This review focuses on organellar AAA/FtsH proteases, whose proteolytic and chaperone-like activity is a crucial component of the protein quality control systems of mitochondrial and chloroplast membranes. We compare the AAA/FtsH proteases from yeast, mammals and plants. The nature of the complexes formed by AAA/FtsH proteases and the current view on their involvement in degradation of non-native organellar proteins or assembly of membrane complexes are discussed. Additional functions of AAA proteases not directly connected with protein quality control found in yeast and mammals but not yet in plants are also described shortly. Following an overview of the molecular functions of the AAA/FtsH proteases we discuss physiological consequences of their inactivation in yeast, mammals and plants. The molecular basis of phenotypes associated with inactivation of the AAA/FtsH proteases is not fully understood yet, with the notable exception of those observed in m-AAA protease-deficient yeast cells, which are caused by impaired maturation of mitochondrial ribosomal protein. Finally, examples of cytosolic events affecting protein quality control in mitochondria and chloroplasts are given. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Hardly anything is known about translational control of plant mitochondrial gene expression. Here, we provide evidence for differential translation of mitochondrial transcripts in Arabidopsis thaliana. We found that silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein S10 disturbs the ratio between the small and large subunits of mitoribosomes, with an excess of the latter. Moreover, a portion of the small subunits are incomplete, lacking at least the S10 protein. rps10 cells also have an increased mitochondrial DNA copy number per cell, causing an upregulation of all mitochondrial transcripts. Mitochondrial translation is also altered so that it largely overrides the hyperaccumulation of transcripts, and as a consequence, only ribosomal proteins are oversynthesized, whereas oxidative phosphorylation subunits are downregulated. Expression of nuclear-encoded components of mitoribosomes and oxidative phosphorylation system (OXPHOS) complexes seems to be less affected. The ultimate coordination of expression of the nuclear and mitochondrial genomes occurs at the complex assembly level. These findings indicate that mitoribosomes can regulate gene expression by varying the efficiency of translation of mRNAs for OXPHOS and ribosomal proteins.

ATP-dependent proteases from three families have been identified experimentally in Arabidopsis mitochondria: four FtsH proteases (AtFtsH3, AtFtsH4, AtFtsH10, and AtFtsH11), two Lon proteases (AtLon1 and AtLon4), and one Clp protease (AtClpP2 with regulatory subunit AtClpX). In this review we discuss their submitochondrial localization, expression profiles and proposed functions, with special emphasis on their impact on plant growth and development. The best characterized plant mitochondrial ATP-dependent proteases are AtLon1 and AtFtsH4. It has been proposed that AtLon1 is necessary for proper mitochondrial biogenesis during seedling establishment, whereas AtFtsH4 is involved in maintaining mitochondrial homeostasis late in rosette development under short-day photoperiod.

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The existence of a proteolytic system which can specifically recognize and cleave proteins in mitochondria is now well established. The components of this system comprise processing peptidases, ATP-dependent peptidases and oligopeptidases. A short overview of experimentally confirmed proteases mainly from Arabidopsis thaliana is provided. The role of the mitochondrial peptidases in plant growth and development is emphasized. We also discuss the possibility of existence of as yet unidentified plant homologs of yeast mitochondrial ATP-independent proteases.