title: Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.
abstract: We have combined classical subcellular fractionation with large-scale quantitative mass spectrometry to identify proteins that enrich specifically with peroxisomes of Saccharomyces cerevisiae. In two complementary experiments, isotope-coded affinity tags and tandem mass spectrometry were used to quantify the relative enrichment of proteins during the purification of peroxisomes. Mathematical modeling of the data from 306 quantified proteins led to a prioritized list of 70 candidates whose enrichment scores indicated a high likelihood of them being peroxisomal. Among these proteins, eight novel peroxisome-associated proteins were identified. The top novel peroxisomal candidate was the small GTPase Rho1p. Although Rho1p has been shown to be tethered to membranes of the secretory pathway, we show that it is specifically recruited to peroxisomes upon their induction in a process dependent on its interaction with the peroxisome membrane protein Pex25p. Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.
authors.forename: Marcello
authors.initials: M
authors.lastname: Marelli
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Smith
authors.forename: Sunhee
authors.initials: S
authors.lastname: Jung
authors.forename: Eugene
authors.initials: E
authors.lastname: Yi
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: Rowan H
authors.initials: RH
authors.lastname: Christmas
authors.forename: Ramsey A
authors.initials: RA
authors.lastname: Saleem
authors.forename: Yuen Yi C
authors.initials: YY
authors.lastname: Tam
authors.forename: Andrei
authors.initials: A
authors.lastname: Fagarasanu
authors.forename: David R
authors.initials: DR
authors.lastname: Goodlett
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Richard A
authors.initials: RA
authors.lastname: Rachubinski
authors.forename: John D
authors.initials: JD
authors.lastname: Aitchison
mesh_terms: D000199:Actins / Q000032:analysis / Q000378:metabolism*; D020558:GTP Phosphohydrolases / Q000378:metabolism; D007425:Intracellular Membranes / Q000378:metabolism*; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008962:Models, Theoretical; D000074401:Peroxins; D020675:Peroxisomes / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D020741:rho GTP-Binding Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D000199:Actins; D008565:Membrane Proteins; C475282:PEX25 protein, S cerevisiae; D000074401:Peroxins; D029701:Saccharomyces cerevisiae Proteins; D020558:GTP Phosphohydrolases; C051302:RHO1 protein, S cerevisiae; D020741:rho GTP-Binding Proteins