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Abstract
The lamin B2 locus is the only mammalian origin whose replication initiation points (RIPs) have been mapped. Although this paper was published 8 years ago, no further mammalian RIP-mapping studies have been reported, largely due to technical difficulties of ligation-mediated (LM)-PCR used by the authors. Here, we report the development of a simple, one-way PCR-based protocol that allows one to accurately determine RIPs at mammalian origins. The procedure can be completed within 48 h from the time of cell lysis in the agarose gel. Nascent DNA is then isolated from the same gel after DNA is separated by alkaline gel electrophoresis. Subsequently, RIPs are determined by one-way PCR-based primer extension using labeled primers. Using this protocol, we have successfully mapped RIPs in the human DBF4 locus. As one-way PCR is routinely used by many scientists, this protocol will provide a powerful new tool for studying DNA replication in many organisms including mammalian cells.
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Le Breton M, Henneke G, Norais C, Flament D, Myllykallio H, Querellou J, Raffin JP. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? J Mol Biol 2007; 374:1172-85. [PMID: 17991487 DOI: 10.1016/j.jmb.2007.10.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 11/27/2022]
Abstract
We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and deoxyribonucleotides, and its activity was dependent on the presence of Mg2+ and Mn2+. Interestingly, Pab DNA primase also displayed DNA polymerase, gap-filling, and strand-displacement activities. Genetic analyses undertaken in Haloferax volcanii suggested that the eukaryotic-type heterodimeric primase is essential for survival in archaeal cells. Our results are in favor of a multifunctional archaeal primase involved in priming and repair.
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Affiliation(s)
- Magali Le Breton
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, Ifremer, BP 70, F-29280 Plouzané, France
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53
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Gaudier M, Schuwirth BS, Westcott SL, Wigley DB. Structural basis of DNA replication origin recognition by an ORC protein. Science 2007; 317:1213-6. [PMID: 17761880 DOI: 10.1126/science.1143664] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.
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Affiliation(s)
- Martin Gaudier
- Cancer Research UK Clare Hall Laboratories, London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK
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54
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Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1. BMC Genet 2007; 8:31. [PMID: 17559652 PMCID: PMC1906834 DOI: 10.1186/1471-2156-8-31] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 06/08/2007] [Indexed: 11/22/2022] Open
Abstract
Background Information transfer systems in Archaea, including many components of the DNA replication machinery, are similar to those found in eukaryotes. Functional assignments of archaeal DNA replication genes have been primarily based upon sequence homology and biochemical studies of replisome components, but few genetic studies have been conducted thus far. We have developed a tractable genetic system for knockout analysis of genes in the model halophilic archaeon, Halobacterium sp. NRC-1, and used it to determine which DNA replication genes are essential. Results Using a directed in-frame gene knockout method in Halobacterium sp. NRC-1, we examined nineteen genes predicted to be involved in DNA replication. Preliminary bioinformatic analysis of the large haloarchaeal Orc/Cdc6 family, related to eukaryotic Orc1 and Cdc6, showed five distinct clades of Orc/Cdc6 proteins conserved in all sequenced haloarchaea. Of ten orc/cdc6 genes in Halobacterium sp. NRC-1, only two were found to be essential, orc10, on the large chromosome, and orc2, on the minichromosome, pNRC200. Of the three replicative-type DNA polymerase genes, two were essential: the chromosomally encoded B family, polB1, and the chromosomally encoded euryarchaeal-specific D family, polD1/D2 (formerly called polA1/polA2 in the Halobacterium sp. NRC-1 genome sequence). The pNRC200-encoded B family polymerase, polB2, was non-essential. Accessory genes for DNA replication initiation and elongation factors, including the putative replicative helicase, mcm, the eukaryotic-type DNA primase, pri1/pri2, the DNA polymerase sliding clamp, pcn, and the flap endonuclease, rad2, were all essential. Targeted genes were classified as non-essential if knockouts were obtained and essential based on statistical analysis and/or by demonstrating the inability to isolate chromosomal knockouts except in the presence of a complementing plasmid copy of the gene. Conclusion The results showed that ten out of nineteen eukaryotic-type DNA replication genes are essential for Halobacterium sp. NRC-1, consistent with their requirement for DNA replication. The essential genes code for two of ten Orc/Cdc6 proteins, two out of three DNA polymerases, the MCM helicase, two DNA primase subunits, the DNA polymerase sliding clamp, and the flap endonuclease.
