메뉴 건너뛰기




Volumn 12, Issue 1, 2006, Pages 1-14

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories

Author keywords

Base composition; RNA secondary structure; Selection; Self organization

Indexed keywords

RIBOSOME RNA;

EID: 29844452150     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2183806     Document Type: Article
Times cited : (47)

References (38)
  • 2
    • 2942571539 scopus 로고    scopus 로고
    • The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
    • Cannone, J., Subramanian, S., Schnare, M., Collett, J., D'Souza, L., Du, Y., Feng, B., Lin, N., Madabusi, L., Muller, K., et al. 2002. The Comparative RNA Web (CRW) Site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
    • (2002) BMC Bioinformatics , vol.3 , pp. 2
    • Cannone, J.1    Subramanian, S.2    Schnare, M.3    Collett, J.4    D'Souza, L.5    Du, Y.6    Feng, B.7    Lin, N.8    Madabusi, L.9    Muller, K.10
  • 5
    • 50449121567 scopus 로고
    • Evidence of common regularities in the composition of pentose nucleic acids
    • Elson, D. and Chargaff, E. 1955. Evidence of common regularities in the composition of pentose nucleic acids. Biochim. Biophys. Acta 17: 367-376.
    • (1955) Biochim. Biophys. Acta , vol.17 , pp. 367-376
    • Elson, D.1    Chargaff, E.2
  • 6
    • 0030900384 scopus 로고    scopus 로고
    • Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes
    • Galtier, N. and Lobry, J. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J. Mol. Evol. 44: 632-636.
    • (1997) J. Mol. Evol. , vol.44 , pp. 632-636
    • Galtier, N.1    Lobry, J.2
  • 8
    • 0036600570 scopus 로고    scopus 로고
    • The accuracy of ribosomal RNA comparative structure models
    • Gutell, R., Lee, J., and Cannone, J. 2002. The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12: 301-310.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 301-310
    • Gutell, R.1    Lee, J.2    Cannone, J.3
  • 9
    • 5444276316 scopus 로고    scopus 로고
    • Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication
    • Guy, L. and Roten, C. 2004. Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene 340: 45-52.
    • (2004) Gene , vol.340 , pp. 45-52
    • Guy, L.1    Roten, C.2
  • 11
    • 0035220937 scopus 로고    scopus 로고
    • A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes
    • Knight, R., Freeland, S., and Landweber, L. 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2: http://genomebiology.com.
    • (2001) Genome Biol. , vol.2
    • Knight, R.1    Freeland, S.2    Landweber, L.3
  • 12
    • 4344641945 scopus 로고    scopus 로고
    • Bayesfold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences
    • Knight, R., Birmingham, A., and Yarus, M. 2004. Bayesfold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences. RNA 10: 1323-1336.
    • (2004) RNA , vol.10 , pp. 1323-1336
    • Knight, R.1    Birmingham, A.2    Yarus, M.3
  • 13
    • 0034006790 scopus 로고    scopus 로고
    • Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine
    • Lao, P. and Forsdyke, D. 2000. Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Res. 10: 228-236.
    • (2000) Genome Res. , vol.10 , pp. 228-236
    • Lao, P.1    Forsdyke, D.2
  • 14
    • 17844366343 scopus 로고    scopus 로고
    • Recurrent structural RNA motifs, isostericity matrices, and sequence alignments
    • Lescoute, A., Leontis, N.B., Massire, C., and Westhof, E. 2005. Recurrent structural RNA motifs, isostericity matrices, and sequence alignments. Nucleic Acids Res. 33: 2395-2409.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2395-2409
    • Lescoute, A.1    Leontis, N.B.2    Massire, C.3    Westhof, E.4
  • 15
    • 0031593216 scopus 로고    scopus 로고
    • Influence of genomic G+C content on average aminoacid composition of proteins from 59 bacterial species
    • Lobry, J. 1997. Influence of genomic G+C content on average aminoacid composition of proteins from 59 bacterial species. Gene 205: 309-316.
    • (1997) Gene , vol.205 , pp. 309-316
    • Lobry, J.1
  • 16
    • 0037179524 scopus 로고    scopus 로고
    • Asymmetric directional mutation pressures in bacteria
    • Lobry, J. and Sueoka, N. 2002. Asymmetric directional mutation pressures in bacteria. Genome Biol. 3: http://genomebiology.com.
    • (2002) Genome Biol. , vol.3
    • Lobry, J.1    Sueoka, N.2
  • 17
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D.H., Sabina, J., Zuker, M., and Turner, D. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.4
  • 18
    • 0029129682 scopus 로고
    • Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: Thermodynamic and spectroscopic applications
