Optimization of Gene Expression through Divergent Mutational Paths

Cell Reports

Volumn 1, Issue 2, 2012, Pages 133-140

  Chou, Hsin Hung ^a,c   Marx, Christopher J ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; CONTROLLED STUDY; CONVERGENT EVOLUTION; ENZYME ACTIVITY; FGHA GENE; FLHA GENE; GENE CASSETTE; GENE DOSAGE; GENE EXPRESSION; GENE MAPPING; GENE OVEREXPRESSION; GENETIC STABILITY; GENETIC VARIABILITY; GENOTYPE PHENOTYPE CORRELATION; HAPLOTYPE MAP; METABOLIC REGULATION; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; PHENOTYPIC VARIATION; PROCESS OPTIMIZATION; PROMOTER REGION; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; FLOW CYTOMETRY; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC FITNESS; GLUTATHIONE; HAPLOTYPES; METABOLIC ENGINEERING; METHANOL; METHYLOBACTERIUM EXTORQUENS; MOLECULAR SEQUENCE DATA; MUTATION; PLASMIDS;

BACTERIA (MICROORGANISMS);

EID: 84861135633     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2011.12.003     Document Type: Article

References (51)

1. Abzhanov A., Kuo W.P., Hartmann C., Grant B.R., Grant P.R., Tabin C.J. The calmodulin pathway and evolution of elongated beak morphology in Darwin's finches. Nature 2006, 442:563-567.
2. Akashi H., Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 2002, 99:3695-3700.
3. Andersson D.I., Hughes D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 2009, 43:167-195.
4. Barrett R.D., MacLean R.C., Bell G. Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations. Biol. Lett. 2006, 2:236-238.
5. Barrick J.E., Yu D.S., Yoon S.H., Jeong H., Oh T.K., Schneider D., Lenski R.E., Kim J.F. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 2009, 461:1243-1247.
6. Bedford T., Hartl D.L. Optimization of gene expression by natural selection. Proc. Natl. Acad. Sci. USA 2009, 106:1133-1138.
7. Berg T., Firth N., Apisiridej S., Hettiaratchi A., Leelaporn A., Skurray R.A. Complete nucleotide sequence of pSK41: evolution of staphylococcal conjugative multiresistance plasmids. J. Bacteriol. 1998, 180:4350-4359.
8. Brand A.H., Perrimon N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 1993, 118:401-415.
9. Brown C.J., Todd K.M., Rosenzweig R.F. Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol. Biol. Evol. 1998, 15:931-942.
10. Cereghino J.L., Helinski D.R. Essentiality of the three carboxyl-terminal amino acids of the plasmid RK2 replication initiation protein TrfA for DNA binding and replication activity in gram-negative bacteria. J. Biol. Chem. 1993, 268:24926-24932.
11. Chistoserdov A.Y., Chistoserdova L.V., McIntire W.S., Lidstrom M.E. Genetic organization of the mau gene cluster in Methylobacterium extorquens AM1: complete nucleotide sequence and generation and characteristics of mau mutants. J. Bacteriol. 1994, 176:4052-4065.
12. Chou H.H., Berthet J., Marx C.J. Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation. PLoS Genet. 2009, 5:e1000652.
13. Chou H.H., Chiu H.C., Delaney N.F., Segrè D., Marx C.J. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 2011, 332:1190-1192.
14. Cohen S.N. Transposable genetic elements and plasmid evolution. Nature 1976, 263:731-738.
15. Dabizzi S., Ammannato S., Fani R. Expression of horizontally transferred gene clusters: activation by promoter-generating mutations. Res. Microbiol. 2001, 152:539-549.
16. Dekel E., Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436:588-592.
17. Desai M.M., Fisher D.S., Murray A.W. The speed of evolution and maintenance of variation in asexual populations. Curr. Biol. 2007, 17:385-394.
18. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 1998, 95:14863-14868.
19. Field Y., Fondufe-Mittendorf Y., Moore I.K., Mieczkowski P., Kaplan N., Lubling Y., Lieb J.D., Widom J., Segal E. Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat. Genet. 2009, 41:438-445.
20. Gresham D., Desai M.M., Tucker C.M., Jenq H.T., Pai D.A., Ward A., DeSevo C.G., Botstein D., Dunham M.J. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 2008, 4:e1000303.
21. Hall B.G. Spectra of spontaneous growth-dependent and adaptive mutations at ebgR. J. Bacteriol. 1999, 181:1149-1155.
