DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase

Erdem, Ayşen L.; Jaszczur, Malgorzata; Bertram, Jeffrey G.; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

doi:10.7554/elife.02384

Cited by 23 publications

(81 citation statements)

References 31 publications

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“…25 We recovered a form of pol V Mut (UmuD′ 2 C-RecA) devoid of both ATPγS/ATP and polymerase activity. 25 Restoration of pol V Mut activity occurred upon addition of new ATPγS/ATP.…”

Section: Tls After 2006 Reca* Trans-activationmentioning

confidence: 99%

“…25 We recovered a form of pol V Mut (UmuD′ 2 C-RecA) devoid of both ATPγS/ATP and polymerase activity. 25 Restoration of pol V Mut activity occurred upon addition of new ATPγS/ATP. Therefore, an adenosine nucleoside triphosphate cofactor ATP, dATP or ATPγS was necessary as an integral component of pol V Mut to catalyze DNA synthesis on undamaged and damaged (TLS) DNA templates.…”

Section: Tls After 2006 Reca* Trans-activationmentioning

confidence: 99%

“…Pol V Mut has an intrinsic DNA-dependent ATPase activity that appears to act as internal clock to regulate polymerase processivity. 25 The RecA* activation of pol V is spatially regulated, most likely occurring at the cell membrane. 26 The last observation connects current research with the mid-‘80s observation of Evelyn Witkin that RecA* is localized on the membrane in E. coli lysates.…”

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confidence: 99%

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Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword

et al. 2016

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1953, the year of Watson and Crick, bore witness to a less acclaimed, yet highly influential discovery. Jean Weigle demonstrated that upon infection of Escherichia coli, λ phage deactivated by UV radiation, and thus unable to form progeny, could be reactivated by irradiation of the bacterial host. Evelyn Witkin and Miroslav Radman later revealed the presence of the SOS regulon. The more than 40 regulon genes are repressed by LexA protein and induced by the coproteolytic cleavage of LexA, catalyzed by RecA protein bound to single-stranded (ss)DNA, the RecA* nucleoprotein filament. Several SOS-induced proteins are engaged in repairing both cellular and extracellular damaged DNA. There’s no “free lunch”, however, because error-free repair is accompanied by error-prone translesion DNA synthesis (TLS), involving E. coli DNA polymerase V (UmuD′2C) and RecA*. This review describes the biochemical mechanisms of pol V-mediated TLS. Pol V is active only as a mutasomal complex, pol V Mut = UmuD′2C-RecA-ATP. RecA* donates a single RecA subunit to pol V. We highlight three recent insights: 1) pol V Mut has an intrinsic DNA-dependent ATPase activity that governs polymerase binding and dissociation from DNA; 2) active and inactive states of pol V Mut are determined at least in part by the distinct interactions between RecA and UmuC; 3) pol V is activated by RecA*, not at a blocked replisome, but at the inner cell membrane.

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“…25 We recovered a form of pol V Mut (UmuD′ 2 C-RecA) devoid of both ATPγS/ATP and polymerase activity. 25 Restoration of pol V Mut activity occurred upon addition of new ATPγS/ATP.…”

Section: Tls After 2006 Reca* Trans-activationmentioning

confidence: 99%

Section: Tls After 2006 Reca* Trans-activationmentioning

confidence: 99%

mentioning

confidence: 99%

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Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword

et al. 2016

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“…The unresolved question was why. The answer that we arrived at while I was writing these Reflections is that pol V Mut function is regulated by an intrinsic DNA-dependent ATPase activity (41). The binding of a single ATP molecule to pol V Mut is required to bind the polymerase to primer-template DNA.…”

Section: The Unexpected Identification Of Pol V Mut As Dna-dependent mentioning

confidence: 99%

“…Mutational lethality can be avoided by restricting low-fidelity DNA synthesis to short DNA segments confined to replication forks blocked by DNA damage and to replication restart at stalled replication forks on undamaged DNA. Keeping pol V Mut processivity in check appears to be role of the internal ATPase that triggers polymerase dissociation from primer-template DNA (41). In essence, the enzyme has evolved to do the absolute minimum to get cellular DNA synthesis restarted.…”

Section: The Unexpected Identification Of Pol V Mut As Dna-dependent mentioning

confidence: 99%

The Discovery of Error-prone DNA Polymerase V and Its Unique Regulation by RecA and ATP

Goodman

2014

Journal of Biological Chemistry

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My career pathway has taken a circuitous route, beginning with a Ph.D. degree in electrical engineering from The Johns Hopkins University, followed by five postdoctoral years in biology at Hopkins and culminating in a faculty position in biological sciences at the University of Southern California. My startup package in 1973 consisted of $2,500, not to be spent all at once, plus an ancient Packard scintillation counter that had a series of rapidly flashing light bulbs to indicate a radioactive readout in counts/minute. My research pathway has been similarly circuitous. The discovery of Escherichia coli DNA polymerase V (pol V) began with an attempt to identify the mutagenic DNA polymerase responsible for copying damaged DNA as part of the well known SOS regulon. Although we succeeded in identifying a DNA polymerase, one that was induced as part of the SOS response, we actually rediscovered DNA polymerase II, albeit in a new role. A decade later, we discovered a new polymerase, pol V, whose activity turned out to be regulated by bound molecules of RecA protein and ATP. This Reflections article describes our research trajectory, includes a review of key features of DNA damage-induced SOS mutagenesis leading us to pol V, and reflects on some of the principal researchers who have made indispensable contributions to our efforts.

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Better living with hyper‐mutation

Goodman

2016

Environ and Mol Mutagen

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The simplest forms of mutations, base substitutions, typically have negative consequences, aside from their existential role in evolution and fitness. Hypermutations, mutations on steroids, occurring at frequencies of 10−2 – 10−4 per base pair, straddle a domain between fitness and death, depending on the presence or absence of regulatory constraints. We portray two facets of hypermutation, one in Escherichia coli involving DNA polymerase V (pol V), the other in humans, involving activation-induced deoxycytidine deaminase (AID). Pol V is induced as part of the DNA-damage-induced SOS regulon, and is responsible for generating the lion’s share of mutations when catalyzing translesion DNA synthesis (TLS). Four regulatory mechanisms, temporal, internal, conformational, and spatial, activate pol V to copy damaged DNA and then deactivate it. On the flip side of the coin, SOS-induced pols V, IV and II mutate undamaged DNA, thus providing genetic diversity heightening long-term survival and evolutionary fitness. Fitness in humans is principally the domain of a remarkably versatile immune system marked by somatic hypermutations (SHM) in immunoglobulin variable (IgV) regions that ensure antibody (Ab) diversity. AID initiates SHM by deaminating C → U, favoring hot WRC (W = A/T, R = A/G) motifs. Since there are large numbers of trinucleotide motif targets throughout IgV, AID must exercise considerable catalytic restraint to avoid attacking such sites repeatedly, which would otherwise compromise diversity. Processive, random, and inefficient AID-catalyzed dC deamination simulates salient features of SHM, yet generates B-cell lymphomas when working at the wrong time in the wrong place.

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DNA polymerase V activity is autoregulated by a novel intrinsic DNA-dependent ATPase

Cited by 23 publications

References 31 publications

Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword

Mutations for Worse or Better: Low-Fidelity DNA Synthesis by SOS DNA Polymerase V Is a Tightly Regulated Double-Edged Sword

The Discovery of Error-prone DNA Polymerase V and Its Unique Regulation by RecA and ATP

Better living with hyper‐mutation

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