Predicting gene expression level from codon usage bias

Molecular Biology and Evolution

Volumn 24, Issue 1, 2007, Pages 10-12

  Henry, Ian ^a   Sharp, Paul M ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Codon usage; Escherichia coli; Gene expression; Predicted highly expressed genes; Shewanella oneidensis

Indexed keywords

ARTICLE; BACTERIAL STRAIN; CODON; CORRELATION ANALYSIS; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENOME; NONHUMAN; SHEWANELLA ONEIDENSIS;

CODON; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; SHEWANELLA;

ESCHERICHIA COLI; PROKARYOTA; SHEWANELLA ONEIDENSIS;

EID: 33845874641     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl148     Document Type: Article

References (22)

1. DiRienzo JM, Nakamura K, Inouye M. 1978. The outer membrane proteins of gram-negative bacteria: biosynthesis, assembly, and functions. Annu Rev Biochem. 47:481-532.
2. Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:7055-7074.
3. Heidelberg J, Paulsen I, Nelson K, et al. (43 co-authors). 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat Biotechnol. 20:1118-1123.
4. Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein coding genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 151:389-409.
5. Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34.
6. Karlin S, Barnett MJ, Campbell A, Fisher RF, Mrazek J. 2003. Predicting gene expression levels from codon biases in α-proteobacterial genomes. Proc Natl Acad Sci USA. 100:7313-7318.
7. Karlin S, Brocchieri L, Mrazek J, Kaiser D. 2006. Distinguishing features of δ-proteobacterial genomes. Proc Natl Acad Sci USA. 103:11352-11357.
8. Karlin S, Mrazek J. 2000. Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol. 182:5238-5250.
9. Karlin S, Mrazek J. 2001. Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage. Proc Natl Acad Sci USA. 98:5240-5245.
10. Karlin S, Mrazek J, Campbell A, Kaiser D. 2001. Characterizations of highly expressed genes of four fast-growing bacteria. J Bacteriol. 183:5025-5040.
11. Karlin S, Mrazek J, Ma J, Brocchieri L. 2005. Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci USA. 102:7303-7308.
12. Karlin S, Theriot J, Mrazek J. 2004. Comparative analysis of gene expression among low G+C gram-positive genomes. Proc Natl Acad Sci USA. 101:6182-6187.
13. Kerr ARW, Peden JF, Sharp PM. 1997. Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae. Mol Microbiol. 25:1177-1179.
14. Lafay B, Atherton JC, Sharp PM. 2000. Absence of translationally selected codon usage bias in Helicobacter pylori. Microbiology. 146:851-860.
15. Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. 1999. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27:1642-1649.
16. Ma J, Campbell A, Karlin S. 2002. Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol. 184:5733-5745.
17. Mrazek J, Bhaya D, Grossman AR, Karlin S. 2001. Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29:1590-1601.
18. Mrazek J, Spoorman AM, Karlin S. 2006. Genomic comparisons among γ-proteobacteria. Environ Microbiol. 8:273-288.
19. Pedersen S, Bloch PL, Reeh S, Neidhardt FC. 1978. Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates. Cell. 14:179-190.
20. Post LE, Nomura M. 1980. DNA sequences from the str operon of Escherichia coli. J Biol Chem. 255:4660-4666.
21. Sharp PM, Bailes E, Grocock RJ, Peden JF, Sockett RE. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33:1141-1153.
22. Sharp PM, Li W-H. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.