Publications described by ALEdb projects

Pputida TALE ethylene glycoln

Li, W., Jayakody, L. N., Franden, M. A., Wehrmann, M., Daun, T., Hauer, B., et al. (2019). Laboratory evolution reveals the metabolic and regulatory basis of ethylene glycol metabolism by Pseudomonas putida KT2440. Environ. Microbiol. 21:3669–3682. doi: 10.1111/1462-2920.14703

W3110 Benzoate Tolerization

Kaitlin E. Creamer, Frederick S. Ditmars, Preston J. Basting, Karina S. Kunka, Issam N. Hamdallah, Sean P. Bush, Zachary Scott, Amanda He, Stephanie R. Penix, Alexandra S. Gonzales, Elizabeth K. Eder, Dominic W. Camperchioli, Adama Berndt, Michelle W. Clark, Kerry A. Rouhier, Joan L. Slonczewski. Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution. Applied and Environmental Microbiology. 2016. doi:10.10.1128/AEM.02736-16

GYD

LaCroix RA, Palsson BO, Feist AM. A Model for Designing Adaptive Laboratory Evolution Experiments. Applied and Environmental Microbiology Mar 2017, 83 (8) e03115-16; doi: 10.1128/AEM.03115-16

OxyR

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

OxidizeME

Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, MonK JM et al. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proceedings of the National Academy of Sciences. 2019. doi: 10.1073/pnas.1905039116

E. coli chemical tolerance

Lennen RM, Jensen K, Mohammed ET, Malla S, Börner RA, Chekina K, et al. Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production [Internet]. bioRxiv. 2019. p. 634105. doi:10.1101/634105

isobutanol-resistant Ecoli

Atsumi, Shota, Tung-Yun Wu, Iara M. P. Machado, Wei-Chih Huang, Pao-Yang Chen, Matteo Pellegrini, and James C. Liao. 2010. “Evolution, Genomic Analysis, and Reconstruction of Isobutanol Tolerance in Escherichia Coli.” Molecular Systems Biology 6 (December): 449.

Genome-reduced E. coli

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.

Enzyme Promiscuity Novel Substrates PALE ALE

Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, et al. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol. 2019;15: e8462.

Central carbon knockout pgi

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.

Central carbon knockout sdh

Central carbon knockout gnd

Central carbon knockout glucose evolution

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.

Central carbon knockout PTS

Central carbon knockout glucose evolution

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.

Central carbon knockout tpiA

Central carbon knockout glucose evolution

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

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

C321

C321.∆A

C321.∆A.earlyfix

ECNR2.1

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.

PGI

Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, et al. Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene. PLoS Genet. Public Library of Science; 2010;6: e1001186

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

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. 2016;11: e0151130
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
42C Tenaillon Tenaillon, Olivier, Alejandra Rodríguez-Verdugo, Rebecca L. Gaut, Pamela McDonald, Albert F. Bennett, Anthony D. Long, and Brandon S. Gaut. 2012. “The Molecular Diversity of Adaptive Convergence.” Science 335 (6067): 457–61
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.
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
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

SSW AC

SSW GLY

SSW XYL

SSW GLU AC

SSW GLU GLY

SSW GLY XYL

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

LTEE

LTEE ARA

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

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.
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.