[Frontiers in Bioscience 16, 3164-3182, June 1, 2011]

Escherichia coli Y family DNA polymerases

Jason M. Walsh1, Lisa A. Hawver1, Penny J. Beuning1, 2

1Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA, 2Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA

TABLE OF CONTENTS

1. Abstract
2. Introduction
3. Transcriptional and post-translational regulation
4. DNA polymerase IV: DinB
4.1. DinB in general stress responses
4.2. Specificity
4.3. DinB variants
4.4. Cellular interactions of DinB
5. DNA polymerase V: UmuD′2C
5.1. Discovery of pol V and SOS mutagenesis
5.2. Roles of Pol V in responding to replication stress
5.3. Specificity
5.4. UmuC variants
5.5. Cellular interactions of UmuC
6. Polymerase switching
7. Summary
8. Acknowledgments
9. References

1. ABSTRACT

DNA damage is ubiquitous, arising from both environmental and endogenous sources. All organisms have evolved multiple pathways to respond to DNA damage and maintain genomic integrity. Escherichia coli possesses two DNA polymerases, pol IV and pol V, that are members of the Y family. These polymerases are characterized by their specialized ability to copy damaged DNA as well as their relatively low fidelity on undamaged DNA. Pol IV and pol V are regulated by the SOS response to DNA damage and by their multiple interactions with other proteins. These two Y family DNA polymerases copy DNA damaged by distinct agents. Pol IV is capable of replicating DNA containing N2-dG adducts, while pol V bypasses abasic sites and thymine-thymine dimers, which result from exposure to UV radiation. In addition to their roles in copying damaged DNA, the two Y family DNA polymerases in E. coli act in regulation of DNA replication and contribute to bacterial mutagenesis in response to cellular stress.

2. INTRODUCTION

The process by which DNA polymerases replicate damaged DNA is known as translesion synthesis (TLS) and was first described 35 years ago (1). It was observed that DNA damage induced the E. coli SOS response, which is accompanied by mutagenesis of the DNA (1). Originally DNA damage-induced mutagenesis was thought to result from the modification of replicative DNA polymerases, which allowed them to bypass DNA damage, albeit sometimes mutagenically (2). However it was later discovered that the UmuC/UmuD′ complex (UmuD′2C, pol V) and DinB (pol IV) are Y family DNA polymerases that have the specialized ability to carry out potentially mutagenic TLS (3).

Y family DNA polymerases (4), found throughout all domains of life, have five conserved sequence motifs but the overall size of the proteins can vary considerably (Figure 1) (3, 5-9). In addition to bacterial pol IV and pol V, the eukaryotic members of the family include Rev1, pol eta, pol kappa, and pol iota (4). The domains of both replicative and Y family DNA polymerases are named for their general resemblance to the parts of a right hand, including thumb, palm, and finger domains. Y family polymerases also possess a domain known as the 'little finger' domain found only in the Y family (10). The Y family polymerases are characterized by small finger and thumb domains relative to replicative DNA polymerases, which result in an open, solvent-accessible active site in the palm domain of Y family members (3, 11). The active site of replicative polymerases contains an 'O-helix', the role of which is to act as a steric check on fidelity and allow only a correct base pair to be formed (12-14). Y family polymerases lack the O-helix, contributing to their more open and flexible active sites and allowing them to accommodate lesions on the DNA template (10, 15). The available crystal structures of Y family DNA polymerases (6) tend to support the model of an open active site, as seen in the structure of Sulfolobus solfataricus Dpo4 in complex with DNA containing a thymine-thymine (T-T) cyclobutane pyrimidine dimer (16). This structure demonstrates that both thymines are accommodated in the active site simultaneously (16). Structures of other Y family DNA polymerases with or without DNA also generally show that these proteins have small finger domains and open, solvent-accessible active sites, suggesting a structural basis both for their ability to accommodate DNA lesions and for their low fidelity when copying undamaged DNA (3, 6, 10-11, 17-18).

3. TRANSCRIPTIONAL AND POST-TRANSLATIONAL REGULATION

In E. coli, the expression of Y family polymerases along with other genes is induced via the SOS response to damaged DNA. This cellular response was named the SOS response by Miroslav Radman because there is a "danger signal which induces SOS repair" (19). That "danger signal" is usually considered to be a DNA lesion that disrupts normal DNA replication (5, 19). Evelyn Witkin suggested that there was a pathway in E. coli that is controlled by a repressor whose function is inactivated when DNA damage occurs and that again becomes activated as a repressor once the repair of DNA damage is complete (20). This repressor was discovered to be the LexA protein, the repressor of the SOS genes. The SOS response is initiated when a lesion in the DNA template prevents replicative polymerases from continuing with efficient replication, causing a region of single-stranded DNA (ssDNA) to develop (Figure 2). RecA is activated upon binding to ssDNA, forming a RecA/ssDNA nucleoprotein filament (5). LexA then binds the RecA/ssDNA nucleoprotein filament, inducing LexA to cleave itself at its Ala84-Gly85 bond, approximately in the middle of the protein (21). Once LexA is cleaved it no longer represses the SOS genes, allowing at least 57 genes, including umuC, umuD, and dinB, to be expressed during the SOS response (5, 22). In addition to its role in initiating the SOS response, RecA also plays more direct roles in the ability of Pol V to bypass lesions (see Section 5.5).

The umuD gene products contribute an additional level of regulation of Y family DNA polymerases in E. coli (5). Upon expression, UmuD2 binds to the RecA/ssDNA nucleoprotein filament, stimulating the ability of UmuD to cleave itself at its Cys24-Gly25 bond and removing its N-terminal 24-amino acids to form UmuD′2 by a mechanism similar to that of LexA (23-25). The full-length UmuD2 protein persists for approximately 20-40 min after expression is induced, after which time the cleaved form UmuD′2 becomes the predominant form (Figure 2) (26). Full-length UmuD2 and cleaved UmuD′2 play distinct roles in the cellular response to DNA damage; UmuD2 contributes to accurate DNA replication and repair while UmuD′2 facilitates mutagenesis (26-32). Therefore, this lag in the appearance of UmuD′2 delays the use of a potentially mutagenic pathway, in part via direct interactions between the umuD gene products and Y family DNA polymerases.

4. DNA POLYMERASE IV: DinB

DinB is one of two Y family polymerases found in E. coli (29, 31, 33). The dinB (damage-inducible) gene was identified as being induced upon treatment with DNA damaging agents (9, 34). Subsequently, the dinB gene product was demonstrated to be a DNA-dependent DNA polymerase (33). DinB was also shown to possess the ability to accommodate misaligned or bulged primer-template structures into its active site and to lack intrinsic 3′-5′ exonuclease proofreading activity (33).

4.1. DinB in general stress responses

DinB is expressed at a level of approximately 250 molecules per cell under non-SOS induced conditions (35). However, this number increases 10-fold after SOS induction; therefore DinB is the most abundant DNA polymerase in E. coli during times of cellular stress (35). This level of upregulation of DinB leads to inhibition of pol III, decreasing the ability of pol III to access DNA and ultimately leading to cell death (36-37).

A phenomenon known as adaptive mutagenesis involves dinB-dependent increased mutability in starving, non-dividing cells (38-39). It has been suggested that adaptive mutagenesis provides mutations that confer a selective advantage in times of cellular stress (40). DinB induction occurs late in stationary phase and the higher levels may be maintained for at least several days with maximum expression and mutagenesis occurring in cells that have active RNA polymerase sigma factor (RpoS) (41-42). Adaptive mutagenesis is a cellular starvation stress response system, which is partially distinct from the SOS response. Notably, of the SOS genes, only DinB at elevated levels is required for stress-induced mutagenesis (43), although the exact molecular mechanism of adaptive mutagenesis may not be entirely clear (44-46). A variety of aspects of adaptive mutagenesis have been reviewed recently (40, 47-49). The GroE heat shock response chaperone system has also been shown to influence DinB protein levels as well as adaptive mutagenesis, although no direct interaction between GroE and DinB has been detected (50).

Classically, expression of the dinB gene is repressed by LexA and induced as part of the SOS response (22, 34). However, the dinB gene can also be expressed under other conditions of cellular stress. For example, dinB expression is induced by beta-lactam antibiotic-mediated inhibition of the synthesis of the bacterial cell wall independent of LexA (51). This suggests that transcription of the dinB gene can be considered a general stress response mechanism. Increased mutagenesis by DinB, and possibly pol V, may be a contributing factor to antigenic variation or antibiotic resistance (52-55).

4.2. Specificity

DinB displays a preference for certain damaged DNA substrates. For example, DinB possesses a 15-fold preference to insert C opposite N2-furfuryl-dG and a 25-fold preference to extend from a base pair with N2-furfuryl-dG in comparison to undamaged dG in a DNA template (Figure 3) (56-57). While the endogenous source of N2-furfuryl-dG has not yet been determined, by analogy to the formation of kinetin (N6-furfuryl-dA), it may be a product of ribose oxidation (58). Strains in which dinB has been deleted show a striking sensitivity to nitrofurazone and 4-nitroquinoline-1-oxide (4NQO), both of which are thought to form N2-dG adducts, as well as possibly other adducts (5, 56). DinB also efficiently and accurately bypasses N2-(1-carboxyethyl)-2′-deoxyguanine (N2-CEdG), which was detected in 1 in 107 bases in melanoma cells and is formed as an adduct of methylglyoxal, a common byproduct of glycolysis (Figure 3) (59). The presence of DinB significantly increases bypass of the N2-dG adduct of benzo(a)pyrene (B(a)P), a potent carcinogen consisting of a large, bulky polycyclic hydrocarbon (Figure 3) (60-63). However, efficient bypass of some isomers of B(a)P also requires pol V, suggesting that even subtle changes in the conformation of adducts can alter how they are processed by DinB (60). Acrolein is a potent toxin and has tumor initiating properties, but it is also an endogenous byproduct of fatty acid metabolism (64). DinB inserts dCTP across from gamma-hydroxypropano-deoxyguanosine (HOPdG), the N2-dG adduct of acrolein, as well as peptide cross-links to gamma-HOPdG (Figure 3) (64). In addition to bypass of DNA-peptide cross-links, DinB is also proficient in bypassing N2-N2-dG interstrand cross-links (65). DinB may have a functional duality as a bypass polymerase for certain metabolism-induced DNA lesions such as HOPdG, N2-CEdG, and N2-furfuryl-dG, and as a general bypass polymerase capable of negotiating larger N2-dG adducts such as benzo(a)pyrene.

