טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentPenias Navon Sharon
SubjectShort Peptide Sequences Inhibit Prokaryotic Translation:
A New Way of Looking at Biological Information
DepartmentDepartment of Chemistry
Supervisor Professor Noam Adir
Full Thesis textFull thesis text - English Version


Abstract

During translation all nascent polypeptides must pass through the ribosomal exit tunnel. This tunnel is formed primarily by rRNA nucleotides and few protein residues, and must permit the transit of all of the different peptide sequences. However, some peptide sequences have been found to interact with the tunnel, thereby affecting the protein elongation cycle of the ribosome. This suggests that the tunnel may consist of a series of dynamic regulatory gates that inspect the nascent chain as it passes through.

Previous research has revealed the importance of short amino acid sequences in biological processes, but very little research has been done on those amino acid sequences that are missing. We hypothesized that if there are short amino acid sequences that form strong interactions with the ribosomal exit tunnel that lead to translational arrest and loss of cell viability, then, their incidence might be reduced by evolutionary pressure. In this work we scanned the E. coli proteome databases and indeed found a few short amino acid sequences which are significantly under-represented (URSs).

In order to explore the effect of the URS on the protein production and cell viability we embedded them into normal overexpressed proteins. We found that protein expression of the mutants that carry the URS was inhibited both in vivo and in vitro, suggesting that their translation is inhibited. In addition, we found that the expression of proteins containing URS sequences, inhibit the translation of other proteins in vitro, indicating that the rate of ribosome recycling is also inhibited.

The viability of bacteria cells that overexpressed the proteins carrying the URS, decreased. We believe that the arrest of ribosome translation by the protein containing URS also inhibits the translation of other proteins in vivo, to an extent that causes cell death. However, embedding the E. coli URSs in GFP expressed in human HeLa cells had no effect on translation efficiency, showing that URSs are species specific. Analysis of proteomes of prokaryotes, archea and eukaryote URSs show significant variability most likely due to differences between ribosome peptide exit tunnels.

We believe that this research reveal a simple methodology that can be used to identify URSs that have a potential to harm the cell. This data could potentially help us understand protein expression difficulties and even more enticingly, to be the basis for the development of a completely novel class of antimicrobials.