Synergic and Opposing Activities of Thermophilic RecQ-like Helicase and Topoisomerase 3 Proteins in Holliday Junction Processing and Replication Fork Stabilization

Valenti, Anna; Felice, Maurilio De; Perugino, Giuseppe; Bizard, Anna H.; Nadal, Marc; Rossi, Mosè; Ciaramella, Maria

doi:10.1074/jbc.m112.366377

Cited by 13 publications

(13 citation statements)

References 47 publications

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“…For the direct homolog Hel112 from S. solfataricus, it was previously shown in vitro that Cy-labeled HJ substrates were mostly unwound to Y-shaped intermediates but, unlike our findings, not to ssDNA (44). When we used Cy3-labeled substrates instead of radioactively labeled DNA, we obtained similar results; in addition, we could not completely boil these substrates to ssDNA (data not shown).…”

Section: Figsupporting

confidence: 72%

“…RecQ helicases are referred to as conserved guardians of genomic integrity (69) and are reported to be involved in multiple pathways for the maintenance of genomic stability, including HR (69-73). As was shown for its previously studied ortholog in S. solfataricus (Sso0112 or Hel112) (44,45), we demonstrated that Saci_1500 shows typical RecQ-like DNA binding and unwinding activities. It catalyzes the processing of HR intermediates, such as Holliday junctions and Y-shaped DNA, and unwinds dsDNA with an overhang in a 3=-to-5=-dependent fashion.…”

Section: Figsupporting

confidence: 49%

“…When we used Cy3-labeled substrates instead of radioactively labeled DNA, we obtained similar results; in addition, we could not completely boil these substrates to ssDNA (data not shown). We therefore assume that the Cy labels cause crosslinking between DNA strands of the HJ substrate, making it impossible to show the full unwinding of the HJ substrates in the mentioned study (44), as was shown by us in Fig. 5F.…”

Section: Figmentioning

confidence: 98%

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DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

Wolferen

Albers

2015

J Bacteriol

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The ups operon of Sulfolobus species is highly induced upon UV stress. Previous studies showed that the pili encoded by this operon are involved in cellular aggregation, which is essential for subsequent DNA exchange between cells, resulting in homologous recombination. The presence of this pilus system increases the fitness of Sulfolobus cells under UV light-induced stress conditions, as the transfer of DNA takes place in order to repair UV-induced DNA lesions via homologous recombination. Four conserved genes (saci_1497 to saci_1500) which encode proteins with putative DNA processing functions are present downstream of the ups operon. In this study, we show that after UV treatment the cellular aggregation of strains with saci_1497, saci_1498, and saci_1500 deletions is similar to that of wild-type strains; their survival rates, however, were reduced and similar to or lower than those of the pilus deletion strains, which could not aggregate anymore. DNA recombination assays indicated that saci_1498, encoding a ParB-like protein, plays an important role in DNA transfer. Moreover, biochemical analysis showed that the endonuclease III encoded by saci_1497 nicks UV-damaged DNA. In addition, RecQ-like helicase Saci_1500 is able to unwind homologous recombination intermediates, such as Holliday junctions. Interestingly, a saci_1500 deletion mutant was more sensitive to UV light but not to the replication-stalling agents hydroxyurea and methyl methanesulfonate, suggesting that Saci_1500 functions specifically in the UV damage pathway. Together these results suggest a role of Saci_1497 to Saci_1500 in the repair or transfer of DNA that takes place after UV-induced damage to the genomic DNA of Sulfolobus acidocaldarius. IMPORTANCESulfolobales species increase their fitness after UV stress by a UV-inducible pilus system that enables high rates of DNA exchange between cells. Downstream of the pilus operon, three genes that seem to play a role in the repair or transfer of the DNA between Sulfolobus cells were identified, and their possible functions are discussed. Next to the previously described role of UV-inducible pili in the exchange of DNA, we have thereby increased our knowledge of DNA transfer at the level of DNA processing. This paper therefore contributes to the overall understanding of the DNA exchange mechanism among Sulfolobales cells. In all domains of life, DNA repair is crucial for maintenance of genome integrity upon exposure to intra-or extracellular DNAdamaging threats (1). Unlike DNA repair in bacteria, archaeal DNA repair and its regulation are still far from well understood (1, 2). Homology searches revealed that the proteins in archaeal DNA repair pathways show similarities to both bacterial and eukaryotic proteins. In addition, DNA repair proteins with unique archaeal features exist (3).Previously, it was speculated that archaea might have SOS-like responses similar to those in certain bacteria (4); however, microarray studies revealed that neither Haloarchaea (5, 6) nor Sulfolobus species (7...

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Section: Figsupporting

confidence: 72%

Section: Figsupporting

confidence: 49%

Section: Figmentioning

confidence: 98%

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DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

Wolferen

Albers

2015

J Bacteriol

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“…Combined unwinding/branch migration and annealing activities are shared by eukaryotic and archaeal helicases (37)(38)(39)(40)(41). The discovery that PcalRG holds such activities enabling the HJ resolution by a true ATP-dependent mechanism, at least in vitro, might support previous results suggesting the involvement of RG in recombination and/or repair (7)(8)(9)(10).…”

Section: Discussionsupporting

confidence: 77%

“…Substrates used in DNA binding and unwinding assays were prepared by annealing oligonucleotides in appropriate combinations: M-HJ, A1-A2-A3-A4; IM-HJ, A1-A2-A5-A6; Y-shaped Fork, A1-A2; 40 bp-double strand (ds), A2-A7; Flap, A1-21lead (30); dsFork, A1ϩA2 ϩ 30Lag and 21Lead (39). The single strand (ss) 70 bp Lead and Lag oligonucleotides (39) were used for annealing assays.…”

Section: Methodsmentioning

confidence: 99%

The Reverse Gyrase from Pyrobaculum calidifontis, a Novel Extremely Thermophilic DNA Topoisomerase Endowed with DNA Unwinding and Annealing Activities

Jamroze

Perugino

Valenti

et al. 2014

Journal of Biological Chemistry

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Background:The thermophilic DNA topoisomerase reverse gyrase induces DNA-positive supercoiling. Results: The novel reverse gyrase, PcalRG, is presented. Conclusion: PcalRG is the most efficient and robust reverse gyrase known, and the first inducing ATP-dependent unwinding of Holliday junctions and annealing of single-stranded oligonucleotides. Significance: PcalRG shares structural and functional features with evolutionary conserved helicase-topoisomerase complexes involved in genome stability.

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Type IA DNA Topoisomerases: A Universal Core and Multiple Activities

Garnier

Débat

Nadal

2017

Methods in Molecular Biology

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All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.

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Synergic and Opposing Activities of Thermophilic RecQ-like Helicase and Topoisomerase 3 Proteins in Holliday Junction Processing and Replication Fork Stabilization

Cited by 13 publications

References 47 publications

DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

The Reverse Gyrase from Pyrobaculum calidifontis, a Novel Extremely Thermophilic DNA Topoisomerase Endowed with DNA Unwinding and Annealing Activities

Type IA DNA Topoisomerases: A Universal Core and Multiple Activities

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