Pol kappa is the eukaryotic ortholog of DinB. Although mammalian pol kappa, like DinB, exhibits a preference for N2-furfuryl-dG (56), there are differences in the abilities of the two enzymes to replicate DNA containing other adducts. Notably, the C8-dG adducts of N-2-acetylaminofluorene (2-AAF) and aminofluorine (2-AF), which are prototypical aromatic amides and carcinogens, are readily bypassed by human pol kappa, but these same adducts block insertion and extension by E. coli DinB (66).

DinB exhibits varying efficiency for bypass of a number of lesions resulting from reactive oxygen species, including 8-oxoG, 2-oxoA, thymine glycol, 5-formyluracil, and 5-hydroxymethyluracil (67) and is able to incorporate into DNA the oxidized nucleotides 2-oxo-dATP and 8-oxo-dGTP (68). DinB has been shown to bypass abasic (AP) sites in vitro generating either -1 or -2 frameshift mutations (69-70). The presence of accessory proteins, specifically the beta processivity clamp and the gamma clamp loader, greatly increase the efficiency of bypass (70) and decrease frameshift mutagenesis (69).

On undamaged DNA, DinB has a relatively high error frequency of 2.1 x 10-4 for frameshift mutations and 5.1 x 10-5 for base substitution mutations (69). The majority of the frameshift mutations are single base deletions (~81%), whereas a substantial number of frameshift mutations are two base deletions (~15%) (69). The mechanisms by which the -1 frameshift mutations occur in TLS by DinB is most likely a combination of Streisinger slippage (71) and dNTP-stabilized misalignment in which a nucleotide downstream from the primer terminus is flipped out of the DNA helix and is skipped by DinB generating a -1 frameshift mutation (Figure 4) (69, 72-73). The dNTP-mediated mechanism may be at odds however with the recently published mechanism of template slippage on homopolymeric runs by DinB (73). This type of slippage, which generates -1 frameshift mutations, is inhibited by UmuD2 (Figure 4) (73). Base skipping occurs as the template strand opposite the 5′ terminus folds into the extrahelical space and the next nucleotide on the template strand becomes the base opposite the primer terminus (74-75). This mechanism was also observed in similar studies with the DinB ortholog Sulfolobus acidocaldaricus Dbh (76).

4.3. DinB variants

Currently, there is no high-resolution structure of DinB but homology models (56, 77) have been constructed based on the crystal structures of other homologous proteins: Sulfolobus solfataricus Dpo4 (10) and Sulfolobus acidocaldaricus Dbh (17). Therefore, interpretation of experiments in which DinB variants have been constructed relies on the use of homology models. Cells containing overexpressed wild-type DinB had a mutation frequency of 68,466.5 x 107 (33), which is approximately 3600-fold greater than cells without overexpressed DinB (33). DinB mutations D8A, D8H, R49A, R49F, D103A, D103N (dinB003), and E104A led to between 850- and 3700-fold lower mutation frequencies (Figure 5) (33). D103 and E104 reside in the S(LI)DE box whose negatively charged residues in the active site coordinate the divalent magnesium ions needed for adding the incoming nucleotide to the DNA primer (10, 33). Along with D103 and E104, D8 is strictly conserved (33). R49 is predicted to lie in a loop region that is near the incoming nucleotide.

The steric gate is a single residue in DNA polymerases that prevents the incorporation of ribonucleotides into DNA by sterically occluding nucleotides with a 2′ hydroxyl group (78). The steric gate residue of Y family DNA polymerases is most frequently tyrosine or phenylalanine (56, 79-80). Mutation of the steric gate residue F13 in DinB increases the frequency of ribonucleotide misincorporation from <10-5 to 10-3 (56). It was hypothesized that the pocket in which F13 resides is involved in the accommodation of a lesion in the active site (Figure 5) (56). The substitution F13V inhibits the ability of DinB to bypass N2-furfuryl-dG and also slightly enhances the ability of DinB to replicate undamaged DNA (56).

Near the steric gate residue and conserved among all orthologous DinBs, Y79 is hypothesized to regulate the function of the steric gate residue (57). Mutations at this position have a modest effect on primer extension on undamaged DNA but prevent DinB from extending more than a few nucleotides beyond a lesion and result in extreme cellular sensitivity to nitrofurazone (57). As demonstrated in these studies, single mutations can have a large effect on both the DNA replication and TLS activities of DinB.

4.4. Cellular interactions of DinB

DinB is regulated through protein-protein interactions with UmuD2, RecA, and NusA, as well as with the beta clamp (27, 81). Addition of RecA and UmuD2 to a primer extension assay in which there are correctly paired bases at the primer terminus increases the polymerization proficiency of DinB (27). It appears that the deleterious -1 frameshift mutator activity of DinB is a result of the elevated number of molecules of DinB present in a cell relative to the amount of UmuD2 present (27). Indeed, co-upregulation of both UmuD2 and DinB suppresses the -1 frameshift mutation activity, while -1 frameshift mutations are elevated in the absence of umuD (Figure 4) (27). Modeling studies suggest that RecA and UmuD2 may suppress the -1 frameshift activity innate to DinB by decreasing the openness of the DinB active site (27). This regulation may explain the dual nature of the polymerase activity of DinB, which accurately bypasses bulky N2-dG adducts but is also responsible for highly mutagenic -1 frameshift mutations (56, 69, 82). Deletion of umuD did not affect DinB-dependent resistance to nitrofurazone, suggesting that the -1 frameshift mutator activity and TLS functions are to some extent distinct (27). DinB residue F172 is highly conserved in DinB sequences from organisms that also harbor umuD and has been shown to mediate the interaction between DinB and UmuD (Figure 5) (27).

DinB also interacts physically with the beta processivity clamp. In the presence of the beta clamp, DinB is recruited to the primer terminus to form a stable complex with DNA, which substantially stimulates its processivity (81). The specific residues involved in this protein-protein interaction have been identified as 346QLVLGL351 (83-84), which is at the C-terminus of DinB (Figure 5). The co-crystal structure of the little finger domain of DinB with the beta clamp reveals a second interaction site between the two proteins at DinB residues 303VWP305 and near the dimer interface of beta (85). When the structure of full-length Dpo4 was superimposed on the structure of the DinB little finger, the DNA polymerase did not seem to be in the proper position to access the primer terminus (85). This suggests that this conformation, while likely not catalytically relevant, may be one way in which the beta processivity clamp facilitates recruitment of DinB to replication forks (85-86). DinB can remove pol III from the beta clamp when pol III is stalled at a primer terminus in vitro thus inhibiting the continuation of DNA synthesis by the pol III holoenzyme (37).

Recently, a role for the NusA protein in stress-induced mutagenesis has been found involving an interaction with DinB. NusA plays an important role in the elongation, termination, and anti-termination phases of transcription (87-89). It was shown that DinB and NusA physically interact with one another, so it was proposed that NusA recruits DinB to gaps that stall RNA polymerase during transcription (90). Though the exact location of the interaction has yet to be identified, the C-terminal domain of NusA and surface residues near the nusA11Ts mutation are likely sites (90-91). Genetic interactions have been observed between nusA and both dinB and umuDC, which may indicate a genetic link between TLS and transcription (90). Moreover, NusA plays a role in transcription-coupled nucleotide excision repair as well as in recruiting DinB for transcription-coupled TLS of lesions that result in gaps in the DNA template that disrupt RNA polymerase (92). Additionally, NusA has been found to be required for DinB-dependent stress-induced, or adaptive, mutagenesis (93).

5. DNA POLYMERASE V: UmuD′2C

Y family DNA polymerase pol V, discovered in an experiment to identify nonmutable mutants of E. coli, is encoded by the umuDC genes and induced by the SOS response (94-95). This specialized polymerase consists of one molecule of UmuC which possesses the polymerase activity, and one UmuD′2 dimer, therefore pol V is also referred to as UmuD′2C. Pol V is responsible for the majority of UV-induced mutagenesis in E. coli and it has been shown to bypass common lesions from UV radiation.

5.1. Discovery of pol V and SOS mutagenesis

The umuC gene was discovered by characterizing mutants of E. coli that were deficient for UV-induced mutagenesis but were still viable (95). Kato and Shinoura screened for UV-nonmutable (Umu) mutants by using the mutagen 4-nitroquinoline-1-oxide (4NQO) and then using UV irradiation in a second screen (95). The umuC gene appeared to encode a protein that participates in "mutagenic repair" as well as reactivation by UV irradiation (95). Steinborn independently discovered uvm mutants that are deficient in UV mutability using a similar method to Kato and Shinoura (96). It was thought that perhaps the uvm gene was related to umuC in that they displayed similar nonmutable characteristics when uvm mutants were exposed to UV light, a phenotype of UmuC that is now well known (96). Characterization of the umuC gene and its role in SOS mutagenesis was carried out long before the biochemical function of its gene product in translesion synthesis was determined.

Polymerase V is an error-prone DNA polymerase that is responsible for most SOS mutagenesis. It was first suggested that the UmuC and UmuD proteins were mediators that enabled DNA polymerase III holoenzyme (pol III HE), which typically stalls at sites of damage, to bypass DNA lesions (97-98). This stalling may occur for one of two reasons: either the polymerase cannot recognize the lesion as an instructional base, or the exonucleolytic proofreading subunit of pol III HE recognizes any base insertion as incorrect and hydrolyzes the newly incorporated nucleotide (2, 5, 99-101). It was thought that UmuC-UmuD′ allows pol III HE to successfully replicate past a DNA lesion but with low fidelity (2, 98). A two-step model for UV mutagenesis was proposed. In the model, the first step involves a RecA-mediated misincorporation event opposite the lesion. In the second step, umuC extends the primer from the misincorporated nucleotide, allowing replication to continue beyond this point (97, 100). At the same time, it was discovered that the umuD gene product participates along with UmuC in this two-step process (97).

