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Volumn 50, Issue 3, 2000, Pages 249-257

The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes

Author keywords

Analysis of variance; Bacterial genomes; Base composition; Gene direction; Prokaryote genomes; Replication orientation; Skews

Indexed keywords

SIGNAL PEPTIDE;

EID: 0033935187     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002399910029     Document Type: Article
Times cited : (154)

References (45)
  • 1
    • 0025297285 scopus 로고
    • Codon preferences in free-living organisms
    • Andersson SG, Kurland CG (1990). Codon preferences in free-living organisms. Microbiol Rev 54:98-210
    • (1990) Microbiol Rev , vol.54 , pp. 98-210
    • Andersson, S.G.1    Kurland, C.G.2
  • 3
    • 0030462462 scopus 로고    scopus 로고
    • Transcription-induced mutations: Increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli
    • Beletskii A, Bhagwat A (1996) Transcription-induced mutations: Increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci USA 93: 13919-13924
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13919-13924
    • Beletskii, A.1    Bhagwat, A.2
  • 4
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner FR, Plunkett G, Bloch CA, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474
    • (1997) Science , vol.277 , pp. 1453-1474
    • Blattner, F.R.1    Plunkett, G.2    Bloch, C.A.3
  • 5
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschil
    • Bull CJ, White O, Olsen GJ, et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschil. Science 273:1058-1073
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bull, C.J.1    White, O.2    Olsen, G.J.3
  • 8
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3
  • 9
    • 0030976320 scopus 로고    scopus 로고
    • Strand asymmetries in DNA evolution
    • Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13:240-245
    • (1997) Trends Genet , vol.13 , pp. 240-245
    • Francino, M.P.1    Ochman, H.2
  • 10
    • 0029874447 scopus 로고    scopus 로고
    • Asymmetries generated by transcription-coupled repair in enterobacterial genes
    • Francino MP, Chao L, Riley MA, Ochman H (1996) Asymmetries Generated by transcription-coupled repair in enterobacterial genes. Science 272:107-109
    • (1996) Science , vol.272 , pp. 107-109
    • Francino, M.P.1    Chao, L.2    Riley, M.A.3    Ochman, H.4
  • 11
    • 0028829125 scopus 로고
    • The minimal gene complement of Mycoplasma genitalium
    • Fraser CM, Gocayne JD, White O, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397-403
    • (1995) Science , vol.270 , pp. 397-403
    • Fraser, C.M.1    Gocayne, J.D.2    White, O.3
  • 12
    • 0031470826 scopus 로고    scopus 로고
    • Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
    • Fraser CM, Casjens S, Huang WM, et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-586
    • (1997) Nature , vol.390 , pp. 580-586
    • Fraser, C.M.1    Casjens, S.2    Huang, W.M.3
  • 13
    • 0032540874 scopus 로고    scopus 로고
    • Complete genome sequence of Treponema pallidum, the syphilis spirochete
    • Fraser CM, Norris SJ, Weinstock GM, et al. (1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375-388
    • (1998) Science , vol.281 , pp. 375-388
    • Fraser, C.M.1    Norris, S.J.2    Weinstock, G.M.3
  • 15
    • 0032524384 scopus 로고    scopus 로고
    • Analysing genomes with cumulative skew diagrams
    • Grigoriev A (1998) Analysing genomes with cumulative skew diagrams. Nucleic Acids Res 26:2286-2290
    • (1998) Nucleic Acids Res , vol.26 , pp. 2286-2290
    • Grigoriev, A.1
  • 18
    • 0030606608 scopus 로고    scopus 로고
    • Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions
    • Kaneko T, Sato S, Kotani H, et al. (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:185-209
    • (1996) DNA Res , vol.3 , pp. 185-209
    • Kaneko, T.1    Sato, S.2    Kotani, H.3
  • 19
    • 0032815103 scopus 로고    scopus 로고
    • Bacterial DNA strand asymmetry
    • Karlin S. (1999) Bacterial DNA strand asymmetry. Trends Microbiol 7:305-308
    • (1999) Trends Microbiol , vol.7 , pp. 305-308
    • Karlin, S.1
  • 20
    • 0032579989 scopus 로고    scopus 로고
    • Complete sequence and gene organization of the genome of a hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3
