What traits are carried on mobile genetic elements, and why

Heredity

Volumn 106, Issue 1, 2011, Pages 1-10

  Rankin, D J ^a,b   Rocha, E P C ^c   Brown, S P ^d  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c CNRS   (France)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

microbial ecology; Mobile genetic elements; mutualisms; plasmid addiction; social evolution; toxin antitoxin

Indexed keywords

EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENOME; HERITABILITY; MICROBIAL ECOLOGY; MUTUALISM; PLASMID; PROKARYOTE; TOXIN;

BACTERIAL GENOME; BACTERIUM; GENETICS; HORIZONTAL GENE TRANSFER; INTERSPERSED REPEAT; PLASMID; REVIEW;

BACTERIA; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; INTERSPERSED REPETITIVE SEQUENCES; PLASMIDS;

BACTERIA (MICROORGANISMS); PROKARYOTA;

EID: 78650305634     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2010.24     Document Type: Review

References (121)

1. Achtman M (1975). Mating aggregates in Escherichia coli conjugation. J Bacteriol 123: 505-515.
2. Ackermann M, Stecher B, Freed NE, Songhet P, Hardt W-D, Doebeli M (2008). Self-destructive cooperation mediated by phenotypic noise. Nature 454: 987-990.
3. Ahmer BMM, Tran M, Heron F (1999). The virulence plasmid of Salmonella typhimurium is self-transmissible. J Bacteriol 181: 1364-1368.
4. Alizon S, Hurford A, Mideo N, van Baalen M (2009). Virulence evolution and the trade-off hypothesis: history, current state of affairs and the future. J Evol Biol 22: 245-259.
5. Amabile-Cuevas CF, Heinemann JA (2004). Shooting the messenger of antibiotic resistance: plasmid elimination as a counter-evolutionary tactic. Drug Discov Today 9: 465-467.
6. Anderson RM, May RM (1979). Population biology of infectious diseases: part I. Nature 280: 361-367.
7. Anderson RM, May RM (1992). Infectious Diseases of Humans: Dynamics and Control. Oxford University Press: Oxford.
8. Arcus VL, Rainey PB, Turner SJ (2005). The PIN-domain toxin-antitoxin array in mycobacteria. Trends Microbiol 13: 360-365.
9. Bahl MI, Hansen LH, Licht TR, Sorensen SJ (2007a). Conjugative transfer facilitates stable maintenance of IncP-1 plasmid pKJK5 in Escherichia coli cells colonizing the gastrointestinal tract of the germfree rat. Appl Environ Microbiol 73: 341-343.
10. Bahl MI, Lars Hestbjerg H, Sren JS (2007b). Impact of conjugal transfer on the stability of IncP-1 plasmid pKJK5 in bacterial populations. FEMS Microbiol Lett 266: 250-256.
11. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315: 1709-1712.
12. Bergstrom CT, Lipsitch M, Levin BR (2000). Natural selection, infectious transfer and the existence conditions for bacterial plasmids. Genetics 155: 1505-1519.
13. Bordenstein SR, Reznikoff WS (2005). Mobile DNA in obligate intracellular bacteria. Nat Rev Microbiol 3: 688-699.
14. Bouma JE, Lenski RE (1988). Evolution of a bacteria plasmid association. Nature 335: 351-352.
15. Brown SP, Buckling A (2008). A social life for discerning microbes. Cell 135: 600-604.
16. Brown SP, Inglis RF, Taddei F (2009a). Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence. Evol Appl 2: 32-39.
17. Brown SP, Le Chat L, De Paepe M, Taddei F (2006). Ecology of microbial invasions: amplification allows virus carriers to invade more rapidly when rare. Curr Biol 16: 2048-2052.
18. Brown SP, West SA, Diggle SP, Griffin AS (2009b). Social evolution in micro-organisms and a Trojan horse approach to medical intervention strategies. Philos Trans R Soc London B Biol Sci 364: 3157-3168.
19. Buchrieser C, Glaser P, Rusniok C, Nedjari H, D'Hauteville H, Kunst F et al. (2000). The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol Microbiol 38: 760-771.
20. Bushman F (2002). Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbour University Press: Cold Spring Harbour, NY.
21. Buts L, Lah J, Dao-Thi M-H, Wyns L, Loris R (2005). Toxinantitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci 30: 672-679.
22. Cascales E, Buchanan SK, Duche D, Kleanthous C, Lloubes R, Postle K et al. (2007). Colicin biology. Microbiol Mol Biol Rev 71: 158-229.
23. Cascales E, Christie PJ (2003). The versatile bacterial type IV secretion systems. Nat Rev Microbiol 1: 137-149.
