PCA of H8-loop-H9 motifs in proteobacterial GluRS
To probe further, a separate PCA was performed only on the
H8-L -H9 motifs from proteobacterial GluRSs (Figure 3B). As was
seen earlier (Figure 3A), the tRNAGln-discriminatory
and non-discriminatory GluRSs separated well on the PC1-PC2 plane, with
the separation dominantly along the PC1 axis. The non-discriminatory
GluRSs formed three subclusters along the PC1 axis – (A)
α-proteobacterial T2-GluRS (α-T2), (B) δ-proteobacterial
T2-GluRS/ND-GluRS (δ-T2) and γ-proteobacterial T2-GluRS (γ-T2) and (C)
α-proteobacterial ND-GluRS (α-ND) and ε-proteobacterial T2-GluRS (ε-T2)
– indicating phylum-specific differences in the H8-L -H9 motif
among tRNAGln-non-discriminating GluRSs. The
tRNAGln-discriminating proteobacterial GluRSs also
showed clustering: (D) γ-proteobacterial D(+)-GluRS2 (γ-D+) (E)
α-proteobacterial T1-GluRS (α-T1) and β-proteobacterial D(+)-GluRS2
(β-D+). Cluster F contained the rest of the
tRNAGln-discriminating proteobacterial GluRSs
(including some γ-D+, α-T1 and β-D+ some members of the three classes
that appeared in clusters D and F). Exceptions to the overall
differential appearance of
tRNAGln-discriminating/non-discriminating GluRS were
three members of the α-ND group that appeared in the
tRNAGln-discriminating half, two in cluster-F (CCRCaulobacter vibrioides ; PZU Phenylobacterium zucineum ) and
one in cluster-E (PUB Candidatus Pelagibacter ubique ), and one
member of γ-T1 group that appeared in the
tRNAGln-non-discriminatory half, in cluster-B (TGRThioalkalivibrio sulfidiphilus ). In summary, the distinct
separation between discriminatory and non-discriminatory proteobacterial
GluRSs indicated a significant role of the H8-L -H9 motif in
tRNAGln-discrimination. The phylum-specific variations
indicated that the H8-L -H9 motif may have evolved to facilitate
tRNAGln-discrimination in a phylum-specific way.