1
|
Dagva O, Thibessard A, Lorenzi JN, Labat V, Piotrowski E, Rouhier N, Myllykallio H, Leblond P, Bertrand C. Correction of non-random mutational biases along a linear bacterial chromosome by the mismatch repair endonuclease NucS. Nucleic Acids Res 2024; 52:5033-5047. [PMID: 38444149 PMCID: PMC11109965 DOI: 10.1093/nar/gkae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/07/2024] Open
Abstract
The linear chromosome of Streptomyces exhibits a highly compartmentalized structure with a conserved central region flanked by variable arms. As double strand break (DSB) repair mechanisms play a crucial role in shaping the genome plasticity of Streptomyces, we investigated the role of EndoMS/NucS, a recently characterized endonuclease involved in a non-canonical mismatch repair (MMR) mechanism in archaea and actinobacteria, that singularly corrects mismatches by creating a DSB. We showed that Streptomyces mutants lacking NucS display a marked colonial phenotype and a drastic increase in spontaneous mutation rate. In vitro biochemical assays revealed that NucS cooperates with the replication clamp to efficiently cleave G/T, G/G and T/T mismatched DNA by producing DSBs. These findings are consistent with the transition-shifted mutational spectrum observed in the mutant strains and reveal that NucS-dependent MMR specific task is to eliminate G/T mismatches generated by the DNA polymerase during replication. Interestingly, our data unveil a crescent-shaped distribution of the transition frequency from the replication origin towards the chromosomal ends, shedding light on a possible link between NucS-mediated DSBs and Streptomyces genome evolution.
Collapse
Affiliation(s)
- Oyut Dagva
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | | | | | - Victor Labat
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Emilie Piotrowski
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Nicolas Rouhier
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Hannu Myllykallio
- Ecole Polytechnique, INSERM U696-CNRS UMR 7645 LOB, 91128 Palaiseau, France
| | - Pierre Leblond
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| | - Claire Bertrand
- Université de Lorraine, INRAE, UMR 1128 DynAMic, 54000 Nancy, France
| |
Collapse
|
2
|
Wörtz J, Smith V, Fallmann J, König S, Thuraisingam T, Walther P, Urlaub H, Stadler PF, Allers T, Hille F, Marchfelder A. Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair. Front Microbiol 2022; 13:822304. [PMID: 35495653 PMCID: PMC9051519 DOI: 10.3389/fmicb.2022.822304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways, either by regulating their expression or via direct protein-protein contact and enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but an additional role in cellular DNA repair pathways has been proposed previously. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to act upon DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to reduced survival rates following stress induction. In addition, our results indicate that Cas1 is directly involved in DNA repair as the enzymatically active site of the protein is crucial for growth under oxidative conditions. Based on biochemical assays, we propose a mechanism by which Cas1 plays a similar function to DNA repair protein Fen1 by cleaving branched intermediate structures. The present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display equivalent roles during archaeal DNA damage repair.
Collapse
Affiliation(s)
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jörg Fallmann
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Sabine König
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Peter F. Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
- Santa Fe Institute, Santa Fe, NM, United States
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Anita Marchfelder
- Biology II, Ulm University, Ulm, Germany
- *Correspondence: Anita Marchfelder,
| |
Collapse
|
3
|
Control of Genome Stability by EndoMS/NucS-Mediated Non-Canonical Mismatch Repair. Cells 2021; 10:cells10061314. [PMID: 34070467 PMCID: PMC8228993 DOI: 10.3390/cells10061314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
The DNA repair endonuclease EndoMS/NucS is highly conserved in Archaea and Actinobacteria. This enzyme is able to recognize and cleave dsDNA carrying a mismatched base pair, and its activity is enhanced by the interaction with the sliding clamp of the replisome. Today, EndoMS/NucS has been established as the key protein of a non-canonical mismatch repair (MMR) pathway, acting specifically in the repair of transitions and being essential for maintaining genome stability. Despite having some particularities, such as its lower activity on transversions and the inability to correct indels, EndoMS/NucS meets the main hallmarks of a MMR. Its absence leads to a hypermutator phenotype, a transition-biased mutational spectrum and an increase in homeologous recombination. Interestingly, polymorphic EndoMS/NucS variants with a possible effect in mutation rate have been detected in clinical isolates of the relevant actinobacterial pathogen Mycobacterium tuberculosis. Considering that MMR defects are often associated with the emergence of resistant bacteria, the existence of EndoMS/NucS-defective mutators could have an important role in the acquisition of antibiotic resistance in M. tuberculosis. Therefore, a further understanding of the EndoMS/NucS-mediated non-canonical MMR pathway may reveal new strategies to predict and fight drug resistance. This review is focused on the recent progress in NucS, with special emphasis on its effect on genome stability and evolvability in Actinobacteria.
Collapse
|
4
|
Pérez-Arnaiz P, Dattani A, Smith V, Allers T. Haloferax volcanii-a model archaeon for studying DNA replication and repair. Open Biol 2020; 10:200293. [PMID: 33259746 PMCID: PMC7776575 DOI: 10.1098/rsob.200293] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
The tree of life shows the relationship between all organisms based on their common ancestry. Until 1977, it comprised two major branches: prokaryotes and eukaryotes. Work by Carl Woese and other microbiologists led to the recategorization of prokaryotes and the proposal of three primary domains: Eukarya, Bacteria and Archaea. Microbiological, genetic and biochemical techniques were then needed to study the third domain of life. Haloferax volcanii, a halophilic species belonging to the phylum Euryarchaeota, has provided many useful tools to study Archaea, including easy culturing methods, genetic manipulation and phenotypic screening. This review will focus on DNA replication and DNA repair pathways in H. volcanii, how this work has advanced our knowledge of archaeal cellular biology, and how it may deepen our understanding of bacterial and eukaryotic processes.
