메뉴 건너뛰기




Volumn 11, Issue 2, 2011, Pages 343-348

Ongoing purifying selection on intergenic spacers in group A streptococcus

Author keywords

Bacterial spacers; Group A streptococcus; Purifying selection; Slightly deleterious mutations; Streptococcus pyogenes

Indexed keywords

SPACER DNA;

EID: 79951956217     PISSN: 15671348     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meegid.2010.11.005     Document Type: Article
Times cited : (7)

References (51)
  • 3
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: an approach using the bootstrap
    • Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 4
    • 36048967894 scopus 로고    scopus 로고
    • MSOAR: a high-throughput ortholog assignment system based on genome rearrangement
    • Fu Z., Chen X., Vacic V., Nan P., Zhong Y., Jiang T. MSOAR: a high-throughput ortholog assignment system based on genome rearrangement. J. Comput. Biol. 2007, 14:1160-1175.
    • (2007) J. Comput. Biol. , vol.14 , pp. 1160-1175
    • Fu, Z.1    Chen, X.2    Vacic, V.3    Nan, P.4    Zhong, Y.5    Jiang, T.6
  • 5
    • 33947404017 scopus 로고    scopus 로고
    • Mutations of the act promoter in Myxococcus xanthus
    • Gronewold T.M.A., Kaiser D. Mutations of the act promoter in Myxococcus xanthus. J. Bacteriol. 2007, 189:1836-1844.
    • (2007) J. Bacteriol. , vol.189 , pp. 1836-1844
    • Gronewold, T.M.A.1    Kaiser, D.2
  • 6
    • 70449700233 scopus 로고    scopus 로고
    • Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence
    • Horler R.S.P., Vanderpool C.K. Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence. Nucleic Acids Res. 2009, 37:5465-5476.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5465-5476
    • Horler, R.S.P.1    Vanderpool, C.K.2
  • 7
    • 29144525031 scopus 로고    scopus 로고
    • High level of functional polymorphism indicates a unique role of natural selection at human immune system loci
    • Hughes A., Packer B., Welch R., Chanock S., Yeager M. High level of functional polymorphism indicates a unique role of natural selection at human immune system loci. Immunogenetics 2005, 57:821-827.
    • (2005) Immunogenetics , vol.57 , pp. 821-827
    • Hughes, A.1    Packer, B.2    Welch, R.3    Chanock, S.4    Yeager, M.5
  • 9
    • 11244292387 scopus 로고    scopus 로고
    • Patterns of sequence divergence in 5′ intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories
    • Hughes A.L., Friedman R. Patterns of sequence divergence in 5′ intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories. Genetics 2004, 168:1795-1803.
    • (2004) Genetics , vol.168 , pp. 1795-1803
    • Hughes, A.L.1    Friedman, R.2
  • 10
    • 15544381275 scopus 로고    scopus 로고
    • Evidence for abundant slightly deleterious polymorphisms in bacterial populations
    • Hughes A.L. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 2005, 169:533-538.
    • (2005) Genetics , vol.169 , pp. 533-538
    • Hughes, A.L.1
  • 11
    • 16844373373 scopus 로고    scopus 로고
    • Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus
    • Hughes A.L., Friedman R. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus. J. Bacteriol. 2005, 187:2698-2704.
    • (2005) J. Bacteriol. , vol.187 , pp. 2698-2704
    • Hughes, A.L.1    Friedman, R.2
  • 12
    • 34748817463 scopus 로고    scopus 로고
    • Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    • Hughes A.L. Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity 2007, 99:364-373.
    • (2007) Heredity , vol.99 , pp. 364-373
    • Hughes, A.L.1
  • 13
    • 33845793082 scopus 로고    scopus 로고
    • Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium
    • Hughes A.L., French J.O. Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene 2007, 387:31-37.
    • (2007) Gene , vol.387 , pp. 31-37
    • Hughes, A.L.1    French, J.O.2
  • 14
    • 35248860855 scopus 로고    scopus 로고
    • More effective purifying selection on RNA viruses than in DNA viruses
    • Hughes A.L., Hughes M.A.K. More effective purifying selection on RNA viruses than in DNA viruses. Gene 2007, 404:117-125.
    • (2007) Gene , vol.404 , pp. 117-125
    • Hughes, A.L.1    Hughes, M.A.K.2
  • 15
    • 33947507808 scopus 로고    scopus 로고
    • Coding sequence polymorphism in avian mitochondrial genomes reflects population histories
    • Hughes A.L., Hughes M.A.K. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Mol. Ecol. 2007, 17:1369-1376.