Tang et al. showed that UmuD′2C in the presence of RecA, beta clamp, gamma clamp loader, SSB, and either polymerase III or II facilitates the bypass of an abasic lesion, at which time it was speculated that UmuD′2C had polymerase activity (102). By 1999, two separate groups reported purifying different forms of the UmuC protein. The Livneh group purified a soluble form of UmuC, an N-terminal fusion with maltose binding protein (MBP) (29). The Woodgate and Goodman groups collaborated to purify a soluble complex UmuD′2C (31, 102-103). Both groups determined that UmuD′2C is in fact a DNA polymerase (29, 31). UmuC had weak DNA polymerase activity, but with the addition of cofactors such as UmuD′, RecA, and SSB, this activity increased despite the absence of pol III HE (29). The UmuD′2C complex also inhibits homologous recombination mediated by RecA, suggesting that the appearance of pol V actively prevents the relatively accurate recombination repair pathway while enabling SOS mutagenesis (104-106).

5.2. Roles of Pol V in responding to replication stress

Upon DNA damage, replication forks undergo regression; these regressed forks are stabilized by RecA and RecF (107-108). RecJ and RecQ partially degrade nascent DNA at stalled replication forks, while preventing TLS from occurring (109). Recovery of DNA synthesis typically occurs once the generally accurate nucleotide excision repair process removes the lesion (110). If the capacity of nucleotide excision repair is exhausted, pol V specifically allows DNA replication to recover (111). In the absence of umuDC, recovery of DNA synthesis is modestly delayed (110). However, in the absence of recJ, replication restart is significantly delayed and in the absence of both recJ and umuDC, replication essentially does not recover. Without RecJ present to process the stalled replication fork, TLS by pol V is required for survival (110, 112).

When UmuC and UmuD are overexpressed in E. coli, strains are cold sensitive, meaning the cells exhibit extremely slow growth at 30 �C without a growth defect at 42 �C. The cold sensitivity phenotype correlates with a specific decrease in the rate of DNA replication (28). This decrease in the rate of replication likely delays restart of replication in response to DNA damage to allow time for accurate methods of DNA repair such as nucleotide excision repair to operate and therefore may serve as a primitive DNA damage checkpoint (26). In this model, cleavage of UmuD to form UmuD′ releases the checkpoint, in part because UmuD′ has lower affinity for the beta clamp than does UmuD (113-114), and allows TLS to occur (26, 30, 115). The cold sensitivity phenotype conferred by UmuD and UmuC is independent of their roles in TLS (30). Taken together, these observations suggest that inappropriate levels of the umuDC gene products, whether because they are deleted or overexpressed, disrupt the cellular responses to DNA damage or replication stress.

5.3. Specificity of pol V

Polymerase V bypasses common lesions that result from UV radiation, such as thymine-thymine (T-T) cis-syn cyclobutane pyrimidine dimers (CPD) and T-T (6-4) photoproducts, as well as abasic sites and the C8-dG adduct formed from N-2-acetylaminofluorine (C8-AAF) (Figure 6) (101, 116-119). Pol V efficiently bypasses UV photoproducts as well as abasic sites when in the presence of the beta clamp, RecA/ssDNA, and SSB (118). Pol V inserts G six-fold more frequently than it inserts A opposite the 3′-T of T-T (6-4) photoproducts, consistent with its mutagenic signature in vivo (116, 118). The CPD UV photoproduct is bypassed in an error-free manner (116, 118). N-2-acetylaminofluorine forms adducts at the C8 position of the guanine base (117), giving C8-AAF-dG, which is bypassed in an error-free manner by pol V when the lesion occurs in the context of (5′-GGCGAAFCC-) (117). These lesions also commonly cause -2 frameshift mutations in continuous G sequences, including the NarI sequence, as well as -1 frameshift mutations in sequences containing three or four continuous Gs (5). Pol V efficiently bypasses N6-benzo(a)pyrene-dA and is implicated in bypass of some N2-benzo(a)pyrene-dG adducts (Figure 3), as well as some oxidized bases (60-61, 63, 120). Pol V displays error rates of 10-3 - 10-4 when copying undamaged DNA, therefore it is even less accurate than DinB (118).

5.4. UmuC variants

There is currently no crystal structure of UmuC, so interpretation of experiments with UmuC variants must rely on models based on homology to Dpo4 and other Y family DNA polymerases (121-122). UmuC variants with mutations at several residues have been characterized (Figure 7). Due to the lack of an efficient purification scheme for pol V, most characterization of variants has been carried out in vivo using complementation assays. Residues D101, E102, and D6 are strictly conserved catalytic residues for metal ion binding, with D101 and E102 part of the conserved S(LI)DE motif (10, 96). The UmuC D101N (umuC104) variant made by Steinborn cannot carry out UV-induced mutagenesis and polymerase activity is severely diminished (10, 96).

The steric gate residue of UmuC has been identified as Y11 (Figure 7) (80). F10 is the residue N-terminal to the steric gate residue and was chosen for analysis based on analogy to the F13 steric gate residue of DinB (80). Mutating either UmuC F10 or Y11 to alanine caused cells harboring these variants to be hypersensitive to UV light, which was alleviated by combining either of these mutations with ablation of the beta-binding motif in UmuC (80). This observation suggests that the toxic effect of the F10 or Y11 variants is conferred via their access to replication forks.

Cells harboring the UmuC variant A39V were very sensitive to UV radiation and had decreased UV-induced mutagenesis (Figure 7). Also, the A39V mutation fails to complement the umuDC-dependent cold sensitivity phenotype (123). Even though pol V contributes substantially to UV-induced mutagenesis, it contributes only modestly to survival after exposure to UV (5). However, mutations at F10, Y11, and A39 are examples of point mutations in UmuC that confer dramatically increased sensitivity to UV on cells that harbor them.

Several residues were proposed to be important for UmuC activity based on analysis of the active site region thought to accommodate bulky lesions (77, 122, 124). Residues 31SNN33 are metaphorically referred to as the "flue" of a "chimney," meaning these residues perhaps control the size of the active site opening of UmuC, which in turn would control the size of the adducts that can be bypassed (Figure 7) (124). S31 was shown experimentally to be important for UV-induced mutagenesis, while I38 and V39 contribute to bypass of benzo(a)pyrene (77, 125). N32 theoretically plugs the chimney hole, controlling the size of the opening (Figure 7) (124). V29, L30, V37, and I38 are thought to anchor an active site loop, referred to as loop 1, of UmuC. Furthermore, I38 is identified as the "roof" amino acid which influences dNTP insertion due to its location directly adjacent to the incoming nucleotide. L30 is a "flue handle" that controls the flue opening of the chimney (77, 124).

Strains harboring the umuC36 allele (E75K) were rendered nonmutable (126). E75 is potentially a site of interaction between UmuC and UmuD′2, because in strains with UmuD′2 present at elevated levels, the non-mutable phenotype was suppressed (126-127). The T290K mutation (umuC25) causes strains harboring it to be non-mutable (126). By analogy to Dpo4, T290 is predicted to be in the hydrophobic core of the little finger and may contribute to protein stability (Figure 7) (8).

The model of UmuC shown in Figure 7 is a truncation, with the last residue in the model indicated at Q353, as the C-terminal domain of UmuC lacks homology to proteins of known structure. The UmuC C-terminal domain is important for UV-induced mutagenesis as well as for interactions with UmuD and UmuD′ (30). The UmuC beta-binding motif 357QLNLF361 would be located just C-terminal to the end of the model, Q353 (83, 121, 128). Mutations in this motif cause almost a complete loss in UmuC-dependent UV-induced mutagenesis (83, 121). The second area of interaction between UmuC and the beta clamp, 313LTP315, did not cause a loss in UV-induced mutagenesis when mutated. However, the UmuC-dependent cold-sensitivity phenotype was suppressed when either of these sites was mutated (121).

5.5. Cellular interactions of UmuC

Initial characterization through a series of co-immunoprecipitation experiments showed that UmuC interacts with UmuD2 and interacts more strongly with UmuD′2 (2). UmuD′2 is the form of the umuD gene products that is active in mutagenesis, with the presence of UmuD′2 specifically required to facilitate mutagenesis (24). Moreover, induction of umuDC is all that is required for SOS mutagenesis (129). It was not until approximately twenty years after the discovery of the umuDC genes and their roles in SOS mutagenesis that UmuD′2C was found to be a DNA polymerase capable of copying damaged DNA (29, 31).

Several additional proteins facilitate TLS by UmuD′2C. These proteins include RecA, the beta clamp and gamma clamp loader, and SSB. Activated RecA is strictly required for pol V-dependent TLS, although the exact mechanism by which RecA must be activated in still in question (see below). The use of a variety of experimental systems by three separate groups to study the biochemical properties of pol V has contributed to different conclusions about the roles and requirements of these accessory proteins (summarized in Figure 8). First, different forms of UmuC have been used, with one group using a maltose binding protein tag (MBP) to purify UmuC (29) while others purified a native UmuC-UmuD′ complex (31, 117). Another major experimental difference among the three groups is the DNA substrate used (Figure 8). The Livneh group used a gapped plasmid with an ssDNA region of approximately 339 nucleotides (29, 130-132). The Goodman group originally used linear ssDNA with the lesion located 50 nucleotides from the 5′ end (31, 118-119); in their more recent work the length of the DNA varies (133-136). Lastly, the Fuchs group used circular ssDNA that is about 2700 nucleotides in length (101, 117, 137). These differences in experimental design possibly set the stage for the discrepancies in biochemical requirements for pol V as summarized in Figure 8 and discussed below.

RecA is a 38-kDa protein that is the product of the recA gene (138). In addition to the significant roles RecA is known to play in responses to DNA damage, including homologous recombination, induction of the SOS response by serving as a coprotease in the autoproteolytic cleavage of LexA, and the regulation of SOS mutagenesis by cleavage of UmuD2 to UmuD′2, RecA also has a direct role in TLS (139-140). Furthermore, it was proposed that RecA has two distinct roles in pol V-mediated TLS (134). First, RecA at the 3′ end of a primer stimulates pol V for TLS activity. Second, RecA bound to the template strand mediates extension past the lesion (134). The RecA nucleoprotein filament may provide an "activated" RecA monomer for TLS, but the filament itself may or may not participate in the actual TLS reaction. A six-nucleotide overhang can only bind two RecA monomers, and TLS still occurs, an observation that argues against the need for a RecA filament (134). Bypass of an abasic site in a three-nucleotide gap in the DNA to which RecA can still bind was successful as well; however, bypass of a lesion in a two-nucleotide gap was not (134).

