Pputida TALE ethylene glycoln
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W3110 Benzoate Tolerization
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GYD
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OxyR
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Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. Molecular Biology and Evolution. 25 October 2019. doi: 10.1093/molbev/msz251
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OxidizeME
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E. coli chemical tolerance
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isobutanol-resistant Ecoli
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Genome-reduced E. coli
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Choe D, Lee JH, Yoo M, Hwang S, Sung BH, Cho S, Palsson B, Kim SC, Cho BK. Adaptive laboratory evolution of a genome-reduced Escherichia coli. Nature Communications. 2019;10:935. doi: 10.1038/s41467-019-08888-6.
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Enzyme Promiscuity Novel Substrates PALE ALE
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Central carbon knockout pgi
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McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, et al. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018.
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Central carbon knockout sdh
Central carbon knockout gnd
Central carbon knockout glucose evolution
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McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, et al. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018;9: 1793.
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Central carbon knockout PTS
Central carbon knockout glucose evolution
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McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, et al. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng. 2018;48: 233–242.
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Central carbon knockout tpiA
Central carbon knockout glucose evolution
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McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, et al. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng. 2018;48: 82–93. |
Auxotrophic strains hisD gltA
Auxotrophic strains hisD gltB
Auxotrophic strains hisD pyrC
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Lloyd CJ, King Z, Sandberg T, Hefner Y, Olson C, Phaneuf P, et al. Model-driven design and evolution of non-trivial synthetic syntrophic pairs [Internet]. bioRxiv. 2018. p. 327270. doi:10.1101/327270
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C321
C321.∆A
C321.∆A.earlyfix
ECNR2.1
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Wannier TM, Kunjapur AM, Rice DP, McDonald MJ, Desai MM, Church GM. Adaptive evolution of genomically recoded Escherichia coli. Proc Natl Acad Sci U S A. 2018;115: 3090–3095.
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PGI |
Charusanti P, Conrad TM, Knight EM,
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Long CP, Gonzalez JE, Feist AM, Palsson BO,
Antoniewicz MR. Dissecting the genetic and metabolic
mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli. Proc
Natl Acad Sci U S A. 2018;115: 222–227
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C13 |
Sandberg TE, Long CP, Gonzalez JE, Feist AM,
Antoniewicz MR, Palsson BO. Evolution of E. coli on
[U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology. PLoS One.
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42C |
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde
M, Herrgard MJ, et al. Evolution of
Escherichia coli to 42 °C and subsequent genetic engineering reveals adaptive mechanisms and novel
mutations. Mol Biol Evol. 2014;31: 2647–2662
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42C Tenaillon |
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Rebecca L. Gaut, Pamela McDonald, Albert F. Bennett, Anthony D. Long, and Brandon S. Gaut. 2012.
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Epistasis2011 |
Chou, Hsin-Hung, Hsuan-Chao Chiu, Nigel
F. Delaney, Daniel Segrè, and Christopher J. Marx. 2011. “Diminishing Returns Epistasis among
Beneficial Mutations Decelerates Adaptation.” Science 332 (6034): 1190–92.
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GLU |
LaCroix RA, Sandberg TE, O’Brien EJ, Utrilla J,
Ebrahim A, Guzman GI, et al. Use of adaptive
laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655
on glucose minimal medium. Appl Environ Microbiol. 2015;81: 17–30
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SER |
Mundhada H, Seoane JM, Schneider K, Koza A,
Christensen HB, Klein T, et al. Increased production of
L-serine in Escherichia coli through Adaptive Laboratory Evolution. Metab Eng. 2017;39: 141–150
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SSW AC
SSW GLY
SSW XYL
SSW GLU AC
SSW GLU GLY
SSW GLY XYL
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Sandberg TE, Lloyd CJ, Palsson BO, Feist AM.
Laboratory Evolution to Alternating Substrate
Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies. Appl Environ Microbiol.
2017;83
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LTEE
LTEE ARA
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Tenaillon O, Barrick JE, Ribeck N, Deatherage DE,
Blanchard JL, Dasgupta A, et al. Tempo and mode of
genome evolution in a 50,000-generation experiment. Nature. 2016;536: 165–170
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TEE
TEE ARA
|
Deatherage, Daniel E., Jamie L. Kepner, Albert F.
Bennett, Richard E. Lenski, and Jeffrey E. Barrick. 2017. “Specificity of Genome Evolution in
Experimental Populations of Escherichia Coli Evolved at Different Temperatures.” Proceedings of the
National Academy of Sciences of the United States of America 114 (10): E1904–12.
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TM GluGly |
Latif, Haythem, Joshua A. Lerman, Vasiliy A.
Portnoy, Yekaterina Tarasova, Harish Nagarajan, Alexandra C. Schrimpe-Rutledge, Richard D. Smith, et
al. 2013. “The Genome Organization of Thermotoga Maritima Reflects Its Lifestyle.” PLoS Genetics 9
(4): e1003485.
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