Evolution in microbes

Annual Review of Biophysics

Volumn 42, Issue 1, 2013, Pages 493-514

  Kussell, Edo ^a  

^a POLYTECHNIC UNIVERSITY   (United States)

Author keywords

bacteria; cooperation; ecology; evolutionary dynamics; experimental evolution; fitness; physiology; yeast

Indexed keywords

BETA LACTAM ANTIBIOTIC; CEFOTAXIME; CHLORAMPHENICOL; DNA TOPOISOMERASE; PROTEOME; SUCROSE;

ADAPTATION; AGING; ANTIBIOTIC RESISTANCE; BACTERIAL GROWTH; BIOFILM; CARBON SOURCE; DNA SEQUENCE; EPISTASIS; ESCHERICHIA COLI; EVOLUTION; EVOLUTIONARY ADAPTATION; GENE MUTATION; GENETIC VARIABILITY; METHYLOBACTERIUM EXTORQUENS; MICROBIAL GENETICS; MICROORGANISM; NONHUMAN; PHENOTYPE; POPULATION DENSITY; PRIORITY JOURNAL; QUORUM SENSING; REVIEW; RIBOSOME; TEMPERATURE; THERMODYNAMICS;

ADAPTATION, PHYSIOLOGICAL; BIOLOGICAL EVOLUTION; EPISTASIS, GENETIC; ESCHERICHIA COLI; GENETIC FITNESS; SELECTION, GENETIC;

EID: 84877729488     PISSN: 1936122X     EISSN: 19361238     Source Type: Book Series    
DOI: 10.1146/annurev-biophys-083012-130320     Document Type: Review

References (108)

