Characterization of a New LexA Binding Motif in the Marine Magnetotactic Bacterium Strain MC-1

Henestrosa, Antonio R. Fernández de; Cuñé, Jordi; Mazón, Gerard; Dubbels, Bradley L.; Bazylinski, Dennis A.; Barbé, Jordi

doi:10.1128/jb.185.15.4471-4482.2003

Cited by 16 publications

(13 citation statements)

References 37 publications

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“…Furthermore, the results also establish that the LexA proteins clustering with the Gallionellales LexA share a ancestor and target variations of a LexA-binding motif similar to that reported in B. subtilis. The small size of the putative SOS regulon in these Gallionellales cluster species, and specifically the loss of recA regulation by LexA, has been described before in association with rapidly diverging lexA genes, lexA duplications and putative LGT (26,39,59,(61)(62)(63)(64). In this setting, the description in S. lithotrophicus of a more elaborate LexA regulon, including a signature gene of the canonical Betaproteobacteria SOS response (splB) points to a process of convergent evolution toward the regulation of this gene.…”

Section: Resultsmentioning

confidence: 99%

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

et al. 2015

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The SOS response is a transcriptional regulatory network governed by the LexA repressor that activates in response to DNA damage. In the Betaproteobacteria, LexA is known to target a palindromic sequence with the consensus sequence CTGT-N 8 -ACAG. We report the characterization of a LexA regulon in the iron-oxidizing betaproteobacterium Sideroxydans lithotrophicus. In silico and in vitro analyses show that LexA targets six genes by recognizing a binding motif with the consensus sequence GAACGaaCGTTC, which is strongly reminiscent of the Bacillus subtilis LexA-binding motif. We confirm that the closely related Gallionella capsiferriformans shares the same LexA-binding motif, and in silico analyses indicate that this motif is also conserved in the Nitrosomonadales and the Methylophilales. 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 the Betaproteobacteria. However, their lexA gene is unrelated to the standard Betaproteobacteria lexA, and there is evidence of its spread through lateral gene transfer. In contrast to other reported cases of noncanonical LexA-binding motifs, the regulon of S. lithotrophicus is comparable in size and function to that of many other Betaproteobacteria, suggesting that a convergent SOS regulon has reevolved under the control of a new LexA protein. Analysis of the DNA-binding domain of S. lithotrophicus LexA 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 the B. 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.

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Section: Resultsmentioning

confidence: 99%

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

et al. 2015

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“…In the bacteria "Dehalococcoides ethenogenes" (22), Bdellovibrio bacteriovorus (9), a "Magnetococcus" sp. (23), Petrotoga miotherma (38), Acidobacterium capsulatum (39), Deinococcus radiodurans (44), and Geobacter sulfurreducens (29), recA is not regulated by LexA. There are also lexA genes that are not autoregulated, as in Leptospira interrogans (15).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the SOS Regulon ofCaulobacter crescentus

et al. 2008

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The SOS regulon is a paradigm of bacterial responses to DNA damage. A wide variety of bacterial species possess homologs of lexA and recA, the central players in the regulation of the SOS circuit. Nevertheless, the genes actually regulated by the SOS have been determined only experimentally in a few bacterial species. In this work, we describe 37 genes regulated in a LexA-dependent manner in the alphaproteobacterium Caulobacter crescentus. In agreement with previous results, we have found that the direct repeat GTTCN 7 GTTC is the SOS operator of C. crescentus, which was confirmed by site-directed mutagenesis studies of the imuA promoter. Several potential promoter regions containing the SOS operator were identified in the genome, and the expression of the corresponding genes was analyzed for both the wild type and the lexA strain, demonstrating that the vast majority of these genes are indeed SOS regulated. Interestingly, many of these genes encode proteins with unknown functions, revealing the potential of this approach for the discovery of novel genes involved in cellular responses to DNA damage in prokaryotes, and illustrating the diversity of SOSregulated genes among different bacterial species.

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“…Collections of binding sites to construct both PSWM were obtained from previous publications. For LexA1, 23 experimentally verified binding sites from E. coli (15,23,29,31) were used to construct the PSWM, while seven LexA2 binding sites from several Pseudomonas and Xanthomonas species were used to construct the LexA2 PSWM (1,41). Genomic sequences were all downloaded from the NCBI GenBank repository through its FTP server (ftp.ncbi.nlm.nih.gov).…”

Section: Methodsmentioning

confidence: 99%

Cohabitation of Two DifferentlexARegulons inPseudomonas putida

et al. 2007

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In contrast to the vast majority of the members of the domain Bacteria, several Pseudomonas and Xanthomonas species have two lexA genes, whose products have been shown to recognize different LexA binding motifs, making them an interesting target for studying the interplay between cohabiting LexA regulons in a single species. Here we report an analysis of the genetic composition of the two LexA regulons of Pseudomonas putida KT2440 performed with a genomic microarray. The data obtained indicate that one of the two LexA proteins (LexA1) seems to be in control of the conventional Escherichia coli-like SOS response, while the other LexA protein (LexA2) regulates only its own transcriptional unit, which includes the imuA, imuB, and dnaE2 genes, and a gene (PP_3901) from a resident P. putida prophage. Furthermore, PP_3901 is also regulated by LexA1 and is required for DNA damage-mediated induction of several P. putida resident prophage genes. In silico searches suggested that this marked asymmetry in regulon contents also occurs in other Pseudomonas species with two lexA genes, and the implications of this asymmetry in the evolution of the SOS network are discussed.

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Characterization of a New LexA Binding Motif in the Marine Magnetotactic Bacterium Strain MC-1

Cited by 16 publications

References 37 publications

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria

Characterization of the SOS Regulon ofCaulobacter crescentus

Cohabitation of Two DifferentlexARegulons inPseudomonas putida

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