One viewpoint is that a "minimal mutasome," which includes pol V, ATP, and two RecA molecules, one bound to UmuC and one bound to UmuD′2, is the active form in TLS (136, 141). Furthermore, in this model, RecA acts in trans, such that the RecA/ssDNA filament is formed on a DNA strand not actively being copied by pol V (135). In other words, the trans RecA/ssDNA transfers a RecA monomer as well as a molecule of ATP from its 3′ end to a molecule of pol V, thereby activating pol V for TLS (133). The newly activated pol V then performs a single round of TLS, and upon dissociation from the DNA is inactivated and must once again be activated by RecA and ATP (133). On the other hand, there is also evidence that the RecA/ssDNA nucleoprotein filament primarily acts in cis for TLS by forming a filament on the single-stranded DNA downstream from the lesion on the primer strand, thus facilitating TLS by pol V (137).

The beta clamp significantly increases the processivity of the replicative DNA polymerase pol III (142). This enhancement of processivity extends to other polymerases as well, including pol V. The beta clamp and gamma clamp loader provide additional stability to the complex and may help pol V remain tethered to DNA (119). However, the beta clamp only increases processivity of pol V modestly, with determinations ranging from three- to five-fold to ~100-fold (117, 131). It has been consistently observed that the beta clamp stimulates Pol V, but to varying extents and with different requirements for co-factors (Figure 8) (29, 31, 101-102, 117-119, 131). The Livneh and Fuchs groups determined that with native ATP, the presence of the beta clamp increased processivity of Pol V (117, 131), whereas the Goodman group observed a three- to five-fold increase in processivity with the beta clamp present but only with ATP-gamma-S and SSB also present (119). The Fuchs group suggested that SSB must be present when ATP-gamma-S is used, perhaps to destabilize the highly stabilized RecA filament that is formed in the presence of ATP-gamma-S (62).

A direct physical interaction has been detected between UmuC and single-stranded DNA binding protein (SSB) (130). SSB coats single-stranded DNA and helps to prevent dissociation of RecA from the ssDNA formed after a replicative polymerase stalls at a lesion (143). SSB also stimulates the formation of the RecA filament by over 50-fold (144). Lesion bypass using MBP-UmuC (29) was at its most efficient when the concentration of SSB in the reaction was 50 nM and ATP was present (132). Using a purified UmuD′2C complex, it was determined that lesion bypass was optimal at 60 nM SSB and that SSB stimulated TLS by 1,040-fold when ATP-gamma-S was present (119). Similarly, SSB likely helps to form the RecA nucleoprotein filament in the presence of ATP (132). In a lesion bypass experiment in the absence of SSB in which a functional RecA/ssDNA nucleoprotein filament was formed, no bypass was observed, leading to the conclusion that SSB may have a second function in TLS besides stimulation of RecA nucleoprotein filament formation (132). On the other hand, it has been suggested that SSB is not absolutely required for Pol V TLS in the presence of ATP, but SSB may be needed to disrupt the more stable RecA filament formed in the presence of ATP-gamma-S (117). Furthermore, it is thought that SSB may play a direct role in recruiting pol V to the 3′ end of the primer coated with RecA via a direct interaction with UmuC (130), as SSB interacts with pol V at the C-terminus of SSB (130). It is important again to consider the differences in the form of pol V as well as the DNA substrate used for these experiments, which is summarized in Figure 8.

6. Polymerase Switching

There are a variety of models used to describe how the multiple DNA polymerases in E. coli are utilized appropriately. The beta clamp facilitates polymerase switching that must take place in order for pol V to replace pol III on the DNA template (101, 117, 137, 145). In E. coli, it was observed that the beta clamp is donated by pol III to recruit pol V to the DNA template near the lesion (101). The "dynamic processivity" model was suggested from experiments using a catalytically inactive variant of the T4 DNA polymerase gp43 that was exchanged in less than a minute to replace the wild-type replicative polymerase (146). Thus, this model suggests that DNA polymerases may exchange in a stochastic and rapid manner. The observation that elevated levels of DinB inhibit pol III suggests a model of rapid replacement of polymerases at the replication fork in E. coli as well (36-37). Another model of polymerase switching is the "tool belt" model, which holds that multiple DNA polymerases are tethered to the beta clamp at the same time, allowing several DNA polymerases to be present at the replication fork and used when needed (5, 147). However, the observation that only one binding site on the beta clamp is used to facilitate a switch between pol III and pol IV is inconsistent with the tool-belt model (148). Finally, the gap filling model suggests that gaps are left at lesion sites when a replicative polymerase cannot bypass the lesion. Replication is initiated downstream of the lesion and the resulting gap is subsequently filled in by Y family polymerases performing TLS (149-152). These models are not mutually exclusive.

Although pol V is very poorly processive, the processivity offered by the beta clamp to pol V allows the polymerase to synthesize an appropriate-length "TLS patch." This patch of at least six nucleotides allows pol V to bypass the lesion and extend past it far enough for pol III to resume DNA synthesis without triggering proofreading at the newly bypassed lesion (101). Pol III can detect distortions in DNA caused by inserting a nucleotide opposite a lesion even when pol III is recruited back to the replication fork four to five nucleotides after the lesion so a TLS polymerase must extend at least beyond that point.

Mutations in the beta clamp, notably a poly-A sequence substituted at residues 148-152 (replacing 148HQDVR152) severely inhibited DNA replication by pol IV, but did not affect the polymerase functionality of pol III (153). Even though pol IV has been observed to inhibit replication by pol III (36-37), pol IV only displaces an impaired pol III that is not actively replicating and does not seem to displace an actively replicating pol III (148). Pol IV is proposed to accomplish this by two separate interactions with the beta clamp, at what is termed the 'cleft' and the 'rim' dimer interface regions of the beta clamp (85-86, 148). First, DinB binds the rim adjacent to the cleft bound by a replicating pol III alpha subunit and then gains control of the cleft once the replicative polymerase stalls at a lesion site (148). The DinB little finger-rim interaction is dispensable for TLS but necessary for recruitment of pol IV to replication forks (86).

Other work suggests that the situation is more complicated than a simple exchange between two DNA polymerases, as apparently several polymerases can compete or cooperate to bypass specific lesions (111, 120, 154-157). The presence of pol III, pol II, pol IV and pol V influence one another's ability to access the primer terminus of the replication fork (158). The two Y family DNA polymerases contribute to bypass of benzo(a)pyrene, for example (60, 63). Additionally, by using the characteristic mutagenic signature of each DNA polymerase, it was found that the polymerases in E. coli compete for access to DNA and that both pol IV and pol V contribute to spontaneous mutagenesis (154).

7. SUMMARY

E. coli Y family DNA polymerases play important roles in conferring resistance to DNA damaging agents. The two Y family polymerases present in E. coli are proficient for bypassing distinct sets of DNA lesions, which suggests that they play roles complementary to each other in cells faced with DNA damage. The Y family polymerases also regulate DNA replication in response to DNA damage and other replication stress. Because of their role in mutagenesis, the Y family polymerases may be involved in antigenic variation or antibiotic resistance. Thus, understanding both the regulation and the inherent basis of specificity of Y family DNA polymerases is critical.

8. ACKNOWLEDGEMENTS

Jason M. Walsh and Lisa A. Hawver contributed equally to this article. This work was supported by the National Science Foundation (CAREER Award, MCB-0845033 to PJB), the NU Office of the Provost, and a New Faculty Award from the Camille & Henry Dreyfus Foundation (to PJB). PJB is a Cottrell Scholar of the Research Corporation for Science Advancement.

9. REFERENCES

1.Miroslav Radman: SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Basic Life Sci 5A, 355-367 (1975)

2.Roger Woodgate, Malini Rajagopalan, Chi Lu and Harrison Echols: UmuC mutagenesis protein of Escherichia coli: purification and interaction with UmuD and UmuD'. Proc Natl Acad Sci U S A 86, 7301-7305 (1989)
doi:10.1073/pnas.86.19.7301

3.Wei Yang: Portraits of a Y-family DNA polymerase. FEBS Letters 579, 868-872 (2005)
doi:10.1016/j.febslet.2004.11.047

4.Haruo Ohmori, Errol Friedberg, Robert Fuchs, Myron Goodman, Fumio Hanaoka, David Hinkle, Thomas Kunkel, Christopher Lawrence, Zvi Livneh, Takehiko Nohmi, Louise Prakash, Satya Prakash, Takeshi Todo, Graham Walker, Zhigang Wang and Roger Woodgate: The Y-family of DNA polymerases. Mol Cell 8, 7-8 (2001)
doi:10.1016/S1097-2765(01)00278-7

5.Errol Friedberg, Graham Walker, Wolfram Siede, Richard Wood, Roger Schultz and Tom Ellenberger. DNA Repair and Mutagenesis, ASM Press, Washington DC, 2 edition, (2006)

6.Janice Pata: Structural diversity of the Y-family DNA polymerases. Biochem Biophys Acta 1804, 1124-1135 (2010)

7.Wei Yang and Roger Woodgate: What a different a decade makes: Insights into translesion DNA synthesis. Proc Natl Acad Sci U S A 104, 15591-15598 (2007)
doi:10.1073/pnas.0704219104

8.Francois Boudsocq, Hong Ling, Wei Yang and Roger Woodgate: Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass. DNA Repair 1, 343-358 (2002)
doi:10.1016/S1568-7864(02)00019-8

9.Haruo Ohmori, Eriko Hatada, Yun Qiao, Masaharu Tsuji and Ryuji Fukuda: dinP, a new gene in Escherichia coli, whose product shows similarities to UmuC and its homologues. Mutat Res 347, 1-7 (1995)
doi:10.1016/0165-7992(95)90024-1