Collapse
Affiliation(s)
| | | | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| |
Collapse
|
5
|
Hogrel G, Lu Y, Alexandre N, Bossé A, Dulermo R, Ishino S, Ishino Y, Flament D. Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea. Biomolecules 2020; 10:E1045. [PMID: 32674430 PMCID: PMC7407445 DOI: 10.3390/biom10071045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/03/2020] [Accepted: 07/09/2020] [Indexed: 01/20/2023] Open
Abstract
Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.
Collapse
Affiliation(s)
- Gaëlle Hogrel
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Yang Lu
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Nicolas Alexandre
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Audrey Bossé
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Rémi Dulermo
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka 819-0395, Japan; (S.I.); (Y.I.)
| | - Didier Flament
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS, Univ Brest, 29280 Plouzané, France; (G.H.); (Y.L.); (N.A.); (A.B.); (R.D.)
- LIA1211 MICROBSEA, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Xiamen-Plouzané, France
| |
Collapse
|
6
|
Ishino S, Skouloubris S, Kudo H, l'Hermitte-Stead C, Es-Sadik A, Lambry JC, Ishino Y, Myllykallio H. Activation of the mismatch-specific endonuclease EndoMS/NucS by the replication clamp is required for high fidelity DNA replication. Nucleic Acids Res 2019; 46:6206-6217. [PMID: 29846672 PMCID: PMC6159515 DOI: 10.1093/nar/gky460] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/14/2018] [Indexed: 12/02/2022] Open
Abstract
The mismatch repair (MMR) system, exemplified by the MutS/MutL proteins, is widespread in Bacteria and Eukarya. However, molecular mechanisms how numerous archaea and bacteria lacking the mutS/mutL genes maintain high replication fidelity and genome stability have remained elusive. EndoMS is a recently discovered hyperthermophilic mismatch-specific endonuclease encoded by nucS in Thermococcales. We deleted the nucS from the actinobacterium Corynebacterium glutamicum and demonstrated a drastic increase of spontaneous transition mutations in the nucS deletion strain. The observed spectra of these mutations were consistent with the enzymatic properties of EndoMS in vitro. The robust mismatch-specific endonuclease activity was detected with the purified C. glutamicum EndoMS protein but only in the presence of the β-clamp (DnaN). Our biochemical and genetic data suggest that the frequently occurring G/T mismatch is efficiently repaired by the bacterial EndoMS-β−clamp complex formed via a carboxy-terminal sequence motif of EndoMS proteins. Our study thus has great implications for understanding how the activity of the novel MMR system is coordinated with the replisome and provides new mechanistic insight into genetic diversity and mutational patterns in industrially and clinically (e.g. Mycobacteria) important archaeal and bacterial phyla previously thought to be devoid of the MMR system.
Collapse
Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Stéphane Skouloubris
- Department of Biology, Univ. Paris-Sud, Univ. Paris-Saclay, Orsay F-91405, France.,Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Hanae Kudo
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | | | - Asmae Es-Sadik
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Jean-Christophe Lambry
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Hannu Myllykallio
- Laboratory of Optics and Biosciences, CNRS-INSERM-Ecole Polytechnique, 91128 Palaiseau France
| |
Collapse
|
7
|
Hogrel G, Lu Y, Laurent S, Henry E, Etienne C, Phung DK, Dulermo R, Bossé A, Pluchon PF, Clouet-d'Orval B, Flament D. Physical and functional interplay between PCNA DNA clamp and Mre11-Rad50 complex from the archaeon Pyrococcus furiosus. Nucleic Acids Res 2019; 46:5651-5663. [PMID: 29741662 PMCID: PMC6009593 DOI: 10.1093/nar/gky322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/18/2018] [Indexed: 01/10/2023] Open
Abstract
Several archaeal species prevalent in extreme environments are particularly exposed to factors likely to cause DNA damages. These include hyperthermophilic archaea (HA), living at temperatures >70°C, which arguably have efficient strategies and robust genome guardians to repair DNA damage threatening their genome integrity. In contrast to Eukarya and other archaea, homologous recombination appears to be a vital pathway in HA, and the Mre11–Rad50 complex exerts a broad influence on the initiation of this DNA damage response process. In a previous study, we identified a physical association between the Proliferating Cell Nuclear Antigen (PCNA) and the Mre11–Rad50 (MR) complex. Here, by performing co-immunoprecipitation and SPR analyses, we identified a short motif in the C- terminal portion of Pyrococcus furiosus Mre11 involved in the interaction with PCNA. Through this work, we revealed a PCNA-interaction motif corresponding to a variation on the PIP motif theme which is conserved among Mre11 sequences of Thermococcale species. Additionally, we demonstrated functional interplay in vitro between P. furiosus PCNA and MR enzymatic functions in the DNA end resection process. At physiological ionic strength, PCNA stimulates MR nuclease activities for DNA end resection and promotes an endonucleolytic incision proximal to the 5′ strand of double strand DNA break.
Collapse
Affiliation(s)
- Gaëlle Hogrel
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Yang Lu
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Etienne Henry
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Clarisse Etienne
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Duy Khanh Phung
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Rémi Dulermo
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Pierre-François Pluchon
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Béatrice Clouet-d'Orval
- Université de Toulouse; UPS, 118 Route de Narbonne, F-31062 Toulouse, France; CNRS; LMGM; F-31062 Toulouse, France
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France.,CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| |
Collapse
|
8
|
Lemor M, Kong Z, Henry E, Brizard R, Laurent S, Bossé A, Henneke G. Differential Activities of DNA Polymerases in Processing Ribonucleotides during DNA Synthesis in Archaea. J Mol Biol 2018; 430:4908-4924. [PMID: 30342933 DOI: 10.1016/j.jmb.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/09/2018] [Accepted: 10/12/2018] [Indexed: 12/11/2022]
Abstract
Consistent with the fact that ribonucleotides (rNTPs) are in excess over deoxyribonucleotides (dNTPs) in vivo, recent findings indicate that replicative DNA polymerases (DNA Pols) are able to insert ribonucleotides (rNMPs) during DNA synthesis, raising crucial questions about the fidelity of DNA replication in both Bacteria and Eukarya. Here, we report that the level of rNTPs is 20-fold higher than that of dNTPs in Pyrococcus abyssi cells. Using dNTP and rNTP concentrations present in vivo, we recorded rNMP incorporation in a template-specific manner during in vitro synthesis, with the family-D DNA Pol (PolD) having the highest propensity compared with the family-B DNA Pol and the p41/p46 complex. We also showed that ribonucleotides accumulate at a relatively high frequency in the genome of wild-type Thermococcales cells, and this frequency significantly increases upon deletion of RNase HII, the major enzyme responsible for the removal of RNA from DNA. Because ribonucleotides remain in genomic DNA, we then analyzed the effects on polymerization activities by the three DNA Pols. Depending on the identity of the base and the sequence context, all three DNA Pols bypass rNMP-containing DNA templates with variable efficiency and nucleotide (mis)incorporation ability. Unexpectedly, we found that PolD correctly base-paired a single ribonucleotide opposite rNMP-containing DNA templates. An evolutionary scenario is discussed concerning rNMP incorporation into DNA and genome stability.
