Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels

Crézé, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, J.-M.; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

doi:10.1074/jbc.m112.346361

Cited by 21 publications

(31 citation statements)

References 66 publications

(70 reference statements)

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“…Numerous client proteins of the PCNA interact with the replication clamp via a PIP box [24,35,45], a structure which is shown to be well conserved in the C-terminal end of the Pab0431 sequence (Figure 4B). …”

Section: Resultsmentioning

confidence: 99%

An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs

et al. 2013

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In Archaea, the proteins involved in the genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of eukaryotes. Characterizations of components of the eukaryotic-type replication machinery complex provided many interesting insights into DNA replication in both domains. In contrast, DNA repair processes of hyperthermophilic archaea are less well understood and very little is known about the intertwining between DNA synthesis, repair and recombination pathways. The development of genetic system in hyperthermophilic archaea is still at a modest stage hampering the use of complementary approaches of reverse genetics and biochemistry to elucidate the function of new candidate DNA repair gene. To gain insights into genomic maintenance processes in hyperthermophilic archaea, a protein-interaction network centred on informational processes of Pyrococcus abyssi was generated by affinity purification coupled with mass spectrometry. The network consists of 132 interactions linking 87 proteins. These interactions give insights into the connections of DNA replication with recombination and repair, leading to the discovery of new archaeal components and of associations between eucaryotic homologs. Although this approach did not allow us to clearly delineate new DNA pathways, it provided numerous clues towards the function of new molecular complexes with the potential to better understand genomic maintenance processes in hyperthermophilic archaea. Among others, we found new potential partners of the replication clamp and demonstrated that the single strand DNA binding protein, Replication Protein A, enhances the transcription rate, in vitro, of RNA polymerase. This interaction map provides a valuable tool to explore new aspects of genome integrity in Archaea and also potentially in Eucaryotes.

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Section: Resultsmentioning

confidence: 99%

An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs

et al. 2013

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“…This procedure avoids loss of ligand from the DNR hemes upon addition. Fluorescence anisotropy was measured following a procedure as described (21) in a Cary Eclipse fluorometer equipped with a manual polarization device, with an excitation beam centered at 590 nm and scanning the Texas red emission spectrum. Anisotropy data were fitted to a hyperbolic binding curve (Langmuir equation) to determine the binding constant (K d ).…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the Heme-binding Bacterial Gas-sensing Dissimilative Nitrate Respiration Regulator (DNR) and Activation Barriers for Ligand Binding and Escape

Lobato

Bouzhir-Sima

Yamashita

et al. 2014

Journal of Biological Chemistry

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Background: DNR is a recently discovered transcriptional regulator homologous to the CO sensor CooA. Results: NO binding to heme selectively allows activation; ligand dynamics energetics implies common mechanism for 6-coordinate heme proteins. Conclusion: DNR is an NO sensor acting as ligand trap. Significance: Demonstration of NO-sensing function helps unravel signaling in the pathogen P. aeruginosa and describes common mechanism in emerging class of 6-coordinate heme proteins.

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“…Therefore it appears that the presence of three identical surfaces on PCNA may restrict and direct the access of target proteins. In this respect, Creze et al [46] recently described the functional and structural characterization of the complex formed between PCNA and NucS, a structure-specific DNA endonuclease. They demonstrated that only one molecule of the NucS homodimer binds to the outside surface of the PCNA homotrimer via the PIP (PCNA-interacting protein)/IDCL (interdomain connecting loop) interface, leading to the conclusion that this particular stoichiometry could be due RNA primer removal in Archaea 279 to long-range conformational changes on PCNA that in turn could regulate the recruitment of additional partners [46].…”

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In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways

Henneke

2012

Biochemical Journal

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Using model DNA substrates and purified recombinant proteins from Pyrococcus abyssi, I have reconstituted the enzymatic reactions involved in RNA primer elimination in vitro. In my dual-labelled system, polymerase D performed efficient strand displacement DNA synthesis, generating 5'-RNA flaps which were subsequently released by Fen1, before ligation by Lig1. In this pathway, the initial cleavage event by RNase HII facilitated RNA primer removal of Okazaki fragments. In addition, I have shown that polymerase B was able to displace downstream DNA strands with a single ribonucleotide at the 5'-end, a product resulting from a single cut in the RNA initiator by RNase HII. After RNA elimination, the combined activities of strand displacement DNA synthesis by polymerase B and flap cleavage by Fen1 provided a nicked substrate for ligation by Lig1. The unique specificities of Okazaki fragment maturation enzymes and replicative DNA polymerases strongly support the existence of two pathways in the resolution of RNA fragments.

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Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels

Cited by 21 publications

References 66 publications

An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs

An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs

Dynamics of the Heme-binding Bacterial Gas-sensing Dissimilative Nitrate Respiration Regulator (DNR) and Activation Barriers for Ligand Binding and Escape

In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways

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