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Volumn 5, Issue JULY, 2014, Pages

Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery

Author keywords

Archaea; DNA polymerases; DNA replication; Enzyme inactivation; Mobile genetic elements

Indexed keywords

DNA POLYMERASE;

EID: 84905451755     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00354     Document Type: Review
Times cited : (58)

References (67)
  • 1
    • 0032529457 scopus 로고    scopus 로고
    • Phosphoesterase domains associated with DNA polymerases of diverse origins
    • doi: 10.1093/nar/26.16.3746
    • Aravind, L., and Koonin, E. V. (1998). Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 26, 3746-3752. doi: 10.1093/nar/26.16.3746
    • (1998) Nucleic Acids Res , vol.26 , pp. 3746-3752
    • Aravind, L.1    Koonin, E.V.2
  • 2
    • 33744929889 scopus 로고    scopus 로고
    • His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus
    • doi: 10.1016/j.virol.2006.02.005
    • Bath, C., Cukalac, T., Porter, K., and Dyall-Smith, M. L. (2006). His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350, 228-239. doi: 10.1016/j.virol.2006.02.005
    • (2006) Virology , vol.350 , pp. 228-239
    • Bath, C.1    Cukalac, T.2    Porter, K.3    Dyall-Smith, M.L.4
  • 3
    • 84857853904 scopus 로고    scopus 로고
    • Kinetics and fidelity of polymerization by DNA polymerase III from Sulfolobus solfataricus
    • doi: 10.1021/bi201799a
    • Bauer, R. J., Begley, M. T., and Trakselis, M. A. (2012). Kinetics and fidelity of polymerization by DNA polymerase III from Sulfolobus solfataricus. Biochemistry 51, 1996-2007. doi: 10.1021/bi201799a
    • (2012) Biochemistry , vol.51 , pp. 1996-2007
    • Bauer, R.J.1    Begley, M.T.2    Trakselis, M.A.3
  • 4
    • 84899860411 scopus 로고    scopus 로고
    • Structure-Function Studies of DNA Polymerase lambda
    • doi: 10.1021/bi4017236
    • Bebenek, K., Pedersen, L. C., and Kunkel, T. A. (2014). Structure-Function Studies of DNA Polymerase lambda. Biochemistry 53, 2781-2792. doi: 10.1021/bi4017236
    • (2014) Biochemistry , vol.53 , pp. 2781-2792
    • Bebenek, K.1    Pedersen, L.C.2    Kunkel, T.A.3
  • 5
    • 0035997368 scopus 로고    scopus 로고
    • DNA replication in eukaryotic cells
    • doi: 10.1146/annurev.biochem.71.110601.135425
    • Bell, S. P., and Dutta, A. (2002). DNA replication in eukaryotic cells. Annu. Rev. Biochem. 71, 333-374. doi: 10.1146/annurev.biochem.71.110601.135425
    • (2002) Annu. Rev. Biochem , vol.71 , pp. 333-374
    • Bell, S.P.1    Dutta, A.2
  • 6
    • 0035941229 scopus 로고    scopus 로고
    • Eukaryotic DNA polymerases: proposal for a revised nomenclature
    • doi: 10.1074/jbc.R100056200
    • Burgers, P. M., Koonin, E. V., Bruford, E., Blanco, L., Burtis, K. C., Christman, M. F., et al. (2001). Eukaryotic DNA polymerases: proposal for a revised nomenclature. J. Biol. Chem. 276, 43487-43490. doi: 10.1074/jbc.R100056200
    • (2001) J. Biol. Chem , vol.276 , pp. 43487-43490
    • Burgers, P.M.1    Koonin, E.V.2    Bruford, E.3    Blanco, L.4    Burtis, K.C.5    Christman, M.F.6
  • 7
    • 0032564361 scopus 로고    scopus 로고
    • A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase
    • doi: 10.1073/pnas.95.24.14250
    • Cann, I. K., Komori, K., Toh, H., Kanai, S., and Ishino, Y. (1998). A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 95, 14250-14255. doi: 10.1073/pnas.95.24.14250
    • (1998) Proc. Natl. Acad. Sci. U.S.A , vol.95 , pp. 14250-14255
    • Cann, I.K.1    Komori, K.2    Toh, H.3    Kanai, S.4    Ishino, Y.5
  • 8
    • 32044468517 scopus 로고    scopus 로고
    • Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans
    • doi: 10.1016/j.jmb.2005.12.036