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55
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Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP. DNA Polymerase Switching on Homotrimeric PCNA at the Replication Fork of the Euryarchaea Pyrococcus abyssi. J Mol Biol 2007; 369:343-55. [PMID: 17442344 DOI: 10.1016/j.jmb.2007.03.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 03/15/2007] [Accepted: 03/19/2007] [Indexed: 12/28/2022]
Abstract
DNA replication in Archaea, as in other organisms, involves large protein complexes called replisomes. In the Euryarchaeota subdomain, only two putative replicases have been identified, and their roles in leading and lagging strand DNA synthesis are still poorly understood. In this study, we focused on the coupling of proliferating cell nuclear antigen (PCNA)-loading mechanisms with DNA polymerase function in the Euryarchaea Pyrococcus abyssi. PCNA spontaneously loaded onto primed DNA, and replication factor C dramatically increased this loading. Surprisingly, the family B DNA polymerase (Pol B) also increased PCNA loading, probably by stabilizing the clamp on primed DNA via an essential motif. In contrast, on an RNA-primed DNA template, the PCNA/Pol B complex was destabilized in the presence of dNTPs, allowing the family D DNA polymerase (Pol D) to perform RNA-primed DNA synthesis. Then, Pol D is displaced by Pol B to perform processive DNA synthesis, at least on the leading strand.
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Affiliation(s)
- Christophe Rouillon
- IFREMER, UMR 6197, Laboratoire de Microbiologie et Environnements Extrêmes, BP 70, F-29280 Plouzané, France
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56
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Matsunaga F, Glatigny A, Mucchielli-Giorgi MH, Agier N, Delacroix H, Marisa L, Durosay P, Ishino Y, Aggerbeck L, Forterre P. Genomewide and biochemical analyses of DNA-binding activity of Cdc6/Orc1 and Mcm proteins in Pyrococcus sp. Nucleic Acids Res 2007; 35:3214-22. [PMID: 17452353 PMCID: PMC1904270 DOI: 10.1093/nar/gkm212] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of DNA replication (oriC) of the hyperthermophilic archaeon Pyrococcus abyssi contains multiple ORB and mini-ORB repeats that show sequence similarities to other archaeal ORB (origin recognition box). We report here that the binding of Cdc6/Orc1 to a 5 kb region containing oriC in vivo was highly specific both in exponential and stationary phases, by means of chromatin immunoprecipitation coupled with hybridization on a whole genome microarray (ChIP-chip). The oriC region is practically the sole binding site for the Cdc6/Orc1, thereby distinguishing oriC in the 1.8 M bp genome. We found that the 5 kb region contains a previously unnoticed cluster of ORB and mini-ORB repeats in the gene encoding the small subunit (dp1) for DNA polymerase II (PolD). ChIP and the gel retardation analyses further revealed that Cdc6/Orc1 specifically binds both of the ORB clusters in oriC and dp1. The organization of the ORB clusters in the dp1 and oriC is conserved during evolution in the order Thermococcales, suggesting a role in the initiation of DNA replication. Our ChIP-chip analysis also revealed that Mcm alters the binding specificity to the oriC region according to the growth phase, consistent with its role as a licensing factor.
