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Chapter 15 : Mutagenesis and Translesion Synthesis in Prokaryotes

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Mutagenesis and Translesion Synthesis in Prokaryotes, Page 1 of 2

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Abstract:

This chapter traces the key intellectual advances that led to the recognition of translesion DNA synthesis in prokaryotes as an important DNA damage tolerance mechanism, as well as the cause of most SOS mutagenesis resulting from DNA damage. Despite the many pieces of evidence indicating that the underlying mechanism of most UV radiation and chemical mutagenesis results from SOS-induced translesion synthesis and the major advances in understanding various levels of regulation of the umuDC gene products, it took many years before the actual molecular mechanism of SOS mutagenesis was understood. The chapter summarizes some other experiments that were important because they yielded additional insights into the complexity of the mechanism, ruled out particular models, or contributed to the intellectual development of the field. The DNA template used in this study was a P-labeled primer annealed to a linear 7.2-kb M13 DNA template carrying an AP site located 50 bp from the 5’ end. Importantly, the preparation of purified UmuD’C could not carry out translesion synthesis unless RecA was present, an observation that was consistent with the additional requirement in vivo for RecA in SOS mutagenesis.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15

Key Concept Ranking

Mobile Genetic Elements
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DNA Synthesis
0.46852642
Genetic Recombination
0.4482224
Family Y DNA Polymerase
0.42132992
Nuclear Magnetic Resonance Spectroscopy
0.40665233
0.7258296
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Figures

Image of Figure 15–1
Figure 15–1

Translesion synthesis. A polymerase incorporates an incorrect nucleotide opposite a noninstructional or misinstructive lesion (represented by the gold circle) and then continues synthesis.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–2
Figure 15–2

Screen used to isolate and mutants ( ).

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–3
Figure 15–3

(A) Frequency of UV-induced His mutations in umu (black) and (gold) strains. Data from reference . (B) UV survival curves of a strain compared with and recA(Def). (Adapted from references and .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–4
Figure 15–4

MMS-induced reversion of the mutation in a strain mediated by pKM101 and pGW1700 To 2 ml of top agar supplemented with limiting (0.05 mM) arginine and nonlimiting concentrations of all other growth requirements were added 0.1 ml of a fresh stationary-phase culture and the appropriate amount of a freshly prepared solution of MMS in dimethyl sulfoxide. The top agar was then poured on minimal-glucose plates, which were incubated at 37°C for 4 days. Spontaneous revertants have been subtracted. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–5
Figure 15–5

RecA-mediated cleavage of UmuD. UmuD ( μg) was incubated with wild-type or mutant RecA at 37°C for 90 min in the presence of ssDNA (40 ng) and ATPγ-S (1 mM) (or 2 mM dATP where indicated). To avoid depletion of the dATP by the dATPase activity of RecA, an additional 2 mM dATP was added after 45 min of incubation. The products of the reaction were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (19% polyacrylamide), and the proteins were visualized by staining with Coomassie blue. Migration positions are indicated for RecA, UmuD, and the largest cleavage fragment of UmuD (UmuD’). Lanes: 1, no RecA; 2, 0.5 μg of RecA441 plus ATPγ-S; 3, 1 μg of RecA441 plus ATPγ-S; 4, 1 μg of RecA441 plus dATP; 5, 0.5 μg of RecA plus ATPγ-S; 6, 1 μg of RecA plus ATPγ-S; 7, 1 μg of RecA plus dATP; 8, 0.5 μg of RecA430 plus ATPγ-S; 9, 1 μg of RecA430 plus ATPγ-S; 10, 1 μg of RecA430 plus dATP. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–6
Figure 15–6

