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Volumn 241, Issue 2, 2006, Pages 321-332

Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences

Author keywords

Deamination; Experimental test; Heavy strand; Mutation; Origin of light strand replication; Phylogeny; Secondary structure; Stepwise evolution; Time spent single stranded; tRNA

Indexed keywords

TRANSFER RNA;

EID: 33745746528     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2005.11.035     Document Type: Article
Times cited : (64)

References (40)
  • 1
    • 0036044139 scopus 로고    scopus 로고
    • Mitogenomic analyses of eutherian relationships
    • Arnason U., and Janke A. Mitogenomic analyses of eutherian relationships. Cytogenet. Genome Res. 96 (2002) 20-32
    • (2002) Cytogenet. Genome Res. , vol.96 , pp. 20-32
    • Arnason, U.1    Janke, A.2
  • 2
    • 0038109027 scopus 로고    scopus 로고
    • The mitochondrial replication bubble has not burst
    • Bogenhagen D.F., and Clayton D.A. The mitochondrial replication bubble has not burst. Trends Biochem. Sci. 28 (2003) 357-360
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 357-360
    • Bogenhagen, D.F.1    Clayton, D.A.2
  • 3
    • 0042157173 scopus 로고    scopus 로고
    • Concluding remarks: the mitochondrial DNA replication bubble has not burst
    • Bogenhagen D.F., and Clayton D.A. Concluding remarks: the mitochondrial DNA replication bubble has not burst. Trends Biochem. Sci. 28 (2003) 404-405
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 404-405
    • Bogenhagen, D.F.1    Clayton, D.A.2
  • 5
    • 0019978703 scopus 로고
    • Replication of animal mitochondrial DNA
    • Clayton D.A. Replication of animal mitochondrial DNA. Cell 28 (1982) 693-705
    • (1982) Cell , vol.28 , pp. 693-705
    • Clayton, D.A.1
  • 6
    • 0033646639 scopus 로고    scopus 로고
    • Transcription and replication of mitochondrial DNA
    • Clayton D.A. Transcription and replication of mitochondrial DNA. Hum. Reprod. 15 (2000) 11-17
    • (2000) Hum. Reprod. , vol.15 , pp. 11-17
    • Clayton, D.A.1
  • 7
    • 0025743302 scopus 로고
    • Mitochondrial DNA in the sea urchin Arbacia lixula: nucleotide sequence differences between two polymorphic molecules indicate asymmetry of mutations
    • De Giorgi C., De Luca F., and Saccone C. Mitochondrial DNA in the sea urchin Arbacia lixula: nucleotide sequence differences between two polymorphic molecules indicate asymmetry of mutations. Gene 103 (1991) 249-252
    • (1991) Gene , vol.103 , pp. 249-252
    • De Giorgi, C.1    De Luca, F.2    Saccone, C.3
  • 8
    • 0025343497 scopus 로고
    • Sequence and gene organization of the chicken mitochondrial genome-a novel gene order in higher vertebrates
    • Desjardins P., and Morais R. Sequence and gene organization of the chicken mitochondrial genome-a novel gene order in higher vertebrates. J. Mol. Biol. 212 (1990) 599-634
    • (1990) J. Mol. Biol. , vol.212 , pp. 599-634
    • Desjardins, P.1    Morais, R.2
  • 9
    • 0033531780 scopus 로고    scopus 로고
    • The non-monophyletic origin of the tRNA molecule
    • Di Giulio M. The non-monophyletic origin of the tRNA molecule. J. Theor. Biol. 197 (1999) 403-414
    • (1999) J. Theor. Biol. , vol.197 , pp. 403-414
    • Di Giulio, M.1
  • 10
    • 0345276409 scopus 로고    scopus 로고
    • The origin of the tRNA molecule: implications for the origin of protein synthesis
    • Di Giulio M. The origin of the tRNA molecule: implications for the origin of protein synthesis. J. Theor. Biol. 226 (2004) 89-93
    • (2004) J. Theor. Biol. , vol.226 , pp. 89-93
    • Di Giulio, M.1
  • 11
    • 13344279384 scopus 로고    scopus 로고
    • Doshi, K.J., Cannone, J.J., Cobaugh, C.W., Gutell, R.R., 2004. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5: Art. No. 105.
  • 12
    • 0036094907 scopus 로고    scopus 로고
    • Genomewide comparison of DNA sequences between humans and chimpanzees
    • Ebersberger I., Metzler D., Schwarz C., and Paabo S. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70 (2002) 1490-1497
    • (2002) Am. J. Hum. Genet. , vol.70 , pp. 1490-1497
    • Ebersberger, I.1    Metzler, D.2    Schwarz, C.3    Paabo, S.4
  • 13
    • 0242318326 scopus 로고    scopus 로고
    • Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes
    • Faith J.J., and Pollock D.D. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics 165 (2003) 735-745
