Artykuły w czasopismach: „UvrD helicase”

1

LeCuyer, Brian E., Alison K. Criss i H. Steven Seifert. "Genetic Characterization of the Nucleotide Excision Repair System of Neisseria gonorrhoeae". Journal of Bacteriology 192, nr 3 (20.11.2009): 665–73. http://dx.doi.org/10.1128/jb.01018-09.

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ABSTRACT Nucleotide excision repair (NER) is universally used to recognize and remove many types of DNA damage. In eubacteria, the NER system typically consists of UvrA, UvrB, UvrC, the UvrD helicase, DNA polymerase I, and ligase. In addition, when DNA damage blocks transcription, transcription-repair coupling factor (TRCF), the product of the mfd gene, recruits the Uvr complex to repair the damage. Previous work using selected mutants and assays have indicated that pathogenic Neisseria spp. carry a functional NER system. In order to comprehensively examine the role of NER in Neisseria gonorrhoeae DNA recombination and repair processes, the predicted NER genes (uvrA, uvrB, uvrC, uvrD, and mfd) were each disrupted by a transposon insertion, and the uvrB and uvrD mutants were complemented with a copy of each gene in an ectopic locus. Each uvr mutant strain was highly sensitive to UV irradiation and also showed sensitivity to hydrogen peroxide killing, confirming that all of the NER genes in N. gonorrhoeae are functional. The effect of RecA expression on UV survival was minor in uvr mutants but much larger in the mfd mutant. All of the NER mutants demonstrated wild-type levels of pilin antigenic variation and DNA transformation. However, the uvrD mutant exhibited higher frequencies of PilC-mediated pilus phase variation and spontaneous mutation, a finding consistent with a role for UvrD in mismatch repair. We conclude that NER functions are conserved in N. gonorrhoeae and are important for the DNA repair capabilities of this strict human pathogen.

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Moolenaar, Geri F., Celine Moorman i Nora Goosen. "Role of the Escherichia coli Nucleotide Excision Repair Proteins in DNA Replication". Journal of Bacteriology 182, nr 20 (15.10.2000): 5706–14. http://dx.doi.org/10.1128/jb.182.20.5706-5714.2000.

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ABSTRACT DNA polymerase I (PolI) functions both in nucleotide excision repair (NER) and in the processing of Okazaki fragments that are generated on the lagging strand during DNA replication.Escherichia coli cells completely lacking the PolI enzyme are viable as long as they are grown on minimal medium. Here we show that viability is fully dependent on the presence of functional UvrA, UvrB, and UvrD (helicase II) proteins but does not require UvrC. In contrast, ΔpolA cells grow even better when theuvrC gene has been deleted. Apparently UvrA, UvrB, and UvrD are needed in a replication backup system that replaces the PolI function, and UvrC interferes with this alternative replication pathway. With specific mutants of UvrC we could show that the inhibitory effect of this protein is related to its catalytic activity that on damaged DNA is responsible for the 3′ incision reaction. Specific mutants of UvrA and UvrB were also studied for their capacity to support the PolI-independent replication. Deletion of the UvrC-binding domain of UvrB resulted in a phenotype similar to that caused by deletion of the uvrC gene, showing that the inhibitory incision activity of UvrC is mediated via binding to UvrB. A mutation in the N-terminal zinc finger domain of UvrA does not affect NER in vivo or in vitro. The same mutation, however, does give inviability in combination with the ΔpolA mutation. Apparently the N-terminal zinc-binding domain of UvrA has specifically evolved for a function outside DNA repair. A model for the function of the UvrA, UvrB, and UvrD proteins in the alternative replication pathway is discussed.

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Ordabayev, Yerdos A., Binh Nguyen, Alexander G. Kozlov, Haifeng Jia i Timothy M. Lohman. "UvrD helicase activation by MutL involves rotation of its 2B subdomain". Proceedings of the National Academy of Sciences 116, nr 33 (30.07.2019): 16320–25. http://dx.doi.org/10.1073/pnas.1905513116.

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Escherichia coli UvrD is a superfamily 1 helicase/translocase that functions in DNA repair, replication, and recombination. Although a UvrD monomer can translocate along single-stranded DNA, self-assembly or interaction with an accessory protein is needed to activate its helicase activity in vitro. Our previous studies have shown that an Escherichia coli MutL dimer can activate the UvrD monomer helicase in vitro, but the mechanism is not known. The UvrD 2B subdomain is regulatory and can exist in extreme rotational conformational states. By using single-molecule FRET approaches, we show that the 2B subdomain of a UvrD monomer bound to DNA exists in equilibrium between open and closed states, but predominantly in an open conformation. However, upon MutL binding to a UvrD monomer–DNA complex, a rotational conformational state is favored that is intermediate between the open and closed states. Parallel kinetic studies of MutL activation of the UvrD helicase and of MutL-dependent changes in the UvrD 2B subdomain show that the transition from an open to an intermediate 2B subdomain state is on the pathway to helicase activation. We further show that MutL is unable to activate the helicase activity of a chimeric UvrD containing the 2B subdomain of the structurally similar Rep helicase. Hence, MutL activation of the monomeric UvrD helicase is regulated specifically by its 2B subdomain.

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Nguyen, Binh, Yerdos Ordabayev, Joshua E. Sokoloski, Elizabeth Weiland i Timothy M. Lohman. "Large domain movements upon UvrD dimerization and helicase activation". Proceedings of the National Academy of Sciences 114, nr 46 (30.10.2017): 12178–83. http://dx.doi.org/10.1073/pnas.1712882114.

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Escherichia coli UvrD DNA helicase functions in several DNA repair processes. As a monomer, UvrD can translocate rapidly and processively along ssDNA; however, the monomer is a poor helicase. To unwind duplex DNA in vitro, UvrD needs to be activated either by self-assembly to form a dimer or by interaction with an accessory protein. However, the mechanism of activation is not understood. UvrD can exist in multiple conformations associated with the rotational conformational state of its 2B subdomain, and its helicase activity has been correlated with a closed 2B conformation. Using single-molecule total internal reflection fluorescence microscopy, we examined the rotational conformational states of the 2B subdomain of fluorescently labeled UvrD and their rates of interconversion. We find that the 2B subdomain of the UvrD monomer can rotate between an open and closed conformation as well as two highly populated intermediate states. The binding of a DNA substrate shifts the 2B conformation of a labeled UvrD monomer to a more open state that shows no helicase activity. The binding of a second unlabeled UvrD shifts the 2B conformation of the labeled UvrD to a more closed state resulting in activation of helicase activity. Binding of a monomer of the structurally similar Escherichia coli Rep helicase does not elicit this effect. This indicates that the helicase activity of a UvrD dimer is promoted via direct interactions between UvrD subunits that affect the rotational conformational state of its 2B subdomain.

