Co-occurrence of AprX with a σ⁵⁴-promoter consensus sequence upstream of xrpA in Rhodobacterales.

A, The species phylogeny is based on RpoC and includes representative species that have xrpA. The Family is indicated by the branch color: blue (Paracoccaceae) and magenta (Roseobacteraceae). The presence of RpoN and AprX is indicated by green dots and yellow triangles, respectively. The red stars indicate the presence of a putative σ⁵⁴-promoter upstream of xrpA. The collapsed branches include 70 species of Roseobacteraceae that do not have an AprX homologue and do not show a σ⁵⁴-promoter sequence upstream of xrpA. Complete information for each species, including the GenBank accession number for each genome, as well as for the proteins RpoC, XrpA, and AprX, is provided in S2 Table. B, Sequence LOGO representation of the conserved motif found upstream of xrpA; the sequences from the 28 species that have an xrpA homologous gene were included in the analysis. The sequence is highly similar to the RpoN binding motif previously reported for S. typhimurium (see Fig 4).