Bifunctional role of the bc1 complex in plants. Mitochondrial bc1 complex catalyses both electron transport and protein processing

The lowdown on breakdown: Open questions in plant proteolysis

Proteolysis, including post-translational proteolytic processing as well as protein degradation and amino acid recycling, is an essential component of the growth and development of living organisms. In this article, experts in plant proteolysis pose and discuss compelling open questions in their areas of research. Topics covered include the role of proteolysis in the cell cycle, DNA damage response, mitochondrial function, the generation of N-terminal signals (degrons) that mark many proteins for degradation (N-terminal acetylation, the Arg/N-degron pathway, and the chloroplast N-degron pathway), developmental and metabolic signaling (photomorphogenesis, abscisic acid and strigolactone signaling, sugar metabolism, and postharvest regulation), plant responses to environmental signals (endoplasmic-reticulum-associated degradation, chloroplast-associated degradation, drought tolerance, and the growth-defense trade-off), and the functional diversification of peptidases. We hope these thought-provoking discussions help to stimulate further research.

Structure and function of the S. pombe III-IV-cyt c supercomplex

The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII2), via a mobile electron carrier, cytochrome c. In the present study, we isolated the CIII2CIV supercomplex from the fission yeast Schizosaccharomyces pombe and determined its structure with bound cyt. c using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn2+, coordinated in the CIII subunit Cor1, which is encoded by the same gene (qcr1) as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIII2CIV supercomplex displays proteolytic activity suggesting a dual role of CIII2 in S. pombe. As in the supercomplex from S. cerevisiae, subunit Cox5 of CIV faces towards one CIII monomer, but in S. pombe, the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. c binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. c bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII2 respiratory system and indicates a two-dimensional cyt. c diffusion mechanism within the CIII2-CIV supercomplex.

The biogenesis and regulation of the plant oxidative phosphorylation system

Mitochondria are central organelles for respiration in plants. At the heart of this process is oxidative phosphorylation (OXPHOS) system, which generates ATP required for cellular energetic needs. OXPHOS complexes comprise of multiple subunits that originated from both mitochondrial and nuclear genome, which requires careful orchestration of expression, translation, import, and assembly. Constant exposure to reactive oxygen species due to redox activity also renders OXPHOS subunits to be more prone to oxidative damage, which requires coordination of disassembly and degradation. In this review, we highlight the composition, assembly, and activity of OXPHOS complexes in plants based on recent biochemical and structural studies. We also discuss how plants regulate the biogenesis and turnover of OXPHOS subunits and the importance of OXPHOS in overall plant respiration. Further studies in determining the regulation of biogenesis and activity of OXPHOS will advances the field, especially in understanding plant respiration and its role to plant growth and development.

Proteolytic regulation of mitochondrial oxidative phosphorylation components in plants

Mitochondrial function relies on the homeostasis and quality control of their proteome, including components of the oxidative phosphorylation (OXPHOS) pathway that generates energy in form of ATP. OXPHOS subunits are under constant exposure to reactive oxygen species due to their oxidation-reduction activities, which consequently make them prone to oxidative damage, misfolding, and aggregation. As a result, quality control mechanisms through turnover and degradation are required for maintaining mitochondrial activity. Degradation of OXPHOS subunits can be achieved through proteomic turnover or modular degradation. In this review, we present multiple protein degradation pathways in plant mitochondria. Specifically, we focus on the intricate turnover of OXPHOS subunits, prior to protein import via cytosolic proteasomal degradation and post import and assembly via intra-mitochondrial proteolysis involving multiple AAA+ proteases. Together, these proteolytic pathways maintain the activity and homeostasis of OXPHOS components.

Protein Processing in Plant Mitochondria Compared to Yeast and Mammals

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.

Parasite powerhouse: A review of the Toxoplasma gondii mitochondrion

Toxoplasma gondii is a member of the apicomplexan phylum, a group of single-celled eukaryotic parasites that cause significant human morbidity and mortality around the world. T. gondii harbors two organelles of endosymbiotic origin: a non-photosynthetic plastid, known as the apicoplast, and a single mitochondrion derived from the ancient engulfment of an α-proteobacterium. Due to excitement surrounding the novelty of the apicoplast, the T. gondii mitochondrion was, to a certain extent, overlooked for about two decades. However, recent work has illustrated that the mitochondrion is an essential hub of apicomplexan-specific biology. Development of novel techniques, such as cryo-electron microscopy, complexome profiling, and next-generation sequencing have led to a renaissance in mitochondrial studies. This review will cover what is currently known about key features of the T. gondii mitochondrion, ranging from its genome to protein import machinery and biochemical pathways. Particular focus will be given to mitochondrial features that diverge significantly from the mammalian host, along with discussion of this important organelle as a drug target.

Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites

The mitochondrion is critical for the survival of apicomplexan parasites. Several major anti-parasitic drugs, such as atovaquone and endochin-like quinolones, act through inhibition of the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase complex (Complex III). Despite being an important drug target, the protein composition of Complex III of apicomplexan parasites has not been elucidated. Here, we undertake a mass spectrometry-based proteomic analysis of Complex III in the apicomplexan Toxoplasma gondii. Along with canonical subunits that are conserved across eukaryotic evolution, we identify several novel or highly divergent Complex III components that are conserved within the apicomplexan lineage. We demonstrate that one such subunit, which we term TgQCR11, is critical for parasite proliferation, mitochondrial oxygen consumption and Complex III activity, and establish that loss of this protein leads to defects in Complex III integrity. We conclude that the protein composition of Complex III in apicomplexans differs from that of the mammalian hosts that these parasites infect.

