Repeated, selection-driven genome reduction of accessory genes in experimental populations

PLoS Genetics

Volumn 8, Issue 5, 2012, Pages

  Lee, Ming Chun ^a,c   Marx, Christopher J ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENE DELETION; GENE LOSS; GENE REPLICATION; GENE SEQUENCE; GENETIC DRIFT; GENETIC SELECTION; GENOME ANALYSIS; METHYLOBACTERIUM EXTORQUENS; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; REDUCTION KINETICS; SEQUENCE ANALYSIS; ADAPTATION; CHROMOSOME; DIRECTED MOLECULAR EVOLUTION; GENETICS; GENOME SIZE; METABOLISM; MUTATION; PHYSIOLOGICAL STRESS;

BACTERIA (MICROORGANISMS); METHYLOBACTERIUM EXTORQUENS;

ADAPTATION, PHYSIOLOGICAL; CHROMOSOMES; COMPARATIVE GENOMIC HYBRIDIZATION; DIRECTED MOLECULAR EVOLUTION; GENE DELETION; GENETIC DRIFT; GENOME SIZE; GENOME, BACTERIAL; METHYLOBACTERIUM EXTORQUENS; MUTATION; PLASMIDS; SELECTION, GENETIC; STRESS, PHYSIOLOGICAL;

EID: 84863668598     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002651     Document Type: Article

References (34)

1. Kuo C, Moran NA, Ochman H, (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 1450-1454.
2. Lynch M, (2006) Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol 60: 327-349.
3. Lawrence JG, Ochman H, (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95: 9413-9417.
4. Welch RA, Burland V, Plunkett G, Redford P, Roesch P, et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99: 17020-17024.
5. Lan R, Reeves PR, (2000) Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol 8: 396-401.
6. Moran NA, Mira A, (2001) The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol 2: research0054.
7. Moran NA, (2002) Microbial minimalism: Genome reduction in bacterial pathogens. Cell 108: 583-586.
8. Ochman H, Moran NA, (2001) Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-1099.
9. McCutcheon JP, Moran NA, (2011) Extreme genome reduction in symbiotic bacteria. Nat Rev Microbiol 10: 13-26.
10. Dufresne A, Garczarek L, Partensky F, (2005) Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol 6: R14.
11. Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 1242-1245.
12. Frost LS, Leplae R, Summers AO, Toussaint A, (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722-732.
13. Cramer N, Klockgether J, Wrasman K, Schmidt M, Davenport CF, et al. (2011) Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ Microbiol 13: 1690-1704.
14. Ernst RK, D'Argenio DA, Ichikawa JK, Bangera MG, Selgrade S, et al. (2003) Genome mosaicism is conserved but not unique in Pseudomonas aeruginosa isolates from the airways of young children with cystic fibrosis. Environ Microbiol 5: 1341-1349.
15. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 103: 8487-8492.
16. Maurelli AT, Fernández RE, Bloch CA, Rode CK, Fasano A, (1998) "Black holes" and bacterial pathogenicity: a large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli. Proc Natl Acad Sci USA 95: 3943-3948.
17. Nilsson A, Koskiniemi S, Eriksson S, Kugelberg E, Hinton J, et al. (2005) Bacterial genome size reduction by experimental evolution. Proc Natl Acad Sci USA 102: 12112-12116.
18. 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: 1243-1247.
19. Zhong S, Khodursky A, Dykhuizen DE, Dean AM, (2004) Evolutionary genomics of ecological specialization. Proc Natl Acad Sci USA 101: 11719-11724.
20. Cooper VS, Schneider D, Blot M, Lenski RE, (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J Bacteriol 183: 2834-2841.
21. Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, et al. (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci USA 106: 16428-16433.
22. Lee M-C, Chou H-H, Marx CJ, (2009) Asymmetric, bimodal trade-offs during adaptation of Methylobacterium to distinct growth substrates. Evolution 63: 2816-2830.
23. Vuilleumier S, Chistoserdova L, Lee M-C, Bringel F, Lajus A, et al. (2009) Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of c1 compounds from natural and industrial sources. PLoS ONE 4: e5584.
24. Chou H-H, Chiu H-C, Delaney NF, Segrè D, Marx CJ, (2011) Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 332: 1190-1192.
25. Moran NA, McLaughlin HJ, Sorek R, (2009) The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria. Science 323: 379-382.
26. Novichkov PS, Wolf YI, Dubchak I, Koonin EV, (2009) Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol 191: 65-73.
27. Harrison PW, Lower RPJ, Kim NKD, Young JPW, (2010) Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol 18: 141-148.
28. Gourion B, Rossignol M, Vorholt JA, (2006) A proteomic study of Methylobacterium extorquens reveals a response regulator essential for epiphytic growth. Proc Natl Acad Sci USA 103: 13186-13191.
29. Notley-McRobb L, King T, Ferenci T, (2002) rpoS mutations and loss of general stress resistance in Escherichia coli populations as a consequence of conflict between competing stress responses. J Bacteriol 184: 806-811.
30. Finkel SE, (2006) Long-term survival during stationary phase: evolution and the GASP phenotype. Nat Rev Microbiol 4: 113-120.
31. Marx C, (2008) Development of a broad-host-range sacB-based vector for unmarked allelic exchange. BMC Res Notes 1: 1.
32. Okubo Y, Skovran E, Guo X, Sivam D, Lidstrom ME, (2007) Implementation of microarrays for Methylobacterium extorquens AM1. Omics 11: 325-340.
33. Marx CJ, Lidstrom ME, (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33: 1062-1067.
34. Vasi F, Travisano M, Lenski RE, (1994) Long-term experimental evolution in Escherichia coli. II. Changes in life-history traits during adaptation to a seasonal environment. Am Nat 144: 432-456.