Protomer alignment modulates specificity of RNA substrate recognition by Ire1

The unfolded protein response (UPR) maintains protein folding homeostasis in the endoplasmic reticulum (ER). In metazoan cells, the Ire1 branch of the UPR initiates two functional outputs-- non-conventional mRNA splicing and selective mRNA decay (RIDD). By contrast, Ire1 orthologs from Saccharomyces cerevisiae and Schizosaccharomyces pombe are specialized for only splicing or RIDD, respectively. The functional specialization lies in Ire1s RNase activity, which is either stringently splice-site specific (as in S. cerevisiae) or promiscuous (as in S. pombe). Here, we developed an assay that reports on Ire1s RNase promiscuity. We found that conversion of two amino acids within the RNase domain of S. cerevisiae Ire1 to their S. pombe counterparts rendered it promiscuous. Using biochemical assays and computational modeling, we show that the mutations rewired a pair of salt bridges at Ire1 RNase domains dimer interface, changing its protomer alignment. Thus, Ire1 protomer alignment affects its substrates specificity.