메뉴 건너뛰기




Volumn 107, Issue 47, 2010, Pages 20500-20505

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

Author keywords

Kinetics; Stringent response; Transcription

Indexed keywords

CARBON; RIBOSOME RNA; RNA POLYMERASE;

EID: 78650546051     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0911253107     Document Type: Article
Times cited : (190)

References (44)
  • 1
    • 0023749808 scopus 로고
    • Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance
    • Jin DJ, Gross CA (1988) Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J Mol Biol 202:45-58.
    • (1988) J Mol Biol , vol.202 , pp. 45-58
    • Jin, D.J.1    Gross, C.A.2
  • 2
    • 0024319151 scopus 로고
    • Characterization of the pleiotropic phenotypes of rifampinresistant rpoB mutants of Escherichia coli
    • Jin DJ, Gross CA (1989) Characterization of the pleiotropic phenotypes of rifampinresistant rpoB mutants of Escherichia coli. J Bacteriol 171:5229-5231.
    • (1989) J Bacteriol , vol.171 , pp. 5229-5231
    • Jin, D.J.1    Gross, C.A.2
  • 3
    • 0032539903 scopus 로고    scopus 로고
    • The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli
    • Zhou YN, Jin DJ (1998) The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli. Proc Natl Acad Sci USA 95:2908-2913.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 2908-2913
    • Zhou, Y.N.1    Jin, D.J.2
  • 4
    • 33645119890 scopus 로고    scopus 로고
    • Structural perspective on mutations affecting the function of multisubunit RNA polymerases
    • Trinh V, Langelier MF, Archambault J, Coulombe B (2006) Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev 70:12-36.
    • (2006) Microbiol Mol Biol Rev , vol.70 , pp. 12-36
    • Trinh, V.1    Langelier, M.F.2    Archambault, J.3    Coulombe, B.4
  • 5
    • 65549147541 scopus 로고    scopus 로고
    • Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes
    • Klein-Marcuschamer D, Santos CN, Yu H, Stephanopoulos G (2009) Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microbiol 75:2705-2711.
    • (2009) Appl Environ Microbiol , vol.75 , pp. 2705-2711
    • Klein-Marcuschamer, D.1    Santos, C.N.2    Yu, H.3    Stephanopoulos, G.4
  • 6
    • 0347536251 scopus 로고    scopus 로고
    • Isolation of RNA polymerase suppressors of a (p)ppGpp deficiency
    • Murphy H, Cashel M (2003) Isolation of RNA polymerase suppressors of a (p)ppGpp deficiency. Methods Enzymol 371:596-601.
    • (2003) Methods Enzymol , vol.371 , pp. 596-601
    • Murphy, H.1    Cashel, M.2
  • 7
    • 33751544539 scopus 로고    scopus 로고
    • Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    • Herring CD, et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38:1406-1412.
    • (2006) Nat Genet , vol.38 , pp. 1406-1412
    • Herring, C.D.1
  • 8
    • 47249153619 scopus 로고    scopus 로고
    • Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli
    • Applebee MK, Herrgård MJ, Palsson BO (2008) Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. J Bacteriol 190: 5087-5094.
    • (2008) J Bacteriol , vol.190 , pp. 5087-5094
    • Applebee, M.K.1    Herrgård, M.J.2    Palsson, B.O.3
  • 9
    • 0025992789 scopus 로고
    • Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations
    • Xiao H, et al. (1991) Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem 266: 5980-5990.
    • (1991) J Biol Chem , vol.266 , pp. 5980-5990
    • Xiao, H.1
  • 11
    • 45449099933 scopus 로고    scopus 로고
    • Advances in bacterial promoter recognition and its control by factors that do not bind DNA
    • Haugen SP, Ross W, Gourse RL (2008) Advances in bacterial promoter recognition and its control by factors that do not bind DNA. Nat Rev Microbiol 6:507-519.
    • (2008) Nat Rev Microbiol , vol.6 , pp. 507-519
    • Haugen, S.P.1    Ross, W.2    Gourse, R.L.3
  • 12
    • 0019427787 scopus 로고
    • A direct effect of guanosine tetraphosphate on pausing of Escherichia coli RNA polymerase during RNA chain elongation
    • Kingston RE, Nierman WC, Chamberlin MJ (1981) A direct effect of guanosine tetraphosphate on pausing of Escherichia coli RNA polymerase during RNA chain elongation. J Biol Chem 256:2787-2797.
    • (1981) J Biol Chem , vol.256 , pp. 2787-2797
    • Kingston, R.E.1    Nierman, W.C.2    Chamberlin, M.J.3
  • 13
    • 0028220191 scopus 로고
    • High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli
    • Sørensen MA, Jensen KF, Pedersen S (1994) High concentrations of ppGpp decrease the RNA chain growth rate. Implications for protein synthesis and translational fidelity during amino acid starvation in Escherichia coli. J Mol Biol 236:441-454.
    • (1994) J Mol Biol , vol.236 , pp. 441-454
    • Sørensen, M.A.1    Jensen, K.F.2    Pedersen, S.3
  • 14
    • 0037417962 scopus 로고    scopus 로고
    • Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli
    • Cooper TF, Rozen DE, Lenski RE (2003) Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc Natl Acad Sci USA 100: 1072-1077.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 1072-1077
