Figure 3.

Evolutionary significance of various identified CSIs in the RNA polymerase β subunit. (A) A portion of the RpoB sequence alignment showing a large insert (boxed) that is distinctive characteristic of all Proteobacteria and some Gram-negative phyla (Chlamydiae-Verrucomicrobiae, Aquificales, Planctomycetes, and Bacteroidetes-Chlorobi), but not found in other phyla of bacteria. Due to the large size of the insert, its entire sequence is not shown. Dashes (–) indicate identity with the amino acid on the top line. On the right is a linear representation of prokaryotic relationships based on the presence and absence of this CSI. The numbers in the brackets indicate the species of each phylum, which have been identified to contain the CSI. (B) A schematic representation of the sequence for E. coli RNA polymerase β subunit (RpoB) showing some functionally important regions and the positions of different lineage-specific inserts that have been identified within this protein. The large insert depicted in (A) (≈ 100 aa in E. coli) is shown in solid black. The positions of CSIs for different groups are roughly indicated using arrows. The values in the brackets identify the number of organisms in each respective group and the number of these species to harbour the indicated CSI. In all cases no organism outside of the indicated group was identified to contain the indel. The indicated CSIs have been described in earlier work (Griffiths and Gupta, 2004b, 2007b; Gupta and Mok, 2007; Gao et al., 2009; Gupta and Bhandari, 2011; Naushad and Gupta, 2012).