22. Hegreness M., Shoresh N., Hartl D., Kishony R. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 2006, 311:1615-1617.
23. Henkin T.M., Sonenshein A.L. Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis. Mol. Gen. Genet. 1987, 209:467-474.
24. Iost I., Dreyfus M. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J. 1995, 14:3252-3261.
25. Kaberdin V.R., Bläsi U. Translation initiation and the fate of bacterial mRNAs. FEMS Microbiol. Rev. 2006, 30:967-979.
26. Kasak L., Hõrak R., Kivisaar M. Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria. Proc. Natl. Acad. Sci. USA 1997, 94:3134-3139.
27. Kassen R., Bataillon T. Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat. Genet. 2006, 38:484-488.
28. Khaitovich P., Tang K., Franz H., Kelso J., Hellmann I., Enard W., Lachmann M., Pääbo S. Positive selection on gene expression in the human brain. Curr. Biol. 2006, 16:R356-R358.
29. Kurland C.G., Dong H. Bacterial growth inhibition by overproduction of protein. Mol. Microbiol. 1996, 21:1-4.
30. Lee C.L., Ow D.S., Oh S.K. Quantitative real-time polymerase chain reaction for determination of plasmid copy number in bacteria. J. Microbiol. Methods 2006, 65:258-267.
31. Lenski R.E., Rose M.R., Simpson S.C., Tadler S.C. Long-term experimental evolution in Escherichia coli. 1. adaptation and divergence during 2,000 generations. Am. Nat. 1991, 138:1315-1341.
32. Lin J., Helinski D.R. Analysis of mutations in trfA, the replication initiation gene of the broad-host-range plasmid RK2. J. Bacteriol. 1992, 174:4110-4119.
33. Mahillon J., Chandler M. Insertion sequences. Microbiol. Mol. Biol. Rev. 1998, 62:725-774.
34. Marciano D.C., Karkouti O.Y., Palzkill T. A fitness cost associated with the antibiotic resistance enzyme SME-1 β-lactamase. Genetics 2007, 176:2381-2392.
35. Monod J., Jacob F. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 1961, 26:389-401.
36. Notley-McRobb L., Ferenci T. Adaptive mgl-regulatory mutations and genetic diversity evolving in glucose-limited Escherichia coli populations. Environ. Microbiol. 1999, 1:33-43.
37. Notley-McRobb L., Ferenci T. The generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose-limited populations of Escherichia coli. Environ. Microbiol. 1999, 1:45-52.
38. R: A Language and Environment for Statistical Computing 2009, R Development Core Team, R Foundation for Statistical Computing, Vienna.
39. Rubens C.E., McNeill W.F., Farrar W.E. Evolution of multiple-antibiotic-resistance plasmids mediated by transposable plasmid deoxyribonucleic acid sequences. J. Bacteriol. 1979, 140:713-719.
40. Saint-Dic D., Kehrl J., Frushour B., Kahng L.S. Excess SeqA leads to replication arrest and a cell division defect in Vibrio cholerae. J. Bacteriol. 2008, 190:5870-5878.
41. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
42. Spradling A.C., Rubin G.M. The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene. Cell 1983, 34:47-57.
43. Stern D.L. Roberts and Company Publishers 2011, The Predictable Genome. In Evolution, Development, and the Predictable Genome, Greenwood Village, the United States, 149-174.
44. Stern D.L., Orgogozo V. Is genetic evolution predictable?. Science 2009, 323:746-751.
45. Stoebel D.M., Dean A.M., Dykhuizen D.E. The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 2008, 178:1653-1660.
46. Sun S., Berg O.G., Roth J.R., Andersson D.I. Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium. Genetics 2009, 182:1183-1195.
47. Thompson A., Gasson M.J. Location effects of a reporter gene on expression levels and on native protein synthesis in Lactococcus lactis and Saccharomyces cerevisiae. Appl. Environ. Microbiol. 2001, 67:3434-3439.
48. Toyama H., Anthony C., Lidstrom M.E. Construction of insertion and deletion mxa mutants of Methylobacterium extorquens AM1 by electroporation. FEMS Microbiol. Lett. 1998, 166:1-7.
49. 1 compounds from natural and industrial sources. PLoS ONE 2009, 4:e5584.
50. Willenbrock H., Ussery D.W. Chromatin architecture and gene expression in Escherichia coli. Genome Biol. 2004, 5:252.
51. Wood T.E., Burke J.M., Rieseberg L.H. Parallel genotypic adaptation: when evolution repeats itself. Genetica 2005, 123:157-170.