This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Gatto, G. J. Articles by Berg, J. M. Search for Related Content PubMed PubMed Citation Articles by Gatto, G. J., Jr. Articles by Berg, J. M. Social Bookmarking                   What's this?

LETTER

Nonrandom Tripeptide Sequence Distributions at Protein Carboxyl Termini

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

The availability of complete genome sequences enables the statistical analysis of sequence features without significant database-imposed bias. The carboxyl termini of proteins often contain regions associated with protein targeting and enhanced translational termination. We analyzed the frequency of occurrence of C-terminal tripeptides in representative archaeal, bacterial, and eukaryotic genomes. The sequence distribution in prokaryotic genomes nearly matches that generated by the randomization of the observed tripeptide set. In contrast, eukaryotic genomes contain large numbers of overrepresented sequences. Some of these correspond to highly repeated sequences from either duplicated endogenous genes or transposon open reading frames. Gratifyingly, others represent previously known targeting signals or sequences associated with an increase in translational termination efficiency. However, a number of overrepresented tripeptides have not been previously noted and may represent novel functional sequences. For example, the sequence XSS may enhance translational termination efficiency in plants, whereas FWC may be a targeting or processing signal for certain amino acid permeases in yeast.

E-MAIL jberg{at}jhmi.edu; FAX (410) 502-6910.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.667603.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				J. R. Gog, E. D. S. Afonso, R. M. Dalton, I. Leclercq, L. Tiley, D. Elton, J. C. von Kirchbach, N. Naffakh, N. Escriou, and P. Digard Codon conservation in the influenza A virus genome defines RNA packaging signals Nucleic Acids Res., March 19, 2007; 35(6): 1897 - 1907. [Abstract] [Full Text] [PDF]

				I. Williams, J. Richardson, A. Starkey, and I. Stansfield Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae Nucleic Acids Res., December 15, 2004; 32(22): 6605 - 6616. [Abstract] [Full Text] [PDF]