Mutagenesis Advance Access originally published online on April 11, 2008
Mutagenesis 2008 23(4):317-323; doi:10.1093/mutage/gen017
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In vivo role of Escherichia coli single-strand exonucleases in SOS induction by gamma radiation
Departamento de Biología, Instituto Nacional de Investigaciones Nucleares, Apartado Postal 18-1027, México DF 110801, México 1Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, México DF 04510, México
Ionizing radiation causes different types of genetic damage, ranging from base modifications to single- and double-stranded DNA breaks, which may be deleterious or even lethal to the cell. There are different repair or tolerance mechanisms to counteract the damage. Among them is the Escherichia coli SOS system: a set of genes that becomes activated upon DNA damage to confer better opportunities for cell survival. However, since this response is triggered by single-stranded DNA regions, most lesions have to be processed or modified prior to SOS activation. Several genes such as recO, recB and recJ that seem to be required to induce the response have already been reported. The results of this work indicate that the four known E.coli single-strand exonucleases take part in processing gamma radiation damage, though RecJ and ExoI proved to be more important than ExoVII or ExoX. In addition, ExoV as well as glycosylases such as Nth and, to a lesser extent, Fpg are also required. A model intended to explain the role of all these genes in damage processing is presented.
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Introduction |
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Ionizing radiation causes a plethora of lesions upon striking DNA that can be grouped as double-strand breaks (DSB), single-strand breaks (ssb) and base damages (1
). Among the many mechanisms that cope with DNA damage in Escherichia coli, there is the SOS response: a set of 
60 genes involved in repair or tolerance whose ultimate purpose is to increase the cell's chances of surviving (2,3). This response is regulated by the products of recA and lexA. Under normal circumstances, the latter attaches to a consensus sequence present in all SOS operators, repressing gene expression, but when DNA damage occurs, an induction signal is generated, activating RecA as a co-protease to promote LexA self-cleavage and hence triggering the response. Once lesions have been eliminated, the induction signal is lost, LexA binds again to all SOS operators and the system is turned off (4). It was thought in the beginning that any type of DNA damage would promptly activate the system; however, it has been established that the induction signal is single-stranded DNA (5,6). Consequently, most types of DNA lesions, such as DSBs, different kinds of base damage or even nicks, are not suitable substrates for RecA and have to be modified or processed to induce SOS (4,7,8). In a previous report, we demonstrated that in gamma-irradiated bacteria, lack of functional recB, recJ and recO decreased SOS activation (7), indicating that these genes take part in damage processing prior to SOS activation. This is in agreement with the findings of other authors (9–11). According to preliminary experiments, xonA (sbcB) might also be involved. Interestingly, both recJ and xonA code for single-strand RecJ and ExoI exonucleases, respectively. Therefore, we decided to investigate whether previous SOS damage processing is a general feature of all E.coli single-strand-exonucleases. In this work, we present data supporting the proposed role of the single-strand-enzymes ExoI, ExoVII and ExoX in processing gamma radiation-induced damage to generate the single-stranded DNA that triggers the SOS response. Since recB-defective mutants exhibit lower radiation-induced SOS activity (7,8), we decided to test the influence of multifunctional heterotrimer enzyme RecBCD—especially its RecD subunit—exonucleolytic activity, which degrades linear double-stranded DNA (12). |
Methods |
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Bacterial strains used for this work are listed in Table I. Strains were either part of this laboratory collection or constructed by P1 general transduction (13
). Strains defective in xseA and exoX were constructed by precise deletion using the methodology described by Datsenko and Wanner (14). Strain BW25113 and plasmids pKD4, pKD46 and pCP20 were obtained through the Yale University E. coli Genetic Stock Center. PCR products containing the kan gene and 40 bp of homology to sequences flanking the target gene were produced by using primers reported elsewhere (15) and pKD4 as the template. Upstream disruption primers terminated in the common sequence 5'-TGTAGGCTGGAGCTGCTTCG and downstream primers terminated in the sequence 5'-CATATGAATATCCTCCTTAG, which served to amplify the kan gene flanked by directly repeated FLP recognition target (FLP recombinase) sites. In addition, primers contained the following open reading frame-specific 40-base sequences at their 5' ends: 5'-GACTGAATAACCTGCTGATTTAGAATTTGATCTCGCTCAC (xseA upstream), 5'-ATGGCTTGATATCGAAAAAACGCGTTGAATTCGTGCTGGC (xseA downstream), 5'-TCATTCCATTACGCTAGGCTTTTTCGGCCTGGAGCATGCC (exoX upstream) and 5'-CGCTGGCGCAGGGAACATTACCCGCTACGCCTGCGGACTA (exoX downstream). BW25113 strain-containing plasmid pKD46, which expresses 
