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Volumn 3, Issue 4, 2012, Pages

The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; ANTIBIOSIS; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CELL LINEAGE; CONTROLLED STUDY; FRAMESHIFT MUTATION; GENE FREQUENCY; GENE SEQUENCE; MICROBIAL DIVERSITY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PLASMID; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN STABILITY; PYROSEQUENCING; REPLICON; SINGLE NUCLEOTIDE POLYMORPHISM; TRFA1 GENE; CLONAL EVOLUTION; GENETICS; METABOLISM; MUTATION; PHYSIOLOGY; SHEWANELLA;

EID: 84865726800     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00077-12     Document Type: Article
Times cited : (33)

References (45)
  • 3
    • 23944499633 scopus 로고    scopus 로고
    • Horizontal gene transfer, genome innovation and evolution
    • Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3:679-687.
    • (2005) Nat. Rev. Microbiol , vol.3 , pp. 679-687
    • Gogarten, J.P.1    Townsend, J.P.2
  • 4
    • 0023506940 scopus 로고
    • Incompatibility group P plasmids: Genetics, evolution, and use in genetic manipulation
    • Thomas CM, Smith CA. 1987. Incompatibility group P plasmids: genetics, evolution, and use in genetic manipulation. Annu. Rev. Microbiol. 41:77-101.
    • (1987) Annu. Rev. Microbiol , vol.41 , pp. 77-101
    • Thomas, C.M.1    Smith, C.A.2
  • 5
    • 0024074288 scopus 로고
    • Molecular genetic analysis of bacterial plasmid promiscuity
    • Krishnapillai V. 1988. Molecular genetic analysis of bacterial plasmid promiscuity. FEMS Microbiol. Lett. 54:223-237.
    • (1988) FEMS Microbiol. Lett , vol.54 , pp. 223-237
    • Krishnapillai, V.1
  • 7
    • 33847231339 scopus 로고    scopus 로고
    • Stability of a promiscuous plasmid in different hosts: No guarantee for a long-term relationship
    • De Gelder L, Ponciano JM, Joyce P, Top EM. 2007. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology 153:452-463.
    • (2007) Microbiology , vol.153 , pp. 452-463
    • de Gelder, L.1    Ponciano, J.M.2    Joyce, P.3    Top, E.M.4
  • 8
    • 78649446843 scopus 로고    scopus 로고
    • Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein
    • Sota M, et al. 2010. Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein. ISME J. 4:1568-1580.
    • (2010) ISME J , vol.4 , pp. 1568-1580
    • Sota, M.1
  • 9
    • 33847234930 scopus 로고    scopus 로고
    • Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host
    • Heuer H, Fox RE, Top EM. 2007. Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host. FEMS Microbiol. Ecol. 59:738-748.
    • (2007) FEMS Microbiol. Ecol , vol.59 , pp. 738-748
    • Heuer, H.1    Fox, R.E.2    Top, E.M.3
  • 10
    • 45849099491 scopus 로고    scopus 로고
    • Adaptive plasmid evolution results in host-range expansion of a broadhost- range plasmid
    • De Gelder L, Williams JJ, Ponciano JM, Sota M, Top EM. 2008. Adaptive plasmid evolution results in host-range expansion of a broadhost- range plasmid. Genetics 178:2179-2190.
    • (2008) Genetics , vol.178 , pp. 2179-2190
    • de Gelder, L.1    Williams, J.J.2    Ponciano, J.M.3    Sota, M.4    Top, E.M.5
  • 11
    • 0023445840 scopus 로고
    • Effects of segregation and selection on instability of plasmid pACYC184 in Escherichia coli B
    • Lenski RE, Bouma JE. 1987. Effects of segregation and selection on instability of plasmid pACYC184 in Escherichia coli B. J. Bacteriol. 169: 5314-5316.
