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

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902 · see citing works

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288 · see citing works

Statistical significance for genomewide studies

Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692 · see citing works

Escherichia coli and Salmonella.

Neidhart, F. C. (1996) · Cited by 1,584 · see citing works

Escherichia coli O157:H7

Mead, P. S., & Griffin, P. M. (1998) · The Lancet · doi:10.1016/s0140-6736(98)01267-7 · Cited by 1,031 · see citing works

Residual guanosine 3‘,5‘-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations.

Xiao, H., Kálmán, M., Ikehara, K., Zemel, S., Glaser, G., & Cashel, M. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)67694-5 · Cited by 721 · see citing works

Mapping and sequencing of mutations in the Escherichia colirpoB gene that lead to rifampicin resistance

Jin, D. J., & Gross, C. A. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90517-7 · Cited by 678 · see citing works

ppGpp: a global regulator in Escherichia coli

Magnusson, L. U., Farewell, A., & Nyström, T. (2005) · Trends in Microbiology · doi:10.1016/j.tim.2005.03.008 · Cited by 644 · see citing works

The global, ppGpp‐mediated stringent response to amino acid starvation in Escherichia coli

Traxler, M. F., Summers, S. M., Nguyen, H., Zacharia, V. M., Hightower, G. A., Smith, J. T., & Conway, T. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06229.x · Cited by 519 · see citing works

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, K. F. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.11.3401-3407.1993 · Cited by 509 · see citing works

DksA

Paul, B. J., Berkmen, M. B., Ross, W., Schneider, D. A., Webb, C., Foster, J. W., & Gourse, R. L. (2004) · Cell · doi:10.1016/j.cell.2004.07.009 · Cited by 479 · see citing works

Parallel changes in gene expression after 20,000 generations of evolution in <i>Escherichia</i> <i>coli</i>

Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334340100 · Cited by 440 · see citing works

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale

Herring, C. D., Raghunathan, A., Honisch, C., Patel, T., Applebee, M. K., Joyce, A. R., Albert, T. J., Blattner, F. R., van den Boom, D., Cantor, C. R., et al. (2006) · Nature Genetics · doi:10.1038/ng1906 · Cited by 381 · see citing works

Transcription Profiling of the Stringent Response in Escherichia coli

Durfee, T., Hansen, A., Zhi, H., Blattner, F. R., & Jin, D. J. (2007) · Journal of Bacteriology · doi:10.1128/jb.01092-07 · Cited by 374 · see citing works

Preprocessing of oligonucleotide array data

Wu, Z. J., & Irizarry, R. A. (2004) · Nature Biotechnology · doi:10.1038/nbt0604-656b · Cited by 364 · see citing works

Ubiquitous Transcriptional Pausing Is Independent of RNA Polymerase Backtracking

Neuman, K. C., Abbondanzieri, E. A., Landick, R. C., Gelles, J., & Block, S. M. (2003) · Cell · doi:10.1016/s0092-8674(03)00845-6 · Cited by 327 · see citing works

Advances in bacterial promoter recognition and its control by factors that do not bind DNA

Haugen, S. P., Ross, W., & Gourse, R. L. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1912 · Cited by 320 · see citing works

Parallel adaptive evolution cultures of<i>Escherichia coli</i>lead to convergent growth phenotypes with different gene expression states

Fong, S. S., Joyce, A. R., & Palsson, B. Ø. (2005) · Genome Research · doi:10.1101/gr.3832305 · Cited by 265 · cited 1× · see citing works

The regulatory roles and mechanism of transcriptional pausing

Landick, R. C. (2006) · Biochemical Society Transactions · doi:10.1042/bst0341062 · Cited by 251 · see citing works

rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase

Haugen, S. P., Berkmen, M. B., Ross, W., Gaál, T., Ward, C. S., & Gourse, R. L. (2006) · Cell · doi:10.1016/j.cell.2006.04.034 · Cited by 218 · see citing works

The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like “stringent” RNA polymerases in Escherichia coli

Zhou, Y. N., & Jin, D. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.6.2908 · Cited by 218 · see citing works

A Central Role of the RNA Polymerase Trigger Loop in Active-Site Rearrangement during Transcriptional Pausing

Toulokhonov, I., Zhang, J., Palangat, M., & Landick, R. C. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.06.008 · Cited by 201 · see citing works

