메뉴 건너뛰기




Volumn 68, Issue 9, 2014, Pages 2559-2570

Less is more: Selective advantages can explain the prevalent loss of biosynthetic genes in bacteria

Author keywords

Adaptive gene loss; Auxotrophy; Black queen hypothesis; Cross feeding; Prototrophy; Symbiosis

Indexed keywords

GENE EXPRESSION; GENOME; GROWTH RATE; METABOLITE; MICROBIAL ACTIVITY; MUTATION; POPULATION GENETICS; SURVIVORSHIP; SYMBIOSIS;

EID: 84907962466     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/evo.12468     Document Type: Article
Times cited : (174)

References (62)
  • 1
    • 0028946084 scopus 로고
    • Phylogenetic identification and in-situ detection of individual microbial cells without cultivation
    • Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in-situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.H.3
  • 2
    • 0032127258 scopus 로고    scopus 로고
    • Reductive evolution of resident genomes
    • Andersson, S. G. E., and C. G. Kurland. 1998. Reductive evolution of resident genomes. Trends Microbiol. 6:263-268.
    • (1998) Trends Microbiol. , vol.6 , pp. 263-268
    • Andersson, S.G.E.1    Kurland, C.G.2
  • 5
    • 33746197428 scopus 로고    scopus 로고
    • Adaptive linear stepup procedures that control the false discovery rate
    • Benjamini, Y., A. M. Krieger, and D. Yekutieli. 2006. Adaptive linear stepup procedures that control the false discovery rate. Biometrika 93:491-507.
    • (2006) Biometrika , vol.93 , pp. 491-507
    • Benjamini, Y.1    Krieger, A.M.2    Yekutieli, D.3
  • 6
    • 84855246842 scopus 로고    scopus 로고
    • Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity
    • Bernstein, H. C., S. D. Paulson, and R. P. Carlson. 2012. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. J. Biotechnol. 157:159-166.
    • (2012) J. Biotechnol. , vol.157 , pp. 159-166
    • Bernstein, H.C.1    Paulson, S.D.2    Carlson, R.P.3
  • 7
    • 9344269395 scopus 로고    scopus 로고
    • Self-generated diversity produces "insurance effects" in biofilm communities
    • Boles, B. R., M. Thoendel, and P. K. Singh. 2004. Self-generated diversity produces "insurance effects" in biofilm communities. Proc. Natl. Acad. Sci. USA 101:16630-16635.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 16630-16635
    • Boles, B.R.1    Thoendel, M.2    Singh, P.K.3
  • 10
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • Dekel, E., and U. Alon. 2005. Optimality and evolutionary tuning of the expression level of a protein. Nature 436:588-592.
    • (2005) Nature , vol.436 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 11
    • 28044436397 scopus 로고    scopus 로고
    • Accelerated evolution associated with genome reduction in a free-living prokaryote
    • Dufresne, A., L. Garczarek, and F. Partensky. 2005. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6:R14.
    • (2005) Genome Biol. , vol.6 , pp. R14
    • Dufresne, A.1    Garczarek, L.2    Partensky, F.3
  • 12
    • 0017803808 scopus 로고
    • Selection for tryptophan auxotrophs of Escherichia coli in glucose-limited chemostats as a test of energy-conservation hypothesis of evolution
    • Dykhuizen, D. 1978. Selection for tryptophan auxotrophs of Escherichia coli in glucose-limited chemostats as a test of energy-conservation hypothesis of evolution. Evolution 32:125-150.
    • (1978) Evolution , vol.32 , pp. 125-150
    • Dykhuizen, D.1
  • 14
    • 84863644574 scopus 로고    scopus 로고
    • Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival
    • Ensminger, A. W., Y. Yassin, A. Miron, and R. R. Isberg. 2012. Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival. PloS Pathogens 8:e1002731. doi:10.1371/journal.ppat.1002731.
    • (2012) PloS Pathogens , vol.8
    • Ensminger, A.W.1    Yassin, Y.2    Miron, A.3    Isberg, R.R.4
  • 18
    • 0035970874 scopus 로고    scopus 로고
    • Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut
    • Giraud, A., I. Matic, O. Tenaillon, A. Clara, M. Radman, M. Fons, and F. Taddei. 2001. Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut. Science 291:2606-2608.
    • (2001) Science , vol.291 , pp. 2606-2608
    • Giraud, A.1    Matic, I.2    Tenaillon, O.3    Clara, A.4    Radman, M.5    Fons, M.6    Taddei, F.7
  • 19
    • 34547640056 scopus 로고    scopus 로고
    • Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction
    • Gómez-Valero, L., E. P. C. Rocha, A. Latorre, and F. J. Silva. 2007. Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction. Genome Res. 17:1178-1185.
    • (2007) Genome Res. , vol.17 , pp. 1178-1185
    • Gómez-Valero, L.1    Rocha, E.P.C.2    Latorre, A.3    Silva, F.J.4
  • 21
    • 0031662188 scopus 로고    scopus 로고
    • Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity
    • Hugenholtz, P., B. M. Goebel, and N. R. Pace. 1998. Impact of cultureindependent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765-4774.
    • (1998) J. Bacteriol. , vol.180 , pp. 4765-4774
    • Hugenholtz, P.1    Goebel, B.M.2    Pace, N.R.3
  • 22
    • 34447500551 scopus 로고    scopus 로고
    • Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli
    • Ihssen, J., E. Grasselli, C. Bassin, P. François, J.-C. Piffaretti, W. Köster, J. Schrenzel, and T. Egli. 2007. Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli. Microbiology 153:2052-2066.
    • (2007) Microbiology , vol.153 , pp. 2052-2066
    • Ihssen, J.1    Grasselli, E.2    Bassin, C.3    François, P.4    Piffaretti, J.-C.5    Köster, W.6    Schrenzel, J.7    Egli, T.8
  • 24
    • 84055224165 scopus 로고    scopus 로고
    • Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome
    • Karberg, K. A., G. J. Olsen, and J. J. Davis. 2011. Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. Proc. Natl. Acad. Sci. USA 108:20154-20159.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 20154-20159
    • Karberg, K.A.1    Olsen, G.J.2    Davis, J.J.3
  • 26
    • 79957948242 scopus 로고    scopus 로고
    • Negative epistasis between beneficial mutations in an evolving bacterial population
    • Khan, A. I., D. M. Dinh, D. Schneider, R. E. Lenski, and T. F. Cooper. 2011. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 332:1193-1196.
    • (2011) Science , vol.332 , pp. 1193-1196
    • Khan, A.I.1    Dinh, D.M.2    Schneider, D.3    Lenski, R.E.4    Cooper, T.F.5
  • 28
    • 68149175229 scopus 로고    scopus 로고
    • The consequences of genetic drift for bacterial genome complexity
    • Kuo, C.-H., N. A. Moran, and H. Ochman. 2009. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-1454.
    • (2009) Genome Res. , vol.19 , pp. 1450-1454
    • Kuo, C.-H.1    Moran, N.A.2    Ochman, H.3
  • 29
    • 84863668598 scopus 로고    scopus 로고
    • Repeated, selection-driven genome reduction of accessory genes in experimental populations
    • Lee, M.-C., and C. J. Marx. 2012. Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet. 8:e1002651.
    • (2012) PLoS Genet. , vol.8
    • Lee, M.-C.1    Marx, C.J.2
  • 30
    • 0026279651 scopus 로고
    • Long-term experimental evolution in Escherichia coli. 1. Adaptation and divergence during 2,000 generations
    • Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental evolution in Escherichia coli. 1. Adaptation and divergence during 2,000 generations. Am. Nat. 138:1315-1341.
    • (1991) Am. Nat. , vol.138 , pp. 1315-1341
    • Lenski, R.E.1    Rose, M.R.2    Simpson, S.C.3    Tadler, S.C.4
  • 31
    • 78149470831 scopus 로고    scopus 로고
    • Comparison of 61 sequenced Escherichia coli genomes
    • Lukjancenko, O., T. M. Wassenaar, and D. W. Ussery. 2010. Comparison of 61 sequenced Escherichia coli genomes. Microb. Ecol. 60:708-720.
    • (2010) Microb. Ecol. , vol.60 , pp. 708-720
    • Lukjancenko, O.1    Wassenaar, T.M.2    Ussery, D.W.3
  • 32
    • 33745277137 scopus 로고    scopus 로고
    • The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis
    • Maughan, H., V. Callicotte, A. Hancock, C. W. Birky, W. L. Nicholson, and J. Masel. 2006. The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis. Evolution 60:686-695.
    • (2006) Evolution , vol.60 , pp. 686-695
    • Maughan, H.1    Callicotte, V.2    Hancock, A.3    Birky, C.W.4    Nicholson, W.L.5    Masel, J.6
  • 33
    • 37649023694 scopus 로고    scopus 로고
    • Parallel genomic evolution and metabolic interdependence in an ancient symbiosis
    • McCutcheon, J. P., and N. A. Moran. 2007. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. Proc. Natl. Acad. Sci. USA 104:19392-19397.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 19392-19397
    • McCutcheon, J.P.1    Moran, N.A.2
  • 34
    • 77958507828 scopus 로고    scopus 로고
    • Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution
    • McCutcheon, J. P., and N. A. Moran. 2010. Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol. Evol. 2:708-718.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 708-718
    • McCutcheon, J.P.1    Moran, N.A.2
  • 35
    • 80051978497 scopus 로고    scopus 로고
    • An interdependent metabolic patchwork in the nested symbiosis of mealybugs
    • McCutcheon, J. P., and C. D. von Dohlen. 2011. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr. Biol. 21:1366-1372.
    • (2011) Curr. Biol. , vol.21 , pp. 1366-1372
    • McCutcheon, J.P.1    von Dohlen, C.D.2
  • 36
    • 84890290025 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strainspecific adaptations to nutritional environments
    • Monk, J. M., P. Charusanti, R. K. Aziz, J. A. Lerman, N. Premyodhin, J. D. Orth, A. M. Feist, and B. Ø. Palsson. 2013. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strainspecific adaptations to nutritional environments. Proc. Natl. Acad. Sci. USA 110:20338-20343.
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 20338-20343
    • Monk, J.M.1    Charusanti, P.2    Aziz, R.K.3    Lerman, J.A.4    Premyodhin, N.5    Orth, J.D.6    Feist, A.M.7    Palsson, B.Ø.8
  • 37
    • 0037040394 scopus 로고    scopus 로고
    • Microbial minimalism: genome reduction in bacterial pathogens
    • Moran, N. A. 2002. Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583-586.
    • (2002) Cell , vol.108 , pp. 583-586
    • Moran, N.A.1
  • 38
    • 8644224924 scopus 로고    scopus 로고
    • Genomic changes following host restriction in bacteria
    • Moran, N. A., and G. R. Plague. 2004. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev. 14:627-633.
    • (2004) Curr. Opin. Genet. Dev. , vol.14 , pp. 627-633
    • Moran, N.A.1    Plague, G.R.2
  • 39
    • 58449125407 scopus 로고    scopus 로고
    • Genomics and evolution of heritable bacterial symbionts
    • Moran, N. A., J. P. McCutcheon, and A. Nakabachi. 2008. Genomics and evolution of heritable bacterial symbionts. Annu. Rev. Genet. 42:165-190.
    • (2008) Annu. Rev. Genet. , vol.42 , pp. 165-190
    • Moran, N.A.1    McCutcheon, J.P.2    Nakabachi, A.3
  • 40
    • 84860511582 scopus 로고    scopus 로고
    • The black queen hypothesis: evolution of dependencies through adaptive gene loss
    • Morris, J. J., R. E. Lenski, and E. R. Zinser. 2012. The black queen hypothesis: evolution of dependencies through adaptive gene loss. Mbio 3:e00036-12.
    • (2012) Mbio , vol.3
    • Morris, J.J.1    Lenski, R.E.2    Zinser, E.R.3
  • 41
    • 0027428477 scopus 로고
    • Concentrations and fluxes of organic carbon substrates in the aquatic environment
    • Münster, U. 1993. Concentrations and fluxes of organic carbon substrates in the aquatic environment. Antonie Leeuwenhoek 63:243-274.
    • (1993) Antonie Leeuwenhoek , vol.63 , pp. 243-274
    • Münster, U.1
  • 43
    • 0035843908 scopus 로고    scopus 로고
    • Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis
    • Ochman, H., and N. A. Moran. 2001. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science 292:1096-1099.
    • (2001) Science , vol.292 , pp. 1096-1099
    • Ochman, H.1    Moran, N.A.2
  • 45
    • 0015919109 scopus 로고