10.Hong Ling, Francois Boudsocq, Roger Woodgate and Wei Yang: Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102 (2001)
doi:10.1016/S0092-8674(01)00515-3

11.Sushil Chandani, Christopher Jacobs and Edward Loechler: Architecture of Y-Family DNA Polymerases Relevant to Translesion DNA Synthesis as Revealed in Structural and Molecular Modeling Studies. Journal of Nucleic Acids 2010, Article ID 784081 20 pages (2010)

12.William Beard and Samuel Wilson: Structural Insights into the Origins of DNA Polymerase Fidelity. Structure 11, 489-496 (2003)
doi:10.1016/S0969-2126(03)00051-0

13.Neerja Kaushik, Virendra Pandey and Mukund Modak: Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket. Biochemistry 35, 7256-66 (1996)
doi:10.1021/bi960537i

14.Masonori Ogawa, Aki Tosaka, Yasutomo Ito, Shonen Yoshida and Motoshi Suzuki: Enhanced ribonucleotide incorporation by an O-helix mutant of Thermus aquaticus DNA polymerase I. Mutat Res 485, 197-207 (2001)

15.Daniel Jarosz, Penny Beuning, Susan Cohen and Graham Walker: Y-family DNA polymerases in Escherichia coli. Trends Microbiol 15, 70-77 (2007)
doi:10.1016/j.tim.2006.12.004

16.Hong Ling, Francois Boudsocq, Brian Plosky, Roger Woodgate and Wei Yang: Replication of a cis-syn thymine dimer at atomic resolution. Nature 424, 1083-1087 (2003)
doi:10.1038/nature01919

17.Laura Silvian, Eric Toth, Phuong Pham, Myron Goodman and Tom Ellenberger: Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat Struct Biol 8, 984-989 (2001)
doi:10.1038/nsb1101-984

18.Bo-Lu Zhou, Janice Pata and Thomas Steitz: Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol Cell 8, 427-37 (2001)
doi:10.1016/S1097-2765(01)00310-0

19.Miroslav Radman. Phenomenology of an inducible mutagenic DNA repair pathway in Escherichia coli: SOS repair hypothesis. In Molecular and environmental aspects of mutagenesis (Louise Prakash, Fred Sherman, Morton W. Miller, Christopher W. Lawrence, Harry Warren Taber and John W. Stewart, eds.), pp. xv, 289 p. Thomas, Springfield, Ill., (1974)

20.Evelyn Witkin: The radiation sensitivity of Escherichia coli B: a hypothesis relating filament formation and prophage induction. Proc Natl Acad Sci U S A 57, 1275-1279 (1967)
doi:10.1073/pnas.57.5.1275

21.Toshihiro Horii, Tomoko Ogawa, Tomoyuki Nakatani, Toshiharu Hase, Hiroshi Matsubara and Hideyuki Ogawa: Regulation of SOS functions: purification of E. coli LexA protein and determination of its specific site cleaved by the RecA protein. Cell 27, 515-522 (1981)
doi:10.1016/0092-8674(81)90393-7

22.Lyle Simmons, James Foti, Susan Cohen and Graham Walker. Chapter 5.4.3 The SOS Regulatory Network. In EcoSal--Escherichia coli and Salmonella: cellular and molecular biology (A. Bock, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nystrom, J. M. Slauch, C. L. Squires and D. Ussary, eds.). ASM Press, Washington, D.C. (2008)

23.Sabine Burckhardt, Roger Woodgate, Richard Scheuermann and Harrison Echols: UmuD mutagenesis protein of Escherichia coli: overproduction, purification, and cleavage by RecA. Proc Natl Acad Sci U S A 85, 1811-1815 (1988)
doi:10.1073/pnas.85.6.1811

24.Takehiko Nohmi, John Battista, Lori Dodson and Graham Walker: RecA-mediated cleavage activates UmuD for mutagenesis: mechanistic relationship between transcriptional derepression and posttranslational activation. Proc Natl Acad Sci U S A 85, 1816-1820 (1988)
doi:10.1073/pnas.85.6.1816

25.Hideo Shinagawa, Hiroshi Iwasaki, Takesi Kato and Atsuo Nakata: RecA protein-dependent cleavage of UmuD protein and SOS mutagenesis. Proc Natl Acad Sci U S A 85, 1806-1810 (1988)
doi:10.1073/pnas.85.6.1806

26.Timothy Opperman, Sumati Murli, Bradley Smith and Graham Walker: A model for a umuDC-dependent prokaryotic DNA damage checkpoint. Proc Natl Acad Sci U S A 96, 9218-9223 (1999)
doi:10.1073/pnas.96.16.9218

27.Veronica Godoy, Daniel Jarosz, Sharotka Simon, Alexej Abyzov, Valentin Ilyin and Graham Walker: UmuD and RecA Directly Modulate the Mutagenic Potential of the Y Family DNA Polymerase DinB. Molecular Cell 28, 1058-1070 (2007)
doi:10.1016/j.molcel.2007.10.025

28.Lorraine Marsh and Graham Walker: Cold sensitivity induced by overproduction of UmuDC in Escherichia coli. J Bacteriol 162, 155-161 (1985)

29.Nina Reuven, Gali Arad, Ayelet Maor-Shoshani and Zvi Livneh: The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J Biol Chem 274, 31763-31766 (1999)
doi:10.1074/jbc.274.45.31763

30.Mark Sutton and Graham Walker: umuDC-mediated cold sensitivity is a manifestation of functions of the UmuD(2)C complex involved in a DNA damage checkpoint control. J Bacteriol 183, 1215-1224 (2001)
doi:10.1128/JB.183.4.1215-1224.2001

31.Mengjia Tang, Xuan Shen, Ekatarine Frank, Michael O'Donnell, Roger Woodgate and Myron Goodman: UmuD'(2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc Natl Acad Sci U S A 96, 8919-8924 (1999)
doi:10.1073/pnas.96.16.8919

32.Jaylene Ollivierre, Jing Fang and Penny Beuning: The roles of UmuD in regulating mutagenesis. J Nucleic Acids 2010, 947680 (2010)

33.Jerome Wagner, Petr Gruz, Su-Rang Kim, Masami Yamada, Keiko Matsui, Robert Fuchs and Takehiko Nohmi: The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis. Mol Cell 4, 281-286 (1999)
doi:10.1016/S1097-2765(00)80376-7

34.Cynthia Kenyon and Graham Walker: DNA-damaging agents stimulate gene expression at specific loci in Escherichia coli. Proc Natl Acad Sci U S A 77, 2819-2823 (1980)
doi:10.1073/pnas.77.5.2819

35.Su-Ryang Kim, Keiko Matsui, Masami Yamada, Petr Gruz and Takehiko Nohmi: Roles of chromosomal and episomal dinB genes encoding DNA pol IV in targeted and untargeted mutagenesis in Escherichia coli. Mol Genet Genomics 266, 207-215 (2001)
doi:10.1007/s004380100541

36.Kaori Uchida, Asako Furukohri, Yutaka Shinozaki, Tetsuya Mori, Daichi Ogawara, Shigehiko Kanaya, Takehiko Nohmi, Hisaji Maki and Masahiro Akiyama: Overproduction of Escherichia coli DNA polymerase DinB (Pol IV) inhibits replication fork progression and is lethal. Mol Microbiol 70, 608-622 (2008)
doi:10.1111/j.1365-2958.2008.06423.x

37.Asako Furukohri, Myron Goodman and Hisaji Maki: A dynamic polymerase exchange with Escherichia coli DNA polymerase IV replacing DNA polymerase III on the sliding clamp. J Biol Chem 283, 11260-11269 (2008)
doi:10.1074/jbc.M709689200

38.Gregory McKenzie, Peter Lee, Mary-Jane Lombardo, PJ Hastings and Susan Rosenberg: SOS mutator DNA polymerase IV functions in adaptive mutation and not adaptive amplification. Mol Cell 7, 571-579 (2001)
doi:10.1016/S1097-2765(01)00204-0

39.Joshua Tompkins, Jennifer Nelson, Jill Hazel, Stacey Leugers, Jefferey Stumpf and Patricia Foster: Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli. J Bacteriol 185, 3469-3472 (2003)
doi:10.1128/JB.185.11.3469-3472.2003

40.Patricia Foster: Stress-Induced Mutagenesis in Bacteria Crit Rev in Biochem and Molec Biol 42, 373-397 (2007)

41.Jill Layton and Patricia Foster: Error-prone DNA polymerase IV is controlled by the stress-response sigma factor, RpoS, in Escherichia coli. Mol Microbiol 50, 549-561 (2003)
doi:10.1046/j.1365-2958.2003.03704.x

42.Mary-Jane Lombardo, Ildiko Aponyi and Susan Rosenberg: General stress response regulator RpoS in adaptive mutation and amplification in Escherichia coli. Genetics 166, 669-680 (2004)
doi:10.1534/genetics.166.2.669

43.Rodrigo Galhardo, Robert Do, Masami Yamada, Errol Friedberg, PJ Hastings, Takehiko Nohmi and Susan Rosenberg: DinB upregulation is the sole role of the SOS response in stress-induced mutagenesis in Escherichia coli. Genetics 182, 55-68 (2009)
doi:10.1534/genetics.109.100735

44.Gregory McKenzie, Daniel Magner, Peter Lee and Susan Rosenberg: The dinB operon and spontaneous mutagenesis in Escherichia coli. Journal of Bacteriology 185, 3972-3977 (2003)
doi:10.1128/JB.185.13.3972-3977.2003

45.E. Susan Slechta, Kim Bunny, Elisabeth Kugelberg, Eric Kofoid, Dan Andersson and John Roth: Adaptive mutation: general mutagenesis is not a programmed response to stress but results from rare coamplification of dinB with lac. Proc Natl Acad Sci U S A 100, 12847-12852 (2003)
doi:10.1073/pnas.1735464100

46.Megan Hersh, Rebecca Ronder, PJ Hastings and Susan Rosenberg: Adaptive mutation and amplication in Escherichia coli: two pathways of genome amplification under stress. Res Microbiol 155, 352-359 (2004)
doi:10.1016/j.resmic.2004.01.020