    • Choi, J. J., Nam, K. H., Min, B., Kim, S. J., Soll, D., and Kwon, S. T. (2006). Protein trans-splicing and characterization of a split family B-type DNA polymerase from the hyperthermophilic archaeal parasite Nanoarchaeum equitans. J. Mol. Biol. 356, 1093-1106. doi: 10.1016/j.jmb.2005.12.036
    • (2006) J. Mol. Biol , vol.356 , pp. 1093-1106
    • Choi, J.J.1    Nam, K.H.2    Min, B.3    Kim, S.J.4    Soll, D.5    Kwon, S.T.6
  • 9
    • 80052406753 scopus 로고    scopus 로고
    • Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication
    • doi: 10.1074/jbc.M111.258038
    • Choi, J. Y., Eoff, R. L., Pence, M. G., Wang, J., Martin, M. V., Kim, E. J., et al. (2011). Roles of the four DNA polymerases of the crenarchaeon Sulfolobus solfataricus and accessory proteins in DNA replication. J. Biol. Chem. 286, 31180-31193. doi: 10.1074/jbc.M111.258038
    • (2011) J. Biol. Chem , vol.286 , pp. 31180-31193
    • Choi, J.Y.1    Eoff, R.L.2    Pence, M.G.3    Wang, J.4    Martin, M.V.5    Kim, E.J.6
  • 10
    • 84877977688 scopus 로고    scopus 로고
    • Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis
    • doi: 10.1128/JB.02037-12
    • Cubonova, L., Richardson, T., Burkhart, B. W., Kelman, Z., Connolly, B. A., Reeve, J. N., et al. (2013). Archaeal DNA polymerase D but not DNA polymerase B is required for genome replication in Thermococcus kodakarensis. J. Bacteriol. 195, 2322-2328. doi: 10.1128/JB.02037-12
    • (2013) J. Bacteriol , vol.195 , pp. 2322-2328
    • Cubonova, L.1    Richardson, T.2    Burkhart, B.W.3    Kelman, Z.4    Connolly, B.A.5    Reeve, J.N.6
  • 11
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: a fingerprint of proteins that physically interact
    • doi: 10.1016/S0968-0004(98)01274-2
    • Dandekar, T., Snel, B., Huynen, M., and Bork, P. (1998). Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324-328. doi: 10.1016/S0968-0004(98)01274-2
    • (1998) Trends Biochem. Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 12
    • 84860271761 scopus 로고    scopus 로고
    • DNA polymerases: mechanistic insight from biochemical and biophysical studies
    • doi: 10.2741/3941
    • Delagoutte, E. (2012). DNA polymerases: mechanistic insight from biochemical and biophysical studies. Front. Biosci. (Landmark Ed). 17, 509-544. doi: 10.2741/3941
    • (2012) Front. Biosci. (Landmark Ed) , vol.17 , pp. 509-544
    • Delagoutte, E.1
  • 13
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: multiple sequence alignment with high accuracy and high throughput
    • doi: 10.1093/nar/gkh340
    • Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic. Acids Res. 32, 1792-1797. doi: 10.1093/nar/gkh340
    • (2004) Nucleic. Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 14
    • 0031822199 scopus 로고    scopus 로고
    • Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases
    • doi: 10.1093/oxfordjournals.molbev.a026028
    • Edgell, D. R., Malik, S. B., and Doolittle, W. F. (1998). Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Mol. Biol. Evol. 15, 1207-1217. doi: 10.1093/oxfordjournals.molbev.a026028
    • (1998) Mol. Biol. Evol , vol.15 , pp. 1207-1217
    • Edgell, D.R.1    Malik, S.B.2    Doolittle, W.F.3
  • 15
    • 0036107982 scopus 로고    scopus 로고
    • Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins
    • doi: 10.1007/s00239-001-0078-x
    • Filee, J., Forterre, P., Sen-Lin, T., and Laurent, J. (2002). Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins. J. Mol. Evol. 54, 763-773. doi: 10.1007/s00239-001-0078-x
    • (2002) J. Mol. Evol , vol.54 , pp. 763-773
    • Filee, J.1    Forterre, P.2    Sen-Lin, T.3    Laurent, J.4
  • 16
    • 84884223995 scopus 로고    scopus 로고
    • The major role of viruses in cellular evolution: facts and hypotheses
    • doi: 10.1016/j.coviro.2013.06.013
    • Forterre, P., and Prangishvili, D. (2013). The major role of viruses in cellular evolution: facts and hypotheses. Curr. Opin. Virol. 3, 558-565. doi: 10.1016/j.coviro.2013.06.013