    • Feedback regulation in anthranilate aggregate from wild-type and mutant strains of Escherichia coli
    • Pabst, M. J., J. C. Kuhn, and R. l. Somervil. 1973. Feedback regulation in anthranilate aggregate from wild-type and mutant strains of Escherichia coli. J. Biol. Chem. 248:901-914.
    • (1973) J. Biol. Chem. , vol.248 , pp. 901-914
    • Pabst, M.J.1    Kuhn, J.C.2    Somervil, R.L.3
  • 47
  • 48
    • 84914179053 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing
    • The R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team. 2013. R: a language and environment for statistical computing. The R Foundation for Statistical Computing, Vienna, Austria.
    • (2013)
  • 50
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: origins and consequences
    • Scott, M., C. W. Gunderson, E. M. Mateescu, Z. Zhang, and T. Hwa. 2010. Interdependence of cell growth and gene expression: origins and consequences. Science 330:1099-1102.
    • (2010) Science , vol.330 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 51
    • 77953115788 scopus 로고    scopus 로고
    • Cost of unneeded proteins in E. coil is reduced after several generations in exponential growth
    • Shachrai, I., A. Zaslaver, U. Alon, and E. Dekel. 2010. Cost of unneeded proteins in E. coil is reduced after several generations in exponential growth. Mol. Cell 38:758-767.
    • (2010) Mol. Cell , vol.38 , pp. 758-767
    • Shachrai, I.1    Zaslaver, A.2    Alon, U.3    Dekel, E.4
  • 52
    • 0034618559 scopus 로고    scopus 로고
    • Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp
    • Shigenobu, S., H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407:81-86.
    • (2000) APS. Nature , vol.407 , pp. 81-86
    • Shigenobu, S.1    Watanabe, H.2    Hattori, M.3    Sakaki, Y.4    Ishikawa, H.5
  • 53
    • 79251610629 scopus 로고    scopus 로고
    • Computational design of auxotrophydependent microbial biosensors for combinatorial metabolic engineering experiments
    • Tepper, N., and T. Shlomi. 2011. Computational design of auxotrophydependent microbial biosensors for combinatorial metabolic engineering experiments. PLoS One 6:e16274.
    • (2011) PLoS One , vol.6
    • Tepper, N.1    Shlomi, T.2
  • 59
    • 0023096283 scopus 로고
    • Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum-physical analysis of Tn5 and Tn5-Mob insertion mutants
    • Vanstockem, M., K. Michiels, J. Vanderleyden, and A. P. Vangool. 1987. Transposon mutagenesis of Azospirillum brasilense and Azospirillum lipoferum-physical analysis of Tn5 and Tn5-Mob insertion mutants. Appl. Environ. Microbiol. 53:410-415.
    • (1987) Appl. Environ. Microbiol. , vol.53 , pp. 410-415
    • Vanstockem, M.1    Michiels, K.2    Vanderleyden, J.3    Vangool, A.P.4
  • 60
    • 0012262121 scopus 로고
    • Feedback inhibition of acetylglutamate synthetase by arginine in Escherichia coli
    • Vyas, S., and W. K. Maas. 1963. Feedback inhibition of acetylglutamate synthetase by arginine in Escherichia coli. Arch. Biochem. Biophys. 100:542-546.
    • (1963) Arch. Biochem. Biophys. , vol.100 , pp. 542-546
    • Vyas, S.1    Maas, W.K.2
  • 61
    • 79960610255 scopus 로고    scopus 로고
    • Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs
    • Wessely, F., M. Bartl, R. Guthke, P. Li, S. Schuster, and C. Kaleta. 2011. Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol. Syst. Biol. 7:515.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 515
    • Wessely, F.1    Bartl, M.2    Guthke, R.3    Li, P.4    Schuster, S.5    Kaleta, C.6
  • 62
    • 0014192938 scopus 로고
    • Study of microbial evolution through loss of biosynthetic functions-establishment of defective mutants
    • Zamenhof, S., and H.H. Eichhorn. 1967. Study of microbial evolution through loss of biosynthetic functions-establishment of defective mutants. Nature 216:456-458.
    • (1967) Nature , vol.216 , pp. 456-458
    • Zamenhof, S.1    Eichhorn, H.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.