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Yokota, Hiroaki. "Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD". International Journal of Molecular Sciences 22, nr 3 (20.01.2021): 1018. http://dx.doi.org/10.3390/ijms22031018.

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Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

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SaiSree, L., Manjula Reddy i J. Gowrishankar. "lon Incompatibility Associated with Mutations Causing SOS Induction: Null uvrD Alleles Induce an SOS Response in Escherichia coli". Journal of Bacteriology 182, nr 11 (1.06.2000): 3151–57. http://dx.doi.org/10.1128/jb.182.11.3151-3157.2000.

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ABSTRACT The uvrD gene in Escherichia coli encodes a 720-amino-acid 3′-5′ DNA helicase which, although nonessential for viability, is required for methyl-directed mismatch repair and nucleotide excision repair and furthermore is believed to participate in recombination and DNA replication. We have shown in this study that null mutations in uvrD are incompatible withlon, the incompatibility being a consequence of the chronic induction of SOS in uvrD strains and the resultant accumulation of the cell septation inhibitor SulA (which is a normal target for degradation by Lon protease). uvrD-lonincompatibility was suppressed by sulA,lexA3(Ind−), or recA (Def) mutations. Other mutations, such as priA, dam,polA, and dnaQ (mutD) mutations, which lead to persistent SOS induction, were also lonincompatible. SOS induction was not observed in uvrC andmutH (or mutS) mutants defective, respectively, in excision repair and mismatch repair. Nor wasuvrD-mediated SOS induction abolished by mutations in genes that affect mismatch repair (mutH), excision repair (uvrC), or recombination (recB andrecF). These data suggest that SOS induction inuvrD mutants is not a consequence of defects in these three pathways. We propose that the UvrD helicase participates in DNA replication to unwind secondary structures on the lagging strand immediately behind the progressing replication fork, and that it is the absence of this function which contributes to SOS induction inuvrD strains.

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Mechanic, Leah E., Marcy E. Latta i Steven W. Matson. "A Region Near the C-Terminal End ofEscherichia coli DNA Helicase II Is Required for Single-Stranded DNA Binding". Journal of Bacteriology 181, nr 8 (15.04.1999): 2519–26. http://dx.doi.org/10.1128/jb.181.8.2519-2526.1999.

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ABSTRACT The role of the C terminus of Escherichia coli DNA helicase II (UvrD), a region outside the conserved helicase motifs, was investigated by using three mutants: UvrDΔ107C (deletion of the last 107 C-terminal amino acids), UvrDΔ102C, and UvrDΔ40C. This region, which lacks sequence similarity with other helicases, may function to tailor UvrD for its specific in vivo roles. Genetic complementation assays demonstrated that mutant proteins UvrDΔ107C and UvrDΔ102C failed to substitute for the wild-type protein in methyl-directed mismatch repair and nucleotide excision repair. UvrDΔ40C protein fully complemented the loss of helicase II in both repair pathways. UvrDΔ102C and UvrDΔ40C were purified to apparent homogeneity and characterized biochemically. UvrDΔ102C was unable to bind single-stranded DNA and exhibited a greatly reduced single-stranded DNA-stimulated ATPase activity in comparison to the wild-type protein (k cat = 0.01% of the wild-type level). UvrDΔ40C was slightly defective for DNA binding and was essentially indistinguishable from wild-type UvrD when single-stranded DNA-stimulated ATP hydrolysis and helicase activities were measured. These results suggest a role for a region near the C terminus of helicase II in binding to single-stranded DNA.

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Shukla, Kaustubh, Roshan Singh Thakur, Debayan Ganguli, Desirazu Narasimha Rao i Ganesh Nagaraju. "Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures". Biochemical Journal 474, nr 21 (18.10.2017): 3579–97. http://dx.doi.org/10.1042/bcj20170587.

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G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria gonorrhoeae UvrD in resolving G4 tetraplexes. EcUvrD and N. gonorrhoeae UvrD were proficient in unwinding previously characterized tetramolecular G4 structures. Notably, EcUvrD was equally efficient in resolving tetramolecular and bimolecular G4 DNA that were derived from the potential G4-forming sequences from the genome of E. coli. Interestingly, in addition to resolving intermolecular G4 structures, EcUvrD was robust in unwinding intramolecular G4 structures. These data for the first time provide evidence for the role of UvrD in the resolution of G4 structures, which has implications for the in vivo role of UvrD helicase in G4 DNA resolution and genome maintenance.

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Shankar, Jay, i Renu Tuteja. "UvrD helicase of Plasmodium falciparum". Gene 410, nr 2 (marzec 2008): 223–33. http://dx.doi.org/10.1016/j.gene.2007.12.015.

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Lovett, S. T., i V. A. Sutera. "Suppression of recJ exonuclease mutants of Escherichia coli by alterations in DNA helicases II (uvrD) and IV (helD)." Genetics 140, nr 1 (1.05.1995): 27–45. http://dx.doi.org/10.1093/genetics/140.1.27.

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Abstract The recJ gene encodes a single-strand DNA-specific exonuclease involved in homologous recombination. We have isolated a pseudorevertant strain in which recJ mutant phenotypes were alleviated. Suppression of recJ was due to at least three mutations, two of which we have identified as alterations in DNA helicase genes. A recessive amber mutation, "uvrD517am," at codon 503 of the gene encoding helicase II was sufficient to suppress recJ partially. The uvrD517am mutation does not eliminate uvrD function because it affects UV survival only weakly; moreover, a uvrD insertion mutation could not replace uvrD517am as a suppressor. However, suppression may result from differential loss of uvrD function: mutation rate in a uvrD517am derivative was greatly elevated, equal to that in a uvrD insertion mutant. The second cosuppressor mutation is an allele of the helD gene, encoding DNA helicase IV, and could be replaced by insertion mutations in helD. The identity of the third cosuppressor "srjD" is not known. Strains carrying the three cosuppressor mutations exhibited hyperrecombinational phenotypes including elevated excision of repeated sequences. To explain recJ suppression, we propose that loss of antirecombinational helicase activity by the suppressor mutations stabilizes recombinational intermediates formed in the absence of recJ.