-Red recombinase, was transformed with the PCR products using the methodology described by Chung et al. (16). It was plated on Luria–Bertani (LB) agar (13) supplemented with 20 µg/ml of kanamycin, and resistant colonies were selected and tested for sensitivity to mitomycin C (1 µM) and up to 9/Jm of ultraviolet (UV) light (wavelength 254). The disrupted allele was introduced into PQ30 by P1 transduction to kanamycin resistance. To construct the xseA, exoX double mutant, excision of the kan gene was later accomplished by transformation of temperature-sensitive plasmid pCP20, which expresses FLP recombinase, into the appropriate strain at 30°C. Growth at 42°C resulted in the loss of pCP20, yielding kanamycin-sensitive deletion derivatives. The new strains were screened for their sensitivity to both mitomycin C and UV light against parental strains.
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Irradiations
Liquid cultures were grown overnight, diluted 50-fold in fresh LB broth and incubated in a water bath shaker at 37°C until reaching mid-logarithmic growth (2 x 108 cells/ml). They were subsequently centrifuged and re-suspended in the same volume of 10–2 M phosphate buffer at pH 7.0. Radiation treatments were performed at room temperature without any stirring or oxygen saturation, using a Gammacell Co60 source, at a dose rate of 5 Gy/min. Cultures were diluted afterwards and immediately plated for viable counts or further incubated for SOS measurements.
SOS activity
SOS activity was evaluated by means of the chromotest (7,17). In brief, aliquots of the irradiated cell suspensions were diluted 10-fold in LB, incubated at 37°C for the appropriate time to allow the expression of the SOS response at its maximum according to kinetic experiments (data not shown) and mixed afterwards with the proper buffer and β-galactosidase substrate (o-nitrophenyl-β-D-galactopyranoside). Another series of tubes was prepared similarly for the alkaline phosphatase assays with p-nitrophenyl phosphate as substrate. Both series were then incubated until a yellow colour appeared (or up to 90 min). The reactions were then stopped as indicated by Quillardet and Hofnung (17), absorbency was read spectrophotometrically at 420 nm, and the SOS induction factor was calculated.
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Results |
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Strains used in this work are listed in Table I. All of them have lacZ inserted in sulA (formerly known as sfiA), so β-galactosidase expression is regulated by the SOS response. In addition, alkaline phosphatase is constitutively expressed to certify that transcription is unaffected. All results are the mean of at least three independent experiments. When available, most of the survival results are comparable with previous reports (18
–20).
Figure 1a shows the gamma radiation survival curves of recJ and xonA strains, as well as of the recJ, xonA double mutant. At the highest dose, survival in either single mutant decreases 100-fold compared to the wild-type (wt) strain PQ30, whereas in the recJ, xonA double mutant, survival decreases considerably more, suggesting that both ExoI and RecJ enzymes play comparatively equivalent roles and seem to complement each other, at least partially. As for the SOS response, it can be noticed that recJ- and xonA-defective bacteria have markedly lower levels than the wt strain, whereas in the case of the recJ, xonA mutant, even at the highest doses, it scarcely doubles the basal level (Figure 1b). These results show again that RecJ as well as ExoI exonucleases are required for SOS expression as a consequence of ionizing radiation-induced DNA damage and both seem to be partially redundant.
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Exonucleases coded by either xseA or exoX genes proved to be less important for survival to gamma radiation, since viability in either mutant tested shows a modest decrease when compared to PQ30, as corroborated by survival plots, which are approximately the same in either single mutant as in the xseA,exoX double mutant (Figure 2a). At doses up to 100 Gy, all strains reach SOS expression levels very much the same as those in the wt. However, beyond that level a decrease is observed, suggesting that at higher doses both ExoVII and ExoX nucleases seem to be required for DNA damage processing prior to SOS activation, as supported by the response of the double mutant, whose activity is almost half of that for the wt strain at all the doses (Figure 2b).
