Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response

Butala, Matej; Klose, Daniel; Hodnik, Vesna; Rems, Ana; Podlesek, Zdravko; Klare, Johann P.; Anderluh, Gregor; Busby, Stephen J. W.; Steinhoff, Heinz‐Jürgen; Žgur-Bertok, Darja

doi:10.1093/nar/gkr265

Cited by 67 publications

(93 citation statements)

References 43 publications

(99 reference statements)

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“…Biochemical analyses showed that only the DNAfree form of LexA is cleaved by activated RecA protein (Butala et al 2011). This study has implications that relate the relative strength of LexA binding sites to the sequential order of induction of genes during the damage response.…”

Section: How Exactly Is Sos Induced?mentioning

confidence: 81%

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

Kreuzer

2013

Cold Spring Harbor Perspectives in Biology

205

185

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Recent advances in the area of bacterial DNA damage responses are reviewed here. The SOS pathway is still the major paradigm of bacterial DNA damage response, and recent studies have clarified the mechanisms of SOS induction and key physiological roles of SOS including a very major role in genetic exchange and variation. When considering diverse bacteria, it is clear that SOS is not a uniform pathway with one purpose, but rather a platform that has evolved for differing functions in different bacteria. Relating in part to the SOS response, the field has uncovered multiple apparent cell-cycle checkpoints that assist cell survival after DNA damage and remarkable pathways that induce programmed cell death in bacteria. Bacterial DNA damage responses are also much broader than SOS, and several important examples of LexA-independent regulation will be reviewed. Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized. Since the publication of DNA Repair and Mutagenesis in 2006 (Friedberg et al. 2006), our understanding of bacterial DNA damage responses has progressed significantly. Some studies have refined known pathways and filled in important details, whereas other studies have uncovered surprising new pathways such as bacterial programmed cell death and a form of replicative repair that reconstitutes severely shattered genomes. This review will focus on these recent advances, with only limited discussion and citation to work that precedes the 2006 tome. THE SOS RESPONSEAs scientists have studied the SOS response in Escherichia coli and other bacteria over the last decade, our understanding of SOS has changed in unexpected ways and the pathway has been found integrated in diverse cellular processes. Our understanding of the mechanism of SOS induction has also advanced in recent years, including a view of induction at the single-cell level. A surprising finding is that the functions of the SOS pathway are not uniform between bacterial species, and so the view of SOS as

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Section: How Exactly Is Sos Induced?mentioning

confidence: 81%

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

Kreuzer

2013

Cold Spring Harbor Perspectives in Biology

205

185

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“…Thus, these two regulators cannot account for the positive effects of CsrA on uvrY transcription. Another candidate is LexA, which coordinates the SOS response (47,48), because a LexA binding site is predicted to be located between nt Ϫ120 and Ϫ139 upstream of the uvrY start site (49). CsrA-dependent modulation of uvrY translation might also be indirect, because no apparent CsrA binding sequences are present in the 5=-UTR of the uvrY transcript.…”

Section: Resultsmentioning

confidence: 99%

Effects of the Global Regulator CsrA on the BarA/UvrY Two-Component Signaling System

et al. 2015

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The hybrid sensor kinase BarA and its cognate response regulator UvrY, members of the two-component signal transduction family, activate transcription of CsrB and CsrC noncoding RNAs. These two small RNAs act by sequestering the RNA binding protein CsrA, which posttranscriptionally regulates translation and/or stability of its target mRNAs. Here, we provide evidence that CsrA positively affects, although indirectly, uvrY expression, at both the transcriptional and translational levels. We also demonstrate that CsrA is required for properly switching BarA from its phosphatase to its kinase activity. Thus, the existence of a feedback loop mechanism that involves the Csr and BarA/UvrY global regulatory systems is exposed. The BarA/UvrY two-component signal transduction system (TCS) of Escherichia coli consists of the membrane-bound sensor kinase BarA and its cognate response regulator UvrY (1). BarA, which belongs to the subfamily of tripartite sensor kinases (2, 3), senses and responds to the presence of formate and acetate but also to that of other short-chain fatty acids (4). Phosphorylated BarA catalyzes the transphosphorylation of UvrY (1), a typical response regulator of the FixJ family (1, 5), which in turn activates expression of the noncoding RNAs of the carbon storage regulation (Csr) system, CsrB and CsrC. These small regulatory RNAs possess repeated sequence elements that allow them to interact with multiple copies of the RNA binding protein CsrA and thereby prevent its regulatory interaction with its mRNA targets (6).CsrA is a small, dimeric RNA binding protein that coordinates gene expression by positively or negatively regulating the translation, stability, and/or elongation of its target transcripts (7,8). CsrA directly interacts with the 5= untranslated leaders of target mRNAs at sites characterized by a GGA sequence that is often located within the loop of a short stem-loop structure (9-11). In this way, CsrA activates exponential-phase processes while it represses several stationary-phase functions (12). CsrA is widely distributed among eubacteria (13) and regulates expression of genes for virulence factors (14, 15), quorum sensing (16, 17), motility (18,19), carbon metabolism (20, 21), biofilm formation (22, 23), cyclic di-GMP synthesis (24), and peptide uptake (10).Curiously, activation of csrB transcription, which depends directly on UvrY-P, does not take place in a csrA mutant strain (25). Therefore, it has been suggested that CsrA has a positive effect on the BarA/UvrY TCS. In this study, we confirmed and extended these results by examining the effects of CsrA on either the expression or the activity of BarA and UvrY. Our results demonstrate that CsrA, apparently indirectly, is required for proper uvrY expression and also for activation of the BarA kinase activity. MATERIALS AND METHODSBacterial strains, plasmids, and growth conditions. The strains and plasmids used in this work are listed in csrB-lacZ) construction, the barA gene was deleted by homologous recombination using the lambda Red ...

