메뉴 건너뛰기




Volumn 12, Issue SUPPL. 9, 2011, Pages

Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY RATE; GENE EXPRESSION LEVELS; KLEBSIELLA PNEUMONIAE; MUTATION RATES; PROKARYOTIC GENOMES; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SELECTION PRESSURES; SUBSTITUTION RATES;

EID: 80053558877     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S9-S19     Document Type: Article
Times cited : (7)

References (31)
  • 1
    • 0035718858 scopus 로고    scopus 로고
    • Flip-flop around the origin and terminus of replication in prokaryotic genomes
    • 138987, 11790247
    • Mackiewicz P, Mackiewicz D, Kowalczuk M, Cebrat S. Flip-flop around the origin and terminus of replication in prokaryotic genomes. Genome Biol 2001, 2(12):INTERACTIONS1004. 138987, 11790247.
    • (2001) Genome Biol , vol.2 , Issue.12
    • Mackiewicz, P.1    Mackiewicz, D.2    Kowalczuk, M.3    Cebrat, S.4
  • 2
    • 0034568798 scopus 로고    scopus 로고
    • Evidence for symmetric chromosomal inversions around the replication origin in bacteria
    • 16139, 11178265
    • Eisen JA, Heidelberg JF, White O, Salzberg SL. Evidence for symmetric chromosomal inversions around the replication origin in bacteria. Genome Biol 2000, 1(6):RESEARCH0011. 16139, 11178265.
    • (2000) Genome Biol , vol.1 , Issue.6
    • Eisen, J.A.1    Heidelberg, J.F.2    White, O.3    Salzberg, S.L.4
  • 3
    • 76749094639 scopus 로고    scopus 로고
    • Co-orientation of replication and transcription preserves genome integrity
    • 10.1371/journal.pgen.1000810, 2797598, 20090829
    • Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD. Co-orientation of replication and transcription preserves genome integrity. PLoS Genet 2010, 6(1):e1000810. 10.1371/journal.pgen.1000810, 2797598, 20090829.
    • (2010) PLoS Genet , vol.6 , Issue.1
    • Srivatsan, A.1    Tehranchi, A.2    MacAlpine, D.M.3    Wang, J.D.4
  • 4
    • 0033676887 scopus 로고    scopus 로고
    • Replication orientation affects the rate and direction of bacterial gene evolution
    • Tillier ER, Collins RA. Replication orientation affects the rate and direction of bacterial gene evolution. J Mol Evol 2000, 51(5):459-463.
    • (2000) J Mol Evol , vol.51 , Issue.5 , pp. 459-463
    • Tillier, E.R.1    Collins, R.A.2
  • 7
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • 10.1016/j.cell.2008.05.042, 2696314, 18662548
    • Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134(2):341-352. 10.1016/j.cell.2008.05.042, 2696314, 18662548.
    • (2008) Cell , vol.134 , Issue.2 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 8
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • 1383730, 12045149
    • Jordan IK, Rogozin IB, Wolf YI, Koonin EV. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12(6):962-968. 1383730, 12045149.
    • (2002) Genome Res , vol.12 , Issue.6 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 9
    • 77951570815 scopus 로고    scopus 로고
    • Forces that influence the evolution of codon bias
    • 10.1098/rstb.2009.0305, 2871821, 20308095
    • Sharp PM, Emery LR, Zeng K. Forces that influence the evolution of codon bias. Philos Trans R Soc Lond B Biol Sci 2010, 365(1544):1203-1212. 10.1098/rstb.2009.0305, 2871821, 20308095.
    • (2010) Philos Trans R Soc Lond B Biol Sci , vol.365 , Issue.1544 , pp. 1203-1212
    • Sharp, P.M.1    Emery, L.R.2    Zeng, K.3
  • 10
    • 0036667696 scopus 로고    scopus 로고
    • Gene location and bacterial sequence divergence
    • Mira A, Ochman H. Gene location and bacterial sequence divergence. Mol Biol Evol 2002, 19(8):1350-1358.