The peptidases involved in plant mitochondrial protein import

The endosymbiotic origin of the mitochondrion and the subsequent transfer of its genome to the host nucleus has resulted in intricate mechanisms of regulating mitochondrial biogenesis and protein content. The majority of mitochondrial proteins are nuclear encoded and synthesized in the cytosol, thus requiring specialized and dedicated machinery for the correct targeting import and sorting of its proteome. Most proteins targeted to the mitochondria utilize N-terminal targeting signals called presequences that are cleaved upon import. This cleavage is carried out by a variety of peptidases, generating free peptides that can be detrimental to organellar and cellular activity. Research over the last few decades has elucidated a range of mitochondrial peptidases that are involved in the initial removal of the targeting signal and its sequential degradation, allowing for the recovery of single amino acids. The significance of these processing pathways goes beyond presequence degradation after protein import, whereby the deletion of processing peptidases induces plant stress responses, compromises mitochondrial respiratory capability, and alters overall plant growth and development. Here, we review the multitude of plant mitochondrial peptidases that are known to be involved in protein import and processing of targeting signals to detail how their activities can affect organellar protein homeostasis and overall plant growth.

Arabidopsis DGD1 SUPPRESSOR1 Is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis

Mitochondrial and plastid biogenesis requires the biosynthesis and assembly of proteins, nucleic acids, and lipids. In Arabidopsis (Arabidopsis thaliana), the mitochondrial outer membrane protein DGD1 SUPPRESSOR1 (DGS1) is part of a large multi-subunit protein complex that contains the mitochondrial contact site and cristae organizing system 60-kD subunit, the translocase of outer mitochondrial membrane 40-kD subunit (TOM40), the TOM20s, and the Rieske FeS protein. A point mutation in DGS1, dgs1-1, altered the stability and protease accessibility of this complex. This altered mitochondrial biogenesis, mitochondrial size, lipid content and composition, protein import, and respiratory capacity. Whole plant physiology was affected in the dgs1-1 mutant as evidenced by tolerance to imposed drought stress and altered transcriptional responses of markers of mitochondrial retrograde signaling. Putative orthologs of Arabidopsis DGS1 are conserved in eukaryotes, including the Nuclear Control of ATP Synthase2 (NCA2) protein in yeast (Saccharomyces cerevisiae), but lost in Metazoa. The genes encoding DGS1 and NCA2 are part of a similar coexpression network including genes encoding proteins involved in mitochondrial fission, morphology, and lipid homeostasis. Thus, DGS1 links mitochondrial protein and lipid import with cellular lipid homeostasis and whole plant stress responses.

Assembly of the Complexes of the Oxidative Phosphorylation System in Land Plant Mitochondria

Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants-compared with those described in fungal and animal models-we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.

Plant mitochondrial protein import: the ins and outs

The majority of the mitochondrial proteome, required to fulfil its diverse range of functions, is cytosolically synthesised and translocated via specialised machinery. The dedicated translocases, receptors, and associated proteins have been characterised in great detail in yeast over the last several decades, yet many of the mechanisms that regulate these processes in higher eukaryotes are still unknown. In this review, we highlight the current knowledge of mitochondrial protein import in plants. Despite the fact that the mechanisms of mitochondrial protein import have remained conserved across species, many unique features have arisen in plants to encompass the developmental, tissue-specific, and stress-responsive regulation in planta. An understanding of unique features and mechanisms in plants provides us with a unique insight into the regulation of mitochondrial biogenesis in higher eukaryotes.

Biogenesis of the bc1 Complex of the Mitochondrial Respiratory Chain

The oxidative phosphorylation system contains four respiratory chain complexes that connect the transport of electrons to oxygen with the establishment of an electrochemical gradient over the inner membrane for ATP synthesis. Due to the dual genetic source of the respiratory chain subunits, its assembly requires a tight coordination between nuclear and mitochondrial gene expression machineries. In addition, dedicated assembly factors support the step-by-step addition of catalytic and accessory subunits as well as the acquisition of redox cofactors. Studies in yeast have revealed the basic principles underlying the assembly pathways. In this review, we summarize work on the biogenesis of the bc₁ complex or complex III, a central component of the mitochondrial energy conversion system.

Shredding the signal: targeting peptide degradation in mitochondria and chloroplasts

The biogenesis and functionality of mitochondria and chloroplasts depend on the constant turnover of their proteins. The majority of mitochondrial and chloroplastic proteins are imported as precursors via their N-terminal targeting peptides. After import, the targeting peptides are cleaved off and degraded. Recent work has elucidated a pathway involved in the degradation of targeting peptides in mitochondria and chloroplasts, with two proteolytic components: the presequence protease (PreP) and the organellar oligopeptidase (OOP). PreP and OOP are specialized in degrading peptides of different lengths, with the substrate restriction being dictated by the structure of their proteolytic cavities. The importance of the intraorganellar peptide degradation is highlighted by the fact that elimination of both oligopeptidases affects growth and development of Arabidopsis thaliana.

Protein import into plant mitochondria: signals, machinery, processing, and regulation

The majority of more than 1000 proteins present in mitochondria are imported from nuclear-encoded, cytosolically synthesized precursor proteins. This impressive feat of transport and sorting is achieved by the combined action of targeting signals on mitochondrial proteins and the mitochondrial protein import apparatus. The mitochondrial protein import apparatus is composed of a number of multi-subunit protein complexes that recognize, translocate, and assemble mitochondrial proteins into functional complexes. While the core subunits involved in mitochondrial protein import are well conserved across wide phylogenetic gaps, the accessory subunits of these complexes differ in identity and/or function when plants are compared with Saccharomyces cerevisiae (yeast), the model system for mitochondrial protein import. These differences include distinct protein import receptors in plants, different mechanistic operation of the intermembrane protein import system, the location and activity of peptidases, the function of inner-membrane translocases in linking the outer and inner membrane, and the association/regulation of mitochondrial protein import complexes with components of the respiratory chain. Additionally, plant mitochondria share proteins with plastids, i.e. dual-targeted proteins. Also, the developmental and cell-specific nature of mitochondrial biogenesis is an aspect not observed in single-celled systems that is readily apparent in studies in plants. This means that plants provide a valuable model system to study the various regulatory processes associated with protein import and mitochondrial biogenesis.