1. Acar M, Mettetal JT, van Oudenaarden A. 2008. Stochastic switching as a survival strategy in fluctuating environments. Nat. Genet. 40:471-755
2. Ackermann M, Chao L, Bergstrom CT, Doebeli M. 2007. On the evolutionary origin of aging. Aging Cell 6:235-444
3. AckermannM, Schauerte A, Stearns SC, Jenal U. 2007. Experimental evolution of aging in a bacterium. BMC Evol. Biol. 7:1266
4. Ackermann M, Stearns SC, Jenal U. 2003. Senescence in a bacterium with asymmetric division. Science 300:19200
5. Balaban NQ,Merrin J, Chait R, Kowalik L, Leibler S. 2004. Bacterial persistence as a phenotypic switch. Science 305:1622-255
6. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, et al. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-477
7. Beaumont HJE, Gallie J, Kost C, Ferguson GC,Rainey PB. 2009. Experimental evolution of bet hedging. Nature 462:90-933
8. Bennett AF, Lenski RE. 2007. An experimental test of evolutionary trade-offs during temperature adaptation. Proc. Natl. Acad. Sci. USA 104(Suppl. 1):8649-544
9. Bischofs IB, Hug JA, Liu AW, Wolf DM, Arkin AP. 2009. Complexity in bacterial cell-cell communication: Quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay. Proc. Natl. Acad. Sci. USA 106:6459-644
10. Blount ZD, Borland CZ, Lenski RE. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. USA 105:7899-9066
11. Bronikowski AM, Bennett AF, Lenski RE. 2001. Evolutionary adaptation to temperature. VII. Effects of temperature on growth rate in natural isolates of Escherichia coli and Salmonella enterica from different thermal environments. Evolution 55:33-400
12. Bull JJ, Molineux IJ. 2008. Predicting evolution from genomics: Experimental evolution of the bacteriophage T7. Heredity 100:453-633
13. Burt A, Trivers R. 2006. Genes in Conflict: The Biology of Selfish Genetic Elements.Cambridge,MA: Harvard Univ. Press
14. Chao L. 2010. A model for damage load and its implications for the evolution of bacterial aging. PLoS Genet. 6:e10010766
15. Chao L, Cox EC. 1983. Competition between high and low mutating strains of Escherichia coli. Evolution 37:125-344
16. Chao L, Vargas C, Spear BB, Cox EC. 1983. Transposable elements as mutator genes in evolution. Nature 303:633-355
17. Chou HH, Chiu HC, Delaney NF, Segre D, Marx CJ. 2011. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332:1190-922
18. Chuang JS, Rivoire O, Leibler S. 2009. Simpson's paradox in a synthetic microbial system. Science 323:272-755
19. Damore JA, Gore J. 2012. Understanding microbial cooperation. J. Theor. Biol. 299:31-411
20. de Vladar HP, Barton NH. 2011. The contribution of statistical physics to evolutionary biology. Trends Ecol. Evol. 26:424-322
21. Desai MM, Fisher DS. 2007. Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176:1759-988
22. Desai MM, Fisher DS. 2011. The balance between mutators and nonmutators in asexual populations. Genetics 188:997-10144
23. Eames M, Kortemme T. 2012. Cost-benefit tradeoffs in engineered lac operons. Science 336:911-155
24. Erjavec N, Cvijovic M, KlippE,NyströmT. 2008. Selective benefits of damage partitioning in unicellular systems and its effects on aging. Proc. Natl. Acad. Sci. USA 105:18764-699
25. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. 2009. The bacterial species challenge: Making sense of genetic and ecological diversity. Science 323:741-466
26. Frey E. 2010. Evolutionary game theory: Theoretical concepts and applications to microbial communities. Physica A 389:4265-988
27. Gilbert JA, Dupont CL. 2011. Microbial metagenomics: Beyond the genome. Annu. Rev. Mar. Sci. 3:347-711
28. Good BG, Rouzine IM, Balick DJ, Hallatschek O, Desai MM. 2012. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc. Natl. Acad. Sci. USA 109:4950-555
29. Gore J, Youk H, van Oudenaarden A. 2009. Snowdrift game dynamics and facultative cheating in yeast. Nature 459:253-566
30. Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, et al. 2008. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 4: E10003033
31. Hallatschek H, Korolev KS. 2009. Fisher waves in the strong noise limit. Phys. Rev. Lett. 103:1081033
32. Hallatschek O, Nelson DR. 2008. Gene surfing in expanding populations. Theor. Popul. Biol. 73: 158-700
33. Hallatschek O, Nelson DR. 2010. Life at the front of an expanding population. Evolution 64:193-2066
34. Hansen SK, Rainey PB, Haagensen JAJ, Molin S. 2007. Evolution of species interactions in a biofilm community. Nature 445:533-366
35. Hegreness M, Shoresh N, Hartl D, Kishony R. 2006. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311:1615-177
36. Hekstra DR, Leibler S. 2012. Contingency and statistical laws in replicate microbial closed ecosystems. Cell 149:1164-733
37. Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC. 2012. Experimental evolution. Trends Ecol. Evol. 27:547-600
38. Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF. 2011. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332:1193-966
39. Klumpp S, Zhang Z, Hwa T. 2009. Growth rate-dependent global effects on gene expression in bacteria. Cell 139:1366-755
40. Kobayashi I. 2001. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29:3742-566
41. Korolev KS, Avlund M, Hallatschek O, Nelson DR. 2010. Genetic demixing and evolution in linear stepping stone models. Rev. Mod. Phys. 82:1691-7188
42. Korolev KS, MuellerMJI, Karahan N,Murray AW, Hallatschek O, Nelson DR. 2012. Selective sweeps in growing microbial colonies. Phys. Biol. 9:0260088
43. Korolev KS, Xavier JB, Nelson DR, Foster KR. 2011. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies. Am. Nat. 178(4):538-522
44. Kryazhimskiy S, Rice DP,DesaiMM.2012. Population subdivision and adaptation in asexual populations of Saccharomyces cerevisiae. Evolution 66:1931-411
45. Kryazhimskiy S, Tkacik G, Plotkin JB. 2009. The dynamics of adaptation on correlated fitness landscapes. Proc. Natl. Acad. Sci. USA 106:18638-433
46. Kussell E, Leibler S. 2005. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309:2075-788
47. Lang GI, Botstein D, Desai MM. 2011. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 188:647-611
48. LeeM-C, Chou H-H, Marx CJ. 2009. Asymmetric, bimodal trade-offs during adaptation ofmethylobacterium to distinct growth substrates. Evolution 63:2816-300
49. Leibler S, Kussell E. 2010. Individual histories and selection in heterogeneous populations. Proc. Natl. Acad. Sci. USA 107:13183-888
50. Lenski RE, Rose MR, Simpson SC, Tadler SC. 1991. Long-term experimental evolution in Escherichia coli. 1. Adaptation and divergence during 2,000 generations. Am. Nat. 138:1315-411
51. Lenski RE,Winkworth CL, Riley MA. 2003. Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations. J. Mol. Evol. 56:498-5088
52. Levin BR. 2010. Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria. PLoS Genet. 6:e10011711
53. Levin BR, Cornejo OE. 2009. The population and evolutionary dynamics of homologous gene recombination in bacteria. PLoS Genet. 5:e10006011
54. Levin BR, Rozen DE. 2006. Non-inherited antibiotic resistance. Nat. Rev. Microbiol. 4:556-622
55. Levy SF, Ziv N, Siegal ML. 2012. Bet hedging in yeast by heterogeneous, age-correlated expression of a stress protectant. PLoS Biol. 10:e10013255
56. Lim HN, van Oudenaarden A. 2007. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat. Genet. 39:269-755
57. Lin WH, Kussell E. 2012. Evolutionary pressures on simple sequence repeats in prokaryotic coding regions. Nucleic Acids Res. 40:2399-4133
58. Lindner AB, Madden R, Dernarez A, Stewart EJ, Taddei F. 2008. Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation. Proc. Natl. Acad. Sci. USA 105: 3076-811
59. Locke JCW, ElowitzMB. 2009. Using movies to analyse gene circuit dynamics in single cells. Nat. Rev. Microbiol. 7:383-922
60. LongT,Tu KC, Wang Y, Mehta P,Ong NP, et al. 2009. Quantifying the integration of quorum-sensing signals with single-cell resolution. PLoS Biol. 7:640-499
61. Marraffini LA, SontheimerEF. 2010.CRISPRinterference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11:181-900
62. Mehta P, Goyal S, Long T, Bassler BL, Wingreen NS. 2009. Information processing and signal integration in bacterial quorum sensing. Mol. Syst. Biol. 5:3255
63. Meyer JR, Agrawal AA, Quick RT, Dobias DT, Schneider D, Lenski RE. 2010. Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection. Evolution 64:3024-344
64. Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE. 2012. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-322
65. Monod J. 1942. Recherches sur la Croissance des Cultures Bactriennes. Paris: Hermann & Cie
66. Moxon R, Bayliss C,Hood D. 2006. Bacterial contingency loci: The role of simple sequenceDNA repeats in bacterial adaptation. Annu. Rev. Genet. 40:307-333
67. Murray NE. 2002. Immigration control of DNA in bacteria: Self versus non-self. Microbiology 148:3-200
68. Mustonen V, Lässig M. 2009. From fitness landscapes to seascapes: Non-equilibrium dynamics of selection and adaptation. Trends Genet. 25:111-199
69. Nadell CD, Bassler BL. 2011. A fitness trade-off between local competition and dispersal in Vibrio cholerae biofilms. Proc. Natl. Acad. Sci. USA 108(34):14181-855
70. Nadell CD, Foster KR, Xavier JB. 2010. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Comput. Biol. 6:E10007166
71. Nagel AC, Joyce P, Wichman HA, Miller CR. 2012. Stickbreaking: A novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution. Genetics 190:655-677
72. Neher RA, Shraiman BI, Fisher DS. 2010. Rate of adaptation in large sexual populations. Genetics 184:467-811
73. Ng W-L, Bassler BL. 2009. Bacterial quorum-sensing network architectures. Annu. Rev. Genet. 43:197- 2222