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As expected, the recB-defective strain is highly sensitive to gamma radiation, while at the highest dose, recD strain survival is slightly lower than that in the wt strain (Figure 3a). However, despite the differences in sensitivity between them, SOS levels are almost identical in both and are approximately half the expression levels reached by PQ30. These results in turn indicate that a lack of ExoV nuclease activity may be the main cause of this SOS decrease (Figure 3b).
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Single-strand exonucleases take part in several mechanisms related to DNA recombination or damage repair within the cell (21
,22). For example, in base excision repair, ss-exonucleases are supposed to enlarge nicks left by the joint action of glycosylases and apurinic/apyrimidinic endonucleases as part of the process (23). Since ionizing radiation causes base modifications as well, we decided to test the role of some glycosylases in processing damage that could in turn lead to SOS induction, using previously constructed strains defective in either fpg or nth glycosylase genes. Results in Figure 4b show that the absence of either gene, especially the nth, lowers the activity of the response, suggesting that both genes may play a role in damage processing prior to SOS induction. The survival data show a slight reduction in viability of these mutants, demonstrating for the first time that nth increase the sensitivity to ionizing radiation (Figure 4a).
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Survival
In E.coli, DNA DSBs, caused either by radiation itself or as a result of the encounter of replication forks with ssb, are repaired mainly by homologous recombination through the RecBCD pathway, whereby information can be fully restored. The natural substrate for the RecBCD enzyme is linear duplex DNA with blunt ends or with short (up to 25 nucleotides) single-stranded DNA tails where the enzyme binds and simultaneously unwinds and cuts both strands, though the 3'-ended strand is degraded to a greater extent than the 5'. When encountering a specific octanucleotide DNA sequence known as Chi (
), the enzyme undergoes activity modification, and thereafter the nuclease shows an attenuated 5' exonuclease activity while retaining its helicase activity, loading at the same time RecA onto the 3' end, thus generating a nucleoproteic filament able to search and bind to a homologous sequence in an intact double-stranded DNA (24). Accordingly, the recB mutant shows high sensitivity to gamma radiation, in agreement with previous reports (18,25). RecBCD acts as a helicase and a nuclease (the latter due to the RecD subunit), but when RecD is missing, RecBC keeps acting as a helicase, so recombination can be efficiently performed (26). This would explain why our recD mutant is almost as resistant as the wt. As stated above, RecBCD only recognizes DSBs with blunt or nearly blunt ends, so in the case of breaks with protruding ends longer than 25 nucleotides, ss-exonucleases such as RecJ and ExoI trim the overhanging tails, making the substrate adequate for RecBCD. Survival to gamma radiation of recJ and xonA strains show similar sensitivity, suggesting that both RecJ and ExoI play an analogous function in processing DSB, most probably converting sticky ends into blunt or near-blunt ends that could be recognized by RecBCD to initiate recombinational repair (27). The strong sensitivity of the recJ, xonA double mutant supports this idea since without these enzymes a good deal of DSB remains unrepaired and finally leads to cell death. As for ExoVII and ExoX, the results indicate that they have a lesser participation in such a process, most likely because both RecJ and ExoI are functional. It must be stressed that ExoVII and ExoX have a limited activity in the cell. Indeed, Chase and Richardson (28), using crude extracts of E.coli ExoI- and ExoVII-defective mutants on labelled, denatured DNA, reported that ExoVII was responsible for only 2–4% of the total 3'-exonuclease degradation, whereas the enzyme ExoX was discovered not because of its activity, but by its similarities to conserved sequences in the DnaQ nuclease family (29).
SOS response
As stated above, to induce the SOS response, it is essential that RecA binds to single-stranded DNA to form a nucleoprotein filament. However, RecA has to compete for single-stranded DNA regions with single-strand binding protein (SSB). When SSB is pre-bound to an ssDNA site, it creates a significant kinetic barrier that prevents RecA nucleation onto this region. To overcome this barrier, the participation of RecFOR seems to be required (9,12,30). RecFOR displaces SSB and promotes RecA binding onto this kind of region (9,31,32). It has been reported that RecJ and ExoI participate in this pathway (33), generating the single-stranded region required to start the process, so when these enzymes are not functional, SOS expression is very low compared to a wt strain. Moreover, radiation-induced SOS levels of recO (7), xonA and recJ mutants are practically the same, indicating that their products take part in different steps of a process, starting from ssb or damaged bases and leading to the single-strand DNA that in turn induces the response.