Formation of heterodimers of UmuD and UmuD’. UmuD and UmuD’ were present at 10 nM in 10 mM phosphate buffer (pH 6.8)-100 mM NaCl. Glutaraldehyde cross-linking was carried out by adding glutaraldehyde to 0.05%, incubating for 3 min at room temperature, and stopping the reaction by the addition of Tris-HCl and freezing quickly. Samples were subjected to electrophoresis on a polyacrylamide gel containing sodium dodecyl sulfate. Lanes: 1 and 2, UmuD with no treatment and with glutaraldehyde, respectively; 3 and 4, UmuD’ with no treatment and with glutaraldehyde, respectively; 5, UmuD and UmuD’ with no treatment; 6 to 11, UmuD and UmuD’ treated with glutaraldehyde after 1, 3, 5, 10, 20, and 30 min of incubation, respectively. D•D and D’•D’ are cross-linked homodimers of UmuD and UmuD’, respectively. D•D’ are cross-linked UmuD•UmuD’ heterodimers. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–7
Figure 15–7

Effect of plasmids encoding both or either one of the NH- or C-terminal polypeptides of UmuD on UV radiation mutagenesis in a strain. The plasmids used were pGW2020 (umuD), pGW2117 (both polypeptides), pGW2122 (C-terminal polypeptide), and pGW2119 (N-terminal polypeptide). The curve for a strain without a plasmid is the same as that for the strain carrying pGW2119. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–8
Figure 15–8

Plasmids encoding the C-terminal polypeptide of UmuD restore UV mutability to a lexA71::Tn5(Def) strain. The plasmids used were pGW2020 (umuD), pGW2117 (both UmuD polypeptides), and pGW2122 (C-terminal polypeptide of UmuD). GW2735 is a lexA71::Tn5 strain carrying pGW2020 (umuD). (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–9
Figure 15–9

Post-translational cleavage of UmuD activates it for its role in SOS mutagenesis. Once RecA has been activated in response to an SOS-inducing treatment, it mediates the proteolytic cleavage of LexA. This leads to increased expression of the SOS-regulated genes including the operon. RecA then mediates the proteolytic cleavage of UmuD at its Cys24-Gly25 bond in a process that is mechanistically and evolutionarily related to the cleavage of LexA. The carboxyl-terminal domain of UmuD (termed UmuD’) is the active form of UmuD that is necessary and sufficient for the role of in SOS mutagenesis. UmuD appears to participate in a DNA damage checkpoint. Both UmuD and UmuD’ form homodimers.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–10
Figure 15–10

(A) Operator-constitutive (O) mutant of enhances survival of and mutagenesis in (Ind) cells. bacteria carrying (gold) and (black) plasmids were UV irradiated (doses are given on the abscissa). → His reversions are shown in the left panel, and cell survival is shown in the right panel. (B) No restoration of SOS mutagenesis by mutant of in a (Ind) strain. bacteria carrying (gold) or and (black) were UV irradiated. — His reversions are shown in the left panel, and cell survival is shown in the right panel. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–11
Figure 15–11

Evidence for a umuDC-dependent DNA damage checkpoint. (A) The activities of uncleaved UmuD and UmuD’ in combination with UmuC increase resistance to DNA damage. Survival after UV irradiation of isogenic strains of GW8023 Δ ( ) that differ in the genotype of and carried on a plasmid: black line, [pSE117] ( ); dotted gold line, [pGW3751] ( ); solid gold line, umuD(S60A) [pTO4] ( ); dotted grey line, Δ [pBR322kan] ( ). (B) The resistance to killing by DNA damage provided by uncleaved UmuD and UmuC depends on. NER. Survival after UV irradiation of isogenic strains of GW8101 Δ ( ) that differ in the genotype of and carried on a plasmid. The line colors are the same as in panel A. (C) Uncleaved UmuD and UmuC regulate growth in response to DNA damage in exponentially growing cultures. The effect of various plasmid-situated gene products on the growth of GW8023 [recA Δ after UV irradiation (25 J/m) is shown. The dotted black line indicates Δ (pBR322kan); the gold line indicates (pSE117); the solid black line indicates umuD(S60A) (pTO4) ( ). (D to G) Uncleaved UmuD and UmuC regulate DNA synthesis in response to DNA damage. The effect of various gene products on inhibition and recovery (replication restart/IRR) of DNA synthesis caused by UV irradiation in isogenic strains of GW8024 Δ lex(Def)] that differ in the genotype of carried on a plasmid is shown. The rate of DNA synthesis (amount of [H]thymidine incorporated into trichloroacetic acid-insoluble counts during a 2-min pulse [black line] and the optical density at 600 nm [gold line] were measured at various times before and after UV irradiation (indicated by the arrow) in isogenic strains that differ only in the genotype of carried on a plasmid. (D) Δ (pBR322kan) ( ); (E) (pSE117) ( ); (F) (pGW3751) ( ); (D) umuD(S60A) (pTO4) ( ). (H) Model showing how multiple levels of post-translational control ensure that checkpoint and translesion synthesis roles of the gene product occur in a temporally ordered fashion ( ). (Adapted from references and .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–12
Figure 15–12

