Analysis of Mitochondrial Membrane Protein Complexes by Electron Cryo-tomography.

Aqueous channels are at the core of the translocase of the outer membrane (TOM) and the translocase of the inner membrane for the transport of preproteins (TIM23), the translocases mediating the transport of proteins across the outer and inner mitochondrial membranes. Yet, the existence of a channel associated to the translocase of the inner membrane for the insertion of multitopic protein (TIM22) complex has been arguable, as its function relates to the insertion of multispanning proteins into the inner membrane. For the first time, we report conditions for detecting a channel activity associated to the TIM22 translocase in organelle, i.e. intact mitoplasts. An internal signal peptide in the intermembrane space of mitochondria is a requisite to inducing this channel, which is otherwise silent. The channel showed slightly cationic and high conductance activity of 1000 pS with a predominant half-open substate. Despite their different composition, the channels of the three mitochondrial translocases were thus remarkably similar, in agreement with their common task as pores transiently trapping proteins en route to their final destination. The opening of the TIM22 channel was a step-up process depending on the signal peptide concentration. Interestingly, low membrane potentials kept the channel fully open, providing a threshold level of the peptide is present. Our results portray TIM22 as a dynamic channel solely active in the presence of its cargo proteins. In its fully open conformation, favored by the combined action of internal signal peptide and low membrane potential, the channel could embrace the in-transit protein. As insertion progressed and initial interaction with the signal peptide faded, the channel would close, sustaining its role as a shunt that places trapped proteins into the membrane.

The TIM23 complex is the major translocase of the mitochondrial inner membrane responsible for the import of essentially all matrix proteins and a number of inner membrane proteins. Tim23 and Tim50, two essential proteins of the complex, expose conserved domains into the intermembrane space that interact with each other. Here, we describe in vitro reconstitution of this interaction using recombinantly expressed and purified intermembrane space domains of Tim50 and Tim23. We established two independent methods, chemical cross-linking and surface plasmon resonance, to track their interaction. In addition, we identified mutations in Tim23 that abolish its interaction with Tim50 in vitro. These mutations also destabilized the interaction between the two proteins in vivo, leading to defective import of preproteins via the TIM23 complex and to cell death at higher temperatures. This is the first study to describe the reconstitution of the Tim50-Tim23 interaction in vitro and to identify specific residues of Tim23 that are vital for the interaction with Tim50.

The mitochondrial inner membrane of most organisms studied so far contains about a dozen proteins made by the mitochondrial genetic system and on the order of 10 proteins imported from the cytoplasm. This review briefly describes the two major pathways by which proteins made inside or outside the mitochondria are inserted into the inner membrane. These pathways were discovered only during the past few years; one of them involves a novel family of chaperone-like proteins in the mitochondrial intermembrane space. Import of proteins from the cytoplasm into mitochondria occurs by distinct routes that are dictated by the properties and final destination of each protein within the mitochondria (1–3). However, most of the different routes described until recently have been variants of the general “matrix pathway.” In this pathway, a protein carrying a positively charged amphiphilic helix at its N terminus is bound by cytosolic chaperones, delivered to an array of import receptors on the mitochondrial surface, and then transported across two distinct, hetero-oligomeric protein translocation channels, the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. During transport, the two complexes are transiently linked by the translocating precursor chain (4, 5). Transport across the TOM complex appears to be driven by binding of the basic N-terminal “presequence” to a series of acidic receptor domains of increasing avidity (“acid chain hypothesis”) (6, 7); insertion of the presequence into the TIM23 complex is driven electrophoretically by the potential across the inner membrane; and complete transport of the precursor into the matrix is driven by an ATP-powered import motor attached to the inner mouth of the TIM23 complex. Proteins destined for compartments other than the matrix can diverge from the general matrix pathway at different points (8–10). Some proteins destined for the outer membrane can arrest in the TOM complex and then escape into the outer membrane (11); and some intermembrane space proteins can arrest in the TIM23 complex and then be proteolytically released into the intermembrane space (8). A few years ago it seemed likely that a variation of this general matrix pathway would also sort proteins to the inner membrane. According to this view, a protein destined for the inner membrane would arrest in the TIM23 complex and escape “sidewise” into the phospholipid bilayer of the inner membrane. So far, however, no inner membrane protein has been shown to follow such a pathway. Arrest in the TIM23 complex has only been found for some proteins destined for the intermembrane space.

Nearly all mitochondrial proteins need to be targeted for import from the cytosol. For the majority, the first port of call is the translocase of the outer membrane (TOM complex), followed by a procession of alternative molecular machines, conducting transport to their final destination. The pre-sequence translocase of the inner membrane (TIM23-complex) imports proteins with cleavable pre-sequences. Progress in understanding these transport mechanisms has been hampered by the poor sensitivity and time resolution of import assays. However, with the development of an assay based on split NanoLuc luciferase, we can now explore this process in greater detail. Here, we apply this new methodology to understand how ∆ψ and ATP hydrolysis, the two main driving forces for import into the matrix, contribute to the transport of pre-sequence-containing precursors (PCPs) with varying properties. Notably, we found that two major rate-limiting steps define PCP import time: passage of PCP across the outer membrane and initiation of inner membrane transport by the pre-sequence – the rates of which are influenced by PCP size and net charge. The apparent distinction between transport through the two membranes (passage through TOM is substantially complete before PCP-TIM engagement) is in contrast with the current view that import occurs through TOM and TIM in a single continuous step. Our results also indicate that PCPs spend very little time in the TIM23 channel – presumably rapid success or failure of import is critical for maintenance of mitochondrial fitness.