Collapse
Affiliation(s)
- Mélanie Lemor
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Etienne Henry
- CNRS, Ifremer, Univ Brest, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280, Plouzané, France
| | - Raphaël Brizard
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Sébastien Laurent
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Audrey Bossé
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France
| | - Ghislaine Henneke
- Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, F-29280 Plouzané, France.
| |
Collapse
|
9
|
Wilson RHC, Biasutto AJ, Wang L, Fischer R, Baple EL, Crosby AH, Mancini EJ, Green CM. PCNA dependent cellular activities tolerate dramatic perturbations in PCNA client interactions. DNA Repair (Amst) 2016; 50:22-35. [PMID: 28073635 PMCID: PMC5264654 DOI: 10.1016/j.dnarep.2016.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 01/04/2023]
Abstract
We assess the cellular effects of the mutation that causes PARD (PCNAS228I). Cells from affected individuals are sensitive to T2AA and T3. PCNAS228I impairs interactions between PCNA and Cdt1, DNMT1, PolD3 and PolD4. The PIP-box of p21 retains binding to PCNAS228I. PCNA-dependent degradation and the cell cycle are only subtly altered by PCNAS228I.
Proliferating cell nuclear antigen (PCNA) is an essential cofactor for DNA replication and repair, recruiting multiple proteins to their sites of action. We examined the effects of the PCNAS228I mutation that causes PCNA-associated DNA repair disorder (PARD). Cells from individuals affected by PARD are sensitive to the PCNA inhibitors T3 and T2AA, showing that the S228I mutation has consequences for undamaged cells. Analysis of the binding between PCNA and PCNA-interacting proteins (PIPs) shows that the S228I change dramatically impairs the majority of these interactions, including that of Cdt1, DNMT1, PolD3p66 and PolD4p12. In contrast p21 largely retains the ability to bind PCNAS228I. This property is conferred by the p21 PIP box sequence itself, which is both necessary and sufficient for PCNAS228I binding. Ubiquitination of PCNA is unaffected by the S228I change, which indirectly alters the structure of the inter-domain connecting loop. Despite the dramatic in vitro effects of the PARD mutation on PIP-degron binding, there are only minor alterations to the stability of p21 and Cdt1 in cells from affected individuals. Overall our data suggests that reduced affinity of PCNAS228I for specific clients causes subtle cellular defects in undamaged cells which likely contribute to the etiology of PARD.
Collapse
Affiliation(s)
- Rosemary H C Wilson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Antonio J Biasutto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Lihao Wang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Emma L Baple
- University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Erika J Mancini
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RH, UK
| | - Catherine M Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
| |
Collapse
|
10
|
Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease. Structure 2016; 24:1960-1971. [PMID: 27773688 DOI: 10.1016/j.str.2016.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/08/2016] [Accepted: 09/28/2016] [Indexed: 01/17/2023]
Abstract
Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.
Collapse
|
11
|
PCNA-binding proteins in the archaea: novel functionality beyond the conserved core. Curr Genet 2016; 62:527-32. [PMID: 26886233 PMCID: PMC4929162 DOI: 10.1007/s00294-016-0577-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 11/30/2022]
Abstract
Sliding clamps play an essential role in coordinating protein activity in DNA metabolism in all three domains of life. In eukaryotes and archaea, the sliding clamp is PCNA (proliferating cell nuclear antigen). Across the diversity of the archaea PCNA interacts with a highly conserved set of proteins with key roles in DNA replication and repair, including DNA polymerases B and D, replication factor C, the Fen1 nuclease and RNAseH2, but this core set of factors is likely to represent a fraction of the PCNA interactome only. Here, I review three recently characterised non-core archaeal PCNA-binding proteins NusS, NreA/NreB and TIP, highlighting what is known of their interactions with PCNA and their functions in vivo and in vitro. Gaining a detailed understanding of the non-core PCNA interactome will provide significant insights into key aspects of chromosome biology in divergent archaeal lineages.
Collapse
|
12
|
Giroux X, MacNeill SA. A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner. Mol Microbiol 2015; 99:1-14. [PMID: 26337406 DOI: 10.1111/mmi.13210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2015] [Indexed: 01/11/2023]
Abstract
The sliding clamp proliferating cell nuclear antigen (PCNA) plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and that has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis. Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.
Collapse
Affiliation(s)
- Xavier Giroux
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| |
Collapse
|
13
|
Abstract
Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea.
