Redundant mitochondrial targeting signals in yeast adenylate kinase

The mitochondrial intermembrane space: the most constricted mitochondrial sub-compartment with the largest variety of protein import pathways

The mitochondrial intermembrane space (IMS) is the most constricted sub-mitochondrial compartment, housing only about 5% of the mitochondrial proteome, and yet is endowed with the largest variability of protein import mechanisms. In this review, we summarize our current knowledge of the major IMS import pathway based on the oxidative protein folding pathway and discuss the stunning variability of other IMS protein import pathways. As IMS-localized proteins only have to cross the outer mitochondrial membrane, they do not require energy sources like ATP hydrolysis in the mitochondrial matrix or the inner membrane electrochemical potential which are critical for import into the matrix or insertion into the inner membrane. We also explore several atypical IMS import pathways that are still not very well understood and are guided by poorly defined or completely unknown targeting peptides. Importantly, many of the IMS proteins are linked to several human diseases, and it is therefore crucial to understand how they reach their normal site of function in the IMS. In the final part of this review, we discuss current understanding of how such IMS protein underpin a large spectrum of human disorders.

Antifungal activity, kinetics and molecular mechanism of action of garlic oil against Candida albicans

The antifungal activity, kinetics, and molecular mechanism of action of garlic oil against Candida albicans were investigated in this study using multiple methods. Using the poisoned food technique, we determined that the minimum inhibitory concentration of garlic oil was 0.35 μg/mL. Observation by transmission electron microscopy indicated that garlic oil could penetrate the cellular membrane of C. albicans as well as the membranes of organelles such as the mitochondria, resulting in organelle destruction and ultimately cell death. RNA sequencing analysis showed that garlic oil induced differential expression of critical genes including those involved in oxidation-reduction processes, pathogenesis, and cellular response to drugs and starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, representing vital cellular processes such as oxidative phosphorylation, the spliceosome, the cell cycle, and protein processing in the endoplasmic reticulum. In addition, four upregulated proteins selected after two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE) analysis were identified with high probability by mass spectrometry as putative cytoplasmic adenylate kinase, pyruvate decarboxylase, hexokinase, and heat shock proteins. This is suggestive of a C. albicans stress responses to garlic oil treatment. On the other hand, a large number of proteins were downregulated, leading to significant disruption of the normal metabolism and physical functions of C. albicans.

Mechanisms and physiological impact of the dual localization of mitochondrial intermembrane space proteins

Eukaryotic cells developed diverse mechanisms to guide proteins to more than one destination within the cell. Recently, the proteome of the IMS (intermembrane space) of mitochondria of yeast cells was identified showing that approximately 20% of all soluble IMS proteins are dually localized to the IMS, as well as to other cellular compartments. Half of these dually localized proteins are important for oxidative stress defence and the other half are involved in energy homoeostasis. In the present review, we discuss the mechanisms leading to the dual localization of IMS proteins and the implications for mitochondrial function.

Mdm35p imports Ups proteins into the mitochondrial intermembrane space by functional complex formation

Ups1p, Ups2p, and Ups3p are three homologous proteins that control phospholipid metabolism in the mitochondrial intermembrane space (IMS). The Ups proteins are atypical IMS proteins in that they lack the two major IMS-targeting signals, bipartite presequences and cysteine motifs. Here, we show that Ups protein import is mediated by another IMS protein, Mdm35p. In vitro import assays show that import of Ups proteins requires Mdm35p. Loss of Mdm35p led to a decrease in steady state levels of Ups proteins in mitochondria. In addition, mdm35Delta cells displayed a similar phenotype to ups1Deltaups2Deltaups3Delta cells. Interestingly, unlike typical import machineries, Mdm35p associated stably with Ups proteins at a steady state after import. Demonstrating that Mdm35p is a functional component of Ups-Mdm35p complexes, restoration of Ups protein levels in mdm35Delta mitochondria failed to restore phospholipid metabolism. These findings provide a novel mechanism in which the formation of functional protein complexes drives mitochondrial protein import.

Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55

In eukaryotes, each subcellular compartment harbors a specific group of proteins that must accomplish specific tasks. Nfs1 is a highly conserved mitochondrial cysteine desulfurase that participates in iron-sulfur cluster assembly as a sulfur donor. Previous genetic studies, in Saccharomyces cerevisiae, have suggested that this protein distributes between the mitochondria and the nucleus with biochemically undetectable amounts in the nucleus (termed "eclipsed distribution"). Here, we provide direct evidence for Nfs1 nuclear localization (in addition to mitochondria) using both alpha-complementation and subcellular fractionation. We also demonstrate that mitochondrial and nuclear Nfs1 are derived from a single translation product. Our data suggest that the Nfs1 distribution mechanism involves at least partial entry of the Nfs1 precursor into mitochondria, and then retrieval of a minor subpopulation (probably by reverse translocation) into the cytosol and then the nucleus. To further elucidate the mechanism of Nfs1 distribution we determined the N-terminal mitochondrial sequence of Nfs1 by Edman degradation. This led to the discovery of a novel mitochondrial processing enzyme, Icp55. This enzyme removes three amino acids from the N terminus of Nfs1 after cleavage by mitochondrial processing peptidase. Intriguingly, Icp55 protease (like its substrate Nfs1) appears to be dual distributed between the nucleus and mitochondria.

Dual mitochondrial localization and different roles of the reversible reaction of mammalian ferrochelatase

Ferrochelatase catalyzes the insertion of ferrous ions into protoporphyrin IX to produce heme. Previously, it was found that this enzyme also participates in the reverse reaction of iron removal from heme. To clarify the role of the reverse reaction of ferrochelatase in cells, mouse liver mitochondria were fractionated to examine the localization of ferrochelatase, and it was found that the enzyme localizes not only to the inner membrane, but also to the outer membrane. Observations by immunoelectron microscopy confirmed the dual localization of ferrochelatase in ferrochelatase-expressing human embryonic kidney cells and mouse liver mitochondria. The conventional (zinc-insertion) activities of the enzyme in the inner and outer membranes were similar, whereas the iron-removal activity was high in the outer membrane. 2D gel analysis revealed that two types of the enzyme with different isoelectric points were present in mitochondria, and the acidic form, which was enriched in the outer membrane, was found to be phosphorylated. Mutation of human ferrochelatase showed that serine residues at positions 130 and 303 were phosphorylated, and serine at position 130 may be involved in the balance of the reversible catalytic reaction. When mouse erythroleukemia cells were treated with 12-O-tetradecanoyl-phorbol 13-acetate, an activator of protein kinase C, or hemin, phospho-ferrochelatase levels increased, with a concomitant decrease in zinc-insertion activity and a slight increase in iron-removal activity. These results suggest that ferrochelatase localizes to both the mitochondrial outer and inner membranes and that the change in the equilibrium position of the forward and reverse activities may be regulated by the phosphorylation of ferrochelatase.

Dual targeted mitochondrial proteins are characterized by lower MTS parameters and total net charge

BACKGROUND

In eukaryotic cells, identical proteins can be located in different subcellular compartments (termed dual-targeted proteins).

METHODOLOGY/PRINCIPAL FINDINGS

We divided a reference set of mitochondrial proteins (published single gene studies) into two groups: i) Dual targeted mitochondrial proteins and ii) Exclusive mitochondrial proteins. Mitochondrial proteins were considered dual-targeted if they were also found or predicted to be localized to the cytosol, the nucleus, the endoplasmic reticulum (ER) or the peroxisome. We found that dual localized mitochondrial proteins have i) A weaker mitochondrial targeting sequence (MitoProtII score, hydrophobic moment and number of basic residues) and ii) a lower whole-protein net charge, when compared to exclusive mitochondrial proteins. We have also generated an annotation list of dual-targeted proteins within the predicted yeast mitochondrial proteome. This considerably large group of dual-localized proteins comprises approximately one quarter of the predicted mitochondrial proteome. We supported this prediction by experimental verification of a subgroup of the predicted dual targeted proteins.

