Impact of transcriptional properties on essentiality and evolutionary rate

Genetics

Volumn 175, Issue 1, 2007, Pages 199-206

  Jung, Kyoon Choi ^a   Sang, Cheol Kim ^b   Seo, Jungmin ^a   Kim, Sangsoo ^c   Bhak, Jong ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b Yonsei University   (South Korea)

^c Soongsil University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EUKARYOTE; EVOLUTION; GENE EXPRESSION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN TRANSPORT; REGRESSION ANALYSIS; STATISTICAL ANALYSIS; TRANSLATION REGULATION; YEAST;

ANIMALS; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; HUMANS; MICE; MODELS, GENETIC; PLANTS; RATS; SACCHAROMYCES CEREVISIAE; SELECTION (GENETICS);

EUKARYOTA; RATTUS;

EID: 33846479811     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.066027     Document Type: Article

References (50)

1. AKASHI, H., 1997 Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 205: 269-278.
2. AKASHI, H., 2001 Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11: 660-666.
3. AKASHI, H., 2003 Translational selection and yeast proteome evolution. Genetics 164: 1291-1303.
4. AKASHI, H., and T. GOJOBORI, 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl. Acad. Sci. USA 99: 3695-3700.
5. BLAKE, W. J., M. KAERN, C. R. CANTOR and J. J. COLLINS, 2003 Noise in gene expression. Nature 422: 633-637.
6. BLOOM, J. D., and C. ADAMI, 2003 Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol. Biol. 3: 21.
7. BLOOM, J. D., and C. ADAMI, 2004 Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. BMC Evol. Biol. 4: 14.
8. CHUANG, J. H., and H. LI, 2004 Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome. PLoS Biol. 2: e29.
9. DENVER, D. R., K. MORRIS, J. T. STREELMAN, S. K. KIM, M. LYNCH et al., 2005 The transcriptional consequences of mutation and natural selection in Caenohabditis elegans. Nat. Genet. 37: 544-548.
10. DOS REIS, M., R. SAVVA and L. WERNISCH, 2004 Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32: 5036-5044.
11. DRUMMOND, D. A., J. D. BLOOM, C. ADAMI, C. O. WILKE and F. H. ARNOLD, 2005 Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102: 14338-14343.
12. DRUMMOND, D. A., A. RAVAL and C. O. WILKE, 2006 A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23: 327-337.
13. DURET, L., and D. MOUCHIROUD, 2000 Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17: 68-74.
14. ELOWITZ, M. B., A. J. LEVINE, E. D. SIGGIA and P. S. SWAIN, 2002 Stochastic gene expression in a single cell. Science 297: 1183-1186.
15. ENARD, W., P. KHAITOVICH, J. KLOSE, S. ZOLLNER, F. HEISSIG et al., 2002 Intra- and interspecific variation in primate gene expression patterns. Science 296: 340-343.
16. FRASER, H. B., and A. E. HIRSH, 2004 Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol. Biol. 4: 13.
17. FRASER, H. B., A. E. HIRSH, L. M. STEINMETZ, C. SCHARFE and M. W. FELDMAN, 2002 Evolutionary rate in the protein interaction network. Science 296: 750-752.
18. FRASER, H. B., A. E. HIRSH, G. GIAEVER, J. KUMM and M. B. EISEN, 2004 Noise minimization in eukaryotic gene expression. PLoS Biol. 2: e137.
19. GIAEVER, G., P. FLAHERTY, J. KUMM, M. PROCTOR, C. NISLOW et al., 2004 Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. USA 101: 793-798.
20. GU, X., 2004 Statistical framework for phylogenomic analysis of gene family expression profiles. Genetics 167: 531-542.
21. GU, X., Z. ZHANG and W. HUANG, 2005 Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc. Natl. Acad. Sci. USA 102: 707-712.
22. GU, Z., S. A. RIFKIN, K. P. WHITE and W.-H. LI, 2004 Duplicate genes increase gene expression diversity within and between species. Nat. Genet. 36: 577-579.