Conformational differences between UmuD’ structures determined by NMR and X-ray crystallography. Ser60 and Lys97, which constitute the catalytic dyad, are shown. (A) Solution structure of UmuD’ determined by NMR ( ). The N terminus (Gly25 by UmuD numbering) and C teminus are indicated. The first 14 residues of UmuD’ are free in solution and are depicted in an arbitrary conformation. Lys97 is too far from Ser60 to activate it. (B) The structure of UmuD’ determined by X-ray cystallography ( ) but showing the dimer interface found in solution ( ). The first 7 amino acids were disordered in the crystal, and so the N terminus shown (N*) is D32 (by UmuD numbering). The two C-terminal residues, residues 138 and , were also disordered in the crystal. Conformational changes caused by crystal packing forces result in Lys97 being close enough to Ser60 to activate it.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–13
Figure 15–13

Model of the structure of the UmuD homodimer based on NMR ( ), cross-linking studies using a collection of UmuD dicysteine derivatives and other approaches ( ), and the structures of mutant forms of LexA protein ( ). Briefly, the model of UmuD was built by basing the position of both arms (thin portion in the picture), i.e., residues 15 to 39 of UmuD (equivalent to residues 75 to 99 of LexA), on the position of the corresponding arm of LexA in the catalytically active conformation but creating a dimer. Because of the absence of structural information for the corresponding 8 residues in the LexA crystal structure, residues 26 to 34 were built as a “loop.” Residues 1 to 14 of UmuD are in an arbitrary “extended” conformation. (Coordinates of the model courtesy of Daniel Barsky and Adam Zemla, Lawrence Livermore National Laboratory.)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–14
Figure 15–14

Schematic representation of how intact UmuD targets its partner within a UmuD-UmuD’ heterodimer for degradation by ClpXP. A tethering motif (shown as an oval) on the UmuD (D) subunit binds to the N-terminal domain (N) of ClpX, thereby leashing its UmuD’ (D’) partner to the enzyme and allowing a weak degradation tag (shown as a square) to interact with the central protein-processing pore. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–15
Figure 15–15

Multiple levels of post-translational control of the gene products by RecA, Lon, ClpXP, and GroESL. See the text for details.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–16
Figure 15–16

Amber mutations induced by UV ( ), 4-NQO ( ), and benzo[a]pyrene ( ) in the gene. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–17
Figure 15–17

Distribution of dominant base pair substitutions and frameshifts in the wild-type (A) and (B) strains. The assumption is made that the mutations are originating from lesions at dipyrimidine targets. Thus, mutations originating from dipyrimidine targets in the non-transcribed strand appear at C or T in this figure (since the nontranscribed strand is the strand displayed). Conversely, mutations arising from dipyrimidine targets on the transcribed strand appear at G or A. Grey areas indicate mutations at C or T bases; gold areas indicate mutations at G or A bases. Mutations above the DNA sequence are base pair substitutions; those below are single-base frameshifts. Underlined bases indicate ambiguity in the position of the missing base. The G → A transition at position 31 is included for completeness, although it is not a dominant mutation. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–18
Figure 15–18