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Affiliation(s)
- Fujihiko Matsunaga
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Annie Glatigny
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Marie-Hélène Mucchielli-Giorgi
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Nicolas Agier
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Hervé Delacroix
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Laetitia Marisa
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Patrice Durosay
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Yoshizumi Ishino
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Lawrence Aggerbeck
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
| | - Patrick Forterre
- Institut de Génétique et Microbiologie, UMR8621, Bât. 409, Université Paris-Sud, 91405 Orsay Cedex, France, Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan and Gif/Orsay DNA Microarray Platform (GODMAP), Centre de Génétique Moléculaire UPR2167, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, Associated with the Université Pierre et Marie Curie-Paris 6, Paris F-75005, France
- *To whom correspondence should be addressed. Tel: +33 1 69 157489; Fax: +33 1 69 157808;
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57
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Pei H, Liu J, Li J, Guo A, Zhou J, Xiang H. Mechanism for the TtDnaA-Tt-oriC cooperative interaction at high temperature and duplex opening at an unusual AT-rich region in Thermoanaerobacter tengcongensis. Nucleic Acids Res 2007; 35:3087-99. [PMID: 17452366 PMCID: PMC1888806 DOI: 10.1093/nar/gkm137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Revised: 02/21/2007] [Accepted: 02/22/2007] [Indexed: 11/19/2022] Open
Abstract
Thermoanaerobacter tengcongensis is an anaerobic low-GC thermophilic bacterium. To further elucidate the replication initiation of chromosomal DNA at high temperature, the interaction between the replication initiator (TtDnaA) and the putative origin (Tt-oriC) in this thermophile was investigated. We found that efficient binding of TtDnaA to Tt-oriC at high temperature requires (i) at least two neighboring DnaA boxes, (ii) the specific feature of the TtDnaA Domain IV and (iii) the self-oligomerization of TtDnaA. Replacement of the TtDnaA Domain IV by the counterpart of Escherichia coli DnaA or disruption of its oligomerization by amino acid mutations (W9A/L20S) abolished the oriC-binding activity of TtDnaA at 60 degrees C, but not at 37 degrees C. Moreover, ATP-TtDnaA, but not ADP-TtDnaA or the oligomerization-deficient mutants was able to unwind the Tt-oriC duplex. The minimal oriC required for this duplex opening in vitro was demonstrated to consist of DnaA boxes 1-8 and an unusual AT-rich region. Interestingly, although no typical ATP-DnaA box was found in this AT-rich region, it was exclusively bound by ATP-TtDnaA and acted as the duplex-opening and replication-initiation site. Taken together, we propose that oligomerization of ATP-DnaA and simultaneously binding of several DnaA boxes and/or AT-rich region may be generally required in replication initiation at high temperature.
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Affiliation(s)
- Huadong Pei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
| | - Jingfang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
| | - Aobo Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
| | - Jian Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China, Graduate University of Chinese Academy of Sciences, Beijing 100039, P. R. China and School of Pharmaceutical Science, Peking University Health Science Center, Beijing 100083, P. R. China
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58
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Geslin C, Gaillard M, Flament D, Rouault K, Le Romancer M, Prieur D, Erauso G. Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi. J Bacteriol 2007; 189:4510-9. [PMID: 17449623 PMCID: PMC1913373 DOI: 10.1128/jb.01896-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Only one virus-like particle (VLP) has been reported from hyperthermophilic Euryarchaeotes. This VLP, named PAV1, is shaped like a lemon and was isolated from a strain of "Pyrococcus abyssi," a deep-sea isolate. Its genome consists of a double-stranded circular DNA of 18 kb which is also present at a high copy number (60 per chromosome) free within the host cytoplasm but is not integrated into the host chromosome. Here, we report the results of complete analysis of the PAV1 genome. All the 25 predicted genes, except 3, are located on one DNA strand. A transcription map has been made by using a reverse transcription-PCR assay. All the identified open reading frames (ORFs) are transcribed. The most significant similarities relate to four ORFs. ORF 180a shows 31% identity with ORF 181 of the pRT1 plasmid isolated from Pyrococcus sp. strain JT1. ORFs 676 and 678 present similarities with a concanavalin A-like lectin/glucanase domain, which could be involved in the process of host-virus recognition, and ORF 59 presents similarities with the transcriptional regulator CopG. The genome of PAV1 displays unique features at the nucleic and proteinic level, indicating that PAV1 should be attached at least to a novel genus or virus family.
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Affiliation(s)
- C Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR 6197 (CNRS, UBO, IFREMER), Place Nicolas Copernic, Technopôle Brest-Iroise, 29280 Plouzané, France.
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59
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Abstract
The archaeal DNA replication machinery bears striking similarity to that of eukaryotes and is clearly distinct from the bacterial apparatus. In recent years, considerable advances have been made in understanding the biochemistry of the archaeal replication proteins. Furthermore, a number of structures have now been obtained for individual components and higher-order assemblies of archaeal replication factors, yielding important insights into the mechanisms of DNA replication in both archaea and eukaryotes.
