Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes

Abstract

Background: The SOS response is a well-known regulatory network present in most bacteria and aimed at addressing DNA damage. It has also been linked extensively to stress-induced mutagenesis, virulence and the emergence and dissemination of antibiotic resistance determinants. Recently, the SOS response has been shown to regulate the activity of integrases in the chromosomal superintegrons of the Vibrionaceae, which encompasses a wide range of pathogenic species harboring multiple chromosomes. Here we combine in silico and in vitro techniques to perform a comparative genomics analysis of the SOS regulon in the Vibrionaceae, and we extend the methodology to map this transcriptional network in other bacterial species harboring multiple chromosomes.

Results: Our analysis provides the first comprehensive description of the SOS response in a family (Vibrionaceae) that includes major human pathogens. It also identifies several previously unreported members of the SOS transcriptional network, including two proteins of unknown function. The analysis of the SOS response in other bacterial species with multiple chromosomes uncovers additional regulon members and reveals that there is a conserved core of SOS genes, and that specialized additions to this basic network take place in different phylogenetic groups. Our results also indicate that across all groups the main elements of the SOS response are always found in the large chromosome, whereas specialized additions are found in the smaller chromosomes and plasmids.

Conclusions: Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and dissemination of antibiotic resistance, and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an essential role in these organisms and sheds light into the mechanisms of evolution of global transcriptional networks involved in adaptability and rapid response to environmental changes, suggesting that small chromosomes may act as evolutionary test beds for the rewiring of transcriptional networks.

Figure 1

Tabulated description of the LexA regulon of the Vibrionaceae. Colors indicate the presence and location of the gene and patterns denote presence (plain) or absence (patterned) of one or more LexA-binding sites in its promoter region. E. coli genes and their corresponding regulation are shown for comparative purposes. Abbreviations are as follows: Eco, E. coli; Vch, V. cholerae; Vha, V. harveyi; Vpa, V. parahaemolyticus; Vsp, Vibrio splendidus; Vvu, V. vulnificus; Asa, A. salmonicida; Vfi, V. fischeri; Ppr, Photobacterium profundum.

Figure 2

Schematic representation of the uvrA-ssb divergent pair and the ruvCAB operon in different Vibrionaceae species. The figure illustrates the persistence of ssb regulation despite gene insertions and the disruption of the ruvCAB operon by gene insertions in some Vibrio species. Genes are represented by filled arrows. Grey-filled arrows correspond to genes that do not constitute part of the canonical uvrA-ssb and ruvCAB elements. Black triangles indicate predicted LexA-binding sites. GenBank accession numbers and absolute genome coordinates for each bacterial species are provided for reference.

Figure 3

EMSA of the promoter region for several V. parahaemolyticus genes in the presence (+) or absence (-) of purified LexA protein from this organism. Competition assays (Additional file 3) were conducted to validate the specificity of LexA binding. The absence of purified LexA protein is used as a negative control for each EMSA. The lexA, recA and imuA promoter regions are used as positive controls.

Figure 4

Tabulated description of the predicted LexA regulon of α-Proteobacteria species with multiple chromosome genomes. Colors indicate the presence and location of the gene and patterns denote presence (plain) or absence (patterned) of one or more LexA-binding sites in its promoter region. E. coli genes and their corresponding regulation are shown for comparative purposes. Eco, E. coli; Arad, Agrobacterium radiobacter; Atu, A. tumefaciens; Avi, Agrobacterium vitis; Bab, Brucella abortus; Bca, Brucella canis; Bme, Brucella melitensis; Bov, Brucella ovis; Bsu, Brucella suis; Oant, Ochrobactrum anthropi; Pden, Paracoccus denitrificans; Rsph, Rhodobacter sphaeroides; Sme, S. meliloti.

Figure 5

Tabulated description of the predicted LexA regulon of β-Proteobacteria species with multiple chromosome genomes. Colors indicate the presence and location of the gene and patterns denote presence (plain) or absence (patterned) of one or more LexA-binding sites in its promoter region. E. coli genes and their corresponding regulation are shown for comparative purposes. Eco, E. coli; B. 383, Burkholderia sp.; Bamb, Burkholderia ambifaria; Bcen, Burkholderia cenocepacia; Bglu, Burkholderia glumae; Bmal, Burkholderia mallei; Bmul, Burkholderia multivorans; Bphy, Burkholderia phymatum; Bphyt, Burkholderia phytofirmans; Bpse, Burkholderia pseudomallei; Btha, Burkholderia thailandensis; Bvie, Burkholderia vietnamiensis; Bxen, Burkholderia xenovorans; Reut, Ralstonia eutropha; Rmet, Ralstonia metallidurans; Rpic, Ralstonia pickettii; Ctai, Cupriavidus taiwanensis; Vpar, Variovorax paradoxus.