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Volumn 20, Issue 7, 2003, Pages 1134-1142

Retroids in Archaea: Phylogeny and lateral origins

Author keywords

Archaea; Group II intron; Methanosarcina; Origin of introns; Retroelement; Retron

Indexed keywords

RNA DIRECTED DNA POLYMERASE;

EID: 0037743892     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg135     Document Type: Article
Times cited : (64)

References (51)
  • 2
    • 0029043298 scopus 로고
    • Transcription: New insights from studies on Archaea
    • Baumann, P., S. A. Qureshi, and S. P. Jackson. 1995. Transcription: new insights from studies on Archaea. Trends Genet. 11:279-283.
    • (1995) Trends Genet. , vol.11 , pp. 279-283
    • Baumann, P.1    Qureshi, S.A.2    Jackson, S.P.3
  • 3
    • 0026089167 scopus 로고
    • Reverse transcriptase in archaebacteria: Purification and characterization of a primase-reverse-transcriptase complex from Halobacterium halobium
    • Ben-Mahrez, K., I. Sorokine, M. Nakayama, and M. Kohiyama. 1991. Reverse transcriptase in archaebacteria: purification and characterization of a primase-reverse-transcriptase complex from Halobacterium halobium. Eur. J. Biochem. 195:157-162.
    • (1991) Eur. J. Biochem. , vol.195 , pp. 157-162
    • Ben-Mahrez, K.1    Sorokine, I.2    Nakayama, M.3    Kohiyama, M.4
  • 4
    • 0026111327 scopus 로고
    • Group II twintron: An intron within an intron in a chloroplast cytochrome b-559 gene
    • Copertino, D. W., and R. B. Hallick. 1991. Group II twintron: an intron within an intron in a chloroplast cytochrome b-559 gene. EMBO J. 10:433-442.
    • (1991) EMBO J. , vol.10 , pp. 433-442
    • Copertino, D.W.1    Hallick, R.B.2
  • 5
    • 0030034289 scopus 로고    scopus 로고
    • Retrohoming: cDNA-mediated mobility of group II introns requires a catalytic RNA
    • Curcio, M. J., and M. Belfort. 1996. Retrohoming: cDNA-mediated mobility of group II introns requires a catalytic RNA. Cell 84:9-12.
    • (1996) Cell , vol.84 , pp. 9-12
    • Curcio, M.J.1    Belfort, M.2
  • 6
    • 0036493198 scopus 로고    scopus 로고
    • Compilation and analysis of group II intron insertions in bacterial genomes: Evidence for retroelement behavior
    • Dai, L., and S. Zimmerly. 2002. Compilation and analysis of group II intron insertions in bacterial genomes: evidence for retroelement behavior. Nucleic Acids Res. 30:1091-1102.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1091-1102
    • Dai, L.1    Zimmerly, S.2
  • 7
    • 0037278926 scopus 로고    scopus 로고
    • ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs
    • -. 2003. ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs. RNA 9:14-19.
    • (2003) RNA , vol.9 , pp. 14-19
  • 8
    • 0035988323 scopus 로고    scopus 로고
    • The genome of Methanosarcina mazei: Evidence for lateral gene transfer between Bacteria and Archaea
    • Deppenmeier, U., A. Johann, T. Hartsch et al. (22 co-authors). 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and Archaea. J. Mol. Microbiol. Biotechnol. 4:453-461.
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , pp. 453-461
    • Deppenmeier, U.1    Johann, A.2    Hartsch, T.3
  • 9
    • 0036017382 scopus 로고    scopus 로고
    • rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
    • Dimmic, M. W., J. S. Rest, D. P. Mindell, and R. A. Goldstein. 2002. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 55:65-73.
    • (2002) J. Mol. Evol. , vol.55 , pp. 65-73
    • Dimmic, M.W.1    Rest, J.S.2    Mindell, D.P.3    Goldstein, R.A.4
  • 12
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • -. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
  • 13
    • 0033552870 scopus 로고    scopus 로고
