DNA Polymerase V and RecA Protein, a Minimal Mutasome

Schlacher, Katharina; Leslie, Kris; Wyman, Claire; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

doi:10.1016/j.molcel.2005.01.006

Cited by 94 publications

(121 citation statements)

References 42 publications

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“…AFM, which yields topographic images of molecules deposited on a surface, can be used effectively for examining the oligomerization states of proteins (33,34,(37)(38)(39)(40)(41)(42). Specifically, it has been demonstrated that the volume of proteins (V) measured by AFM exhibits a linear dependence on molecular weight (MW) with V ϭ 1.2 ϫ MW Ϫ 14.7 (33,34).…”

Section: Resultsmentioning

confidence: 99%

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

Chelico

Sacho

Erie

et al. 2008

Journal of Biological Chemistry

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218

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APOBEC3G (A3G) restricts HIV-1 infection by catalyzingprocessive C 3 U deaminations on single-stranded DNA (ssDNA) with marked 3 3 5 deamination polarity. Here we show that A3G exists in oligomeric states whose composition is dictated primarily by interactions with DNA, with salt playing an important, yet secondary, role. Directional deaminations correlate with the presence of dimers, tetramers, and larger oligomers observed by atomic force microscopy, and random deaminations appear to correlate mainly with monomers. The presence of a 30-nt weakly deaminated "dead" zone located at the 3-ssDNA end implies the presence of a preferred asymmetric direction for A3G catalysis. Single turnover reaction rates reveal a salt-dependent inhibition of C deamination toward the 3-ssDNA region, offering a molecular basis underlying A3G deamination polarity. Presteady state analysis demonstrates rapid diffusionlimited A3G-ssDNA binding, a slower salt-dependent conformational change, possibly indicative of DNA wrapping, and long (5-15 min) protein-DNA complex lifetimes. We suggest that diverse A3G oligomerization modes contribute to the human immunodeficiency virus, type 1, proviral DNA mutational bias.In 2002, Sheehy et al.(1) determined that APOBEC3G (A3G), originally called CEM15, a proposed cytidine deaminase based on sequence analysis, is the nonpermissive host factor that blocks virion infectivity factor-defective (⌬vif) HIV-1 infection of T cells. The experimental determination that CEM15 was a cytidine deaminase belonging to the APOBEC family followed soon after with experiments demonstrating G 3 A-induced hypermutation of proviral DNA in a ⌬vif HIV-1 virion (2, 3). A3G has a duplicated deaminase domain structure, but only the C-terminal domain is responsible for the single-stranded DNA (ssDNA) 2 deamination activity (4, 5).Apart from A3G-catalyzed deamination, A3G may also have the capacity for blocking reverse transcription, (ϩ)-DNA synthesis, and provirus formation either by interacting with RNA or DNA of HIV-1 (6 -8) or by possibly interacting with HIV-1 proteins (9, 10). However, these noncatalytic effects on HIV inhibition may be attributable to the overexpression of A3G and may not be occurring during normal infection (11-13).It is important to bear in mind that any actions of A3G on DNA, catalytic and possibly noncatalytic, are balanced in vivo against cellular RNA binding, which forms a high molecular mass A3G-RNA complex, which may prevent A3G incorporation into virions (7, 14 -16), and against HIV RNA binding, which forms an intravirion A3G complex in which A3G must be activated by HIV RNase H for DNA deamination to ensue (16).We have shown that A3G-catalyzed deamination occurs processively while exhibiting a 3Ј 3 5Ј polarity favoring deamination toward the 5Ј-region of ssDNA (15). Directional deamination is an intrinsic property of A3G, occurring in the absence of an obvious source of energy (e.g. ATP or GTP) (15) and can in principle contribute to the HIV-1 G 3 A mutational bias, increasing in a 3Ј-direction ...

