Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.

Mol Cell
Authors
Keywords
Abstract

Obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. We recently developed a method to map proteomes in living cells with an engineered peroxidase (APEX) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when applied to unbounded regions that allow APEX-generated radicals to escape. Here, we combine APEX technology with a SILAC-based ratiometric tagging strategy to substantially reduce unwanted background and achieve nanometer spatial resolution. This is applied to map the proteome of the mitochondrial intermembrane space (IMS), which can freely exchange small molecules with the cytosol. Our IMS proteome of 127 proteins has >94% specificity and includes nine newly discovered mitochondrial proteins. This approach will enable scientists to map proteomes of cellular regions that were previously inaccessible.

Year of Publication
2014
Journal
Mol Cell
Volume
55
Issue
2
Pages
332-41
Date Published
2014 Jul 17
ISSN
1097-4164
URL
DOI
10.1016/j.molcel.2014.06.003
PubMed ID
25002142
PubMed Central ID
PMC4743503
Links
Grant list
DP1 OD003961 / OD / NIH HHS / United States
Howard Hughes Medical Institute / United States