Collapse
|
14
|
Cooper SE, Hodimont E, Green CM. A fluorescent bimolecular complementation screen reveals MAF1, RNF7 and SETD3 as PCNA-associated proteins in human cells. Cell Cycle 2015; 14:2509-19. [PMID: 26030842 PMCID: PMC4613188 DOI: 10.1080/15384101.2015.1053667] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The proliferating cell nuclear antigen (PCNA) is a conserved component of DNA replication factories, and interactions with PCNA mediate the recruitment of many essential DNA replication enzymes to these sites of DNA synthesis. A complete description of the structure and composition of these factories remains elusive, and a better knowledge of them will improve our understanding of how the maintenance of genome and epigenetic stability is achieved. To fully characterize the set of proteins that interact with PCNA we developed a bimolecular fluorescence complementation (BiFC) screen for PCNA-interactors in human cells. This 2-hybrid type screen for interactors from a human cDNA library is rapid and efficient. The fluorescent read-out for protein interaction enables facile selection of interacting clones, and we combined this with next generation sequencing to identify the cDNAs encoding the interacting proteins. This method was able to reproducibly identify previously characterized PCNA-interactors but importantly also identified RNF7, Maf1 and SetD3 as PCNA-interacting proteins. We validated these interactions by co-immunoprecipitation from human cell extracts and by interaction analyses using recombinant proteins. These results show that the BiFC screen is a valuable method for the identification of protein-protein interactions in living mammalian cells. This approach has potentially wide application as it is high throughput and readily automated. We suggest that, given this interaction with PCNA, Maf1, RNF7, and SetD3 are potentially involved in DNA replication, DNA repair, or associated processes.
Collapse
Affiliation(s)
- Simon E Cooper
- a Department of Zoology ; University of Cambridge ; Cambridge , UK
| | | | | |
Collapse
|
15
|
Gerits N, Johannessen M, Tümmler C, Walquist M, Kostenko S, Snapkov I, van Loon B, Ferrari E, Hübscher U, Moens U. Agnoprotein of polyomavirus BK interacts with proliferating cell nuclear antigen and inhibits DNA replication. Virol J 2015; 12:7. [PMID: 25638270 PMCID: PMC4318453 DOI: 10.1186/s12985-014-0220-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
Background The human polyomavirus BK expresses a 66 amino-acid peptide referred to as agnoprotein. Though mutants lacking agnoprotein are severely reduced in producing infectious virions, the exact function of this peptide remains incompletely understood. To elucidate the function of agnoprotein, we searched for novel cellular interaction partners. Methods Yeast-two hybrid assay was performed with agnoprotein as bait against human kidney and thymus libraries. The interaction between agnoprotein and putative partners was further examined by GST pull down, co-immunoprecipitation, and fluorescence resonance energy transfer studies. Biochemical and biological studies were performed to examine the functional implication of the interaction of agnoprotein with cellular target proteins. Results Proliferating cell nuclear antigen (PCNA), which acts as a processivity factor for DNA polymerase δ, was identified as an interaction partner. The interaction between agnoprotein and PCNA is direct and occurs also in human cells. Agnoprotein exerts an inhibitory effect on PCNA-dependent DNA synthesis in vitro and reduces cell proliferation when ectopically expressed. Overexpression of PCNA restores agnoprotein-mediated inhibition of cell proliferation. Conclusion Our data suggest that PCNA is a genuine interaction partner of agnoprotein and the inhibitory effect on PCNA-dependent DNA synthesis by the agnoprotein may play a role in switching off (viral) DNA replication late in the viral replication cycle when assembly of replicated genomes and synthesized viral capsid proteins occurs. Electronic supplementary material The online version of this article (doi:10.1186/s12985-014-0220-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ugo Moens
- UiT - The Arctic University of Norway, Faculty of Health Sciences, Department of Medical Biology, Molecular Inflammation Research Group, Tromsø NO-9037, Norway.
| |
Collapse
|
16
|
Molecular Genetic Methods to Study DNA Replication Protein Function in Haloferax volcanii, A Model Archaeal Organism. Methods Mol Biol 2015; 1300:187-218. [PMID: 25916714 DOI: 10.1007/978-1-4939-2596-4_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Successful high-fidelity chromosomal DNA replication is fundamental to all forms of cellular life and requires the complex interplay of a variety of essential and nonessential protein factors in a spatially and temporally coordinated manner. Much of what is known about the enzymes and mechanisms of chromosome replication has come from analysis of simple microbial model systems, such as yeast and archaea. Archaea possess a highly simplified eukaryotic-like replication apparatus, making them an excellent model for gaining novel insights into conserved aspects of protein function at the heart of the replisome. Amongst the thermophilic archaea, a number of species have proved useful for biochemical analysis of protein function, but few of these organisms are suited to genetic analysis. One archaeal organism that is genetically tractable is the mesophilic euryarchaeon Haloferax volcanii, a halophile that grows aerobically in high salt medium at an optimum temperature of 40-45 °C and with a doubling time of 2-3 h. The Hfx. volcanii genome has been sequenced and a range of methods have been developed to allow reverse genetic analysis of protein function in vivo, including techniques for gene replacement and gene deletion, transcriptional regulation, point mutation and gene tagging. Here we briefly summarize current knowledge of the chromosomal DNA replication machinery in the haloarchaea before describing in detail the molecular methods available to probe protein structure and function within the Hfx. volcanii replication apparatus.
