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Nucleic Acids Res. 2004; 32(22): 6617–6626.
Published online Dec 16, 2004. doi:  10.1093/nar/gkh996
PMCID: PMC545464

Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics

Abstract

The LexA regulon encompasses an ensemble of genes involved in preserving cell viability under massive DNA damage and is present in most bacterial phyla. Up to date, however, the scope of this network had only been assessed in the Gamma Proteobacteria. Here, we report the structure of the LexA regulon in the Alpha Proteobacteria, using a combined approach that makes use of in vitro and in vivo techniques to assist and validate the comparative genomics in silico methodology. This leads to the first experimentally validated description of the LexA regulon in the Alpha Proteobacteria, and comparison of regulon core structures in both classes suggests that a least common multiple set of genes (recA, ssb, uvrA and ruvCAB) might be a defining property of the Proteobacteria LexA network.

INTRODUCTION

Preservation of genetic material is one of the main functions of living beings, and it is perhaps in bacteria where the mechanisms for DNA preservation have been more clearly identified and studied. A global mechanism to respond to DNA lesions (the SOS system) was first described (1) and has been extensively studied (2,3) in the enteric Gamma Proteobacteria Escherichia coli. The SOS response of E.coli comprises the DNA damage-mediated induction of at least 40 genes involved in DNA repair and cell survival (2,3) and is regulated by the LexA and RecA proteins. Under normal circumstances, E.coli LexA represses the expression of SOS genes by specifically binding to a palindromic motif (CTGTN8ACAG) in their promoter: the SOS box (1). In the advent of DNA damage, RecA acquires an active state (RecA*) through binding to single-stranded regions of DNA generated by either DNA damage-mediated replication inhibition or enzymatic processing of broken DNA ends (4). The RecA* complex then promotes the autocatalytic cleavage of the Ala84–Gly85 bond of E.coli LexA (5). This cleavage, similar to that carried out by serine proteases (5,6), renders LexA unable to bind SOS regulatory motifs and, thereby, results in a global induction of the SOS response. Once DNA lesions have been repaired, the intracellular concentration of RecA* diminishes as new RecA is promptly produced due to SOS induction. Non-cleaved LexA, which is also induced by the SOS response, returns rapidly to normal levels, repressing again the SOS genes and itself.

So far, presence of the lexA gene has been reported in almost all bacterial phyla, and distinct LexA-binding motifs have been described for different bacterial phyla and classes. The Gram-positive, for instance, present a highly conserved LexA recognition motif with consensus sequence CGAACRNRYGTTYC (7,8) that is highly similar to that reported for Cyanobacteria [RGTACNNNDGTWCB; (9)]. Then again, the LexA recognition sequence of E.coli has been reported in several Gamma Proteobacteria families (e.g. Pseudomonaceae, Aeromonadaceae or Vibrionaceae) and in some Beta Proteobacteria (e.g. Ralstonia solanacearum; (10), while a markedly different LexA-binding motif, a direct repeat with consensus sequence GAACN7GAAC or GTTCN7GTTC, has been described in the Alpha Proteobacteria class (11,12) that comprises, among other, the Caulobacterales, the Rhizobiales and the Rhodobacterales orders. Interestingly, all reported LexA-binding motifs are monophyletic for the phyla and classes presenting them, suggesting that they may be reliable indicators of branching points in the evolution of bacteria (10).

In contrast to LexA-binding sequences, little is known about the composition of the LexA regulon beyond E.coli. In silico analyses have shown that a LexA regulated SOS network with the E.coli SOS box is present in all the Gamma Proteobacteria sequenced so far and in some Beta Proteobacteria (10). In all these species, LexA controls a gene network related to that of E.coli, which comprises error-prone polymerases (umuDC, dinP), recombinases (recA, recN), excision repair nucleases (uvrAB) and helicases (uvrD) and a cell-division inhibitor (sulA). However, and in spite of the experimentally reported presence of LexA and of some regulated genes in the Gram-positive bacteria (13,14), the Cyanobacteria (9) and the Alpha Proteobacteria (12), no systematic analyses of the LexA regulon structure in these phyla has been carried out so far. Still, indications on regulon composition are of substantial interest because they can pinpoint subtler differences between species than regulatory motifs (10,15) and because they can yield hints on how the nature and function of the SOS response may have been shaped across different phyla and in response to particular environments.

