Determining the relationship of gene expression and global mRNA stability in Drosophila melanogaster and Escherichia coli using linear models

Gene

Volumn 424, Issue 1-2, 2008, Pages 102-107

  Eck, Sebastian ^a   Stephan, Wolfgang ^b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

Codon usage bias; D. melanogaster; E. coli; EST; expressed sequence tag; FOP; frequency of optimal codons; GC content; Gene expression; mRNA stability

Indexed keywords

MESSENGER RNA;

ARTICLE; CODON USAGE; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENE STRUCTURE; MICROARRAY ANALYSIS; MULTIPLE REGRESSION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA STABILITY; SERUM GROUP GC SYSTEM; STATISTICAL MODEL; THERMODYNAMICS;

ANIMALS; DROSOPHILA MELANOGASTER; DRUG STABILITY; ESCHERICHIA COLI; GENE EXPRESSION; NUCLEIC ACID CONFORMATION; REGRESSION ANALYSIS; RNA, BACTERIAL; RNA, MESSENGER;

DROSOPHILA MELANOGASTER; ESCHERICHIA COLI;

EID: 52949118471     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.07.033     Document Type: Article

References (33)

1. Akashi H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136 (1994) 927-935
2. Akashi H. Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11 (2001) 660-666
3. Akashi H. Translational selection and yeast proteome evolution. Genetics 164 (2003) 1291-1303
4. Akashi H., and Eyre-Walker A. Translational selection and molecular evolution. Curr. Opin. Genet. Dev. 8 (1998) 688-693
5. Blattner F.R., et al. The complete genome sequence of Escherichia coli K-12. Science 277 (1997) 1453-1474
6. Carlini D.B., and Stephan W. In vivo introduction of unpreferred synonymous codons into the Drosophila adh gene results in reduced levels of adh protein. Genetics 163 (2003) 239-243
7. Carlini D.B., Chen Y., and Stephan W. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes adh and adhr. Genetics 159 (2001) 623-633
8. Chen Y., and Stephan W. Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster ADH gene. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 11499-11504
9. dos Reis M., Wernisch L., and Savva R. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 31 (2003) 6976-6985
10. Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16 (2000) 287-289
11. Duret L., and Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 4482-4487
12. Fahrmeir L., Künstler R., Pigeot I., and Tutz G. Statistik (2004) (2004), Springer Verlag
13. Gibson G., et al. Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics 167 (2004) 1791-1799
14. Glasner J.D., et al. Asap, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 (2003) 147-151
15. Hambuch T.M., and Parsch J. Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression. Genetics 170 (2005) 1691-1700
16. Hofacker I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31 (2003) 3429-3431
17. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M., and Schuster P. Fast folding and comparison of RNA secondary structures. Chem. Mon. 125 (1994) 167-188
18. Hofacker I.L., Fekete M., and Stadler P.F. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319 (2002) 1059-1066
19. Hutter S., Saminadin-Peter S., Stephan W., and Parsch J. Gene expression variation in african and european populations of Drosophila melanogaster. Genome Biol. 9 (2008)
20. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151 (1981) 389-409
21. Jia M., and Li Y. The relationship among gene expresseion, folding free energy and codon usage bias in Escherichia coli. FEBS Lett. 579 (2005) 5333-5337
22. Kanaya S., Yamada Y., Kinouchi M., Kudo Y., and Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol. Evol. 53 (2001) 290-298
23. Mathews D.H., Sabina J., Zucker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
24. Moriyama E.N., and Powell J.R. Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45 (1997) 514-523
25. Munoz E.T., Bogarad L.D., and Deem M.W. Microarray and est database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans. BMC Genomics 5 (2004)
26. Norusis M. SPSS 10.0 guide to data analysis (2000), Prentice Hall
27. Notredame C., Higgins D.G., and Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
28. Parsch J., Tanda S., and Stephan W. Site-directed mutations reveal long-range compensatory interactions in the Adh gene of Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 928-933
29. Parsch J., Braverman J.M., and Stephan W. Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154 (2000) 909-921
30. Ringnér M., and Krogh M. Folding free energies of 5′-UTRs impact post-transcriptional regulation on a genomic scale in yeast. PLoS. Comput. Biol. 1 (2005) e72
31. Stenøien H.K., and Stephan W. Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias. J. Mol. Evol. 61 (2005) 306-314
32. Watson J.D., and Crick F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171 (1953) 737-738
33. Zucker M., Mathews D., and Turner D. Algorithems and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszweski J., and Clark B.F.C. (Eds). RNA biochemistry and biotechnology (1999), Kluwer Academic Publishers