Control of Carbon Flux to Acetate Excretion During Growth of Escherichia coli in Batch and Continuous Cultures

El-Mansi, E. M. T., & HOLMS, W. H. (1989) · Microbiology · doi:10.1099/00221287-135-11-2875 · Cited by 201 · see citing works

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, T. M., Joyce, A. R., Applebee, M. K., Barrett, C. L., Xie, B., Gao, Y., & Palsson, B. Ø. (2009) · Genome biology · doi:10.1186/gb-2009-10-10-r118 · Cited by 196 · see citing works

Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli

Herring, C. D., Glasner, J. D., & Blattner, F. R. (2003) · Gene · doi:10.1016/s0378-1119(03)00585-7 · Cited by 177 · see citing works

Characterization of the pleiotropic phenotypes of rifampin-resistant rpoB mutants of Escherichia coli

Jin, D. J., & Gross, C. A. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.9.5229-5231.1989 · Cited by 165 · see citing works

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

Goodarzi, H., Bennett, B. D., Amini, S., Reaves, M. L., Hottes, A. K., Rabinowitz, J. D., & Tavazoie, S. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.33 · Cited by 155 · see citing works

A direct effect of guanosine tetraphosphate on pausing of Escherichia coli RNA polymerase during RNA chain elongation.

Kingston, R. E., Nierman, W. C., & Chamberlin, M. J. (1981) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)69683-3 · Cited by 150 · see citing works

Evolution of global regulatory networks during a long‐term experiment with<i>Escherichia coli</i>

Philippe, N., Crozat, E., Lenski, R. E., & Schneider, D. (2007) · BioEssays · doi:10.1002/bies.20629 · Cited by 145 · see citing works

Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination

Klumpp, S., & Terence Hwa, B. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806084105 · Cited by 143 · see citing works

Co-overexpression of Escherichia coliRNA Polymerase Subunits Allows Isolation and Analysis of Mutant Enzymes Lacking Lineage-specific Sequence Insertions

Artsimovitch, I., Svetlov, V. V., Murakami, K. S., & Landick, R. C. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211214200 · Cited by 139 · see citing works

DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade

Lemke, J. J., Durfee, T., & Gourse, R. L. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06939.x · Cited by 98 · see citing works

The Downstream DNA Jaw of Bacterial RNA Polymerase Facilitates Both Transcriptional Initiation and Pausing

Ederth, J., Artsimovitch, I., Isaksson, L. A., & Landick, R. C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207038200 · Cited by 94 · see citing works

Mouse Intestine Selects Nonmotile flhDC Mutants of Escherichia coli MG1655 with Increased Colonizing Ability and Better Utilization of Carbon Sources

Leatham, M. P., Stevenson, S. J., Gauger, E. J., Krogfelt, K. A., Lins, J. J., Haddock, T. L., Autieri, S. M., Conway, T., & Cohen, P. S. (2005) · Infection and Immunity · doi:10.1128/iai.73.12.8039-8049.2005 · Cited by 93 · see citing works

Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes

Klein‐Marcuschamer, D., Santos, C. N. S., Yu, H., & Stephanopoulos, G. N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01888-08 · Cited by 84 · see citing works

RpoB8, a rifampicin-resistant termination-proficient RNA polymerase, has an increased Km for purine nucleotides during transcription elongation

Jin, D., & Gross, C. A. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)98711-9 · Cited by 83 · see citing works

Isolation of RNA Polymerase Suppressors of a (p)ppGpp Deficiency

Murphy, H., & Cashel, M. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)71044-1 · Cited by 81 · see citing works

Effects of the Antiterminator BoxA on Transcription Elongation Kinetics and ppGpp Inhibition of Transcription Elongation in Escherichia coli

Vogel, U. B., & Jensen, K. F. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.31.18335 · Cited by 73 · see citing works

High Concentrations of ppGpp Decrease the RNA Chain Growth Rate

Sørensen, M. A., Jensen, K. F., & Pedersen, S. B. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1156 · Cited by 72 · see citing works

Structural Perspective on Mutations Affecting the Function of Multisubunit RNA Polymerases

Trinh, V. Q., Langelier, M.-F., Archambault, J., & Coulombe, B. (2006) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.70.1.12-36.2006 · Cited by 70 · see citing works

Mutations of the beta subunit of RNA polymerase alter both transcription pausing and transcription termination in the trp operon leader region in vitro.