Premutagenic lesions for SOS mutagenesis. (A) T-T CPD; (B) T-T CPD; (C) T-T (6–4) normal isomer; (D) T-T (6–4) Dewar valence isomer; (E) T-C (6–4) normal isomer; (F) T-C (6–4) Dewar valence isomer; (G) N-(2’-deoxyguanosin-8-yl)-AAF.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–19
Figure 15–19

Two ways in which closely opposed lesions could generate a substrate-requiring translesion bypass. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–20
Figure 15–20

Proposed structure of the bivalent AP site/strand break lesion induced by neocarzinostatin. The arrow shows the strand break with 3’-phosphate and 5’-aldehyde termini. The AP site probably involves oxidation of C-1’ to a lactone. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–21
Figure 15–21

(A) Spontaneous amber (black bars) and ochre (gold bars) mutations occurring in strains. The height of each bar represents the number of independent occurrences in a collection of 306 nonsense mutations. (The ochre bar heights have been normalized to account for a small sample size.) Arrows indicate the positions of nonsense sites at which there were zero occurrences in this collection. Asterisks indicate 5-methylcytosine residues. The positions of sites in the gene are indicated on the horizontal axis by the number of the corresponding amino acid in the repressor. (B) Distribution of 586 spontaneous amber and ochre mutations occurring in a strain at 42°C. Each mutation is of independent origin and corresponds to the actual number collected (no normalizations). (Panel A adapted from reference ; panel B adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–22
Figure 15–22

Loss of photoreversibility of UV-induced mutations in a strain at 34°C (gold) and 43°C (black). (A) Bacteria were incubated at 34°C after UV exposure for 15 min before the culture was divided (indicated by the arrow); half was incubated at 34°C, and half was incubated at 43°C. (B) Similar experiment with a 22.5-min postirradiation incubation at 34°C before the temperature shift. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–23
Figure 15–23

Unrooted phylogenetic tree of the Y family of polymerases. Members of the family were identified by a BlastP search of the nonredundant protein database, using the IMS (ImpB/MucB/SamB) consensus as the query. Nearly 100 hits were obtained, and the results were filtered by the removal of fragments or sequences with over 97% identity. Proteins were aligned using the ClustalX program and modified manually to ensure the correct alignment of conserved motifs. The tree can be broadly divided into several branches that include UmuC gram negative (shaded in medium gold), UmuC gram positive (shaded in light gold), DinB (shaded in medium grey), Rev1 (shaded in dark gold), Rad30B (shaded in light grey), and Rad30A (shaded in dark grey). The abbreviations used in the figure are as follows. Bacteria: Ban, Bha, Bsu, Eco, Efa, Lla, Mtu, Nme, Pae, Pmu, Psy, Sco, Sma, Spn, Sth, serovar Typhi; Sty, serovar Typhimurium; Vco, Archaea: Hai, sp. strain NRC-11; Sso, Eukaryotes: At, Ce, Dm, Hs, Lm, Mm, Sc, Sp, (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–24
Figure 15–24

Evidence that UmuD’C (DNA Pol V) is a translesion DNA polymerase and its cofactor requirements. (A) Each reaction mixture for lanes 1 to 9 contains 1.5 μl of a Superdex fraction of UmuD’C that has no detectable Pol III, Pol I antibody, and various combinations of RecA, β,γ- complex, and SSB, as indicated ( ). Running-start reactions, in which C is incorporated opposite template G to reach the abasic site, were carried out at 37°C, with all four dNTPs present in lanes 1 to , but with dCTP omitted in lane 9. Reactions were run in the presence of 5% polyethylene glycol. A portion of the template sequence is shown at the right of lane , where X represents an abasic site. The left-hand lane contains the primer (P) in the absence of proteins. Standing-start reactions, in which the first incorporated nucleotide occurs opposite X, were run for wild-type UmuD’C (lane ) and for the mutant UmuD’C104 (D101N) (lane ), each at a concentration of 200 nM. A portion of the template, shown at the right of lane , has the same sequence as the running-start template but uses a primer terminating 1 base before the lesion. The asterisk (*) designates a P label at the 5’ primer terminus. (B) Translesion replication by the UmuC fusion protein in the presence of UmuD’, RecA, and SSB. The DNA substrate used in the lesion bypass assay was gapped plasmid GP21 carrying a site-specific synthetic abasic site ( ). A time course of translesion replication was performed with 10 or 50 nM MalB-UmuC as indicated. DNA Pol I in the control reactions (lanes 12 and ) was present at 90 nM. After restriction, the reaction products were analyzed by urea-polyacrylamide gel electrophoresis fractionation and PhosphoImager analysis. Unextended primer corresponds to 19 nucleotides, and replication arrested at the lesion corresponds to 29 nucleotides. Lane 14 contains a P-labeled 47-mer marker oligonucleotide, representing the expected bypass product. (Adapted from references and .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–25
Figure 15–25