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Affiliation(s)
- Elizabeth R Barry
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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60
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Ito N, Matsui I, Matsui E. Molecular basis for the subunit assembly of the primase from an archaeon Pyrococcus horikoshii. FEBS J 2007; 274:1340-51. [PMID: 17286576 DOI: 10.1111/j.1742-4658.2007.05690.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Archaeal/eukaryotic primases form a heterodimer consisting of a small catalytic subunit (PriS) and a large subunit (PriL). The heterodimer complex synthesizes primer oligoribonucleotides that are required for chromosomal replication. Here, we describe crystallographic and biochemical studies of the N-terminal domain (NTD) of PriL (PriL(NTD); residues 1-222) that bind to PriS from a hyperthermophilic archaeon, Pyrococcus horikoshii, at 2.9 A resolution. The PriL(NTD) structure consists of two subdomains, the helix-bundle and twisted-strand domains. The latter is structurally flexible, and is expected to contain a PriS interaction site. Pull-down and surface plasmon resonance analyses of structure-based deletion and alanine scanning mutants showed that the conserved hydrophobic Tyr155-Tyr156-Ile157 region near the flexible region is the PriS-binding site, as the Y155A/Y156A/I157A mutation markedly reduces PriS binding, by 1000-fold. These findings and a structural comparison with a previously reported PriL(NTD)-PriS complex suggest that the presented alternative conformations of the twisted-strand domain facilitate the heterodimer assembly.
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Affiliation(s)
- Nobutoshi Ito
- Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, Wako, Saitama, Japan
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61
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Sun C, Zhou M, Li Y, Xiang H. Molecular characterization of the minimal replicon and the unidirectional theta replication of pSCM201 in extremely halophilic archaea. J Bacteriol 2006; 188:8136-44. [PMID: 16997958 PMCID: PMC1698213 DOI: 10.1128/jb.00988-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A 3,463-bp plasmid, pSCM201, was isolated from a halophilic archaeon, Haloarcula sp. strain AS7094. The minimal replicon that is essential and sufficient for autonomous replication and stable maintenance in Haloarcula hispanica was determined by deletion analysis of the plasmid. This minimal replicon ( approximately 1.8 kb) consisted of only two functionally related segments: (i) a putative origin (ori201) containing an AT-rich region and sets of repeats and (ii) an adjacent gene encoding a putative replication initiation protein (Rep201). Electron microscopic observation and Southern blotting analysis demonstrated that pSCM201 replicates via a theta mechanism. Precise mapping of the putative origin suggested that the replication initiated from a fixed site close to the AT-rich region and proceeded unidirectionally toward the downstream rep201 gene, which was further confirmed by electron microscopic analysis of the ClaI-digested replication intermediates. To our knowledge, this is the first unidirectional theta replication plasmid experimentally identified in the domain of archaea. It provides a novel plasmid system to conduct research on archaeal DNA replication.
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Affiliation(s)
- Chaomin Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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62
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Rytkönen AK, Vaara M, Nethanel T, Kaufmann G, Sormunen R, Läärä E, Nasheuer HP, Rahmeh A, Lee MYWT, Syväoja JE, Pospiech H. Distinctive activities of DNA polymerases during human DNA replication. FEBS J 2006; 273:2984-3001. [PMID: 16762037 DOI: 10.1111/j.1742-4658.2006.05310.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The contributions of human DNA polymerases (pols) alpha, delta and epsilon during S-phase progression were studied in order to elaborate how these enzymes co-ordinate their functions during nuclear DNA replication. Pol delta was three to four times more intensely UV cross-linked to nascent DNA in late compared with early S phase, whereas the cross-linking of pols alpha and epsilon remained nearly constant throughout the S phase. Consistently, the chromatin-bound fraction of pol delta, unlike pols alpha and epsilon, increased in the late S phase. Moreover, pol delta neutralizing antibodies inhibited replicative DNA synthesis most efficiently in late S-phase nuclei, whereas antibodies against pol epsilon were most potent in early S phase. Ultrastructural localization of the pols by immuno-electron microscopy revealed pol epsilon to localize predominantly to ring-shaped clusters at electron-dense regions of the nucleus, whereas pol delta was mainly dispersed on fibrous structures. Pol alpha and proliferating cell nuclear antigen displayed partial colocalization with pol delta and epsilon, despite the very limited colocalization of the latter two pols. These data are consistent with models where pols delta and epsilon pursue their functions at least partly independently during DNA replication.