Alternatively and according to our data, when RecA is loaded onto single-strand DNA by RecBCD from DSB, most of it would go to homologous recombination, and just a small portion could actually induce SOS. To further support this proposal, we constructed recB, recO and recD, recO double mutants and none of them showed any SOS activity whatsoever after exposure to gamma radiation (Figure 5), clearly demonstrating that these pathways are essential for SOS induction, in agreement with previous reports of experiments using UV light (34,35).
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Since radiation-induced DSBs are recognized by the RecBCD enzyme, the SOS activity decrease in the recB strain would indicate the DSB fraction actually leading to the induction of the response. Alternatively, the fact that recB and recD strains show equivalent SOS levels indicates that the nuclease activity of RecBCD is responsible for generating the SOS induction signal. Furthermore, since RecD exonuclease activity takes place before encountering a
site, and since the recD mutant is proficient in homologous recombination (26) as supported by survival results, it is likely that the RecA nucleoproteic filament loaded by RecBC may be leading to the homologous recombination repair pathway, rather than triggering the SOS response.
Single-strand exonucleases participate in several repair or recombination pathways within the cell, such as BER (23), methyl-directed mismatch repair (21), homologous recombination (27,36) and P1 transduction (22). RecJ and ExoI play an important role in degrading single-stranded DNA, and as observed in the present work, both are essential for DNA damage processing prior to SOS induction, whereas ExoVII as well as ExoX seem to be secondary, and as indicated by the results in the xseA, exoX double mutant are not indispensable for SOS to occur. It is important to point out that RecJ and ExoI share several common features: they both have a very similar tri-dimensional structure, including a narrow cleft just about the active site that promotes tight single-strand DNA binding while excluding duplex DNA to achieve a potent processive nuclease function (37–39); they both have been reported to act in the same mechanisms (36) and they both have direct protein–protein interaction with RecQ helicase and SSB, two proteins that are also important for SOS induction (39–41).
In an attempt to explain the results obtained in this work, a model suggesting how different kinds of gamma radiation-induced lesions may be processed and the role played by different repair enzymes in leading to the induction of the SOS response is proposed (Figure 6).
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To allow full SOS expression, bacterial cultures were grown to exponential phase, and consequently there were several replication forks in progress, which when encountering ssb were able to be converted to DSBs. Those with blunt ends, together with the rest caused by radiation itself, may be directly recognized by RecBCD to be repaired by homologous recombination, while only a small portion could actually induce SOS. As supported by the strong radiation sensitivity of the recJ,xonA double mutant, DSBs with sticky ends would be trimmed by single-strand-exonucleases, mainly RecJ and ExoI, to become a proper substrate for RecBCD-directed recombination repair.
ssb could be recognized and enlarged by single-strand-exonucleases, probably assisted by helicases such as RecQ (41,42), to become single-strand DNA suitable to be coated by SSB and later by RecA with the participation of RecFOR, as suggested by the fact that recJ-, recO- and xonA-defective mutants have equally low induced SOS levels.
Nearly 74% of gamma radiation-induced DNA damage occurs at base level (43). A great deal of these lesions (such as dihydroxy-dihydrothymidine, hydroxy-deoxyuridine, hydroxymethyl-deoxyuridine, formyl-deoxyuridine, dihydro-deoxyadenosine, dihydro-deoxyguanosine, diamino-formamidopyrimidine and diamino-hydroxy-formamidopyrimidine) are recognized by Nth or Fpg glycosylases (44,45) and AP endonucleases, causing nicks that upon encountering replication forks may cause DSBs or, by single-strand-exonucleolytic extension, lead to SOS induction (46). It was demonstrated earlier that DNA replication arrest leads to SOS activation (47,48). However, and as opposed to UV light, only a small portion of gamma radiation base damage can actually block replication forks. Indeed, the difference in SOS levels between proficient and uvrA-defective strains is relatively small (7), suggesting that DNA polymerase illegible lesions of the type recognized by the UvrABC endonuclease complex (49) hardly contribute to overall SOS activation.