74. Nogueira T, Rankin DJ, TouchonM, Taddei F, Brown SP, Rocha EPC. 2009. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr. Biol. 19:1683-911
75. Pearl S, Gabay C, Kishony R, Oppenheim A, Balaban NQ. 2008. Nongenetic individuality in the hostphage interaction. PLoS Biol. 6:957-644
76. Poelwijk FJ, de Vos MGJ, Tans SJ. 2011. Tradeoffs and optimality in the evolution of gene regulation. Cell 146:462-700
77. Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ. 2007. Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445:383-866
78. Qian L, Kussell E. 2012. Evolutionary dynamics of restriction site avoidance. Phys. Rev. Lett. 108:1581055
79. Quan S, Ray JCJ, Kwota Z, Duong T, Balazsi G, et al. 2012. Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli. PLoS Genet. 8:e10024444
80. Rando OJ, Verstrepen KJ. 2007. Timescales of genetic and epigenetic inheritance. Cell 128:655-688
81. Rang CU, Peng AY, Chao L. 2011. Temporal dynamics of bacterial aging and rejuvenation. Curr. Biol. 21:1813-166
82. Rokney A, Shagan M, Kessel M, Smith Y, Rosenshine I, Oppenheim AB. 2009. E. coli transports aggregated proteins to the poles by a specific and energy-dependent process. J. Mol. Biol. 392:589-6011
83. Rokyta DR, Joyce P, Caudle SB, Miller C, Beisel CJ, Wichman HA. 2011. Epistasis between beneficial mutations and the phenotype-to-fitness map for a ssDNA virus. PLoS Genet. 7:e10020755
84. Rotem E, Loinger A, Ronin I, Levin-Reisman I, Gabay C, et al. 2010. Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc. Natl. Acad. Sci. USA 107: 12541-466
85. Rouzine IM, Wakeley J, Coffin JM. 2003. The solitary wave of asexual evolution. Proc. Natl. Acad. Sci. USA 100:587-922
86. Rozen DE, Philippe N, Arjan de Visser J, Lenski RE, Schneider D. 2009. Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol. Lett. 12:34-444
87. Schaechter M, Maaloe O, Kjeldgaard NO. 1958. Dependency of medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium. J. Gen. Microbiol. 19: 592-6066
88. ScottM,Gunderson CW,Mateescu EW, Zhang Z, HwaT. 2010. Interdependence of cell growth and gene expression: Origins and consequences. Science 330:1099-1022
89. Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, et al. 2012. Population genomics of early events in the ecological differentiation of bacteria. Science 336:48-511
90. Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. 2008. A mechanism for asymmetric segregation of age during yeast budding. Nature 454:728-344
91. Sniegowski PD, Gerrish PJ, Lenski RE. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703-55
92. Stewart EJ, Madden R, Paul G, Taddei F. 2005. Aging and death in an organism that reproduces by morphologically symmetric division. PLoS Biol. 3:295-3000
93. Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. 2006. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440:545-500
94. Teng S-W, Schaffer JN,Tu KC, Mehta P, LuW, et al. 2011. Active regulation of receptor ratios controls integration of quorum-sensing signals in Vibrio harveyi. Mol. Syst. Biol. 7:4911
95. Thattai M, van Oudenaarden A. 2004. Stochastic gene expression in fluctuating environments. Genetics 167:523-300
96. van der Woude MW, Bäumler AJ. 2004. Phase and antigenic variation in bacteria. Clin. Microbiol. Rev. 17:581-6111
97. Vilar JMG, Guet CC, Leibler S. 2003. Modeling network dynamics: The lac operon, a case study. J. Cell Biol. 161:471-766
98. Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ. 2009. Unstable tandem repeats in promoters confer transcriptional evolvability. Science 324:1213-166
99. Wakamoto Y, Grosberg AY, Kussell E. 2012. Optimal lineage principle for age-structured populations. Evolution 66:115-344
100. Measures growth and cell death in E. coli cells with a novel microfluidics device. 100. Wang P, Robert L, Pelletier J, Dang WL, Taddei F, et al. 2010. Robust growth of Escherichia coli. Curr. Biol. 20:1099-1033
101. Waters CM, Bassler BL. 2005. Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21:319-466
102. Weinberger AD, Sun CL, Plucinski MM, Denef VJ, Thomas BC, et al. 2012. Persisting viral sequences shape microbial CRISPR-based immunity. PLoS Comput. Biol. 8:e10024755
103. Weinreich DM, Delaney NF, DePristoMA, Hartl DL. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312:111-144
104. Wolf DM, Vazirani VV, Arkin AP. 2005. Diversity in times of adversity: Probabilistic strategies in microbial survival games. J. Theor. Biol. 234:227-533
105. Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331:1433-366
106. Xavier JB, Foster KR. 2007. Cooperation and conflict in microbial biofilms. Proc. Natl. Acad. Sci. USA 104:876-811
107. Xavier JB, Kim W, Foster KR. 2011. A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa. Mol. Microbiol. 79:166-799
108. Yamaguchi Y, Inouye M. 2011. Regulation of growth and death in Escherichia coli by toxin-antitoxin systems. Nat. Rev. Microbiol. 9:779-900