The evolutionary emergence of stochastic phenotype switching in bacteria

Microbial Cell Factories

Volumn 10, Issue SUPPL. 1, 2011, Pages

  Rainey, Paul B ^a,b   Beaumont, Hubertus J E ^c   Ferguson, Gayle C ^a   Gallie, Jenna ^d   Kost, Christian ^e   Libby, Eric ^a   Zhang, Xue Xian ^a  

^a MASSEY UNIVERSITY   (New Zealand)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^c DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^d UNIVERSITY OF WASHINGTON   (United States)

^e MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ANTIGENIC VARIATION; ARTICLE; BACTERIUM; ENVIRONMENTAL FACTOR; EXPERIMENTAL DESIGN; EXPERIMENTAL STUDY; GENE MUTATION; GENETICS; HAEMOPHILUS INFLUENZAE; IMMUNE RESPONSE; MATHEMATICAL MODEL; MORPHOLOGY; NONHUMAN; PHENOTYPE; PSEUDOMONAS; SIMULATION; STOCHASTIC PHENOTYPE SWITCHING; THEORETICAL STUDY; ADAPTATION; BACTERIAL PHENOMENA AND FUNCTIONS; EVOLUTION; GROWTH, DEVELOPMENT AND AGING; PHYSIOLOGY; STATISTICS;

BACTERIA (MICROORGANISMS);

ADAPTATION, PHYSIOLOGICAL; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; BIOLOGICAL EVOLUTION; PHENOTYPE; STOCHASTIC PROCESSES;

EID: 80052244698     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-10-S1-S14     Document Type: Article

References (49)