Collapse
|
17
|
Pluchon PF, Fouqueau T, Crezé C, Laurent S, Briffotaux J, Hogrel G, Palud A, Henneke G, Godfroy A, Hausner W, Thomm M, Nicolas J, Flament D. An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs. PLoS One 2013; 8:e79707. [PMID: 24244547 PMCID: PMC3820547 DOI: 10.1371/journal.pone.0079707] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Pierre-François Pluchon
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Thomas Fouqueau
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Christophe Crezé
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Sébastien Laurent
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Julien Briffotaux
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Gaëlle Hogrel
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Adeline Palud
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Ghislaine Henneke
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Anne Godfroy
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
| | - Winfried Hausner
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Michael Thomm
- Lehrstuhl für Mikrobiologie, Universität Regensburg, Regensburg, Germany
| | - Jacques Nicolas
- IRISA-INRIA, Campus de Beaulieu, Rennes, France
- * E-mail: (DF); (JN)
| | - Didier Flament
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- Université de Bretagne Occidentale, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- CNRS, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, France
- * E-mail: (DF); (JN)
| |
Collapse
|
18
|
Sun F, Huang L. Sulfolobus chromatin proteins modulate strand displacement by DNA polymerase B1. Nucleic Acids Res 2013; 41:8182-95. [PMID: 23821667 PMCID: PMC3783171 DOI: 10.1093/nar/gkt588] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Strand displacement by a DNA polymerase serves a key role in Okazaki fragment maturation, which involves displacement of the RNA primer of the preexisting Okazaki fragment into a flap structure, and subsequent flap removal and fragment ligation. We investigated the role of Sulfolobus chromatin proteins Sso7d and Cren7 in strand displacement by DNA polymerase B1 (PolB1) from the hyperthermophilic archaeon Sulfolobus solfataricus. PolB1 showed a robust strand displacement activity and was capable of synthesizing thousands of nucleotides on a DNA-primed 72-nt single-stranded circular DNA template. This activity was inhibited by both Sso7d and Cren7, which limited the flap length to 3–4 nt at saturating concentrations. However, neither protein inhibited RNA displacement on an RNA-primed single-stranded DNA minicircle by PolB1. Strand displacement remained sensitive to modulation by the chromatin proteins when PolB1 was in association with proliferating cell nuclear antigen. Inhibition of DNA instead of RNA strand displacement by the chromatin proteins is consistent with the finding that double-stranded DNA was more efficiently bound and stabilized than an RNA:DNA duplex by these proteins. Our results suggest that Sulfolobus chromatin proteins modulate strand displacement by PolB1, permitting efficient removal of the RNA primer while inhibiting excessive displacement of the newly synthesized DNA strand during Okazaki fragment maturation.
Collapse
Affiliation(s)
- Fei Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | |
Collapse
|
19
|
In vitro reconstitution of RNA primer removal in Archaea reveals the existence of two pathways. Biochem J 2012; 447:271-80. [PMID: 22849643 DOI: 10.1042/bj20120959] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
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.
Collapse
|
20
|
Creze C, Ligabue A, Laurent S, Lestini R, Laptenok SP, Khun J, Vos MH, Czjzek M, Myllykallio H, Flament D. Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels. J Biol Chem 2012; 287:15648-60. [PMID: 22431731 DOI: 10.1074/jbc.m112.346361] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.
Collapse
Affiliation(s)
- Christophe Creze
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Beattie TR, Bell SD. Coordination of multiple enzyme activities by a single PCNA in archaeal Okazaki fragment maturation. EMBO J 2012; 31:1556-67. [PMID: 22307085 PMCID: PMC3321178 DOI: 10.1038/emboj.2012.12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 01/09/2012] [Indexed: 11/16/2022] Open
Abstract
In vitro reconstitution of Okazaki fragment processing shows that DNA polymerase, flap endonuclease and DNA ligase need to simultaneously bind to the same PCNA-sliding clamp molecule during DNA lagging strand replication. Chromosomal DNA replication requires one daughter strand—the lagging strand—to be synthesised as a series of discontinuous, RNA-primed Okazaki fragments, which must subsequently be matured into a single covalent DNA strand. Here, we describe the reconstitution of Okazaki fragment maturation in vitro using proteins derived from the archaeon Sulfolobus solfataricus. Six proteins are necessary and sufficient for coupled DNA synthesis, RNA primer removal and DNA ligation. PolB1, Fen1 and Lig1 provide the required catalytic activities, with coordination of their activities dependent upon the DNA sliding clamp, proliferating cell nuclear antigen (PCNA). S. solfataricus PCNA is a heterotrimer, with each subunit having a distinct specificity for binding PolB1, Fen1 or Lig1. Our data demonstrate that the most efficient coupling of activities occurs when a single PCNA ring organises PolB1, Fen1 and Lig1 into a complex.
Collapse
Affiliation(s)
- Thomas R Beattie
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
| | | |
Collapse
|
22
|
Finger LD, Atack JM, Tsutakawa S, Classen S, Tainer J, Grasby J, Shen B. The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcell Biochem 2012; 62:301-26. [PMID: 22918592 PMCID: PMC3728657 DOI: 10.1007/978-94-007-4572-8_16] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Processing of Okazaki fragments to complete lagging strand DNA synthesis requires coordination among several proteins. RNA primers and DNA synthesised by DNA polymerase α are displaced by DNA polymerase δ to create bifurcated nucleic acid structures known as 5'-flaps. These 5'-flaps are removed by Flap Endonuclease 1 (FEN), a structure-specific nuclease whose divalent metal ion-dependent phosphodiesterase activity cleaves 5'-flaps with exquisite specificity. FENs are paradigms for the 5' nuclease superfamily, whose members perform a wide variety of roles in nucleic acid metabolism using a similar nuclease core domain that displays common biochemical properties and structural features. A detailed review of FEN structure is undertaken to show how DNA substrate recognition occurs and how FEN achieves cleavage at a single phosphate diester. A proposed double nucleotide unpairing trap (DoNUT) is discussed with regards to FEN and has relevance to the wider 5' nuclease superfamily. The homotrimeric proliferating cell nuclear antigen protein (PCNA) coordinates the actions of DNA polymerase, FEN and DNA ligase by facilitating the hand-off intermediates between each protein during Okazaki fragment maturation to maximise through-put and minimise consequences of intermediates being released into the wider cellular environment. FEN has numerous partner proteins that modulate and control its action during DNA replication and is also controlled by several post-translational modification events, all acting in concert to maintain precise and appropriate cleavage of Okazaki fragment intermediates during DNA replication.