    • (2013) Curr. Opin. Virol , vol.3 , pp. 558-565
    • Forterre, P.1    Prangishvili, D.2
  • 17
    • 39749200124 scopus 로고    scopus 로고
    • Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant
    • doi: 10.1128/JB.01463-07
    • Gawel, D., Pham, P. T., Fijalkowska, I. J., Jonczyk, P., and Schaaper, R. M. (2008). Role of accessory DNA polymerases in DNA replication in Escherichia coli: analysis of the dnaX36 mutator mutant. J. Bacteriol. 190, 1730-1742. doi: 10.1128/JB.01463-07
    • (2008) J. Bacteriol , vol.190 , pp. 1730-1742
    • Gawel, D.1    Pham, P.T.2    Fijalkowska, I.J.3    Jonczyk, P.4    Schaaper, R.M.5
  • 18
    • 84898989880 scopus 로고    scopus 로고
    • A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2
    • doi: 10.1093/nar/gkt1385
    • Gill, S., Krupovic, M., Desnoues, N., Beguin, P., Sezonov, G., and Forterre, P. (2014). A highly divergent archaeo-eukaryotic primase from the Thermococcus nautilus plasmid, pTN2. Nucleic Acids Res. 42, 3707-3719. doi: 10.1093/nar/gkt1385
    • (2014) Nucleic Acids Res , vol.42 , pp. 3707-3719
    • Gill, S.1    Krupovic, M.2    Desnoues, N.3    Beguin, P.4    Sezonov, G.5    Forterre, P.6
  • 20
    • 82355180998 scopus 로고    scopus 로고
    • The archaeal 'TACK' superphylum and the origin of eukaryotes
    • doi: 10.1016/j.tim.2011.09.002
    • Guy, L., and Ettema, T. J. (2011). The archaeal 'TACK' superphylum and the origin of eukaryotes. Trends Microbiol. 19, 580-587. doi: 10.1016/j.tim.2011.09.002
    • (2011) Trends Microbiol , vol.19 , pp. 580-587
    • Guy, L.1    Ettema, T.J.2
  • 21
    • 84888643083 scopus 로고    scopus 로고
    • Accelerated growth in the absence of DNA replication origins
    • doi: 10.1038/nature12650
    • Hawkins, M., Malla, S., Blythe, M. J., Nieduszynski, C. A., and Allers, T. (2013). Accelerated growth in the absence of DNA replication origins. Nature 503, 544-547. doi: 10.1038/nature12650
    • (2013) Nature , vol.503 , pp. 544-547
    • Hawkins, M.1    Malla, S.2    Blythe, M.J.3    Nieduszynski, C.A.4    Allers, T.5
  • 22
    • 20444377771 scopus 로고    scopus 로고
    • The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication
    • doi: 10.1016/j.jmb.2005.04.042
    • Henneke, G., Flament, D., Hubscher, U., Querellou, J., and Raffin, J. P. (2005). The hyperthermophilic euryarchaeota Pyrococcus abyssi likely requires the two DNA polymerases D and B for DNA replication. J. Mol. Biol. 350, 53-64. doi: 10.1016/j.jmb.2005.04.042
    • (2005) J. Mol. Biol , vol.350 , pp. 53-64
    • Henneke, G.1    Flament, D.2    Hubscher, U.3    Querellou, J.4    Raffin, J.P.5
  • 23
    • 0033616725 scopus 로고    scopus 로고
    • Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius
    • doi: 10.1073/pnas.96.7.3600
    • Hopfner, K. P., Eichinger, A., Engh, R. A., Laue, F., Ankenbauer, W., Huber, R., et al. (1999). Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc. Natl. Acad. Sci. U.S.A. 96, 3600-3605. doi: 10.1073/pnas.96.7.3600
    • (1999) Proc. Natl. Acad. Sci. U.S.A , vol.96 , pp. 3600-3605
    • Hopfner, K.P.1    Eichinger, A.2    Engh, R.A.3    Laue, F.4    Ankenbauer, W.5    Huber, R.6
  • 24
    • 22444435033 scopus 로고    scopus 로고
    • Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members
    • doi: 10.1093/nar/gki702
    • Iyer, L. M., Koonin, E. V., Leipe, D. D., and Aravind, L. (2005). Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res. 33, 3875-3896. doi: 10.1093/nar/gki702
    • (2005) Nucleic Acids Res , vol.33 , pp. 3875-3896
    • Iyer, L.M.1    Koonin, E.V.2    Leipe, D.D.3    Aravind, L.4
  • 25
    • 33846695786 scopus 로고    scopus 로고
    • Y-family DNA polymerases in Escherichia coli
    • doi: 10.1016/j.tim.2006.12.004
    • Jarosz, D. F., Beuning, P. J., Cohen, S. E., and Walker, G. C. (2007). Y-family DNA polymerases in Escherichia coli. Trends Microbiol. 15, 70-77. doi: 10.1016/j.tim.2006.12.004