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Affiliation(s)
- Anna K Rytkönen
- Biocenter Oulu and Department of Biochemistry, University of Oulu, Finland
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63
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DasSarma S, Berquist BR, Coker JA, DasSarma P, Müller JA. Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. SALINE SYSTEMS 2006; 2:3. [PMID: 16542428 PMCID: PMC1447603 DOI: 10.1186/1746-1448-2-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 03/16/2006] [Indexed: 11/21/2022]
Abstract
Halobacteriumsp. NRC-1 is an extremely halophilic archaeon that is easily cultured and genetically tractable. Since its genome sequence was completed in 2000, a combination of genetic, transcriptomic, proteomic, and bioinformatic approaches have provided insights into both its extremophilic lifestyle as well as fundamental cellular processes common to all life forms. Here, we review post-genomic research on this archaeon, including investigations of DNA replication and repair systems, phototrophic, anaerobic, and other physiological capabilities, acidity of the proteome for function at high salinity, and role of lateral gene transfer in its evolution.
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Affiliation(s)
- Shiladitya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Brian R Berquist
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - James A Coker
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Priya DasSarma
- University of Maryland Biotechnology Institute, Center of Marine Biotechnology, 701 E. Pratt Street, Suite 236, Baltimore, MD 21202, USA
| | - Jochen A Müller
- Department of Biology, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA
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Yamashiro K, Yokobori SI, Oshima T, Yamagishi A. Structural analysis of the plasmid pTA1 isolated from the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles 2006; 10:327-35. [PMID: 16493526 DOI: 10.1007/s00792-005-0502-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 12/04/2005] [Indexed: 11/25/2022]
Abstract
Thermoplasma acidophilum is a thermoacidophilic archaeon that grows optimally at pH1.8 and 56 degrees C and has no cell wall. Plasmid pTA1 was found in some strains of the species. We sequenced plasmid pTA1 and analyzed the open reading frames (ORFs). pTA1 was found to be a circular DNA molecule of 15,723 bp. Eighteen ORFs were found; none of the gene products except ORF1 had sequence similarity to known proteins. ORF1 showed similarity to Cdc6, which is involved in genome-replication initiation in Eukarya and Archaea. T. acidophilum has two Cdc6 homologues in the genome. The homologue found in pTA1 is most similar to Tvo3, one of the three Cdc6 homologues found in the genome of Thermoplasma volcanium, among all of the Cdc6 family proteins. The phylogenetic analysis suggested that plasmid pTA1 is possibly originated from the chromosomal DNA of Thermoplasma.
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Affiliation(s)
- Kan Yamashiro
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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65
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Kelman Z, White MF. Archaeal DNA replication and repair. Curr Opin Microbiol 2005; 8:669-76. [PMID: 16242991 DOI: 10.1016/j.mib.2005.10.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 10/05/2005] [Indexed: 11/22/2022]
Abstract
Since the first archaeal genome was sequenced, much attention has been focused on the study of these unique microorganisms. We have learnt that although archaeal DNA metabolic processes (replication, recombination and repair) are more similar to the metabolic processes of Eukarya than those of Bacteria, Archaea are not simply 'mini Eukarya'. They are, in fact, a mosaic of the eukaryal and bacterial systems that also possess archaeal-specific features. Recent biochemical and structural studies of the proteins that participate in archaeal DNA replication and repair have increased our understanding of these processes.
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Affiliation(s)
- Zvi Kelman
- University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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66
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Abstract
Three DNA polymerases are thought to function at the eukaryotic DNA replication fork. Currently, a coherent model has been derived for the composition and activities of the lagging strand machinery. RNA-DNA primers are initiated by DNA polymerase ot-primase. Loading of the proliferating cell nuclear antigen, PCNA, dissociates DNA polymerase ca and recruits DNA polymerase S and the flap endonuclease FEN1 for elongation and in preparation for its requirement during maturation, respectively. Nick translation by the strand displacement action of DNA polymerase 8, coupled with the nuclease action of FEN1, results in processive RNA degradation until a proper DNA nick is reached for closure by DNA ligase I. In the event of excessive strand displacement synthesis, other factors, such as the Dna2 nuclease/helicase, are required to trim excess flaps. Paradoxically, the composition and activity of the much simpler leading strand machinery has not been clearly established. The burden of evidence suggests that DNA polymerase E normally replicates this strand,but under conditions of dysfunction, DNA polymerase 8 may substitute.