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Newton, Kelley N., Charmain T. Courcelle i Justin Courcelle. "UvrD Participation in Nucleotide Excision Repair Is Required for the Recovery of DNA Synthesis following UV-Induced Damage inEscherichia coli". Journal of Nucleic Acids 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/271453.

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UvrD is a DNA helicase that participates in nucleotide excision repair and several replication-associated processes, including methyl-directed mismatch repair and recombination. UvrD is capable of displacing oligonucleotides from synthetic forked DNA structuresin vitroand is essential for viability in the absence of Rep, a helicase associated with processing replication forks. These observations have led others to propose that UvrD may promote fork regression and facilitate resetting of the replication fork following arrest. However, the molecular activity of UvrD at replication forksin vivohas not been directly examined. In this study, we characterized the role UvrD has in processing and restoring replication forks following arrest by UV-induced DNA damage. We show that UvrD is required for DNA synthesis to recover. However, in the absence of UvrD, the displacement and partial degradation of the nascent DNA at the arrested fork occur normally. In addition, damage-induced replication intermediates persist and accumulate inuvrDmutants in a manner that is similar to that observed in other nucleotide excision repair mutants. These data indicate that, following arrest by DNA damage, UvrD is not required to catalyze fork regressionin vivoand suggest that the failure ofuvrDmutants to restore DNA synthesis following UV-induced arrest relates to its role in nucleotide excision repair.

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Atkinson, John, Colin P. Guy, Chris J. Cadman, Geri F. Moolenaar, Nora Goosen i Peter McGlynn. "Stimulation of UvrD Helicase by UvrAB". Journal of Biological Chemistry 284, nr 14 (10.02.2009): 9612–23. http://dx.doi.org/10.1074/jbc.m808030200.

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Curti, Elena, Stephen J. Smerdon i Elaine O. Davis. "Characterization of the Helicase Activity and Substrate Specificity of Mycobacterium tuberculosis UvrD". Journal of Bacteriology 189, nr 5 (8.12.2006): 1542–55. http://dx.doi.org/10.1128/jb.01421-06.

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ABSTRACT UvrD is a helicase that is widely conserved in gram-negative bacteria. A uvrD homologue was identified in Mycobacterium tuberculosis on the basis of the homology of its encoded protein with Escherichia coli UvrD, with which it shares 39% amino acid identity, distributed throughout the protein. The gene was cloned, and a histidine-tagged form of the protein was expressed and purified to homogeneity. The purified protein had in vitro ATPase activity that was dependent upon the presence of DNA. Oligonucleotides as short as four nucleotides were sufficient to promote the ATPase activity. The DNA helicase activity of the enzyme was only fueled by ATP and dATP. UvrD preferentially unwound 3′-single-stranded tailed duplex substrates over 5′-single-stranded ones, indicating that the protein had a duplex-unwinding activity with 3′-to-5′ polarity. A 3′ single-stranded DNA tail of 18 nucleotides was required for effective unwinding. By using a series of synthetic oligonucleotide substrates, we demonstrated that M. tuberculosis UvrD has an unwinding preference towards nicked DNA duplexes and stalled replication forks, representing the likely sites of action in vivo. The potential role of M. tuberculosis UvrD in maintenance of bacterial genomic integrity makes it a promising target for drug design against M. tuberculosis.

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Kang, Josephine, i Martin J. Blaser. "UvrD Helicase Suppresses Recombination and DNA Damage-Induced Deletions". Journal of Bacteriology 188, nr 15 (1.08.2006): 5450–59. http://dx.doi.org/10.1128/jb.00275-06.

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ABSTRACT UvrD, a highly conserved helicase involved in mismatch repair, nucleotide excision repair (NER), and recombinational repair, plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species. In this report, we focus on the UvrD homolog in Helicobacter pylori, a genetically diverse organism that lacks many known DNA repair proteins, including those involved in mismatch repair and recombinational repair, and that is noted for high levels of inter- and intragenomic recombination and mutation. H. pylori contains numerous DNA repeats in its compact genome and inhabits an environment rich in DNA-damaging agents that can lead to increased rearrangements between such repeats. We find that H. pylori UvrD functions to repair DNA damage and limit homologous recombination and DNA damage-induced genomic rearrangements between DNA repeats. Our results suggest that UvrD and other NER pathway proteins play a prominent role in maintaining genome integrity, especially after DNA damage; thus, NER may be especially critical in organisms such as H. pylori that face high-level genotoxic stress in vivo.

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HOEIJMAKERS, J. H. J. "How Relevant is the Escherichia coli UvrABC Model for Excision Repair in Eukaryotes?" Journal of Cell Science 100, nr 4 (1.12.1991): 687–91. http://dx.doi.org/10.1242/jcs.100.4.687.

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Knowledge about the DNA excision repair system is increasing rapidly. A detailed model for this process in Escherichia coli has emerged in which a lesion in the DNA is first recognized by the UvrA2B helicase complex. Subsequently, UvrC mediates incision on both sites of the DNA injury. Finally, the concerted action of helicase II (UvrD), polymerase and ligase takes care of removal of the damage-containing oligonucleotide, DNA resynthesis and sealing of the residual nick. In the eukaryotes, yeast and mammals a total of 10 excision repair genes have been analysed thus far. However, little is still known about the molecular mechanism of this repair reaction. Amino acid sequence comparison suggests that at least three DNA helicases operate in eukaryotic nucleotide excision. In addition, a striking sequence conservation is noted between human and yeast repair proteins. But no eukaryotic homologs of the UvrABC proteins have been identified. In this Commentary the parallels and differences between the prokaryotic and eukaryotic excision repair pathways are weighed in an attempt to assess the relevance of the E. coli model for the eukaryotic system.

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Mendonca, V. M., i S. W. Matson. "Genetic analysis of delta helD and delta uvrD mutations in combination with other genes in the RecF recombination pathway in Escherichia coli: suppression of a ruvB mutation by a uvrD deletion." Genetics 141, nr 2 (1.10.1995): 443–52. http://dx.doi.org/10.1093/genetics/141.2.443.

