Recovering from a bad start: Rapid adaptation and tradeoffs to growth below a threshold density

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Marx, Christopher J ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; BACTERIUM; DENSITY DEPENDENCE; DILUTION; ENVIRONMENTAL CONDITIONS; GROWTH RATE; METHANOL; MICROBIAL ECOLOGY; PHYSIOLOGICAL RESPONSE; SPECIALIZATION; THRESHOLD; TRADE-OFF;

BACTERIA (MICROORGANISMS); METHYLOBACTERIUM EXTORQUENS;

ACCLIMATIZATION; ARTICLE; EVOLUTION; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; METHYLOBACTERIUM EXTORQUENS; REPRODUCTIVE FITNESS;

ACCLIMATIZATION; BIOLOGICAL EVOLUTION; GENETIC FITNESS; GENOTYPE; METHYLOBACTERIUM EXTORQUENS;

EID: 84863202796     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-109     Document Type: Article

References (35)

1. Bacterial growth: constant obsession with dN/dt. Neidhardt FC, J Bacteriol 1999 181 24 7405 7408 10601194
2. Single-nutrient microbial competition: qualitative agreement between experimental and theoretically forecast outcomes. Hansen SR, Hubbell SP, Science 1980 207 4438 1491 1493 10.1126/science.6767274 6767274
3. Selection in chemostats. Dykhuizen DE, Hartl DL, Microbiol Rev 1983 47 2 150 168 6308409
4. Long-term experimental evolution in Escherichia coli. II. Changes in life-history traits during adaptation to a seasonal environment. Vasi F, Travisano M, Lenski RE, Am Nat 1994 144 432 456 10.1086/285685
5. The Prisoners Dilemna and polymorphism in yeast SUC genes. Grieg D, Travisano M, Proc Biol Sci 2004 271 suppl 25 26 10.1098/rsbl.2003.0083
6. Snowdrift game dynamics and facultative cheating in yeast. Gore J, Youk H, van Oudenaarden A, Nature 2009 459 7244 253 256 10.1038/nature07921 19349960
7. Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. Koschwanez JH, Foster KR, Murray AW, PLoS Biol 2011 9 8 1001122 10.1371/journal.pbio.1001122 21857801
8. Siderophore-mediated cooperation and virulence in Pseudomonas aeruginosa. Buckling A, Harrison F, Vos M, Brockhurst MA, Gardner A, West SA, Griffin A, FEMS Microbiol Ecol 2007 62 2 135 141 10.1111/j.1574-6941.2007.00388.x 17919300
9. Evolutionary theory of bacterial quorum sensing: when is a signal not a signal? Diggle SP, Gardner A, West SA, Griffin AS, Phil Trans Royal Soc B 2007 362 1483 1241 1249 10.1098/rstb.2007.2049
10. Do bacteria need to communicate with each other for growth? Kaprelyants AS, Kell DB, Trends Microbiol 1996 4 6 237 242 10.1016/0966-842X(96)10035-4 8795160
11. Multistability in the lactose utilization network of Escherichia coli. Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A, Nature 2004 427 6976 737 740 10.1038/nature02298 14973486
12. Enzyme Induction as an All-or-None Phenomenon. Novick A, Weiner M, Proc Natl Acad Sci U S A 1957 43 7 553 566 10.1073/pnas.43.7.553 16590055
13. New strategies for cultivation and detection of previously uncultured microbes. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA, Appl Environ Microbiol 2004 70 8 4748 4755 10.1128/AEM.70.8.4748-4755.2004 15294811
14. SAR11 marine bacteria require exogenous reduced sulphur for growth. Tripp HJ, Kitner JB, Schwalbach MS, Dacey JW, Wilhelm LJ, Giovannoni SJ, Nature 2008 452 7188 741 744 10.1038/nature06776 18337719
15. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. Gresham D, Desai MM, Tucker CM, Jenq HT, Pai DA, Ward A, DeSevo CG, Botstein D, Dunham MJ, PLoS Genet 2008 4 12 1000303 10.1371/journal.pgen.1000303 19079573
16. Transport by the lactose permease of Escherichia coli as the basis of lactose killing. Dykhuizen D, Hartl D, J Bacteriol 1978 135 3 876 882 99437
17. C1 transfer enzymes and coenzymes linking methylotrophic bacteria and methanogenic Archaea. Chistoserdova L, Vorholt JA, Thauer RK, Lidstrom ME, Science 1998 281 5373 99 102 9651254
