An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria
ABSTRACTThe SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In theBetaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N8-ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacteriumSideroxydans lithotrophicus.In silicoandin vitroanalyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of theBacillus subtilisLexA-binding motif. We confirm that the closely relatedGallionella capsiferriformansshares the same LexA-binding motif, andin silicoanalyses indicate that this motif is also conserved in theNitrosomonadalesand theMethylophilales. Phylogenetic analysis of LexA and the alpha subunit of DNA polymerase III (DnaE) reveal that the organisms harboring this noncanonical LexA form a compact taxonomic cluster within theBetaproteobacteria. However, theirlexAgene is unrelated to the standardBetaproteobacterialexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon ofS. lithotrophicusis comparable in size and function to that of many otherBetaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain ofS. lithotrophicusLexA reveals little sequence similarity with that of other LexA proteins targeting similar binding motifs, suggesting that network structure may limit site evolution or that structural constrains make theB. subtilis-type motif an optimal interface for multiple LexA sequences.IMPORTANCEUnderstanding the evolution of transcriptional systems enables us to address important questions in microbiology, such as the emergence and transfer potential of different regulatory systems to regulate virulence or mediate responses to stress. The results reported here constitute the first characterization of a noncanonical LexA protein regulating a standard SOS regulon. This is significant because it illustrates how a complex transcriptional program can be put under the control of a novel transcriptional regulator. Our results also reveal a substantial degree of plasticity in the LexA recognition domain, raising intriguing questions about the space of protein-DNA interfaces and the specific evolutionary constrains faced by these elements.