    • (2007) Mol. Ecol. , vol.17 , pp. 1369-1376
    • Hughes, A.L.1    Hughes, M.A.K.2
  • 16
    • 33846608204 scopus 로고    scopus 로고
    • Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes
    • Hughes A.L., Langley K.J. Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes. Infect. Genet. Evol. 2007, 7:188-196.
    • (2007) Infect. Genet. Evol. , vol.7 , pp. 188-196
    • Hughes, A.L.1    Langley, K.J.2
  • 17
    • 45249106003 scopus 로고    scopus 로고
    • Near neutrality: leading edge of the neutral theory of molecular evolution
    • Hughes A.L. Near neutrality: leading edge of the neutral theory of molecular evolution. Ann. N.Y. Acad. Sci. 2008, 1133:162-179.
    • (2008) Ann. N.Y. Acad. Sci. , vol.1133 , pp. 162-179
    • Hughes, A.L.1
  • 18
    • 51649122447 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes
    • Hughes A.L., Friedman R., Rivailler P., French J.O. Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol. Biol. Evol. 2008, 25:2199-2209.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2199-2209
    • Hughes, A.L.1    Friedman, R.2    Rivailler, P.3    French, J.O.4
  • 20
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Academic Press, New York, H. Munro (Ed.)
    • Jukes T., Cantor C. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. Academic Press, New York. H. Munro (Ed.).
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.1    Cantor, C.2
  • 21
    • 0017368336 scopus 로고
    • Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution
    • Kimura M. Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 1977, 267:275-276.
    • (1977) Nature , vol.267 , pp. 275-276
    • Kimura, M.1
  • 23
    • 10644272391 scopus 로고    scopus 로고
    • Benjamin Cummings
    • Lewin B. Genes VIII 2003, Benjamin Cummings.
    • (2003) Genes VIII
    • Lewin, B.1
  • 24
    • 23044471766 scopus 로고    scopus 로고
    • An algorithm for progressive multiple alignment of sequences with insertions
    • Loytynoja A., Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:10557-10562.
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 10557-10562
    • Loytynoja, A.1    Goldman, N.2
  • 25
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • Loytynoja A., Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320:1632-1635.
    • (2008) Science , vol.320 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 27
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Madan Babu M., Teichmann S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 2003, 31:1234-1244.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1234-1244
    • Madan Babu, M.1    Teichmann, S.A.2
  • 28
    • 0642368358 scopus 로고    scopus 로고
    • Position specific variation in the rate of evolution in transcription factor binding sites
    • Moses A., Chiang D., Kellis M., Lander E., Eisen M. Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol. Biol. 2003, 3:19.
    • (2003) BMC Evol. Biol. , vol.3 , pp. 19
    • Moses, A.1    Chiang, D.2    Kellis, M.3    Lander, E.4    Eisen, M.5
  • 29
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 31
    • 0015722319 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta T. Slightly deleterious mutant substitutions in evolution. Nature 1973, 246:96-98.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 32
    • 0017220894 scopus 로고
    • Role of very slightly deleterious mutations in molecular evolution and polymorphism
    • Ohta T. Role of very slightly deleterious mutations in molecular evolution and polymorphism. Theor. Popul. Biol. 1976, 10:254-275.
    • (1976) Theor. Popul. Biol. , vol.10 , pp. 254-275
    • Ohta, T.1
  • 33
    • 0037058932 scopus 로고    scopus 로고
    • Near-neutrality in evolution of genes and gene regulation
    • Ohta T. Near-neutrality in evolution of genes and gene regulation. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:16134-16137.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 16134-16137
    • Ohta, T.1
  • 34
    • 70449435697 scopus 로고    scopus 로고
    • A genome-wide analysis of small regulatory RNAs in the human pathogen group A streptococcus
    • Perez N., Trevino J., Liu Z., Ho S.C.M., Babitzke P., Sumby P. A genome-wide analysis of small regulatory RNAs in the human pathogen group A streptococcus. PLoS ONE 2009, 4:e7668.
    • (2009) PLoS ONE , vol.4
