Archaeal DNA replication and repair: new genetic, biophysical and molecular tools for discovering and characterizing enzymes, pathways and mechanisms.
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[1] M. Adams,et al. Natural Competence in the Hyperthermophilic Archaeon Pyrococcus furiosus Facilitates Genetic Manipulation: Construction of Markerless Deletions of Genes Encoding the Two Cytoplasmic Hydrogenases , 2011, Applied and Environmental Microbiology.
[2] Z. Kelman,et al. Thermococcus kodakarensis encodes three MCM homologs but only one is essential , 2011, Nucleic acids research.
[3] Boris G. Mirkin,et al. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell , 2005, Nucleic acids research.
[4] G. Wilson. Organization of restriction-modification systems. , 1991, Nucleic acids research.
[5] Z. Kelman,et al. Do Archaea Need an Origin of Replication? , 2017, Trends in Microbiology.
[6] Nicholas E. Dixon,et al. Replicative DNA polymerases. , 2013, Cold Spring Harbor perspectives in biology.
[7] Kin-Fan Au,et al. PacBio Sequencing and Its Applications , 2015, Genom. Proteom. Bioinform..
[8] H. Daiyasu,et al. Comparative analyses of the two proliferating cell nuclear antigens from the hyperthermophilic archaeon, Thermococcus kodakarensis , 2012, Genes to cells : devoted to molecular & cellular mechanisms.
[9] H. Daiyasu,et al. Biochemical and genetical analyses of the three mcm genes from the hyperthermophilic archaeon, Thermococcus kodakarensis , 2011, Genes to cells : devoted to molecular & cellular mechanisms.
[10] Mary E. Miller,et al. Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae Model System , 2014, Genetics.
[11] M. Botchan,et al. Mechanisms and regulation of DNA replication initiation in eukaryotes , 2017, Critical reviews in biochemistry and molecular biology.
[12] Jerard Hurwitz,et al. Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis , 2011, Proceedings of the National Academy of Sciences.
[13] Z. Kelman,et al. Unwinding the structure and function of the archaeal MCM helicase , 2009, Molecular microbiology.
[14] Joanna Bybee,et al. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes , 2015, Nucleic acids research.
[15] Y. Ishino,et al. Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication , 2016, Nucleic acids research.
[16] Travis H. Hileman,et al. A novel mechanism for regulating the activity of proliferating cell nuclear antigen by a small protein , 2014, Nucleic acids research.
[17] T. Fukui,et al. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. , 2005, Genome research.
[18] S. MacNeill,et al. Structure and function of the GINS complex, a key component of the eukaryotic replisome. , 2010, The Biochemical journal.
[19] E V Koonin,et al. Phosphoesterase domains associated with DNA polymerases of diverse origins. , 1998, Nucleic acids research.
[20] J. W. Picking,et al. Genetic techniques for the archaea. , 2013, Annual review of genetics.
[21] B. Stillman,et al. Principles and concepts of DNA replication in bacteria, archaea, and eukarya. , 2013, Cold Spring Harbor perspectives in biology.
[22] Dongwan D. Kang,et al. The Epigenomic Landscape of Prokaryotes , 2016, PLoS genetics.
[23] Z. Kelman,et al. Archaeal DNA Polymerase D but Not DNA Polymerase B Is Required for Genome Replication in Thermococcus kodakarensis , 2013, Journal of bacteriology.
[24] T. Boulikas,et al. Common structural features of replication origins in all life forms , 1996, Journal of cellular biochemistry.
[25] S. Onesti,et al. Structure and evolutionary origins of the CMG complex , 2013, Chromosoma.
[26] P. Kenis,et al. Comparative Analyses , 2020, Institutional Responses to Drug Demand in Central Europe.
[27] Daniel L. Vera,et al. Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq , 2018, Nature Protocols.
[28] A. Camilli,et al. Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.
[29] J. van der Oost,et al. The chromosome copy number of the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 , 2015, Extremophiles.
[30] M. DePamphilis. 2 Origins of DNA Replication , 1996 .
[31] Z. Kelman,et al. Characterization of DNA Primase Complex Isolated from the Archaeon, Thermococcus kodakaraensis* , 2012, The Journal of Biological Chemistry.
[32] J. Reeve,et al. Chromosome packaging by archaeal histones. , 2001, Advances in applied microbiology.
[33] Antoine M. van Oijen,et al. Single-molecule studies of the replisome. , 2010, Annual review of biophysics.