Fisher, R. F., & Yanofsky, C. (1983) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)82040-7 · Cited by 66 · see citing works

Impact of Individual Mutations on Increased Fitness in Adaptively Evolved Strains of Escherichia coli

Applebee, M. K., Herrgård, M. J., & Palsson, B. Ø. (2008) · Journal of Bacteriology · doi:10.1128/jb.01976-07 · Cited by 51 · see citing works

Direct Versus Limited-step Reconstitution Reveals Key Features of an RNA Hairpin-stabilized Paused Transcription Complex

Kyzer, S., Ha, K. S., Landick, R. C., et al. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m701483200 · Cited by 47 · see citing works

Role of the spacer boxA of Escherichia coli ribosomal RNA operons in efficient 23 S rRNA synthesis in vivo

Pfeiffer, T., & Hartmann, R. K. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0744 · Cited by 22 · see citing works

Modeling and analysis of the E. coli transcriptional regulatory network: An assessment of its properties, plasticity, and role in adaptive evolution

Joyce, A. R. (2007) · eScholarship (California Digital Library) · Cited by 4 · see citing works

Adaptive laboratory evolution—Principles and applications for biotechnology

Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827 · see citing works

The Molecular Diversity of Adaptive Convergence

Tenaillon, O., Rodríguez-Verdugo, A., Gaut, R. L., McDonald, P., Bennett, A. F., Long, A. D., & Gaut, B. S. (2012) · Science · doi:10.1126/science.1212986 · Cited by 815 · see citing works

Adaptive laboratory evolution — harnessing the power of biology for metabolic engineering

Portnoy, V. A., Bezdan, D., & Zengler, K. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.03.007 · Cited by 309 · see citing works

Evolutionary insight from whole‐genome sequencing of experimentally evolved microbes

DETTMAN, J. R., RODRIGUE, N., MELNYK, A. H., WONG, A., BAILEY, S. F., & KASSEN, R. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05484.x · Cited by 160 · see citing works

Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

Lu, H., Li, F., Yuan, L., Domenzain, I., Yu, R., Wang, H., Li, G., Chen, Y., Ji, B., Kerkhoven, E. J., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110427 · Cited by 44 · see citing works

Laboratory evolution of <i>Geobacter sulfurreducens</i> for enhanced growth on lactate via a single-base-pair substitution in a transcriptional regulator

Summers, Z. M., Ueki, T., Ismail, W., Haveman, S. A., & Lovley, D. R. (2012) · The ISME Journal · doi:10.1038/ismej.2011.166 · Cited by 39 · see citing works

The role of cellular objectives and selective pressures in metabolic pathway evolution

Nam, H., Conrad, T. M., & Lewis, N. E. (2011) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2011.03.006 · Cited by 32 · see citing works

<i>In Vitro</i> Gut Modeling as a Tool for Adaptive Evolutionary Engineering of <i>Lactiplantibacillus plantarum</i>

Isenring, J., Geirnaert, A., Hall, A. R., Jans, C., Lacroix, C., & Stevens, M. J. A. (2021) · mSystems · doi:10.1128/msystems.01085-20 · Cited by 17 · see citing works

High Temperature Induction of a Stringent Response in the dnaK(Ts) and dnaJ(Ts) Mutants of Escherichia coli

Itikawa, H., Fujita, H., & Wada, M. (1986) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a135648 · Cited by 17 · see citing works

The Mechanism of E. coli RNA Polymerase Regulation by ppGpp Is Suggested by the Structure of their Complex

Zuo, Y., Wang, Y., & Steitz, T. A. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.03.020 · Cited by 176 · see citing works

ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response

Ross, W., Sanchez‐Vazquez, P., Chen, A. Y., Lee, J.-H., Burgos, H. L., & Gourse, R. L. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.04.029 · Cited by 250 · see citing works

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

Sanchez‐Vazquez, P., Dewey, C. N., Kitten, N., Ross, W., & Gourse, R. L. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1819682116 · Cited by 224 · see citing works

Properties of Escherichia coli RNA polymerase from a strain devoid of the stringent response alarmone ppGpp.

Szalewska-Pałasz, A. (2008) · Acta Biochimica Polonica · doi:10.18388/abp.2008_3078 · Cited by 3 · see citing works