    • Mobile introns: Retrohoming by complete reverse splicing
    • Eickbush, T. H. 1999. Mobile introns: retrohoming by complete reverse splicing. Curr. Biol. 9:R11-14.
    • (1999) Curr. Biol. , vol.9
    • Eickbush, T.H.1
  • 14
    • 0033646667 scopus 로고    scopus 로고
    • Retroelements contribute to the excess low-copy-number DNA in pine
    • Elsik, C. G., and C. G. Williams. 2000. Retroelements contribute to the excess low-copy-number DNA in pine. Mol. Gen. Genet. 264:47-55.
    • (2000) Mol. Gen. Genet. , vol.264 , pp. 47-55
    • Elsik, C.G.1    Williams, C.G.2
  • 15
    • 0028206859 scopus 로고
    • Multiple group II self-splicing introns in mobile DNA from Escherichia coli
    • Ferat, J. L., M. Le Gouar, and F. Michel. 1994. Multiple group II self-splicing introns in mobile DNA from Escherichia coli. C. R. Acad. Sci. Serie III Sci. Vie 317:141-148.
    • (1994) C. R. Acad. Sci. Serie III Sci. Vie , vol.317 , pp. 141-148
    • Ferat, J.L.1    Le Gouar, M.2    Michel, F.3
  • 16
    • 0036225678 scopus 로고    scopus 로고
    • The genome of M. acetivorans reveals extensive metabolic and physiological diversity
    • Galagan, J. E., C. Nusbaum, A. Roy et al. (55 co-authors). 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
    • (2002) Genome Res , vol.12 , pp. 532-542
    • Galagan, J.E.1    Nusbaum, C.2    Roy, A.3
  • 17
    • 0022448120 scopus 로고
    • On the antiquity of introns
    • Gilbert, W., M. Marchionni, and G. McKnight. 1986. On the antiquity of introns. Cell 46:151-153.
    • (1986) Cell , vol.46 , pp. 151-153
    • Gilbert, W.1    Marchionni, M.2    McKnight, G.3
  • 18
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 20
    • 0031796215 scopus 로고    scopus 로고
    • Weighting hidden Markov models for maximum discrimination
    • Karchin, R., and R. Hughey. 1998. Weighting hidden Markov models for maximum discrimination. Bioinformatics 14:772-782.
    • (1998) Bioinformatics , vol.14 , pp. 772-782
    • Karchin, R.1    Hughey, R.2
  • 21
    • 0026693137 scopus 로고
    • Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor
    • Kohlstaedt, L. A., J. Wang, J. M. Friedman, P. A. Rice, and T. A. Steitz. 1992. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-1790.
    • (1992) Science , vol.256 , pp. 1783-1790
    • Kohlstaedt, L.A.1    Wang, J.2    Friedman, J.M.3    Rice, P.A.4    Steitz, T.A.5
  • 22
    • 0036237968 scopus 로고    scopus 로고
    • Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron
    • Kudla, J., F. J. Albertazzi, D. Blazevic, M. Hermann, and R. Bock. 2002. Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron. Mol. Genet. Genomics 267:223-230.
    • (2002) Mol. Genet. Genomics , vol.267 , pp. 223-230
    • Kudla, J.1    Albertazzi, F.J.2    Blazevic, D.3    Hermann, M.4    Bock, R.5
  • 23
    • 0027305131 scopus 로고
    • Introns as mobile genetic elements
    • Lambowitz, A. M., and M. Belfort. 1993. Introns as mobile genetic elements. Annu. Rev. Biochem. 62:587-622.
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 587-622
    • Lambowitz, A.M.1    Belfort, M.2
  • 25
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B., and D. L. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 26
    • 0031737389 scopus 로고    scopus 로고
    • The recent origins of spliceosomal introns revisited
    • Logsdon, J. M. Jr. 1998. The recent origins of spliceosomal introns revisited. Curr. Opin. Genet. Dev. 8:637-648.
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 637-648
    • Logsdon J.M., Jr.1
  • 27
    • 0028556367 scopus 로고
    • Dynamic RNA-RNA interactions in the spliceosome
    • Madhani, H. D., and C. Guthrie. 1994. Dynamic RNA-RNA interactions in the spliceosome. Annu. Rev. Genet. 28:1-26.