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“…The SOS gene network is controlled by the LexA repressor, and LexA-regulated genes exhibit heterogeneous expression in a culture not subject to an external SOSinducing treatment . The heterogeneity of expression is a result of stochastic factors resulting from the binding affinity of LexA to different SOS boxes and intrinsic DNA damage (Pennington and Rosenberg 2007;Kamensek et al 2010;Butala et al 2011). Combined heterogeneity of the expression of the target and the repair mechanism translates into a wide spectrum of phenotypic states and hence varied susceptibility to a FQ.…”

mentioning

confidence: 99%

Tolerance ofEscherichia colito Fluoroquinolone Antibiotics Depends on Specific Components of the SOS Response Pathway

2013

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Bacteria exposed to bactericidal fluoroquinolone (FQ) antibiotics can survive without becoming genetically resistant. Survival of these phenotypically resistant cells, commonly called "persisters," depends on the SOS gene network. We have examined mutants in all known SOS-regulated genes to identify functions essential for tolerance in Escherichia coli. The absence of DinG and UvrD helicases and the Holliday junction processing enzymes RuvA and RuvB leads to a decrease in survival. Analysis of the respective mutants indicates that, in addition to repair of double-strand breaks, tolerance depends on the repair of collapsed replication forks and stalled transcription complexes. Mutation in recF results in increased survival, which identifies RecAF recombination as a poisoning mechanism not previously linked to FQ lethality. DinG acts upstream of SOS promoting its induction, whereas RuvAB participates in repair only. UvrD directly promotes all repair processes initiated by FQ-induced damage and prevents RecAF-dependent misrepair, making it one of the crucial SOS functions required for tolerance. IN the face of a potentially lethal stress, the presence of phenotypic variants of genetically identical bacterial cells can make a difference between survival of the lineage and extermination. A clonal population of cells of a strain genetically susceptible to an antibiotic can harbor tolerant phenocopies that will survive the antibiotic challenge. These cells are termed "persisters" and are of special interest because of their ability to influence the outcome of antibiotic treatments (Lewis 2010;Mulcahy et al. 2010). Toxins from chromosomally encoded toxin-antitoxin (TA) modules have been shown to play a role in persister formation under certain condition (Keren et al. 2004;Dörr et al. 2010;Gerdes and Maisonneuve 2012) To date, screening of E. coli mutant libraries has yielded no single mutants that completely lack persisters (Spoering 2006;Hansen et al. 2008). These studies have shown that there are many pathways that lead to persister formation (Lewis 2010). We have shown that tolerance to fluoroquinolone (FQ) antibiotics depends on a functional SOS response (Dörr et al. 2009). The SOS-regulated tisAB/istR TA locus contributes to tolerance to ciprofloxacin (Dörr et al. 2010). When overproduced, the membrane peptide TisB decreases proton motive force and intracellular ATP levels (Gurnev et al. 2012). During SOS induction, tisB is overexpressed, which may induce stasis and prevent killing by the antibiotic. However, it influences tolerance only at high ciprofloxacin concentration [1003 minimal inhibitory concentration (MIC)]; therefore, it is not the only mechanism of FQ tolerance.Fluoroquinolones target gyrase and topoisomerase IV (Drlica and Zhao 1997). Upon FQ binding, these enzymes become endonucleases introducing double-strand breaks (DSBs) into the bacterial chromosome (Malik et al. 2006). Cells repair DSBs largely through the DNA-damage-inducible SOS gene network (Radman 1975;Friedberg et al. 2006). The su...

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Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response

Cited by 67 publications

References 43 publications

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks

Effects of the Global Regulator CsrA on the BarA/UvrY Two-Component Signaling System

Tolerance ofEscherichia colito Fluoroquinolone Antibiotics Depends on Specific Components of the SOS Response Pathway

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