    • Kawarabayasi Y, Sawada M, Horikawa H, et al. (1998) Complete sequence and gene organization of the genome of a hyperthermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res 5:55-76
    • (1998) DNA Res , vol.5 , pp. 55-76
    • Kawarabayasi, Y.1    Sawada, M.2    Horikawa, H.3
  • 21
    • 0031458333 scopus 로고    scopus 로고
    • The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
    • Klenk HP, Clayton RA, Tomb JF, et al. (1997) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370
    • (1997) Nature , vol.390 , pp. 364-370
    • Klenk, H.P.1    Clayton, R.A.2    Tomb, J.F.3
  • 22
    • 0030731108 scopus 로고    scopus 로고
    • The complete genome sequence of the gram-positive bacterium Bacillus subtilis
    • Kunst F, Ogasawara N, Moszer I, et al. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256
    • (1997) Nature , vol.390 , pp. 249-256
    • Kunst, F.1    Ogasawara, N.2    Moszer, I.3
  • 23
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland, MA
    • Li, W-H. (1997) Molecular evolution. Sinauer Associates, Sunderland, MA
    • (1997) Molecular Evolution
    • Li, W.-H.1
  • 24
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strand of bacteria
    • Lobry JR (1996a) Asymmetric substitution patterns in the two DNA strand of bacteria. Mol Biol Evol 13:660-665
    • (1996) Mol Biol Evol , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 25
    • 0029805251 scopus 로고    scopus 로고
    • A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria
    • Lobry JR (1996b) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie 78: 323-326
    • (1996) Biochimie , vol.78 , pp. 323-326
    • Lobry, J.R.1
  • 26
    • 0029938912 scopus 로고    scopus 로고
    • Origin of replication of Mycoplasma genitalium
    • Lobry JR (1996c) Origin of replication of Mycoplasma genitalium. Science 272:745-746
    • (1996) Science , vol.272 , pp. 745-746
    • Lobry, J.R.1
  • 27
    • 0032999415 scopus 로고    scopus 로고
    • How does replication-associated mutational pressure influence amino acid composition of proteins
    • Mackiewicz P, Gielik A, Kowalczuk M, Dudek M, Cebrat S (1999) How does replication-associated mutational pressure influence amino acid composition of proteins. Genome Res 9:409-416
    • (1999) Genome Res , vol.9 , pp. 409-416
    • Mackiewicz, P.1    Gielik, A.2    Kowalczuk, M.3    Dudek, M.4    Cebrat, S.5
  • 28
    • 0027490882 scopus 로고
    • Bacterial chromosome origins of replication
    • Marczynski G, Shapiro L (1993) Bacterial chromosome origins of replication. Curr Opin Genet Dev 3:775-782
    • (1993) Curr Opin Genet Dev , vol.3 , pp. 775-782
    • Marczynski, G.1    Shapiro, L.2
  • 29
    • 0017711419 scopus 로고
    • A DNA fragment containing the origin of replication of the Escherichia coli chromosome
    • Marsh R, Worcel A (1977) A DNA fragment containing the origin of replication of the Escherichia coli chromosome. Proc Natl Acad Sci USA 74:2720-2724
    • (1977) Proc Natl Acad Sci USA , vol.74 , pp. 2720-2724
    • Marsh, R.1    Worcel, A.2
  • 30
    • 0032169578 scopus 로고    scopus 로고
    • Replication and transcriptional selection on codon usage in Borrelia burgdorfori
    • McInemey JO (1998) Replication and transcriptional selection on codon usage in Borrelia burgdorfori. Proc Natl Acad Sci USA 95:10698-10703
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 10698-10703
    • McInemey, J.O.1
  • 31
    • 0032417093 scopus 로고    scopus 로고
    • Base composition skews, replication orientation and gene orientation in 12 prokaryotic genomes
    • McLean M, Wolfe KH, Devine KM (1998) Base composition skews, replication orientation and gene orientation in 12 prokaryotic genomes. J Mol Evol 47:691-696
    • (1998) J Mol Evol , vol.47 , pp. 691-696
    • McLean, M.1    Wolfe, K.H.2    Devine, K.M.3
  • 32
    • 0032584101 scopus 로고    scopus 로고
    • Strand compositional asymmetry in bacterial and large viral genomes
    • Mrázek J, Karlin S (1998) Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 95:3720-3725
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 3720-3725
    • Mrázek, J.1    Karlin, S.2
  • 33
    • 0026591035 scopus 로고
