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Co-evolution of RNA polymerase with RbpA in the phylum Actinobacteria

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ABSTRACT

The role of RbpA in the backdrop of M. smegmatis showed that it rescues mycobacterial RNA polymerase from rifampicin-mediated inhibition (Dey et al., 2010; Dey et al., 2011). Paget and co-workers (Paget et al., 2001; Newell et al., 2006) have revealed that RbpA homologs occur exclusively in actinobacteria. Newell et al. (2006) showed that MtbRbpA, when complemented in a ∆rbpA mutant of S. coelicolor, showed a low recovery of MIC (from 0.75 to 2 μg/ml) as compared to complementation by native RbpA of S. coelicolor (MIC increases from 0.75 to 11 μg/ml). Our studies on MsRbpA show that it is a differential marker for M. smegmatis RNA polymerase as compared to E. coli RNA polymerase at IC50 levels of rifampicin. A recent sequence-based analysis by Lane and Darst (2010) has shown that RNA polymerases from Proteobacteria and Actinobacteria have had a divergent evolution. E. coli is a representative of Proteobacteria and M. smegmatis is an Actinobacterium. RbpA has an exclusive occurrence in Actinobacteria. Since protein–protein interactions might not be conserved across different species, therefore, the probable reason for the indifference of MsRbpA toward E. coli RNA polymerase could be the lineage-specific differences between actinobacterial and proteobacterial RNA polymerases. These observations led us to ask the question as to whether the evolution of RbpA in Actinobacteria followed the same route as that of RNA polymerase subunits from actinobacterial species. We show that the exclusivity of RbpA in Actinobacteria and the unique evolution of RNA polymerase in this phylum share a co-evolutionary link. We have addressed this issue by a blending of experimental and bioinformatics based approaches. They comprise of induction of bacterial cultures coupled to rifampicin-tolerance, transcription assays and statistical comparison of phylogenetic trees for different pairs of proteins in actinobacteria.

No MeSH data available.


A. Phylogenetic tree of RbpA in Actinobacteria.B: Phylogenetic tree of RNA polymerase β-subunit in Actinobacteria.C: Phylogenetic tree of RNA polymerase β'-subunit in Actinobacteria.D: Phylogenetic tree of RNA polymerase α-subunit.E: Phylogenetic tree of RNA polymerase ω-subunit.F: Phylogenetic tree of GroEL1.G: Phylogenetic tree of glucose-6-phosphate dehydrogenase in Actinobacteria.
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f0020: A. Phylogenetic tree of RbpA in Actinobacteria.B: Phylogenetic tree of RNA polymerase β-subunit in Actinobacteria.C: Phylogenetic tree of RNA polymerase β'-subunit in Actinobacteria.D: Phylogenetic tree of RNA polymerase α-subunit.E: Phylogenetic tree of RNA polymerase ω-subunit.F: Phylogenetic tree of GroEL1.G: Phylogenetic tree of glucose-6-phosphate dehydrogenase in Actinobacteria.

Mentions: Phylogenetic analysis has shown that the trees of RbpA, RNA polymerase β and RNA polymerase β' subunits (Fig. 4A, B, and C) share a similarity in their appearance. As a control, the phylogenetic tree for the gene glucose-6-phosphate dehydrogenase (from same set of species) did not show a similar appearance (Fig. 4G). We have also analyzed the phylogenetic trees of RNA polymerase subunits α and ω, GroEL1 (Fig. 4D, E and F) as well as other genes (as mentioned in the Materials and methods; see Supplementary material). In order to ascertain that the observed similarity was not anecdotal, it was important to calculate the statistical relationship between tree similarities. For this purpose, we computed the pairwise distances between the members of each phylogenetic tree (for the same set of species; the values of the phylogenetic distances have been enlisted in Table 3A to D). Similar data analyses were carried out for the remaining set of trees obtained from the phylogenetic analyses of the other genes (mentioned in Materials and methods; see Supplementary material).


