Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability

Characterization of murine SIRT3 transcript variants and corresponding protein products

SIRT3 is one of the seven mammalian sirtuin homologs of the yeast SIR2 gene. SIRT3 possesses NAD(+)-dependent protein deacetylase activity. Recent studies indicate that the murine SIRT3 gene expresses different transcript variants, resulting in three possible SIRT3 protein isoforms with various lengths at the N-terminus: M1 (aa 1-334), M2 (aa 15-334), and M3 (aa 78-334). The transcript variants 1 and 3 can only produce M3 protein, while M1 and M2 proteins are translationally initiated from different in-frame ATG sites in transcript 2. Here we report that three transcript variants of the mouse SIRT3 gene are broadly expressed in various mouse tissues. By expressing these SIRT3 isoforms in HEK293 cells through transient transfection, we confirmed recent reports that two longer murine SIRT3 proteins (M1 and M2) are targeted to mitochondria with higher efficiency than the shorter M3 isoform. Additionally, the M1 and M2 proteins are processed into a mature form. Using Edman degradation we identify Ile38 (majority) or Val42 as the N-terminal amino acid of the mature M1 isoform, and Met78 or Val79 as the N-terminal amino acid of the M3 isoform. Interestingly, we found that even upon mutation of the M2 ATG site in the M1 cDNA, a processed mature protein could still be produced. In terms of deacetylase activity, we found that although only the mature protein derived from M1 or M2 proteins were active against acetylated peptide substrates, all three forms had equal deacetylase activity towards a full-length native protein substrate, acetyl CoA synthetase 2.

Inventory control: cytochrome c oxidase assembly regulates mitochondrial translation

Mitochondria maintain genome and translation machinery to synthesize a small subset of subunits of the oxidative phosphorylation system. To build up functional enzymes, these organellar gene products must assemble with imported subunits that are encoded in the nucleus. New findings on the early steps of cytochrome c oxidase assembly reveal how the mitochondrial translation of its core component, cytochrome c oxidase subunit 1 (Cox1), is directly coupled to the assembly of this respiratory complex.

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes

The increasing ability to generate large-scale, quantitative proteomic data has brought with it the challenge of analyzing such data to discover the sequence elements that underlie systems-level protein behavior. Here we show that short, linear protein motifs can be efficiently recovered from proteome-scale datasets such as sub-cellular localization, molecular function, half-life, and protein abundance data using an information theoretic approach. Using this approach, we have identified many known protein motifs, such as phosphorylation sites and localization signals, and discovered a large number of candidate elements. We estimate that ∼80% of these are novel predictions in that they do not match a known motif in both sequence and biological context, suggesting that post-translational regulation of protein behavior is still largely unexplored. These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental validation.

An in silico analysis of the mitochondrial protein import apparatus of plants

BACKGROUND

An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.

RESULTS

The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, (C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes (S. moellendorffii) and gymnosperms (P. glauca). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria.

CONCLUSIONS

It is proposed that the observed functional divergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, diversity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or diverged in a lineage specific manner.

Mosaic origin of the mitochondrial proteome

Although the origin of mitochondria from the endosymbiosis of an α-proteobacterium is well established, the nature of the host cell, the metabolic complexity of the endosymbiont and the subsequent evolution of the proto-mitochondrion into all its current appearances are still the subject of discovery and sometimes debate. Here we review what has been inferred about the original composition and subsequent evolution of the mitochondrial proteome and essential mitochondrial systems. The evolutionary mosaic that currently constitutes mitochondrial proteomes contains (i) endosymbiotic proteins (15-45%), (ii) proteins without detectable orthologs outside the eukaryotic lineage (40%), and (iii) proteins that are derived from non-proteobacterial Bacteria, Bacteriophages and Archaea (15%, specifically multiple tRNA-modification proteins). Protein complexes are of endosymbiotic origin, but have greatly expanded with novel eukaryotic proteins; in contrast to mitochondrial enzymes that are both of proteobacterial and non-proteobacterial origin. This disparity is consistent with the complexity hypothesis, which argues that proteins that are a part of large, multi-subunit complexes are unlikely to undergo horizontal gene transfer. We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do.

Prediction of subcellular locations of proteins: where to proceed?