    • Genes and their organization in the replication origin region of the bacterial chromosome
    • Ogasawara N, Yoshikawa H (1992) Genes and their organization in the replication origin region of the bacterial chromosome. Mol Microbiol 6:629-634
    • (1992) Mol Microbiol , vol.6 , pp. 629-634
    • Ogasawara, N.1    Yoshikawa, H.2
  • 34
    • 0021702490 scopus 로고
    • Replication origin of the Bacillus subtilis chromosome determined by hybridization of the first-replicating DNA with cloned fragments from the replication region of the chromosome
    • Ogasawara N, Mizumoto S, Yoshikawa H (1984) Replication origin of the Bacillus subtilis chromosome determined by hybridization of the first-replicating DNA with cloned fragments from the replication region of the chromosome. Gene 30:173-182
    • (1984) Gene , vol.30 , pp. 173-182
    • Ogasawara, N.1    Mizumoto, S.2    Yoshikawa, H.3
  • 35
    • 0032581609 scopus 로고    scopus 로고
    • Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: Translational selection versus mutational bias
    • Pan A, Dutta C, Das J (1998) Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: Translational selection versus mutational bias. Gene 215:405-413
    • (1998) Gene , vol.215 , pp. 405-413
    • Pan, A.1    Dutta, C.2    Das, J.3
  • 36
    • 0030472379 scopus 로고    scopus 로고
    • Correspondence discriminant analysis: A multivariate method for comparing classes of protein and nucleic acid sequences
    • Perriere G, Lobry JR, Thioulouse J (1996) Correspondence discriminant analysis: A multivariate method for comparing classes of protein and nucleic acid sequences. Comput Appl Biosci 12:519-524
    • (1996) Comput Appl Biosci , vol.12 , pp. 519-524
    • Perriere, G.1    Lobry, J.R.2    Thioulouse, J.3
  • 37
    • 0032898516 scopus 로고    scopus 로고
    • Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome
    • Picardeau M, Lobry JR, Hinnebusch BJ (1999) Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol Microbiol 32:437-445
    • (1999) Mol Microbiol , vol.32 , pp. 437-445
    • Picardeau, M.1    Lobry, J.R.2    Hinnebusch, B.J.3
  • 38
    • 0032910674 scopus 로고    scopus 로고
    • Universal replication biases in bacteria
    • Rocha EPC, Danchin, Vlari A (1999a) Universal replication biases in bacteria. Mol Microbiol 32:11-16
    • (1999) Mol Microbiol , vol.32 , pp. 11-16
    • Rocha, E.P.C.1    Danchin2    Vlari, A.3
  • 39
    • 0032800845 scopus 로고    scopus 로고
    • Bacterial DNA strand compositional asymmetry: Response
    • Rocha EPC, Danchin, Viari A (1999b) Bacterial DNA strand compositional asymmetry: Response. Trends Microbiol 7:308
    • (1999) Trends Microbiol , vol.7 , pp. 308
    • Rocha, E.P.C.1    Danchin2    Viari, A.3
  • 41
    • 0023650543 scopus 로고
    • The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH (1987) The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281-1295
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 42
    • 0023652058 scopus 로고
    • Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases
    • Shields DC, Sharp PM (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res 15:8023-8040
    • (1987) Nucleic Acids Res , vol.15 , pp. 8023-8040
    • Shields, D.C.1    Sharp, P.M.2
  • 43
    • 15644383855 scopus 로고    scopus 로고
    • Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics
    • Smith DR, Doucette-Stamm LA, Deloughery C, et al. (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J Bacteriol 179:7135-7155
    • (1997) J Bacteriol , vol.179 , pp. 7135-7155
    • Smith, D.R.1    Doucette-Stamm, L.A.2    Deloughery, C.3
  • 44
    • 0032561496 scopus 로고    scopus 로고
    • Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis
    • Stephens RS, Kalman S, Lammel C, et al. (1998) Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science 282:754-759
    • (1998) Science , vol.282 , pp. 754-759
    • Stephens, R.S.1    Kalman, S.2    Lammel, C.3
  • 45
    • 0030835739 scopus 로고    scopus 로고
    • The complete genome sequence of the gastric pathogen Helicobacter pylori
    • Tomb JF, White O, Kerlavage AR, et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547
    • (1997) Nature , vol.388 , pp. 539-547
    • Tomb, J.F.1    White, O.2    Kerlavage, A.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.