    • Perez, N.1    Trevino, J.2    Liu, Z.3    Ho, S.C.M.4    Babitzke, P.5    Sumby, P.6
  • 35
    • 0030000951 scopus 로고    scopus 로고
    • Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans
    • Rand D.M., Kann L.M. Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 1996, 13:735-748.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 735-748
    • Rand, D.M.1    Kann, L.M.2
  • 36
    • 33749172711 scopus 로고    scopus 로고
    • Defining the Mga regulon: comparative transcriptome analysis reveals both direct and indirect regulation by Mga in the group A streptococcus
    • Ribardo D.A., McIver K.S. Defining the Mga regulon: comparative transcriptome analysis reveals both direct and indirect regulation by Mga in the group A streptococcus. Mol. Microbiol. 2006, 62:491-508.
    • (2006) Mol. Microbiol. , vol.62 , pp. 491-508
    • Ribardo, D.A.1    McIver, K.S.2
  • 37
    • 1642512330 scopus 로고    scopus 로고
    • Evolution of cis-regulatory elements versus codifying regions
    • Rodriguez-Trelles F., Tarrio R., Ayala F.J. Evolution of cis-regulatory elements versus codifying regions. Int. J. Dev. Biol. 2003, 47:665-673.
    • (2003) Int. J. Dev. Biol. , vol.47 , pp. 665-673
    • Rodriguez-Trelles, F.1    Tarrio, R.2    Ayala, F.J.3
  • 39
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 40
    • 0036999964 scopus 로고    scopus 로고
    • Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura
    • Schaeffer S.W. Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genet. Res. 2002, 80:163-175.
    • (2002) Genet. Res. , vol.80 , pp. 163-175
    • Schaeffer, S.W.1
  • 41
    • 43349089766 scopus 로고    scopus 로고
    • Maximum-likelihood analysis using TREE-PUZZLE
    • Wiley and Sons, New York, (Supplement 17, Unit 6.6), A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, L. Stein (Eds.)
    • Schmidt H.A., von Haeseler A. Maximum-likelihood analysis using TREE-PUZZLE. Current Protocols in Bioinformatics 2007, Wiley and Sons, New York, (Supplement 17, Unit 6.6). A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, L. Stein (Eds.).
    • (2007) Current Protocols in Bioinformatics
    • Schmidt, H.A.1    von Haeseler, A.2
  • 42
    • 0032873606 scopus 로고    scopus 로고
    • Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA
    • Sharples G.J., Ingleston S.M., Lloyd R.G. Holliday junction processing in bacteria: insights from the evolutionary conservation of RuvABC, RecG, and RusA. J. Bacteriol. 1999, 181:5543-5550.
    • (1999) J. Bacteriol. , vol.181 , pp. 5543-5550
    • Sharples, G.J.1    Ingleston, S.M.2    Lloyd, R.G.3
  • 43
    • 77955324319 scopus 로고    scopus 로고
    • Functional annotations in bacterial genomes based on small RNA signatures
    • Sridhar J., Rafi Z.A. Functional annotations in bacterial genomes based on small RNA signatures. Bioinformation 2008, 2:284-295.
    • (2008) Bioinformation , vol.2 , pp. 284-295
    • Sridhar, J.1    Rafi, Z.A.2
  • 44
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 45
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 46
    • 33747885768 scopus 로고    scopus 로고
    • Evolution of cis-regulatory sequence and function in Diptera
    • Wittkopp P.J. Evolution of cis-regulatory sequence and function in Diptera. Heredity 2006, 97:139-147.
    • (2006) Heredity , vol.97 , pp. 139-147
    • Wittkopp, P.J.1
  • 48
    • 0030683599 scopus 로고    scopus 로고
    • PAML: a program package for phylogenetic analysis by maximum likelihood
    • Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 1997, 13:555-556.
    • (1997) Bioinformatics , vol.13 , pp. 555-556
    • Yang, Z.1
  • 49
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z., Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 2000, 17:32-43.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 50
    • 0019224628 scopus 로고
    • The mechanism of action of penicillin. Penicillin acylates the active site of Bacillus stearothermophilus d-alanine carboxypeptidase
    • Yocum R.R., Rasmussen J.R., Strominger J.L. The mechanism of action of penicillin. Penicillin acylates the active site of Bacillus stearothermophilus d-alanine carboxypeptidase. J. Biol. Chem. 1980, 255:3977-3986.
    • (1980) J. Biol. Chem. , vol.255 , pp. 3977-3986
    • Yocum, R.R.1    Rasmussen, J.R.2    Strominger, J.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.