Since the proposal of the signal hypothesis on protein subcellular sorting, a number of computational analyses have been performed in this field. A typical example is the development of prediction algorithms for the subcellular localization sites of input protein sequences. In this review, we mainly focus on the biological grounds of the prediction methods rather than the algorithmic issues because we believe the former will be more fruitful for future development. Recent advances on the study of protein sorting signals will hopefully be incorporated into future prediction methods. Unfortunately, many of the state-of-the-art methods are published without sufficient objective tests. In fact, a simple test employed in this article shows that the performance of specifically developed predictors is not significantly better than that of a homology search. We suspect that this is a general problem associated with the interpretation of genome sequences, which have evolved through gene duplication and speciation.

Dual targeting of mitochondrial proteins: mechanism, regulation and function

One solution found in evolution to increase the number of cellular functions, without increasing the number of genes, is distribution of single gene products to more than one cellular compartment. It is well documented that in eukaryotic cells, molecules of one protein can be located in several subcellular locations, a phenomenon termed dual targeting, dual localization, or dual distribution. The differently localized proteins are coined in this review "echoforms" indicating repetitious forms of the same protein (echo in Greek denotes repetition) distinctly placed in the cell. This term replaces the term to "isoproteins" or "isoenzymes" which are reserved for proteins with the same activity but different amino acid sequences. Echoforms are identical or nearly identical, even though, as referred to in this review may, in some cases, surprisingly have a totally different function in the different compartments. With regard to mitochondria, our operational definition of dual targeted proteins refers to situations in which one of the echoforms is translocated through/into a mitochondrial membrane. In this review we ask how, when and why mitochondrial proteins are dual localized in the cell. We describe mechanisms of dual targeting of proteins between mitochondria and other compartments of the eukaryotic cell. In particular, we have paid attention to situations in which dual localization is regulated in time, location or function. In addition, we have attempted to provide a broader view concerning the phenomenon of dual localization of proteins by looking at mechanisms that are beyond our simple definition of dual targeting. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.

The approaches for manipulating mitochondrial proteome

Over the past decade a large volume of research data has accumulated which has established a fundamental role for mitochondria in normal cellular functioning, as well as in various pathologies. Mitochondria play a pivotal role in metabolism and energy production, and are one of the key players involved in programmed cell death. On the other hand, mitochondrial dysfunction is implicated, directly or indirectly in numerous pathological conditions including inherited mitochondrial disorders, diabetes, cardiovascular and neurodegenerative diseases, and a variety of malignancies. The ability to modulate mitochondrial function by altering the diverse protein component of this organelle may be of great value for developing future therapeutic interventions. This review will discuss approaches used to introduce proteins into mitochondria. One group of methods utilizes strategies aimed at expressing proteins from genes in the nucleus. These include overexpression of nuclear-encoded mitochondrial proteins, allotopic expression, which is the re-coding and relocation of mitochondrial genes to the nucleus for expression and subsequent delivery of their gene products to mitochondria, and xenotopic expression, which is the nuclear expression of genes coding electron transport chain components from distant species, for delivery of their products to mammalian mitochondria. Additionally, antigenomic and progenomic strategies which focus on expression of mitochondrially targeted nuclear proteins involved in the maintenance of mtDNA will be discussed. The second group of methods considered will focus on attempts to use purified proteins for mitochondrial delivery. Special consideration has been given to the complexities involved in targeting exogenous proteins to mitochondria.

Proteomic techniques and activity-based probes for the system-wide study of proteolysis

Proteolysis constitutes a major post-translational modification but specificity and substrate selectivity of numerous proteases have remained elusive. In this review, we highlight how advanced techniques in the areas of proteomics and activity-based probes can be used to investigate i) protease active site specificity; ii) protease in vivo substrates; iii) protease contribution to proteome homeostasis and composition; and iv) detection and localization of active proteases. Peptide libraries together with genetical or biochemical selection have traditionally been used for active site profiling of proteases. These are now complemented by proteome-derived peptide libraries that simultaneously determine prime and non-prime specificity and characterize subsite cooperativity. Cell-contextual discovery of protease substrates is rendered possible by techniques that isolate and quantitate protein termini. Here, a novel approach termed Terminal Amine Isotopic Labeling of Substrates (TAILS) provides an integrated platform for substrate discovery and appropriate statistical evaluation of terminal peptide identification and quantification. Proteolytically generated carboxy-termini can now also be analyzed on a proteome-wide level. Proteolytic regulation of proteome composition is monitored by quantitative proteomic approaches employing stable isotope coding or label free quantification. Activity-based probes specifically recognize active proteases. In proteomic screens, they can be used to detect and quantitate proteolytic activity while their application in cellular histology allows to locate proteolytic activity in situ. Activity-based probes - especially in conjunction with positron emission tomography - are also promising tools to monitor proteolytic activities on an organism-wide basis with a focus on in vivo tumor imaging. Together, this array of methodological possibilities enables unveiling physiological protease substrate repertoires and defining protease function in the cellular- and organism-wide context.