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Abstract Helicase II (uvrD gene product) and helicase IV (helD gene product) have been shown previously to be involved in the RecF pathway of recombination. To better understand the role of these two proteins in homologous recombination in the RecF pathway [recBCsbcB(C) background, we investigated the interactions between helD, uvrD and the following RecF pathway genes: recF, recO, recN and ruvAB. We observed synergistic interactions between uvrD ant the recF, recN, recO and recG genes in both conjugational recombination and the repair of methylmethane sulfonate (MMS)-induced DNA damage. No synergistic interactions were detected between helD and the recF, recO and regN genes when conjugational recombination was analyzed. We did, however, detect synergistic interactions between helD and recF/recO in recombinational repair. Surprisingly, the uvrD deletion completely suppressed the phenotype of a ruvB mutation in a recBCsbcB(C) background. Both conjugational recombination efficiency and MMS-damaged DNA repair proficiency returned to wild-type levels in the deltauvrDruvB9 double mutant. Suppression of the effects of the ruvB mutation by a uvrD deletion was dependent on the recG and recN genes and not dependent on the recF/O/R genes. These data are discussed in the context of two "RecF" homologous recombination pathways operating in a recBCsbcB(C) strain background.

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Sedman, Tiina, Silja Kuusk, Sirje Kivi i Juhan Sedman. "A DNA Helicase Required for Maintenance of the Functional Mitochondrial Genome in Saccharomyces cerevisiae". Molecular and Cellular Biology 20, nr 5 (1.03.2000): 1816–24. http://dx.doi.org/10.1128/mcb.20.5.1816-1824.2000.

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ABSTRACT A novel DNA helicase, a homolog of several prokaryotic helicases, including Escherichia coli Rep and UvrD proteins, is encoded by the Saccharomyces cerevisiae nuclear genome open reading frame YOL095c on the chromosome XV. Our data demonstrate that the helicase is localized in the yeast mitochondria and is loosely associated with the mitochondrial inner membrane during biochemical fractionation. The sequence of the C-terminal end of the 80-kDa helicase protein is similar to a typical N-terminal mitochondrial targeting signal; deletions and point mutations in this region abolish transport of the protein into mitochondria. The C-terminal signal sequence of the helicase targets a heterologous carrier protein into mitochondria in vivo. The purified recombinant protein can unwind duplex DNA molecules in an ATP-dependent manner. The helicase is required for the maintenance of the functional ([rho +]) mitochondrial genome on both fermentable and nonfermentable carbon sources. However, the helicase is not essential for the maintenance of several defective ([rho −]) mitochondrial genomes. We also demonstrate that the helicase is not required for transcription in mitochondria.

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Tuteja, Renu. "In silico analysis ofPlasmodiumspecies specific UvrD helicase". Communicative & Integrative Biology 6, nr 2 (marzec 2013): e23125. http://dx.doi.org/10.4161/cib.23125.

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Brosh, Jr., Robert M. "UvrD helicase: The little engine that could". Cell Cycle 13, nr 8 (4.03.2014): 1213–15. http://dx.doi.org/10.4161/cc.28382.

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Ordabayev, Yerdos A., Binh Nguyen, Anita Niedziela-Majka i Timothy M. Lohman. "Regulation of UvrD Helicase Activity by MutL". Journal of Molecular Biology 430, nr 21 (październik 2018): 4260–74. http://dx.doi.org/10.1016/j.jmb.2018.08.022.

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Ordabayev, Yerdos, Binh Nguyen, Anita Niedziela-Majka i Timothy Lohman. "Regulation of UvrD Helicase Activity by MutL". Biophysical Journal 114, nr 3 (luty 2018): 444a. http://dx.doi.org/10.1016/j.bpj.2017.11.2455.

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Delagoutte, Emmanuelle, i Peter H. von Hippel. "Helicase mechanisms and the coupling of helicases within macromolecular machines Part II: Integration of helicases into cellular processes". Quarterly Reviews of Biophysics 36, nr 1 (27.01.2003): 1–69. http://dx.doi.org/10.1017/s0033583502003864.