1. Kelly JL. A new interpretation of information rate. Bell Syst Tech J 1956, 35:917-926.
2. Shannon CE. A mathematical theory of communication. Bell Syst Tech J 1949, 27:379-423. 623-656.
3. Stearns SC. Daniel Bernoulli (1738): evolution and economics under risk. J Bioscience 2000, 25:221-228.
4. Slatkin M. Hedging one's evolutionary bets. Nature 1974, 250:704-705.
5. Bergstrom CT, Lachmann M. Shannon information and biological fitness. IEEE Information Theory Workshop; IEEE 2004, 50-54.
6. Via S, Lande R. Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 1985, 39:505-522.
7. Cohen D. Optimizing reproduction in a randomly varying environment. J Theor Biol 1966, 12:119-129. 10.1016/0022-5193(66)90188-3, 6015423.
8. Seger JB, Brockmann H. What is bet hedging?. Oxford Surveys in Evolutionary Biology 1987, 182-211. Oxford Oxford University Press, Harvey P, Partridge L.
9. Bull JJ. Evolution of phenotypic variance. Evolution 1987, 41:303-315.
10. King OD, Masel J. The evolution of bet-hedging adaptations to rare scenarios. Theor Pop Biol 2007, 72:560-575.
11. Childs DZ, Metcalf CJ, Rees M. Evolutionary bet-hedging in the real world: empirical evidence and challenges revealed by plants. Proc R Soc B 2010, 277:3055-3064. 10.1098/rspb.2010.0707, 20573624.
12. Andrewes FW. Studies in group-agglutination. I. The Salmonella group and its antigenic structure. J Path Bacteriol 1922, 25:505-521.
13. Moxon ER, Rainey PB, Nowak MA, Lenski RE. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 1994, 4:24-33. 10.1016/S0960-9822(00)00005-1, 7922307.
14. Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005, 6:451-464. 10.1038/nrg1615, 15883588.
15. Smits WK, Kuipers OP, Veening JW. Phenotypic variation in bacteria: the role of feedback regulation. Nat Rev Microbiol 2006, 4:259-271. 10.1038/nrmicro1381, 16541134.
16. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science 2002, 297:1183-1186. 10.1126/science.1070919, 12183631.
17. Maamar H, Raj A, Dubnau D. Noise in gene expression determines cell fate in Bacillus subtilis. Science 2007, 317:526-529. 10.1126/science.1140818, 17569828.
18. Lim HN, van Oudenaarden A. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 2007, 39:269-725. 10.1038/ng1956, 17220888.
19. Freed NE, Silander OK, Stecher B, Bohm A, Hardt WD, Ackermann M. A simple screen to identify promoters conferring high levels of phenotypic noise. PLoS Genet 2008, 4:e1000307. 10.1371/journal.pgen.1000307, 2588653, 19096504.
20. Dubnau D, Losick R. Bistability in bacteria. Mol Microbiol 2006, 61:564-572. 10.1111/j.1365-2958.2006.05249.x, 16879639.
21. Keren I, Kaldalu N, Spoering A, Wang Y, Lewis K. Persister cells and tolerance to antimicrobials. FEMS Microbiol Lett 2004, 230:13-18. 10.1016/S0378-1097(03)00856-5, 14734160.
22. Balaban NQ, Merrin J, Chait R, Kowalik L, Leibler S. Bacterial persistence as a phenotypic switch. Science 2004, 305:1622-1625. 10.1126/science.1099390, 15308767.
23. Kussell E, Leibler S. Phenotypic diversity, population growth, and information in fluctuating environments. Science 2005, 309:2075-2078. 10.1126/science.1114383, 16123265.
24. Johnsen PJ, Dubnau D, Levin BR. Episodic selection and the maintenance of competence and natural transformation in Bacillus subtilis. Genetics 2009, 181:1521-1533. 10.1534/genetics.108.099523, 2666517, 19189946.
25. Moxon ER, Bayliss C, Hood DW. Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Annu Rev Genet 2006, 40:307-333. 10.1146/annurev.genet.40.110405.090442, 17094739.
26. Maizels N. Immunoglobulin gene diversification. Annu Rev Genet 2005, 39:23-46. 10.1146/annurev.genet.39.073003.110544, 16285851.
27. Levinson G, Gutman GA. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol Biol Evol 1987, 4:203-221.
28. Simons AM. Fluctuating natural selection accounts for the evolution of diversification bet hedging. Proc R Soc B 2009, 276:1987-1992. 10.1098/rspb.2008.1920, 2677257, 19324774.
29. Meyers LA, Bull JJ. Fighting change with change: Adaptive variation in an uncertain world. Trends Ecol Evol 2002, 17:551-557.
30. Frank SA, Bush RM. Barriers to antigenic escape by pathogens: trade-off between reproductive rate and antigenic mutability. BMC Evol Biol 2007, 7:229. 10.1186/1471-2148-7-229, 2217548, 18005440.
31. Kussell E, Kishony R, Balaban NQ, Leibler S. Bacterial persistence: a model of survival in changing environments. Genetics 2005, 169:1807-1814. 10.1534/genetics.104.035352, 1449587, 15687275.
32. Acar M, Mettetal JT, van Oudenaarden A. Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 2008, 40:471-475. 10.1038/ng.110, 18362885.
33. Gaal B, Pitchford JW, Wood AJ. Exact results for the evolution of stochastic switching in variable asymmetric environments. Genetics 2010, 184:1113-1119. 10.1534/genetics.109.113431, 2865911, 20100938.
34. Wolf DM, Vazirani VV, Arkin AP. A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation. J Theor Biol 2005, 234:255-262. 10.1016/j.jtbi.2004.11.021, 15757682.
35. Donaldson-Matasci MC, Bergstrom CT, Lachmann M. The fitness value of information. Oikos 2010, 119:219-230.
36. Levins R. Theory of fitness in a heterogeneous environment. I. The fitness set and adaptive function. Am Nat 1962, 96:361-373.
37. Donaldson-Matasci MC, Lachmann M, Bergstrom CT. Phenotypic diversity as an adaptation to environmental uncertainty. Evol Ecol Res 2008, 10:493-515.
38. Visco P, Allen RJ, Majumdar SN, Evans MR. Switching and growth for microbial populations in catastrophic responsive environments. Biophys J 2010, 98:1099-1108. 10.1016/j.bpj.2009.11.049, 2849059, 20371309.
39. Salathe M, Van Cleve J, Feldman MW. Evolution of stochastic switching rates in asymmetric fitness landscapes. Genetics 2009, 182:1159-1164. 10.1534/genetics.109.103333, 2728856, 19474199.
40. Ribeiro AS. Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments. Phys Rev E 2008, 78:061902.
41. Beaumont HJ, Gallie J, Kost C, Ferguson GC, Rainey PB. Experimental evolution of bet hedging. Nature 2009, 462:90-93. 10.1038/nature08504, 19890329.
42. Rainey PB, Travisano M. Adaptive radiation in a heterogeneous environment. Nature 1998, 394:69-72. 10.1038/27900, 9665128.
43. McDonald MJ, Gehrig SM, Meintjes PL, Zhang XX, Rainey PB. Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 2009, 183:1041-1053. 10.1534/genetics.109.107110, 2778958, 19704015.
44. de Jong IG, Haccou P, Kuipers OP. Bet hedging or not? A guide to proper classification of microbial survival strategies. Bioessays 2011, 33:215-223. 10.1002/bies.201000127, 21254151.
45. Simons AM. Modes of response to environmental change and the elusive empirical evidence for bet hedging. Proc R Soc B 2011, 278:1601-1609. 10.1098/rspb.2011.0176, 21411456.
46. Libby E, Rainey PB. Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching. Proc R Soc B 2011, doi: 10.1098/rspb.2011.0146.
47. Buckling A, Rainey PB. Antagonistic coevolution between a bacterium and a bacteriophage. Proc R Soc B 2002, 269:931-936. 10.1098/rspb.2001.1945, 1690980, 12028776.
48. Veening JW, Stewart EJ, Berngruber TW, Taddei F, Kuipers OP, Hamoen LW. Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci USA 2008, 105:4393-4398. 10.1073/pnas.0700463105, 2393751, 18326026.
49. Monteiro SM, Clemente JJ, Henriques AO, Gomes RJ, Carrondo MJ, Cunha AE. A procedure for high-yield spore production by Bacillus subtilis. Biotechnol Prog 2005, 21:1026-1031.