Interspecies regulation of the recA gene of gram-negative bacteria lacking an E. coli-like SOS operator

Multiple Ku orthologues mediate DNA non-homologous end-joining in the free-living form and during chronic infection of Sinorhizobium meliloti

The bacterial non-homologous end-joining (NHEJ) apparatus is a two-component system that uses Ku and LigD to repair DNA double-strand breaks. Although the reaction mechanism has been extensively studied, much less is known about the physiological role of bacterial NHEJ. Recent studies suggest that NHEJ acts under conditions where DNA replication is reduced or absent (such as in a spore or stationary phase). Interestingly, genes encoding Ku and LigD have been identified in a wide range of bacteria that can chronically infect eukaryotic hosts. Strikingly, Sinohizobium meliloti, an intracellular symbiont of legume plants, carries four genes encoding Ku homologues (sku1 to sku4). Deletion analysis of the sku genes indicated that all Ku homologues are functional. One of these genes, sku2, is strongly expressed in free-living cells, as well as in bacteroid cells residing inside of the host plant. To visualize the NHEJ apparatus in vivo, SKu2 protein was fused to yellow fluorescent protein (YFP). Ionizing radiation (IR) induced focus formation of SKu2-YFP in free-living cells in a dosage-dependent manner. Moreover, SKu2-YFP foci formed in response to IR in non-dividing bacteroids, indicating that NHEJ system is functional even during the chronic infection phase of symbiosis.

Aeons of distress: an evolutionary perspective on the bacterial SOS response

The SOS response of bacteria is a global regulatory network targeted at addressing DNA damage. Governed by the products of the lexA and recA genes, it co-ordinates a comprehensive response against DNA lesions and its description in Escherichia coli has stood for years as a textbook paradigm of stress-response systems in bacteria. In this paper we review the current state of research on the SOS response outside E. coli. By retracing research on the identification of multiple diverging LexA-binding motifs across the Bacteria Domain, we show how this work has led to the description of a minimum regulon core, but also of a heterogeneous collection of SOS regulatory networks that challenges many tenets of the E. coli model. We also review recent attempts at reconstructing the evolutionary history of the SOS network that have cast new light on the SOS response. Exploiting the newly gained knowledge on LexA-binding motifs and the tight association of LexA with a recently described mutagenesis cassette, these works put forward likely evolutionary scenarios for the SOS response, and we discuss their relevance on the ultimate nature of this stress-response system and the evolutionary pressures driving its evolution.

Mutational analysis of the Rhizobium etli recA operator

Based upon our earlier studies (A. Tapias, A. R. Fernández de Henestrosa, and J. Barbé, J. Bacteriol. 179:1573-1579, 1997) we hypothesized that the regulatory sequence of the Rhizobium etli recA gene was TTGN11CAA. However, further detailed analysis of the R. etli recA operator described in the present work suggests that it may in fact be GAACN7GTAC. This new conclusion is based upon PCR mutagenesis analysis carried out in the R. etli recA operator, which indicates that the GAAC and GTAC submotifs found in the sequence GAACN7GTAC are required for the maximal stimulation of in vivo transcription and in vitro DNA-protein complex formation. This DNA-protein complex is also detected when the GAACN7GTAC wild-type sequence is modified to obtain GAACN7GAAC, GTACN7GTAC, or GAACN7GTTC. The wild-type promoters of the Rhizobium meliloti and Agrobacterium tumefaciens recA genes, which also contain the GAACN7GTAC sequence, compete with the R. etli recA promoter for the DNA-protein complex formation but not with mutant derivatives in any of these motifs, indicating that the R. etli, R. meliloti, and A. tumefaciens recA genes present the same regulatory sequence.

Identification of the Rhodobacter sphaeroides SOS box

Gel-mobility shift assays with crude cell extracts of Rhodobacter sphaeroides, which belongs to the alpha group of the proteobacteria, have shown that a protein binds to the promoter of its recA gene, resulting in two retardation bands. Analysis of the minimal region of the R. sphaeroides recA gene required for the formation of the DNA-protein complexes, revealed the presence of the motifs GTTCN7GATC and GAACN7GAAC, which are centred at positions -21 and +8 from the transcriptional starting point respectively. Using PCR mutagenesis, we have demonstrated that these two motifs are required for the formation of both DNA-protein complexes in vitro as well as for the DNA damage-mediated inducibility of the recA gene in vivo. Furthermore, the level of the recA gene expression in the constitutive mutants is the same as that achieved by the wild-type cells after DNA damage, indicating that the binding protein must be a repressor. The motif GTTCN7GTTC is also present upstream of the R. sphaeroides uvrA promoter, which in vitro specifically binds to a protein and whose expression is DNA damage inducible. Mutagenesis of this motif abolishes both the binding of this protein to the uvrA promoter and the DNA damage-mediated expression of this gene. The fact that the recA and uvrA wild-type promoters compete with each other for the retardation band formation, but not with their mutant derivatives in any of these motifs, indicates that the same repressor binds to the operator of both genes. All these results lead us to propose the sequence GTTCN7GTTC as the SOS box of R. sphaeroides. This is the first SOS box known whose sequence is a direct repeat and not a palindrome.