47.John R. Roth, Elisabeth Kugelberg, Andrew B. Reams, Eric Kofoid and Dan I. Andersson: Origin of Mutations Under Selection: The Adaptive Mutation Controversy. Annu Rev Microbiol 60, 477-501 (2006)

48.Rodrigo S. Galhardo, Philip J. Hastings and Susan M. Rosenberg: Mutation as a Stress Response and the Regulation of Evolvability. Crit Rev in Biochem and Molec Biol 42, 399-435 (2007)

49.Philip J. Hastings: Adaptive Amplification. Crit Rev in Biochem and Molec Biol 42, 271-283 (2007)
doi:10.1080/10409230701507757

50.Jill Layton and Patricia Foster: Error-prone DNA polymerase IV is regulated by the heat shock chaperone GroE in Escherichia coli. J Bacteriol 187, 449-457 (2005)
doi:10.1128/JB.187.2.449-457.2005

51.Tatiana Perez-Capilla, Maria-Rosario Baquero, Jose-Maria Gomez-Gomez, Alina Ionel, Soledad Martin and Jesus Blazquez: SOS-Independent Induction of dinB Transcription by {beta}-Lactam-Mediated Inhibition of Cell Wall Synthesis in Escherichia coli. J. Bacteriol. 187, 1515-1518 (2005)
doi:10.1128/JB.187.4.1515-1518.2005

52.Gregory McKenzie and Susan Rosenberg: Adaptive mutations, mutator DNA polymerases and genetic change strategies of pathogens. Curr Opin Microbiol 4, 586-594 (2001)
doi:10.1016/S1369-5274(00)00255-1

53.Peter Smith and Floyd Romesberg: Combating bacteria and drug resistance by inhibiting mechanisms of persistence and adaptation. Nat Chem Biol 3, 549-556 (2007)
doi:10.1038/nchembio.2007.27

54.Ryan Cirz and Floyd Romesberg: Controlling Mutation: Intervention in Evolution as a Therapeutic Strategy Crit Rev in Biochem and Molec Biol 42, 341-354 (2007)

55.Joseph Petrosino, Rodrigo Galhardo, Liza Morales and Susan Rosenberg: Stress-induced beta-lactam antibiotic resistance mutation and sequences of stationary-phase mutations in the Escherichia coli chromosome. J Bacteriol 191, 5881-5889 (2009)
doi:10.1128/JB.00732-09

56.Daniel Jarosz, Veronica Godoy, James Delaney, John Essigmann and Graham Walker: A single amino acid governs enhanced activity of DinB DNA polymerases on damaged templates. Nature 439, 225-228 (2006)
doi:10.1038/nature04318

57.Daniel Jarosz, Susan Cohen, James Delaney, John Essigmann and Graham Walker: A DinB variant reveals diverse physiological consequences of incomplete TLS extension by a Y-family DNA polymerase. Proc Natl Acad Sci U S A 106, 21137-21142 (2009)
doi:10.1073/pnas.0907257106

58.Jan Barciszewski, Miroslawa Barciszewska, Gunhild Siboska, Suresh Rattan and Brian Clark: Some unusual nucleic acid bases are products of hydroxyl radical oxidation of DNA and RNA. Mol Biol Reports 26, 231-238 (1999)
doi:10.1023/A:1007058602594

59.Bifeng Yuan, Huachuan Cao, Yong Jiang, Haizheng Hong and Yinsheng Wang: Efficient and accurate bypass of N2-(1-carboxyethyl)-2'-deoxyguanosine by DinB DNA polymerase in vitro and in vivo. Proc Natl Acad Sci U S A 105, 8679-8684 (2008)
doi:10.1073/pnas.0711546105

60.Kwang Seo, Arumugam Nagalingam, Shadi Miri, Jun Yin, Sushil Chandani, Aleksandr Kolbanovskiy, Anant Shastry and Edward Loechler: Mirror image stereoisomers of the major benzo(a)pyrene N2-dG adduct are bypassed by different lesion-bypass DNA polymerases in E. coli. DNA Repair (Amst) 5, 515-522 (2006)
doi:10.1016/j.dnarep.2005.12.009

61.Xuan Shen, Jane Sayer, Heiko Kroth, Ingrid Ponten, Michael O'Donnell, Roger Woodgate, Donald Jerina and Myron Goodman: Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo(a)pyrene-7,8-diol 9,10-epoxide A and G adducts. J Biol Chem 277, 5265-5274 (2002)
doi:10.1074/jbc.M109575200

62.Robert Fuchs, Shingo Fujii and Jerome Wagner: Properties and functions of Escherichia coli: Pol IV and Pol V. Adv Protein Chem 69, 229-264 (2004)
doi:10.1016/S0065-3233(04)69008-5

63.Nathalie Lenne-Samuel, Regine Janel-Bintz, Aleksandr Kolbanovskiy, Nicholas Geacintov and Robert Fuchs: The processing of a Benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli. Mol Microbiol 38, 299-307 (2000)
doi:10.1046/j.1365-2958.2000.02116.x

64.Irina Minko, Kinrin Yamanaka, Ivan Kozekov, Albena Kozekova, Chiara Indiani, Michael O'Donnell, Qingfei Jiang, Myron Goodman, Carmelo Rizzo and R. Stephen Lloyd: Replication bypass of the acrolein-mediated deoxyguanine DNA-peptide cross-links by DNA polymerases of the DinB family. Chem Res Toxicol 21, 1983-1990 (2008)
doi:10.1021/tx800174a

65.Anuradha Kumari, Irina Minko, Michael Harbut, Steven Finkel, Myron Goodman and R. Stephen Lloyd: Replication bypass of interstrand cross-link intermediates by Escherichia coli DNA polymerase IV. J Biol Chem 283, 27433-27437 (2008)
doi:10.1074/jbc.M801237200

66.Naomi Suzuki, Eiji Ohashi, Ken Hayashi, Haruo Ohmori, Arthur Grollman and Shinya Shibutani: Translesional synthesis past acetylaminofluorene-derived DNA adducts catalyzed by human DNA polymerase kappa and Escherichia coli DNA polymerase IV. Biochemistry 40, 15176-15183 (2001)
doi:10.1021/bi010702g

67.Masaki Hori, Shin-Ichiro Yonekura, Takehiko Nohmi, Petr Gruz, Hiroshi Sugiyama, Shuji Yonei and Qiu-Mei Zhang-Akiyama: Error-prone translesion DNA synthesis by Escherichia coli DNA polymerase IV (DinB) on templates containing 1,2-dihydro-2-oxoadenine. J Nucleic Acids 2010, 807579 (2010)

68.Masami Yamada, Tatsuo Nunoshiba, Masatomi Shimizu, Petr Gruz, Hiroyuki Kamiya, Hideyoshi Harashima and Takehiko Nohmi: Involvement of Y-family DNA polymerases in mutagenesis caused by oxidized nucleotides in Escherichia coli. J Bacteriol 188, 4992-4995 (2006)
doi:10.1128/JB.00281-06

69.Sawami Kobayashi, Michael Valentine, Phuong Pham, Mike O'Donnell and Myron Goodman: Fidelity of Escherichia coli DNA polymerase IV. Preferential generation of small deletion mutations by dNTP-stabilized misalignment. J Biol Chem 277, 34198-34207 (2002)
doi:10.1074/jbc.M204826200

70.Ayelet Maor-Shoshani, Ken Hayashi, Haruo Ohmori and Zvi Livneh: Analysis of translesion replication across an abasic site by DNA polymerase IV of Escherichia coli. DNA Repair 2, 1227-1238 (2003)
doi:10.1016/S1568-7864(03)00142-3

71.George Streisinger, Yohei Okada, Jaqueline Emrich, J Newton, A. Tsugita, E. Terzaghi and M. Inouye: Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol 31, 77-84 (1966)

72.Brigette Tippin, Sawami Kobayashi, Jeffrey Bertram and Myron Goodman: To slip or to skip, visualizing frameshift mutation dynamics for error-prone DNA polymerases. J Biol Chem 279, 45360-45368 (2004)
doi:10.1074/jbc.M408600200

73.James Foti, Angela DeLucia, Catherine Joyce and Graham Walker: UmuD(2) inhibits a non-covalent step during DinB-mediated template slippage on homopolymeric nucleotide runs. J Biol Chem 285, 23086-23095 (2010)
doi:10.1074/jbc.M110.115774

74.Thomas Kunkel and Aruna Soni: Mutagenesis by transient misalignment. J Biol Chem 263, 14784-14789 (1988)

75.Katarzyna Bebenek and Thomas Kunkel: Frameshift errors initiated by nucleotide misincorporation. Proc Natl Acad Sci U S A 87, 4946-4950 (1990)
doi:10.1073/pnas.87.13.4946

76.Angela DeLucia, Nigel Grindley and Catherine Joyce: Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence. Biochemistry 46, 10790-10803 (2007)
doi:10.1021/bi7006756

77.Kwang Seo, Jun Yin, Prashant Donthamsetti, Sushil Chandani, Chui Lee and Edward Loechler: Amino acid architecture that influences dNTP insertion efficiency in Y-family DNA polymerase V of E. coli. J Mol Biol 392, 270-282 (2009)
doi:10.1016/j.jmb.2009.07.016

78.Mekbib Astatke, Kimmie Ng, Nigel Grindley and Catherine Joyce: A single side chain prevents Escherichia coli DNA polymerase I (Klenow fragment) from incorporating ribonucleotides. Proc Natl Acad Sci U S A 95, 3402-3407 (1998)
doi:10.1073/pnas.95.7.3402

79.Angela DeLucia, Santanov Chaudhuri, Olga Potapova, Nigel Grindley and Catherine Joyce: The properties of steric gate mutants reveal different constraints within the active sites of Y-family and A-family DNA polymerases. J Biol Chem 281, 27286-27291 (2006)
doi:10.1074/jbc.M604393200

80.Brenna Shurtleff, Jaylene Ollivierre, Mohammed Tehrani, Graham Walker and Penny Beuning: Steric gate variants of UmuC confer UV hypersensitivity on Escherichia coli. J Bacteriol 191, 4815-4823 (2009)
doi:10.1128/JB.01742-08

81.Jerome Wagner, Shingo Fujii, Petr Gruz, Takehiko Nohmi and Robert Fuchs: The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity. EMBO Rep 1, 484-488 (2000)