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Affiliation(s)
- Parie Garg
- Washington University School of Medicine, St. Louis, MO 63110, USA
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67
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Henneke G, Flament D, Hübscher U, Querellou J, Raffin JP. The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication. J Mol Biol 2005; 350:53-64. [PMID: 15922358 DOI: 10.1016/j.jmb.2005.04.042] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 04/11/2005] [Accepted: 04/19/2005] [Indexed: 11/25/2022]
Abstract
DNA polymerases carry out DNA synthesis during DNA replication, DNA recombination and DNA repair. During the past five years, the number of DNA polymerases in both eukarya and bacteria has increased to at least 19 and multiple biological roles have been assigned to many DNA polymerases. Archaea, the third domain of life, on the other hand, have only a subset of the eukaryotic-like DNA polymerases. The diversity among the archaeal DNA polymerases poses the intriguing question of their functional tasks. Here, we focus on the two identified DNA polymerases, the family B DNA polymerase B (PabpolB) and the family D DNA polymerase D (PabpolD) from the hyperthermophilic euryarchaeota Pyrococcus abyssi. Our data can be summarized as follows: (i) both Pabpols are DNA polymerizing enzymes exclusively; (ii) their DNA binding properties as tested in gel shift competition assays indicated that PabpolD has a preference for a primed template; (iii) PabPolD is a primer-directed DNA polymerase independently of the primer composition whereas PabpolB behaves as an exclusively DNA primer-directed DNA polymerase; (iv) PabPCNA is required for PabpolD to perform efficient DNA synthesis but not PabpolB; (v) PabpolD, but not PabpolB, contains strand displacement activity; (vii) in the presence of PabPCNA, however, both Pabpols D and B show strand displacement activity; and (viii) we show that the direct interaction between PabpolD and PabPCNA is DNA-dependent. Our data imply that PabPolD might play an important role in DNA replication likely together with PabpolB, suggesting that archaea require two DNA polymerases at the replication fork.
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Affiliation(s)
- Ghislaine Henneke
- IFREMER, UMR 6197, Laboratoire de Microbiologie et Environnements Extrêmes, DRV/VP/LM2E, BP 70, F-29280 Plouzané, France.
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68
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Abstract
Replication of DNA is essential for the propagation of life. It is somewhat surprising then that, despite the vital nature of this process, cellular organisms show a great deal of variety in the mechanisms that they employ to ensure appropriate genome duplication. This diversity is manifested along classical evolutionary lines, with distinct combinations of replicon architecture and replication proteins being found in the three domains of life: the Bacteria, the Eukarya and the Archaea. Furthermore, although there are mechanistic parallels, even within a given domain of life, the way origins of replication are defined shows remarkable variation.
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Affiliation(s)
- Nicholas P Robinson
- MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, UK
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69
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Zhang R, Zhang CT. Identification of replication origins in archaeal genomes based on the Z-curve method. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2005; 1:335-46. [PMID: 15876567 PMCID: PMC2685548 DOI: 10.1155/2005/509646] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Z-curve is a three-dimensional curve that constitutes a unique representation of a DNA sequence, i.e., both the Z-curve and the given DNA sequence can be uniquely reconstructed from the other. We employed Z-curve analysis to identify one replication origin in the Methanocaldococcus jannaschii genome, two replication origins in the Halobacterium species NRC-1 genome and one replication origin in the Methanosarcina mazei genome. One of the predicted replication origins of Halobacterium species NRC-1 is the same as a replication origin later identified by in vivo experiments. The Z-curve analysis of the Sulfolobus solfataricus P2 genome suggested the existence of three replication origins, which is also consistent with later experimental results. This review aims to summarize applications of the Z-curve in identifying replication origins of archaeal genomes, and to provide clues about the locations of as yet unidentified replication origins of the Aeropyrum pernix K1, Methanococcus maripaludis S2, Picrophilus torridus DSM 9790 and Pyrobaculum aerophilum str. IM2 genomes.
