Targeting APEX2 to the mRNA encoding fatty acid synthase β in yeast identifies interacting proteins that control its abundance in the cell cycle.

Profiling the repertoire of proteins associated with a given mRNA during the cell cycle is unstudied. Furthermore, it is easier to ask and answer what mRNAs a specific protein might bind to than the other way around. Here, we implemented an RNA-centric proximity labeling technology at different points in the cell cycle in highly synchronous yeast cultures. To understand how the abundance of , encoding fatty acid synthase, peaks late in the cell cycle, we identified proteins that interact with the transcript in a cell cycle-dependent manner. We used dCas13d-APEX2 fusions to target and label nearby proteins, which were then identified by mass spectrometry. The glycolytic enzyme Tdh3p, a known RNA-binding protein, interacted with the mRNA, and it was necessary for the periodic abundance of Fas1p in the cell cycle. These results point to unexpected connections between major metabolic pathways. They also underscore the role of mRNA-protein interactions for gene expression during cell division.