Collapse
Affiliation(s)
- L. David Finger
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - John M. Atack
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - Susan Tsutakawa
- Life Sciences Division, Lawrence Berkeley National, Laboratory, Berkeley, CA 94720, USA
| | - Scott Classen
- Physical Biosciences Division, The Scripps Research, Institute, La Jolla, CA 92037, USA
| | - John Tainer
- Life Sciences Division, Lawrence Berkeley, National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA
| | - Jane Grasby
- Department of Chemistry, Centre for Chemical Biology, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - Binghui Shen
- Division of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
23
|
Dobosy JR, Rose SD, Beltz KR, Rupp SM, Powers KM, Behlke MA, Walder JA. RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers. BMC Biotechnol 2011; 11:80. [PMID: 21831278 PMCID: PMC3224242 DOI: 10.1186/1472-6750-11-80] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 08/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background The polymerase chain reaction (PCR) is commonly used to detect the presence of nucleic acid sequences both in research and diagnostic settings. While high specificity is often achieved, biological requirements sometimes necessitate that primers are placed in suboptimal locations which lead to problems with the formation of primer dimers and/or misamplification of homologous sequences. Results Pyrococcus abyssi (P.a.) RNase H2 was used to enable PCR to be performed using blocked primers containing a single ribonucleotide residue which are activated via cleavage by the enzyme (rhPCR). Cleavage occurs 5'-to the RNA base following primer hybridization to the target DNA. The requirement of the primer to first hybridize with the target sequence to gain activity eliminates the formation of primer-dimers and greatly reduces misamplification of closely related sequences. Mismatches near the scissile linkage decrease the efficiency of cleavage by RNase H2, further increasing the specificity of the assay. When applied to the detection of single nucleotide polymorphisms (SNPs), rhPCR was found to be far more sensitive than standard allele-specific PCR. In general, the best discrimination occurs when the mismatch is placed at the RNA:DNA base pair. Conclusion rhPCR eliminates the formation of primer dimers and markedly improves the specificity of PCR with respect to off-target amplification. These advantages of the assay should find utility in challenging qPCR applications such as genotyping, high level multiplex assays and rare allele detection.
Collapse
Affiliation(s)
- Joseph R Dobosy
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, IA 5224, USA
| | | | | | | | | | | | | |
Collapse
|
24
|
Abstract
Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.
Collapse
|
25
|
Structure and function of a novel endonuclease acting on branched DNA substrates. Biochem Soc Trans 2011; 39:145-9. [PMID: 21265762 DOI: 10.1042/bst0390145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Branched DNA structures that occur during DNA repair and recombination must be efficiently processed by structure-specific endonucleases in order to avoid cell death. In the present paper, we summarize our screen for new interaction partners for the archaeal replication clamp that led to the functional characterization of a novel endonuclease family, dubbed NucS. Structural analyses of Pyrococcus abyssi NucS revealed an unexpected binding site for ssDNA (single-stranded DNA) that directs, together with the replication clamp, the nuclease activity of this protein towards ssDNA-dsDNA (double-stranded DNA) junctions. Our studies suggest that understanding the detailed architecture and dynamic behaviour of the NucS (nuclease specific for ssDNA)-PCNA (proliferating-cell nuclear antigen) complex with DNA will be crucial for identification of its physiologically relevant activities.
Collapse
|
26
|
Li Z, Pan M, Santangelo TJ, Chemnitz W, Yuan W, Edwards JL, Hurwitz J, Reeve JN, Kelman Z. A novel DNA nuclease is stimulated by association with the GINS complex. Nucleic Acids Res 2011; 39:6114-23. [PMID: 21459845 PMCID: PMC3152336 DOI: 10.1093/nar/gkr181] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromosomal DNA replication requires the spatial and temporal coordination of the activities of several complexes that constitute the replisome. A previously uncharacterized protein, encoded by TK1252 in the archaeon Thermococcus kodakaraensis, was shown to stably interact with the archaeal GINS complex in vivo, a central component of the archaeal replisome. Here, we document that this protein (TK1252p) is a processive, single-strand DNA-specific exonuclease that degrades DNA in the 5′ → 3′ direction. TK1252p binds specifically to the GINS15 subunit of T. kodakaraensis GINS complex and this interaction stimulates the exonuclease activity in vitro. This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed.
Collapse
Affiliation(s)
- Zhuo Li
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes. Biochem Soc Trans 2011; 39:70-6. [DOI: 10.1042/bst0390070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5′-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.
Collapse
|
28
|
Bubeck D, Reijns MAM, Graham SC, Astell KR, Jones EY, Jackson AP. PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res 2011; 39:3652-66. [PMID: 21245041 PMCID: PMC3089482 DOI: 10.1093/nar/gkq980] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Ribonuclease H2 is the major nuclear enzyme degrading cellular RNA/DNA hybrids in eukaryotes and the sole nuclease known to be able to hydrolyze ribonucleotides misincorporated during genomic replication. Mutation in RNASEH2 causes Aicardi–Goutières syndrome, an auto-inflammatory disorder that may arise from nucleic acid byproducts generated during DNA replication. Here, we report the crystal structures of Archaeoglobus fulgidus RNase HII in complex with PCNA, and human PCNA bound to a C-terminal peptide of RNASEH2B. In the archaeal structure, three binding modes are observed as the enzyme rotates about a flexible hinge while anchored to PCNA by its PIP-box motif. PCNA binding promotes RNase HII activity in a hinge-dependent manner. It enhances both cleavage of ribonucleotides misincorporated in DNA duplexes, and the comprehensive hydrolysis of RNA primers formed during Okazaki fragment maturation. In addition, PCNA imposes strand specificity on enzyme function, and by localizing RNase H2 and not RNase H1 to nuclear replication foci in vivo it ensures that RNase H2 is the dominant RNase H activity during nuclear replication. Our findings provide insights into how type 2 RNase H activity is directed during genome replication and repair, and suggest a mechanism by which RNase H2 may suppress generation of immunostimulatory nucleic acids.
