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.