Homologous desensitization of guanylyl cyclase A, the receptor for atrial natriuretic peptide, is associated with a complex phosphorylation pattern

Atrial natriuretic peptide (ANP), via its guanylyl cyclase A (GC-A) receptor and intracellular guanosine 3',5'-cyclic monophosphate production, is critically involved in the regulation of blood pressure. In patients with chronic heart failure, the plasma levels of ANP are increased, but the cardiovascular actions are severely blunted, indicating a receptor or postreceptor defect. Studies on metabolically labelled GC-A-overexpressing cells have indicated that GC-A is extensively phosphorylated, and that ANP-induced homologous desensitization of GC-A correlates with receptor dephosphorylation, a mechanism which might contribute to a loss of function in vivo. In this study, tandem MS analysis of the GC-A receptor, expressed in the human embryonic kidney cell line HEK293, revealed unambiguously that the intracellular domain of the receptor is phosphorylated at multiple residues: Ser487, Ser497, Thr500, Ser502, Ser506, Ser510 and Thr513. MS quantification based on multiple reaction monitoring demonstrated that ANP-provoked desensitization was accompanied by a complex pattern of receptor phosphorylation and dephosphorylation. The population of completely phosphorylated GC-A was diminished. However, intriguingly, the phosphorylation of GC-A at Ser487 was selectively enhanced after exposure to ANP. The functional relevance of this observation was analysed by site-directed mutagenesis. The substitution of Ser487 by glutamate (which mimics phosphorylation) blunted the activation of the GC-A receptor by ANP, but prevented further desensitization. Our data corroborate previous studies suggesting that the responsiveness of GC-A to ANP is regulated by phosphorylation. However, in addition to the dephosphorylation of the previously postulated sites (Ser497, Thr500, Ser502, Ser506, Ser510), homologous desensitization seems to involve the phosphorylation of GC-A at Ser487, a newly identified site of phosphorylation. The identification and further characterization of the specific mechanisms involved in the downregulation of GC-A responsiveness to ANP may have important pathophysiological implications.

The many faces of the mitochondrial TIM23 complex

The TIM23 complex in the inner membrane of mitochondria mediates import of essentially all matrix proteins and a large number of inner membrane proteins. Here we present an overview on the latest insights into the structure and function of this remarkable molecular machine.

On the mechanism of preprotein import by the mitochondrial presequence translocase

Mitochondria are organelles of endosymbiontic origin that contain more than one thousand different proteins. The vast majority of these proteins is synthesized in the cytosol and imported into one of four mitochondrial subcompartments: outer membrane, intermembrane space, inner membrane and matrix. Several import pathways exist and are committed to different classes of precursor proteins. The presequence translocase of the inner mitochondrial membrane (TIM23 complex) mediates import of precursor proteins with cleavable amino-terminal presequences. Presequences direct precursors across the inner membrane. The combination of this presequence with adjacent regions determines if a precursor is fully translocated into the matrix or laterally sorted into the inner mitochondrial membrane. The membrane-embedded TIM23(SORT) complex mediates the membrane potential-dependent membrane insertion of precursor proteins with a stop-transfer sequence downstream of the mitochondrial targeting signal. In contrast, translocation of precursor proteins into the matrix requires the recruitment of the presequence translocase-associated motor (PAM) to the TIM23 complex. This ATP-driven import motor consists of mitochondrial Hsp70 and several membrane-associated co-chaperones. These two structurally and functionally distinct forms of the TIM23 complex (TIM23(SORT) and TIM23(MOTOR)) are in a dynamic equilibrium with each other. In this review, we discuss recent advances in our understanding of the mechanisms of matrix translocation and membrane insertion by the TIM23 machinery.