    • (2007) Trends Microbiol , vol.15 , pp. 70-77
    • Jarosz, D.F.1    Beuning, P.J.2    Cohen, S.E.3    Walker, G.C.4
  • 26
    • 2342597828 scopus 로고    scopus 로고
    • Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D
    • doi: 10.1093/nar/gkh558
    • Jokela, M., Eskelinen, A., Pospiech, H., Rouvinen, J., and Syvaoja, J. E. (2004). Characterization of the 3' exonuclease subunit DP1 of Methanococcus jannaschii replicative DNA polymerase D. Nucleic Acids Res. 32, 2430-2440. doi: 10.1093/nar/gkh558
    • (2004) Nucleic Acids Res , vol.32 , pp. 2430-2440
    • Jokela, M.1    Eskelinen, A.2    Pospiech, H.3    Rouvinen, J.4    Syvaoja, J.E.5
  • 27
    • 0033214481 scopus 로고    scopus 로고
    • Isolation and characterization of a split B-type DNA polymerase from the archaeon Methanobacterium thermoautotrophicum deltaH
    • doi: 10.1074/jbc.274.40.28751
    • Kelman, Z., Pietrokovski, S., and Hurwitz, J. (1999). Isolation and characterization of a split B-type DNA polymerase from the archaeon Methanobacterium thermoautotrophicum deltaH. J. Biol. Chem. 274, 28751-28761. doi: 10.1074/jbc.274.40.28751
    • (1999) J. Biol. Chem , vol.274 , pp. 28751-28761
    • Kelman, Z.1    Pietrokovski, S.2    Hurwitz, J.3
  • 28
    • 67650409702 scopus 로고    scopus 로고
    • 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases
    • doi: 10.1038/emboj.2009.150
    • Klinge, S., Nunez-Ramirez, R., Llorca, O., and Pellegrini, L. (2009). 3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases. Embo J. 28, 1978-1987. doi: 10.1038/emboj.2009.150
    • (2009) Embo J , vol.28 , pp. 1978-1987
    • Klinge, S.1    Nunez-Ramirez, R.2    Llorca, O.3    Pellegrini, L.4
  • 29
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics, minimal gene-sets and the last universal common ancestor
    • doi: 10.1038/nrmicro751
    • Koonin, E. V. (2003). Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat. Rev. Microbiol. 1, 127-136. doi: 10.1038/nrmicro751
    • (2003) Nat. Rev. Microbiol , vol.1 , pp. 127-136
    • Koonin, E.V.1
  • 30
    • 84905513696 scopus 로고    scopus 로고
    • The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes
    • doi: 10.1101/cshperspect.a016188
    • Koonin, E. V., and Yutin, N. (2014). The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb. Perspect. Biol. 6:a016188. doi: 10.1101/cshperspect.a016188
    • (2014) Cold Spring Harb. Perspect. Biol , vol.6
    • Koonin, E.V.1    Yutin, N.2
  • 31
    • 84872257668 scopus 로고    scopus 로고
    • Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids
    • doi: 10.1371/journal.pone.0049044
    • Krupovic, M., Gonnet, M., Hania, W. B., Forterre, P., and Erauso, G. (2013). Insights into dynamics of mobile genetic elements in hyperthermophilic environments from five new Thermococcus plasmids. PLoS ONE 8:e49044. doi: 10.1371/journal.pone.0049044
    • (2013) PLoS ONE , vol.8
    • Krupovic, M.1    Gonnet, M.2    Hania, W.B.3    Forterre, P.4    Erauso, G.5
  • 32
    • 78649370567 scopus 로고    scopus 로고
    • The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements
    • doi: 10.1093/molbev/msq161
    • Krupovic, M., Gribaldo, S., Bamford, D. H., and Forterre, P. (2010). The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements. Mol. Biol. Evol. 27, 2716-2732. doi: 10.1093/molbev/msq161
    • (2010) Mol. Biol. Evol , vol.27 , pp. 2716-2732
    • Krupovic, M.1    Gribaldo, S.2    Bamford, D.H.3    Forterre, P.4
  • 33
    • 84902203191 scopus 로고    scopus 로고
    • Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity
    • doi: 10.1186/1741-7007-12-36
    • Krupovic, M., Makarova, K. S., Forterre, P., Prangishvili, D., and Koonin, E. V. (2014a). Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. BMC Biol. 12:36. doi: 10.1186/1741-7007-12-36