In recent years, the increasing availability of sequenced genomes has fostered the design of algorithms to predict regulatory binding sites and thus extend the knowledge on or discover new regulatory networks through in silico analyses (2,16). Based on different statistical approaches, consensus-building (17), expectation maximization (18), oligonucleotide-frequency analysis (19) and Gibbs-sampling method (20) algorithms have been devised to locate new regulatory sites. Simple in silico screening, though, is too inaccurate to extract solid knowledge if it is not assisted by prior experimental knowledge on the nature of the regulon (21), thus limiting the application scope of such analyses. More recently, and with the assumption that gene networks and regulatory motifs ought to be dependably conserved across related species (15), comparative genomics analyses have been carried out (22,23) making use of known regulon structures in related genomes as a means to strengthen and focus motif-prediction algorithms in previously unstudied species. However, even with the comparative genomics approach, extensive experimental knowledge of the regulon under study must still be available in closely related species in order to derive conclusive facts.

In this work, we have made use of a consensus-building algorithm (10,17) to conduct a comparative genomics analysis of the LexA regulon of Alpha Proteobacteria. Based on prior experimental data (12) and on the known structure of the Gamma Proteobacteria SOS regulon (10), the analysis has been refined through experimental validation of its preliminary results, thus circumventing the lack of extensive experimental knowledge of the LexA regulon in an Alpha Proteobacteria species, to achieve the first consistent outline of the SOS response network in this bacterial class. These results, together with previously published thorough analyses of both the E.coli (2) and Gamma Proteobacteria (10) LexA regulons, allow for the first time a direct comparison of the LexA regulon between different Proteobacteria classes. Such a straight comparison is particularly appealing because, apart from the established phylogenetic divergence between the Alpha and Gamma Proteobacteria (24,25), both these classes have been shown also to present markedly divergent LexA-binding motifs (10,12).

MATERIALS AND METHODS

Bacterial strains and growth conditions

The Sinorhizobium meliloti 2021 strain used in the present work was grown at 30°C in LB medium (26). All plasmid constructions and cloning experiments were performed in E.coli DH5α using the pGEM-T vector. Plasmid DNA was transformed into competent E.coli cells as described previously (27).

Nucleic acids techniques

RNA and DNA total extraction was carried out by standard methods (26). Genes and promoter fragments for electrophoretic mobility shift assays were isolated by PCR from total DNA extraction, using suitable oligonucleotide primers designed in accordance to the S.meliloti published sequence. RT–PCR analyses of gene expression were performed for all genes as reported (28), using specific internal oligonucleotide primers for each one. In all cases, the RNA concentration of the gene to be analyzed was always normalized to that of the S.meliloti trpA gene, since expression of the latter is not affected by DNA damage (3).

Purification of LexA protein

The S.meliloti lexA gene was cloned by PCR using specific primers designed from its published sequence. The 5′ end of the upper primer contained an NdeI restriction site in which the ATG initial triplet of the lexA gene was included. The lower primer started 200 bp downstream of the translational stop codon of the lexA gene. The PCR fragment containing the S.meliloti lexA gene was cloned into a pGEM-T vector and, afterwards, inserted into a pGEX4T1 expression vector. The pGEX4T1-derivative containing the S.meliloti lexA gene was transformed into the E.coli lexA (Def) BL21(DE3) codon plus strain (2) for over-expression of its encoding LexA protein, which was subsequently purified using the Talon™ Metal Affinity Resin Kit (Clontech) as reported in (9). The S.meliloti LexA protein obtained was above 95% purity as determined with Coomassie Blue staining of SDS–PAGE (15%) polyacrylamide gels (data not shown) following standard methodology (29).

Electrophoresis mobility shift assays

LexA–DNA binding was analyzed for each gene promoter by electrophoresis mobility shift assays (EMSAs) using purified S.meliloti LexA protein. DNA probes were prepared by PCR amplification with one of the primers labeled at its 5′ end with digoxigenin (DIG) and purifying each product in a 2–3% low-melting-point agarose gel. DNA–protein reactions (20 μl) typically containing 20 ng of the DIG–DNA-labeled probe and 80 nM of purified LexA protein were incubated in binding buffer: 10 mM HEPES, NaOH (pH 8), 10 mM Tris–HCl (pH 8), 5% glycerol, 50 mM KCl, 1 mM EDTA, 1 mM DTT, 1 mg/ml of salmon DNA and 50 μg/ml BSA. After 30 min at 30°C, the mixture was loaded onto a 6% non-denaturing Tris–glycine polyacrylamide gel (pre-run for 30 min at 10 V/cm in 25 mM Tris–HCl (pH 8.5), 250 mM glycine, 1 mM EDTA). DNA–protein complexes were separated at 150 V for 60 min, followed by transfer to a Biodine B nylon membrane (Pall Gelman Laboratory). DIG-labeled DNA–protein complexes were detected following the manufacturer protocol (Roche). For the binding-competition experiments, a 300-fold molar excess of either specific or nonspecific-unlabeled competitor DNA was also included in the mixture. All EMSAs were repeated a minimum of three times to ensure reproducibility of results.