CONCLUSIONS/SIGNIFICANCE

Taken together, these results establish dual targeting as a widely abundant phenomenon that should affect our concepts of gene expression and protein function. Possible relationships between the MTS/mature sequence traits and protein dual targeting are discussed.

Profiling the Monascus pilosus proteome during nitrogen limitation

Monascus species have the unique ability to economically produce many secondary metabolites. However, the influence of nitrogen limitation on Monascus secondary metabolite production and metabolic performance remains unclear. Varying the carbon/nitrogen (C/N) ratios in the range from 20 to 60 in cultivation of Monascus pilosus by glucose nitrate medium, our resulting data showed that red pigment production was significantly suppressed and more sensitive to nitrogen limitation than cellular biomass growth at a C/N ratio of 60. Using a comparative proteomic approach, combining two-dimensional gel electrophoresis, matrix-assisted laser desorption ionization time-of-flight/time-of-flight liquid chromatography-mass spectrometry, and tandem mass spectrometry, proteins with modified expression in the nitrogen-limited (C/N ratio 60) Monascus filamentous cells were identified. The results revealed that the deregulated proteins identified were involved in amino acid biosynthesis, protein translation, antioxidant-related enzymes, glycolysis, and transcriptional regulation. The results suggested that, under nitrogen limitation-induced suppression of protein translation and of expression of the related energy-generating enzymes, nitrogen limitation induced a switch of metabolic flux from glycolysis to the tricarboxylic acid (TCA) cycle for maintaining cellular energy homeostasis, resulting in repression of the metabolic shift of the polyketide biosynthesis pathway for red pigment production.

Protein kinase CK2 activates the atypical Rio1p kinase and promotes its cell-cycle phase-dependent degradation in yeast

Using co-immunoprecipitation combined with MS analysis, we identified the alpha' subunit of casein kinase 2 (CK2) as an interaction partner of the atypical Rio1 protein kinase in yeast. Co-purification of Rio1p with CK2 from Deltacka1 or Deltacka2 mutant extracts shows that Rio1p preferentially interacts with Cka2p in vitro. The C-terminal domain of Rio1p is essential and sufficient for this interaction. Six C-terminally located clustered serines were identified as the only CK2 sites present in Rio1p. Replacement of all six serine residues by aspartate, mimicking constitutive phosphorylation, stimulates Rio1p kinase activity about twofold in vitro compared with wild-type or the corresponding (S > A)(6) mutant proteins. Both mutant alleles (S > A)(6) or (S > D)(6) complement in vivo, however, growth of the RIO1 (S > A)(6) mutant is greatly retarded and shows a cell-cycle phenotype, whereas the behaviour of the RIO1 (S > D)(6) mutant is indistinguishable from wild-type. This suggests that phosphorylation by protein kinase CK2 leads to moderate activation of Rio1p in vivo and promotes cell proliferation. Physiological studies indicate that phosphorylation by CK2 renders the Rio1 protein kinase susceptible to proteolytic degradation at the G(1)/S transition in the cell-division cycle, whereas the non-phosphorylated version is resistant.