One would expect then that radiation-induced SOS levels would be lowered in glycosylase-defective mutants, as is the case with the results obtained using nth- or fpg-defective strains—especially the former. Moreover, preliminary experiments exposing these defective mutants to tert-butyl-hydroperoxide show, as expected, lowered SOS levels (data not shown), supporting the idea that part of the response is due to oxidized bases caused by gamma radiation.
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Conclusions |
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The results obtained in this work indicate that in vivo, all single-strand-exonucleases analysed, as well as some glycosylases, seem to participate in processing gamma radiation-induced damage to generate single-stranded DNA regions that lead to induction of the SOS response. It was also demonstrated that the nuclease activity of RecD is responsible for the small percentage of SOS induced by DNA DSBs. Taken together, the results suggest that SOS induction occurs mainly when RecA is loaded onto single-stranded DNA by RecFOR and, to a lesser degree, by RecBCD.
It was stated initially that SOS was one of multiple alternatives for survival. However, when comparing SOS-proficient strains with those with poor SOS levels, differences in survival are relatively modest. This in turn indicates that, if not essential for survival, this response may be a backup system, and its actual importance lies rather in the increase in genetic variability through the error-prone polymerases, and consequently in enhancing chances for advantageous mutations to occur, as suggested previously (50,51).
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Consejo Nacional de Ciencia y Tecnología, México (194870) to J.S.-G.
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Acknowledgments |
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The authors wish to thank Susan Lovett for bacterial strain STL2694, Dr Richard Kolodner for strain RDK1848, Dr Richard Cunningham for strain BW434, Dr Barry Wanner for the set of strains used in the gene disruption methodology and Dr Philippe Qullardet for PQ30 strain; Jessica Ponce-Malagón, Magdalena Aguilar-Moreno and Alicia González-Medina for technical assistance. Our special thanks to Dr Rafael Camacho-Carranza and Dr Manuel Uribe-Alcocer for their helpful comments throughout this work.
Conflict of interest statement: None declared.
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Notes |
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* To whom correspondence should be addressed. Tel: +52 55 5329 7230; Fax: +52 55 5329 7387; Email: josg{at}nuclear.inin.mx
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-
1. Téoule R. Radiation-induced DNA damage and its repair. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. (1987) 51:573–589.[Medline]
2. Fernández de Henestrosa AR, Ogi T, Aoyagi S, Chafin D, Hayes JJ, Ohmori H, Woodgate R. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. (2000) 35:1560–1572.[CrossRef][Web of Science][Medline]
3. Courcelle J, Khodursky A, Peter B, Brown P, Hanawalt P. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Genetics (2001) 158:41–64.
4. Walker GC. The SOS response of Escherichia coli. In: Escherichia coli and Salmonella:—Neidhardt FC, et al, eds. (1996) Washington, DC: Cellular and Molecular Biology. ASM Press. 1400–1416.
5. Little JW. Autodigestion of lexA and phage repressors. Proc. Natl Acad. Sci. USA (1984) 81:1375–1379.
6. Higashitani N, Higashitani A, Horiuchi K. SOS induction in Escherichia coli by single-stranded DNA of mutant filamentous phage: monitoring by cleavage of LexA repressor. J. Bacteriol. (1995) 177:3610–3612.
7. Breña M, Serment J. SOS induction by gamma radiation in E. coli strains defective in repair and/or recombination mechanisms. Mutagenesis (1998) 13:637–641.
8. Tavera L, Breña M, Pérez M, Serment J, Balcázar M. Response to alpha and gamma radiations of Escherichia coli strains defective in repair or protective mechanisms. Radiat. Meas. (2003) 36:591–595.[CrossRef][Web of Science]
9. Umezu K, Kolodner R. Protein interactions in genetic recombination in Escherichia coli: interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA binding protein. J. Biol. Chem. (1994) 269:30005–30013.