Genome sequences

Available complete genome sequences for the Alpha Proteobacteria species analyzed here were obtained from the NCBI Entrez genomes database (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome) or from The Institute for Genomic Research (TIGR) Microbial Genome Database (http://www.tigr.org/tdb/mdb/mdb.html).

In silico analyses

In silico analyses of regulon structure were carried out using RCGScanner (Recursive Comparative Genome Scanner), a consensus-building software for the prediction of regulatory motifs that has been previously described (10). Essentially, the program scans a local raw genome file searching for direct or inverted repeats in the vicinity of putative Open Reading Frames (ORFs). After scanning, the program filters out sequences according to their Heterology Index [HI; (30)], using both direct cut-off and iterative filtering techniques. NCBI Genbank database is then queried through BLAST (31) to obtain functional definitions for the ORFs that are adjacent to filter-passing motifs. RCGScanner allows two different modes of operation, depending on the availability of experimental information concerning the regulon and organism under study. If such information is available, in the form of known regulatory motifs, RCGScanner uses these motifs to directly generate the consensus sequence that is applied in filtering. Conversely, if no binding motifs are known for the species under study, the program takes as input a known regulon structure in the form of regulon genes sequences. Gene homologues are then searched for through BLAST in the genome of the species under study and, if found, putative regulatory motifs are sought in their promoters. These putative motifs are then used to create the consensus sequence for filtering.

RESULTS AND DISCUSSION

Initial analysis of the Alpha Proteobacteria LexA regulon

Since the structure of the LexA regulon has only been clearly defined in E.coli (2) and close relatives (10), experimental validation of in silico results was necessary to elucidate the structure of the LexA regulon in the distant Alpha Proteobacteria, which present a markedly divergent LexA-binding motif (12). Therefore, a two-step analytical procedure was implemented as described previously (10). In the initial analysis, the consensus-building software was run against Alpha Proteobacteria complete genomes using the E.coli LexA regulon structure as input. Protein sequences of genes that are known to form part of the E.coli SOS network (2) were automatically searched for in the analyzed genomes using BLAST and a minimum identity level of 60% as threshold. The promoter regions of the resulting conserved genes were then scanned for putative GTTCN7GTTC or GAACN7GAAC direct repeats, and these were used to build a preliminary consensus matrix for filtering.

The results of this initial analysis (Table (Table1)1) revealed that a LexA core regulon structure (lexA, recA, uvrA and ssb) similar to that of Gamma Proteobacteria (10) might be present in the Alpha Proteobacteria. Using the aforementioned consensus matrix, motifs were filtered using astringent selection criteria (10). For each motif putatively regulating a given gene, these criteria impose a HI score below 6 and the presence of a motif upstream of a homologue of that same gene in at least another bacterial species. After filtering, several high-scoring LexA-binding sites upstream of contrasted SOS gene homologues (lexA, recA, uvrA, ssb, sulA and dinP) were identified in almost all the Alpha Proteobacteria genomes analyzed, as well as upstream of some DNA-repair associated genes (ruvC and dnaE) that had not been previously described as LexA-regulated in either Alpha or Gamma Proteobacteria. The only exceptions to this trend were the intracellular parasites Rickettsia conorii and Rickettsia prowazekii, which present a deletion of their lexA gene due to drastic genome reduction. The LexA-binding motifs thus selected, together with experimentally determined LexA boxes of several Alpha Proteobacteria [(12), Table Table1],1], were then used to define a robust interspecies consensus sequence (Figure (Figure1)1) to carry out a second, more accurate filtering step.

Figure 1
Interspecies consensus sequences for Alpha Proteobacteria LexA-binding sites derived from the preliminary analysis and available experimental data (Table (Table1).1). Sequence logos were produced using the WebLogo service at http://weblogo.berkeley.edu ...
Table 1.
Regulatory motifs used to build the interspecies consensus for the second phase of the analysis

Experimental validation of the in silico approach

Prior to conducting a full-fledged analysis of the Alpha Proteobacteria LexA regulon using the interspecies consensus sequence obtained in the initial analysis, a pilot study was carried out in the nodule-forming soil bacterium S.meliloti to validate the reliability of the in silico approach. Of the 29 S.meliloti genes presenting at least one putative regulatory motif with HI < 6 in this second round of filtering (Table (Table2),2), 6 of those not previously reported to be DNA-damage inducible in the Alpha Proteobacteria (ruvC, dinP, sulA1, parE, yigN and SMc03093), together with lexA, were arbitrarily elicited for experimental validation.

