Open AccessIn silico analysis of the σ 54 ‐dependent enhancer‐binding proteins in Pirellula species strain 1
Author(s) -
Studholme David J,
Dixon Ray
Publication year - 2004
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1016/s0378-1097(03)00897-8
Subject(s) - regulon , biology , sigma factor , enhancer , rpon , genetics , gene , response regulator , in silico , promoter , rna polymerase , escherichia coli , mutant , gene expression
The planctomycetes are a phylogenetically distinct group of bacteria, widespread in aquatic and terrestrial environments. Their cell walls lack peptidoglycan and their compartmentalised cells undergo a yeast‐like budding cell division process. Many bacteria regulate a subset of their genes by an enhancer‐dependent mechanism involving the alternative sigma factor σ 54 (RpoN, σ N ) in association with σ 54 ‐dependent transcriptional activators known as enhancer‐binding proteins (EBPs). The σ 54 ‐dependent regulon has previously been studied in several groups of bacteria, but not in the planctomycetes. We wished to exploit the recently published complete genome sequence of Pirellula species strain 1 to predict and analyse the σ 54 ‐dependent regulon in this interesting group of bacteria. The genome of Pirellula species strain 1 encodes one homologue of σ 54 , and 16 σ 54 ‐dependent EBPs, including 10 two‐component response regulators and a homologue of Escherichia coli RtcR. Two EBPs contain forkhead‐associated domains, representing a novel protein domain combination not previously observed in bacterial EBPs and suggesting a novel link between the enhancer‐dependent regulon and ‘eukaryotic‐like’ protein phosphorylation in bacterial signal transduction. We identified several potential σ 54 ‐dependent promoters upstream of genes and operons including two homologues of csrA , which encodes the global regulator CsrA, and rtcBA , encoding a RNA 3′‐terminal phosphate cyclase. Phylogenetic analysis of EBP sequences from a wide range of bacterial taxa suggested that planctomycete EBPs fall into several distinct clades. Also the phylogeny of the σ 54 factors is broadly consistent with that of the host organisms. These results are consistent with a very ancient origin of σ 54 within the bacterial lineage. The repertoire of functions predicted to be under the control of the σ 54 ‐dependent regulon in Pirellula shares some similarities (e.g. rtcBA ) as well as exhibiting differences with that in other taxonomic groups of bacteria, reinforcing the evolutionarily dynamic nature of this regulon.