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Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):7166-70. doi: 10.1073/pnas.1606518113. Epub 2016 Jun 15.

Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences.

Author information

1
Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel;
2
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126.
3
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126 puglisi@stanford.edu nadir@tx.technion.ac.il.
4
Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel; puglisi@stanford.edu nadir@tx.technion.ac.il.

Abstract

Bioinformatic analysis of Escherichia coli proteomes revealed that all possible amino acid triplet sequences occur at their expected frequencies, with four exceptions. Two of the four underrepresented sequences (URSs) were shown to interfere with translation in vivo and in vitro. Enlarging the URS by a single amino acid resulted in increased translational inhibition. Single-molecule methods revealed stalling of translation at the entrance of the peptide exit tunnel of the ribosome, adjacent to ribosomal nucleotides A2062 and U2585. Interaction with these same ribosomal residues is involved in regulation of translation by longer, naturally occurring protein sequences. The E. coli exit tunnel has evidently evolved to minimize interaction with the exit tunnel and maximize the sequence diversity of the proteome, although allowing some interactions for regulatory purposes. Bioinformatic analysis of the human proteome revealed no underrepresented triplet sequences, possibly reflecting an absence of regulation by interaction with the exit tunnel.

KEYWORDS:

bioinformatics; single-molecule methods; stalling peptides; translation; underrepresented sequences

PMID:
27307442
PMCID:
PMC4932979
DOI:
10.1073/pnas.1606518113
[Indexed for MEDLINE]
Free PMC Article

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