Respiratory electron transfer pathways in plant mitochondria

The respiratory electron transport chain (ETC) couples electron transfer from organic substrates onto molecular oxygen with proton translocation across the inner mitochondrial membrane. The resulting proton gradient is used by the ATP synthase complex for ATP formation. In plants, the ETC is especially intricate. Besides the "classical" oxidoreductase complexes (complex I-IV) and the mobile electron transporters cytochrome c and ubiquinone, it comprises numerous "alternative oxidoreductases." Furthermore, several dehydrogenases localized in the mitochondrial matrix and the mitochondrial intermembrane space directly or indirectly provide electrons for the ETC. Entry of electrons into the system occurs via numerous pathways which are dynamically regulated in response to the metabolic state of a plant cell as well as environmental factors. This mini review aims to summarize recent findings on respiratory electron transfer pathways in plants and on the involved components and supramolecular assemblies.

Evidence for interactions between the mitochondrial import apparatus and respiratory chain complexes via Tim21-like proteins in Arabidopsis

The mitochondrial import machinery and the respiratory chain complexes of the inner membrane are highly interdependent for the efficient import and assembly of nuclear encoded respiratory chain components and for the generation of a proton motive force essential for protein translocation into or across the inner membrane. In plant and non-plant systems functional, physical, and evolutionary associations have been observed between proteins of the respiratory chain and protein import apparatus. Here we identify two novel Tim21-like proteins encoded by At2g40800 and At3g56430 that are imported into the mitochondrial inner membrane. We propose that Tim21-like proteins may associate with respiratory chain Complex I, III, in addition to the TIM17:23 translocase of the inner membrane. These results are discussed further with regards to the regulation of mitochondrial activity and biogenesis.

Import determinants of organelle-specific and dual targeting peptides of mitochondria and chloroplasts in Arabidopsis thaliana

Most of the mitochondrial and chloroplastic proteins are synthesized in the cytosol as precursor proteins carrying an N-terminal targeting peptide (TP) directing them specifically to a correct organelle. However, there is a group of proteins that are dually targeted to mitochondria and chloroplasts using an ambiguous N-terminal dual targeting peptide (dTP). Here, we have investigated pattern properties of import determinants of organelle-specific TPs and dTPs combining mathematical multivariate data analysis (MVDA) with in vitro organellar import studies. We have used large datasets of mitochondrial and chloroplastic proteins found in organellar proteomes as well as manually selected data sets of experimentally confirmed organelle-specific TPs and dTPs from Arabidopsis thaliana. Two classes of organelle-specific TPs could be distinguished by MVDA and potential patterns or periodicity in the amino acid sequence contributing to the separation were revealed. dTPs were found to have intermediate sequence features between the organelle-specific TPs. Interestingly, introducing positively charged residues to the dTPs showed clustering towards the mitochondrial TPs in silico and resulted in inhibition of chloroplast, but not mitochondrial import in in vitro organellar import studies. These findings suggest that positive charges in the N-terminal region of TPs may function as an 'avoidance signal' for the chloroplast import.

Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function

The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.

A molecular link between mitochondrial preprotein transporters and respiratory chain complexes

The TIM17:23 complex on the mitochondrial inner membrane is responsible for import of the majority of mitochondrial proteins in plants. In Arabidopsis, Tim17 and Tim23 belong to a large gene family consisting of 16 members termed the Preprotein and Amino acid transporters (PRAT). Recently, two members of this protein family, Tim23-2 and the Complex I subunit B14.7, have been shown to assemble into both Complex I of the respiratory chain and the TIM17:23 complex (Wang et al., 2012), adding to other examples of links between respiratory and protein import complexes. These associations provide a mechanism to coordinate mitochondrial activity and biogenesis.

A novel mitochondrial and chloroplast peptidasome, PreP

A novel mitochondrial and chloroplast peptidasome, the Presequence Protease (PreP) degrades organellar targeting peptides as well as other unstructured peptides up to 65 amino acid residues in length. PreP belongs to the pitrilysin oligopeptidase family (M16C) containing an inverted zinc-binding motif. The crystal structure of Arabidopsis thaliana PreP, AtPreP, refined at 2.1 Å, revealed a novel mechanism of proteolysis in which two halves of the enzyme connected by a hinge region enclose a large catalytic chamber opening and closing in response to peptide binding. Double knock-out mutant of AtPreP1 and AtPreP2 results in a severe phenotype, including decreased size and growth rate, chlorosis and organellar abnormalities, such as altered chloroplast starch content, partial loss of the integrity of the inner mitochondrial membrane and reduced mitochondrial respiration. PreP homologues are also present in yeast and humans. Interestingly, human PreP has been associated with Alzheimer's disease as it is responsible for degradation of amyloid-β peptide in brain mitochondria.

