Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

Abstract

Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.

Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites

“…7A and 8A) suggests that MPP activity may persist independent of complex III integrity, since dQ is not expected to bypass more general defects in MPP processing. Biochemical precedent for autonomous MPP function is provided by yeast and humans, in which MPP is a soluble matrix enzyme that functions independent of complex III (61).…”

KOMPEITO, an Atypical Arabidopsis Rhomboid-Related Gene, Is Required for Callose Accumulation and Pollen Wall Development

“…The deduced KOM peptide encoded 385 amino acid residues with a signal anchor domain at its N-terminus and 7 predicted transmembrane domains; it belonged to the Rhomboid family of proteins ( Figure 3 D), which are conserved in bacteria, animals and plants [ 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 ]. Unlike many members of the Rhomboid family [ 31 , 38 ], KOM did not contain a conserved His residue at TMD6, which, in all other Rhomboids, is required for the serine protease activity.…”

“…Most Rhomboid-like proteins are distributed through the secretory pathway [ 39 ], although some members act in mitochondria [ 33 , 40 ]. Arabidopsis Rhomboid-like proteins were also experimentally shown or predicted to localize several subcellular organelles [ 31 , 41 , 42 ].…”

The CLP and PREP protease systems coordinate maturation and degradation of the chloroplast proteome in Arabidopsis thaliana

“…Chloroplasts and mitochondria contain multiple ATP‐dependent and ATP‐independent peptidases that together break down proteins into individual amino acids and must be part of a network of unfolding and peptidase activity (Majsec et al ., 2017; Nishimura et al ., 2017; Ghifari et al ., 2019; Rodriguez‐Concepcion et al ., 2019; Bouchnak & van Wijk, 2021; Luo & Kim, 2021; Heidorn‐Czarna et al ., 2022). How these protease activities are coordinated and positioned within these organellar networks is only partially understood.…”