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Unlabelled: Caspase proteases are responsible for the regulated disassembly of the cell into apoptotic bodies during mammalian apoptosis. Structural homologues of the caspase family (called metacaspases) are involved in programmed cell death in single-cell eukaryotes, yet the molecular mechanisms that contribute to death are currently undefined. Recent evidence revealed that a programmed cell death process is induced by acetic acid (AA-PCD) in Saccharomyces cerevisiae both in the presence and absence of metacaspase encoding gene YCA1. Here, we report an unexpected role for the yeast metacaspase in protein quality and metabolite control. By using an "omics" approach, we focused our attention on proteins and metabolites differentially modulated en route to AA-PCD either in wild type or YCA1-lacking cells. Quantitative proteomic and metabolomic analyses of wild type and Δyca1 cells identified significant alterations in carbohydrate catabolism, lipid metabolism, proteolysis and stress-response, highlighting the main roles of metacaspase in AA-PCD. Finally, deletion of YCA1 led to AA-PCD pathway through the activation of ceramides, whereas in the presence of the gene yeast cells underwent an AA-PCD pathway characterized by the shift of the main glycolytic pathway to the pentose phosphate pathway and a proteolytic mechanism to cope with oxidative stress., Significance: The yeast metacaspase regulates both proteolytic activities through the ubiquitin-proteasome system and ceramide metabolism as revealed by proteome and metabolome profiling of YCA1-knock-out cells during acetic-acid induced programmed cell death., (Copyright © 2015 Elsevier B.V. All rights reserved.)

With the aim of studying the involvement of the mitochondrial genome in the impairment of heart function, mitochondrial DNA was analyzed by modified primer shift-polymerase chain reaction in a panel of young patients affected by primary cardiomyopathies. Mitochondrial DNA molecules harboring the 7436 bp deletion were specifically found in cardiomyopathic patients as compared with a panel of control subjects. The 4977 bp deletion was commonly detected among the subjects analyzed whereas none of the specific tRNA gene point mutations generally associated with the cardiomyopathic trait were detected. The presence of the 7436 bp deletion as a consequence of a premature aging of the heart muscle, secondary to heart dysfunction, is discussed.

Sensitivity to digestion with pronase has been used to show that the precursor form of mitochondrial aspartate aminotransferase, the form lacking the N-terminal presequence, that with a deletion of the first 9 residues and mutants of the mature enzyme in which residue Cys-166 is mutated to alanine or serine, all retain unfolded conformations after synthesis in a reticulocyte lysate. In the presence of lysed mitochondria the various forms of mitochondrial aspartate aminotransferase retained their susceptibilities to pronase in a way that mirrored the efficiencies with which they are imported into intact mitochondria. The results are interpreted as showing that the presequence of mitochondrial aspartate aminotransferase is not uniquely required for interaction with cytosolic factors required to maintain the newly synthesised protein in a form competent for interacting with, and being imported into, mitochondria.

Mutant genes were constructed which coded for the precursor form of mitochondrial aspartate aminotransferase in which residue cysteine 166 was mutated to either serine or alanine and for forms of the protein lacking both the presequence and residues 1-9 of the mature protein but carrying the same cysteine mutations. The protein products of all of these mutant genes were imported into mitochondria that had been added to the expression system but with varying degrees of efficiency. The results showed that the effects of mutation of cysteine 166 and of deletion of residues 1-9 of the mature protein on sequestration into mitochondria were essentially cumulative, suggesting that these parts of the protein are involved in distinct steps on the recognition/uptake pathway.

Two fused genes were constructed which encode for two chimeric proteins in which either 10 or 191 N-terminal amino acids of mature mitochondrial aspartate aminotransferase had been attached to the entire polypeptide chain of cytosolic dihydrofolate reductase. The precursor and mature form of mitochondrial aspartate aminotransferase, dihydrofolate reductase and both chimeric proteins were synthesized in vitro and their import into isolated mitochondria was studied. Both chimeric proteins were taken up by isolated organelles, where they became protease resistant, thus indicating the ability of the N-terminal portion of the mature moiety of the precursor of mitochondrial aspartate aminotransferase to direct cytosolic dihydrofolate reductase into mitochondria.

To gain some insight into the role played by certain protein domains in the import of mitochondrial aspartate aminotransferase in isolated mitochondria, three protein mutants were constructed by using the plasmid pOTS-mAspAT, which contains the nucleotide sequence encoding for the mature form of this enzyme. Two mutant proteins in which Cys-166 was substituted with either serine or alanine and another protein lacking the nine N-terminal amino acids were all synthesized in a cell-free transcription/translation system. Comparison was made among the newly synthesized mutant proteins and the newly synthesized wild type aspartate aminotransferase with respect to their capability to enter mitochondria. All the mutant proteins proved to be able to enter mitochondria even though with a lower efficiency than the wild type enzyme. Interestingly the thiol reagent mersalyl proved to inhibit import of both wild type enzyme and serine mutant, whereas import of alanine mutant was found to be insensitive to mersalyl, thus showing that Cys-166 is the unique -SH group involved in import. Import of mitochondrial aspartate aminotransferase by mitochondria is shown to involve certain protein domains present in the mature protein, two of them being the Cys-166 and the N-terminal regions.

Both the precursor and the mature form of mitochondrial aspartate aminotransferase were synthesized in a cell-free coupled transcription/translation system directed by the recombinant expression plasmid pOTS-pmAspAT and pOTS-mAspAT, respectively. Both newly synthesized forms of the protein were imported into isolated mitochondria, with the precursor correctly processed to the mature form. In both cases the import process showed resistance to externally added pronase and was abolished in mitochondria treated with the uncoupler carbonyl cyanide m-chlorophenylhydrazone. Moreover the imported products showed the same intramitochondrial localization as judged by a subfractionation procedure. In both cases import was time dependent and was completed in about 15 min. Finally a competitive inhibition of the import of the precursor of aspartate aminotransferase was found due to externally added purified aspartate aminotransferase.

To gain insight into the uptake of mature aspartate aminotransferase by isolated mitochondria, the capability of certain cyanogen bromide peptides from mature beef heart mitochondrial aspartate aminotransferase to inhibit enzyme uptake was kinetically tested. N-terminal peptides (1-9 and 10-31) proved to inhibit the rate of aspartate aminotransferase uptake respectively in purely competitive and non-competitive ways, whereas other peptides distal from the N-terminus (203-217, 321-327 and 328-353) were found to be completely ineffective.

Fumarate permeation in isolated rat liver mitochondria was demonstrated by measuring malate and phosphate efflux caused by fumarate added externally to the mitochondrial suspension. The existence of two specific fumarate translocators, fumarate/malate and fumarate/phosphate, is shown here. These carriers are distinguished in the light of different kinetic parameters (Km values are 50 microM and 150 microM, and Vmax values are 17 and 40 nmoles/min X mg mitochondrial protein, respectively) and of differing sensitivity to non-penetrant compounds. Fumarate was found to cause oxaloacetate efflux from mitochondria by means of an indirect process which involves the cooperation of both fumarate/malate and malate/oxaloacetate translocators. Results are discussed in the light of the physiological role played by fumarate translocation in both ureogenesis and aminoacid metabolism.