The Yeast Mitochondrial Proteome, a Study of Fermentative and Respiratory Growth

Abstract

Saccharomyces cerevisiae is able to switch from fermentation to respiration (diauxic shift) with major changes in metabolic activity. This phenomenon has been previously studied on the transcriptional level. Here we present a parallel analysis of the yeast mitochondrial proteome and the corresponding transcriptional activity in cells grown on glucose (fermentation) and glycerol (respiration). A two-dimensional reference gel for this organelle proteome was established (available at www.biochem.oulu.fi/proteomics/), which contains about 800 intense spots. From 459 spots 253 individual proteins were identified, among them low abundant and hydrophobic proteins, and 37 proteins previously deemed hypothetical, with partially unknown cellular localization. After the diauxic shift, mitochondrial levels of only 18 proteins were changed (17 increased, with 1 decreased), among them proteins involved in the tricarboxylic acid cycle (Sdh1p, Sdh2p, and Sdh4p) and the respiratory chain (Cox4p, Cyb2p, and Qcr7p), proteins contributing to other respiratory pathways (Ach1p, Adh2p, Ald4p, Cat2p, Icl2p, and Pdh1p), and two proteins with unknown function (Om45p and Ybr230p). Apart from an overall increase in mitochondrial protein mass, the mitochondrial proteome remains remarkably constant, even in a major metabolic adaptation. This seemingly disagrees with results of the DNA microarray analyses, where a rather heterogenous up-or down-regulation of genes encoding mitochondrial proteins implies large changes in the proteome. We propose that the discrepancy between proteome and transcriptional regulation, apart from different translation efficiency, indicates a changed turnover rate of proteins in different physiological conditions.

Role of Protein Kinase C-mediated Protein Phosphorylation in Mitochondrial Translocation of Mouse CYP1A1, Which Contains a Non-canonical Targeting Signal

“…In the case of various CYP and glutathione S-transferase proteins, detailed analysis of targeting mechanism shows a need for the activation of chimeric MT-targeting signals by physiological factors (9 -11, 14). These results on bimodal targeting are also supported by recent proteomic data showing a large number of proteins identified as part of mitochondrial proteome are also localized to extramitochondrial compartments, including the cytosol, peroxisomes, and ER membrane (5)(6)(7)(8). It is therefore highly likely that the bimodal targeting, driven by chimeric NH 2 -terminal signals as shown for various CYP and glutathione S-transferase enzymes, represents a precisely evolved physiological process with functional significance.…”

“…It remains to be determined if this step is also an important regulatory step that determines the extent of MT targeting. It is becoming increasingly apparent that mitochondria from lower eukaryotes as well as from mammalian cells contain a large number of proteins that were previously thought to be exclusively extramitochondrial in their location and function (5)(6)(7)(8). It is estimated that nearly 50% of the Ͼ1500 proteins associated with mammalian mitochondria may lack canonical mitochondrial-targeting signals.…”

Yeast Contain a Non-proteinaceous Pool of Copper in the Mitochondrial Matrix

“…The known assembly factors involved in copper ion metallation of CcO are not likely to contribute to the mitochondrial copper pool because they are low abundance proteins. A recent mitochondrion proteomic study showed Sco1 to be a low abundant protein comparable in levels of the CcO subunit Cox6 (42).…”

Use of selective extraction and fast chromatographic separation combined with electrophoretic methods for mapping of membrane proteins

“…The purity of organelles and other protein complexes is crucial to subcellular proteome research [13][14][15][16][17]. For the isolation of subcellular structures and organelles several methods, such as differential-and density-gradient centrifugation [18][19][20], immunoisolation [8], affinity purification, [21], and freeflow electrophoresis [22], have been applied. It has been shown that such fractionations improved identification of proteins from targeted subcellular structures [8,10,[12][13][14][15].…”