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Affiliation(s)
- Ren Zhang
- Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
| | - Chun-Ting Zhang
- Department of Physics, Tianjin University, Tianjin 300072, China
- Corresponding author ()
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70
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Abstract
The replication of the chromosome is among the most essential functions of the bacterial cell and influences many other cellular mechanisms, from gene expression to cell division. Yet the way it impacts on the bacterial chromosome was not fully acknowledged until the availability of complete genomes allowed one to look upon genomes as more than bags of genes. Chromosomal replication includes a set of asymmetric mechanisms, among which are a division in a lagging and a leading strand and a gradient between early and late replicating regions. These differences are the causes of many of the organizational features observed in bacterial genomes, in terms of both gene distribution and sequence composition along the chromosome. When asymmetries or gradients increase in some genomes, e.g. due to a different composition of the DNA polymerase or to a higher growth rate, so do the corresponding biases. As some of the features of the chromosome structure seem to be under strong selection, understanding such biases is important for the understanding of chromosome organization and adaptation. Inversely, understanding chromosome organization may shed further light on questions relating to replication and cell division. Ultimately, the understanding of the interplay between these different elements will allow a better understanding of bacterial genetics and evolution.
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Affiliation(s)
- Eduardo P C Rocha
- Atelier de Bioinformatique, Université Pierre et Marie Curie, 12, Rue Cuvier, 75005 Paris, and Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
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71
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Zhang R, Zhang CT. Identification of replication origins in the genome of the methanogenic archaeon, Methanocaldococcus jannaschii. Extremophiles 2004; 8:253-8. [PMID: 15197606 DOI: 10.1007/s00792-004-0385-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Accepted: 02/10/2004] [Indexed: 10/26/2022]
Abstract
Methanocaldococcus jannaschii has been notorious as an archaeon in which the replication origins are difficult to identify. Although extensive efforts have been exerted on this issue, the locations of replication origins still remain elusive 7 years after the publication of its complete genome sequence in 1996. Ambiguous results were obtained in identifying the replication origins of M. jannaschii based on all theoretical and experimental approaches. In the genome of M. jannaschii, we found that an ORF (MJ0774), annotated as a hypothetical protein, is a homologue of the Cdc6 protein. The position of the gene is at a global minimum of the x component of the Z curve, i.e., RY disparity curve, which has been used to identify replication origins in other Archaea. In addition, an intergenic region (694,540-695,226 bp) that is between the cdc6 gene and an adjacent ORF shows almost all the characteristics of known replication origins, i.e., it is highly rich in AT composition (80%) and contains multiple copies of repeat elements and AT stretches. Therefore, these lines of evidence strongly suggest that the identified region is a replication origin, which is designated as oriC1. The analysis of the y component of the Z curve, i.e., MK disparity curve, suggests the presence of another replication origin corresponding to one of the peaks in the MK disparity curve at around 1,388 kb of the genome.
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Affiliation(s)
- Ren Zhang
- Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, 300060 Tianjin, China
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72
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Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 2004; 116:25-38. [PMID: 14718164 DOI: 10.1016/s0092-8674(03)01034-1] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Eukaryotic chromosomes possess multiple origins of replication, whereas bacterial chromosomes are replicated from a single origin. The archaeon Pyrococcus abyssi also appears to have a single origin, suggesting a common rule for prokaryotes. However, in the current work, we describe the identification of two active origins of replication in the single chromosome of the hyperthermophilic archaeon Sulfolobus solfataricus. Further, we identify conserved sequence motifs within the origins that are recognized by a family of three Sulfolobus proteins that are homologous to the eukaryotic initiator proteins Orc1 and Cdc6. We demonstrate that the two origins are recognized by distinct subsets of these Orc1/Cdc6 homologs. These data, in conjunction with an analysis of the levels of the three Orc1/Cdc6 proteins in different growth phases and cell cycle stages, lead us to propose a model for the roles for these proteins in modulating origin activity.