    • (2003) Genetics , vol.165 , pp. 735-745
    • Faith, J.J.1    Pollock, D.D.2
  • 14
    • 0030900384 scopus 로고    scopus 로고
    • Relationships between genomic G+C content, RNA secondary structures, and optimal group temperature in prokaryotes
    • Galtier N., and Lobry J.R. Relationships between genomic G+C content, RNA secondary structures, and optimal group temperature in prokaryotes. J. Mol. Evol. 44 (1997) 632-636
    • (1997) J. Mol. Evol. , vol.44 , pp. 632-636
    • Galtier, N.1    Lobry, J.R.2
  • 15
    • 1542358790 scopus 로고    scopus 로고
    • Nuclear control of cloverleaf structure of human mitochondrial tRNA(Lys)
    • Helm M., and Attardi G. Nuclear control of cloverleaf structure of human mitochondrial tRNA(Lys). J. Mol. Biol. 337 (2004) 545-560
    • (2004) J. Mol. Biol. , vol.337 , pp. 545-560
    • Helm, M.1    Attardi, G.2
  • 16
    • 0032052242 scopus 로고    scopus 로고
    • The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA
    • Helm M., Brulé H., Degoul F., Cepanec C., Leroux J.P., Giegé R., and Florentz C. The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucl. Acids Res. 26 (1998) 1636-1643
    • (1998) Nucl. Acids Res. , vol.26 , pp. 1636-1643
    • Helm, M.1    Brulé, H.2    Degoul, F.3    Cepanec, C.4    Leroux, J.P.5    Giegé, R.6    Florentz, C.7
  • 17
    • 0023019723 scopus 로고
    • Both the conserved stem-loop and divergent 5′-flanking sequences are required for initiation at the human mitochondrial origin of light-strand replication
    • Hixson J.E., Wong T.W., and Clayton D.A. Both the conserved stem-loop and divergent 5′-flanking sequences are required for initiation at the human mitochondrial origin of light-strand replication. J. Biol. Chem. 261 (1986) 2384-2390
    • (1986) J. Biol. Chem. , vol.261 , pp. 2384-2390
    • Hixson, J.E.1    Wong, T.W.2    Clayton, D.A.3
  • 18
    • 0038825342 scopus 로고    scopus 로고
    • Response: the mitochondrial DNA replication bubble has not burst
    • Holt I.J., and Jacobs H.T. Response: the mitochondrial DNA replication bubble has not burst. Trends Biochem. Sci. 28 (2003) 355-356
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 355-356
    • Holt, I.J.1    Jacobs, H.T.2
  • 19
    • 0034598918 scopus 로고    scopus 로고
    • Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA
    • Holt I.J., Lorimer H.E., and Jacobs H.T. Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell 100 (2000) 515-524
    • (2000) Cell , vol.100 , pp. 515-524
    • Holt, I.J.1    Lorimer, H.E.2    Jacobs, H.T.3
  • 20
    • 33745739846 scopus 로고    scopus 로고
    • Krishnan, N.M., Seligmann, H., Raina, S.Z., Pollock, D.D., 2004a. Phylogenetic analyses detect site-specific perturbations in asymmetric mutation gradients in primate mitochondria. In: Gramada, A., Bourne, P.E. (Eds.), Currents in Computational Molecular Biology. pp. 266-267.
  • 21
    • 22944472360 scopus 로고    scopus 로고
    • Analysis of among-site variation in asymmetric substitution patterns
    • Krishnan N.M., Raina S.Z., and Pollock D.D. Analysis of among-site variation in asymmetric substitution patterns. Biol. Proc. Online 6 (2004) 180-188
    • (2004) Biol. Proc. Online , vol.6 , pp. 180-188
    • Krishnan, N.M.1    Raina, S.Z.2    Pollock, D.D.3
  • 22
    • 16644398041 scopus 로고    scopus 로고
    • Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes
    • Krishnan N.M., Seligmann H., Raina S.Z., and Pollock D.D. Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes. DNA Cell Biol. 23 (2004) 707-714
    • (2004) DNA Cell Biol. , vol.23 , pp. 707-714
    • Krishnan, N.M.1    Seligmann, H.2    Raina, S.Z.3    Pollock, D.D.4
  • 25
    • 13544268333 scopus 로고    scopus 로고
    • Bidirectional replication initiates at sites throughout the mitochondrial genome of birds
    • Reyes A., Yang M.Y., Bowmaker M., and Holt I.J. Bidirectional replication initiates at sites throughout the mitochondrial genome of birds. J. Biol. Chem. 280 (2005) 3242-3250
    • (2005) J. Biol. Chem. , vol.280 , pp. 3242-3250
    • Reyes, A.1    Yang, M.Y.2    Bowmaker, M.3    Holt, I.J.4
  • 26
    • 0027276319 scopus 로고
    • Transfer-RNAs with complementary anticodons-could they reflect early evolution of discriminative genetic-code adapters?
    • Rodin S., Ohno S., and Rodin A. Transfer-RNAs with complementary anticodons-could they reflect early evolution of discriminative genetic-code adapters?. Proc. Natl Acad. Sci. USA 90 (1993) 4723-4727