10. Hedge S, Sandler J, Clark A, Madiraju M. recO and recR mutations delay induction of the SOS response in Escherichia coli. Mol. Gen. Genet. (1995) 246:254–258.[CrossRef][Web of Science][Medline]
11. Whitby C, Lloyd R. Altered SOS induction associated with mutation in recF, recO and recR. Mol. Gen. Genet. (1995) 246:174–179.[CrossRef][Web of Science][Medline]
12. Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage . Microbiol. Mol. Biol. Rev. (1999) 63:751–813.
13. Miller J. A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (1991) Cold Spring Harbour, NY: Cold Spring Harbour Laboratory Press. 456.
14. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA (2000) 97:6640–6645.
15. Feschenko VV, Rajman LA, Lovett ST. Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases. Proc. Natl Acad. Sci. USA (2003) 100:31134–31139.
16. Chung CT, Niemela SL, Miller RH. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc. Natl Acad. Sci. USA (1989) 86:2172–2175.
17. Quillardet P, Hofnung M. The SOS chromotest, a colorimetric bacterial assay for genotoxins: procedures. Mutat. Res. (1985) 147:65–78.[Web of Science][Medline]
18. Sargentini NJ, Smith KC. Quantitation of the involvement of the recA, recB, recC, recF, recJ, recN, lexA, radA, radB, uvrD, and umuC genes in the repair of X-ray-induced DNA double-strand breaks in Escherichia coli. Radiat. Res. (1986) 107:58–72.[Web of Science][Medline]
19. Cunningham P, Weiss B. Endonuclease III (nth) mutants of Escherichia coli. Proc. Natl Acad. Sci. USA (1985) 82:474–478.
20. Boiteux S, Huisman O. Isolation of a formamidopyrimidine-DNA glycosylase (fpg) mutant of Escherichia coli K12. Mol. Gen. Genet. (1989) 215:300–305.[CrossRef][Web of Science][Medline]
21. Burdett V, Baitinger C, Viswanathan M, Lovett ST, Modrich P. In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc. Natl Acad. Sci. USA (2001) 98:6765–6770.
22. 
ermic D. Functions of multiple exonucleases are essential for cell viability, DNA repair and homologous recombination in recD mutants of Escherichia coli. Genetics (2006) 172:2057–2069.
23. Cooper DL, Lahue RS, Modrich P. Methyl-directed mismatch repair is bidirectional. J. Biol. Chem. (1993) 268:11823–11829.
24. Anderson DG, Kowalczykowski SC. The recombination hot spot x is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme. Genes Dev. (1997) 11:571–581.
25. Br
i
-Kosti K, Salaj-
mic E, Mar
i N, Kaji S, Stojiljkovi I, Trgovccaronevi 
. Interaction of RecBCD enzyme with DNA damaged by gamma radiation. Mol. Gen. Genet. (1991) 228:136–142.[CrossRef][Web of Science][Medline]
26. Churchill J, Anderson D, Kowalczykowski S. The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of x, resulting in constitutive recombination activation. Genes Dev. (1999) 13:901–911.
27. Thoms B, Wackernagel W. Interaction of RecBCD enzyme with DNA at double-strand breaks produced in UV-irradiated Escherichia coli: requirement for DNA end processing. J. Bacteriol. (1998) 180:5639–5645.
28. Chase JW, Richardson CC. Exonuclease VII of Escherichia coli; purification and properties. J. Biol. Chem. (1974) 249:4545–4552.
29. Viswanathan M, Lovett ST. Exonuclease X of E. coli, a novel 3'-5' DNase and DnaQ superfamily member involved in DNA repair. J. Biol. Chem. (1999) 274:30094–30100.
30. Shan Q, Bork JM, Webb BL, Inman RB, Cox MM. RecA protein filaments: end-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins. J. Mol. Biol. (1997) 265:519–540.[CrossRef][Web of Science][Medline]
31. Hobbs MD, Sakai A, Cox M. SSB protein limits RecOR binding onto single-stranded DNA. J. Biol. Chem. (2007) 282:11058–11067.
32. Kowalczykowski SC. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. (2000) 25:156–165.[CrossRef][Web of Science][Medline]
33. Viswanathan M, Lanjuin A, Lovett ST. Identification of RNase T as a high-copy suppressor of the UV sensitivity associated with single-strand DNA exonuclease deficiency in Escherichia coli. Genetics (1999) 151:929–934.