Processing peptidases in mitochondria and chloroplasts

Most of the mitochondrial and chloroplastic proteins are nuclear encoded and synthesized in the cytosol as precursor proteins with N-terminal extensions called targeting peptides. Targeting peptides function as organellar import signals, they are recognized by the import receptors and route precursors through the protein translocons across the organellar membranes. After the fulfilled function, targeting peptides are proteolytically cleaved off inside the organelles by different processing peptidases. The processing of mitochondrial precursors is catalyzed in the matrix by the Mitochondrial Processing Peptidase, MPP, the Mitochondrial Intermediate Peptidase, MIP (recently called Octapeptidyl aminopeptidase 1, Oct1) and the Intermediate cleaving peptidase of 55kDa, Icp55. Furthermore, different inner membrane peptidases (Inner Membrane Proteases, IMPs, Atp23, rhomboids and AAA proteases) catalyze additional processing functions, resulting in intra-mitochondrial sorting of proteins, the targeting to the intermembrane space or in the assembly of proteins into inner membrane complexes. Chloroplast targeting peptides are cleaved off in the stroma by the Stromal Processing Peptidase, SPP. If the protein is further translocated to the thylakoid lumen, an additional thylakoid-transfer sequence is removed by the Thylakoidal Processing Peptidase, TPP. Proper function of the D1 protein of Photosystem II reaction center requires its C-terminal processing by Carboxy-terminal processing protease, CtpA. Both in mitochondria and in chloroplasts, the cleaved targeting peptides are finally degraded by the Presequence Protease, PreP. The organellar proteases involved in precursor processing and targeting peptide degradation constitute themselves a quality control system ensuring the correct maturation and localization of proteins as well as assembly of protein complexes, contributing to sustenance of organelle functions. Dysfunctions of several mitochondrial processing proteases have been shown to be associated with human diseases. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Unique components of the plant mitochondrial protein import apparatus

The basic mitochondrial protein import apparatus was established in the earliest eukaryotes. Over the subsequent course of evolution and the divergence of the plant, animal and fungal lineages, this basic import apparatus has been modified and expanded in order to meet the specific needs of protein import in each kingdom. In the plant kingdom, the arrival of the plastid complicated the process of protein trafficking and is thought to have given rise to the evolution of a number of unique components that allow specific and efficient targeting of mitochondrial proteins from their site of synthesis in the cytosol, to their final location in the organelle. This includes the evolution of two unique outer membrane import receptors, plant Translocase of outer membrane 20 kDa subunit (TOM20) and Outer membrane protein of 64 kDa (OM64), the loss of a receptor domain from an ancestral import component, Translocase of outer membrane 22 kDa subunit (TOM22), evolution of unique features in the disulfide relay system of the inter membrane space, and the addition of an extra membrane spanning domain to another ancestral component of the inner membrane, Translocase of inner membrane 17 kDa subunit (TIM17). Notably, many of these components are encoded by multi-gene families and exhibit differential sub-cellular localisation and functional specialisation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Deletion of an organellar peptidasome PreP affects early development in Arabidopsis thaliana

A novel peptidasome PreP is responsible for degradation of targeting peptides and other unstructured peptides in mitochondria and chloroplasts. Arabidopsis thaliana contains two PreP isoforms, AtPreP1, and AtPreP2. Here we have characterized single and double prep knockout mutants. Immunoblot analysis of atprep1 and atprep2 mutants showed that both isoforms are expressed in all tissues with the highest expression in flowers and siliques; additionally, AtPreP1 accumulated to a much higher level in comparison to AtPreP2. The atprep2 mutant behaved like wild type, whereas deletion of AtPreP1 resulted in slightly pale-green seedlings. Analysis of the atprep1 atprep2 double mutant revealed a chlorotic phenotype in true leaves with diminished chlorophyll a and b content, but unchanged Chl a/b ratio indicating a proportional decrease of both PSI and PSII complexes. Mitochondrial respiratory rates (state 3) were lower and the mitochondria were partially uncoupled. EM pictures on cross sections of the first true leaves showed aberrant chloroplasts, including less grana stacking and less starch granules. Mitochondria with extremely variable size could also be observed. At later developmental stages the plants appeared almost normal. However, all through the development there was a statistically significant decrease of approximately 40% in the accumulated biomass in the double mutant plants in comparison to wild type. In mitochondria, deletion of AtPreP was not compensated by activation of any peptidolytic activity, whereas chloroplast membranes contained a minor peptidolytic activity not related to AtPreP. In summary, the AtPreP peptidasome is required for efficient plant growth and organelle function particularly during early development.

Building the Powerhouse: What are the Signals Involved in Plant Mitochondrial Biogenesis?

With a central role in respiration and ATP production, regulation of mitochondrial form and function is essential for cell and organism survival. Our understanding of the molecular mechanisms and signaling events underlying plant mitochondrial biogenesis is limited. In a recent paper published in the Journal of Biological Chemistry we have demonstrated aspects of mitochondrial biogenesis that are dependent on an oxygen signal in the monocot model, rice. Specifically, we identified (1) a set of genes encoding mitochondrial components that are responsive to oxygen levels and (2) that a lack of oxygen represses the normal increase in the mitochondrial protein import capacity during germination, and that these changes culminate in a modified mitochondrial proteome and altered respiratory activity. These findings can be combined with an earlier study, which gave insights into the characteristics of promitochondrial structures found in dry seeds and how they change during the germination process. Together they provide evidence for regulation of mitochondrial biogenesis by developmental and environmental cues and transcriptional and post-transcriptional events. This information can be used to build a model of plant mitochondrial biogenesis within the context of seed germination and oxygen availability.

Oxygen initiation of respiration and mitochondrial biogenesis in rice

Rice growth under aerobic and anaerobic conditions allowed aspects of mitochondrial biogenesis to be identified as dependent on or independent of an oxygen signal. Analysis of transcripts encoding mitochondrial components found that a subset of these genes respond to oxygen (defined as aerobic), whereas others are relatively unaffected by oxygen availability. Mitochondria formed during growth in anaerobic conditions had reduced protein levels of tricarboxylic acid cycle components and cytochrome-containing complexes of the respiratory chain and repressed respiratory functionality. In general, the capacity of the general import pathway was found to be significantly lower in mitochondria isolated from tissue grown under anaerobic conditions, whereas the carrier import pathway capacity was not affected by changes in oxygen availability. Transcript levels of genes encoding components of the protein import apparatus were generally not affected by the absence of oxygen, and their protein abundance was severalfold higher in mitochondria isolated from anaerobically grown tissue. However, both transcript and protein abundances of the subunits of the mitochondrial processing peptidase, which in plants is integrated into the cytochrome bc(1) complex, were repressed under anaerobic conditions. Therefore, in this system, an increase in import capacity is correlated with an increase in the abundance of the cytochrome bc(1) complex, which is ultimately dependent on the presence of oxygen, providing a link between the respiratory chain and protein import apparatus.

