The goal of our research group is to elucidate the molecular mechanisms underlying the initiation phase of protein synthesis in eukaryotic organisms. We use the yeast saccharomyces cerevisiae as a model system and employ a range of approaches - from genetics to biochemistry to structural biology - in collaboration with Alan Hinnebusch and Tom Devers labs at NICHD and several other research groups around the world. Eukaryotic translation initiation is a key control point in the regulation of gene expression. It begins when an initiator methionyl tRNA (Met-tRNAi) is loaded onto the small (40S) ribosomal subunit. Met-tRNAi binds to the 40S subunit as a ternary complex (TC) with the GTP-bound form of the initiation factor eIF2. Three other factors eIF1, eIF1A and eIF3 also bind to the 40S subunit and promote the loading of the TC. The resulting 43S pre-initiation complex (PIC) is then loaded onto the 5-end of an mRNA with the aid of eIF3 and the eIF4 group of factors the RNA helicase eIF4A; the 5-7-methylguanosine cap-binding protein eIF4E; the scaffolding protein eIF4G; and the 40S subunit- and RNA-binding protein eIF4B. Both eIF4A and eIF4E bind to eIF4G and form the eIF4F complex. Once loaded onto the mRNA, the 43S PIC is thought to scan along the mRNA in search of an AUG start codon. This process is ATP-dependent and likely requires multiple RNA helicases, including the DEAD-box protein Ded1p. Recognition of the start site begins with base pairing between the anticodon of tRNAi and the AUG codon. This base pairing then triggers downstream events that commit the PIC to continuing initiation from that point on the mRNA. These events include ejection of eIF1 from its binding site on the 40S subunit, movement of the C-terminal tail (CTT) of eIF1A, and release of phosphate from eIF2, which converts it to its GDP-bound state. In addition, the initiator tRNA moves from a position that is not fully engaged in the ribosomal P site (termed P(OUT)) to one that is (P(IN)) and the PIC as a whole converts from an open conformation that is conducive for scanning to a closed one that is not. At this stage eIF2GDP dissociates from the PIC and eIF1A and a second GTPase factor, eIF5B, coordinate joining of the large ribosomal subunit to form the 80S initiation complex. eIF5B hydrolyzes GTP, which appears to result in a conformational reorganization of the complex, and then dissociates along with eIF1A. This year we made progress in understanding the role of the DEAD box RNA helicase Ded1 in promoting mRNA recruitment to the PIC. Our data indicate that Ded1 unwinds stable structures in the 5'-UTRs of mRNAs. It appears to act as part of a quaternary complex with eIF4A, eIF4G and eIF4E, but on some mRNAs it has an additional function outside of this complex. Different mRNAs are differentially dependent for efficient recruitment on each of the multiple interactions between Ded1 and the other components of the quaternary complex indicating that the factor acts in distinct ways dependent on the mRNA. This observation is consistent with the idea that because each mRNA has a unique shape a single mode of interaction between Ded1 and mRNAs is unlikely to be able to accommodate the need to act on the myriad of scenarios presented by each different structure. In our ribosome profiling studies we have been analyzing cases in which temperature-dependent changes in 5'-upstream open reading frame (uORF) translation is inversely correlated with changes in main ORF translation, as these could be physiologically significant gene regulatory events. In addition, we have been examining cases in which translation of an N-terminal extension of the main ORF is altered by changes in temperature. We have recently started a new project to probe the mechanistic role of the N-terminal tail of eIF1 in start codon recognition. This work is utilizing both yeast genetic and in vitro biochemical approaches.
