An unusual primary sigma factor in the Bacteroidetes phylum.

The presence of housekeeping gene promoters with a unique consensus sequence in Bacteroides fragilis, previously described by Bayley et al. (2000, FEMS Microbiol Lett 193: 149-154), suggested the existence of a particular primary sigma factor. The single rpoD-like gene observed in the B. fragilis genome, and similarly in those of other members of the Bacteroidetes phylum, was found to be essential. It encodes a protein, sigma(ABfr), of only 32.7 kDa that is produced with equal abundance during all phases of growth and was concluded to be the primary sigma factor. sigma(ABfr) and its orthologues in the Bacteroidetes are unusual primary sigma factors in that they lack region 1.1, have a unique signature made up of 29 strictly identical amino acids and are the only RpoD factors that cluster with the RpoS factors. Although binding to the Escherichia coli core RNA polymerase, sigma(ABfr) does not support transcription initiation from any promoter when it is part of the heterologous holoenzyme, while in the reconstituted homologous holoenzyme it does so only from typical B. fragilis, including rrs, promoters but not from the lacUV5 or RNA I promoters.