Mitochondrial signal peptidases of yeast: the rhomboid peptidase Pcp1 and its substrate cytochrome C peroxidase

The rhomboid peptidase Pcp1 of yeast is the first mitochondrial enzyme of this new class of serine peptidases. Pcp1 is an integral part of the inner membrane and was identified by its signal peptidase activity responsible for processing of the intermediate of cytochrome c peroxidase (iCcp1) to the mature enzyme. Here we describe studies on the expression of the PCP1 gene. Proteolytic processing of Pcp1 itself was found. The precursor and the intermediate of Ccp1 were localized to the inner membrane. The results confirm our previous report on a two-step processing pathway of cytochrome c peroxidase and the identification of the signal peptidases involved.

Protein import into mitochondria: origins and functions today (review)

Mitochondria are organelles derived from alpha-proteobacteria over the course of one to two billion years. Mitochondria from the major eukaryotic lineages display some variation in functions and coding capacity but sequence analysis demonstrates them to be derived from a single common ancestral endosymbiont. The loss of assorted functions, the transfer of genes to the nucleus, and the acquisition of various 'eukaryotic' proteins have resulted in an organelle that contains approximately 1000 different proteins, with most of these proteins imported into the organelle across one or two membranes. A single translocase in the outer membrane and two translocases in the inner membrane mediate protein import. Comparative sequence analysis and functional complementation experiments suggest some components of the import pathways to be directly derived from the eubacterial endosymbiont's own proteins, and some to have arisen 'de novo' at the earliest stages of 'mitochondrification' of the endosymbiont. A third class of components appears lineage-specific, suggesting they were incorporated into the process of protein import long after mitochondria was established as an organelle and after the divergence of the various eukaryotic lineages. Protein sorting pathways inherited from the endosymbiont have been co-opted and play roles in intraorganelle protein sorting after import. The import apparatus of animals and fungi show significant similarity to one another, but vary considerably to the plant apparatus. Increasing complexity in the eukaryotic lineage, i.e., from single celled to multi-cellular life forms, has been accompanied by an expansion in genes encoding each component, resulting in small gene families encoding many components. The functional differences in these gene families remain to be elucidated, but point to a mosaic import apparatus that can be regulated by a variety of signals.

The N-terminal extension of plant mitochondrial carrier proteins is removed by two-step processing: the first cleavage is by the mitochondrial processing peptidase

In contrast to yeast, many plants encode mitochondrial inner membrane carrier proteins with an N-terminal extension that is removed upon organelle import. Investigations using yeast and plant mitochondria models and purified general mitochondrial processing peptidase (MPP) indicate that the extension was removed in a two-step process. The first processing was carried out by MPP, while the second processing most probably occurs in the inter-membrane space by an as yet undefined peptidase, putatively a serine protease. Purified MPP from potato processed two carrier proteins to an intermediate size, this processing was sensitive to an MPP inhibitor (1,10-phenanthroline) and further, processing could be inhibited by changing arginine residues to glycine residues at a -3 arginine consensus processing site for MPP. Interestingly, yeast mitochondria only processed plant mitochondrial carrier proteins to the same intermediate size as purified plant MPP, and this intermediary processing did not occur in a temperature sensitive yeast mutant for MPP at the restrictive temperature. Incubation of carrier proteins with intact or lysed plant mitochondria under conditions designed to slow down the rate of import revealed that the MPP processed intermediate could be observed and chased to the mature form. The second processing step is inhibited by Pefabloc, suggesting it is carried out by a serine protease. A model for the processing of the N-terminal extension of plant mitochondrial carrier proteins is presented.

Redox-induced transitions in bovine cytochrome bc1 complex studied by perfusion-induced ATR-FTIR spectroscopy

Redox transitions in a film of detergent-purified bovine cytochrome bc(1) complex were investigated by perfusion-induced attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. The technique provides a flexible method for generating redox-induced IR changes of components of bovine cytochrome bc(1) complex at a high signal:noise ratio. These IR redox difference spectra arise from perturbations of prosthetic groups and surrounding protein. Visible difference spectra were recorded synchronously using a light beam reflected from the exposed prism surface and provided a quantitative means of determining the redox transitions that were occurring. IR and visible redox difference spectra of iron-sulfur protein/cytochrome c(1), heme b(H), and heme b(L) were separated by selective reduction and/or oxidation that extends published data on the homologous bacterial enzyme. Several bands could be tentatively assigned to redox-sensitive modes of hemes and ubiquinone and changes in the surrounding protein by comparison with available data for bacterial bc(1) complex, other related heme proteins, and model compounds. Some tentative assignments of further signals to specific amino acids are made on the basis of known crystal structures.

Determination of the cleavage site of the presequence by mitochondrial processing peptidase on the substrate binding scaffold and the multiple subsites inside a molecular cavity

Mitochondrial processing peptidase (MPP) recognizes a large variety of basic presequences of mitochondrial preproteins and cleaves the single site, often including arginine, at the -2 position (P(2)). To elucidate the recognition and specific processing of the preproteins by MPP, we mutated to alanines at acidic residues conserved in a large internal cavity formed by the MPP subunits, alpha-MPP and beta-MPP, and analyzed the processing efficiencies for various preproteins. We report here that alanine mutations at a subsite in rat beta-MPP interacting with the P(2) arginine cause a shift in the processing site to the C-terminal side of the preprotein. Because of reduced interactions with the P(2) arginine, the mutated enzymes recognize not only the N-terminal authentic cleavage site with P(2) arginine but also the potential C-terminal cleavage site without a P(2) arginine. In fact, it competitively cleaves the two sites of the preprotein. Moreover, the acidified site of alpha-MPP, which binds to the distal basic site in the long presequence, recognized the authentic P(2) arginine as the distal site in compensation for ionic interaction at the proximal site in the mutant MPP. Thus, MPP seems to scan the presequence from beta- to alpha-MPP on the substrate binding scaffold inside the MPP cavity and finds the distal and P(2) arginines on the multiple subsites on both MPP subunits. A possible mechanism for substrate recognition and cleavage is discussed here based on the notable character of a subsite-deficient mutant of MPP in which the substrate specificity is altered.