Collapse
Affiliation(s)
- Doryen Bubeck
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | | | | |
Collapse
|
29
|
Abstract
Faithful DNA replication involves the removal of RNA residues from genomic DNA prior to the ligation of nascent DNA fragments in all living organisms. Because the physiological roles of archaeal type 2 RNase H are not fully understood, the substrate structure requirements for the detection of RNase H activity need further clarification. Biochemical characterization of a single RNase H detected within the genome of Pyrococcus abyssi showed that this type 2 RNase H is an Mg- and alkaline pH-dependent enzyme. PabRNase HII showed RNase activity and acted as a specific endonuclease on RNA-DNA/DNA duplexes. This specific cleavage, 1 nucleotide upstream of the RNA-DNA junction, occurred on a substrate in which RNA initiators had to be fully annealed to the cDNA template. On the other hand, a 5' RNA flap Okazaki fragment intermediate impaired PabRNase HII endonuclease activity. Furthermore, introduction of mismatches into the RNA portion near the RNA-DNA junction decreased both the specificity and the efficiency of cleavage by PabRNase HII. Additionally, PabRNase HII could cleave a single ribonucleotide embedded in a double-stranded DNA. Our data revealed PabRNase HII as a dual-function enzyme likely required for the completion of DNA replication and DNA repair.
Collapse
|
30
|
Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 2010; 5:e9605. [PMID: 20333302 PMCID: PMC2841640 DOI: 10.1371/journal.pone.0009605] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 02/11/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
Collapse
Affiliation(s)
- Amber L. Hartman
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Cédric Norais
- Institut de Génétique et Microbiologie, Université Paris-Sud, Paris, France
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jonathan H. Badger
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Stéphane Delmas
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Sam Haldenby
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Ramana Madupu
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Jeffrey Robinson
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Qinghu Ren
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mecky Pohlschroder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Charles Daniels
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Thorsten Allers
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan A. Eisen
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
| |
Collapse
|
31
|
Castrec B, Laurent S, Henneke G, Flament D, Raffin JP. The glycine-rich motif of Pyrococcus abyssi DNA polymerase D is critical for protein stability. J Mol Biol 2010; 396:840-8. [PMID: 20070946 DOI: 10.1016/j.jmb.2010.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 12/03/2009] [Accepted: 01/05/2010] [Indexed: 12/11/2022]
Abstract
A glycine-rich motif described as being involved in human polymerase delta proliferating cell nuclear antigen (PCNA) binding has also been identified in all euryarchaeal DNA polymerase D (Pol D) family members. We redefined the motif as the (G)-PYF box. In the present study, Pol D (G)-PYF box motif mutants from Pyrococcus abyssi were generated to investigate its role in functional interactions with the cognate PCNA. We demonstrated that this motif is not essential for interactions between PabPol D (P. abyssi Pol D) and PCNA, using surface plasmon resonance and primer extension studies. Interestingly, the (G)-PYF box is located in a hydrophobic region close to the active site. The (G)-PYF box mutants exhibited altered DNA binding properties. In addition, the thermal stability of all mutants was reduced compared to that of wild type, and this effect could be attributed to increased exposure of the hydrophobic region. These studies suggest that the (G)-PYF box motif mediates intersubunit interactions and that it may be crucial for the thermostability of PabPol D.
Collapse
Affiliation(s)
- Benoît Castrec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie et Environnements Extrêmes, BP 70, F-29280 Plouzané, France
| | | | | | | | | |
Collapse
|
32
|
Eum NS, Kim DE, Yeom SH, Kang BH, Kim KJ, Park CS, Kang SW. Variable wavelength surface plasmon resonance (SPR) in biosensing. Biosystems 2009; 98:51-5. [DOI: 10.1016/j.biosystems.2009.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/08/2009] [Accepted: 05/17/2009] [Indexed: 11/16/2022]
|
33
|
Castrec B, Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP. Binding to PCNA in Euryarchaeal DNA Replication requires two PIP motifs for DNA polymerase D and one PIP motif for DNA polymerase B. J Mol Biol 2009; 394:209-18. [PMID: 19781553 DOI: 10.1016/j.jmb.2009.09.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 09/16/2009] [Accepted: 09/17/2009] [Indexed: 01/07/2023]
Abstract
Replicative DNA polymerases possess a canonical C-terminal proliferating cell nuclear antigen (PCNA)-binding motif termed the PCNA-interacting protein (PIP) box. We investigated the role of the PIP box on the functional interactions of the two DNA polymerases, PabPol B (family B) and PabPol D (family D), from the hyperthermophilic euryarchaeon Pyrococcus abyssi, with its cognate PCNA. The PIP box was essential for interactions of PabPol B with PCNA, as shown by surface plasmon resonance and primer extension studies. In contrast, binding of PabPol D to PCNA was affected only partially by removing the PIP motif. We identified a second palindromic PIP box motif at the N-terminus of the large subunit of PabPol D that was required for the interactions of PabPol D with PCNA. Thus, two PIP motifs were needed for PabPol D for binding to PabPCNA. Moreover, the C-terminus of PabPCNA was essential for stimulation of PabPol D activity but not for stimulation of PabPol B activity. Neither DNA polymerase interacted with the PabPCNA interdomain connecting loop. Our data suggest that distinct processes are involved in PabPol D and PabPol B binding to PCNA, raising the possibility that Archaea require two mechanisms for recruiting replicative DNA polymerases at the replication fork.
Collapse
Affiliation(s)
- Benoît Castrec
- Université de Bretagne Occidentale, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, BP 70, F-29280 Plouzané, France
| | | | | | | | | | | |
Collapse
|
34
|
Winter JA, Christofi P, Morroll S, Bunting KA. The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation. BMC STRUCTURAL BIOLOGY 2009; 9:55. [PMID: 19698123 PMCID: PMC2737543 DOI: 10.1186/1472-6807-9-55] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 08/22/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The high intracellular salt concentration required to maintain a halophilic lifestyle poses challenges to haloarchaeal proteins that must stay soluble, stable and functional in this extreme environment. Proliferating cell nuclear antigen (PCNA) is a fundamental protein involved in maintaining genome integrity, with roles in both DNA replication and repair. To investigate the halophilic adaptation of such a key protein we have crystallised and solved the structure of Haloferax volcanii PCNA (HvPCNA) to a resolution of 2.0 A. RESULTS The overall architecture of HvPCNA is very similar to other known PCNAs, which are highly structurally conserved. Three commonly observed adaptations in halophilic proteins are higher surface acidity, bound ions and increased numbers of intermolecular ion pairs (in oligomeric proteins). HvPCNA possesses the former two adaptations but not the latter, despite functioning as a homotrimer. Strikingly, the positive surface charge considered key to PCNA's role as a sliding clamp is dramatically reduced in the halophilic protein. Instead, bound cations within the solvation shell of HvPCNA may permit sliding along negatively charged DNA by reducing electrostatic repulsion effects. CONCLUSION The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the pore region, to facilitate functional interactions with DNA. In this way, HvPCNA may harness its environment as opposed to simply surviving in extreme halophilic conditions.