Most of the mitochondrial outer membrane (MOM) proteins contain helical transmembrane domains. Some of the single-span proteins and all known multiple-span proteins are inserted into the membrane in a pathway that depends on the MOM protein Mitochondrial Import 1 (Mim1). So far it has been unknown whether additional proteins are required for this process. Here, we describe the identification and characterization of Mim2, a novel protein of the MOM that has a crucial role in the biogenesis of MOM helical proteins. Mim2 physically and genetically interacts with Mim1, and both proteins form the MIM complex. Cells lacking Mim2 exhibit a severely reduced growth rate and lower steady-state levels of helical MOM proteins. In addition, absence of Mim2 leads to compromised assembly of the translocase of the outer mitochondrial membrane (TOM complex), hampered mitochondrial protein import, and defects in mitochondrial morphology. In summary, the current study demonstrates that Mim2 is a novel central player in the biogenesis of MOM proteins.

Dual Role of Mitochondrial Porin in Metabolite Transport across the Outer Membrane and Protein Transfer to the Inner Membrane

The mitochondrial membranes contain translocation machineries ("preprotein translocases") which facilitate transport of proteins from the cytosol into the mitochondria. The TOM complex is localized in the outer membrane. Two translocases have been characterized in the inner membrane: the Tim23-Tim17 complex and the Tim22 complex which differ in their specificities for preproteins. The TOM and TIM complexes can act in a coordinated fashion to facilitate the insertion of preproteins into the mitochondrial membranes as well as the translocation into the internal compartments, the intermembrane space and the matrix. We discuss insights into the function of components of the translocases, illustrated by examples for mechanisms of protein sorting into the different compartment of mitochondria.

The preprotein translocase of the outer mitochondrial membrane is a multi-subunit complex with receptors and a general import pore. We report the molecular identification of Tom7, a small subunit of the translocase that behaves as an integral membrane protein. The deletion of TOM7 inhibited the mitochondrial import of the outer membrane protein porin, whereas the import of preproteins destined for the mitochondrial interior was impaired only slightly. However, protein import into the mitochondrial interior was strongly inhibited when it occurred in two steps: preprotein accumulation at the outer membrane in the absence of a membrane potential and subsequent further import after the re-establishment of a membrane potential. The delay of protein import into tom7delta mitochondria seemed to occur after the binding of preproteins to the outer membrane receptor sites. A lack of Tom7 stabilized the interaction between the receptors Tom20 and Tom22 and the import pore component Tom40. This indicated that Tom7 exerts a destabilizing effect on part of the outer membrane translocase, whereas Tom6 stabilizes the interaction between the receptors and the import pore. Synthetic growth defects of the double mutants tom7delta tom20delta and tom7delta tom6delta provided genetic evidence for the functional relationship of Tom7 with Tom20 and Tom6. These results suggest that (i) Tom7 plays a role in sorting and accumulation of the preproteins at the outer membrane, and (ii) Tom7 and Tom6 perform complementary functions in modulating the dynamics of the outer membrane translocase.

The translocase of the outer membrane (TOM complex) is the central entry gate for nuclear-encoded mitochondrial precursor proteins. All Tom proteins are also encoded by nuclear genes and synthesized as precursors in the cytosol. The channel-forming beta-barrel protein Tom40 is targeted to mitochondria via Tom receptors and inserted into the outer membrane by the sorting and assembly machinery (SAM complex). A further outer membrane protein, Mim1, plays a less defined role in assembly of Tom40 into the TOM complex. The three receptors Tom20, Tom22, and Tom70 are anchored in the outer membrane by a single transmembrane alpha-helix, located at the N terminus in the case of Tom20 and Tom70 (signal-anchored) or in the C-terminal portion in the case of Tom22 (tail-anchored). Insertion of the precursor of Tom22 into the outer membrane requires pre-existing Tom receptors while the import pathway of the precursors of Tom20 and Tom70 is only poorly understood. We report that Mim1 is required for efficient membrane insertion and assembly of Tom20 and Tom70, but not Tom22. We show that Mim1 associates with SAM(core) components to a large SAM complex, explaining its role in late steps of the assembly pathway of Tom40. We conclude that Mim1 is not only required for biogenesis of the beta-barrel protein Tom40 but also for membrane insertion and assembly of signal-anchored Tom receptors. Thus, Mim1 plays an important role in the efficient assembly of the mitochondrial TOM complex.

