Highly expressed proteins have an increased frequency of alanine in the second amino acid position.
BACKGROUND
Although the sequence requirements for translation initiation regions have been frequently analysed, usually the highly expressed genes are not treated as a separate dataset.


RESULTS
To investigate this, we analysed the mRNA regions downstream of initiation codons in nine bacteria, three archaea and three unicellular eukaryotes, comparing the dataset of highly expressed genes to the dataset of all genes. In addition to the detailed analysis of the nucleotide and codon frequencies we compared the N-termini of highly expressed proteins to the N-termini of all proteins coded in the genome.


CONCLUSIONS
The most conserved pattern was observed at the amino acid level: strong alanine over-representation was observed at the second amino acid position of highly expressed proteins. This pattern is well conserved in all three domains of life.
Tats
Age
A
Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia. age.tats@ut.ee
Remm
Maido
M
Tenson
Tanel
T
D000241:Adenosine / Q000032:analysis; D000409:Alanine / Q000032:analysis*; D000818:Animals; D003062:Codon / Q000737:chemistry*; D004926:Escherichia coli / Q000235:genetics; D015870:Gene Expression; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D009711:Nucleotides / Q000032:analysis; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020539:Sequence Analysis, Protein
D003062:Codon; D009711:Nucleotides; D011506:Proteins; D000241:Adenosine; D000409:Alanine