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Affiliation(s)
- Nicholas P Robinson
- Medical Research Council Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
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73
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Abstract
Genome sequences of a number of archaea have revealed an apparent paradox in the phylogenies of the bacteria, archaea, and eukarya, as well as an intriguing set of problems to be resolved in the study of DNA replication. The archaea, long thought to be bacteria, are not only different enough to merit their own domain but also appear to be an interesting mosaic of bacterial, eukaryal, and unique features. Most archaeal proteins participating in DNA replication are more similar in sequence to those found in eukarya than to analogous replication proteins in bacteria. However, archaea have only a subset of the eukaryal replication machinery, apparently needing fewer polypeptides and structurally simpler complexes. The archaeal replication apparatus also contains features not found in other organisms owing, in part, to the broad range of environmental conditions, some extreme, in which members of this domain thrive. In this review the current knowledge of the mechanisms governing DNA replication in archaea is summarized and the similarities and differences of those of bacteria and eukarya are highlighted.
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Affiliation(s)
- Beatrice Grabowski
- University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
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74
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Kaufmann G, Nethanel T. Did an early version of the eukaryal replisome enable the emergence of chromatin? PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 77:173-209. [PMID: 15196893 DOI: 10.1016/s0079-6603(04)77005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Gabriel Kaufmann
- Biochemistry Department, Tel Aviv University, Ramat Aviv 69978, Israel
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75
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Berquist BR, DasSarma S. An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol 2003; 185:5959-66. [PMID: 14526006 PMCID: PMC225043 DOI: 10.1128/jb.185.20.5959-5966.2003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report on the identification and first cloning of an autonomously replicating sequence element from the chromosome of an archaeon, the extreme halophile Halobacterium strain NRC-1. The putative replication origin was identified by association with the orc7 gene and replication ability in the host strain, demonstrated by cloning into a nonreplicating plasmid. Deletion analysis showed that sequences located up to 750 bp upstream of the orc7 gene translational start, plus the orc7 gene and 50 bp downstream, are sufficient to endow the plasmid with replication ability, as judged by expression of a plasmid-encoded mevinolin resistance selectable marker and plasmid recovery after transformation. Sequences located proximal to the two other chromosomally carried haloarchaeal orc genes (orc6 and orc8) are not able to promote efficient autonomous replication. Located within the 750-bp region upstream of orc7 is a nearly perfect inverted repeat of 31 bp, which flanks an extremely AT-rich (44%) stretch of 189 bp. The replication ability of the plasmid was lost when one copy of the inverted repeat was deleted. Additionally, the inverted repeat structure near orc7 homologs in the genomic sequences of two other halophiles, Haloarcula marismortui and Haloferax volcanii, is highly conserved. Our results indicate that, in halophilic archaea, a chromosomal origin of replication is physically linked to orc7 homologs and that this element is sufficient to promote autonomous replication. We discuss the finding of a functional haloarchaeal origin in relation to the large number of orc1-cdc6 homologs identified in the genomes of all haloarchaea to date.
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Affiliation(s)
- Brian R Berquist
- Molecular and Cell Biology Program, University of Maryland, Baltimore, and Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, Maryland 21202, USA
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76
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Abstract
Whereas the process of DNA replication is fundamentally conserved in the three domains of life, the archaeal system is closer to that of eukarya than bacteria. In the time since the complete genome sequences of several members of the archaeal domain became available, there has been a burst of research on archaeal DNA replication. These studies have led to both expected and surprising findings. This review summarizes the search for origins of replication in archaea, and our current knowledge of initiation, the process by which replication origins are recognized, the DNA molecule is unwound and the replicative helicase is loaded onto the DNA in preparation for DNA synthesis. The similarities and differences of the initiation process in archea, bacteria and eukarya are also summarized.
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Affiliation(s)
- Lori M Kelman
- Montgomery College, 20200 Observation Drive, Germantown, MD 20876, USA.
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77
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Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Quérellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 2003; 47:1495-512. [PMID: 12622808 DOI: 10.1046/j.1365-2958.2003.03381.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii, whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.
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Affiliation(s)
- Georges N Cohen
- Institut Pasteur, 25,28 rue du Docteur Roux, 75724 Paris CEDEX 15, France
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