High expression hampers horizontal gene transfer

Genome Biology and Evolution

Volumn 4, Issue 4, 2012, Pages 523-532

  Park, Chungoo ^a   Zhang, Jianzhi ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Evolution; Expression level; Horizontal gene transfer; Prokaryotes

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA;

ESCHERICHIA COLI PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; PHYLOGENY;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE TRANSFER, HORIZONTAL; MODELS, GENETIC; PHYLOGENY;

EID: 84864112797     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs030     Document Type: Conference Paper

References (63)

1. Akashi H. 2003. Translational selection and yeast proteome evolution. Genetics 164:1291-1303. (Pubitemid 37102197)
2. Akashi H, Gojobori T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci U S A. 99:3695-3700. (Pubitemid 34252168)
3. Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29. (Pubitemid 30257031)
4. Battistuzzi FU, Feijao A, Hedges SB. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol. 4:44.
5. Boucher Y, et al. 2003. Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet. 37:283-328. (Pubitemid 38041428)
6. Cherry JL. 2010. Expression level, evolutionary rate, and the cost of expression. Genome Biol Evol. 2:757-769.
7. Cho BK, et al. 2009. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol. 27:1043-1049.
8. Choi IG, Kim SH. 2007. Global extent of horizontal gene transfer. Proc Natl Acad Sci U S A. 104:4489-4494.
9. Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287. (Pubitemid 43334717)
10. Cohen O, Gophna U, Pupko T. 2011. The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol. 28:1481-1489.
11. Dagan T, Artzy-Randrup Y, Martin W. 2008. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad Sci U S A. 105:10039-10044.
12. Daubin V, Moran NA, Ochman H. 2003. Phylogenetics and the cohesion of bacterial genomes. Science 301:829-832. (Pubitemid 36962623)
13. Dekel E, Alon U. 2005. Optimality and evolutionary tuning of the expression level of a protein. Nature 436:588-592. (Pubitemid 41112935)
14. Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
15. Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352. (Pubitemid 352010328)
16. Fournier GP, Gogarten JP. 2008. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol. 190:1124-1127. (Pubitemid 351170956)
17. Fraser HB, Hirsh AE, Wall DP, Eisen MB. 2004. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A. 101:9033-9038. (Pubitemid 38781606)
18. Geiler-Samerotte KA, et al. 2011. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci U S A. 108:680-685.
19. Gogarten JP, Townsend JP. 2005. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol. 3:679-687. (Pubitemid 41195085)
20. Gophna U, Ofran Y. 2011. Lateral acquisition of genes is affected by the friendliness of their products. Proc Natl Acad Sci U S A. 108:343-348.
21. Gout JF, Kahn D, Duret L. 2010. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet. 6:e1000944.
22. Hershberg R, Petrov DA. 2009. General rules for optimal codon choice. PLoS Genet. 5:e1000556.
23. Hu P, et al. 2009. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7:e96.
24. Hubble J, et al. 2009. Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res. 37:D898-D901.
25. Jain R, Rivera MC, Lake JA. 1999. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A. 96:3801-3806. (Pubitemid 29168991)
26. Koonin EV, Makarova KS, Aravind L. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol. 55:709-742. (Pubitemid 32978121)
27. Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255-258.
28. Kurland CG, Canback B, Berg OG. 2003. Horizontal gene transfer: a critical view. Proc Natl Acad Sci U S A. 100:9658-9662. (Pubitemid 37086996)
29. Kutner MH, Nachtsheim CJ, Neter J, Li W. 2005. Applied linear statistical models. New York: McGraw-Hill.
30. Lawrence JG. 1999. Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol. 2:519-523. (Pubitemid 29477180)
31. Lawrence JG, Ochman H. 1997. Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 44:383-397. (Pubitemid 27161335)
32. Lerat E, Daubin V, Ochman H, Moran NA. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3:e130.
33. Lercher MJ, Pal C. 2008. Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol Biol Evol. 25:559-567. (Pubitemid 351301911)
34. Liao BY, Zhang J. 2006. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol. 23:1119-1128. (Pubitemid 43781587)
35. Markowitz VM, et al. 2009. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38:D382-D390.
36. Marraffini LA, Sontheimer EJ. 2010. CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet. 11:181-190.
37. Nakamura Y, Itoh T, Matsuda H, Gojobori T. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet. 36:760-766. (Pubitemid 38886640)
38. Navarre WW, McClelland M, Libby SJ, Fang FC. 2007. Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev. 21:1456-1471. (Pubitemid 46955718)
39. Navarre WW, et al. 2006. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313:236-238. (Pubitemid 44066257)
40. Ochman H, Lawrence JG, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405:299-304. (Pubitemid 30337055)
41. Omer S, Kovacs A, Mazor Y, Gophna U. 2010. Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer. Mol Biol Evol. 27:2441-2445.
42. Pal C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931. (Pubitemid 32552328)
43. Pal C, Papp B, Lercher MJ. 2005. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet. 37:1372-1375. (Pubitemid 41722195)
44. Park C, Makova KD. 2009. Coding region structural heterogeneity and turnover of transcription start sites contribute to divergence in expression between duplicate genes. Genome Biol. 10:R10.
45. Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T. 2011. Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes. Genome Res. 21: 599-609.
46. Qian W, Yang JR, Pearson NM, Maclean C, Zhang J. 2012. Balanced codon usage optimizes eukaryotic translational efficiency. PLoS Genet. 8:e1002603.
47. Rivera MC, Jain R, Moore JE, Lake JA. 1998. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A. 95:6239-6244. (Pubitemid 28248996)
48. Sharp PM, Li WH. 1986. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol. 24:28-38.
49. Sharp PM, Li WH. 1987. The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
50. Sharp PM, Tuohy TM, Mosurski KR. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14:5125-5143.
51. Sorek R, et al. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318:1449-1452. (Pubitemid 350208955)
52. Stoebel DM, Dean AM, Dykhuizen DE. 2008. The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products. Genetics 178:1653-1660.
53. Stoletzki N, Eyre-Walker A. 2007. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol. 24:374-381. (Pubitemid 46204370)
54. Syvanen M. 1994. Horizontal gene transfer: evidence and possible consequences. Annu Rev Genet. 28:237-261.
55. Thomas CM, Nielsen KM. 2005. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol. 3:711-721. (Pubitemid 41195087)
56. Tuller T, et al. 2011. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res. 39:4743-4755.
57. Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B. 2009. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138:198-208.
58. Wagner A. 2005. Energy constraints on the evolution of gene expression. Mol Biol Evol. 22:1365-1374. (Pubitemid 40734188)
59. Wellner A, Gophna U. 2008. Neutrality of foreign complex subunits in an experimental model of lateral gene transfer. Mol Biol Evol. 25:1835-1840.
60. Yang J-R, Liao B-Y, Zhuang S-M, Zhang J. 2012. Protein-misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc Natl Acad Sci U S A. 109:E831-E840.
61. Yang JR, Zhuang SM, Zhang J. 2010. Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol Syst Biol. 6:421.
62. Zhang J, He X. 2005. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol Biol Evol. 22:1147-1155. (Pubitemid 40471427)
63. Zhaxybayeva O, Doolittle WF. 2011. Lateral gene transfer. Curr Biol. 21:R242-246.