Collapse
Affiliation(s)
- Jody A Winter
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | | | | | | |
Collapse
|
35
|
Ren B, Kühn J, Meslet-Cladiere L, Briffotaux J, Norais C, Lavigne R, Flament D, Ladenstein R, Myllykallio H. Structure and function of a novel endonuclease acting on branched DNA substrates. EMBO J 2009; 28:2479-89. [PMID: 19609302 DOI: 10.1038/emboj.2009.192] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 06/18/2009] [Indexed: 11/09/2022] Open
Abstract
We show that Pyrococcus abyssi PAB2263 (dubbed NucS (nuclease for ss DNA) is a novel archaeal endonuclease that interacts with the replication clamp PCNA. Structural determination of P. abyssi NucS revealed a two-domain dumbbell-like structure that in overall does not resemble any known protein structure. Biochemical and structural studies indicate that NucS orthologues use a non-catalytic ssDNA-binding domain to regulate the cleavage activity at another site, thus resulting into the specific cleavage at double-stranded DNA (dsDNA)/ssDNA junctions on branched DNA substrates. Both 3' and 5' extremities of the ssDNA can be cleaved at the nuclease channel that is too narrow to accommodate duplex DNA. Altogether, our data suggest that NucS proteins constitute a new family of structure-specific DNA endonucleases that are widely distributed in archaea and in bacteria, including Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Bin Ren
- Center for Structural Biochemistry, Karolinska Institutet, NOVUM, Huddinge, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
The powerful combination of genetic and biochemical analysis has provided many key insights into the structure and function of the chromosomal DNA replication machineries of bacterial and eukaryotic cells. In contrast, in the archaea, biochemical studies have dominated, mainly due to the absence of efficient genetic systems for these organisms. This situation is changing, however, and, in this regard, the genetically tractable haloarchaea Haloferax volcanii and Halobacterium sp. NRC-1 are emerging as key models. In the present review, I give an overview of the components of the replication machinery in the haloarchaea, with particular emphasis on the protein factors presumed to travel with the replication fork.
Collapse
|
37
|
Chon H, Vassilev A, DePamphilis ML, Zhao Y, Zhang J, Burgers PM, Crouch RJ, Cerritelli SM. Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex. Nucleic Acids Res 2008; 37:96-110. [PMID: 19015152 PMCID: PMC2615623 DOI: 10.1093/nar/gkn913] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Eukaryotic RNase H2 is a heterotrimeric enzyme. Here, we show that the biochemical composition and stoichiometry of the human RNase H2 complex is consistent with the properties previously deduced from genetic studies. The catalytic subunit of eukaryotic RNase H2, RNASEH2A, is well conserved and similar to the monomeric prokaryotic RNase HII. In contrast, the RNASEH2B and RNASEH2C subunits from human and Saccharomyces cerevisiae share very little homology, although they both form soluble B/C complexes that may serve as a nucleation site for the addition of RNASEH2A to form an active RNase H2, or for interactions with other proteins to support different functions. The RNASEH2B subunit has a PIP-box and confers PCNA binding to human RNase H2. Unlike Escherichia coli RNase HII, eukaryotic RNase H2 acts processively and hydrolyzes a variety of RNA/DNA hybrids with similar efficiencies, suggesting multiple cellular substrates. Moreover, of five analyzed mutations in human RNASEH2B and RNASEH2C linked to Aicardi-Goutières Syndrome (AGS), only one, R69W in the RNASEH2C protein, exhibits a significant reduction in specific activity, revealing a role for the C subunit in enzymatic activity. Near-normal activity of four AGS-related mutant enzymes was unexpected in light of their predicted impairment causing the AGS phenotype.
Collapse
Affiliation(s)
- Hyongi Chon
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda MD 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
39
|
Brooks MA, Meslet-Cladiére L, Graille M, Kuhn J, Blondeau K, Myllykallio H, van Tilbeurgh H. The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci 2008; 17:1336-45. [PMID: 18511537 DOI: 10.1110/ps.035493.108] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The genome of Pyrococcus abyssi contains two open reading frames encoding proteins which had been previously predicted to be DNA ligases, Pab2002 and Pab1020. We show that while the former is indeed a DNA ligase, Pab1020 had no effect on the substrate deoxyoligo-ribonucleotides tested. Instead, Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction, suggesting that it is an RNA ligase. We have solved the structure of Pab1020 in complex with the ATP analog AMPPNP by single-wavelength anomalous dispersion (SAD), elucidating a structure with high structural similarity to the catalytic domains of two RNA ligases from the bacteriophage T4. Additional carboxy-terminal domains are also present, and one of these mediates contacts with a second protomer, which is related by noncrystallographic symmetry, generating a homodimeric structure. These C-terminal domains are terminated by short domain swaps which themselves end within 5 A of the active sites of the partner molecules. Additionally, we show that the protein is indeed capable of circularizing RNA molecules in an ATP-dependent reaction. These structural and biochemical results provide an insight into the potential physiological roles of Pab1020.
Collapse
Affiliation(s)
- Mark Adrian Brooks
- IBBMC-CNRS, Université de Paris-Sud, CNRS-UMR8619, IFR115, 91405 Orsay, France
| | | | | | | | | | | | | |
Collapse
|
40
|
Bacart J, Corbel C, Jockers R, Bach S, Couturier C. The BRET technology and its application to screening assays. Biotechnol J 2008; 3:311-24. [DOI: 10.1002/biot.200700222] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|