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1. Helicases as components of macromolecular machines 32. Helicases in replication 72.1 The loading of replicative helicases 72.1.1 Loading Rep helicase at the replication origin of bacteriophage ϕX174 72.1.2 How is a ssDNA strand passed through (and bound in?) the central channel of the hexameric replicative helicases? 82.1.3 Loading of E. coli DnaB helicase in the absence of an auxiliary protein-loading factor 82.1.4 The T7 gp4 primase-helicase is loaded by means of a facilitated ring-opening mechanism 102.1.5 Bacteriophage T4 gp61 primase can be viewed as a loading factor for the homologous gp41 helicase 112.1.6 DnaC serves as the loading factor for E. coli DnaB helicase 112.1.7 The role of bacteriophage T4 gp59 in loading the T4 gp41 helicase 122.1.8 Loading of helicases onto ssDNA covered by ssDNA-binding proteins (SSBPs) 152.2 DNA polymerase and ssDNA-binding proteins can serve as reporters for replicative helicases in their elongation mode 172.2.1 The DNA polymerase, the sliding clamp, and the clamp loader 172.2.2 The role of ssDNA-binding protein 182.2.3 Coupling is achieved by the DNA polymerase and the ssDNA-binding protein 182.3 Arrest of replicative helicases 182.3.1 The Ter sites and termination proteins 192.3.2 Models for orientation-specific fork arrest 203. Helicases in transcription 203.1 Assisted loading of E. coli RNAP by the sigma70 initiation factor 213.1.1 RNAP holoenzyme formation 233.1.2 Formation of closed promoter complexes RPc and RPi 243.1.3 Strand separation and the formation of the open complex 243.1.4 Promoter clearance 243.1.5 Conclusions 253.2 Transcript formation serves as a monitor (reporter) of RNAP helicase activity in the elongation phase of transcription 253.2.1 Structural aspects of transcription complex translocation 263.2.2 Transcript elongation is an approximately isoenergetic process 263.3 Termination of transcription 273.3.1 Intrinsic termination 273.3.2 Termination by transcription-termination helicase Rho 283.3.3 Conclusions 293.4 Loading of the Rho transcription-termination helicase 294. Helicases in nucleotide excision repair (NER) 304.1 The limited strand-separating activity of the UvrAB complex 314.2 UvrB is a DNA helicase adapted for NER 334.2.1 The ATP-binding site of UvrB is similar to that of other helicases 334.2.2 The putative DNA-binding site 334.3 UvrA as a UvrB loader 344.4 Assisted targeting of UvrAB to the transcribed strand of DNA sequences undergoing active transcription 344.4.1 Targeting of UvrAB to damaged DNA sites in the vicinity of promoters is assisted by RNAP 344.4.2 TRCF participates in the assisted targeting of UvrAB to a transcribing RNAP stalled by a DNA lesion 354.4.3 Conclusions 364.5 UvrC endonuclease is the reporter of UvrAB helicase activity in incision 364.6 Post-incision events 364.7 Mechanistic details of the helicase activity of UvrD 374.7.1 Structural organization and conformational changes 374.7.2 Translocation and unwinding activities 384.7.3 Step size of DNA unwinding 384.7.4 Oligomeric state 395. Helicases in recombination 395.1 Role of RecBCD and RecQ in the initiation of recombination 405.1.1 The RecBCD enzyme 405.1.1.1 Loading of RecBCD onto its DNA substrate does not require a separate loading protein 405.1.1.2 The endonuclease activity of RecD, and the binding of SSB protein, serve as reporters of RecBCD helicase activity 405.1.1.3 RecA can also serve as a reporter of RecBCD helicase activity 415.1.1.4 RecBCD step size and unwinding mechanism 415.1.1.5 RecBCD unwinding efficiency 425.1.2 The RecQ protein 435.2 Strand-exchange reaction catalyzed by RecA 435.2.1 The nucleoprotein filament 445.2.2 The strand-exchange reaction 465.2.2.1 A ‘minor-groove’ to ‘major-groove’ triple-helix transition 465.2.2.2 Role of the secondary DNA-binding site of RecA 465.2.2.3 SSB protein stimulates the strand-exchange reaction 465.2.2.4 Cost of the strand-exchange reaction 475.2.3 Conclusion: RecA is a ‘scaffolding’ protein that prepares DNA for a coupled unpairing–reannealing reaction 485.3 Role of the RuvAB helicase in processing recombination intermediates by a branch migration mechanism 485.3.1 A brief description of the RuvA and RuvB proteins 495.3.2 Crystal structures of RuvA and the RuvA–Holliday junction complex 505.3.3 RuvA as a scaffolding protein that prepares the homoduplex for strand separation 515.3.4 Branch migration mechanism 516. RNA unwindases in the spliceosome 526.1 RNA structural rearrangements within the spliceosome: an overview 526.2 The spliceosome consumes chemical free energy 546.3 RNA structural alterations require the concerted (or coupled) action of unwinding and reannealing proteins 546.4 The reannealing proteins of the spliceosome: contribution of the RNA recognition motifs (RRMs) 556.5 The RNA unwindases of the spliceosome 556.6 RNA targets of the RNA unwindases 567. Conclusions and overview 578. Acknowledgments 589. References 59In Part I of this review [Delagoutte & von Hippel, Quarterly Reviews of Biophysics (2002) 35, 431–478] we summarized what is known about the properties, mechanisms, and structures of the various helicases that catalyze the unwinding of double-stranded nucleic acids. Here, in Part II, we consider these helicases as tightly integrated (or coupled) components of the various macromolecular machines within which they operate. The biological processes that are considered explicitly include DNA replication, recombination, and nucleotide excision repair, as well as RNA transcription and splicing. We discuss the activities of the constituent helicases (and their protein partners) in the assembly (or loading) of the relevant complex onto (and into) the specific nucleic acid sites at which the actions of the helicase-containing complexes are to be initiated, the mechanisms by which the helicases (and the complexes) translocate along the nucleic acids in discharging their functions, and the reactions that are used to terminate the translocation of the helicase-containing complexes at specific sites within the nucleic acid ‘substrate’. We emerge with several specific descriptions of how helicases function within the above processes of genetic expression which, we hope, can serve as paradigms for considering how helicases may also be coupled and function within other macromolecular machines.

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Centore, Richard C., i Steven J. Sandler. "UvrD Limits the Number and Intensities of RecA-Green Fluorescent Protein Structures in Escherichia coli K-12". Journal of Bacteriology 189, nr 7 (26.01.2007): 2915–20. http://dx.doi.org/10.1128/jb.01777-06.

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ABSTRACT RecA is important for recombination, DNA repair, and SOS induction. In Escherichia coli, RecBCD, RecFOR, and RecJQ prepare DNA substrates onto which RecA binds. UvrD is a 3′-to-5′ helicase that participates in methyl-directed mismatch repair and nucleotide excision repair. uvrD deletion mutants are sensitive to UV irradiation, hypermutable, and hyper-rec. In vitro, UvrD can dissociate RecA from single-stranded DNA. Other experiments suggest that UvrD removes RecA from DNA where it promotes unproductive reactions. To test if UvrD limits the number and/or the size of RecA-DNA structures in vivo, an uvrD mutation was combined with recA-gfp. This recA allele allows the number of RecA structures and the amount of RecA at these structures to be assayed in living cells. uvrD mutants show a threefold increase in the number of RecA-GFP foci, and these foci are, on average, nearly twofold higher in relative intensity. The increased number of RecA-green fluorescent protein foci in the uvrD mutant is dependent on recF, recO, recR, recJ, and recQ. The increase in average relative intensity is dependent on recO and recQ. These data support an in vivo role for UvrD in removing RecA from the DNA.

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24

Yang, W., i J. Lee. "Stop-action movie of UvrD helicase unwinding DNA". Acta Crystallographica Section A Foundations of Crystallography 64, a1 (23.08.2008): C25. http://dx.doi.org/10.1107/s0108767308099236.

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25

Veaute, Xavier, Stéphane Delmas, Marjorie Selva, Josette Jeusset, Eric Le Cam, Ivan Matic, Francis Fabre i Marie-Agnès Petit. "UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli". EMBO Journal 24, nr 1 (25.11.2004): 180–89. http://dx.doi.org/10.1038/sj.emboj.7600485.

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Criss, Alison K., Kevin M. Bonney, Rhoda A. Chang, Paul M. Duffin, Brian E. LeCuyer i H. Steven Seifert. "Mismatch Correction Modulates Mutation Frequency and Pilus Phase and Antigenic Variation in Neisseria gonorrhoeae". Journal of Bacteriology 192, nr 1 (23.10.2009): 316–25. http://dx.doi.org/10.1128/jb.01228-09.

