An inventory of genes encoding RNA polymerase sigma factors in 31 completely sequenced eubacterial genomes

Sigma factors are important elements involved in transcriptional regulation of gene expression by conferring promoter specificity to RNA polymerase. The number of sigma factor encoding genes in 31 completely sequenced bacterial genomes were compared. Two unrelated families of sigma factors, the sigma70- and the sigma54-family were identified previously. The sigma70-family can be further subdivided into two distantly related groups: the sigma70 subfamily and the poorly characterized ECF subfamily. A total of 215 sigma factors could be attributed to these subfamilies. The construction of phylogenetic trees allows subclassifications of sigma factor encoding genes within the subfamilies. With the exception of Deinococcus radiodurans, all species possess a housekeeping primary sigma factor. Free-living species possess a higher number of both sigma70-type and ECF alternative sigma factors than pathogens or symbionts associated with animals. Different bacterial species exhibit large differences in the number of alternative sigma factor encoding genes and consequently huge flexibility in their transcriptional regulatory patterns. Transcriptional regulation in terms of regulons controlled by alternative sigma factors is a late evolving phenomenon. The current nomenclature for sigma factor encoding genes is confusing and should be revised.