• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Aug 11, 1994; 22(15): 3174–3180.
PMCID: PMC310293

Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes.

Abstract

Multivariate analysis of the amino-acid compositions of 999 chromosome-encoded proteins from Escherichia coli showed that three main factors influence the variability of amino-acid composition. The first factor was correlated with the global hydrophobicity of proteins, and it discriminated integral membrane proteins from the others. The second factor was correlated with gene expressivity, showing a bias in highly expressed genes towards amino-acids having abundant major tRNAs. Just as highly expressed genes have reduced codon diversity in protein coding sequences, so do they have a reduced diversity of amino-acid choice. This showed that translational constraints are important enough to affect the global amino-acid composition of proteins. The third factor was correlated with the aromaticity of proteins, showing that aromatic amino-acid content is highly variable.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.2M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Thioulouse J. Statistical analysis and graphical display of multivariate data on the Macintosh. Comput Appl Biosci. 1989 Oct;5(4):287–292. [PubMed]
  • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105–132. [PubMed]
  • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. [PMC free article] [PubMed]
  • Nishikawa K, Ooi T. Correlation of the amino acid composition of a protein to its structural and biological characters. J Biochem. 1982 May;91(5):1821–1824. [PubMed]
  • Rogers SD, Bhave MR, Mercer JF, Camakaris J, Lee BT. Cloning and characterization of cutE, a gene involved in copper transport in Escherichia coli. J Bacteriol. 1991 Nov;173(21):6742–6748. [PMC free article] [PubMed]
  • Klein P, Kanehisa M, DeLisi C. The detection and classification of membrane-spanning proteins. Biochim Biophys Acta. 1985 May 28;815(3):468–476. [PubMed]
  • Yamao F, Andachi Y, Muto A, Ikemura T, Osawa S. Levels of tRNAs in bacterial cells as affected by amino acid usage in proteins. Nucleic Acids Res. 1991 Nov 25;19(22):6119–6122. [PMC free article] [PubMed]
  • Shpaer EG. Amino acid composition is correlated with protein abundance in Escherichia coli: can this be due to optimization of translational efficiency? Protein Seq Data Anal. 1989 Feb;2(2):107–110. [PubMed]
  • Holmes WM, Goldman E, Miner TA, Hatfield GW. Differential utilization of leucyl-tRNAs by Escherichia coli. Proc Natl Acad Sci U S A. 1977 Apr;74(4):1393–1397. [PMC free article] [PubMed]
  • Goldman E, Holmes WM, Hatfield GW. Specificity of codon recognition by Escherichia coli tRNALeu isoaccepting species determined by protein synthesis in vitro directed by phage RNA. J Mol Biol. 1979 Apr 25;129(4):567–585. [PubMed]
  • Jakubowski H, Goldman E. Quantities of individual aminoacyl-tRNA families and their turnover in Escherichia coli. J Bacteriol. 1984 Jun;158(3):769–776. [PMC free article] [PubMed]
  • Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. [PubMed]
  • Grantham R, Gautier C. Genetic distances from mRNA sequences. Naturwissenschaften. 1980 Feb;67(2):93–94. [PubMed]
  • Grantham R, Gautier C, Gouy M, Mercier R, Pavé A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 1980 Jan 11;8(1):r49–r62. [PMC free article] [PubMed]
  • Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980 May 10;8(9):1893–1912. [PMC free article] [PubMed]
  • Andersson SG, Kurland CG. Codon preferences in free-living microorganisms. Microbiol Rev. 1990 Jun;54(2):198–210. [PMC free article] [PubMed]
  • Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982 Nov 25;10(22):7055–7074. [PMC free article] [PubMed]
  • Gouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C. ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):121–127. [PMC free article] [PubMed]
  • Gouy M, Gautier C, Attimonelli M, Lanave C, di Paola G. ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Comput Appl Biosci. 1985 Sep;1(3):167–172. [PubMed]
  • Gouy M, Gautier C, Milleret F. System analysis and nucleic acid sequence banks. Biochimie. 1985 May;67(5):433–436. [PubMed]
  • Benson D, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res. 1993 Jul 1;21(13):2963–2965. [PMC free article] [PubMed]
  • Hall BG, Sharp PM. Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates. Mol Biol Evol. 1992 Jul;9(4):654–665. [PubMed]
  • Nishikawa K, Kubota Y, Ooi T. Classification of proteins into groups based on amino acid composition and other characters. I. Angular distribution. J Biochem. 1983 Sep;94(3):981–995. [PubMed]
  • Sawers G, Heider J, Zehelein E, Böck A. Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme. J Bacteriol. 1991 Aug;173(16):4983–4993. [PMC free article] [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...