Glu(191) and Asp(195) in rat mitochondrial processing peptidase beta subunit are involved in effective cleavage of precursor protein through interaction with the proximal arginine

Mitochondrial processing peptidase (MPP), consisting of alpha and beta subunits, recognizes a large variety of N-terminal extension peptides of mitochondrial precursor proteins, and generally cleaves a single site of the peptide including arginine at the -2 position (P(2)). We obtained evidence that Glu(191) and Asp(195) of rat beta subunit interact with P(2) arginine of precursor protein through ionic and hydrogen bonds, respectively, using recombinant MPP. Mutation to alanines at Glu(191) and Asp(195) reduced processing activity toward precursors with P(2) arginine, but resulted in no loss of activity toward P(2) alanine precursors. Charge-complementary mutation demonstrated that MPP variants with beta Arg(191) exhibited compensatory processing activity for the precursor with acidic residue at the P(2) position. Thus, Glu(191) and Asp(195) are substrate-binding sites required for cleavage of extension peptides through interaction with P(2) arginine.

Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex

The chicken mitochondrial ubiquinol cytochrome c oxidoreductase (bc(1) complex) is inhibited by Zn(2+) ions, but with higher K(i) ( approximately 3 microM) than the corresponding bovine enzyme. When equilibrated with mother liquor containing 200 microM ZnCl(2) for 7 days, the crystalline chicken bc(1) complex specifically binds Zn(2+) at 4 sites representing two sites on each monomer in the dimer. These two sites are close to the stigmatellin-binding site, taken to be center Q(o) of the Q-cycle mechanism, and are candidates for the inhibitory site. One binding site is actually in the hydrophobic channel between the Q(o) site and the bulk lipid phase, and may interfere with quinone binding. The other is in a hydrophilic area between cytochromes b and c(1), and might interfere with the egress of protons from the Q(o) site to the intermembrane aqueous medium. No zinc was bound near the putative proteolytic active site of subunits 1 and 2 (homologous to mitochondrial processing peptidase) under these conditions.

Characterization and submitochondrial localization of the alpha subunit of the mitochondrial processing peptidase from the aquatic fungus Blastocladiella emersonii

In an effort to investigate the molecular mechanisms responsible for the drastic morphological changes the mitochondria go through during the life cycle of the aquatic fungus Blastocladiella emersonii, the gene encoding the alpha subunit of the mitochondrial processing peptidase (alpha-MPP) was isolated. Nucleotide sequence analysis revealed that the predicted alpha-MPP polypeptide comprises 474 amino acids with a calculated molecular mass of 51,900 Da, presenting a characteristic mitochondrial signal sequence. Northern blot analysis indicated a single 1.4-kb transcript encoding the B. emersonii alpha-MPP, whose levels decrease during sporulation, becoming very low in the zoospore, and increase again during germination. Despite these variations in mRNA concentration, B. emersonii alpha-MPP protein levels do not change significantly during the life cycle of the fungus, as observed in Western blots. Experiments to investigate the submitochondrial localization of B. emersonii alpha-MPP and beta-MPP were also carried out, and the results indicated that both subunits are associated with the mitochondrial inner membrane, possibly as part of the bc1 complex, as described for plants.

Signals required for the import and processing of the alternative oxidase into mitochondria

The critical residues involved in targeting and processing of the soybean alternative oxidase to plant and animal mitochondria was investigated. Import of various site-directed mutants into soybean mitochondria indicated that positive residues throughout the length of the presequence were important for import, not just those in the predicted region of amphiphilicity. The position of the positive residues in the C-terminal end of the presequence was also important for import. Processing assays of the various constructs with purified spinach mitochondrial processing peptidase showed that all the -2-position mutants had a drastic effect on processing. In contrast to the import assay, the position of the positive residue could be changed for processing. Deletion mutants confirmed the site-directed mutagenesis data in that an amphiphilic alpha-helix was not the only determinant of mitochondrial import in this homologous plant system. Import of these constructs into rat liver mitochondria indicated that the degree of inhibition differed and that the predicted region of amphiphilic alpha-helix was more important with rat liver mitochondria. Processing with a rat liver matrix fraction showed little inhibition. These results are discussed with respect to targeting specificity in plant cells and highlight the need to carry out homologous studies and define the targeting requirements to plant mitochondria.

Isolation of an Arabidopsis thaliana cDNA by complementation of a yeast abc1 deletion mutant deficient in complex III respiratory activity

The yeast Abc1 protein acts as a chaperone-like protein essential for the proper conformation and efficient functioning of the respiratory complex III. By functional complementation of a yeast abc1 mutant, we have identified an Arabidopsis thaliana cDNA that corresponds to a single copy gene and encodes a protein sharing 45% similarity with the yeast Abc1p protein. Cytochrome spectra and respiratory activity measurements have shown that the plant protein allows a partial restoration of the complex III activity. No major difference in the steady-state level of ABC1At mRNA was observed in various plant tissues, suggesting that ABC1At is constitutively expressed in A. thaliana. Phylogenetic analysis revealed that the Abc1At protein belongs to a large family of proteins composed of two eukaryotic and one prokaryotic subgroups differing by their degree of similarity and probably by their function.