34. Keller KL, Overbeck-Carrick TL, Beck DJ. Survival and induction of SOS in Escherichia coli treated with cisplatin, UV-irradiation, or mitomycin C are dependent on the function of the RecBC and RecFOR pathways of homologous recombination. Mutat. Res. (2001) 486:21–29.[Web of Science][Medline]
35. Ivani-Bae I, Vlai I, Salaj-mic E, Bri-Kosti K. Genetic evidence for the requirement of RecA loading activity in SOS induction after UV irradiation in Escherichia coli. J. Bacteriol. (2007) 188:5024–5032.[CrossRef][Web of Science]
36. Viswanathan M, Lovett ST. Single-strand DNA specific exonucleases in Escherichia coli: roles in repair and mutation avoidance. Genetics (1998) 149:7–16.
37. Breyer W, Matthews B. Structure of Escherichia coli exonuclease I suggests how processivity is achieved. Nat. Struct. Biol. (2000) 7:1125–1128.[CrossRef][Web of Science][Medline]
38. Yamagata A, Kakuta Y, Masui R, Fukuyama K. The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity. Proc. Natl Acad. Sci. USA (2002) 99:5908–5912.
39. Han ES, Cooper DL, Persky NS, Sutera VA, Whitaker RD, Montello ML, Lovett ST. RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Res. (2006) 34:1084–1091.
40. Sandigursky M, Mendez F, Bases RE, Matsumoto T, Franklin WA. Protein-protein interactions between the Escherichia coli single-stranded DNA-binding protein and exonuclease I. Radiat. Res. (1996) 145:619–623.[Web of Science][Medline]
41. Shereda R, Bernstain DA, Keck J. A central role for SSB in Escherichia coli RecQ DNA helicase function. J. Biol. Chem. (2007) 282:19247–19258.
42. Hishida T, Han YW, Shibata T, Kubota Y, Ishino Y, Iwasaki H, Shinagawa H. Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks. Genes Dev. (2004) 18:1886–1897.
43. Gulston M, Fulford J, Jenner T, de-Lara C, O'Neill P. Clustered damage induced by gamma radiation in human fibroblasts (HF19), hamster (V79-4) calls and plasmid DNA revealed as Fpg and Nth sensitive sites. Nucleic Acids Res. (2002) 30:3464–3472.
44. Frelon S, Douki T, Ravanat J, Pouget J, Tornabene C, Cadet J. High-performance liquid chromatography-tandem mass spectrometry measurement of radiation-induced base damage to isolated and cellular DNA. Chem. Res. Toxicol. (2000) 13:1002–1010.[CrossRef][Web of Science][Medline]
45. Shikazono N, Pearson C, O'Neill P, Thacker J. The roles of specific glycosylases in determining the mutagenic consequences of clustered DNA base damage. Nucleic Acids Res. (2006) 34:3722–3730.
46. Dianov G, Sedwick B, Daly G, Olsson M, Lovett ST, Lindhal T. Release of 5'-terminal deoxyribose-phosphate residues from incised abasic sites in DNA by the Escherichia coli RecJ protein. Nucleic Acids Res. (1994) 22:993–998.
47. Salles B, Defais M. Signal of induction of recA protein in E. coli. Mutat. Res. (1984) 131:53–59.[CrossRef][Web of Science][Medline]
48. Sassanfar M, Roberts J. Nature of the SOS-inducing signal in Escherichia coli; the involvement of DNA replication. J. Mol. Biol. (1990) 212:79–96.[CrossRef][Web of Science][Medline]
49. Roldán-Arjona T, Sedgwick B. DNA base damage induced by ionizing radiation recognized by Escherichia coli UvrABC nuclease but not Nth or Fpg proteins. Mol. Carcinog. (1996) 16:188–196.[CrossRef][Web of Science][Medline]
50. Radman M. Enzymes of evolutionary change. Nature (1999) 401:866–867. 869.[CrossRef][Medline]
51. Friedberg E, Gerlach V. Novel DNA polymerases offer clues to the molecular basis of mutagenesis. Cell (1999) 98:413–416.[CrossRef][Web of Science][Medline]
Received on December 14, 2007; revised on February 15, 2008; revised on March 12, 2008; accepted on March 14, 2008.
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