24. Chao L, Levin BR (1981). Structured habitats and the evolution of anticompetitor toxins in bacteria. Proc Natl Acad Sci USA 78: 6324-6328.
25. Chen I, Dubnau D (2004). DNA uptake during bacterial transformation. Nat Rev Microbiol 2: 241-249.
26. Cooper TF, Heinemann JA (2000). Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competiting plasmids. Proc Natl Acad Sci USA 97: 12643-12648.
27. Cooper TF, Heinemann JA (2005). Selection for plasmid postsegregational killing depends on multiple infection: evidence for the selection of more virulent parasites through parasitelevel competition. Proc R Soc London B Biol Sci 272: 403-410.
28. Crespi BJ (2001). The evolution of social behavior in microorganisms. Trends Ecol Evol 16: 178-183.
29. de la Cruz F, Frost LS, Meyer RJ, Zechner E (2009). Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34: 18-40.
30. Delsuc F, Brinkmann H, Philippe H (2005). Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 6: 361-375.
31. Diaz Ricci JC, Hernandez ME (2000). Plasmid effects on Escherichia coli metabolism. Crit Rev Biotechnol 20: 79-108.
32. Dionisio F (2007). Selfish and spiteful behaviour through parasites and pathogens. Evol Ecol Res 9: 1199-1210.
33. Dionisio F, Matic I, Radman M, Rodrigues OR, Taddei F (2002). Plasmids spread very fast in heterogeneous bacterial communities. Genetics 162: 1525-1532.
34. Dykes GA, Hastings JW (1999). Selection and fitness in bacteriocin-producing bacteria. Proc R Soc London B Biol Sci 264: 683-687.
35. Eberhard WG (1990). Evolution in bacterial plasmids and levels of selection. Q Rev Biol 65: 3-22.
36. Egan ES, Waldor MK (2003). Distinct replication requirements for the two Vibrio cholerae chromosomes. Cell 114: 521-530.
37. Ellis RJ, Lilley AK, Lacey SJ, Murrell D, Godfray HCJ (2007). Frequency-dependent advantages of plasmid carriage by Pseudomonas in homogeneous and spatially structured environments. ISME J 1: 92-95.
38. Faruque SM, Naser IB, Islam MJ, Faruque ASG, Ghosh AN, Nair GB et al. (2005). Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages. Proc Natl Acad Sci USA 102: 1702-1707.
39. Ferdy JB, Godelle B (2005). Diversification of transmission modes and the evolution of mututalism. Am Nat 166: 613-627.
40. Foster KR, Ratnieks FLW, Wenseleers T (2000). Spite in social insects. Trends Ecol Evol 15: 469-470.
41. Foster KR, Wenseleers T (2006). A general model for the evolution of mutualisms. J Evol Biol 19: 1283-1293.
42. Foster KR, Wenseleers T, Ratnieks FLW (2001). Spite: Hamilton's unproven theory. Ann Zool Fennici 38: 229-238.
43. Fox RE, Zhong X, Krone SM, Top EM (2008). Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations. ISME J 2: 1024-1039.
44. Frost LS, Leplae R, Summers AO, Toussaint A (2005). Mobile genetic elements: the agents of open source evolution. Nat Rev Micro 3: 722-732.
45. Gardner A, Hardy ICW, Taylor PD, West SA (2007). Spiteful soldiers and sex ratio conflict in polyembryonic parasitoid wasps. Am Nat 169: 519-533.
46. Gardner A, West SA (2004a). Spite among siblings. Science 305: 1413-1414.
47. Gardner A, West SA (2004b). Spite and the scale of competition. J Evol Biol 17: 1195-1203.
48. Gardner A, West SA (2006). Spite. Curr Biol 16: R662-R664.
49. Gardner A, West SA (2010). Greenbeards. Evolution 64: 25-38.
50. Gardner A, West SA, Buckling A (2004). Bacteriocins, spite and virulence. Proc R Soc London B 271: 1529-1535.
51. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ et al. (2005). Re-evaluating prokaryotic species. Nat Rev Micro 3: 733-739.
52. Gil G, Sabater-Muñoz B, Perez-Brocal V, Silva FJ, Latorre A (2006). Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story. Gene 370: 17-25.
53. Goldenfeld N,Woese C (2007). Biology's next revolution. Nature 445: 369.
54. Griffin AS, West SA, Buckling A (2004). Cooperation and competition in pathogenic bacteria. Nature 430: 1024-1027.
55. Hacker J, Carniel E (2001). Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep 2: 376-381.
56. Haft RJF, Mittler JE, Traxler B (2009). Competition favours reduced cost of plasmids to host bacteria. ISME J 3: 761-769.
57. Hamilton WD (1964). The genetical evolution of social behaviour. I & II. J Theor Biol 7: 1-52.
58. Hamilton WD (1970). Selfish and spiteful behaviour in an evolutionary model. Nature 228: 1218-1220.