    • Cooper, T.F.1    Rozen, D.E.2    Lenski, R.E.3
  • 16
    • 0037020252 scopus 로고    scopus 로고
    • The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing
    • Ederth J, Artsimovitch I, Isaksson LA, Landick R (2002) The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem 277:37456-37463.
    • (2002) J Biol Chem , vol.277 , pp. 37456-37463
    • Ederth, J.1    Artsimovitch, I.2    Isaksson, L.A.3    Landick, R.4
  • 17
    • 0038823636 scopus 로고    scopus 로고
    • Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions
    • Artsimovitch I, Svetlov V, Murakami KS, Landick R (2003) Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J Biol Chem 278:12344-12355.
    • (2003) J Biol Chem , vol.278 , pp. 12344-12355
    • Artsimovitch, I.1    Svetlov, V.2    Murakami, K.S.3    Landick, R.4
  • 18
    • 0021099727 scopus 로고
    • Mutations of the beta subunit of RNA polymerase alter both transcription pausing and transcription termination in the trp operon leader region in vitro
    • Fisher RF, Yanofsky C (1983) Mutations of the beta subunit of RNA polymerase alter both transcription pausing and transcription termination in the trp operon leader region in vitro. J Biol Chem 258:8146-8150.
    • (1983) J Biol Chem , vol.258 , pp. 8146-8150
    • Fisher, R.F.1    Yanofsky, C.2
  • 19
    • 0026329122 scopus 로고
    • RpoB8, a rifampicin-resistant termination-proficient RNA polymerase, has an increased Km for purine nucleotides during transcription elongation
    • Jin DJ, Gross CA (1991) RpoB8, a rifampicin-resistant termination-proficient RNA polymerase, has an increased Km for purine nucleotides during transcription elongation. J Biol Chem 266:14478-14485.
    • (1991) J Biol Chem , vol.266 , pp. 14478-14485
    • Jin, D.J.1    Gross, C.A.2
  • 20
    • 28444483927 scopus 로고    scopus 로고
    • Mouse intestine selects nonmotile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources
    • Leatham MP, et al. (2005) Mouse intestine selects nonmotile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources. Infect Immun 73:8039-8049.
    • (2005) Infect Immun , vol.73 , pp. 8039-8049
    • Leatham, M.P.1
  • 21
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • Fong SS, Joyce AR, Palsson BO (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 15:1365-1372.
    • (2005) Genome Res , vol.15 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.O.3
  • 22
    • 0024416873 scopus 로고
    • Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures
    • el-Mansi EM, Holms WH (1989) Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J Gen Microbiol 135: 2875-2883.
    • (1989) J Gen Microbiol , vol.135 , pp. 2875-2883
    • El-Mansi, E.M.1    Holms, W.H.2
  • 23
    • 4043069926 scopus 로고    scopus 로고
    • DksA: A critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP
    • Paul BJ, et al. (2004) DksA: A critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118:311-322.
    • (2004) Cell , vol.118 , pp. 311-322
    • Paul, B.J.1
  • 24
    • 34547097808 scopus 로고    scopus 로고
    • Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex
    • Kyzer S, Ha KS, Landick R, Palangat M (2007) Direct versus limited-step reconstitution reveals key features of an RNA hairpin-stabilized paused transcription complex. J Biol Chem 282:19020-19028.
    • (2007) J Biol Chem , vol.282 , pp. 19020-19028
    • Kyzer, S.1    Ha, K.S.2    Landick, R.3    Palangat, M.4
  • 25
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM (2003) Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115: 437-447.
    • (2003) Cell , vol.115 , pp. 437-447
    • Neuman, K.C.1    Abbondanzieri, E.A.2    Landick, R.3    Gelles, J.4    Block, S.M.5
  • 26
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • Landick R (2006) The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 34:1062-1066.
    • (2006) Biochem Soc Trans , vol.34 , pp. 1062-1066
    • Landick, R.1
  • 27
    • 0000640710 scopus 로고    scopus 로고
    • Modulation of chemical composition and other parameters of the cell by growth rate
    • ed Neidhardt FC (American Society for Microbiology, Washington, DC), 2nd Ed
    • Bremer H, Dennis PP (1996) Modulation of chemical composition and other parameters of the cell by growth rate. Escherichia coli and Salmonella, ed Neidhardt FC (American Society for Microbiology, Washington, DC), 2nd Ed, pp 1553-1569.
    • (1996) Escherichia Coli and Salmonella , pp. 1553-1569
    • Bremer, H.1    Dennis, P.P.2
  • 28
    • 72049100690 scopus 로고    scopus 로고
    • DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade
    • Lemke JJ, Durfee T, Gourse RL (2009) DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade. Mol Microbiol 74:1368-1379.
    • (2009) Mol Microbiol , vol.74 , pp. 1368-1379
    • Lemke, J.J.1    Durfee, T.2    Gourse, R.L.3
  • 29
    • 34548769341 scopus 로고    scopus 로고
