Orr HA: The genetic theory of adaptation: A brief history. Nat Rev Genet. 2005, 6: 119-127.
Article
CAS
PubMed
Google Scholar
Kimura M: The neutral theory of molecular evolution. 1983, Cambridge: Cambridge University Press
Book
Google Scholar
Schrag SJ, Perrot V, Levin BR: Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc R Soc Lond B. 1997, 264: 1287-1291. 10.1098/rspb.1997.0178.
Article
CAS
Google Scholar
Weinreich DM, Watson RA, Chao L: Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. Evolution. 2005, 59: 1165-1174.
Article
CAS
PubMed
Google Scholar
Gros PA, Le Nagard H, Tenaillon O: The Evolution of epistasis and its links with genetic robustness, complexity and drift in a phenotypic model of adaptation. Genetics. 2009, 182: 277-293. 10.1534/genetics.108.099127.
Article
CAS
PubMed Central
PubMed
Google Scholar
Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF: Negative epistasis between beneficial mutations in an evolving bacterial population. Science. 2011, 332: 1193-1196. 10.1126/science.1203801.
Article
CAS
PubMed
Google Scholar
Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE: Second-order selection for evolvability in a large Escherichia coli population. Science. 2011, 331: 1433-1436. 10.1126/science.1198914.
Article
CAS
PubMed Central
PubMed
Google Scholar
Remold SK, Lenski RE: Contribution of individual random mutations to genotype-by-environment interactions in Escherichia coli. Proc Natl Acad Sci USA. 2001, 98: 11388-11393. 10.1073/pnas.201140198.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ostrowski EA, Rozen DE, Lenski RE: Pleiotropic effects of beneficial mutations in Escherichia coli. Evolution. 2005, 59: 2343-2352.
Article
CAS
PubMed
Google Scholar
Bataillon T, Zhang TY, Kassen R: Cost of adaptation and fitness effects of beneficial mutations in Pseudomonas fluorescens. Genetics. 2011, 189: 939-949. 10.1534/genetics.111.130468.
Article
PubMed Central
PubMed
Google Scholar
MacLean RC, Bell G, Rainey PB: The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc Natl Acad Sci USA. 2004, 101: 8072-8077. 10.1073/pnas.0307195101.
Article
CAS
PubMed Central
PubMed
Google Scholar
Taubes G: The bacteria fight back. Science. 2008, 321: 356-361. 10.1126/science.321.5887.356.
Article
CAS
PubMed
Google Scholar
Andersson DI, Levin BR: The biological cost of antibiotic resistance. Curr Opin Microbiol. 1999, 2: 489-493. 10.1016/S1369-5274(99)00005-3.
Article
CAS
PubMed
Google Scholar
MacLean RC, Hall AR, Perron GG, Buckling A: The population genetics of antibiotic resistance: integrating molecular mechanisms and treatment contexts. Nat Rev Genet. 2010, 11: 405-414. 10.1038/nrg2778.
Article
CAS
PubMed
Google Scholar
Marcusson LL, Frimodt-Moller N, Hughes D: Interplay in the selection of fluoroquinolone resistance and bacterial fitness. PLoS Pathog. 2009, 5: 1553-7366.
Article
Google Scholar
Tupin A, Gualtieri M, Roquet-Baneres F, Morichaud Z, Brodolin K, Leonetti JP: Resistance to rifampicin: at the crossroads between ecological, genomic and medical concerns. Int J Antimicrob Agents. 2010, 35: 519-523. 10.1016/j.ijantimicag.2009.12.017.
Article
CAS
PubMed
Google Scholar
Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S: Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet. 2012, 44: 106-110.
Article
CAS
Google Scholar
Campbell EA, Korzheva N, Mustaev A, Murakami K, Nair S, Goldfarb A, Darst SA: Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell. 2001, 104: 901-912. 10.1016/S0092-8674(01)00286-0.
Article
CAS
PubMed
Google Scholar
Reynolds MG: Compensatory evolution in rifampin-resistant Escherichia coli. Genetics. 2000, 156: 1471-1481.
CAS
PubMed Central
PubMed
Google Scholar
Brandis G, Wrande M, Liljas L, Hughes D: Fitness-compensatory mutations in rifampicin-resistant RNA polymerase. Mol Microbiol. 2012, 85: 142-151. 10.1111/j.1365-2958.2012.08099.x.
Article
CAS
PubMed
Google Scholar
Kassen R, Bataillon T: Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat Genet. 2006, 38: 484-488. 10.1038/ng1751.
Article
CAS
PubMed
Google Scholar
Trindade S, Sousa A, Gordo I: Antibiotic resistance and stress in the light of fisher’s model. Evolution. 2012, 66: 3815-3824. 10.1111/j.1558-5646.2012.01722.x.
Article
PubMed
Google Scholar
Levin BR, Perrot V, Walker N: Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics. 2000, 154: 985-997.
CAS
PubMed Central
PubMed
Google Scholar
Hall AR, MacLean RC: Epistasis buffers the fitness effect of rifampicin-resistance mutations in Pseudomonas aeruginosa. Evolution. 2011, 65: 2370-2379. 10.1111/j.1558-5646.2011.01302.x.
Article
PubMed
Google Scholar
Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS: The molecular diversity of adaptive convergence. Science. 2012, 335: 457-461. 10.1126/science.1212986.
Article
CAS
PubMed
Google Scholar
Lenski RE, Rose MR, Rose MR: Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat. 1991, 138: 1315-1341. 10.1086/285289.
Article
Google Scholar
Lang GI, Botstein D, Desai MM: Genetic variation and the fate of beneficial mutations in asexual populations. Genetics. 2011, 188: 647-661. 10.1534/genetics.111.128942.