Mitochondrial Localization and Putative Signaling Function of Sucrose Synthase in Maize

In many organisms, an increasing number of proteins seem to play two or more unrelated roles. Here we report that maize sucrose synthase (SUS) is distributed in organelles not involved in sucrose metabolism and may have novel roles beyond sucrose degradation. Bioinformatics analysis predicts that among the three maize SUS isoforms, SH1 protein has a putative mitochondrial targeting peptide (mTP). We validated this prediction by the immunodetection of SUS in mitochondria. Analysis with isoform-specific antisera revealed that both SH1 and SUS1 are represented in mitochondria, although the latter lacks a canonical mTP. The SUS2 isoform is not detectable in mitochondria, despite its presence in the cytosol. In maize primary roots, the mitochondrion-associated SUS (mtSUS; which includes SH1 and SUS1) is present mostly in the root tip, indicating tissue-specific regulation of SUS compartmentation. Unlike the glycolytic enzymes that occur attached to the outside of mitochondria, SH1 and SUS1 are intramitochondrial. The low abundance of SUS in mitochondria, its high Km value for sucrose, and the lack of sucrose in mitochondria suggest that mtSUS plays a non-sucrolytic role. Co-immunoprecipitation studies indicate that SUS interacts with the voltage-dependent anion channel in an isoform-specific and anoxia-enhanced manner and may be involved in the regulation of solute fluxes into and out of mitochondria. In several plant species, at least one of the SUS proteins possesses a putative mTP, indicating the conservation of the noncatalytic function across plant species. Taken together, these observations suggest that SUS has a novel noncatalytic function in plant cells.

Chopped, trapped or tacked--protein translocation into the IMS of mitochondria

All proteins of the intermembrane space (IMS) of mitochondria are synthesized in the cytosol. The mechanisms by which these polypeptides are transported into the IMS are strikingly different from other protein-translocation processes in the cell. Recent studies suggest that IMS proteins reach their destination by three alternative principles that differ in the energy sources employed to drive the translocation reactions. The first class of proteins uses both hydrolysis of matrix ATP and the electrochemical potential of the inner membrane. The second class depends on the energy gain of protein folding, and the third on the association of the proteins to high-affinity binding sites in the IMS.

Molecular cloning and characterization of a novel adenylate kinase 3 gene from Clonorchis sinensis

Adenylate kinase (AK) is a ubiquitous enzyme that contributes to the homeostasis of adenine nucleotides in living cells. AK catalyzes reversible high energy phosphoryl transfer reactions between ATP (or GTP) and AMP to generate ADP (or GDP). From a Clonorchis sinensis adult worm cDNA library, we isolated a cDNA clone encoding a novel AK3 isozyme. The 956 bp cDNA encodes a putative protein of 228 amino acids with a predicted molecular mass of 26.2 kDa. The recombinant CsAK3 protein produced in Escherichia coli can be refolded into a functional protein with AK3 activity. The optimum pH and temperature for the enzyme are 8.5 and 40 degrees C, respectively. The calculated activation energy is 56.04 kJ mol-1. The Km of the CsAK3 for AMP and GTP are 118 microM and 359 microM, respectively. CsAK3 is inhibited by Ap5A (>70% inhibition by 2.0 mM AP5A). Ap5A may be a potential lead compound acting on C. sinensis in which AK3 as a drug target.

Adenylate kinase and GTP:AMP phosphotransferase of the malarial parasite Plasmodium falciparum

For coping with energetic and synthetic challenges, parasites require high activities of adenylate kinase (AK; ATP + AMP <==> 2 ADP) and GTP:AMP phosphotransferase (GAK; GTP + AMP <==> GDP + ADP). These enzymes were identified in erythrocytic stages of Plasmodium falciparum. The genes encoding PfAK and PfGAK are located on chromosomes 10 and 4, respectively. Molecular cloning and heterologous expression in E. coli yielded enzymatically active proteins of 28.9 (PfAK) and 28.0 kDa (PfGAK). Recombinant PfAK resembles authentic PfAK in its biochemical characteristics including the possible association with a stabilizing protein and the high specificity for AMP as the mononucleotide substrate. Specificity is less stringent for the triphosphate, with ATP as the best substrate (75 U/mg; kcat = 2160 min(-1) at 25 degrees C). PfAK contains the sequence of the amphiphatic helix that is known to mediate translocation of the cytosolic protein into the mitochondrial intermembrane space. PfGAK exhibits substrate preference for GTP and AMP (100 U/mg; kcat = 2800 min(-1) at 25 degrees C); notably, there is no detectable activity with ATP. In contrast to its human orthologue (AK3), PfGAK contains a zinc finger motif and binds ionic iron. The dinucleoside pentaphosphate compounds AP5A and GP5A inhibited PfAK and PfGAK, respectively, with Ki values of approximately 0.2 microM which is more than 250-fold lower than the KM values determined for the nucleotide substrates. The disubstrate inhibitors are useful for studying the enzymatic mechanism of PfAK and PfGAK as well as their function in adenine nucleotide homeostasis; in addition, the chimeric inhibitors represent interesting lead compounds for developing nucleosides to be used as antiparasitic agents.