    • (1987) J. Bacteriol , vol.169 , pp. 5314-5316
    • Lenski, R.E.1    Bouma, J.E.2
  • 12
    • 0023694037 scopus 로고
    • Evolution of a bacteria/plasmid association
    • Bouma JE, Lenski RE. 1988. Evolution of a bacteria/plasmid association. Nature 335:351-352.
    • (1988) Nature , vol.335 , pp. 351-352
    • Bouma, J.E.1    Lenski, R.E.2
  • 13
    • 25444496227 scopus 로고    scopus 로고
    • The evolution of a conjugative plasmid and its ability to increase bacterial fitness
    • Dionisio F, Conceição IC, Marques ACR, Fernandes L, Gordo I. 2005. The evolution of a conjugative plasmid and its ability to increase bacterial fitness. Biol. Lett. 1:250-252.
    • (2005) Biol. Lett , vol.1 , pp. 250-252
    • Dionisio, F.1    Conceição, I.C.2    Marques, A.C.R.3    Fernandes, L.4    Gordo, I.5
  • 14
    • 0028291689 scopus 로고
    • Genetic analysis of a plasmidencoded, host genotype-specific enhancement of bacterial fitness
    • Lenski RE, Simpson SC, Nguyen TT. 1994. Genetic analysis of a plasmidencoded, host genotype-specific enhancement of bacterial fitness. J. Bacteriol. 176:3140-3147.
    • (1994) J. Bacteriol , vol.176 , pp. 3140-3147
    • Lenski, R.E.1    Simpson, S.C.2    Nguyen, T.T.3
  • 15
    • 0026049049 scopus 로고
    • Coevolution in bacterial-plasmid populations
    • Modi RI, Adams J. 1991. Coevolution in bacterial-plasmid populations. Evolution 45:656-667.
    • (1991) Evolution , vol.45 , pp. 656-667
    • Modi, R.I.1    Adams, J.2
  • 16
    • 77957746208 scopus 로고    scopus 로고
    • Genome-wide mutational diversity in an evolving population of Escherichia coli
    • Barrick JE, Lenski RE. 2009. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74:119-129.
    • (2009) Cold Spring Harb. Symp. Quant. Biol , vol.74 , pp. 119-129
    • Barrick, J.E.1    Lenski, R.E.2
  • 17
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick JE, et al. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247.
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1
  • 18
    • 0035970061 scopus 로고    scopus 로고
    • Fitness effects of advantageous mutations in evolving Escherichia coli populations
    • Imhof M, Schlötterer C. 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc. Natl. Acad. Sci. U. S. A. 98:1113-1117.
    • (2001) Proc. Natl. Acad. Sci. U. S. A , vol.98 , pp. 1113-1117
    • Imhof, M.1    Schlötterer, C.2
  • 19
    • 33746615552 scopus 로고    scopus 로고
    • Clonal adaptive radiation in a constant environment
    • Maharjan R, Seeto S, Notley-McRobb L, Ferenci T. 2006. Clonal adaptive radiation in a constant environment. Science 313:514-517.
    • (2006) Science , vol.313 , pp. 514-517
    • Maharjan, R.1    Seeto, S.2    Notley-McRobb, L.3    Ferenci, T.4
  • 20
    • 42049093984 scopus 로고    scopus 로고
    • Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage F{cyrillic} X 174
    • Pepin KM, Wichman HA. 2008. Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage F{cyrillic} X 174. BMC Evol. Biol. 8:85.
    • (2008) BMC Evol. Biol , vol.8 , pp. 85
    • Pepin, K.M.1    Wichman, H.A.2
  • 21
    • 20444382446 scopus 로고    scopus 로고
    • Adaptive molecular evolution for 13,000 phage generations: A possible arms race
    • Wichman HA, Millstein J, Bull JJ. 2005. Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170:19-31.
    • (2005) Genetics , vol.170 , pp. 19-31
    • Wichman, H.A.1    Millstein, J.2    Bull, J.J.3
  • 23
    • 78951475034 scopus 로고    scopus 로고
    • Mutational effects and population dynamics during viral adaptation challenge current models
    • Miller CR, Joyce P, Wichman HA. 2011. Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 187:185-202.