    • (1994) Annu. Rev. Genet. , vol.28 , pp. 1-26
    • Madhani, H.D.1    Guthrie, C.2
  • 28
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    • Mau, B., M. A. Newton, and B. Larget. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.A.2    Larget, B.3
  • 29
    • 0001862516 scopus 로고    scopus 로고
    • The retroid agents: Disease, function and evolution
    • E. Domingo, R. Webster, and J. Holland, eds. Academic Press, London
    • McClure, M. A. 1999. The retroid agents: disease, function and evolution. Pp. 163-195 in E. Domingo, R. Webster, and J. Holland, eds. Origin and evolution of viruses. Academic Press, London.
    • (1999) Origin and Evolution of Viruses , pp. 163-195
    • McClure, M.A.1
  • 30
    • 0022384634 scopus 로고
    • Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses
    • Michel, F., and B. F. Lang. 1985. Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses. Nature 316:641-643.
    • (1985) Nature , vol.316 , pp. 641-643
    • Michel, F.1    Lang, B.F.2
  • 32
    • 0021276637 scopus 로고
    • Distribution and evolutionary significance of mitochondrial plasmids in Neurospora spp
    • Natvig, D. O., G. May, and J. W. Taylor. 1984. Distribution and evolutionary significance of mitochondrial plasmids in Neurospora spp. J. Bacteriol. 159:288-293.
    • (1984) J. Bacteriol. , vol.159 , pp. 288-293
    • Natvig, D.O.1    May, G.2    Taylor, J.W.3
  • 33
    • 0035106010 scopus 로고    scopus 로고
    • Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria
    • Nesbo, C. L., S. L'Haridon, K. O. Stetter, and W. F. Doolittle. 2001. Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria. Mol. Biol. Evol. 18:362-375.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 362-375
    • Nesbo, C.L.1    L'Haridon, S.2    Stetter, K.O.3    Doolittle, W.F.4
  • 34
    • 0024967081 scopus 로고
    • The mitochondrial plasmid from Neurospora intormedia strain Labelle-1b contains a long open reading frame with blocks of amino acids characteristic of reverse transcriptases and related proteins
    • Pande, S., E. G. Lemire, and F. E. Nargang. 1989. The mitochondrial plasmid from Neurospora intormedia strain Labelle-1b contains a long open reading frame with blocks of amino acids characteristic of reverse transcriptases and related proteins. Nucleic Acids Res. 17:2023-2042.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 2023-2042
    • Pande, S.1    Lemire, E.G.2    Nargang, F.E.3
  • 35
    • 0027293432 scopus 로고
    • Molecular evolution: Why introns-in-pieces?
    • Roger, A. J., and W. F. Doolittle. 1993. Molecular evolution: why introns-in-pieces? Nature 364:289-290.
    • (1993) Nature , vol.364 , pp. 289-290
    • Roger, A.J.1    Doolittle, W.F.2
  • 36
    • 0027377818 scopus 로고
    • Transposition of a group II intron
    • Sellem, C. H., G. Lecellier, and L. Belcour. 1993. Transposition of a group II intron. Nature 366:176-178.
    • (1993) Nature , vol.366 , pp. 176-178
    • Sellem, C.H.1    Lecellier, G.2    Belcour, L.3
  • 37
    • 0022131865 scopus 로고
    • On the origin of RNA splicing and introns
    • Sharp, P. A. 1985. On the origin of RNA splicing and introns. Cell 42:397-400.
    • (1985) Cell , vol.42 , pp. 397-400
    • Sharp, P.A.1
  • 38
    • 0033852426 scopus 로고    scopus 로고
    • A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion
    • Shirasu, K., A. H. Schulman, T. Lahaye, and P. Schulze-Lefert. 2000. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10:908-915.
    • (2000) Genome Res , vol.10 , pp. 908-915
    • Shirasu, K.1    Schulman, A.H.2    Lahaye, T.3    Schulze-Lefert, P.4
  • 39
    • 0037136554 scopus 로고    scopus 로고
    • Eukaryotic evolution: Early origin of canonical introns