Bypass of a benzo]pyrene diol expoxide adduct in DNA by a Pol Y family polymerase. (A) The DinB-type polymerase Dpo4 from was crystallized in complex with DNA containing benzo[a]pyrene diol epoxide adjacent to the active site ( ). Two different conformations of benzo[a]pyrene (B[a]P) were observed in two independent molecules that crystallized. (B) In one conformation, the bulky BAP adduct intercalates between the incoming nucleotide (grey) and the 3’ end of the growing DNA strand, explaining why this DNA modification interferes with replication. (C) In a second conformation, the BAP adduct adopts an exposed, extrahelical conformation that is more favorable for DNA synthesis. The addition of organic solvents such as dimethyl sulfoxide stimulates bypass of BAP by Dpo4 in vitro, apparently by stabilizing the extrahelical conformation of the hydrophobic benzo]pyrene moiety in the major groove of DNA ( ).

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–26
Figure 15–26

Potential involvement of the different DNA polymerases in distinct translesion synthesis (TLS) pathways. (A) Induction of —2 frameshift mutations by an AAF adduct located within the NarI sequence context. The nonslipped and slipped translesion synthesis pathways are strictly dependent on Pol V and Pol II, respectively. (B) Induction of —1 frameshift mutations by an AAF adduct located within the sequence GGG. Both the nonslipped and slipped replication pathways require only Pol V. (C) Induction of base substitution mutations by DNA Pol III and induction of — 1 frameshift mutations by a benzo[a]pyrene (BaP) adduct located within the sequence GGG. Both the error-free nonslipped and — 1 frameshift slipped TLS pathways require Pol IV and Pol V. (Adapted from references and .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–27
Figure 15–27

Model for two modes of disassembly of a RecA-ssDNA filament during translesion synthesis. In this diagram, the translesion synthesis event has resulted in the insertion of an A opposite a lesion. In conjunction with SSB, DNA Pol V catalyzes filament disassembly by stripping RecA molecules from the template strand in a 3’ → 5’ direction in a reaction that does not require ATP hydrolysis, while concomitant ATP-hydrolysis-driven filament disassembly occurs in the 5’ → 3’ direction, resulting in bidirectional filament assembly. UmuC (dark gold), UmuD’ (light gold), RecA (light grey spheres), SSB (dark grey), and β sliding clamp (light grey) are indicated. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–28
Figure 15–28

Model depicting two modes of RecA in translesion synthesis by DNA Pol V. (A) Wild-type RecA exhibits two modes of RecA action: mode 1 stimulation of DNA Pol V when interacting with Pol V at the 3’-OH primer end and mode 2 cocatalysis of translesion synthesis when bound to the DNA template strand at the 5’ side of the lesion. (B) RecA1730 protein (S117F) exhibits mode 1 stimulation of DNA Pol V activity but is essentially unable to cocatalyze translesion synthesis. RecA protein is illustrated as a monomer, but its detailed structure is unknown and it could be a multimer. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–29
Figure 15–29