Absence of an SOS-like system in Neisseria gonorrhoeae

The DNA repair capacities of Neisseria gonorrhoeae have not been well characterised, however, it is known that the gonococcus possesses an excision repair system. The fact that genes in this system are part of the SOS regulon in Escherichia coli prompted this investigation into the transcriptional regulation of genes involved in DNA repair in N. gonorrhoeae. Northern (RNA-DNA) dot blot hybridisation was used to investigate potential DNA damage-mediated induction of the gonococcal recA, uvrA and uvrB genes. In contrast to the situation in E. coli, transcription of these genes in N. gonorrhoeae was not induced in response to treatment with methyl methanesulfonate (MMS) and UV light. These data indicated that the gonococcus does not possess an SOS-like system that is induced in response to DNA damage.

Characterization and expression analysis of a Xanthomonas oryzae pv. oryzae recA

Nucleotide sequence of Xanthomonas oryzae pv. oryzae (Xoo) DNA from pSM-A1 was determined and sequence analysis revealed an ORF with high homology to RecA proteins. Expression analysis using an anti-RecA antibody demonstrates that MMS treatment induces recA in Xanthomonas strains but not in an Escherichia coli harbouring cloned Xoo recA. This indicates the existence of a recA regulatory mechanism in Xanthomonas that is not function in E. coli. In Xoo, recA was highly induced by treatments with chemical mutagens, UV and peroxides, while superoxides, a thiol agent, a heavy metal and heat shock were not inducers. The increased amount of RecA induced by H2O2 or MMS treatments were due to increased transcription of recA. recA showed no growth phase or starvation regulation. The pattern of recA regulation in Xoo could play important roles in stress survival in the environment and during plant-microbe interactions.

Characterization of the promoter of the Rhizobium etli recA gene

The promoter of the Rhizobium etli recA gene has been identified by primer extension and by making deletions affecting several regions located upstream of its coding region. A gel mobility shift assay carried out with crude extracts of cells of R. etli has been used to show that a DNA-protein complex is formed in the R. etli recA promoter region in vitro. Analysis of the minimal region of the recA promoter giving rise to this DNA-protein complex revealed the presence of an imperfect palindrome corresponding to the sequence TTGN11CAA. Site-directed mutation of both halves of this palindrome indicated that both motifs, TTG and CAA, are necessary for both normal DNA-protein complex formation in vitro and full DNA damage-mediated inducibility of the recA gene in vivo. However, the TTG motif seems to be more dispensable than the CAA one. The presence of this same palindrome upstream of the recA genes of Rhizobium meliloti and Agrobacterium tumefaciens, whose expression is also regulated in R. etli cells, suggests that this TTGN11CAA sequence may be the SOS box of at least these three members of the Rhizobiaceae.

The uvrB gene of Pseudomonas aeruginosa is not DNA damage inducible

The uvrB gene of Pseudomonas aeruginosa has been isolated from a genomic library by complementation of an Escherichia coli uvrB mutant. The complete nucleotide sequence of P. aeruginosa uvrB consists of 2,013 bp, encoding a polypeptide of 670 amino acids. A P. aeruginosa SOS consensus region, which functions as a binding site for the LexA repressor molecule, is not present in the upstream region of the uvrB gene isolated. By transcriptional fusions with a reporter gene, it has been demonstrated that, contrary to what happens with the homologous gene of E. coli, the P. aeruginosa uvrB gene is not DNA damage inducible. Nevertheless, the UvrB protein must be functional in P. aeruginosa cells because a uvrB-defective mutant is extremely sensitive to UV radiation.

New mini-Tn5 derivatives for insertion mutagenesis and genetic engineering in gram-negative bacteria

Five mini-Tn5 derivatives encoding resistance to Km, Cm, Gm, Tc, and Sm, coupled with the polylinker of the pBluescriptII plasmid, were constructed. These derivatives are carried by an ampicillin-resistant plasmid that has a conditional origin of replication from plasmid R6K and origin of conjugal transfer from the broad host range plasmid RP4. The new vectors are smaller than those previously described and possess numerous unique restriction sites inside the minitransposons for gene cloning in addition to SfiI and NotI sites found in their predecessors.

Non-reciprocal regulation of Rhodobacter capsulatus and Rhodobacter sphaeroides recA genes expression

The Rhodobacter capsulatus recA gene has been isolated and sequenced. Its deduced amino acid sequence showed the closest identity with the Rhodobacter sphaeroides RecA protein (91% identity). However, the promoter regions of both R. capsulatus and R. sphaeroides recA genes are only 64% similar. An Escherichia coli-like LexA binding site was not present in the upstream region of the R. capsulatus recA gene. Nevertheless, the R. capsulatus recA gene is inducible by DNA damage in both hetero- and phototrophically growing conditions. The R. capsulatus recA gene is poorly induced when inserted into the chromosome of R. sphaeroides, indicating that the recA gene of both bacteria possess different control sequences despite their phylogenetically close relationship.