Article
PubMed Central
PubMed
Google Scholar
R: A language and environment for statistical computing. http://www.R-project.org/,
Datsenko KA, Wanner BL: One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA. 2000, 97: 6640-6645. 10.1073/pnas.120163297.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lenski RE: Quantifying fitness and gene stability in microorganisms. Assessing ecological risks of biotechnology. Edited by: Ginzburg LR. 1991, Boston: Butterworth-Heinemann, 173-192.
Chapter
Google Scholar
Barrick JE, Kauth MR, Strelioff CC, Lenski RE: Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol. 2010, 27: 1338-1347. 10.1093/molbev/msq024.
Article
CAS
PubMed Central
PubMed
Google Scholar
Garibyan L, Huang T, Kim M, Wolff E, Nguyen A, Nguyen T, Diep A, Hu KB, Iverson A, Yang HJ, Miller JH: Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome. DNA Repair. 2003, 2: 593-608. 10.1016/S1568-7864(03)00024-7.
Article
CAS
PubMed
Google Scholar
Christin PA, Weinreich DM, Besnard G: Causes and evolutionary significance of genetic convergence. Trends Genet. 2010, 26: 400-405. 10.1016/j.tig.2010.06.005.
Article
CAS
PubMed
Google Scholar
Severinov K, Soushko M, Goldfarb A, Nikiforov V: RifR mutations in the beginning of the Escherichia coli rpoB gene. Mol Gen Genet. 1994, 244: 120-126.
Article
CAS
PubMed
Google Scholar
Maisnier-Patin S, Berg OG, Liljas L, Andersson DI: Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol Microbiol. 2002, 46: 355-366. 10.1046/j.1365-2958.2002.03173.x.
Article
CAS
PubMed
Google Scholar
Rozen DE, de Visser JA, Gerrish PJ: Fitness effects of fixed beneficial mutations in microbial populations. Curr Biol. 2002, 12: 1040-1045. 10.1016/S0960-9822(02)00896-5.
Article
CAS
PubMed
Google Scholar
Chou HH, Chiu HC, Delaney NF, Segre D, Marx CJ: Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science. 2011, 332: 1190-1192. 10.1126/science.1203799.
Article
CAS
PubMed Central
PubMed
Google Scholar
Gerrish PJ, Lenski RE: The fate of competing beneficial mutations in an asexual population. Genetica. 1998, 102–3: 127-144.
Article
Google Scholar
de Visser JA, Rozen DE: Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli. Genetics. 2006, 172: 2093-2100.
Article
CAS
PubMed Central
PubMed
Google Scholar
Phillips PC: Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 2008, 9: 855-867. 10.1038/nrg2452.
Article
CAS
PubMed Central
PubMed
Google Scholar
Trindade S, Sousa A, Xavier KB, Dionisio F, Ferreira MG, Gordo I: Positive epistasis drives the acquisition of multidrug resistance. PLoS Genet. 2009, 5: e1000578-10.1371/journal.pgen.1000578.
Article
PubMed Central
PubMed
Google Scholar
Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF: Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 2009, 461: 1243-1274. 10.1038/nature08480.
Article
CAS
PubMed
Google Scholar
Studier FW, Daegelen P, Lenski RE, Maslov S, Kim JF: Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E-coli B and K-12 genomes. J Mol Biol. 2009, 394: 653-680. 10.1016/j.jmb.2009.09.021.
Article
CAS
PubMed
Google Scholar
Conrad TM, Frazier M, Joyce AR, Cho BK, Knight EM, Lewis NE, Landick R, Palsson BO: RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. Proc Natl Acad Sci USA. 2010, 107: 20500-20505. 10.1073/pnas.0911253107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Freddolino PL, Goodarzi H, Tavazoie S: Fitness landscape transformation through a single amino acid change in the Rho terminator. PLoS Genet. 2012, 8: e1002744-10.1371/journal.pgen.1002744.
Article
CAS
PubMed Central
PubMed
Google Scholar
Goodarzi H, Hottes AK, Tavazoie S: Global discovery of adaptive mutations. Nat Methods. 2009, 6: 581-583. 10.1038/nmeth.1352.
Article
CAS
PubMed Central
PubMed
Google Scholar
Applebee MK, Herrgard MJ, Palsson BO: Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli. J Bacteriol. 2008, 190: 5087-5094. 10.1128/JB.01976-07.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fong SS, Joyce AR, Palsson BO: Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res. 2005, 15: 1365-1372. 10.1101/gr.3832305.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hindre T, Knibbe C, Beslon G, Schneider D: New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nat Rev Microbiol. 2012, 10: 352-365.
CAS
PubMed
Google Scholar
Singleton R, Amelunxen RE: Protein from thermophilic microorganisms. Bacteriol Rev. 1973, 37: 320-342.
CAS
PubMed Central
PubMed
Google Scholar
Ryals J, Little R, Bremer H: Temperature dependence of RNA synthesis parameters in Escherichia coli. J Bacteriol. 1982, 151: 879-887.
CAS
PubMed Central
PubMed
Google Scholar
Mejia YX, Mao HB, Forde NR, Bustamante C: Thermal probing of E.coli RNA polymerase off-pathway mechanisms. J Mol Biol. 2008, 382: 628-637. 10.1016/j.jmb.2008.06.079.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jin DJ, Walter WA, Gross CA: Characterization of the termination phenotype of rifampicin-resistant mutants. J Mol Biol. 1988, 202: 245-253. 10.1016/0022-2836(88)90455-X.
Article
CAS
PubMed
Google Scholar