    • Molinaro, M. and Tinoco Jr., I. 1995. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: Thermodynamic and spectroscopic applications. Nucleic Acids Res. 23: 3056-3063.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3056-3063
    • Molinaro, M.1    Tinoco Jr., I.2
  • 19
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial evolution
    • Muto,A. and Osawa, S. 1987.The guanine and cytosine content of genomic DNA and bacterial evolution. Proc. Natl. Acad. Sci. 84: 166-169.
    • (1987) Proc. Natl. Acad. Sci. , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 20
    • 0035942248 scopus 로고    scopus 로고
    • RNA tertiary interactions in the large ribosomal subunit: The A-minor motif
    • Nissen, P., Ippolito, J., Ban, N., Moore, P., and Steitz, T. 2001. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. 98: 4899-4903.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 4899-4903
    • Nissen, P.1    Ippolito, J.2    Ban, N.3    Moore, P.4    Steitz, T.5
  • 21
    • 0027049243 scopus 로고
    • The kinemage: A tool for scientific communication
    • Richardson, D. and Richardson, J. 1992. The kinemage: A tool for scientific communication. Protein Sci. 1: 3-9.
    • (1992) Protein Sci. , vol.1 , pp. 3-9
    • Richardson, D.1    Richardson, J.2
  • 22
    • 0030759786 scopus 로고    scopus 로고
    • Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence
    • Schultes, E., Hraber, P., and LaBean, T. 1997. Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence. RNA 3: 792-806.
    • (1997) RNA , vol.3 , pp. 792-806
    • Schultes, E.1    Hraber, P.2    LaBean, T.3
  • 23
    • 0033013683 scopus 로고    scopus 로고
    • Estimating the contributions of selection and selforganization in RNA secondary structure
    • _. 1999. Estimating the contributions of selection and selforganization in RNA secondary structure. J. Mol. Evol. 49: 76-83.
    • (1999) J. Mol. Evol. , vol.49 , pp. 76-83
  • 25
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genomewide bias in the amino acid composition of proteins
    • Singer, G. and Hickey, D. 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17:1581-1588.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1581-1588
    • Singer, G.1    Hickey, D.2
  • 26
    • 73049156042 scopus 로고
    • Compositional correlation between deoxyribonucleic acid and protein
    • Sueoka, N. 1961. Compositional correlation between deoxyribonucleic acid and protein. Cold Spring Harb. Symp. Quant. Biol. 26: 35-43.
    • (1961) Cold Spring Harb. Symp. Quant. Biol. , vol.26 , pp. 35-43
    • Sueoka, N.1
  • 27
    • 3643052747 scopus 로고
    • On the genetic basis of variation and heterogeneity of DNA base composition
    • _. 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. 48: 582-592.
    • (1962) Proc. Natl. Acad. Sci. , vol.48 , pp. 582-592
  • 28
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • _. 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. 85: 2653-2657.
    • (1988) Proc. Natl. Acad. Sci. , vol.85 , pp. 2653-2657
  • 29
    • 0033053160 scopus 로고    scopus 로고
    • Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of at and GC
    • _. 1999. Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of AT and GC. J. Mol. Evol. 49: 49-62.
    • (1999) J. Mol. Evol. , vol.49 , pp. 49-62
  • 30
    • 0030292964 scopus 로고    scopus 로고
    • RNA enzymes: Putting together a large ribozyme
    • Tinoco Jr., I. 1996. RNA enzymes: Putting together a large ribozyme. Curr. Biol. 6: 1374-1376.
    • (1996) Curr. Biol. , vol.6 , pp. 1374-1376
    • Tinoco Jr., I.1
  • 32
    • 0036606141 scopus 로고    scopus 로고
    • Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes
    • Wang, H. and Hickey, D. 2002. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res. 30: 2501-2507.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2501-2507
    • Wang, H.1    Hickey, D.2
  • 33
    • 6044241907 scopus 로고    scopus 로고
    • Evolution of RNA architecture
    • Westhof, E. and Massire, C. 2004. Evolution of RNA architecture. Science 306: 62-63.
    • (2004) Science , vol.306 , pp. 62-63
    • Westhof, E.1    Massire, C.2
  • 35
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops"
    • Woese, C.R., Winker, S., and Gutell, R.R. 1990. Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops." Proc. Natl. Acad. Sci. 87: 8467-8471.
    • (1990) Proc. Natl. Acad. Sci. , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Gutell, R.R.3
  • 38
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker, M. and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133-148.
    • (1981) Nucleic Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.