    • (2014) BMC Biol , vol.12 , pp. 36
    • Krupovic, M.1    Makarova, K.S.2    Forterre, P.3    Prangishvili, D.4    Koonin, E.V.5
  • 34
    • 84893497778 scopus 로고    scopus 로고
    • Unification of the globally distributed spindle-shaped viruses of the Archaea
    • doi: 10.1128/JVI.02941-13
    • Krupovic, M., Quemin, E. R., Bamford, D. H., Forterre, P., and Prangishvili, D. (2014b). Unification of the globally distributed spindle-shaped viruses of the Archaea. J. Virol. 88, 2354-2358. doi: 10.1128/JVI.02941-13
    • (2014) J. Virol , vol.88 , pp. 2354-2358
    • Krupovic, M.1    Quemin, E.R.2    Bamford, D.H.3    Forterre, P.4    Prangishvili, D.5
  • 35
    • 54249092768 scopus 로고    scopus 로고
    • Dividing the workload at a eukaryotic replication fork
    • doi: 10.1016/j.tcb.2008.08.005
    • Kunkel, T. A., and Burgers, P. M. (2008). Dividing the workload at a eukaryotic replication fork. Trends Cell Biol. 18, 521-527. doi: 10.1016/j.tcb.2008.08.005
    • (2008) Trends Cell Biol , vol.18 , pp. 521-527
    • Kunkel, T.A.1    Burgers, P.M.2
  • 36
    • 84873151038 scopus 로고    scopus 로고
    • Thermococcus kodakarensis DNA replication
    • doi: 10.1042/BST20120303
    • Li, Z., Kelman, L. M., and Kelman, Z. (2013). Thermococcus kodakarensis DNA replication. Biochem. Soc. Trans. 41, 332-338. doi: 10.1042/BST20120303
    • (2013) Biochem. Soc. Trans , vol.41 , pp. 332-338
    • Li, Z.1    Kelman, L.M.2    Kelman, Z.3
  • 37
    • 79551480646 scopus 로고    scopus 로고
    • Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1
    • doi: 10.1042/BST0390104
    • Lipps, G. (2011). Structure and function of the primase domain of the replication protein from the archaeal plasmid pRN1. Biochem. Soc. Trans. 39, 104-106. doi: 10.1042/BST0390104
    • (2011) Biochem. Soc. Trans , vol.39 , pp. 104-106
    • Lipps, G.1
  • 38
    • 59749096849 scopus 로고    scopus 로고
    • The haloarchaeal chromosome replication machinery
    • doi: 10.1042/BST0370108
    • MacNeill, S. A. (2009). The haloarchaeal chromosome replication machinery. Biochem. Soc. Trans. 37, 108-113. doi: 10.1042/BST0370108
    • (2009) Biochem. Soc. Trans , vol.37 , pp. 108-113
    • MacNeill, S.A.1
  • 39
    • 84877122234 scopus 로고    scopus 로고
    • Archaeology of eukaryotic DNA replication
    • doi: 10.1101/cshperspect.a012963
    • Makarova, K. S., and Koonin, E. V. (2013). Archaeology of eukaryotic DNA replication. Cold Spring Harb. Perspect. Biol. 5:a012963. doi: 10.1101/cshperspect.a012963
    • (2013) Cold Spring Harb. Perspect. Biol , vol.5
    • Makarova, K.S.1    Koonin, E.V.2
  • 40
    • 84887971081 scopus 로고    scopus 로고
    • The basic building blocks and evolution of CRISPR-Cas systems
    • doi: 10.1042/BST20130038
    • Makarova, K. S., Wolf, Y. I., and Koonin, E. V. (2013). The basic building blocks and evolution of CRISPR-Cas systems. Biochem. Soc. Trans. 41, 1392-1400. doi: 10.1042/BST20130038
    • (2013) Biochem. Soc. Trans , vol.41 , pp. 1392-1400
    • Makarova, K.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 41
    • 84873164495 scopus 로고    scopus 로고
    • From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell
    • doi: 10.1042/BST20120292
    • Martijn, J., and Ettema, T. J. (2013). From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell. Biochem. Soc. Trans. 41, 451-457. doi: 10.1042/BST20120292
    • (2013) Biochem. Soc. Trans , vol.41 , pp. 451-457
    • Martijn, J.1    Ettema, T.J.2
  • 42
    • 79551469840 scopus 로고    scopus 로고
    • Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii
    • doi: 10.1016/j.febslet.2010.12.040
    • Matsui, I., Urushibata, Y., Shen, Y., Matsui, E., and Yokoyama, H. (2011). Novel structure of an N-terminal domain that is crucial for the dimeric assembly and DNA-binding of an archaeal DNA polymerase D large subunit from Pyrococcus horikoshii. FEBS Lett. 585, 452-458. doi: 10.1016/j.febslet.2010.12.040
