Global analysis of condition-specific subcellular protein distribution and abundance.
Cellular control of protein activities by modulation of their abundance or compartmentalization is not easily measured on a large scale. We developed and applied a method to globally interrogate these processes that is widely useful for systems-level analyses of dynamic cellular responses in many cell types. The approach involves subcellular fractionation followed by comprehensive proteomic analysis of the fractions, which is enabled by a data-independent acquisition mass spectrometry approach that samples every available mass to charge channel systematically to maximize sensitivity. Next, various fraction-enrichment ratios are measured for all detected proteins across different environmental conditions and used to group proteins into clusters reflecting changes in compartmentalization and relative conditional abundance. Application of the approach to characterize the response of yeast proteins to fatty acid exposure revealed dynamics of peroxisomes and novel dynamics of MCC/eisosomes, specialized plasma membrane domains comprised of membrane compartment occupied by Can1 (MCC) and eisosome subdomains. It also led to the identification of Fat3, a fatty acid transport protein of the plasma membrane, previously annotated as Ykl187.
Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA.
Sunhee
S
Jung
Jennifer J
JJ
Smith
Priska D
PD
von Haller
David J
DJ
Dilworth
Katherine A
KA
Sitko
Leslie R
LR
Miller
Ramsey A
RA
Saleem
David R
DR
Goodlett
John D
JD
Aitchison
D002458:Cell Fractionation; D003470:Culture Media; D005947:Glucose / Q000378:metabolism; D050356:Lipid Metabolism; D008856:Microscopy, Fluorescence; D058977:Molecular Sequence Annotation; D019301:Oleic Acid / Q000378:metabolism; D015388:Organelles / Q000737:chemistry / Q000378:metabolism; D021381:Protein Transport; D020543:Proteome / Q000737:chemistry / Q000378:metabolism*; D040901:Proteomics; D012441:Saccharomyces cerevisiae / Q000254:growth & development / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism*; D013347:Subcellular Fractions / Q000737:chemistry
D003470:Culture Media; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D019301:Oleic Acid; D005947:Glucose