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In vivo mapping of protein complex organization
Author(s) -
Gingras AnneClaude
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.259.1
Subject(s) - organelle , compartmentalization (fire protection) , biotinylation , biology , microbiology and biotechnology , compartment (ship) , subcellular localization , protein subcellular localization prediction , cell fractionation , computational biology , cellular compartment , biochemistry , nucleic acid , transport protein , function (biology) , chemistry , cell , cytoplasm , membrane , enzyme , gene , oceanography , geology
Compartmentalization is essential for all complex forms of life. In eukaryotic cells, membrane‐bound organelles, as well as a multitude of protein‐ and nucleic acid‐rich subcellular structures, maintain boundaries and serve as enrichment zones to promote and regulate protein function. Consistent with the critical importance of these boundaries, alterations in the machinery that mediate protein transport between these compartments has been implicated in a number of diverse diseases. Understanding the composition of each cellular “compartment” (be it a classical organelle or a large protein complex) remains a challenging task. For soluble protein complexes, approaches such as affinity purification other biochemical fractionation coupled to mass spectrometry provides important insight, but this is not the case for detergent‐insoluble components. Classically, both microscopy and organellar purifications have been employed for identifying the composition of these structures, but these approaches have limitations, notably in resolution for standard high‐throughput fluorescence microscopy and in the difficulty in purifying some of the structures (e.g. p‐bodies) for approaches based on biochemical isolations. Prompted by the recent implementation in vivo biotinylation approaches such as BioID, we report here the systematic mapping of the composition of various subcellular structures, using as baits proteins (or protein fragments) which are well‐characterized markers for a specified location. We defined how relationships between “prey” proteins detected through this approach can help understanding the protein organization inside a cell. We will discuss our low‐resolution map of a human cell containing major organelles and non‐membrane bound structures, but also a higher resolution map of RNA‐containing cellular structures, including the p‐bodies and the stress granules that regulate mRNA stability. This will be presented alongside new computational tools that will help the scientific community to make use of our dataset. Support or Funding Information We acknowledge the support of the Canadian Institutes of Health Research and the Natural Sciences and Engineering Research Council of Canada.A draft map of a human cell using proximity biotinylation