    • (1993) Proc. Natl Acad. Sci. USA , vol.90 , pp. 4723-4727
    • Rodin, S.1    Ohno, S.2    Rodin, A.3
  • 27
    • 0038031633 scopus 로고    scopus 로고
    • Epigenetic silencing may aid evolution by gene duplication
    • Rodin S.N., and Riggs A.D. Epigenetic silencing may aid evolution by gene duplication. J. Mol. Evol. 56 (2003) 718-729
    • (2003) J. Mol. Evol. , vol.56 , pp. 718-729
    • Rodin, S.N.1    Riggs, A.D.2
  • 28
    • 0036220666 scopus 로고    scopus 로고
    • The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA
    • Schmitz J., Ohme M.., and Zischler H. The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA. Mol. Biol. Evol. 19 (2002) 544-553
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 544-553
    • Schmitz, J.1    Ohme, M..2    Zischler, H.3
  • 29
    • 0041426511 scopus 로고    scopus 로고
    • Transitions and transversions in Ki-ras gene in colorectal cancers in Mexican patients
    • Segura-Uribe J., Santiago-Payan H., and Quintero A. Transitions and transversions in Ki-ras gene in colorectal cancers in Mexican patients. Tumori 89 (2003) 259-262
    • (2003) Tumori , vol.89 , pp. 259-262
    • Segura-Uribe, J.1    Santiago-Payan, H.2    Quintero, A.3
  • 30
    • 3042686794 scopus 로고    scopus 로고
    • A comparison of methods for estimating the transition:transversion ratio from DNA sequences
    • Strandberg A.K.K., and Salter L.A. A comparison of methods for estimating the transition:transversion ratio from DNA sequences. Mol. Phylogenet. Evol. 32 (2004) 495-503
    • (2004) Mol. Phylogenet. Evol. , vol.32 , pp. 495-503
    • Strandberg, A.K.K.1    Salter, L.A.2
  • 31
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura K., and Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 32
    • 0027966917 scopus 로고
    • Strand asymmetry in human mitochondrial mutations
    • Tanaka M., and Ozawa T. Strand asymmetry in human mitochondrial mutations. Genomics 22 (1994) 327-335
    • (1994) Genomics , vol.22 , pp. 327-335
    • Tanaka, M.1    Ozawa, T.2
  • 34
    • 0028893838 scopus 로고
    • How often do duplicated genes evolve new functions?
    • Walsh J.B. How often do duplicated genes evolve new functions?. Genetics 139 (1995) 421-428
    • (1995) Genetics , vol.139 , pp. 421-428
    • Walsh, J.B.1
  • 35
    • 0038644195 scopus 로고    scopus 로고
    • Population-genetic models of the fates of duplicate genes
    • Walsh B. Population-genetic models of the fates of duplicate genes. Genetica 118 (2003) 279-294
    • (2003) Genetica , vol.118 , pp. 279-294
    • Walsh, B.1
  • 36
    • 0033572893 scopus 로고    scopus 로고
    • No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    • Workman C., and Krogh A. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucl. Acids Res. 27 (1999) 4816-4822
    • (1999) Nucl. Acids Res. , vol.27 , pp. 4816-4822
    • Workman, C.1    Krogh, A.2
  • 37
    • 0037112343 scopus 로고    scopus 로고
    • Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication
    • Yang M.Y., Bowmaker M., Reyes A., Vergani L., Angeli P., Gringeri E., Jacobs H.T., and Holt I.J. Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication. Cell 111 (2002) 495-505
    • (2002) Cell , vol.111 , pp. 495-505
    • Yang, M.Y.1    Bowmaker, M.2    Reyes, A.3    Vergani, L.4    Angeli, P.5    Gringeri, E.6    Jacobs, H.T.7    Holt, I.J.8
  • 38
    • 0345306317 scopus 로고    scopus 로고
    • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes
    • Zhang Z., and Gerstein M. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucl. Acids Res. 31 (2003) 5338-5348
    • (2003) Nucl. Acids Res. , vol.31 , pp. 5338-5348
    • Zhang, Z.1    Gerstein, M.2
  • 39
    • 0346735285 scopus 로고    scopus 로고
    • Evolutionary history and mode of the amylase multigene family in Drosophila
    • Zhang Z., Inomata N., Yamazaki T., and Kishino H. Evolutionary history and mode of the amylase multigene family in Drosophila. J. Mol. Evol. 57 (2003) 702-709
    • (2003) J. Mol. Evol. , vol.57 , pp. 702-709
    • Zhang, Z.1    Inomata, N.2    Yamazaki, T.3    Kishino, H.4
  • 40
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31 (2003) 3406-3415
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1


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