    • (2011) Genetics , vol.187 , pp. 185-202
    • Miller, C.R.1    Joyce, P.2    Wichman, H.A.3
  • 24
    • 2542583245 scopus 로고    scopus 로고
    • The fate of competing beneficial mutations in an asexual population
    • Gerrish PJ, Lenski RE. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102:127-144.
    • (1998) Genetica , vol.102 , pp. 127-144
    • Gerrish, P.J.1    Lenski, R.E.2
  • 25
    • 33646204788 scopus 로고    scopus 로고
    • Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli
    • De Visser JA, Rozen DE. 2006. Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli. Genetics 172: 2093-2100.
    • (2006) Genetics , vol.172 , pp. 2093-2100
    • de Visser, J.A.1    Rozen, D.E.2
  • 26
    • 61849168524 scopus 로고    scopus 로고
    • Clonal interference, multiple mutations and adaptation in large asexual populations
    • Fogle CA, Nagle JL, Desai MM. 2008. Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics 180: 2163-2173.
    • (2008) Genetics , vol.180 , pp. 2163-2173
    • Fogle, C.A.1    Nagle, J.L.2    Desai, M.M.3
  • 27
    • 79960137718 scopus 로고    scopus 로고
    • Genetic variation and the fate of beneficial mutations in asexual populations
    • Lang GI, Botstein D, Desai MM. 2011. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 188:647-661.
    • (2011) Genetics , vol.188 , pp. 647-661
    • Lang, G.I.1    Botstein, D.2    Desai, M.M.3
  • 28
    • 0033543602 scopus 로고    scopus 로고
    • Clonal interference and the evolution of RNA viruses
    • Miralles R, Gerrish PJ, Moya A, Elena SF. 1999. Clonal interference and the evolution of RNA viruses. Science 285:1745-1747.
    • (1999) Science , vol.285 , pp. 1745-1747
    • Miralles, R.1    Gerrish, P.J.2    Moya, A.3    Elena, S.F.4
  • 29
    • 0030625265 scopus 로고    scopus 로고
    • The cost of antibiotic resistance-from the perspective of a bacterium
    • In Chadwick DJ, Goode J, Wiley, Chichester, United Kingdom
    • Lenski RE. 1997. The cost of antibiotic resistance-from the perspective of a bacterium, p 131-151. In Chadwick DJ, Goode J (ed), Antibiotic resistance: origins, evolution, selection and spread. Wiley, Chichester, United Kingdom.
    • (1997) Antibiotic Resistance: Origins, Evolution, Selection and Spread , pp. 131-151
    • Lenski, R.E.1
  • 30
    • 0030267622 scopus 로고    scopus 로고
    • Antibiotic resistance: Counting the cost
    • Spratt BG. 1996. Antibiotic resistance: counting the cost. Curr. Biol. 6:1219-1221.
    • (1996) Curr. Biol , vol.6 , pp. 1219-1221
    • Spratt, B.G.1
  • 31
    • 0035885022 scopus 로고    scopus 로고
    • Minimizing potential resistance: A population dynamics view
    • Levin BR. 2001. Minimizing potential resistance: a population dynamics view. Clin. Infect. Dis. 33:S161-S169.
    • (2001) Clin. Infect. Dis , vol.33
    • Levin, B.R.1
  • 32
    • 10844248054 scopus 로고    scopus 로고
    • Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic-sensitive mutants in a population of resistant bacteria during experimental evolution
    • De Gelder L, et al. 2004. Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic-sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics 168:1131-1144.
    • (2004) Genetics , vol.168 , pp. 1131-1144
    • de Gelder, L.1
  • 33
    • 0028081662 scopus 로고
    • Balancing the drug-resistance equation
    • Levy SB. 1994. Balancing the drug-resistance equation. Trends Microbiol. 2:341-342.