82.Anne Brotcorne-Lannoye and Genevieve Maenhaut-Michel: Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene. Proc Natl Acad Sci U S A 83, 3904-3908 (1986)
doi:10.1073/pnas.83.11.3904

83.Olivier Becherel, Robert Fuchs and Jerome Wagner: Pivotal role of the beta-clamp in translesion DNA synthesis and mutagenesis in E. coli cells. DNA Repair (Amst) 1, 703-708 (2002)
doi:10.1016/S1568-7864(02)00106-4

84.Nathalie Lenne-Samuel, Jerome Wagner, Helene Etienne and Robert Fuchs: The processivity factor beta controls DNA polymerase IV traffic during spontaneous and tranlesion synthesis in vivo. EMBO Rep 3, 45-49 (2002)
doi:10.1093/embo-reports/kvf007

85.Karen Bunting, S. Mark Roe and Lawrence Pearl: Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J 22, 5883-5892 (2003)
doi:10.1093/emboj/cdg568

86.Jerome Wagner, Helene Etienne, Robert Fuchs, Agnes Cordonnier and Dominique Burnouf: Distinct beta-clamp interactions govern the activities of the Y family PolIV DNA polymerase. Mol Microbiol 74, 1143-1151 (2009)
doi:10.1111/j.1365-2958.2009.06920.x

87.Peggy Farnham, Jack Greenblatt and Terry Platt: Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. Cell 29, 945-951 (1982)
doi:10.1016/0092-8674(82)90457-3

88.Jack Greenblatt and Joyce Li: Interaction of the sigma factor and the nusA gene protein of E. coli with RNA polymerase in the initiation-termination cycle of transcription. Cell 24, 421-428 (1981)
doi:10.1016/0092-8674(81)90332-9

89.Kebin Liu, Yuying Zhang, Konstantin Severinov, Asis Das and Michelle Hanna: Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor NusA. EMBO J 15, 150-161 (1996)

90.Susan Cohen, Veronica Godoy and Graham Walker: Transcriptional modulator NusA interacts with translesion DNA polymerases in Escherichia coli. J Bacteriol 191, 665-672 (2009)
doi:10.1128/JB.00941-08

91.Yoshikazu Nakamura, Saeko Mizusawa, Donald Court and Akiko Tsugawa: Regulatory defects of a conditionally lethal nusAts mutant of Escherichia coli. Positive and negative modulator roles of NusA protein in vivo. J Mol Biol 189, 103-111 (1986)
doi:10.1016/0022-2836(86)90384-0

92.Susan Cohen, Cindi Lewis, Rachel Mooney, Michael Kohanski, James Collins, Robert Landick and Graham Walker: Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A 107, 15517-15522 (2010)
doi:10.1073/pnas.1005203107

93.Susan Cohen and Graham Walker: The transcription elongation factor NusA is required for stress-induced mutagenesis in Escherichia coli. Curr Biol 20, 80-85 (2010)
doi:10.1016/j.cub.2009.11.039

94.Anne Bagg, Cynthia Kenyon and Graham Walker: Inducibility of a gene product required for UV and chemical mutagenesis in Escherichia coli. Proc Natl Acad Sci U S A 78, 5749-5753 (1981)
doi:10.1073/pnas.78.9.5749

95.Takesi Kato and Yukiko Shinoura: Isolation and characterization of mutants of Escherichia coli deficient in induction of mutations by ultraviolet light. Mol Gen Genet 156, 121-131 (1977)
doi:10.1007/BF00283484

96.Gerhard Steinborn: Uvm mutants of Escherichia coli K12 deficient in UV mutagenesis. I. Isolation of uvm mutants and their phenotypical characterization in DNA repair and mutagenesis. Mol Gen Genet 165, 87-93 (1978)
doi:10.1007/BF00270380

97.Bryn Bridges and Roger Woodgate: Mutagenic repair in Escherichia coli: products of the recA gene and of the umuD and umuC genes act at different steps in UV-induced mutagenesis. Proc Natl Acad Sci U S A 82, 4193-4197 (1985)
doi:10.1073/pnas.82.12.4193

98.Malini Rajagopalan, Chi Lu, Roger Woodgate, Mike O'Donnell, Myron Goodman and Harrison Echols: Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III. Proc Natl Acad Sci U S A 89, 10777-10781 (1992)
doi:10.1073/pnas.89.22.10777

99.Graham Walker: Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev 48, 60-93 (1984)

100.Bryn Bridges and Roger Woodgate: The two-step model of bacterial UV mutagenesis. Mutat Res 150, 133-139 (1985)
doi:10.1016/0027-5107(85)90110-1

101.Shingo Fujii and Robert Fuchs: Defining the position of the switches between replicative and bypass DNA polymerases. EMBO J 23, 4342-4352 (2004)
doi:10.1038/sj.emboj.7600438

102.Mengjia Tang, Irina Bruck, Ramon Eritja, Jennifer Turner, Ekatarine Frank, Roger Woodgate, Mike O'Donnell and Myron Goodman: Biochemical basis of SOS-induced mutagenesis in Escherichia coli: reconstitution of in vitro lesion bypass dependent on the UmuD'2C mutagenic complex and RecA protein. Proc Natl Acad Sci U S A 95, 9755-9760 (1998)
doi:10.1073/pnas.95.17.9755

103.Irina Bruck, Roger Woodgate, Kevin McEntee and Myron Goodman: Purification of a soluble UmuD'C complex from Escherichia coli. Cooperative binding of UmuD'C to single-stranded DNA. J Biol Chem 271, 10767-10774 (1996)

104.William Rehrauer, Irina Bruck, Roger Woodgate, Myron Goodman and Stephen Kowalczykowski: Modulation of RecA nucleoprotein function by the mutagenic UmuD'C protein complex. J Biol Chem 273, 32384-32387 (1998)
doi:10.1074/jbc.273.49.32384

105.Suzanne Sommer, Adriana Bailone and Raymond Devoret: The appearance of the UmuD'C protein complex in Escherichia coli switches repair from homologous recombination to SOS mutagenesis. Mol Microbiol 10, 963-971 (1993)
doi:10.1111/j.1365-2958.1993.tb00968.x

106.Hanna Szpilewska, Pascale Bertrand, Adriana Bailone and Marie Dutreix: In vitro inhibition of RecA-mediated homologous pairing by UmuD'C proteins. Biochimie 77, 848-853 (1995)
doi:10.1016/0300-9084(95)90002-0

107.Justin Courcelle, Janet Donaldson, Kin-Hoe Chow and Charmain Courcelle: DNA damage-induced replication fork regression and processing in Escherichia coli. Science 299, 1064-1067 (2003)
doi:10.1126/science.1081328

108.Justin Courcelle and Philip Hanawalt: RecA-dependent recovery of arrested DNA replication forks. Annu Rev Genet 37, 611-646 (2003)
doi:10.1146/annurev.genet.37.110801.142616

109.Justin Courcelle and Philip Hanawalt: Participation of recombination proteins in rescue of arrested replication forks in UV-irradiated Escherichia coli need not involve recombination. Proc Natl Acad Sci U S A 98, 8196-8202 (2001)
doi:10.1073/pnas.121008898

110.Charmain Courcelle, Jerilyn Belle and Justin Courcelle: Nucleotide excision repair or polymerase V-mediated lesion bypass can act to restore UV-arrested replication forks in Escherichia coli. J Bacteriol 187, 6953-6961 (2005)
doi:10.1128/JB.187.20.6953-6961.2005

111.Justin Courcelle: Shifting replication between IInd, IIIrd, and IVth gears. Proc Natl Acad Sci U S A 106, 6027-6028 (2009)
doi:10.1073/pnas.0902226106

112.Charmain Courcelle, Kin-Hoe Chow, Andrew Casey and Justin Courcelle: Nascent DNA processing by RecJ favors lesion repair over translesion synthesis at arrested replication forks in Escherichia coli. Proc Natl Acad Sci U S A 103, 9154-9159 (2006)
doi:10.1073/pnas.0600785103

113.Mark Sutton, Timothy Opperman and Graham Walker: The Escherichia coli SOS mutagenesis proteins UmuD and UmuD' interact physically with the replicative DNA polymerase. Proc Natl Acad Sci U S A 96, 12373-12378 (1999)
doi:10.1073/pnas.96.22.12373

114.Mark Sutton, Issay Narumi and Graham Walker: Posttranslational modification of the umuD-encoded subunit of Escherichia coli DNA polymerase V regulates its interactions with the beta processivity clamp. Proc Natl Acad Sci U S A 99, 5307-5312 (2002)
doi:10.1073/pnas.082322099

115.Mark Sutton. Damage signals triggering the Escherichia coli SOS response. In DNA Damage and Recognition (Wolfram Seide, Yoke Kow and Paul Doetsch, eds.), pp. 781-802. New York : Taylor & Francis (2006)

116.Olivier Becherel and Robert Fuchs: SOS mutagenesis results from up-regulation of translesion synthesis. J Mol Biol 294, 299-306 (1999)
doi:10.1006/jmbi.1999.3272

117.Shingo Fujii, Veronique Gasser and Robert Fuchs: The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. J Mol Biol 341, 405-417 (2004)
doi:10.1016/j.jmb.2004.06.017

118.Mengjia Tang, Phuong Pham, Xuan Shen, John-Stephen Taylor, Michael O'Donnell, Roger Woodgate and Myron Goodman: Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404, 1014-1018 (2000)
doi:10.1038/35010020

119.Phuong Pham, Jeffrey Bertram, Mike O'Donnell, Roger Woodgate and Myron Goodman: A model for SOS-lesion-targeted mutations in Escherichia coli. Nature 409, 366-370 (2001)
doi:10.1038/35053116

120.William Neeley, Sarah Delaney, Yuriy Alekseyev, Daniel Jarosz, James Delaney, Graham Walker and John Essigmann: DNA polymerase V allows bylass of toxic guanine oxidation products in vivo. J Biol Chem 282, 12741-12748 (2007)
doi:10.1074/jbc.M700575200