    • (2011) FEBS Lett , vol.585 , pp. 452-458
    • Matsui, I.1    Urushibata, Y.2    Shen, Y.3    Matsui, E.4    Yokoyama, H.5
  • 43
    • 35748960204 scopus 로고    scopus 로고
    • The X family portrait: structural insights into biological functions of X family polymerases
    • doi: 10.1016/j.dnarep.2007.05.009
    • Moon, A. F., Garcia-Diaz, M., Batra, V. K., Beard, W. A., Bebenek, K., Kunkel, T. A., et al. (2007). The X family portrait: structural insights into biological functions of X family polymerases. DNA Repair (Amst) 6, 1709-1725. doi: 10.1016/j.dnarep.2007.05.009
    • (2007) DNA Repair (Amst) , vol.6 , pp. 1709-1725
    • Moon, A.F.1    Garcia-Diaz, M.2    Batra, V.K.3    Beard, W.A.4    Bebenek, K.5    Kunkel, T.A.6
  • 44
    • 75749086797 scopus 로고    scopus 로고
    • DNA polymerases at the eukaryotic fork-20 years later
    • doi: 10.1016/j.mrfmmm.2009.08.002
    • Pavlov, Y. I., and Shcherbakova, P. V. (2010). DNA polymerases at the eukaryotic fork-20 years later. Mutat. Res. 685, 45-53. doi: 10.1016/j.mrfmmm.2009.08.002
    • (2010) Mutat. Res , vol.685 , pp. 45-53
    • Pavlov, Y.I.1    Shcherbakova, P.V.2
  • 45
    • 34249726708 scopus 로고    scopus 로고
    • Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms
    • doi: 10.1016/j.virol.2007.03.005
    • Peng, X., Basta, T., Haring, M., Garrett, R. A., and Prangishvili, D. (2007). Genome of the Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms. Virology 364, 237-243. doi: 10.1016/j.virol.2007.03.005
    • (2007) Virology , vol.364 , pp. 237-243
    • Peng, X.1    Basta, T.2    Haring, M.3    Garrett, R.A.4    Prangishvili, D.5
  • 46
    • 0036084146 scopus 로고    scopus 로고
    • InBase: the Intein Database
    • doi: 10.1093/nar/30.1.383
    • Perler, F. B. (2002). InBase: the Intein Database. Nucleic Acids Res. 30, 383-384. doi: 10.1093/nar/30.1.383
    • (2002) Nucleic Acids Res , vol.30 , pp. 383-384
    • Perler, F.B.1
  • 47
    • 0028214350 scopus 로고
    • Protein splicing elements: inteins and exteins-a definition of terms and recommended nomenclature
    • doi: 10.1093/nar/22.7.1125
    • Perler, F. B., Davis, E. O., Dean, G. E., Gimble, F. S., Jack, W. E., Neff, N., et al. (1994). Protein splicing elements: inteins and exteins-a definition of terms and recommended nomenclature. Nucleic Acids Res. 22, 1125-1127. doi: 10.1093/nar/22.7.1125
    • (1994) Nucleic Acids Res , vol.22 , pp. 1125-1127
    • Perler, F.B.1    Davis, E.O.2    Dean, G.E.3    Gimble, F.S.4    Jack, W.E.5    Neff, N.6
  • 48
    • 84861309045 scopus 로고    scopus 로고
    • Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea
    • doi: 10.1128/JVI.06915-11
    • Pietila, M. K., Atanasova, N. S., Manole, V., Liljeroos, L., Butcher, S. J., Oksanen, H. M., et al. (2012). Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J. Virol. 86, 5067-5079. doi: 10.1128/JVI.06915-11
    • (2012) J. Virol , vol.86 , pp. 5067-5079
    • Pietila, M.K.1    Atanasova, N.S.2    Manole, V.3    Liljeroos, L.4    Butcher, S.J.5    Oksanen, H.M.6
  • 49
    • 84874681864 scopus 로고    scopus 로고
    • Insights into head-tailed viruses infecting extremely halophilic archaea
    • doi: 10.1128/JVI.03397-12
    • Pietila, M. K., Laurinmaki, P., Russell, D. A., Ko, C. C., Jacobs-Sera, D., Butcher, S. J., et al. (2013). Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87, 3248-3260. doi: 10.1128/JVI.03397-12
    • (2013) J. Virol , vol.87 , pp. 3248-3260
    • Pietila, M.K.1    Laurinmaki, P.2    Russell, D.A.3    Ko, C.C.4    Jacobs-Sera, D.5    Butcher, S.J.6
  • 50
    • 84876741070 scopus 로고    scopus 로고
    • Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
    • doi: 10.1186/1745-6150-8-9
