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Biology
2021 Project Proposal

The Role of eIF3 on the Ribosome and Across the Transcriptome

Colin Aitken (Biology)

Project Type - B - Flexible:  It will be in-person if we are allowed to have URSI students on campus, but it will become a remote project if not.

Translation initiation sets the reading frame of protein synthesis. It is the rate-limiting and the most highly-regulated step in the pathway. In eukaryotes, initiation is mediated by a group of eukaryotic initiation factors (eIFs) that bind to the smaller subunit of ribosome (40S) to assemble the ribosome at the start codon and initiate translation. The process begins with the assembly of a  pre-initiation complex (PIC) on the 40S subunit. The PIC then scans along the mRNA from the 5’ end to the 3’ end until it identifies the start codon. Physical features of the 5’ untranslated region (UTR) such as the length or secondary structure impact the scanning efficiency of the PIC, and thus affect translation initiation. eIF3 is the largest and most complex eIF and it participates in mRNA recruitment, scanning, and start codon recognition. We investigated two Saccharomyces cerevisiae mutants lacking eIF3 or a part of it. One mutant targets the structural eIF3a/b subunits (degron), mimicking the loss of the entire eIF3 complex; the other mutant targets the eIF3i subunit (DDKK), resulting in the loss of both eIF3i and eIF3g subunits from the PIC. We measured the translational efficiency (TE) of individual mRNAs using ribosomal profiling, a technique that tracks the ribosome across the entire genome. In both mutants, the overall translation of mRNAs was reduced, with the degron mutant exhibiting the most severe decrease in translation. In both mutants, the most down-regulated genes tend to have longer and more complex 5’ UTRs. We identified a set of mRNAs strongly affected by each mutation and are working to validate these results in vitro. We also compared the TE changes of degron and DDKK with those observed in the presence of mutations to the DEAD-Box RNA helicase Ded1 and eIF4A and a moderate overlap was observed. These results shed new light on the role of eIF3 in promoting the translation of mRNAs at the transcriptome level.

Prerequisites: One 200-level Biology course

How should students express interest in this project? Students should not contact me directly. I will review the list of applicants and reach out to a short list of students for interviews.

This is an 8-week project running from June 7 – July 31