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Section: Resultsmentioning

confidence: 99%

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

Chelico

Sacho

Erie

et al. 2008

Journal of Biological Chemistry

Self Cite

218

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“…UmuC, together with UmuDЈ 2 and other factors, acts in translesion synthesis, particularly in the bypass of abasic sites and adducts resulting from UV light (16,36,37,40,51). UmuC, together with intact UmuD 2 , plays a role in a primitive DNA damage checkpoint, specifically decreasing the rate of DNA synthesis (27,33,50).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Novel Alleles of the Escherichia coli umuDC Genes Identifies Additional Interaction Sites of UmuC with the Beta Clamp

et al. 2009

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Translesion synthesis is a DNA damage tolerance mechanism by which damaged DNA in a cell can be replicated by specialized DNA polymerases without being repaired. The Escherichia coli umuDC gene products, UmuC and the cleaved form of UmuD, UmuD, comprise a specialized, potentially mutagenic translesion DNA polymerase, polymerase V (UmuD 2 C). The full-length UmuD protein, together with UmuC, plays a role in a primitive DNA damage checkpoint by decreasing the rate of DNA synthesis. It has been proposed that the checkpoint is manifested as a cold-sensitive phenotype that is observed when the umuDC gene products are overexpressed. Elevated levels of the beta processivity clamp along with elevated levels of the umuDC gene products, UmuDC, exacerbate the cold-sensitive phenotype. We used this observation as the basis for genetic selection to identify two alleles of umuD and seven alleles of umuC that do not exacerbate the cold-sensitive phenotype when they are present in cells with elevated levels of the beta clamp. The variants were characterized to determine their abilities to confer the umuDC-specific phenotype UV-induced mutagenesis. The umuD variants were assayed to determine their proficiencies in UmuD cleavage, and one variant (G129S) rendered UmuD noncleaveable. We found at least two UmuC residues, T243 and L389, that may further define the beta binding region on UmuC. We also identified UmuC S31, which is predicted to bind to the template nucleotide, as a residue that is important for UV-induced mutagenesis.

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“…Furthermore, simultaneous residency on the ␤ clamp by Pol III, a replicative polymerase, and Pol IV, a repair polymerase, has also been demonstrated (66). Given the facts that RecA acts at a template lesion to recruit Pol V, the main repair polymerase of E. coli (67), and that Pol V requires the ␤ clamp (52), we expect that further work will reveal exquisite fine tuning among the different DNA polymerases, accessory factors, and recombination proteins that act in concert to perform their functions together at a stalled replication fork.…”

Section: Discussionmentioning

confidence: 99%

Replisome Fate upon Encountering a Leading Strand Block and Clearance from DNA by Recombination Proteins

McInerney¹,

O'Donnell

2007

Journal of Biological Chemistry

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Replication forks that collapse upon encountering a leading strand lesion are reactivated by a recombinative repair process called replication restart. Using rolling circle DNA substrates to model replication forks, we examine the fate of the helicase and both DNA polymerases when the leading strand polymerase is blocked. We find that the helicase continues over 0.5 kb but less than 3 kb and that the lagging strand DNA polymerase remains active despite its connection to a stalled leading strand enzyme. Furthermore, the blocked leading strand polymerase remains stably bound to the replication fork, implying that it must be dismantled from DNA in order for replication restart to initiate. Genetic studies have identified at least four gene products required for replication restart, RecF, RecO, RecR, and RecA. We find here that these proteins displace a stalled polymerase at a DNA template lesion. Implications of these results for replication fork collapse and recovery are discussed.

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DNA Polymerase V and RecA Protein, a Minimal Mutasome

Cited by 94 publications

References 42 publications

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

A Model for Oligomeric Regulation of APOBEC3G Cytosine Deaminase-dependent Restriction of HIV

Characterization of Novel Alleles of the Escherichia coli umuDC Genes Identifies Additional Interaction Sites of UmuC with the Beta Clamp

Replisome Fate upon Encountering a Leading Strand Block and Clearance from DNA by Recombination Proteins

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