    • (1994) Trends Microbiol , vol.2 , pp. 341-342
    • Levy, S.B.1
  • 34
    • 84857934383 scopus 로고    scopus 로고
    • The role of long and short replication initiation proteins in the fate of IncP-1 plasmids
    • Yano H, Deckert GE, Rogers LM, Top EM. 2012. The role of long and short replication initiation proteins in the fate of IncP-1 plasmids. J. Bacteriol. 194:1533-1543.
    • (2012) J. Bacteriol , vol.194 , pp. 1533-1543
    • Yano, H.1    Deckert, G.E.2    Rogers, L.M.3    Top, E.M.4
  • 35
    • 0028094645 scopus 로고
    • Microbial evolution in a simple unstructured environment: Genetic differentiation in Escherichia coli
    • Rosenzweig RF, Sharp RR, Treves DS, Adams J. 1994. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 137:903-917.
    • (1994) Genetics , vol.137 , pp. 903-917
    • Rosenzweig, R.F.1    Sharp, R.R.2    Treves, D.S.3    Adams, J.4
  • 36
    • 0019996193 scopus 로고
    • On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions
    • Albertini AM, Hofer M, Calos MP, Miller JH. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319-328.
    • (1982) Cell , vol.29 , pp. 319-328
    • Albertini, A.M.1    Hofer, M.2    Calos, M.P.3    Miller, J.H.4
  • 37
    • 80052389951 scopus 로고    scopus 로고
    • Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture
    • Nahku R, et al. 2011. Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology 157: 2604-2610.
    • (2011) Microbiology , vol.157 , pp. 2604-2610
    • Nahku, R.1
  • 38
    • 58149215803 scopus 로고    scopus 로고
    • Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing
    • Nusbaum C, et al. 2009. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat. Methods 6:67-69.
    • (2009) Nat. Methods , vol.6 , pp. 67-69
    • Nusbaum, C.1
  • 39
    • 77954202204 scopus 로고    scopus 로고
    • VARiD: A variation detection framework for color-space and letter-space platforms
    • Dalca AV, Rumble SM, Levy S, Brudno M. 2010. VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics 26:i343-i349.
    • (2010) Bioinformatics , vol.26
    • Dalca, A.V.1    Rumble, S.M.2    Levy, S.3    Brudno, M.4
  • 40
    • 37749044450 scopus 로고    scopus 로고
    • The evolution of specificity in evolving and coevolving antagonistic interactions between a bacteria and its phage
    • Poullain V, Gandon S, Brockhurst MA, Buckling A, Hochberg ME. 2008. The evolution of specificity in evolving and coevolving antagonistic interactions between a bacteria and its phage. Evolution 62:1-11.
    • (2008) Evolution , vol.62 , pp. 1-11
    • Poullain, V.1    Gandon, S.2    Brockhurst, M.A.3    Buckling, A.4    Hochberg, M.E.5
  • 41
    • 64049094567 scopus 로고    scopus 로고
    • Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2
    • Betancourt AJ. 2009. Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2. Genetics 181: 1535-1544.
    • (2009) Genetics , vol.181 , pp. 1535-1544
    • Betancourt, A.J.1
  • 42
    • 33846011830 scopus 로고    scopus 로고
    • Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1β plasmids without accessory mobile elements
    • Kamachi K, et al. 2006. Plasmid pBP136 from Bordetella pertussis represents an ancestral form of IncP-1β plasmids without accessory mobile elements. Microbiology 152:3477-3484.
    • (2006) Microbiology , vol.152 , pp. 3477-3484
    • Kamachi, K.1
  • 45
    • 0036842611 scopus 로고    scopus 로고
    • Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis
    • Heidelberg JF, et al. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20: 1118-1123.
    • (2002) Nat. Biotechnol , vol.20 , pp. 1118-1123
    • Heidelberg, J.F.1


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