59. Hardin G (1968). The tragedy of the commons. Science 162: 1243-1248.
60. Harrison F, Browning LE, Vos M, Buckling A (2006). Cooperation and virulence in acute Pseudomonas aeruginosa infections. BMC Biol 4: 21.
61. Johnson LJ (2007). The genome strikes back: the evolutionary importance of defence against mobile elements. Evol Biol 34: 121-129.
62. Keller L, Ross KG (1998). Selfish genes: a green beard in the red fire ant. Nature 394: 573-575.
63. Knothe H, Shah P, Krcmery V, Antal M, Mitsuhashi S (1983). Transferable resistance to cefotaxime, cefoxitin, cefamandole and cefuroxime in clinical isolates of Klebsiella pneumoniae and Serratia marcescens. Infection 11: 315-317.
64. Kobayashi I (2001). Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29: 3742-3756.
65. Korona R, Levin BR (1993). Phage-mediated selection for restriction-modification. Evolution 47: 565-575.
66. Kozlowicz BK, Shi K, Gu ZY, Ohlendorf DH, Earhart CA, Dunny GM (2006). Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides. Mol Microbiol 62: 958-969.
67. Kurland CG, Canback B, Berg OG (2003). Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 100: 9658-9662.
68. Lederberg J, Tatum EL (1946). Gene recombination in E. coli. Nature 158: 558.
69. Lee K, Lee M, Shin JH, Lee MH, Kang SH, Park AJ et al. (2006). Prevalence of plasmid-mediated AmpC b-Lactamases in Escherichia coli and Klebsiella pneumoniae in Korea. Microb Drug Resist 12: 44-49.
70. Lehmann L, Feldman MW, Foster KR (2008). Cultural transmission can inhibit the evolution of altruistic helping. Am Nat 172: 12-24.
71. Lehmann L, Keller L (2006). The evolution of cooperation and altruism-a general framework and a classification of models. J Evol Biol 19: 1365-1376.
72. Lerat E, Ochman H (2004). Psi-Phi: exploring the outer limits of bacterial pseudogenes. Genome Res 14: 2273-2278.
73. Levin BR, Stewart FM (1977). Probability of establishing chimeric plasmids in natural populations of bacteria. Science 196: 218-220.
74. Lili LN, Britton NF, Feil EJ (2007). The persistence of parasitic plasmids. Genetics 177: 399-405.
75. Livermore DM (1995). Beta-Lactamases in laboratory and clinical resistance. Clin Microbiol Rev 8: 557-584.
76. Magnuson RD (2007). Hypothetical functions of toxin-antitoxin systems. J Bacteriol 189: 6089-6092.
77. Martínez JL (2008). Antibiotics and antibiotic resistance genes in natural environments. Science 321: 365-367.
78. Martinez JL (2009). The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc R Soc London B 276: 2521-2530.
79. May RM, Anderson RM (1979). Population biology of infectious diseases: part II. Nature 280: 455-461.
80. Mochizuki A, Yahara K, Kobayashi I, Iwasa Y (2006). Genetic addiction: selfish gene's strategy for symbiosis in the genome. Genetics 172: 1309-1323.
81. Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EP (2009). Gene mobility drives the evolution of bacterial cooperation and virulence. Curr Biol 19: 1683-1691.
82. Norman A, Hansen LH, Sorensen SJ (2009). Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc London B 364: 2275-2289.
83. Nuti MP, Lepidi AA, Prakash RK, Schilperoort RA, Cannon FC (1979). Evidence for nitrogen fixation (nif) genes on indigenous Rhizobium plasmids. Nature 282: 533-535.
84. O'Brien AD, Newland JW, Miller SF, Holmes RK, Smith HW, Formal SB (1984). Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science 226: 694-696.
85. Ochman H, Lawrence JG, Groisman EA (2000). Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
86. Oliver KM, Degnan PH, Hunter MS, Moran NA (2009). Bacteriophages encode factors required for protection in a symbiotic mutualism. Science 325: 992-994.
87. Orgel LE, Crick FHC (1980). Selfish DNA: the ultimate parasite. Nature 284: 604-607.
88. Paulsson J (2002). Multileveled selection on plasmid replication. Genetics 161: 1373-1384.
89. Philppon A, Arlet G, Jacoby GA (2002). Plasmid-determined AmpC-type beta-lactamases. Antimicrob Agents Chemother 46: 1-11.
90. Polzleitner E, Zechner EL, Renner W, Fratte R, Jauk B, Högenauer G et al. (1997). TraM of plasmid R1 controls transfer gene expression as an integrated control element in a complex regulatory network. Mol Microbiol 25: 495-507.
