International Journal of Systematic and Evolutionary Microbiology, Vol 52, 1477-1484, Copyright © 2002 by Society for General Microbiology

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

R. Morse, K. O'Hanlon and M. D. Collins
Food Microbial Sciences Unit, School of Food Biosciences, University of Reading, Whiteknights, PO Box 226, Reading RG6 6AP, UK

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.

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