The signal anchor sequence of mitochondrial Mas70p contains an oligomerization domain

The Mitochondrial Outer Membrane Protein Tom70-Mediator in Protein Traffic, Membrane Contact Sites and Innate Immunity

Tom70 is a versatile adaptor protein of 70 kDa anchored in the outer membrane of mitochondria in metazoa, fungi and amoeba. The tertiary structure was resolved for the Tom70 of yeast, showing 26 α-helices, most of them participating in the formation of 11 tetratricopeptide repeat (TPR) motifs. Tom70 serves as a docking site for cytosolic chaperone proteins and co-chaperones and is thereby involved in the uptake of newly synthesized chaperone-bound proteins in mitochondrial biogenesis. In yeast, Tom70 additionally mediates ER-mitochondria contacts via binding to sterol transporter Lam6/Ltc1. In mammalian cells, TOM70 promotes endoplasmic reticulum (ER) to mitochondria Ca2+ transfer by association with the inositol-1,4,5-triphosphate receptor type 3 (IP3R3). TOM70 is specifically targeted by the Bcl-2-related protein MCL-1 that acts as an anti-apoptotic protein in macrophages infected by intracellular pathogens, but also in many cancer cells. By participating in the recruitment of PINK1 and the E3 ubiquitin ligase Parkin, TOM70 can be implicated in the development of Parkinson's disease. TOM70 acts as receptor of the mitochondrial antiviral-signaling protein (MAVS) and thereby participates in the corresponding system of innate immunity against viral infections. The protein encoded by Orf9b in the genome of SARS-CoV-2 binds to TOM70, probably compromising the synthesis of type I interferons.

Rat Liver Carnitine Palmitoyltransferase 1 Forms an Oligomeric Complex within the Outer Mitochondrial Membrane

Carnitine palmitoyltransferase (CPT) 1A catalyzes the rate-limiting step in the transport of long chain acyl-CoAs from cytoplasm to the mitochondrial matrix by converting them to acylcarnitines. Located within the outer mitochondrial membrane, CPT1A activity is inhibited by malonyl-CoA, its allosteric inhibitor. In this study, we investigate for the first time the quaternary structure of rat CPT1A. Chemical cross-linking studies using intact mitochondria isolated from fed rat liver or from Saccharomyces cerevisiae expressing CPT1A show that CPT1A self-assembles into an oligomeric complex. Size exclusion chromatography experiments using solubilized mitochondrial extracts suggest that the fundamental unit of its quaternary structure is a trimer. When studied in blue native-PAGE, the CPT1A hexamer could be observed, however, suggesting that under these native conditions CPT1A trimers might be arranged as dimers. Moreover, the oligomeric state of CPT1A was found unchanged by starvation and by streptozotocin-induced diabetes, conditions characterized by changes in malonyl-CoA sensitivity of CPT1A. Finally, gel filtration analysis of several yeast-expressed chimeric CPTs demonstrates that the first 147 N-terminal residues of CPT1A, encompassing its two transmembrane segments, trigger trimerization independently of its catalytic C-terminal domain. Deletion of residues 1-82, including transmembrane 1, did not abrogate oligomerization, but the latter is limited to a trimer by the presence of the large catalytic C-terminal domain on the cytosolic face of mitochondria. Based on these findings, we proposed that the oligomeric structure of CPT1A would allow the newly formed acylcarnitines to gain direct access into the intermembrane space, hence facilitating substrate channeling.

Detecting protein-protein interaction in live yeast by flow cytometry

BACKGROUND

The yeast Saccharomyces cerevisiae is the most commonly used organism for studying protein- protein interactions. In this report we demonstrate the use of flow cytometry in observing fluorescence resonance energy transfer (FRET) between cyan and yellow fluorescent fusion proteins (CFP and YFP, respectively) as a marker for protein interaction in live yeast cells. Probability binning is also employed to provide a statistical confirmation of our observations.

METHODS

We coexpressed CFP and YFP fusions containing the N-terminal transmembrane domain (NTM) of Tom70p in yeast and analyzed FRET in live cells with a multilaser flow cytometer. The Tom70p NTM was previously shown to be sufficient for mitochondrial localization and protein-protein interaction (Millar and Shore, 1994, J Biol Chem 269:12229-12232).

RESULTS

FRET was observed only in cells that expressed CFP and YFP fusions that each contained the wild-type NTM. The introduction of mutations previously shown to disrupt NTM interaction eliminated FRET. Probability binning confirmed that differences between the FRET channels of experimental and control samples were statistically and physiologically significant.