Table 2.
S.meliloti genes with at least one regulatory motif displaying a HI < 6 in the second phase of the analysis

After cloning and purifying the LexA protein of S.meliloti, EMSAs were carried out to determine the LexA-binding affinity of promoters for the six chosen genes. Results (Figure (Figure2a)2a) clearly demonstrated that all six promoters are able to bind LexA, suggesting that they might be DNA-damage-inducible genes. To further elucidate this point, RNA was extracted from S.meliloti cultures following exposure to mitomycin C and analyzed through RT–PCR. Again, the results (Figure (Figure2b)2b) clearly established that all six genes were DNA-damage inducible, confirming that the two-step in silico approach taken here and the use of a robust interspecies consensus yielded manifestly reliable results.

Figure 2
(a) Electrophoretic mobility of the S.meliloti lexA promoter in the presence of 80 nM of S.meliloti LexA protein and a 300-fold molar excess of unlabeled fragments comprising about 400 bp of the upstream regions of the genes ruvC, dinP, sulA1, parE, ...

Analysis of the Alpha Proteobacteria LexA regulon

After both in vitro and in vivo validation of the filtering scheme taken in S.meliloti, the second round of analyses was extended to the remaining Alpha Proteobacteria species with published complete genomes (Table (Table3).3). To avoid false positives, a combined astringent filtering procedure was applied, including only those genes that, apart from presenting at least one motif with a HI < 6, were seemingly regulated in at least three different bacterial species.

Table 3.
Distribution of genes with conserved regulatory motifs in the Alpha Proteobacteria

The results (Table (Table3)3) allowed extending the preliminary definition of the Alpha Proteobacteria LexA regulon core (lexA, recA, ssb and uvrA) by imposing the more severe criterion of presence in at least 5 of the 10 bacterial species analyzed. The identified core thus encompasses 13 genes that include previously described Alpha and Gamma Proteobacteria LexA-regulated genes (lexA, recA, ssb and uvrA), several E.coli SOS genes (dinP, yigN and sulA) and some new LexA-regulated genes identified here (parE, dnaE, ruvC, ispE, SMc00865 and comM).

Again, to confirm the validity of these in silico results, those members of the identified regulon core that had not been experimentally validated previously (dnaE, sulA2, ispE, SMc00865 and comM) were analyzed in S.meliloti. EMSA results (Figure (Figure3a)3a) demonstrate that all these genes promoters are able to bind the LexA protein in S.meliloti. Furthermore, subsequent RT–PCR analyses (Figure (Figure3b)3b) revealed that these genes are DNA-damage inducible in S.meliloti, demonstrating that the in silico identified regulon core is indeed functional in this bacterial species. In addition, three other genes (ppdK, dnrV and recG) presented high-scoring LexA-binding motifs in at least three different bacterial species, and were thus considered as optional members of the LexA regulon in the Alpha Proteobacteria. As expected, and in agreement with the results of the initial analysis, there was again no evidence of LexA regulatory motifs in the Rickettsiae, indicating that the loss of lexA must have taken place early in the evolution of these intracellular parasites, and that subsequent genome reduction has removed all traces of former LexA regulation.

Figure 3
(a) Electrophoretic mobility of the S.meliloti lexA promoter in the presence of 80 nM of S.meliloti LexA protein and a 300-fold molar excess of unlabeled fragments comprising about 400 bp of the upstream regions of dnaE, ispE, sulA2, comM, SMc00865 and ...

It should be stressed that these results constitute also the first description of a sulA-like gene under control of the LexA protein in the Alpha Proteobacteria class. Moreover, the surrounding region of the two copies (three in the case of A.tumefaciens) identified here of this LexA-regulated sulA homologue presents the same genetic organization in all the species analyzed. This genetic arrangement, consisting of the own sulA homologue, a DNA polymerase IV homologue (dinP) and a homologue of the alpha subunit of DNA polymerase III (dnaE), has been shown to be a polycistronic transcriptional unit belonging to a broader class of mobile genetic element encoding also the LexA protein in a lexA-sulA-dinP-dnaE cassette organization (33) that is present in some Gamma Proteobacteria. The presence of a cell-division inhibitor homologue in the Alpha Proteobacteria LexA regulon supports the view that postponing cell division under massive DNA damage is a markedly favorable and widespread adaptation, a hypothesis further endorsed by the reported convergent evolution of a similar mechanism mediated by the yneA gene in the Gram-positive bacterium Bacillus subtilis (34).