Translocator protein (18 kDa, TSPO), previously known as the peripheral-type benzodiazepine receptor, is an outer mitochondrial membrane (OMM) protein necessary for cholesterol import and steroid production. We reconstituted the mitochondrial targeting and insertion of TSPO into the OMM to analyze the signals and mechanisms required for this process. Initial studies indicated the formation of a mitochondrial 66 kDa complex through Blue Native-PAGE analysis. The formation of this complex was found to be dependent on the presence of ATP and the cytosolic chaperone Hsp90. Through mutational analysis we identified two areas necessary for TSPO targeting, import, and function: amino acids 103-108 (Schellman motif), which provide the necessary structural orientation for import, and the cholesterol-binding C-terminus required for insertion. Although the translocase of the outer mitochondrial membrane (TOM) complex proteins Tom22 and Tom40 were present in the OMM, the TOM complex did not interact with TSPO. In search of proteins involved in TSPO import, we analyzed complexes known to interact with TSPO by mass spectrometry. Formation of the 66 kDa complex was found to be dependent on an identified protein, Metaxin 1, for formation and TSPO import. The level of import of TSPO into steroidogenic cell mitochondria was increased following treatment of the cells with cAMP. These findings suggest that the initial targeting of TSPO to mitochondria is dependent upon the presence of cytosolic chaperones interacting with the import receptor Tom70. The C-terminus plays an important role in targeting TSPO to mitochondria, whereas its import into the OMM is dependent upon the presence of the Schellman motif. Final integration of TSPO into the OMM occurs via its interaction with Metaxin 1. Import of TSPO into steroidogenic cell mitochondria is regulated by cAMP.

Mitochondria import most of their proteins from the cytosol. Dynamic protein complexes in the mitochondrial outer and inner membranes are responsible for the specific recognition and membrane translocation of preproteins. The preprotein translocase of the outer mitochondrial membrane contains several import receptors and a general import pore. The preprotein translocase of the inner membrane consists of a channel interacting with preproteins in transit and an import motor that includes the matrix heat shock protein Hsp70. Acidic patches of import components are thought to guide the import of positively charged signal sequences (acid chain hypothesis). Energy input is derived from the inner membrane potential and ATP. Proteins in the mitochondrial matrix are required for proteolytic processing and folding of imported proteins. The dynamic nature of the membrane translocase permits sorting of preproteins at distinct stages of the import pathway.

Mechanistic insights into fungal mitochondrial outer membrane protein biogenesis

Mitochondria have gained significant attention in disease models due to their crucial role in cellular energy production and metabolic activity. Understanding how mitochondria maintain their function and interact with other cellular components during stress is of great importance. Import translocases play a vital role in importing cytoplasmically synthesized mitochondrial proteins. Advancements in analytical techniques have provided insights into the independent translocases embedded in the mitochondrial membrane and their coordination in ensuring the proper assembly of nuclear-encoded proteins. While most translocases have been evolutionarily conserved with some modifications, the TIM22 complex in the inner mitochondrial membrane has shown diversification from yeast to humans. Recent identification of the peripheral subunits, TIM29 and AGK, in metazoans has shed light on their role in the TIM22 complex. AGK acts as both a complex subunit and a lipid kinase, contributing to the lipid composition of the inner mitochondrial membrane and facilitating carrier protein import through the TIM22 complex. TIM29 is known to stabilize the complex and interact with small TIM proteins, but further knowledge about the structure and function of the independent subunits is limited. To address this, we employed two tagging methods and conducted a large-scale proteomic analysis. By combining chemical crosslinking and mass spectrometric analysis (XL-MS), we identified the regions of interaction between the subunits, providing insights into their spatial orientation and the flexibility of the hexamer complex involved in substrate transport. Building on this understanding, our focus shifted to investigating the significance of the diversification of peripheral subunits. We performed siRNA-mediated knockdown of TIM23, TIM22, and TIM29 proteins and used TMT-based tagging and LC-MS/MS analysis to assess changes in the mitochondrial proteome. Surprisingly, we observed pronounced effects on TOM complex subunits following TIM29 knockdown. The TOM22 and TOM20 proteins showed significant depletion, while TOM40 displayed a lower complex of approximately 130 kDa alongside the final TOM complex. We confirmed that the TOM40 lower complex results from diminished TOM22 protein levels, ruling out the involvement of other complexes such as SAM and MICOS. The presence of a similar phenotype in TOM5 under TIM29 knockdown and defects in TOM40 biogenesis suggests that the observed lower complex represents an intermediate stage of TOM40 assembly after its release from SAM50. Our findings uncover a novel function of TIM29 in regulating TOM40 biogenesis. However, the precise mechanism through which TIM29 influences TOM22 abundance and the importance of the association between TOM40 and TIM29 during biogenesis remains unclear. Further investigation is needed to understand the essential role of TIM29 in the complex mitochondrial proteome of humans. To summarize, this thesis enhances our understanding of the intersubunit interactions within the TIM22 complex and reveals an additional novel function of TIM29 in maintaining the overall import function of mitochondria.

Regulating mitochondrial outer membrane proteins by ubiquitination and proteasomal degradation

The Mitochondrial Import Complex MIM Functions as Main Translocase for α-Helical Outer Membrane Proteins