23. HASTY, J., and J. J. COLLINS, 2002 Translating the noise. Nat. Genet. 31: 13-14.
24. HE, X., and J. ZHANG, 2006 Why do hubs tend to be essential in protein networks? PLoS Genet. 2: e88.
25. HERBECK, J. T., D. P. WALL and J. J. WERNEGREEN, 2003 Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia. Microbiology 149: 2585-2596.
26. HIRSH, A. E., and H. B. FRASER, 2001 Protein dispensability and rate of evolution. Nature 411: 1046-1048.
27. JORDAN, I. K., I. B. ROGOZIN, Y. I. WOLF and E. V. KOONIN, 2002 Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12: 962-968.
28. JORDAN, I. K., Y. I. WOLF and E. V. KOONIN, 2003 No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3: 1.
29. KHAITOVICH, P., G. WEISS, M. LACHMANN, I. HELLMANN, W. ENARD et al., 2004 A neutral model of transcriptome evolution. PLoS Biol. 2: e132.
30. KING, M. C., and A. C. WILSON, 1975 Evolution at two levels: molecular similarities and biological differences between humans and chimpanzees. Science 188: 107-116.
31. LEMOS, B., C. D. MEIKLEJOHN and D. L. HARTL, 2004 Regulatory evolution across the protein interaction network. Nat. Genet. 36: 1059-1060.
32. LONG, M., E. BETRAN, K. THORNTON and W. WANG, 2003 The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4: 865-875.
33. MEIKLEJOHN, C. D., J. PARSCH, J. M. RANZ and D. L. HARTL, 2003 Rapid evolution of male-based gene expression in Drosophila. Proc. Natl. Acad. Sci. USA 100: 9894-9899.
34. OLEKSIAK, M. F., G. A. CHURCHILL and D. L. CRAWFORD, 2002 Variation in gene expression within and among natural populations. Nat. Genet. 32: 261-266.
35. OZBUDAK, E. M., M. THATTAI, I. KURTSER, A.D. GROSSMAN and A. VAN OUDENAARDEN, 2002 Regulation of noise in the expression of a single gene. Nat. Genet. 31: 69-73.
36. PAL, C., B. PAPP and L. D. HURST, 2001 Highly expressed genes in yeast evolve slowly. Genetics 158: 927-931.
37. PAL, C., B. PAPP and L. D. HURST, 2003 Rate of evolution and gene dispensability. Nature 421: 496-497.
38. RANZ, J. M., C. I. CASTILLO-DAVIS, C. D. MEIKLEJOHN and D. L. HARTL, 2003 Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
39. RASER, J. M., and E. K. O'SHEA, 2004 Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
40. RIFKIN, S. A., J. KIM and K. P. WHITE, 2003 Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33: 138-144.
41. SHARP, P. M., 1991 Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J. Mol. Evol. 33: 23-33.
42. SHARP, P. M., M. AVEROF, A. T. LLOYD, G. MATASSI and J. F. PEDEN, 1995 DNA sequence evolution: the sounds of silence. Philos. Trans. R. Soc. Lond. Ser. B 349: 241-247.
43. SHIELDS, D. C., P. M. SHARP, D. G. HIGGINS and F. WRIGHT, 1988 "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5: 704-716.
44. SUBRAMANIAN, S., and S. KUMAR, 2004 Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168: 373-381.
45. SWAIN, P. S., M. B. ELOWITZ and E. D. SIGGIA, 2002 Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99: 12795-12800.
46. URRUTIA, A. O., and L. D. HURST, 2003 The signature of selection mediated by expression on human genes. Genome Res. 13: 2260-2264.
47. WALL, D. P., A. E. HIRSH, H. B. FRASER, J. KUMM, G. GIAEVER et al., 2005 Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. USA 102: 5483-5488.
48. WRIGHT, S. I., C. B. K. YAU, M. LOOSELEY and B. C. MEYERS, 2004 Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol. Biol. Evol. 21: 1719-1726.
49. WUCHTY, S., Z. N. OLTVAI and A.-L. BARABASI, 2003 Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35: 176-179.
50. YANG, Z., 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.