PCA of H8-loop-H9 motifs in non-proteobacterial GluRS
The non-proteobacterial H8-L -H9 cluster of Figure 3A (cluster C)
was analyzed further using a separate PCA. As can be seen from Figure
3C, the H8-L -H9 motifs, showed a bias in their appearance on the
PC1-PC2 plane depending upon whether they belonged to
tRNAGln-discriminating (red circles) or
non-discriminating (blue circles) GluRS. However, there was substantial
overlap. Since GluRS sequence variation can be highly phylum-specific,
we then looked at only those cases where both discriminating and
non-discriminating GluRSs were present within the same class. Two such
classes, firmicutes (Fi ) and hyperthermophilic bacteria
(Ht ) in our database contained GluRS of both kinds
(T1-GluRS/T2-GluRS for Ht and D(+)-GluRS/ND-GluRS for Fi ).
The GluRS H8-L -H9 motifs in these two classes showed a clear
sequence difference depending on their
tRNAGln-specificity. For Ht (Figure 3D) all
five pairs of T1-GluRS1/T2-GluRS separated into two distinct clusters.
Sequence comparison of the two groups (Figure S3A) showed the unique
presence of HPE(D)GK sequence at the center of the H8-L -H9 loop
in T2-GluRSs absent in T1-GluRSs. Similarly, for Fi (Figure 3E),
all H8-L -H9 motifs were separated into two clusters depending
upon the tRNAGln-specificity of the corresponding
GluRSs. Sequence comparison of the two groups (Figure S3B) showed the
unique presence of Gly in ND-GluRSs (FMA is an exception); the D-GluRSs
either lacked the Gly residue
(replaced by Thr, Glu, Asp or Asn) or contained a 2-residue (WR)
insertion at the center of H8-L -H9 motif.