[34] W. Metcalf,et al. Genetic manipulation of Methanosarcina spp. , 2012, Front. Microbio..
[35] H. Myllykallio,et al. The heterodimeric primase from the euryarchaeon Pyrococcus abyssi: a multifunctional enzyme for initiation and repair? , 2007, Journal of molecular biology.
[36] Friedrich Lottspeich,et al. An exosome‐like complex in Sulfolobus solfataricus , 2003, EMBO reports.
[37] M. O’Donnell,et al. The Eukaryotic CMG Helicase at the Replication Fork: Emerging Architecture Reveals an Unexpected Mechanism. , 2018, BioEssays : news and reviews in molecular, cellular and developmental biology.
[38] Y. Ishino,et al. The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis , 2017, Nucleic acids research.
[39] Kevin A. Fiala,et al. Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu. , 2004, Biochemistry.
[40] P. Forterre,et al. In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[41] F. J. López de Saro. Regulation of Interactions with Sliding Clamps During DNA Replication and Repair , 2009, Current genomics.
[42] S. Jentsch,et al. PCNA, the Maestro of the Replication Fork , 2007, Cell.
[43] M. O’Donnell,et al. Evolution of replication machines , 2016, Critical reviews in biochemistry and molecular biology.
[44] K. Skarstad,et al. Regulating DNA replication in bacteria. , 2013, Cold Spring Harbor perspectives in biology.
[45] Z. Kelman,et al. Archaeal DNA replication. , 2014, Annual review of genetics.
[46] Alessandro Costa,et al. Structural biology of MCM helicases , 2009, Critical reviews in biochemistry and molecular biology.
[47] Margaret R. Heider,et al. Defining the RNaseH2 enzyme-initiated ribonucleotide excision repair pathway in Archaea , 2017, The Journal of Biological Chemistry.
[48] S. Bell. DNA replication: archaeal oriGINS , 2011, BMC Biology.
[49] L. Prakash,et al. Interaction with PCNA is essential for yeast DNA polymerase eta function. , 2001, Molecular cell.
[50] G. Tell,et al. Base excision repair in Archaea: back to the future in DNA repair. , 2014, DNA repair.
[51] M. Dyall-Smith,et al. Construction and analysis of a recombination‐deficient (radA) mutant of Haloferax volcanii , 1997, Molecular microbiology.
[52] K. Eckert,et al. Eukaryotic Replicative DNA Polymerases , 2014 .
[53] Jan Mrázek,et al. Genome-scale analysis of gene function in the hydrogenotrophic methanogenic archaeon Methanococcus maripaludis , 2013, Proceedings of the National Academy of Sciences.
[54] Z. Kelman,et al. Affinity Purification of an Archaeal DNA Replication Protein Network , 2010, mBio.
[55] Eugene V Koonin,et al. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes , 2012, Biology Direct.
[56] Y. Kawarabayasi,et al. Three Proliferating Cell Nuclear Antigen-Like Proteins Found in the Hyperthermophilic Archaeon Aeropyrum pernix: Interactions with the Two DNA Polymerases , 2002, Journal of bacteriology.
[57] P. Forterre,et al. Genetic analysis of DNA repair in the hyperthermophilic archaeon, Thermococcus kodakaraensis. , 2010, Genes & genetic systems.
[58] Thermococcus kodakarensis has two functional PCNA homologs but only one is required for viability , 2013, Extremophiles.
[59] N. Tanner,et al. Visualizing DNA replication at the single-molecule level. , 2010, Methods in enzymology.
[60] Erbay Yigit,et al. A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome , 2015, BMC Genomics.
[61] K. Moore,et al. An alternative beads‐on‐a‐string chromatin architecture in Thermococcus kodakarensis , 2013, EMBO reports.
[62] Z. Kelman. The replication origin of archaea is finally revealed. , 2000, Trends in biochemical sciences.
[63] M. Washington,et al. PCNA structure and function: insights from structures of PCNA complexes and post-translationally modified PCNA. , 2012, Sub-cellular biochemistry.
[64] Margaret R. Heider,et al. The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis , 2017, Journal of bacteriology.
[65] H. Atomi,et al. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. , 2011, FEMS microbiology reviews.
[66] D. MacAlpine,et al. DNA replication origins—where do we begin? , 2016, Genes & development.
[67] Kevin A. Fiala,et al. Pre-steady-state kinetic studies of the fidelity of Sulfolobus solfataricus P2 DNA polymerase IV. , 2004, Biochemistry.