Activation of a matrix processing peptidase from the crystalline cytochrome bc1 complex of bovine heart mitochondria

No mitochondrial processing peptidase (MPP) activity is detected in crystalline bovine heart mitochondrial cytochrome bc1 complex, which possesses full electron transfer activity. However, when the complex is treated with increasing concentrations of Triton X-100 at 37 degreesC, the electron transfer activity decreases, whereas peptidase activity increases. Maximum MPP activity is obtained when the electron transfer activity in the complex is completely inactivated with 1.5 mM of Triton X-100. This result supports our suggestion that the lack of MPP activity in the mammalian cytochrome bc1 complex is because of binding of an inhibitor polypeptide to the active site of MPP located at the interface of core subunits I and II. This suggestion is based on the three-dimensional structural information for the bc1 complex and the sequence homology between subunits of MPP and the core subunits of the beef complex. Triton X-100, at concentrations that disrupt the structural integrity of the bc1 complex as indicated by the loss of its electron transfer activity, weakens the binding of inhibitor polypeptide to the active site of MPP in core subunits, thus activating MPP. The Triton X-100-activated MPP is pH-, buffer system-, ionic strength-, and temperature-dependent. Maximum activity is observed with an assay mixture containing 15 mM Tris-HCl buffer at neutral pH (6.5-8.5) and at 37 degreesC. Activated MPP is completely inhibited by metal ion chelators such as EDTA and o-phenanthroline and partially inhibited by myxothiazol (58%), ferricyanide (28%), and dithiothreitol (81%). The metal ion chelator-inhibited activity can be partially restored by the addition of divalent cations such as Zn2+ (68%), Mg2+ (44%), Mn2+ (54%), Co2+ (62%), and Fe2+ (92%), indicating that metal ion is required for MPP activity. The cleavage site specificity of activated MPP depends more on the length of amino acid sequence from the mature protein portion and less on the presequence portion, when a synthetic peptide composed of NH2-terminal residues of a mature protein and the COOH-terminal residues of its presequence is used as a substrate.

Temporal regulation of in vitro import of precursor proteins into tobacco mitochondria

Protein import into isolated tobacco mitochondria was investigated using mitochondria from leaves harvested at different times of the day and night. Efficient import was only detected with mitochondria isolated from leaves harvested during the dark period of the growth cycle, only low levels of import were detected from leaves harvested during the light period. However, this temporal difference seen in import did not appear to be circadian in nature. This implies that the protein import process in mitochondria isolated from leaves is not constitutive. This has important implications for targeting specificity studies performed in transgenic plants, as unless the plants are tested at the time when import is occurring, the true in vivo targeting abilities of chimeric constructs will not be measured.

Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria

On the basis of x-ray diffraction data to a resolution of 2.9 angstroms, atomic models of most protein components of the bovine cytochrome bc1 complex were built, including core 1, core 2, cytochrome b, subunit 6, subunit 7, a carboxyl-terminal fragment of cytochrome c1, and an amino-terminal fragment of the iron-sulfur protein. The positions of the four iron centers within the bc1 complex and the binding sites of the two specific respiratory inhibitors antimycin A and myxothiazol were identified. The membrane-spanning region of each bc1 complex monomer consists of 13 transmembrane helices, eight of which belong to cytochrome b. Closely interacting monomers are arranged as symmetric dimers and form cavities through which the inhibitor binding pockets can be accessed. The proteins core 1 and core 2 are structurally similar to each other and consist of two domains of roughly equal size and identical folding topology.

A point mutation in the mitochondrial cytochrome b gene obviates the requirement for the nuclear encoded core protein 2 subunit in the cytochrome bc1 complex in Saccharomyces cerevisiae

A yeast mutant (cor2-45) in which approximately half of the C terminus of core protein 2 of the cytochrome bc1 complex is lacking due to a frameshift mutation that introduces a stop at codon 197 in the COR2 gene fails to assemble the cytochrome bc1 complex and does not grow on non-fermentable carbon sources that require respiration. The loss of respiration is more severe with this frameshift mutation than with the complete deletion of the COR2 gene, suggesting deleterious effects of the truncated core 2 protein. A search for extragenic suppressors of the nuclear cor2-45 mutation resulted (in addition to the expected nuclear suppressors) in the isolation of a suppressor mutation in the mitochondrial DNA that replaces serine 223 by proline in cytochrome b. Assembly of the cytochrome bc1 complex and the respiratory deficient phenotype of the cor2-45 mutant are restored by the proline for serine replacement in cytochrome b. Surprisingly, this amino acid replacement in cytochrome b corrects not only the phenotype resulting from the cor2-45 frameshift mutation, but it also obviates the need for core protein 2 in the cytochrome bc1 complex since it alleviates the respiratory deficiency resulting from the complete deletion of the COR2 gene. This is the first report of a homoplasmic missense point mutation of the mitochondrial DNA acting as a functional suppressor of a mutation located in a nuclear gene and the first demonstration that the supernumerary core protein 2 subunit is not essential for the electron transfer and energy transducing functions of the mitochondrial cytochrome bc1 complex.

Protein import into mitochondria

Mitochondria import many hundreds of different proteins that are encoded by nuclear genes. These proteins are targeted to the mitochondria, translocated through the mitochondrial membranes, and sorted to the different mitochondrial subcompartments. Separate translocases in the mitochondrial outer membrane (TOM complex) and in the inner membrane (TIM complex) facilitate recognition of preproteins and transport across the two membranes. Factors in the cytosol assist in targeting of preproteins. Protein components in the matrix partake in energetically driving translocation in a reaction that depends on the membrane potential and matrix-ATP. Molecular chaperones in the matrix exert multiple functions in translocation, sorting, folding, and assembly of newly imported proteins.

