Sickmann online dating elucidating isoniazid resistance using molecular
The mitochondrial proteome comprises ~1000 (yeast)–1500 (human) different proteins, which are distributed into four different subcompartments.
The sublocalization of these proteins within the organelle in most cases remains poorly defined.
Samples were analyzed by SDS–PAGE and radiolabelled proteins visualized by autoradiography.
In case of presequence cleavage upon import a size shift from the precursor to the mature protein can be observed.
c Map data correlation with known submitochondrial localization of components of the translocase of the inner membrane (TIM), the citrate cycle machinery, complex IV of the respiratory chain, and the Coenzyme Q biosynthesis apparatus To further validate how precisely this map reflects the actual protein classes we chose several well-known mitochondrial protein machineries and complexes with established topologies comprising proteins from all three classes, i.e., soluble, peripheral, and integral membrane proteins (Fig. Indeed, all identified proteins of these complexes localized to the expected clusters in our map (Fig. For the Co Q machinery a clear separation of the integral Coq2 protein from the remaining peripheral membrane proteins could be observed.
Interestingly, the remaining Co Q proteins cluster in two distinct sets in the peripheral membrane protein cloud which might indicate a pool of more tightly associated membrane proteins (Coq1 and Coq8) and a more loosely associated pool (Fig. Notably, two components of Complex IV, Cox4 and Cox6, were found in the ambiguous region – indeed, it has been shown that both co-exist in a peripheral membrane bound as well as a soluble form.
This might partially result from the incorporation of bioinformatic predictions without clear experimental support or the direct inclusion of high-throughput data that often bears misannotations.
Large scale tagging approaches for subcellular and suborganellar localization are particularly problematic in case of mitochondria, because tags often interfere with the protein import and sorting machineries, either preventing import or leading to mislocalization of tagged proteins.
We therefore compared their relative abundance within mitochondria and complete yeast cells, based on label free spectral counting and determined Yeast/Mito ratios for all mitochondrial proteins (Fig. The majority of known mitochondrial proteins, but also many of the novel candidates, showed low Yeast/Mito ratios indicating a strong enrichment in the mitochondrial fraction (Supplementary Data 2).
Protein extraction was performed based on sonication to separate membrane proteins (PEL).
Respective SN/PEL SILAC ratios were determined by LC-MS. b Exemplary SILAC results a for Tim proteins representing the three different protein classes analyzed, confirmed by immunoblotting Mapping of mitochondrial proteins into different classes.
[S]labeled precursors of candidate proteins were generated by in vitro transcription/translation and incubated with isolated mitochondria in the presence or absence of the membrane potential (Δψ) or without mitochondria (Mock).
Import reaction was terminated by depletion of the membrane potential and samples were treated with Proteinase K where indicated to remove non-imported precursors.