Table I

Core list of proteins identified as mβcd-responsive in at least two biological replicate experimental sets

Each protein was functionally classified by MapMan (34). p values indicate the significance of the mβcd response. A cutoff p value of 0.05 was used after correction for multiple testing (32). “DRM” refers to proteins identified as mβcd-responsive based on differential analysis of DRM preparations after mβcd treatment of plasma membranes. “sup” identifies mβcd responsiveness based on release of these proteins to the supernatant after pelleting mβcd-treated plasma membranes. Letters indicate proteins previously published as being GPI-anchored (gpi) (35, 36, 50, 51) or present in DRM in Arabidopsis (drm) (15). Localization is taken from the SUBA database of subcellular localizations (39): PM, plasma membrane; EX, extracellular space; P, plastid; V, vacuole; C, cytosol; N, nucleus; M, mitochondrion. AGI, Arabidopsis gene identifier; DREPP, developmentally regulated plasma membrane polypeptide; v-ATPase, vacuolar type H+-ATPase; LYSM, lysin motif.

AGIDescriptionMapMan functional categoryp valueTimes foundExperimentExperimental subcellular localization from SUBADRM/GPI
MSGFP
At3g07390AIR12; extracellular matrix structural constituentHormone metabolism2.06e−064sup, DRMER, EX, PEX, PMgpi
At4g26690MRH5/SHV3; glycerophosphodiester phosphodiesterase/kinaseLipid metabolism2.06e−064sup, DRMER, EX, PM, MEX, PMgpi
At4g31140Glycosyl hydrolase family 17 proteinCell wall2.06e−063sup, DRMER, EX, PMEX, PMgpi
At5g58090Glycosyl hydrolase family 17 proteinNot assigned, no ontology2.06e−064sup, DRMER, EX, PMEX, PMgpi
At5g58480aGlycosyl hydrolase family 17 proteinNot assigned, no ontology2.06e−062DRMC, ER, EX, PM, MPMgpi
At3g13560Glycosyl hydrolase family 17 proteinCell wall2.54e−063sup, DRMER, EX, PM, MEX, PMgpi
At5g44130Fasciclin-like arabinogalactan protein (FLA13)Cell wall7.10e−066sup, DRMER, EX, PM, MEX, PMgpi
At2g25060Plastocyanin-like domain-containing proteinCell wall1.29e−054sup, DRMER, EX, PMEX, PMgpi
At4g25240SKS1 (SKU5 similar 1); copper ion-bindingCell wall1.56e−056sup, DRMER, EX, PMPMdrm, gpi
At5g55480Glycerophosphoryldiester phosphodiesterase family proteinLipid metabolism1.56e−056sup, DRMEX, PM, P, MEX, PMdrm, gpi
At4g31840Plastocyanin-like domain-containing proteinCell wall1.72e−056sup, DRMER, EX, M, VPMgpi
At4g12730Fasciclin-like arabinogalactan protein (FLA2)Cell wall1.84e−056sup, DRMER, EX, PM, MPMgpi
At3g02740Aspartyl protease family proteinProtein degradation3.06e−052sup, DRMER, EX, VPMgpi
At1g64760Glycosyl hydrolase family 17 proteinCell wall4.62e−055sup, DRMER, EX, PMPMgpi
At5g53870Plastocyanin-like domain-containing proteinCell wall5.16e−054sup, DRMER, EX, M, N, VPMgpi
At2g04780Fasciclin-like arabinogalactan protein (FLA7)Cell wall9.75e−056sup, DRMER, EX, PMEX, PMgpi
At2g45470Fasciclin-like arabinogalactan protein (FLA8)Cell wall2.01e−045sup, DRMER, EXEX, PMgpi
At5g55730Fasciclin-like arabinogalactan protein (FLA1)Cell wall2.25e−045sup, DRMER, EX, P, MEX, PMgpi
At3g61260DNA-binding family protein/remorin family proteinRNA regulation of transcription3.35e−042DRMNPM
At3g58100aGlycosyl hydrolase family 17 proteinCell wall3.99e−042DRMEXPMgpi
At2g17120LYM2 (LYSM domain GPI-anchored protein 2)Not assigned, no ontology6.53e−044DRMC, ER, EX, PEX, PMgpi
At5g51480SKS2 (SKU5 similar 2); copper ion bindingCell wall2.20e−036sup, DRMER, EX, PMPMgpi
At2g45820DNA-binding protein, putativeRNA regulation of transcription3.65e−034sup, DRMC, NPM
At5g42100Glycosyl hydrolase family 17 proteinCell wall4.64e−032DRMER, EX, MEX, PMgpi
At3g03520aPhosphoesterase family proteinNot assigned, no ontology6.08e−032supEX, M, NVgpi
At4g12420SKU5 (skewed 5); copper ion bindingNot assigned, no ontology1.28e−022supER, EX, PMEX, PMdrm, gpi
At5g48450SKS3 (SKU5 Similar 3); copper ion bindingCell wall1.39e−022DRMER; EX, VPM
At5g25090Plastocyanin-like domain-containing proteinCell wall1.88e−022DRMER, EX, PM, MEX, PMgpi
At4g30190AHA2 (Arabidopsis H+-ATPase 2); ATPaseTransport, p- and v-ATPases1.91e−022supC, PMPM
At2g01210Leucine-rich repeat transmembrane protein kinase, putativeSignaling, receptor kinases2.05e−022DRMC, ER, EX, PMEX, PM, P
At2g05920Subtilase family proteinProtein degradation2.13e−022DRMER, EX, M, PEX
At4g27520Plastocyanin-like domain-containing proteinCell wall2.64e−023sup, DRMER, EX, NEX, PM, Pgpi
At1g11820Hydrolase, hydrolyzing O-glycosyl compoundsNot assigned, no ontology2.99e−022DRMER, EX, PMEX
At2g38940ATPT2 (phosphate transporter 2)Transport phosphate3.23e−023sup, DRMEX, PM, P, MPM, V
At3g08510ATPLC2 (phospholipase C2); phospholipase CLipid metabolism3.53e−022DRMC, M, PPM
At4g36750Quinone reductase family proteinLipid metabolism4.54e−022DRMC, M, NPMdrm
At4g20260DREPP plasma membrane polypeptide family proteinNot assigned, no ontology4.71e−014sup, DRMM, NPM, P
  • a Proteins identified based on a single peptide (see supplemental Fig. 1 for annotated spectra).