SUT2 is a novel multicopy suppressor of low activity of the cAMP/protein kinase A pathway in yeast

SUT2 was found in a screen for multicopy suppressors of the synthetic slow growth phenotype of a Deltaras2Deltagpa2 double deletion mutant. It failed, however, to cure the lethal phenotype of a Deltaras1Deltaras2 mutant suggesting that it acts upstream of Ras or in a parallel pathway. By testing cAMP-dependent reactions including the accumulation of storage carbohydrates, pseudohyphal differentiation, entry of meiosis as well as the measurement of FLO11 reporter activity we show that Sut2p modulates the activity of protein kinase A (PKA). Additionally, we demonstrate that cellular levels of Ras2p are affected by Sut2p and that Sut2-GFPp accumulates significantly in the nucleus. Based on the observed influence of high SUT2 gene dosage on PKA activity as well as Sut2p's homology to the presumptive transcription factor Sut1p, we suggest that Sut2p contributes to regulation of PKA activity at the level of transcription.

Import of small Tim proteins into the mitochondrial intermembrane space

Proteins of the intermembrane space (IMS) of mitochondria are typically synthesized without presequences. Little is known about their topogenesis. We used Tim13, a member of the 'small Tim protein' family, as model protein to investigate the mechanism of translocation into the IMS. Tim13 contains four conserved cysteine residues that bind a zinc ion as cofactor. Import of Tim13 did not depend on the membrane potential or ATP hydrolysis. Upon import into mitochondria Tim13 adopted a stably folded conformation in the IMS. Mutagenesis of the cysteine residues or pretreatment with metal chelators interfered with folding of Tim13 in vitro and impaired its import into mitochondria. Upon depletion of metal ions or modification of cysteine residues, imported Tim13 diffused back out of the IMS. We propose an import pathway in which (1) Tim13 can pass through the TOM complex into and out of the IMS in an unfolded conformation, and (2) cofactor acquisition stabilizes folding on the trans side of the outer membrane and traps Tim13 in the IMS, and drives unidirectional movement of the protein across the outer membrane of mitochondria.

Mutagenesis reveals a specific role for Cox17p in copper transport to cytochrome oxidase

The provision of copper to cytochrome oxidase is one of the requisite steps in the assembly of the holoenzyme. Several proteins are involved in this process including Cox17p, Sco1p, and Cox11p. Cox17p, an 8-kDa protein, is the only molecule thought to be involved in shuttling copper from the cytoplasm into mitochondria. Given the small size of Cox17p, we have taken a random and site-directed mutagenesis approach to studying structure-function relationships in Cox17p. Mutations have been generated in 70% of the Cox17p amino acid residues, with only a small subset leading to a detectable respiration-deficient phenotype. We have characterized the respiration-deficient cox17 mutants and found in addition to the expected cytochrome oxidase deficiency, a specific lack of Cox2p and the presence of a misassembled cytochrome oxidase in a subset of mutants. These results suggest that Cox17p is involved upstream of Sco1p in delivering copper specifically to subunit 2 of cytochrome oxidase and predict the existence of a subunit 1-specific copper chaperone.