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ABSTRACT The mismatch correction (MMC) system repairs DNA mismatches and single nucleotide insertions or deletions postreplication. To test the functions of MMC in the obligate human pathogen Neisseria gonorrhoeae, homologues of the core MMC genes mutS and mutL were inactivated in strain FA1090. No mutH homologue was found in the FA1090 genome, suggesting that gonococcal MMC is not methyl directed. MMC mutants were compared to a mutant in uvrD, the helicase that functions with MMC in Escherichia coli. Inactivation of MMC or uvrD increased spontaneous resistance to rifampin and nalidixic acid, and MMC/uvrD double mutants exhibited higher mutation frequencies than any single mutant. Loss of MMC marginally enhanced the transformation efficiency of DNA carrying a single nucleotide mismatch but not that of DNA with a 1-kb insertion. Unlike the exquisite UV sensitivity of the uvrD mutant, inactivating MMC did not affect survival after UV irradiation. MMC and uvrD mutants exhibited increased PilC-dependent pilus phase variation. mutS-deficient gonococci underwent an increased frequency of pilin antigenic variation, whereas uvrD had no effect. Recombination tracts in the mutS pilin variants were longer than in parental gonococci but utilized the same donor pilS loci. These results show that gonococcal MMC repairs mismatches and small insertion/deletions in DNA and also affects the recombination events underlying pilin antigenic variation. The differential effects of MMC and uvrD in gonococci unexpectedly reveal that MMC can function independently of uvrD in this human-specific pathogen.

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27

An, Lixin, Wen Tang, Tamara A. Ranalli, Hyun-Jin Kim, Jamie Wytiaz i Huimin Kong. "Characterization of a Thermostable UvrD Helicase and Its Participation in Helicase-dependent Amplification". Journal of Biological Chemistry 280, nr 32 (13.06.2005): 28952–58. http://dx.doi.org/10.1074/jbc.m503096200.

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Yang, Wei. "Lessons Learned from UvrD Helicase: Mechanism for Directional Movement". Annual Review of Biophysics 39, nr 1 (kwiecień 2010): 367–85. http://dx.doi.org/10.1146/annurev.biophys.093008.131415.

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29

Nguyen, Binh, Yerdos Ordabayev, Joshua Sokoloski, Elizabeth Weiland i Timothy M. Lohman. "Large Domain Movements Upon UvrD Dimerization and Helicase Activation". Biophysical Journal 114, nr 3 (luty 2018): 441a. http://dx.doi.org/10.1016/j.bpj.2017.11.2438.

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30

Epshtein, Vitaliy. "UvrD helicase: An old dog with a new trick". BioEssays 37, nr 1 (27.10.2014): 12–19. http://dx.doi.org/10.1002/bies.201400106.

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31

Carney, Sean P., Kevin D. Whitley, Wen Ma, Haifeng Jia, Timothy M. Lohman, Zaida Luthey-Schulten i Yann R. Chemla. "Direct Measurement of Stepping Dynamics of E. coli UvrD Helicase". Biophysical Journal 118, nr 3 (luty 2020): 71a. http://dx.doi.org/10.1016/j.bpj.2019.11.565.

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32

Štambuk, Snježana, i Miroslav Radman. "Mechanism and Control of Interspecies Recombination in Escherichia coli. I. Mismatch Repair, Methylation, Recombination and Replication Functions". Genetics 150, nr 2 (1.10.1998): 533–42. http://dx.doi.org/10.1093/genetics/150.2.533.

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Abstract A genetic analysis of interspecies recombination in Escherichia coli between the linear Hfr DNA from Salmonella typhimurium and the circular recipient chromosome reveals some fundamental aspects of recombination between related DNA sequences. The MutS and MutL mismatch binding proteins edit (prevent) homeologous recombination between these 16% diverged genomes by at least two distinct mechanisms. One is MutH independent and presumably acts by aborting the initiated recombination through the UvrD helicase activity. The RecBCD nuclease might contribute to this editing step, presumably by preventing reiterated initiations of recombination at a given locus. The other editing mechanism is MutH dependent, requires unmethylated GATC sequences, and probably corresponds to an incomplete long-patch mismatch repair process that does not depend on UvrD helicase activity. Insignificant effects of the Dam methylation of parental DNAs suggest that unmethylated GATC sequences involved in the MutH-dependent editing are newly synthesized in the course of recombination. This hypothetical, recombination-associated DNA synthesis involves PriA and RecF functions, which, therefore, determine the extent of MutH effect on interspecies recombination. Sequence divergence of recombining DNAs appears to limit the frequency, length, and stability of early heteroduplex intermediates, which can be stabilized, and the recombinants mature via the initiation of DNA replication.

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33

Zhang, Gang, Enxin Deng, Larry Baugh i Sidney R. Kushner. "Identification and Characterization ofEscherichia coli DNA Helicase II Mutants That Exhibit Increased Unwinding Efficiency". Journal of Bacteriology 180, nr 2 (15.01.1998): 377–87. http://dx.doi.org/10.1128/jb.180.2.377-387.1998.

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ABSTRACT Using a combination of both ethyl methanesulfonate and site-directed mutagenesis, we have identified a region in DNA helicase II (UvrD) from Escherichia coli that is required for biological function but lies outside of any of the seven conserved motifs (T. C. Hodgman, Nature 333:22–23, 1988) associated with the superfamily of proteins of which it is a member. Located between amino acids 403 and 409, alterations in the amino acid sequence DDAAFER lead to both temperature-sensitive and dominant uvrDmutations. The uvrD300 (A406T) and uvrD301(A406V) alleles produce UV sensitivity at 44°C but do not affect sensitivity to methyl methanesulfonate (MMS). In contrast, theuvrD303 mutation (D403AD404A) causes increased sensitivity to both UV and MMS and is dominant to uvrD+ when present at six to eight copies per cell. Several of the alleles demonstrated a strong antimutator phenotype. In addition, conjugal recombination is reduced 10-fold in uvrD303 strains. Of all of the amino acid substitutions tested, only an alanine-to-serine change at position 406 (uvrD302) was neutral. To determine the biochemical basis for the observed phenotypes, we overexpressed and purified the UvrD303 protein from a uvrDΔ294 deletion background and characterized its enzymatic activities. The highly unusual UvrD303 protein exhibits a higher specific activity for ATP hydrolysis than the wild-type control, while itsKm for ATP binding remains unchanged. More importantly, the UvrD303 protein unwinds partial duplex DNA up to 10 times more efficiently than wild-type UvrD. The DNA binding affinities of the two proteins appear comparable. Based on these results, we propose that the region located between amino acids 403 and 409 serves to regulate the unwinding activity of DNA helicase II to provide the proper balance between speed and overall effectiveness in the various DNA repair systems in which the protein participates.

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34

Kumari, Anuradha, Irina G. Minko, Rebecca L. Smith, R. Stephen Lloyd i Amanda K. McCullough. "Modulation of UvrD Helicase Activity by Covalent DNA-Protein Cross-links". Journal of Biological Chemistry 285, nr 28 (4.05.2010): 21313–22. http://dx.doi.org/10.1074/jbc.m109.078964.