Co-evolution of RNA polymerase with RbpA in the phylum Actinobacteria
A. Phylogenetic tree of RbpA in Actinobacteria.B: Phylogenetic tree of RNA polymerase β-subunit in Actinobacteria.C: Phylogenetic tree of RNA polymerase β'-subunit in Actinobacteria.D: Phylogenetic tree of RNA polymerase α-subunit.E: Phylogenetic tree of RNA polymerase ω-subunit.F: Phylogenetic tree of GroEL1.G: Phylogenetic tree of glucose-6-phosphate dehydrogenase in Actinobacteria.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121209&req=5

f0020: A. Phylogenetic tree of RbpA in Actinobacteria.B: Phylogenetic tree of RNA polymerase β-subunit in Actinobacteria.C: Phylogenetic tree of RNA polymerase β'-subunit in Actinobacteria.D: Phylogenetic tree of RNA polymerase α-subunit.E: Phylogenetic tree of RNA polymerase ω-subunit.F: Phylogenetic tree of GroEL1.G: Phylogenetic tree of glucose-6-phosphate dehydrogenase in Actinobacteria.
Mentions: Phylogenetic analysis has shown that the trees of RbpA, RNA polymerase β and RNA polymerase β' subunits (Fig. 4A, B, and C) share a similarity in their appearance. As a control, the phylogenetic tree for the gene glucose-6-phosphate dehydrogenase (from same set of species) did not show a similar appearance (Fig. 4G). We have also analyzed the phylogenetic trees of RNA polymerase subunits α and ω, GroEL1 (Fig. 4D, E and F) as well as other genes (as mentioned in the Materials and methods; see Supplementary material). In order to ascertain that the observed similarity was not anecdotal, it was important to calculate the statistical relationship between tree similarities. For this purpose, we computed the pairwise distances between the members of each phylogenetic tree (for the same set of species; the values of the phylogenetic distances have been enlisted in Table 3A to D). Similar data analyses were carried out for the remaining set of trees obtained from the phylogenetic analyses of the other genes (mentioned in Materials and methods; see Supplementary material).

View Article: PubMed Central - PubMed

ABSTRACT

The role of RbpA in the backdrop of M. smegmatis showed that it rescues mycobacterial RNA polymerase from rifampicin-mediated inhibition (Dey et al., 2010; Dey et al., 2011). Paget and co-workers (Paget et al., 2001; Newell et al., 2006) have revealed that RbpA homologs occur exclusively in actinobacteria. Newell et al. (2006) showed that MtbRbpA, when complemented in a ∆rbpA mutant of S. coelicolor, showed a low recovery of MIC (from 0.75 to 2 μg/ml) as compared to complementation by native RbpA of S. coelicolor (MIC increases from 0.75 to 11 μg/ml). Our studies on MsRbpA show that it is a differential marker for M. smegmatis RNA polymerase as compared to E. coli RNA polymerase at IC50 levels of rifampicin. A recent sequence-based analysis by Lane and Darst (2010) has shown that RNA polymerases from Proteobacteria and Actinobacteria have had a divergent evolution. E. coli is a representative of Proteobacteria and M. smegmatis is an Actinobacterium. RbpA has an exclusive occurrence in Actinobacteria. Since protein–protein interactions might not be conserved across different species, therefore, the probable reason for the indifference of MsRbpA toward E. coli RNA polymerase could be the lineage-specific differences between actinobacterial and proteobacterial RNA polymerases. These observations led us to ask the question as to whether the evolution of RbpA in Actinobacteria followed the same route as that of RNA polymerase subunits from actinobacterial species. We show that the exclusivity of RbpA in Actinobacteria and the unique evolution of RNA polymerase in this phylum share a co-evolutionary link. We have addressed this issue by a blending of experimental and bioinformatics based approaches. They comprise of induction of bacterial cultures coupled to rifampicin-tolerance, transcription assays and statistical comparison of phylogenetic trees for different pairs of proteins in actinobacteria.

No MeSH data available.