[68] Stephen D. Bell,et al. DNA Replication in the Archaea , 2006, Microbiology and Molecular Biology Reviews.
[69] Z. Kelman,et al. High-temperature single-molecule kinetic analysis of thermophilic archaeal MCM helicases , 2016, Nucleic acids research.
[70] Gary D Bader,et al. Chromatin is an ancient innovation conserved between Archaea and Eukarya , 2012, eLife.
[71] M. DePamphilis. DNA replication in eukaryotic cells , 1996 .
[72] Z. Kelman,et al. The diverse spectrum of sliding clamp interacting proteins , 2003, FEBS letters.
[73] C. Lange,et al. Genome Copy Numbers and Gene Conversion in Methanogenic Archaea , 2010, Journal of bacteriology.
[74] P. DasSarma,et al. Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1 , 2007, BMC Genetics.
[75] J. Doudna,et al. The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.
[76] M. Botchan,et al. Mechanisms for initiating cellular DNA replication , 2017, Science.
[77] S. Bell,et al. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. , 2003, Molecular cell.
[78] Z. Kelman,et al. ARCHAEAL DNA REPLICATION: Eukaryal , 2003 .
[79] C. Pittenger,et al. Characterization of a mutant strain of Saccharomyces cerevisiae with a deletion of the RAD27 gene, a structural homolog of the RAD2 nucleotide excision repair gene , 1995, Journal of bacteriology.
[80] Conrad A. Nieduszynski,et al. Accelerated growth in the absence of DNA replication origins , 2013, Nature.
[81] Academic Excellence. Accelerated Growth , 2020, Definitions.
[82] G. Fan,et al. DNA Methylation and Its Basic Function , 2013, Neuropsychopharmacology.
[83] Byung-Kwan Cho,et al. Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1 , 2017, Scientific Reports.
[84] Z. D. Blount,et al. The unexhausted potential of E. coli , 2015, eLife.
[85] T. Kunkel,et al. RNase H2-initiated ribonucleotide excision repair. , 2012, Molecular cell.
[86] K. Komori,et al. Copyright © 1998, American Society for Microbiology A Novel DNA Polymerase Family Found in Archaea , 1997 .
[87] H. Toh,et al. A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[88] Z. Kelman,et al. The Roles of Family B and D DNA Polymerases in Thermococcus Species 9°N Okazaki Fragment Maturation* , 2015, The Journal of Biological Chemistry.
[89] Z. Kelman,et al. The archaeal PCNA proteins. , 2011, Biochemical Society transactions.
[90] D. Kohda,et al. Archaeal primase bridging the gap between RNA and DNA polymerases , 2001, Current Biology.
[91] Haruyuki Atomi,et al. Overview of the genetic tools in the Archaea , 2012, Front. Microbio..
[92] B. Stillman,et al. A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[93] Travis H. Hileman,et al. Genetics Techniques for Thermococcus kodakarensis , 2012, Front. Microbio..
[94] J. McPherson,et al. Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.
[95] Konrad U. Förstner,et al. Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis , 2014, BMC Genomics.
[96] Z. Kelman,et al. The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[97] S. Bell,et al. The promiscuous primase. , 2005, Trends in genetics : TIG.
[98] R. Crouch,et al. The Balancing Act of Ribonucleotides in DNA. , 2016, Trends in biochemical sciences.
[99] A. F. Gardner,et al. Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance* , 2015, The Journal of Biological Chemistry.
[100] D. Patel,et al. Lesion processing: high-fidelity versus lesion-bypass DNA polymerases. , 2008, Trends in biochemical sciences.
[101] Francisco J. López de Saro,et al. Regulation of Interactions with Sliding Clamps During DNA Replication and Repair , 2009 .
[102] M. Wagner,et al. Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius , 2012, Front. Microbio..
[103] E. Koonin,et al. GINS, a central nexus in the archaeal DNA replication fork , 2006, EMBO reports.
[104] Z. Kelman,et al. Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication , 2017, Front. Microbiol..
[105] M. F. White. Homologous recombination in the archaea: the means justify the ends. , 2011, Biochemical Society transactions.
[106] Genetic studies on the virus-like regions in the genome of hyperthermophilic archaeon, Thermococcus kodakarensis , 2012, Extremophiles.
[107] M. F. White,et al. Archaeal DNA replication and repair. , 2005, Current opinion in microbiology.
[108] Jonathan A Eisen,et al. Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii , 2007, PLoS genetics.