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35

Higinbotham, Hugh. "High-Resolution Single-Molecule Analysis of UvrD Helicase using Nanopore Tweezers". Biophysical Journal 114, nr 3 (luty 2018): 91a. http://dx.doi.org/10.1016/j.bpj.2017.11.540.

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Whitley, Kevin D., Matthew J. Comstock, Haifeng Jia, Timothy M. Lohman i Yann R. Chemla. "Direct Observation of the Stepping Behavior of E. Coli UvrD Helicase". Biophysical Journal 110, nr 3 (luty 2016): 561a. http://dx.doi.org/10.1016/j.bpj.2015.11.3000.

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Chiolo, Irene, Marco Saponaro, Anastasia Baryshnikova, Jeong-Hoon Kim, Yeon-Soo Seo i Giordano Liberi. "The Human F-Box DNA Helicase FBH1 Faces Saccharomyces cerevisiae Srs2 and Postreplication Repair Pathway Roles". Molecular and Cellular Biology 27, nr 21 (27.08.2007): 7439–50. http://dx.doi.org/10.1128/mcb.00963-07.

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ABSTRACTTheSaccharomyces cerevisiaeSrs2 UvrD DNA helicase controls genome integrity by preventing unscheduled recombination events. While Srs2 orthologues have been identified in prokaryotic and lower eukaryotic organisms, human orthologues of Srs2 have not been described so far. We found that the human F-box DNA helicase hFBH1 suppresses specific recombination defects ofS. cerevisiae srs2mutants, consistent with the finding that the helicase domain of hFBH1 is highly conserved with that of Srs2. Surprisingly, hFBH1 in the absence ofSRS2also suppresses the DNA damage sensitivity caused by inactivation of postreplication repair-dependent functions leading to PCNA ubiquitylation. The F-box domain of hFBH1, which is not present in Srs2, is crucial for hFBH1 functions in substituting for Srs2 and postreplication repair factors. Furthermore, our findings indicate that an intact F-box domain, acting as an SCF ubiquitin ligase, is required for the DNA damage-induced degradation of hFBH1 itself. Overall, our findings suggest that the hFBH1 helicase is a functional human orthologue of budding yeast Srs2 that also possesses self-regulation properties necessary to execute its recombination functions.

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38

Adebali, Ogun, Yi-Ying Chiou, Jinchuan Hu, Aziz Sancar i Christopher P. Selby. "Genome-wide transcription-coupled repair inEscherichia coliis mediated by the Mfd translocase". Proceedings of the National Academy of Sciences 114, nr 11 (6.02.2017): E2116—E2125. http://dx.doi.org/10.1073/pnas.1700230114.

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We used high-throughput sequencing of short, cyclobutane pyrimidine dimer-containing ssDNA oligos generated during repair of UV-induced damage to study that process at both mechanistic and systemic levels inEscherichia coli. Numerous important insights on DNA repair were obtained, bringing clarity to the respective roles of UvrD helicase and Mfd translocase in repair of UV-induced damage. Mechanistically, experiments showed that the predominant role of UvrD in vivo is to unwind the excised 13-mer from dsDNA and that mutation ofuvrDresults in remarkable protection of that oligo from exonuclease activity as it remains hybridized to the dsDNA. Genome-wide analysis of the transcribed strand/nontranscribed strand (TS/NTS) repair ratio demonstrated that deletion ofmfdglobally shifts the distribution of TS/NTS ratios downward by a factor of about 2 on average for the most highly transcribed genes. Even for the least transcribed genes, Mfd played a role in preferential repair of the transcribed strand. On the other hand, mutation ofuvrD, if anything, slightly pushed the distribution of TS/NTS ratios to higher ratios. These results indicate that Mfd is the transcription repair-coupling factor whereas UvrD plays a role in excision repair by aiding the catalytic turnover of excision repair proteins.

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39

Jeong, Yeon-Tae, Mario Rossi, Lukas Cermak, Anita Saraf, Laurence Florens, Michael P. Washburn, Patrick Sung, Carl L. Schildkraut i Michele Pagano. "FBH1 promotes DNA double-strand breakage and apoptosis in response to DNA replication stress". Journal of Cell Biology 200, nr 2 (14.01.2013): 141–49. http://dx.doi.org/10.1083/jcb.201209002.

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Proper resolution of stalled replication forks is essential for genome stability. Purification of FBH1, a UvrD DNA helicase, identified a physical interaction with replication protein A (RPA), the major cellular single-stranded DNA (ssDNA)–binding protein complex. Compared with control cells, FBH1-depleted cells responded to replication stress with considerably fewer double-strand breaks (DSBs), a dramatic reduction in the activation of ATM and DNA-PK and phosphorylation of RPA2 and p53, and a significantly increased rate of survival. A minor decrease in ssDNA levels was also observed. All these phenotypes were rescued by wild-type FBH1, but not a FBH1 mutant lacking helicase activity. FBH1 depletion had no effect on other forms of genotoxic stress in which DSBs form by means that do not require ssDNA intermediates. In response to catastrophic genotoxic stress, apoptosis prevents the persistence and propagation of DNA lesions. Our findings show that FBH1 helicase activity is required for the efficient induction of DSBs and apoptosis specifically in response to DNA replication stress.

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40

Tuteja, Renu, i Narendra Tuteja. "Analysis of DNA repair helicase UvrD from Arabidopsis thaliana and Oryza sativa". Plant Physiology and Biochemistry 71 (październik 2013): 254–60. http://dx.doi.org/10.1016/j.plaphy.2013.07.022.

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41

Maluf, Nasib K., i Timothy M. Lohman. "Self-association Equilibria of Escherichia coli UvrD Helicase Studied by Analytical Ultracentrifugation". Journal of Molecular Biology 325, nr 5 (styczeń 2003): 889–912. http://dx.doi.org/10.1016/s0022-2836(02)01276-7.

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42

Maluf, Nasib K., Janid A. Ali i Timothy M. Lohman. "Kinetic Mechanism for Formation of the Active, Dimeric UvrD Helicase-DNA Complex". Journal of Biological Chemistry 278, nr 34 (3.06.2003): 31930–40. http://dx.doi.org/10.1074/jbc.m304223200.

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43

Matson, Steven W., i Adam B. Robertson. "The UvrD helicase and its modulation by the mismatch repair protein MutL". Nucleic Acids Research 34, nr 15 (25.08.2006): 4089–97. http://dx.doi.org/10.1093/nar/gkl450.

