D(+)-GluRS, ND-GluRS,
T1-GluRS and T2-GluRS. Table S1 shows the sequence alignment of GluRS
H8-L -H9 motifs for all bacterial GluRSs sequences used in this
work, annotaed with the organism name (3 letter code used in the KEGG
database) and the tRNAGlx-discriminatory status, as
arrived from whole genome analysis.