CONCLUSION

Flow cytometric analysis of FRET in yeast is a powerful technique for studying protein-protein interactions. The use of flow cytometry allows FRET data to be gathered from a large number of individual cells, thus providing important advantages unavailable to other techniques. Its application to yeast presents a new method to a popular system widely used in proteomic studies.

A Biophysical Analysis of the Tetratricopeptide Repeat-rich Mitochondrial Import Receptor, Tom70, Reveals an Elongated Monomer That Is Inherently Flexible, Unstable, and Unfolds via a Multistate Pathway

Proteins destined for all submitochondrial compartments are translocated across the outer mitochondrial membrane by the TOM (translocase of the outer membrane) complex, which consists of a number of specialized receptor subunits that bind mitochondrial precursor proteins for delivery into the translocation channel. One receptor, Tom70, binds large, hydrophobic mitochondrial precursors. The current model of Tom70-mediated import involves multiple dimers of the receptor recognizing a single molecule of substrate. Here we show via a battery of biophysical and spectroscopic techniques that the cytosolic domain of Tom70 is an elongated monomer. Thermal and urea-induced denaturation revealed that the receptor, which unfolds via a multistate pathway, is a relatively unstable molecule undergoing major conformational change at physiological temperatures. The data suggest that the malleability of the monomeric Tom70 receptor is an important factor in mitochondrial import.

Syndapins integrate N-WASP in receptor-mediated endocytosis

Syndapins are potential links between the cortical actin cytoskeleton and endocytosis because this family of dynamin-associated proteins can also interact with the Arp2/3 complex activator N-WASP. Here we provide evidence for involvement of N-WASP interactions in receptor-mediated endocytosis. We reveal that the observed dominant-negative effects of N-WASP are dependent exclusively on the proline-rich domain, the binding interface of syndapins. Our results therefore suggest that syndapins integrate N-WASP functions in endocytosis. Both proteins co-localize in neuronal cells. Consistent with a crucial role for syndapins in endocytic uptake, co-overexpression of syndapins rescued the endocytosis block caused by N-WASP. An in vivo reconstitution of the syndapin-N-WASP interaction at cellular membranes triggered local actin polymerization. Depletion of endogenous N-WASP by sequestering it to mitochondria or by introducing anti-N-WASP antibodies impaired endocytosis. Our data suggest that syndapins may act as important coordinators of N-WASP and dynamin functions during the different steps of receptor-mediated endocytosis and that local actin polymerization induced by syndapin-N-WASP interactions may be a mechanism supporting clathrin-coated vesicle detachment and movement away from the plasma membrane.

Biogenesis of the mitochondrial TOM complex

The translocase at the outer membrane of mitochondria (TOM complex) mediates the initial steps of the import of preproteins into the organelle, which are essential for mitochondrial biogenesis and, therefore, for eukaryotic cell viability. The TOM complex is a multisubunit molecular machine with a dynamic structure. The biogenesis of TOM is of special interest because the complex is required for its own biogenesis. This article describes the mechanisms by which Tom components are targeted to the mitochondria and inserted into the outer membrane. The assembly of newly synthesized subunits into the functional TOM complex might occur via assembly intermediates that are in equilibrium with the mature complex.

Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association

The nature and distribution of amino acids in the helix interfaces of four polytopic membrane proteins (cytochrome c oxidase, bacteriorhodopsin, the photosynthetic reaction center of Rhodobacter sphaeroides, and the potassium channel of Streptomyces lividans) are studied to address the role of glycine in transmembrane helix packing. In contrast to soluble proteins where glycine is a noted helix breaker, the backbone dihedral angles of glycine in transmembrane helices largely fall in the standard alpha-helical region of a Ramachandran plot. An analysis of helix packing reveals that glycine residues in the transmembrane region of these proteins are predominantly oriented toward helix-helix interfaces and have a high occurrence at helix crossing points. Moreover, packing voids are generally not formed at the position of glycine in folded protein structures. This suggests that transmembrane glycine residues mediate helix-helix interactions in polytopic membrane proteins in a fashion similar to that seen in oligomers of membrane proteins with single membrane-spanning helices. The picture that emerges is one where glycine residues serve as molecular notches for orienting multiple helices in a folded protein complex.