18. Formaldehyde-detoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1. Marx CJ, Chistoserdova L, Lidstrom ME, J Bacteriol 2003 185 24 7160 7168 10.1128/JB.185.23.7160-7168.2003 14645276
19. Purification of the formate-tetrahydrofolate ligase from Methylobacterium extorquens AM1 and demonstration of its requirement for methylotrophic growth. Marx CJ, Laukel M, Vorholt JA, Lidstrom ME, J Bacteriol 2003 185 24 7169 7175 10.1128/JB.185.24.7169-7175.2003 14645277
20. Development of an insertional expression vector system for Methylobacterium extorquens AM1 and generation of null mutants lacking mtdA and/or fch. Marx CJ, Lidstrom ME, Microbiology 2004 150 Pt 1 9 19 14702393
21. Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism. Marx CJ, Van Dien SJ, Lidstrom ME, PLoS Biol 2005 3 2 16 10.1371/journal.pbio.0030016 15660163
22. Formate as the main branch point for methylotrophic metabolism in Methylobacterium extorquens AM1. Crowther GJ, Kosaly G, Lidstrom ME, J Bacteriol 2008 190 14 5057 5062 10.1128/JB.00228-08 18502865
23. S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification? Harms N, Ras J, Reijnders WN, van Spanning RJ, Stouthamer AH, J Bacteriol 1996 178 21 6296 6299 8892832
24. Isolation, sequencing, and mutagenesis of the gene encoding NAD- and glutathione-dependent formaldehyde dehydrogenase (GD-FALDH) from Paracoccus denitrificans, in which GD-FALDH is essential for methylotrophic growth. Ras J, Van Ophem PW, Reijnders WN, Van Spanning RJ, Duine JA, Stouthamer AH, Harms N, J Bacteriol 1995 177 1 247 251 7798140
25. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Chou HH, Chiu HC, Delaney NF, Segre D, Marx CJ, Science 2011 332 6034 1190 1192 10.1126/science.1203799 21636771
26. Optimization of gene expression through divergent mutational paths. Chou HH, Marx CJ, Cell Reports 2012 1 2 133 140 10.1016/j.celrep.2011.12.003 22832162
27. Repeated, selection-driven genome reduction of accessory genes in experimental populations. Lee MC, Marx CJ, PLoS Genet 2012 8 5 1002651 10.1371/journal.pgen.1002651 22589730
28. Novel methylotrophy genes of Methylobacterium extorquens AM1 identified by using transposon mutagenesis including a putative dihydromethanopterin reductase. Marx CJ, O'Brien BN, Breezee J, Lidstrom ME, J Bacteriol 2003 185 2 669 673 10.1128/JB.185.2.669-673.2003 12511515
29. Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. Chou HH, Berthet J, Marx CJ, PLoS Genet 2009 5 9 1000652 10.1371/journal.pgen.1000652 19763169
30. Siderophores from neighboring organisms promote the growth of uncultured bacteria. D'Onofrio A, Crawford JM, Stewart EJ, Witt K, Gavrish E, Epstein S, Clardy J, Lewis K, Chem Biol 2010 17 3 254 264 10.1016/j.chembiol.2010.02.010 20338517
31. Purification, overproduction, and partial characterization of beta-RFAP synthase, a key enzyme in the methanopterin biosynthesis pathway. Scott JW, Rasche ME, J Bacteriol 2002 184 16 4442 4448 10.1128/JB.184.16.4442-4448.2002 12142414
32. Development of a broad-host-range sacB-based vector for unmarked allelic exchange. Marx CJ, BMC Res Notes 2008 1 1 1 10.1186/1756-0500-1-1 18710539
33. Genetic characterization of the carotenoid biosynthetic pathway in Methylobacterium extorquens AM1 and isolation of a colorless mutant. Van Dien SJ, Marx CJ, O'Brien BN, Lidstrom ME, Appl Environ Microbiol 2003 69 12 7563 7566 10.1128/AEM.69.12.7563-7566.2003 14660416
34. Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Lee MC, Chou HH, Marx CJ, Evolution 2009 63 11 2816 2830 10.1111/j.1558-5646.2009.00757.x 19545267
35. Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations. Lenski RE, Rose MR, Simpson SC, Tadler SC, Am Nat 1991 138 6 1315 1341 10.1086/285289