    • Simpson, A. G., E. K. MacQuarrie, and A. J. Roger. 2002. Eukaryotic evolution: early origin of canonical introns. Nature 419:270.
    • (2002) Nature , vol.419 , pp. 270
    • Simpson, A.G.1    MacQuarrie, E.K.2    Roger, A.J.3
  • 40
    • 0027739853 scopus 로고
    • The U5 and U6 small nuclear RNAs as active site components of the spliceosome
    • Sontheimer, E. J., and J. A. Steitz. 1993. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 262:1989-1996.
    • (1993) Science , vol.262 , pp. 1989-1996
    • Sontheimer, E.J.1    Steitz, J.A.2
  • 41
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki, Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 43
    • 0034910710 scopus 로고    scopus 로고
    • Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases
    • Toor, N., G. Hausner, and S. Zimmerly. 2001. Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases. RNA 7:1142-1152.
    • (2001) RNA , vol.7 , pp. 1142-1152
    • Toor, N.1    Hausner, G.2    Zimmerly, S.3
  • 44
    • 0033179990 scopus 로고    scopus 로고
    • Linear mitochondrial plasmids of F. oxysporum are novel, telomere-like retroelements
    • Walther, T. C., and J. C. Kennell. 1999. Linear mitochondrial plasmids of F. oxysporum are novel, telomere-like retroelements. Mol. Cell 4:229-238.
    • (1999) Mol. Cell , vol.4 , pp. 229-238
    • Walther, T.C.1    Kennell, J.C.2
  • 45
    • 0033180584 scopus 로고    scopus 로고
    • A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA
    • Wank, H., J. SanFilippo, R. N. Singh, M. Matsuura, and A. M. Lambowitz. 1999. A reverse transcriptase/maturase promotes splicing by binding at its own coding segment in a group II intron RNA. Mol. Cell 4:239-250.
    • (1999) Mol. Cell , vol.4 , pp. 239-250
    • Wank, H.1    SanFilippo, J.2    Singh, R.N.3    Matsuura, M.4    Lambowitz, A.M.5
  • 46
    • 0036431235 scopus 로고    scopus 로고
    • Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
    • Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
    • (2002) Mol. Phylogenet. Evol. , vol.25 , pp. 361-371
    • Wilcox, T.P.1    Zwickl, D.J.2    Heath, T.A.3    Hillis, D.M.4
  • 47
    • 0025006614 scopus 로고
    • Origin and evolution of retroelements based upon their reverse transcriptase sequences
    • Xiong, Y., and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353-3362.
    • (1990) EMBO J. , vol.9 , pp. 3353-3362
    • Xiong, Y.1    Eickbush, T.H.2
  • 48
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
    • Yang, Z. H., and B. Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.H.1    Rannala, B.2
  • 49
    • 0029162089 scopus 로고
    • Group II intron mobility occurs by target DNA-primed reverse transcription
    • Zimmerly, S., H. Guo, P. S. Perlman, and A. M. Lambowitz. 1995. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82:545-554.
    • (1995) Cell , vol.82 , pp. 545-554
    • Zimmerly, S.1    Guo, H.2    Perlman, P.S.3    Lambowitz, A.M.4
  • 50
    • 0035282874 scopus 로고    scopus 로고
    • Phylogenetic relationships among group II intron ORFs
    • Zimmerly, S., G. Hausner, and X. Wu. 2001. Phylogenetic relationships among group II intron ORFs. Nucleic Acids Res. 29:1238-1250.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1238-1250
    • Zimmerly, S.1    Hausner, G.2    Wu, X.3
  • 51
    • 0036567231 scopus 로고    scopus 로고
    • Pyrococcus genome comparison evidences chromosome shuffling-driven evolution
    • Zivanovic, Y., P. Lopez, H. Philippe, and P. Forterre. 2002. Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30:1902-1910.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1902-1910
    • Zivanovic, Y.1    Lopez, P.2    Philippe, H.3    Forterre, P.4


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