    • (2002) Mol Biol Evol , vol.19 , Issue.8 , pp. 1350-1358
    • Mira, A.1    Ochman, H.2
  • 11
    • 84872035464 scopus 로고    scopus 로고
    • GenBank Database
    • GenBank Database. , ftp://ftp.ncbi.nih.gov/genomes/Bacteria/
  • 12
    • 0027432923 scopus 로고
    • Reduced synonymous substitution rate at the start of enterobacterial genes
    • 10.1093/nar/21.19.4599, 311196, 8233796
    • Eyre-Walker A, Bulmer M. Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res 1993, 21(19):4599-4603. 10.1093/nar/21.19.4599, 311196, 8233796.
    • (1993) Nucleic Acids Res , vol.21 , Issue.19 , pp. 4599-4603
    • Eyre-Walker, A.1    Bulmer, M.2
  • 13
    • 0029878715 scopus 로고    scopus 로고
    • The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use
    • 10.1007/BF02198830, 8919857
    • Eyre-Walker A. The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use. J Mol Evol 1996, 42(2):73-78. 10.1007/BF02198830, 8919857.
    • (1996) J Mol Evol , vol.42 , Issue.2 , pp. 73-78
    • Eyre-Walker, A.1
  • 14
    • 78651316211 scopus 로고    scopus 로고
    • OMA 2011: orthology inference among 1000 complete genomes
    • 3013747, 21113020
    • Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Research 2011, 39(suppl 1):D289-D294. 3013747, 21113020.
    • (2011) Nucleic Acids Research , vol.39 , Issue.SUPPL. 1
    • Altenhoff, A.M.1    Schneider, A.2    Gonnet, G.H.3    Dessimoz, C.4
  • 15
    • 0033831910 scopus 로고    scopus 로고
    • Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
    • 10.1093/bioinformatics/16.6.560, 10980154
    • Frank AC, Lobry JR. Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 2000, 16(6):560-561. 10.1093/bioinformatics/16.6.560, 10980154.
    • (2000) Bioinformatics , vol.16 , Issue.6 , pp. 560-561
    • Frank, A.C.1    Lobry, J.R.2
  • 16
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 10.1093/nar/22.22.4673, 308517, 7984417
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 17
    • 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. Comput Appl Biosci 1997, 13(5):555-556.
    • (1997) Comput Appl Biosci , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1
  • 18
    • 0034750390 scopus 로고    scopus 로고
    • Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions
    • Smith NG, Eyre-Walker A. Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions. Mol Biol Evol 2001, 18(11):2124-2126.
    • (2001) Mol Biol Evol , vol.18 , Issue.11 , pp. 2124-2126
    • Smith, N.G.1    Eyre-Walker, A.2
  • 19
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • 10.1093/nar/30.1.207, 99122, 11752295
    • Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 10.1093/nar/30.1.207, 99122, 11752295.
    • (2002) Nucleic Acids Res , vol.30 , Issue.1 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 20
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 21
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • 10.1093/nar/gkn923, 2615629, 19033363
    • Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
    • (2009) Nucleic Acids Res , vol.37 , Issue.1 , pp. 1-13
    • Huang da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 23
    • 26444621352 scopus 로고    scopus 로고
    • Why highly expressed proteins evolve slowly
    • 10.1073/pnas.0504070102, 1242296, 16176987
    • Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A 2005, 102(40):14338-14343. 10.1073/pnas.0504070102, 1242296, 16176987.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.40 , pp. 14338-14343
    • Drummond, D.A.1    Bloom, J.D.2    Adami, C.3    Wilke, C.O.4    Arnold, F.H.5
  • 24
    • 79952196607 scopus 로고    scopus 로고
    • Expression level, evolutionary rate, and the cost of expression
    • 10.1093/gbe/evq059, 2979011, 20884723
    • Cherry JL. Expression level, evolutionary rate, and the cost of expression. Genome Biol Evol 2010, 2:757-769. 10.1093/gbe/evq059, 2979011, 20884723.