    • Podar, M., Makarova, K. S., Graham, D. E., Wolf, Y. I., Koonin, E. V., and Reysenbach, A. L. (2013). Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol. Direct 8:9. doi: 10.1186/1745-6150-8-9
    • (2013) Biol. Direct , vol.8 , pp. 9
    • Podar, M.1    Makarova, K.S.2    Graham, D.E.3    Wolf, Y.I.4    Koonin, E.V.5    Reysenbach, A.L.6
  • 51
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • doi: 10.1371/journal.pone.0009490
    • Price, M. N., Dehal, P. S., and Arkin, A. P. (2010). FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. doi: 10.1371/journal.pone.0009490
    • (2010) PLoS ONE , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 52
    • 68149093715 scopus 로고    scopus 로고
    • Search for a 'Tree of Life' in the thicket of the phylogenetic forest
    • doi: 10.1186/jbiol159
    • Puigbo, P., Wolf, Y. I., and Koonin, E. V. (2009). Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J. Biol. 8, 59. doi: 10.1186/jbiol159
    • (2009) J. Biol , vol.8 , pp. 59
    • Puigbo, P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 53
    • 84884141974 scopus 로고    scopus 로고
    • Differential translation tunes uneven production of operon-encoded proteins
    • doi: 10.1016/j.celrep.2013.07.049
    • Quax, T. E., Wolf, Y. I., Koehorst, J. J., Wurtzel, O., van der Oost, R., Ran, W., et al. (2013). Differential translation tunes uneven production of operon-encoded proteins. Cell Rep. 4, 938-944. doi: 10.1016/j.celrep.2013.07.049
    • (2013) Cell Rep , vol.4 , pp. 938-944
    • Quax, T.E.1    Wolf, Y.I.2    Koehorst, J.J.3    Wurtzel, O.4    van der Oost, R.5    Ran, W.6
  • 54
    • 84901301395 scopus 로고    scopus 로고
    • Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea
    • doi: 10.1093/gbe/evu004
    • Raymann, K., Forterre, P., Brochier-Armanet, C., and Gribaldo, S. (2014). Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol. Evol. 6, 192-212. doi: 10.1093/gbe/evu004
    • (2014) Genome Biol. Evol , vol.6 , pp. 192-212
    • Raymann, K.1    Forterre, P.2    Brochier-Armanet, C.3    Gribaldo, S.4
  • 55
    • 51249094314 scopus 로고    scopus 로고
    • A highly conserved family of inactivated archaeal B family DNA polymerases
    • doi: 10.1186/1745-6150-3-32
    • Rogozin, I. B., Makarova, K. S., Pavlov, Y. I., and Koonin, E. V. (2008). A highly conserved family of inactivated archaeal B family DNA polymerases. Biol. Direct 3:32. doi: 10.1186/1745-6150-3-32
    • (2008) Biol. Direct , vol.3 , pp. 32
    • Rogozin, I.B.1    Makarova, K.S.2    Pavlov, Y.I.3    Koonin, E.V.4
  • 56
    • 26844566830 scopus 로고    scopus 로고
    • Structure and mechanism of DNA polymerases
    • doi: 10.1016/S0065-3233(04)71011-6
    • Rothwell, P. J., and Waksman, G. (2005). Structure and mechanism of DNA polymerases. Adv. Protein Chem. 71, 401-440. doi: 10.1016/S0065-3233(04)71011-6
    • (2005) Adv. Protein Chem , vol.71 , pp. 401-440
    • Rothwell, P.J.1    Waksman, G.2
  • 58
    • 84877925540 scopus 로고    scopus 로고
    • The roles of DNA polymerase zeta and the Y family DNA polymerases in promoting or preventing genome instability
    • doi: 10.1016/j.mrfmmm.2012.11.002
    • Sharma, S., Helchowski, C. M., and Canman, C. E. (2013). The roles of DNA polymerase zeta and the Y family DNA polymerases in promoting or preventing genome instability. Mutat. Res. 743-744, 97-110. doi: 10.1016/j.mrfmmm.2012.11.002
    • Mutat. Res , vol.743-744 , Issue.2013 , pp. 97-110
    • Sharma, S.1    Helchowski, C.M.2    Canman, C.E.3
  • 59
    • 0035920137 scopus 로고    scopus 로고
    • Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii
    • doi: 10.1074/jbc.M011762200
    • Shen, Y., Musti, K., Hiramoto, M., Kikuchi, H., Kawarabayashi, Y., and Matsui, I. (2001). Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii. J. Biol. Chem. 276, 27376-27383. doi: 10.1074/jbc.M011762200
    • (2001) J. Biol. Chem , vol.276 , pp. 27376-27383