Lambda repressor N-terminal DNA-binding domain as an assay for protein transmembrane segment interactions in vivo

To understand the determinants of membrane protein interactions, we have developed an in vivo genetic assay system for detecting homodimerization of transmembrane (TM) segments from integral membrane proteins. Our approach is to generate gene fusions between potentially dimerizing TM segments and a cytoplasmic DNA-binding protein that lacks its intrinsic dimerization domain. This genetic approach allows us to screen and distinguish among known dimerizing domains and weakly dimerizing mutants, as well as non-dimerizing TM segments. We replaced the bacteriophage lambda cI repressor C-terminal dimerization domain with the human erythrocyte glycophorin A transmembrane segment (GpA TM). GpA TM forms SDS-resistant homodimers in vitro. Expression of this membrane-associated fusion in Escherichia coli conferred the same degree of immunity to lambda cI phages as the wild-type, intact lambda repressor. Single amino acid substitutions that disrupt the GpA TM dimer interface were introduced into the lambda-GpA TM fusion proteins. These mutations dramatically reduced immunity of E. coli to lambda cI, such that the efficiency of plating these phages increased by greater than 10,000-fold over that conferred by the wild-type lambda-GpA TM fusion. Introduction of the putatively non-dimerizing first TM from E. coli MalF into the lambda-TM fusion vector resulted in no immunity to lambda cI phages. Fusion of the homodimeric, periplasmically localized, mature alkaline phosphatase domain to the C terminus of the lambda-TM fusion proteins containing weakly to non-dimerizing TM segments restored immunity to lambda cI phages. Results from this in vivo genetic assay system demonstrate that (1) dimerization of the lambda cI DNA-binding domain can be promoted by dimerizing TM segments, (2) strongly, weakly, and non-dimerizing TM segments can be distinguished on the basis of their ability to confer immunity to lambda cI phages, and (3) introduction of a dimerizing periplasmic domain can provide functionality to lambda-TM fusions containing weakly to non-dimerizing TM segments.

Alteration of a mitochondrial outer membrane signal anchor sequence that permits its insertion into the inner membrane. Contribution of hydrophobic residues

Tom70p is targeted and inserted into the mitochondrial outer membrane in the Nin-Ccyto orientation, via an NH2-terminal signal anchor sequence. The signal anchor is comprised of two domains: an NH2-terminal hydrophilic region which is positively charged (amino acids 1-10) followed by the predicted transmembrane segment (amino acids 11-29). Substitution of the NH2-terminal domain with a matrix-targeting signal caused the signal anchor to adopt the reverse orientation in the outer membrane (Ncyto-Cin) or, if presented to mitoplasts, to arrest protein translocation at the inner membrane without insertion. Physically separating the transmembrane segment from the matrix-targeting signal by moving it downstream within the protein resulted in a failure to arrest in either membrane, and consequently the protein was imported to the matrix. However, if the mean hydrophobicity of the Tom70p transmembrane segment was increased in these constructs, the protein inserted into the inner membrane with an Nin-Cout orientation. Therefore we have determined conditions that allow the Tom70p transmembrane domain to insert in either membrane, pass through both membranes, or arrest without insertion in the inner membrane. These results identify the mean hydrophobicity of potential transmembrane domains within bitopic proteins as an important determinant for insertion into the mitochondrial inner membrane.

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.

Signal anchor sequence insertion into the outer mitochondrial membrane. Comparison with porin and the matrix protein targeting pathway

We have addressed the question of overlap between the pathways for protein insertion into the outer mitochondrial membrane and import to the matrix compartment, using competition studies in vitro. A synthetic peptide corresponding to the matrix-targeting signal of pre-ornithine carbamyl transferase competed for outer membrane insertion of porin but did not compete for membrane insertion of outer membrane signal anchor-containing proteins. Conversely, however, a synthetic peptide corresponding to the signal anchor sequence of Tom70 competed for import of all proteins examined. Both peptides competed for a step beyond receptor binding. Import of all precursors examined was inhibited by antibodies raised against the import receptor Tom20. Following binding to the surface of the organelle, outer membrane integration of porin was sensitive to depletion of nucleoside triphosphates by apyrase, whereas signal anchor protein insertion was not. The results demonstrate that outer membrane signal anchor insertion overlaps with a general insertion pathway. However, it exhibits both properties and steps that differ from the pathway followed by porin and matrix-targeted protein.