Studies on protein processing for membrane-bound spinach leaf mitochondrial processing peptidase integrated into the cytochrome bc1 complex and the soluble rat liver matrix mitochondrial processing peptidase

The plant mitochondrial processing peptidase (MPP) that catalyses the cleavage of the presequences from precursor proteins during or after protein import is a membrane-bound enzyme that constitutes an integral part of the bc1 complex of the respiratory chain. In contrast, MPP from mammals is soluble in the matrix space and does not form part of the respiratory chain. In the present study, we have compared the substrate specificity of the isolated spinach leaf bc1/MPP with rat liver MPP using synthetic signal peptides and different mitochondrial precursor proteins. Inhibition studies of processing with synthetic peptides showed a similar inhibition pattern for plant and rat MPP activity. A peptide derived from the presequence of rat liver mitochondrial aldehyde dehydrogenase (ALDH) was a potent inhibitor of the spinach and rat MPP. Two nonprocessed signal peptides, rhodanese and linker-deleted ALDH (a form of ALDH that lacks the RGP linker connecting two helices in the presequence) had lower inhibitory effects towards each protease. The signal peptide from thiolase, another nonprocessed protein, had little inhibitory effect on MPP. Peptides derived from presequence of the plant Nicotiana plumbaginifolia F1 beta also showed a similar inhibitory pattern with rat MPP as with spinach MPP processing. In-vitro synthesised precursors of plant N. plumbaginifolia F1 beta and rat liver ALDH were cleaved to mature form by both spinach and rat MPP. However, the efficiency of processing was higher with the homologous precursor. Linker-deleted ALDH, rhodanese, and thiolase were not processed by the mammalian or plant MPP. However, both forms of MPP cleaved a mutated form of rhodanese that possesses a typical MPP cleavage motif, RXY S. Addition of the same cleavage motif to thiolase did not result in processing by either MPP. These results show that similar higher-order structural elements upstream from the cleavage site are important for processing by both the membrane-bound plant and the soluble mammalian MPP.

Evidence for a link between translocation and processing during protein import into soybean mitochondria

The effect of metal chelators on protein import was investigated using isolated soybean mitochondria and soybean precursor proteins. Adding 1,10-phenanthroline, a metal chelator that can cross both mitochondrial membranes abolished import of both the alternative oxidase, and the F(A)d subunit of the ATP synthase, a matrix located protein. Other metal chelators such as EDTA, 1,7-phenanthroline and 4,7-phenanthroline, which cannot cross the mitochondrial membranes, had no effect on import. When processing, a known metal-dependent step inside mitochondria, was inhibited using a mutagenesis approach (changing a -2 arginine to a -2 glycine in the pre-piece of the precursor), so was import. Thus it would appear that in soybean, at least, translocation of proteins across the mitochondrial membrane, as well as processing, relies on a metal dependent step. Taken together, the data suggest the two processes may be directly connected in these mitochondria.

Characterization of the bifunctional mitochondrial processing peptidase (MPP)/bc1 complex in Spinacia oleracea

The mitochondrial general processing peptidase (MPP) in plant mitochondria constitutes an integral part of the cytochrome bc1 complex of the respiratory chain. Here we present a characterization of this bifunctional complex from spinach leaf mitochondria. The purified MPP/bc1 complex has a molecular mass of 550 kDa, which corresponds to a dimer. Increased ionic strength results in partial dissociation of the dimer as well as loss of the processing activity. Micellar concentrations of nonionic and zwitterionic detergents stimulate the activity by decreasing the temperature optimum of the processing reaction, whereas anionic detergents totally suppress the activity. MPP is a metalloendopeptidase. Interestingly, hemin, a potent regulator of mitochondrial and cytosolic biogenesis and inhibitor of proteosomal degradation, inhibits the processing activity. Measurements of the processing activity at different redox states of the bc1 complex show that despite bifunctionality of the MPP/bc1 complex, there is no correlation between electron transfer and protein processing.

Conversion of a nonprocessed mitochondrial precursor protein into one that is processed by the mitochondrial processing peptidase

Mitochondrial processing peptidase (MPP) cleaves the signal sequence from a variety of mitochondrial precursor proteins. A subset of mitochondrial proteins, including rhodanese and 3-oxoacyl-CoA thiolase, are imported into the matrix space, yet are not processed. Rhodanese signal peptide and translated protein were recognized by MPP, as both were inhibitors of processing. The signal peptide of precursor aldehyde dehydrogenase consists of a helix-linker-helix motif but when the RGP linker is removed, processing no longer occurs (Thornton, K., Wang, Y., Weiner, H., and Gorenstein, D. G. (1993) J. Biol. Chem. 268, 19906-19914). Disruption of the helical signal sequence of rhodanese by the addition of the RGP linker did not allow cleavage to occur. However, addition of a putative cleavage site allowed the protein to be processed. The same cleavage site was added to 3-oxoacyl-CoA thiolase, but this protein was still not processed. Thiolase and linker-deleted aldehyde dehydrogenase signal peptides were poor inhibitors of MPP. It can be concluded that both a processing site and the structure surrounding this site are important for MPP recognition.

The bifunctional cytochrome c reductase/processing peptidase complex from plant mitochondria

Cytochrome c reductase from potato has been extensively studied with respect to its catalytic activities, its subunit composition, and the biogenesis of individual subunits. Molecular characterization of all 10 subunits revealed that the high-molecular-weight subunits exhibit striking homologies with the components of the general mitochondrial processing peptidase (MPP) from fungi and mammals. Some of the other subunits show differences in the structure of their targeting signals or in their molecular composition when compared to their counterparts from heterotrophic organisms. The proteolytic activity of MPP was found in the cytochrome c reductase complexes from potato, spinach, and wheat, suggesting that the integration of the protease into this respiratory complex is a general feature of higher plants.