Comparison of the Alpha and Gamma LexA regulons

The previously described regulon core for the Gamma Proteobacteria (10) consists of six genes besides lexA whose regulation seems conserved across almost all the species analyzed to date. These genes encode, respectively, the DNA strand exchange and recombination protein RecA, both Holliday junction helicase subunits A and B (RuvAB), the single-strand binding protein Ssb, the recombination protein RecN and the excision nuclease subunit A (UvrA). In the case of the Alpha Proteobacteria regulon core, a highly similar structure is present, with recA, ssb and uvrA explicitly regulated, and the ruvAB regulation substituted in this case by the regulation of the equivalent ruvCAB operon present in all the Alpha Proteobacteria species analyzed here, but for the Rickettsiae. Taking this substitution into account, the only protein of the Gamma Proteobacteria regulon core that is missing in the Alpha Proteobacteria one is the recombination protein RecN. In light of the significant phylogenetic divergence between Alpha and Gamma Proteobacteria, such a high degree of similarity in regulon core composition suggests the possibility that there is a least common multiple set of genes that make up the LexA regulon of Proteobacteria: recA, uvrA, ssb and the ruvAB/ruvCAB operon. The definition of such a least common multiple is interesting because it can contribute to reveal the common evolutionary pressures that maintain the essence of the LexA regulon in different bacterial classes. This line of reasoning is further strengthened when different reports confirming LexA regulation of some of these same genes in the Gram-positive Phylum [recA (7), uvrA (35), ssb (36) or ruvC (14)] are taken into account. Thus, similar studies in the near future could reveal a universal least common multiple set of genes for the bacteria LexA regulon, shedding more light on the general mechanisms governing the evolution of the LexA and other complex regulons.

Another interesting point of the straight comparison between regulon cores concerns the additions to the Alpha Proteobacteria regulon core. These additions are significant because they can pinpoint shared evolutionary pressures and are indicative of the flexibility of the LexA regulon in co-opting additional genes. Of the eight additions to the Alpha Proteobacteria LexA regulon core with respect to its Gamma Proteobacteria counterpart, some can be readily explained by their reported involvement in DNA repair or in the overall SOS response of E.coli and other Gamma Proteobacteria. This is the case for the aforementioned sulA homologue (15), the DNA polymerase IV dinP (37), the alpha subunit of DNA polymerase III [dnaE; (38)] and the hypothetical protein yigN (39). The presence of the DNA topoisomerase IV subunit B (parE) could be similarly explained by its reported involvement in mutagenic processes and antimicrobial resistance (40,41). Regarding the other three additions, however, it is difficult to derive sound inferences without further experimental work on their respective protein functions. The comM gene, for instance, has been annotated as a Mg2+ chelatase in B.suis and B.melitensis, and as such it seems feasible that it could be involved in the regulation of polymerase fidelity during the SOS response through the sequestering of magnesium (42). In a different setting, the ispE gene here reported has been annotated as the molybdenum cofactor biosynthesis protein A (moaA) in C.crescentus, a gene that has been linked in E.coli to the detoxifying processes ensuing N-6-hydroxylaminopurine (HAP)-induced lesions (43). Therefore, it seems not farfetched to assume that some environmental factor may have fostered its co-option in the LexA regulon of the Alpha Proteobacteria.

CONCLUSION

In the present work, we have made use of experimental validation to make a robust assessment of regulon structure for a whole bacterial class through comparative genomics. The inclusion of an intermediate experimental stage improves the accuracy of the consensus-building method used and adds a layer of reliability to the results obtained through comparative genomic approaches. This allows extending the range of comparative genomics assays to different bacterial classes with markedly divergent regulatory motifs, as in the case of Gamma and Alpha Proteobacteria LexA regulons. Using this approach, we have analyzed the LexA regulon of Alpha Proteobacteria, providing the first comprehensive description of the LexA regulon in this bacterial class. The results show that a least common multiple set of genes may be the norm in the Proteobacteria LexA regulon, and reveal some interesting additions to the LexA regulon of Alpha Proteobacteria that may be linked to their particular environment and evolution.

ACKNOWLEDGEMENTS

This work was funded by Grants BMC2001-2065 and BFM2004-02768/BMC from the Ministerio de Educación y Ciencia (MEC) de España and 2001SGR-206 from the Departament d'Universitats, Recerca i Societat de la Informació (DURSI) de la Generalitat de Catalunya, and by the Consejo Superior de Investigaciones Científicas (CSIC). M.J. was recipient of a pre-doctoral fellowship from the DURSI and S.C. is recipient of a post-doctoral contract from INIA-IRTA. We are deeply indebted to Joan Ruiz and Dr Pilar Cortés for their excellent technical assistance.

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