Interaction of a Pol Y family polymerase with a sliding clamp. The lesion bypass activities of DinB-type polymerases are stimulated by interaction with the sliding-clamp processivity factor, known as the β clamp. (A) A peptide motif located at the C terminus of DinB (Pol IV) binds to the interdomain linker of the β clamp. The crystal structure of the little-finger domain from DinB (gold) complexed to the β clamp (white) is shown ( ) (cf. Fig. 15–25 ). (B) The hydrophobic sequence QLVLGL located at the C terminus of DinB binds in a channel on the surface of the β clamp, with the side chains of Met343, Leu347, Leu349, and Leu351 inserted into complementary hydrophobic pockets of the β clamp.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–30
Figure 15–30

Initial evidence that UmuD and UmuD’ interact with the a, β, and ε subunits of DNA Pol III. (A) Far-Western blot of crude extracts using derivatives of UmuD or UmuD’ carrying a short amino acid sequence that enables them to be P radiolabeled using heart muscle kinase. Crude cell extracts were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred to a polyvinylidene difluoride membrane. Membranes then were probed with either P-labeled UmuD (A1) or P-labeled UmuD’ (A2). The whole-cell extracts were of a non-SOS-induced strain (AB1157) that harbored either pBR322 or a pBR322 derivative that directed the overproduction of the α, β, ε, or θ subunits of DNA Pol III (A1 and A2). UmuD and UmuD’ interacted specifically with peptides of approximately 28 and 42 kDa (lane 1) that corresponded to the ε and β subunits of DNA Pol III (lanes 2 to 7). Given the results in panel B, it seems likely that a ca. 35-kDa species specific to the α-enriched extract that interacts with both UmuD and UmuD’ represents a proteolytically truncated form of a that arose during the preparation of the extract. The UmuD, β, and ε enriched crude cell extracts were diluted as indicated (1:5 or 1:10) before electrophoresis. Molecular mass markers are given at the left in kilodaltons. (B) Far-Western blot of purified Pol III subunits. UmuD, UmuD’, β, DnaB helicase, and Pol III core were fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred to polyvinylidene difluoride membranes. Membranes then were either stained with Coomassie brilliant blue (B1) or probed with P-labeled UmuD (B2) or UmuD’ (B3). The position of each protein is indicated to the left.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–31
Figure 15–31

RecA-mediated cleavage of UmuD to UmuD’ changes its ability to interact with a variety of other proteins. In a homodimer of intact UmuD, the N-terminal arm of each monomer is folded over the globular portion of its intradimer partner. Cleavage results in the remaining N-terminal arms of UmuD’ (amino acids 25 to 39) becoming disordered in solution and therefore free to make new contacts ( ). The cleavage also results in the exposure of a substantial portion of the globular domain that was previously hidden, thereby enabling UmuD’ to make contacts that are different from those made by UmuD.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–32
Figure 15–32

Model of a slow-growing bacterium bidirectionally replicating its DNA by a stationary-factory replisome (overlapping triangles) that is tethered to the midpoint of a cell. After the origin region is replicated, the two sister origins light grey circles) are extruded from the centrally located replisome and captured on opposite halves of the cell at or near the cell quarters. The terminus region (terC; dark grey square) remains at mid-cell until it is duplicated. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–33
Figure 15–33

Adaptive mutagenesis analyzed using the strain FC40 model system. (A) Accumulation of Lac revertants of FC40 during incubation on lactose minimal medium plates. Left axis: gold line, number of Lac colonies per 10 cells; right axis: black line, number of Lac cells on the plate. (B) Venn diagram illustrating the role of transient mutators in adaptive mutation. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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Image of Figure 15–34
Figure 15–34

(A to C) Postulated base-pairing modes of O-alkylguanine. (A) Scheme proposed on the basis of the original model of Loveless ( ); (B and C) base-pairing of O-alkylguanine with thymine and cytosine, respectively, predicted from two-dimensional NMR studies. (D to F) Postulated base-pairing models of O-alkylthymine. (D) Conventional scheme for mispairing of O-alkylthymine with guanine; (E and F) base-pairing of O-alkylthymine with guanine and adenine, respectively, predicted from two-dimensional NMR studies. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Mutagenesis and Translesion Synthesis in Prokaryotes, p 509-568. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch15
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