    • (2010) Genome Biol Evol , vol.2 , pp. 757-769
    • Cherry, J.L.1
  • 25
    • 0035546157 scopus 로고    scopus 로고
    • Gene expression and molecular evolution
    • 10.1016/S0959-437X(00)00250-1, 11682310
    • Akashi H. Gene expression and molecular evolution. Curr Opin Genet Dev 2001, 11(6):660-666. 10.1016/S0959-437X(00)00250-1, 11682310.
    • (2001) Curr Opin Genet Dev , vol.11 , Issue.6 , pp. 660-666
    • Akashi, H.1
  • 26
    • 0043163746 scopus 로고    scopus 로고
    • Transcription increases multiple spontaneous point mutations in Salmonella enterica
    • 10.1093/nar/gkg651, 169952, 12888512
    • Hudson RE, Bergthorsson U, Ochman H. Transcription increases multiple spontaneous point mutations in Salmonella enterica. Nucleic Acids Res 2003, 31(15):4517-4522. 10.1093/nar/gkg651, 169952, 12888512.
    • (2003) Nucleic Acids Res , vol.31 , Issue.15 , pp. 4517-4522
    • Hudson, R.E.1    Bergthorsson, U.2    Ochman, H.3
  • 27
    • 0036469913 scopus 로고    scopus 로고
    • The connection between transcription and genomic instability
    • 125829, 11823412
    • Aguilera A. The connection between transcription and genomic instability. EMBO J 2002, 21(3):195-201. 125829, 11823412.
    • (2002) EMBO J , vol.21 , Issue.3 , pp. 195-201
    • Aguilera, A.1
  • 28
    • 0024966756 scopus 로고
    • Chromosomal location and evolutionary rate variation in enterobacterial genes
    • 10.1126/science.2683084, 2683084
    • Sharp PM, Shields DC, Wolfe KH, Li WH. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 1989, 246(4931):808-810. 10.1126/science.2683084, 2683084.
    • (1989) Science , vol.246 , Issue.4931 , pp. 808-810
    • Sharp, P.M.1    Shields, D.C.2    Wolfe, K.H.3    Li, W.H.4
  • 29
    • 34248394295 scopus 로고    scopus 로고
    • Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis
    • 10.1073/pnas.0608999104, 1838449, 17372224
    • Wang JD, Berkmen MB, Grossman AD. Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis. Proc Natl Acad Sci U S A 2007, 104(13):5608-5613. 10.1073/pnas.0608999104, 1838449, 17372224.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.13 , pp. 5608-5613
    • Wang, J.D.1    Berkmen, M.B.2    Grossman, A.D.3
  • 30
    • 79959807202 scopus 로고    scopus 로고
    • Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences
    • 10.1371/journal.pbio.1000622, 3114760, 21697975
    • McDonald MJ, Wang WC, Huang HD, Leu JY. Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. PLoS Biol 2011, 9(6):e1000622. 10.1371/journal.pbio.1000622, 3114760, 21697975.
    • (2011) PLoS Biol , vol.9 , Issue.6
    • McDonald, M.J.1    Wang, W.C.2    Huang, H.D.3    Leu, J.Y.4
  • 31
    • 33947432388 scopus 로고    scopus 로고
    • Replication Fork Stalling at Natural Impediments
    • 10.1128/MMBR.00030-06, 1847372, 17347517
    • Mirkin EV, Mirkin SM. Replication Fork Stalling at Natural Impediments. Microbiol Mol Biol Rev 2007, 71(1):13-35. 10.1128/MMBR.00030-06, 1847372, 17347517.
    • (2007) Microbiol Mol Biol Rev , vol.71 , Issue.1 , pp. 13-35
    • Mirkin, E.V.1    Mirkin, S.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.