Tom71, a novel homologue of the mitochondrial preprotein receptor Tom70

The protein Tom71 is encoded by the open reading frame YHR117w (yeast chromosome VIII) and shares 53% amino acid sequence identity with Tom70, a protein import receptor of the mitochondrial outer membrane. We investigated the cellular function of Tom71 and addressed the question of whether Tom71 and Tom70 fulfill similar functions. Like Tom70, Tom71 is anchored to the mitochondrial outer membrane via its N terminus, thereby exposing a large C-terminal domain to the cytosol. Tom71 is associated with the protein import complex of this membrane and can be cross-linked to a protein with a molecular mass of 30-35 kDa. Disruption of the TOM71 gene does not reduce cell growth, except on nonfermentable carbon sources at elevated temperatures. Deletion of both the TOM71 and TOM70 genes does not acerbate this growth defect. In vitro import studies demonstrated no functional requirement for Tom71 in the import of several preproteins destined for each of the mitochondrial subcompartments. In particular, the import of Tom70-dependent preproteins is minimally affected by the deletion of Tom71, irrespective of the presence or absence of the Tom70 receptor. Thus, despite their strikingly similar biochemical properties, Tom71 and Tom70 do not perform identical functions.

An amphiphilic lipid-binding domain influences the topology of a signal-anchor sequence in the mitochondrial outer membrane

Mas70p is targeted and inserted into the mitochondrial outer membrane in the N(in)-C(cyto) orientation, via an NH2-terminal signal-anchor sequence. The signal-anchor is comprised of two domains: an NH2-terminal hydrophilic region which is positively charged (amino acids 1-10), followed by the predicted transmembrane segment (amino acids 11-29). Substitution of the NH2-terminal hydrophilic domain with a matrix-targeting signal caused the signal-anchor to adopt the reverse orientation in the membrane (N(cyto)-C(in)). This substitution resulted in an increase in the net positive charge of the hydrophilic region, from +4 to +8. In contrast to the endoplasmic reticulum and the bacterial inner membrane, where the net positive charge is an important determinant in conferring protein topology in the lipid bilayer, we show here that the reversal of the Mas70p signal-anchor was not due to differences in the number and positions of basic amino acids in the hydrophilic domain. However, a reduction in the hydrophobic moment of predicted amphiphilic helices containing an arginine, obtained by converting the apolar amino acids flanking the arginine to polar residues, caused the otherwise N(cyto)-C(in) signal-anchor to re-adopt the original N(in)-C(cyto) orientation of Mas70p. The reduced hydrophobic moment at the NH2-terminus significantly reduced the ability of this domain to bind to synthetic liposomes whose lipid composition reflected that of the outer membrane. These results identify amphiphilicity as an important determinant in causing retention of the NH2-terminus of a mitochondrial signal-anchor on the cytosolic side of the outer membrane. In addition to potential interactions between this domain and cytosolic-exposed components of the import machinery, this retention may result as well from interaction of the NH2-terminus with the surrounding membrane surface.

The protein import apparatus of the mitochondrial outer membrane

The majority of proteins within mitochondria are synthesized on cytosolic ribosomes and imported into the organelles. Protein complexes in the mitochondrial outer membrane harbour both the receptors that recognize these preproteins, and a translocation pore. These "receptor complexes" are the entry points for most preproteins, which are subsequently targeted to their final submitochondrial locations. The outer membrane complexes cooperate with the import machinery of the inner membrane to target preproteins to the inner membrane itself, the matrix, or, in some cases, to the intermembrane space. In isolated outer membranes, these complexes are capable of accurately importing preproteins destined for the outer membrane. Our current understanding of the composition, function, and biogenesis of these outer membrane receptor complexes is the focus of this article. Key words: mitochondria, outer membrane, protein import, receptors.

Identification of the human mitochondrial protein import receptor, huMas20p. Complementation of delta mas20 in yeast

The human homolog of the S. cerevisiaelN. crassa mitochondrial protein import receptor, Mas20p/MOM19, has been identified and characterized. Sequence similarities between these three proteins is most pronounced within the NH2-terminal third of the molecules. However, the mammalian protein exhibits only weak homology to the tetratricopeptide repeat B domain that is found in Mas20p/MOM19. huMas20p is targeted and inserted into the outer membrane of isolated rat heart mitochondria, in the Nin-Ccyto orientation. Antibodies directed against the soluble portion of huMas20p inhibited in vitro mitochondrial import of a diverse set of precursor proteins (including inner membrane uncoupling protein), but failed to block import of a fusion protein bearing the signal-anchor sequence of Mas20p itself. Finally, expression of huMAS20 complemented the respiratory defect of delta mas20 yeast cells. Together, these results demonstrate that huMAS20p is a component of the mammalian import apparatus.

