DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks
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Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks Kenneth N. Kreuzer Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710 Correspondence: [email protected] 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. ince the publication of DNA Repair and THE SOS RESPONSE SMutagenesis in 2006 (Friedberg et al. 2006), our understanding of bacterial DNA damage As scientists have studied the SOS response in responses has progressed significantly. Some Escherichia coli and other bacteria over the last studies have refined known pathways and filled decade, our understanding of SOS has changed in important details, whereas other studies have in unexpected ways and the pathway has been uncovered surprising new pathways such as bac- found integrated in diverse cellular processes. terial programmed cell death and a form of rep- Our understanding of the mechanism of SOS licative repair that reconstitutes severely shat- induction has also advanced in recent years, tered genomes. This review will focus on these including a view of induction at the single-cell recent advances, with only limited discussion level. A surprising finding is that the functions and citation to work that precedes the 2006 of the SOS pathway are not uniform between tome. bacterial species, and so the view of SOS as Editors: Errol C. Friedberg, Stephen J. Elledge, Alan R. Lehmann, Tomas Lindahl, and Marco Muzi-Falconi Additional Perspectives on DNA Repair,Mutagenesis, and Other Responsesto DNA Damage available at http://www.cshperspectives.org Copyright # 2013 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a012674 Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012674 1 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press K.N. Kreuzer purely a DNA damage response pathway is in- tein in its native state binds to the promoter sufficient. Furthermore, SOS is not the major region of multiple SOS genes during normal DNA damage response pathway in some bac- growth limiting their expression levels. Upon terial species (see “SOS-Independent DNA DNA damage, the RecA protein is activated to Damage Responses” below). From a practical become a coprotease by formation of a filament viewpoint, recent findings also uncover clinical of RecA on single-stranded DNA (ssDNA), significance of the SOS pathway in the response which facilitates the self-cleavage reaction of to diverse antibiotics and also in the spread of LexA. Thus, as LexA repressor levels decrease, virulence and drug-resistance genes. The reader expression levels of SOS regulon genes increase. is referred to several excellent recent reviews The products of SOS regulon genes are involved on various aspects of the SOS response (Michel in specific DNA repair mechanisms, tolerance of 2005; Aertsen and Michiels 2006; Kelley 2006; DNAdamage, andinduceddelayof the cellcycle. Erill et al. 2007; Butala et al. 2009; Ayora et al. LexA also regulates transcription of both 2011) and to Fuchs and Fujii (2013) on bacterial its own gene and the recA gene, which is impor- translesion synthesis (TLS) polymerases for a tant for the overall function of the circuit. In- discussion of this aspect of the SOS response. creased RecA protein levels after DNA damage promotes recombinational repair and effective cleavage of LexA, whereas increased LexA ex- SOS Response in E. coli pression allows the SOS response to be rapidly shut off when the inducing signal of ssDNA The Basic Circuitry of the SOS Response wanes. Activated RecA protein also serves as co- The SOS response in E. coli coordinates the cells protease for the bacteriophage l repressor and response to DNA damage by the action of the for UmuD, an E. coli protein involved in DNA LexA repressor (Fig. 1) (for review, see Friedberg damage tolerance and TLS (as well as homologs et al. 2006, and above-cited reviews). LexA pro- of both proteins). recA lexA SOS regulon genes DNA Damage Checkpoints repair tolerance Figure 1. The E. coli SOS response. The basic circuitry of the E. coli SOS response is summarized. RecA protein- DNA filaments serve as a coprotease to activate self-cleavage of the LexA protein, the global repressor of SOS. As described in the text, RecA can also activate self-cleavage of UmuD and the phage l repressor. 2 Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012674 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press DNA Damage Responses in Prokaryotes Genome-scale approaches have refined our tional analyses of RecA filament surface residues knowledge of the E. coli genes induced by DNA defined a discrete LexA binding region (Adike- damage in both SOS-dependent and -indepen- savan et al. 2011). dent modes (reviewed by Michel 2005; Kelley Bulk approaches for studying SOS induc- 2006; Friedberg et al. 2006). Microarray studies tion have limitations, including the inability to revealed SOS-inducible genes that were largely assess whether all cells in a population induce expected from prior genetic and molecular the pathway similarly. Additional insight can studies in E. coli (Courcelle et al. 2001; Zheng be obtained at the single-cell level, using fusion et al. 2001; Khil and Camerini-Otero 2002). constructs in which the green fluorescent pro- Furthermore, a chromatin immunoprecipita- tein (GFP) fluorescent reporter is coupled to tion (ChIP) on chip study confirmed 25 expect- either an SOS-inducible promoter or to the ed LexA binding sites, and also uncovered five RecA protein itself. One new insight obtained new sites with a LexA consensus sequence and from this approach relates to the subcellular 19 apparent LexA binding sites without any localization of recombination proteins. Prior obvious LexA motif (Wade et al. 2005). studies in eukaryotic cells revealed DNA dam- As described in detail by Friedberg et al. age-induced recombination protein foci in cell (2006), some genes of the E. coli SOS pathway, nuclei, which were implicated as recombina- such as sulA and umuDC, are induced only tional repair factories (Lisby et al. 2001; for re- late and/or with high levels of DNA damage. view, see Lisby and Rothstein 2009). Similar The molecular explanation is that increasing structures were discovered in E. coli using a levels of DNA damage leads to progressively in- RecA-GFP fusion allele (Renzette et al. 2005). creasing RecA-promoted LexA proteolysis and These investigators found that normal undam- thus decreasing LexA concentrations. Thus, a aged E. coli cells often displayed one or even relatively high level of DNA damage is neces- multiple foci, about half of which were in- sary to achieve the very low LexA concentrations ferred to contain DNA (based on sensitivity to that allow induction of genes such as sulA and DAPI [40,6-diamidino-2-phenylindole] treat- umuDC, with their very strong LexA binding ment) and half not (presumed to be RecA stor- sites. This arrangement allows the SOS response age structures). A RecA substitution mutant that to be graded, for example, facilitating DNA re- does not form storage structures in vitro but pair without blocking cell division or inducing is otherwise normal (Eldin et al. 2000) provided TLS polymerase activity at low levels of DNA a simpler tool because a GFP fusion to this mu- damage. tant RecA showed only DNA-containing (DAPI- sensitive) foci (Renzette et al. 2005). Important- ly, DNA damage induced by UV treatment led How Exactly Is SOS Induced? to an increased number of foci, and the foci Recent studies have brought significant molec- relocalized to a position near the cell center. ular detail to our understanding of how the SOS The new position at cell center was proposed response is induced after DNA damage. Bio- to coincide with the sites of replication machin- chemical analyses showed that only the DNA- ery, arguing that the recombination foci were free form of LexA is cleaved by activated RecA actively involved in dealing with DNA damage protein (Butala et al. 2011). This study has at the replication fork (see “Prokaryotic Strate- implications that relate the relative strength of gies for Replicating Damaged DNA” below). LexA binding sites to the sequential order of A second important insight emerged by an- induction of genes during the damage response. alyzing the time course of induction of GFP Using substitution mutants of RecA, Gruenig fused to SOS promoters. Friedman et al. (2005) et al. (2008) provided evidence that RecA fila- showed cascading waves of SOS induction in ment formation, but not ATPase activity, are single cells during a post-UV incubation period. needed for RecA-induced LexA cleavage. Also These waves were not previously detected in relevant to the induction mechanism, muta- bulk cultures because of asynchrony between Cite this article as Cold Spring Harb Perspect Biol 2013;5:a012674 3 Downloaded from http://cshperspectives.cshlp.org/ on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press K.N.