Characterizing the Multiple Binding Interactions of Air1 and Air2 from S. cerevisiae

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Sean Johnson


Air1 and Air2 are highly homologous Eukaryotic proteins (45% sequence identity) that function in multiple nuclear RNA regulatory pathways, including RNA surveillance. The Air proteins are characterized as essential components of the multi-protein TRAMP complex (Trf4- Air2- Mtr4- Polyadenylation complex), which functions in nuclear RNA quality control by identifying RNA substrates and targeting them for degradation by the nuclear exosome. Within the TRAMP complex, Air1/2 mediate protein-protein interactions with both Mtr4 and Trf4. Furthermore, Air1/2 provides an essential RNA binding platform for the complex. Despite the significant role of Air1/2 in TRAMP, the mechanistic details of the critical protein-protein and protein-RNA interactions are poorly understood. Specific questions addressed in this study include: What is the binding interface of Air1/2 with the helicase Mtr4, and how do the Air proteins recognize various RNA substrates? Pull-down experiments using Air1/2 and Mtr4 truncation mutants are being used to identify the minimal binding interface between Air1/2 and Mtr4. A fluorescence based assay has also been developed to monitor Air1/2 interactions with various RNA species. Crystallization trials of viable complexes are ongoing.

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