Insertion of an uncharged polypeptide into the mitochondrial inner membrane does not require a trans-bilayer electrochemical potential: effects of positive charges

Mitochondria with a ruptured outer membrane exhibited impaired import into this membrane of an outer membrane fusion protein containing the signal-anchor sequence of Mas70p. However, the Mas70p signal-anchor efficiently targeted and inserted the protein directly into exposed regions of the inner membrane. Import into the inner membrane was dependent on delta psi and this dependence was due to the presence of the positively-charged amino acids located at positions 2, 7, and 9 of the signal-anchor. In contrast to wild-type signal-anchor, mutants lacking the positively-charged residues mediated import into the inner membrane in both the presence and absence of delta psi. The results suggest two conclusions: (1) delta psi-dependent import of the signal-anchor sequence was due exclusively to an effect of delta psi on the positively-charged domain of the signal-anchor, rather than to an effect of delta psi on a property of the inner membrane import machinery; (2) in the absence of delta psi, the positively-charged domain of the signal-anchor prevented the otherwise import-competent signal-anchor from inserting into the membrane. This suggests that the positively-charged domain leads import across the inner membrane, and that delta psi is required to vectorially clear this domain in order to allow the distal region of the signal-anchor to enter the translocation pathway. The implications of these findings on the mechanism of import into the mitochondrial inner membrane and matrix are discussed.

Import and insertion of proteins into the mitochondrial outer membrane

Nuclear-encoded proteins destined for insertion into the mitochondrial outer membrane, follow the same general pathway for import as proteins that are translocated to interior compartments within the organelle. This observation is true both for beta-barrel-type proteins and for proteins that contain hydrophobic alpha-helical transmembrane segments. In this review, we describe what is known about the various steps leading to protein insertion into the outer membrane, and discuss the energetics that favor vectorial translocation into and across this membrane. The selection of the outer membrane during import may involve a lateral release of the translocating polypeptide from the import machinery so that the appropriate domains of the protein become embedded in the lipid bilayer. One type of topogenic domain that can guarantee such selection of the outer membrane is a signal-anchor sequence of the type characterized for the bitopic protein Mas70p. It is suggested that a signal-anchor sequence selective for the mitochondrial outer membrane causes abrogation of polypeptide translocation and triggers the release of the transmembrane segment into the surrounding lipid bilayer, prior to any possibility for the commitment of translocation to the interior of the organelle. Specific structural features of the signal-anchor sequence specify its orientation in the membrane, and can confer on this sequence the ability to form homo-oligomers and hetero-oligomers. Strategies other than a signal-anchor sequence may be employed by other classes of proteins for selection of the outer-membrane. Of note is the ability of the outer-membrane import machinery to catalyze integration of the correct set of proteins into the outer-membrane bilayer, while allowing proteins that are destined for integration into the bilayer of the inner membrane to pass through unimpeded. Again, however, different proteins may employ different strategies. One model proposes that this can be accomplished by a combination of a matrix-targeting signal and a distal stop-transfer sequence. In this model, the formation of contact sites, which is triggered when the matrix-targeting signal engages the import machinery of the inner membrane, may prevent the outer-membrane translocon from recognizing and responding to the downstream stop-transfer domain. This allows the transmembrane segment to pass across the outer-membrane, and subsequently integrate into the inner membrane.

Specificity and promiscuity in membrane helix interactions

Transmembrane alpha-helices can associate with one another in lipid bilayers. This association is important in the folding and oligomerization of many integral membrane proteins, and may also play a role in their function. The interactions between helices may be highly specific or relatively non-specific, and their roles may differ accordingly. These two cases are discussed.

Specificity and promiscuity in membrane helix interactions

The membrane-spanning portions of many integral membrane proteins consist of one or a number of transmembrane α-helices, which are expected to be independently stable on thermodynamic grounds. Side-by-side interactions between these transmembrane α-helices are important in the folding and assembly of such integral membrane proteins and their complexes. In considering the contribution of these helix–helix interactions to membrane protein folding and oligomerization, a distinction between the energetics and specificity should be recognized. A number of contributions to the energetics of transmembrane helix association within the lipid bilayer will be relatively non-specific, including those resulting from charge–charge interactions and lipid–packing effects. Specificity (and part of the energy) in transmembrane α-helix association, however, appears to rely mainly upon a detailed stereochemical fit between sets of dynamically accessible states of particular helices. In some cases, these interactions are mediated in part by prosthetic groups.