91. Rainey PB, Rainey K (2003). Evolution of cooperation and conflict in experimental bacterial populations. Nature 425: 72-74.
92. Rankin DJ, Bargum K, Kokko H (2007). The tragedy of the commons in evolutionary biology. Trends Ecol Evol 22: 643-651.
93. Rasched I, Oberer E (1986). Ff coliphages: structural and functional relationships. Microbiol Rev 50: 401-427.
94. Riboli-Sasco L, Brown SP, Taddei F (2008). Why teach? The evolutionary origins and ecological consequences of costly information transfer. In: Ettorre P, Hughes D (eds). Communication Among Social Organisms. Oxford University Press.
95. Riley MA, Wertz JE (2002). Bacteriocins: evolution, ecology and application. Annu Rev Microbiol 56: 117-137.
96. Rousset F (2004). Genetic Structure and Selection in Subdivided Populations. Princeton University Press: Princeton.
97. Sachs JL, Mueller UG, Wilcox TP, Bull JJ (2004). The evolution of cooperation. Q Rev Biol 79: 133-160.
98. Sachs JL, Simms EL (2007). Pathways to mutualism breakdown. Trends Ecol Evol 21: 585-592.
99. Sanchez B, Bressollier P, Urdaci MC (2008). Exported proteins in probiotic bacteria: adhesion to intestinal surfaces, host immunomodulation and molecular cross-talking with the host. FEMS Immunol Med Microbiol 54: 1-17.
100. Slater FR, Bailey MJ, Tett AJ, Turner SL (2008). Progress towards understanding the fate of plasmids in bacterial communities. FEMS Microbiol Ecol 66: 3-13.
101. Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW et al. (2009). Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191: 2501-2511.
102. Smith J (2001). The social evolution of bacterial pathogenesis. Proc R Soc London B Biol Sci 268: 61-69.
103. Sorensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005). Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Micro 3: 700-710.
104. Stewart FM, Levin BR (1977). The population biology of bacterial plasmids: a priori conditions for the existence of conjugationally transmitted factors. Genetics 87: 209-228.
105. Thomas CM, Nielsen KM (2005). Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Micro 3: 711-721.
106. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P et al. (2009). Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 5: e1000344.
107. Turner PE (2004). Phenotypic plasticity in bacterial plasmids. Genetics 167: 9-20.
108. Turner PE, Cooper VS, Lenski RE (1998). Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids. Evolution 52: 315-329.
109. van der Ploeg JR (2005). Regulation of Bacteriocin production in Streptococcus mutans by the quorum-sensing system required for development of genetic competence. J Bacteriol 187: 3980-3989.
110. Van Melderen L, De Bast MS (2009). Bacterial toxin-antitoxin systems: more than selfish entities? PLoS Genet 5: e1000437.
111. Wagner A (2009). Transposable elements as genomic diseases. Mol Biosyst 5: 32-35.
112. Waldor MK, Mekalanos J (1996). Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 1910-1914.
113. West SA, Diggle SP, Buckling A, Gardner A, Griffin AS (2007a). The social lives of microbes. Ann Rev Ecol, Evol Syst 38: 53-77.
114. West SA, Griffin AS, Gardner A (2007b). Evolutionary explanations for cooperation. Curr Biol 17: R661-R672.
115. West SA, Griffin AS, Gardner A (2007c). Social semantics: altruism, cooperation, mutualism, strong reciprocity and group selection. J Evol Biol 20: 415-432.
116. West SA, Griffin AS, Gardner A, Diggle SP (2006). Social evolution theory for microorganisms. Nat Rev Microbiol 4: 597-607.
117. White CE, Winans SC (2007). Cell-cell communication in the plant pathogen Agrobacterium tumefaciens. Philos Trans R Soc London B Biol Sci 362: 1135-1148.
118. Xavier JB, Foster KR (2007). Cooperation and conflict in microbial biofilms. Proc Natl Acad Sci USA 104: 876-881.
119. Yates CM, Shaw DJ, Roe AJ, Woolhouse MEJ, Amyes SGB (2006). Enhancement of bacterial competitive fitness by apramycin resistance plasmids from non-pathogenic Escherichia coli. Biol Lett 2: 463-465.
120. Zinder ND, Lederberg J (1952). Genetic exchange in Salmonella. J Bacteriol 64: 679-699.
121. Zupan J, Muth TR, Draper O, Zambryski P (2000). The transfer of DNA from agrobacterium tumefaciens into plants: a feast of fundamental insights. Plant J 23: 11-28.