Abstract
Membrane-associated proteins are required for essential processes like transport, organelle biogenesis, and signaling. Many are expected to function as part of an oligomeric protein complex. However, membrane-associated proteins are challenging to work with, and large-scale data sets on the oligomerization state of this important class of proteins is missing. Here we combined cell fractionation of Arabidopsis leaves with nondenaturing detergent solubilization and LC/MS-based profiling of size exclusion chromatography fractions to measure the apparent masses of >1350 membrane-associated proteins. Our method identified proteins from all of the major organelles, with more than 50% of them predicted to be part of a stable complex. The plasma membrane was the most highly enriched in large protein complexes compared with other organelles. Hundreds of novel protein complexes were identified. Over 150 proteins had a complicated localization pattern, and were clearly partitioned between cytosolic and membrane-associated pools. A subset of these dual localized proteins had oligomerization states that differed based on localization. Our data set is an important resource for the community that includes new functionally relevant data for membrane-localized protein complexes that could not be predicted based on sequence alone. Our method enables the analysis of protein complex localization and dynamics, and is a first step in the development of a method in which LC/MS profile data can be used to predict the composition of membrane-associated protein complexes.
Highlights
Plants provide food, fiber, and a rapidly growing list of renewable bioproducts that supply the energy, pharmaceutical, and chemical industries
This profiling approach allows for the oligomerization state of thousands of proteins to be monitored in a single experiment, an important step toward gaining systems levels knowledge about protein complexes in the endomembrane system
We found that many hydrophobic proteins containing one or more transmembrane domains eluted as complexes; there was not a large difference between the percent of zero, one, or multiple transmembrane domain containing proteins that were predicted with an Rapp Ն2
Summary
Fiber, and a rapidly growing list of renewable bioproducts that supply the energy, pharmaceutical, and chemical industries. In response to increased demand from a growing global population and climate instability, the generation of crops will require rational design and engineering where plant architectures are optimized for specialized environments and metabolism is altered to generate products with increased value [1] This is a tall order to fill, and success on this front will require broad systems-level knowledge about cell function and how proteins, protein complexes, and networks of interacting pathways determine plant traits [2]. The strength of PCP is that thousands of proteins are analyzed in a single experiment for unbiased discovery of stable protein complexes One limitation this method is that elongated protein shapes or high-mass post-translational modifications can lead to false positives. The above profiling articles analyze soluble proteins, and the important membrane-associated proteins were discarded as the troublesome microsomal pellet
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