    • Shen, Y.1    Musti, K.2    Hiramoto, M.3    Kikuchi, H.4    Kawarabayashi, Y.5    Matsui, I.6
  • 60
    • 77953921670 scopus 로고    scopus 로고
    • Structural basis for the suppression of skin cancers by DNA polymerase eta
    • doi: 10.1038/nature09104
    • Silverstein, T. D., Johnson, R. E., Jain, R., Prakash, L., Prakash, S., and Aggarwal, A. K. (2010). Structural basis for the suppression of skin cancers by DNA polymerase eta. Nature 465, 1039-1043. doi: 10.1038/nature09104
    • (2010) Nature , vol.465 , pp. 1039-1043
    • Silverstein, T.D.1    Johnson, R.E.2    Jain, R.3    Prakash, L.4    Prakash, S.5    Aggarwal, A.K.6
  • 61
    • 1642524959 scopus 로고    scopus 로고
    • Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases
    • doi: 10.1098/rstb.2003.1374
    • Steitz, T. A., and Yin, Y. W. (2004). Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases. Philos. Trans. R Soc. Lond. B Biol. Sci. 359, 17-23. doi: 10.1098/rstb.2003.1374
    • (2004) Philos. Trans. R Soc. Lond. B Biol. Sci , vol.359 , pp. 17-23
    • Steitz, T.A.1    Yin, Y.W.2
  • 62
    • 65349186567 scopus 로고    scopus 로고
    • Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors
    • doi: 10.1186/1745-6150-4-11
    • Tahirov, T. H., Makarova, K. S., Rogozin, I. B., Pavlov, Y. I., and Koonin, E. V. (2009). Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol epsilon and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol. Direct 4:11. doi: 10.1186/1745-6150-4-11
    • (2009) Biol. Direct , vol.4 , pp. 11
    • Tahirov, T.H.1    Makarova, K.S.2    Rogozin, I.B.3    Pavlov, Y.I.4    Koonin, E.V.5
  • 63
    • 0036226078 scopus 로고    scopus 로고
    • HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome
    • doi: 10.1046/j.1365-2958.2002.02890.x
    • Tang, S. L., Nuttall, S., Ngui, K., Fisher, C., Lopez, P., and Dyall-Smith, M. (2002). HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome. Mol. Microbiol. 44, 283-296. doi: 10.1046/j.1365-2958.2002.02890.x
    • (2002) Mol. Microbiol , vol.44 , pp. 283-296
    • Tang, S.L.1    Nuttall, S.2    Ngui, K.3    Fisher, C.4    Lopez, P.5    Dyall-Smith, M.6
  • 64
    • 84870950237 scopus 로고    scopus 로고
    • Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
    • doi: 10.1186/1745-6150-7-46
    • Wolf, Y. I., Makarova, K. S., Yutin, N., and Koonin, E. V. (2012). Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 7:46. doi: 10.1186/1745-6150-7-46
    • (2012) Biol. Direct , vol.7 , pp. 46
    • Wolf, Y.I.1    Makarova, K.S.2    Yutin, N.3    Koonin, E.V.4
  • 65
    • 77955268031 scopus 로고    scopus 로고
    • Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases
    • doi: 10.1016/j.febslet.2010.06.026
    • Yamasaki, K., Urushibata, Y., Yamasaki, T., Arisaka, F., and Matsui, I. (2010). Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases. FEBS Lett. 584, 3370-3375. doi: 10.1016/j.febslet.2010.06.026
    • (2010) FEBS Lett , vol.584 , pp. 3370-3375
    • Yamasaki, K.1    Urushibata, Y.2    Yamasaki, T.3    Arisaka, F.4    Matsui, I.5
  • 66
    • 84899827339 scopus 로고    scopus 로고
    • An Overview of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase eta
    • doi: 10.1021/bi500019s
    • Yang, W. (2014). An Overview of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase eta. Biochemistry 53, 2793-2803. doi: 10.1021/bi500019s
    • (2014) Biochemistry , vol.53 , pp. 2793-2803
    • Yang, W.1
  • 67
    • 84861219308 scopus 로고    scopus 로고
    • Phylogenomics of prokaryotic ribosomal proteins
    • doi: 10.1371/journal.pone.0036972
    • Yutin, N., Puigbo, P., Koonin, E. V., and Wolf, Y. I. (2012). Phylogenomics of prokaryotic ribosomal proteins. PLoS ONE 7:e36972. doi: 10.1371/journal.pone.0036972
    • (2012) PLoS ONE , vol.7
    • Yutin, N.1    Puigbo, P.2    Koonin, E.V.3    Wolf, Y.I.4


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