    • Evolution of global regulatory networks during a long-term experiment with Escherichia coli
    • Philippe N, Crozat E, Lenski RE, Schneider D (2007) Evolution of global regulatory networks during a long-term experiment with Escherichia coli. Bioessays 29:846-860.
    • (2007) Bioessays , vol.29 , pp. 846-860
    • Philippe, N.1    Crozat, E.2    Lenski, R.E.3    Schneider, D.4
  • 30
    • 38649092391 scopus 로고    scopus 로고
    • Transcription profiling of the stringent response in Escherichia coli
    • Durfee T, Hansen AM, Zhi H, Blattner FR, Jin DJ (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190:1084-1096.
    • (2008) J Bacteriol , vol.190 , pp. 1084-1096
    • Durfee, T.1    Hansen, A.M.2    Zhi, H.3    Blattner, F.R.4    Jin, D.J.5
  • 31
    • 43449090374 scopus 로고    scopus 로고
    • The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli
    • Traxler MF, et al. (2008) The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 68:1128-1148.
    • (2008) Mol Microbiol , vol.68 , pp. 1128-1148
    • Traxler, M.F.1
  • 32
    • 0029166388 scopus 로고
    • Effects of the antiterminator BoxA on transcription elongation kinetics and ppGpp inhibition of transcription elongation in Escherichia coli
    • Vogel U, Jensen KF (1995) Effects of the antiterminator BoxA on transcription elongation kinetics and ppGpp inhibition of transcription elongation in Escherichia coli. J Biol Chem 270:18335-18340.
    • (1995) J Biol Chem , vol.270 , pp. 18335-18340
    • Vogel, U.1    Jensen, K.F.2
  • 33
    • 0031592481 scopus 로고    scopus 로고
    • Role of the spacer boxA of Escherichia coli ribosomal RNA operons in efficient 23 S rRNA synthesis in vivo
    • Pfeiffer T, Hartmann RK (1997) Role of the spacer boxA of Escherichia coli ribosomal RNA operons in efficient 23 S rRNA synthesis in vivo. J Mol Biol 265:385-393.
    • (1997) J Mol Biol , vol.265 , pp. 385-393
    • Pfeiffer, T.1    Hartmann, R.K.2
  • 34
    • 57449110975 scopus 로고    scopus 로고
    • Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination
    • Klumpp S, Hwa T (2008) Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci USA 105: 18159-18164.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 18159-18164
    • Klumpp, S.1    Hwa, T.2
  • 35
    • 77953237121 scopus 로고    scopus 로고
    • Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli
    • Goodarzi H, et al. (2010) Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli. Mol Syst Biol 6:378.
    • (2010) Mol Syst Biol , vol.6 , pp. 378
    • Goodarzi, H.1
  • 36
    • 0027251266 scopus 로고
    • The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels
    • Jensen KF (1993) The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol 175:3401-3407.
    • (1993) J Bacteriol , vol.175 , pp. 3401-3407
    • Jensen, K.F.1
  • 37
    • 75349114758 scopus 로고    scopus 로고
    • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    • Conrad TM, et al. (2009) Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 10:R118.
    • (2009) Genome Biol , vol.10
    • Conrad, T.M.1
  • 38
    • 34547204502 scopus 로고    scopus 로고
    • A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing
    • Toulokhonov I, Zhang J, Palangat M, Landick R (2007) A central role of the RNA polymerase trigger loop in active-site rearrangement during transcriptional pausing. Mol Cell 27:406-419.
    • (2007) Mol Cell , vol.27 , pp. 406-419
    • Toulokhonov, I.1    Zhang, J.2    Palangat, M.3    Landick, R.4
  • 39
    • 33744981130 scopus 로고    scopus 로고
    • RRNA promoter regulation by nonoptimal binding of sigma region 1.2:Anadditional recognition element for RNA polymerase
    • Haugen SP, et al. (2006) rRNA promoter regulation by nonoptimal binding of sigma region 1.2:Anadditional recognition element for RNA polymerase. Cell 125:1069-1082.
    • (2006) Cell , vol.125 , pp. 1069-1082
    • Haugen, S.P.1
  • 40
    • 0037633360 scopus 로고    scopus 로고
    • Gene replacement without selection: Regulated suppression of amber mutations in Escherichia coli
    • Herring CD, Glasner JD, Blattner FR (2003) Gene replacement without selection: Regulated suppression of amber mutations in Escherichia coli. Gene 311:153-163.
    • (2003) Gene , vol.311 , pp. 153-163
    • Herring, C.D.1    Glasner, J.D.2    Blattner, F.R.3
  • 41
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97:6640-6645.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 42
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 43
    • 2542610720 scopus 로고    scopus 로고
    • Preprocessing of oligonucleotide array data
    • author reply 658
    • Wu Z, Irizarry RA (2004) Preprocessing of oligonucleotide array data. Nat Biotechnol 22:656-658, author reply 658.
    • (2004) Nat Biotechnol , vol.22 , pp. 656-658
    • Wu, Z.1    Irizarry, R.A.2
  • 44
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440-9445.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.