121.Penny Beuning, Dorota Sawicka, Daniel Barsky and Graham Walker: Two processivity clamp interactions differentially alter the dual activities of UmuC. Mol Microbiol 59, 460-474 (2006)
doi:10.1111/j.1365-2958.2005.04959.x

122.Chiu Hong Lee, Sushil Chandani and Edward Loechler: Homology modeling of four Y-family lesion-bypass DNA polymerases: The case that E. coli Pol IV and human Pol kappa are orthologs, and E. coli Pol V and human Pol eta are orthologs. J Mol Graph Model 25, 87-102 (2005)
doi:10.1016/j.jmgm.2005.10.009

123.Lorraine Marsh, Takehiko Nohmi, Sean Hinton and Graham Walker: New mutations in cloned Escherichia coli umuDC genes: novel phenotypes of strains carrying a umuC125 plasmid. Mutat Res 250, 183-197 (1991)
doi:10.1016/0027-5107(91)90175-N

124.Sushil Chandani and Edward Loechler: Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications. J Mol Graph Model 27, 759-769 (2009)
doi:10.1016/j.jmgm.2008.11.003

125.Penny Beuning, Sarah Chan, Lauren Waters, Haripriya Addepalli, Jaylene Ollivierre and Graham Walker: Characterization of novel alleles of the Escherichia coli umuDC genes identifies additional interaction sites of UmuC with the beta clamp. J Bacteriol 191, 5910-5920 (2009)
doi:10.1128/JB.00292-09

126.Walter Koch, Don Ennis, Arthur Levine and Roger Woodgate: Escherichia coli umuDC mutants: DNA sequence alterations and UmuD cleavage. Mol Gen Genet 233, 443-448 (1992)
doi:10.1007/BF00265442

127.Helen Bates, Bryn Bridges and Roger Woodgate: Mutagenic DNA repair in Escherichia coli, XX. Overproduction of UmuD' protein results in suppression of the umuC36 mutation in excision defective bacteria. Mutat Res 250, 199-204 (1991)
doi:10.1016/0027-5107(91)90176-O

128.Brian Dalrymple, Kritaya Kongsuwan, Gene Wijffels, Nicholas Dixon and Philip Jennings: A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc Natl Acad Sci U S A 98, 11627-11632 (2001)
doi:10.1073/pnas.191384398

129.Suzanne Sommer, Jelena Knezevic, Adriana Bailone and Raymond Devoret: Induction of only one SOS operon, umuDC, is required for SOS mutagenesis in Escherichia coli. Mol Gen Genet 239, 137-144 (1993)

130.Gail Arad, Ayal Hendel, Claus Urbanke, Ute Curth and Zvi Livneh: Single-stranded DNA-binding protein recruits DNA polymerase V to primer termini on RecA-coated DNA. J Biol Chem 283, 8274-8282 (2008)
doi:10.1074/jbc.M710290200

131.Ayelet Maor-Shoshani and Zvi Livneh: Analysis of the stimulation of DNA polymerase V of Escherichia coli by processivity proteins. Biochemistry 41, 14438-14446 (2002)
doi:10.1021/bi0262909

132.Nina Reuven, Gali Arad, Alicja Stasiak, Andrzej Stasiak and Zvi Livneh: Lesion bypass by the Escherichia coli DNA polymerase V requires assembly of a RecA nucleoprotein filament. J Biol Chem 276, 5511-5517 (2001)
doi:10.1074/jbc.M006828200

133.Qingfei Jiang, Kiyonobu Karata, Roger Woodgate, Michael Cox and Myron Goodman: The active form of DNA polymerase V is UmuD'(2)C-RecA-ATP. Nature 460, 359-363 (2009)
doi:10.1038/nature08178

134.Phuong Pham, Erica Seitz, Sergel Saveliev, Xuan Shen, Roger Woodgate, Michael Cox and Myron Goodman: Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis. Proc Natl Acad Sci U S A 99, 11061-11066 (2002)
doi:10.1073/pnas.172197099

135.Katharina Schlacher, Michael Cox, Roger Woodgate and Myron Goodman: RecA acts in trans to allow replication of damaged DNA by DNA polymerase V. Nature 442, 883-887 (2006)
doi:10.1038/nature05042

136.Katharina Schlacher, Kris Leslie, Claire Wyman, Roger Woodgate, Michael Cox and Myron Goodman: DNA polymerase V and RecA protein, a minimal mutasome. Mol Cell 17, 561-572 (2005)
doi:10.1016/j.molcel.2005.01.006

137.Shingo Fujii and Robert Fuchs: Biochemical basis for the essential genetic requirements of RecA and the beta-clamp in Pol V activation. Proc Natl Acad Sci U S A 106, 14825-14830 (2009)
doi:10.1073/pnas.0905855106

138.Alvin Clark and Ann Margulies: Isolation and Characterization of Recombination-Deficient Mutants of Escherichia Coli K12. Proc Natl Acad Sci U S A 53, 451-459 (1965)
doi:10.1073/pnas.53.2.451

139.Katharina Schlacher, Phuong Pham, Michael Cox and Myron Goodman: Roles of DNA polymerase V and RecA protein in SOS damage-induced mutation. Chem Rev 106, 406-419 (2006)
doi:10.1021/cr0404951

140.Meghna Patel, Qingfei Jiang, Roger Woodgate, Michael Cox and Myron Goodman: A new model for SOS-induced mutagenesis: how RecA protein activates DNA polymerase V. Crit Rev in Biochem and Molec Biol 45, 171-184 (2010)
doi:10.3109/10409238.2010.480968

141.Joann Sweasy: RecA kicks Pol V into gear. Nat Struct Mol Biol 12, 215-216 (2005)
doi:10.1038/nsmb0305-215

142.Arthur Kornberg and Tania Baker. DNA Replication, W.H. Freeman & Company, New York, Second edition, (1992)

143.Michael Cox, Daniel Soltis, Zvi Livneh and I. R. Lehman: On the role of single-stranded DNA binding protein in recA protein-promoted DNA strand exchange. J Biol Chem 258, 2577-2585 (1983)

144.John Flory and Charles Radding: Visualization of recA protein and its association with DNA: a priming effect of single-strand-binding protein. Cell 28, 747-756 (1982)
doi:10.1016/0092-8674(82)90054-X

145.Dominique Burnouf, Vincent Olieric, Jerome Wagner, Shingo Fujii, J. Reinbolt, Robert Fuchs and Philippe Dumas: Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. J Mol Biol 335, 1187-1197 (2004)
doi:10.1016/j.jmb.2003.11.049

146.Jingsong Yang, Zhizao Zhuang, Rosa Maria Roccasecca, Michael Trakselis and Stephen Benkovic: The dynamic processivity of the T4 DNA polymerase during replication. Proc Natl Acad Sci U S A 101, 8289-8294 (2004)
doi:10.1073/pnas.0402625101

147.Vincent Pages and Robert Fuchs: How DNA lesions are turned into mutations within cells? Oncogene 21, 8957-8966 (2002)
doi:10.1038/sj.onc.1206006

148.Justin Heltzel, Robert Maul, Sarah Scouten Ponticelli and Mark Sutton: A model for DNA polymerase switching involving a single cleft and the rim of the sliding clamp. Proc Natl Acad Sci U S A 106, 12664-9 (2009)
doi:10.1073/pnas.0903460106

149.Ryan Heller and Kenneth Marians: Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439, 557-562 (2006)
doi:10.1038/nature04329

150.Alan Lehmann and Robert Fuchs: Gaps and forks in DNA replication: Rediscovering old models. DNA Repair (Amst) 5, 1495-1498 (2006)
doi:10.1016/j.dnarep.2006.07.002

151.Massimo Lopes, Marco Foiani and Jose Sogo: Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions. Mol Cell 21, 15-27 (2006)
doi:10.1016/j.molcel.2005.11.015

152.Vincent Pages and Robert Fuchs: Uncoupling of leading- and lagging-strand DNA replication during lesion bypass in vivo. Science 300, 1300-1303 (2003)
doi:10.1126/science.1083964

153.Justin Heltzel, Sarah Scouten Ponticelli, Laurie Sanders, Jill Duzen, Vivian Cody, James Pace, Edward Snell and Mark Sutton: Sliding clamp-DNA interactions are required for viability and contribute to DNA polymerase management in Escherichia coli. J Mol Biol 387, 74-91 (2009)
doi:10.1016/j.jmb.2009.01.050

154.Elena Curti, John McDonald, Samantha Mead and Roger Woodgate: DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli. Mol Microbiol 71, 315-331 (2009)
doi:10.1111/j.1365-2958.2008.06526.x

155.Robert Fuchs and Shingo Fujii: Translesion synthesis in Escherichia coli: Lessons from the NarI mutation hot spot. DNA Repair 6, 1032-1041 (2007)
doi:10.1016/j.dnarep.2007.02.021

156.Stéphane Delmas and Ivan Matic: Interplay between replication and recombination in Escherichia coli: impact of the alternative DNA polymerases. Proc Natl Acad Sci U S A 103, 4564-4569 (2006)
doi:10.1073/pnas.0509012103

157.Rita Napolitano, Regine Janel-Bintz, Jerome Wagner and Robert Fuchs: All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J 19, 6259-6265 (2000)
doi:10.1093/emboj/19.22.6259

158.Mark Sutton and Jill Duzen: Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli. DNA Repair (Amst) 5, 312-23 (2006)
doi:10.1016/j.dnarep.2005.10.011

159.Samer Lone, Sharon Townson, Sacha Uljon, Robert Johnson, Amrita Brahma, Deepak Nair, Satya Prakash, Louise Prakash and Aneel Aggarwal: Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Mol Cell 25, 601-614 (2007)
doi:10.1016/j.molcel.2007.01.018

160.Katharina Schlacher, Qingfei Jiang, Roger Woodgate and Myron Goodman: Purification and characterization of Escherichia coli DNA polymerase V. Methods Enzymol 408, 378-390 (2006)
doi:10.1016/S0076-6879(06)08023-2

Key Words: Y family, translesion synthesis, DNA polymerase, pol IV, pol V, UmuD, UmuC, DinB, mutation, DNA damage

Send correspondence to: Penny J. Beuning, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA 02115, USA, Tel: 617-373-2865, Fax: 617-373-8795, E-mail:beuning@neu.edu