Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria

In this study, we have sequenced the rpoB gene, encoding the beta subunit of DNA-dependent RNA polymerase, from a selection of Gram-positive and Gram-negative bacteria. The presence of insertions and deletions (indels) in the beta subunit separate the Gram-positive and Gram-negative bacteria from each other and support the division of the Gram-positive organisms into two clades based on DNA G+C content. Phylogenetic and amino acid content analyses further separate the clostridia from bacilli, leuconostocs, listeriae and relatives, forming an early branch after the common Gram-positive ancestor. The occurrence in the beta subunit of Asn-Ala at positions 471-472 in Porphyromonas cangingivalis and Asn at position 372 in Weissella paramesenteroides are postulated to be the cause of the natural rifampicin resistance of these species.