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Shea, Molly E., i Hiroshi Hiasa. "Distinct Effects of the UvrD Helicase on Topoisomerase- Quinolone-DNA Ternary Complexes". Journal of Biological Chemistry 275, nr 19 (5.05.2000): 14649–58. http://dx.doi.org/10.1074/jbc.275.19.14649.

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Bhattacharyya, Saumitri, i Robert S. Lahue. "Saccharomyces cerevisiae Srs2 DNA Helicase Selectively Blocks Expansions of Trinucleotide Repeats". Molecular and Cellular Biology 24, nr 17 (1.09.2004): 7324–30. http://dx.doi.org/10.1128/mcb.24.17.7324-7330.2004.

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ABSTRACT Trinucleotide repeats (TNRs) undergo frequent mutations in families afflicted with certain neurodegenerative disorders and in model organisms. TNR instability is modulated both by the repeat tract itself and by cellular proteins. Here we identified the Saccharomyces cerevisiae DNA helicase Srs2 as a potent and selective inhibitor of expansions. srs2 mutants had up to 40-fold increased expansion rates of CTG, CAG, and CGG repeats. The expansion phenotype was specific, as mutation rates at dinucleotide repeats, at unique sequences, or for TNR contractions in srs2 mutants were not altered. Srs2 is known to suppress inappropriate genetic recombination; however, the TNR expansion phenotype of srs2 mutants was largely independent of RAD51 and RAD52. Instead, Srs2 mainly functioned with DNA polymerase delta to block expansions. The helicase activity of Srs2 was important, because a point mutant lacking ATPase function was defective in blocking expansions. Purified Srs2 was substantially better than bacterial UvrD helicase at in vitro unwinding of a DNA substrate that mimicked a TNR hairpin. Disruption of the related helicase gene SGS1 did not lead to excess expansions, nor did wild-type SGS1 suppress the expansion phenotype of an srs2 strain. We conclude that Srs2 selectively blocks triplet repeat expansions through its helicase activity and primarily in conjunction with polymerase delta.

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46

Akashi, Motohiro, i Masaharu Takemura. "Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus". Viruses 11, nr 3 (17.03.2019): 267. http://dx.doi.org/10.3390/v11030267.

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The detailed mechanisms of replication initiation, termination and segregation events were not yet known in Acanthamoeba polyphaga mimivirus (APMV). Here, we show detailed bioinformatics-based analyses of chromosomal replication in APMV from initiation to termination mediated by proteins bound to specific DNA sequences. Using GC/AT skew and coding sequence skew analysis, we estimated that the replication origin is located at 382 kb in the APMV genome. We performed homology-modeling analysis of the gamma domain of APMV-FtsK (DNA translocase coordinating chromosome segregation) related to FtsK-orienting polar sequences (KOPS) binding, suggesting that there was an insertion in the gamma domain which maintains the structure of the DNA binding motif. Furthermore, UvrD/Rep-like helicase in APMV was homologous to Bacillus subtilis AddA, while the chi-like quartet sequence 5′-CCGC-3′ was frequently found in the estimated ori region, suggesting that chromosomal replication of APMV is initiated via chi-like sequence recognition by UvrD/Rep-like helicase. Therefore, the replication initiation, termination and segregation of APMV are presumably mediated by DNA repair machineries derived from gram-positive bacteria. Moreover, the other frequently observed quartet sequence 5′-CGGC-3′ in the ori region was homologous to the mitochondrial signal sequence of replication initiation, while the comparison of quartet sequence composition in APMV/Rickettsia-genome showed significantly similar values, suggesting that APMV also conserves the mitochondrial replication system acquired from an ancestral genome of mitochondria during eukaryogenesis.

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47

Feng, W. Y., i J. B. Hays. "DNA structures generated during recombination initiated by mismatch repair of UV-irradiated nonreplicating phage DNA in Escherichia coli: requirements for helicase, exonucleases, and RecF and RecBCD functions." Genetics 140, nr 4 (1.08.1995): 1175–86. http://dx.doi.org/10.1093/genetics/140.4.1175.

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Abstract During infection of homoimmune Escherichia coli lysogens ("repressed infections"), undamaged nonreplicating lambda phage DNA circles undergo very little recombination. Prior UV irradiation of phages dramatically elevates recombinant frequencies, even in bacteria deficient in UvrABC-mediated excision repair. We previously reported that 80-90% of this UvrABC-independent recombination required MutHLS function and unmethylated d(GATC) sites, two hallmarks of methyl-directed mismatch repair. We now find that deficiencies in other mismatch-repair activities--UvrD helicase, exonuclease I, exonuclease VII, RecJ exonuclease--drastically reduce recombination. These effects of exonuclease deficiencies on recombination are greater than previously observed effects on mispair-provoked excision in vitro. This suggests that the exonucleases also play other roles in generation and processing of recombinagenic DNA structures. Even though dsDNA breaks are thought to be highly recombinagenic, 60% of intracellular UV-irradiated phage DNA extracted from bacteria in which recombination is low--UvrD-, ExoI-, ExoVII-, or Rec(J-)--displays (near-)blunt-ended dsDNA ends (RecBCD-sensitive when deproteinized). In contrast, only bacteria showing high recombination (Mut+ UvrD+ Exo+) generate single-stranded regions in nonreplicating UV-irradiated DNA. Both recF and recB recC mutations strikingly reduce recombination (almost as much as a recF recB recC triple mutation), suggesting critical requirements for both RecF and RecBCD activity. The mismatch repair system may thus process UV-irradiated DNA so as to initiate more than one recombination pathway.

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48

Mendonca, V. M., K. Kaiser-Rogers i S. W. Matson. "Double helicase II (uvrD)-helicase IV (helD) deletion mutants are defective in the recombination pathways of Escherichia coli." Journal of Bacteriology 175, nr 15 (1993): 4641–51. http://dx.doi.org/10.1128/jb.175.15.4641-4651.1993.

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Ansari, Abulaish, Mohammed Tarique i Renu Tuteja. "Genetically Engineered Synthetic Miniaturized Versions of Plasmodium falciparum UvrD Helicase Are Catalytically Active". PLoS ONE 9, nr 3 (7.03.2014): e90951. http://dx.doi.org/10.1371/journal.pone.0090951.

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Martínez, Eriel, Evelyne Paly i François-Xavier Barre. "CTXφ Replication Depends on the Histone-Like HU Protein and the UvrD Helicase". PLOS Genetics 11, nr 5 (20.05.2015): e1005256. http://dx.doi.org/10.1371/journal.pgen.1005256.

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