Identification of a novel MIPEP splice variant with altered substrate-binding properties

Mitochondrial intermediate peptidase (MIPEP) is a mitochondrial signal peptidase that removes N-terminal amino acids from mitochondrial matrix proteins. We have identified a novel <i>Mipep</i> splice variant that lacks exons 15 and 16, which we termed "ΔMIPEP". We characterized the molecular features of ΔMIPEP by investigating its expression level in numerous mouse tissues and by performing a computer simulation that allows the prediction of protein structures and substrate-binding properties. <i>ΔMipep</i> mRNA was detected in all mouse tissues examined but at much lower levels than full-length <i>Mipep</i>. Structure prediction and docking simulation of full-length MIPEP and ΔMIPEP with substrates of MIPEP, such as malate dehydrogenase 2 (MDH2) and cytochrome <i>c</i> oxidase subunit 4, showed that entry of these substrates into ΔMIPEP with a low binding energy was greatly restricted. To determine levels of MIPEP substrates in the presence or absence of full-length MIPEP or ΔMIPEP, we created <i>Mipep</i> and <i>ΔMipep</i> overexpression 3T3-L1 cells and <i>Mipep</i> knockout (KO) cells. Western blotting showed that in <i>Mipep</i> KO cells <i>Mipep</i> overexpression slightly decreased the molecular weight of MDH2 and Sirtuin 3, another MIPEP substrate, whereas ΔMipep overexpression did not. These results indicate that ΔMIPEP fails to recognize MIPEP substrate proteins. Together, our findings indicate that ΔMIPEP is a novel splice variant that can contribute to mitochondrial signal peptidase-mediated regulation of mitochondrial protein homeostasis.