Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

Morgenstern, Marcel; Stiller, Sebastian B.; Lübbert, Philipp; Peikert, Christian D.; Dannenmaier, Stefan; Drepper, Friedel; Weill, Uri; Höß, Philipp; Feuerstein, Reinhild; Gebert, Michael; Bohnert, Maria; Laan, Martin van der; Schuldiner, Maya; Schütze, Conny; Oeljeklaus, Silke; Pfanner, Nikolaus; Wiedemann, Nils; Warscheid, Bettina

doi:10.1016/j.celrep.2017.06.014

Cited by 364 publications

(481 citation statements)

References 59 publications

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“…In short, peptides that are facing the cytosol will be sensitive to protease treatment and hence will be lost from MS analysis. This method was recently used to assess yeast mitochondrial protein membrane topology …”

Section: Resultsmentioning

confidence: 99%

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

et al. 2019

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Membrane proteins perform a variety of functions, all crucially dependent on their orientation in the membrane. However, neither the exact number of transmembrane domains (TMDs) nor the topology of most proteins have been experimentally determined. Due to this, most scientists rely primarily on prediction algorithms to determine topology and TMD assignments. Since these can give contradictory results, single‐algorithm‐based predictions are unreliable. To map the extent of potential misanalysis, the predictions of nine algorithms on the yeast proteome are compared and it is found that they have little agreement when predicting TMD number and termini orientation. To view all predictions in parallel, a webpage called TopologYeast: http://www.weizmann.ac.il/molgen/TopologYeast was created. Each algorithm is compared with experimental data and a poor agreement is found. The analysis suggests that more systematic data on protein topology are required to increase the training sets for prediction algorithms and to have accurate knowledge of membrane protein topology.

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Section: Resultsmentioning

confidence: 99%

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

et al. 2019

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“…Mitochondria contain about 1000 proteins in baker's yeast S. cerevisiae and 1500 proteins in human mitochondria . Mitochondria of higher plants are thought to contain even more than 2000 proteins .…”

Section: Channel‐forming Proteins In Protein Transportmentioning

confidence: 99%

“…VDAC is the most abundant outer membrane protein. In yeast, two isoforms exists: the major form Por1 and the low abundant Por2 . In human mitochondria three VDAC isoforms are present .…”

Section: Channel‐forming Proteins In Metabolite Transportmentioning

confidence: 99%

Mitochondrial Outer Membrane Channels: Emerging Diversity in Transport Processes

Becker

Wagner

2018

BioEssays

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Mitochondrial function and biogenesis depend on the transport of a large variety of proteins, ions, and metabolites across the two surrounding membranes. While several specific transporters are present in the inner membrane, transport processes across the outer membrane are less understood. Recent studies reveal that the number of outer membrane channels and their transport mechanisms are more diverse than originally thought. Four protein-conducting channels promote transport of distinct sets of precursor proteins across and into the outer membrane. The voltage-dependent anion channel (VDAC) forms the major channel for small hydrophilic molecules. In addition, three channels with yet unknown substrate specificity exist in the outer membrane. In this review, we outline the emerging functional diversity, selectivity, and regulation of mitochondrial outer membrane channels. The presence of several channel-forming proteins challenges the traditional view that the outer membrane forms an unspecific size-exclusion filter for the flux of small hydrophilic molecules.

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“…Mitochondria are essential cellular organelles that are key sources of ATP generation via oxidative phosphorylation as well as the assembly of iron-sulfur clusters and many other catabolic and anabolic reactions (Attardi and Schatz, 1988). To support mitochondrial function, thousands of nuclearencoded proteins are imported into mitochondria from the cytoplasm (Morgenstern et al, 2017). This has to be coordinated with the gene expression of the mitochondrial genome, which in Saccharomyces cerevisiae contains 13 genes (Borst and Grivell, 1978).…”

Section: Introductionmentioning

confidence: 99%

“…This metabolic change is known to dramatically change the mitochondrial morphology (Egner et al, 2002). The protein content of yeast mitochondria also shows dynamic changes in response to shifting cellular energy demands (Morgenstern et al, 2017;Paulo et al, 2016). Oxidative phosphorylation protein coding mRNAs are known to gradually increase their protein synthesis as the growth environment changes from fermentative growth to respiratory conditions (Couvillion et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins

Tsuboi

Viana

et al. 2019

Preprint

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Mitochondria are dynamic in their size and morphology yet must also precisely control their protein composition according to cellular energy demand. Although nuclear-encoded mRNAs can be localized to the mitochondrial outer membrane, the importance of this localization in altering mitochondrial protein composition is unclear. We have found that, as yeast switch from fermentative to respiratory metabolism, there is an increase in the fraction of the cytoplasm that is mitochondrial. This drives the localization of certain nuclear-encoded mitochondrial mRNAs to the surface of the mitochondria. Through tethering experiments, we show that mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth. Furthermore, we find that ribosome stalling impacts mRNA sensitivity to mitochondrial volume fraction and counterintuitively leads to enhanced protein synthesis by increasing mRNA localization to the mitochondria. This points to a mechanism by which cells are able to use translation elongation and the geometric constraints of the cell to fine-tune organelle-specific gene expression through mRNA localization while potentially circumventing the need to directly coordinate with the nuclear genome. mitochondria | geometric constraints | mRNA localization | translation control

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Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

Cited by 364 publications

References 59 publications

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

Mitochondrial Outer Membrane Channels: Emerging Diversity in Transport Processes

Mitochondrial volume fraction controls translation of nuclear-encoded mitochondrial proteins

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