Table II. Additional trafficking or membrane associated proteins preferentially ubiquitinated with K0 Ub. Ubiquitinated proteins enriched in K0 Ub expressing cells from supplementary Table S1 that are associated with protein sorting, trafficking, or membrane-associated processes, but not included in Table I. Light-to-Heavy (L/H) ratio represents abundance of each target in K0 Ub-expressing cells relative to WT. Protein descriptions are based on SGD http://www.yeastgenome.org.

Systematic name	Protein	Ratio L/H	Protein description
YMR316W	DIA1	12.2	Protein of unknown function, involved in invasive and pseudohyphal growth, target of calcineurin signaling
YDL226C	GCS1	6.1	ADP-ribosylation factor GTPase activating protein (ARF GAP), involved in ER-Golgi transpor
YDR425W	SNX41	5.1	Sorting nexin, involved in the retrieval of late-Golgi SNAREs
YLR219W	MSC3	3.9	Protein of unknown function; may be a component of eisosomes
YDL203C	ACK1	3.5	Protein that functions upstream of Pkc1p in the cell wall integrity pathway
YOR171C	LCB4	3.5	Sphingoid long-chain base kinase, responsible for synthesis of long-chain base phosphates
YJR125C	ENT3	3.0	Protein containing an N-terminal epsin-like domain involved in clathrin recruitment and traffic
YGR086C	PIL1	2.9	Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis
YOR109W	INP53	2.8	Polyphosphatidylinositol phosphatase, dephosphorylates multiple phosphatidylinositols
YMR079W	SEC14	2.7	Phosphatidylinositol/phosphatidylcholine transfer protein
YNL054W	VAC7	2.6	Integral vacuolar membrane protein involved in vacuole inheritance and morphology
YAL002W	VPS8	2.6	Membrane-associated protein that interacts with Vps21p to facilitate soluble vacuolar protein localization
YGR136W	LSB1	2.4	Protein containing an N-terminal SH3 domain
YGR130C	YGR130C	2.4	Putative protein of unknown function; possible component of the eisosome
YIL041W	GVP36	2.1	BAR domain-containing protein that localizes to both early and late Golgi vesicles
YDL029W	ARP2	2.1	Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center
YPL195W	APL5	2.0	Delta adaptin-like subunit of the clathrin associated protein complex (AP-3)
YJL154C	VPS35	1.9	Endosomal subunit of membrane-associated retromer complex required for retrograde transport
YKL212W	SAC1	1.8	Phosphatidylinositol phosphate (PtdInsP) phosphatase involved in hydrolysis of PtdIns[4]P
YCR088W	ABP1	1.8	Actin-binding protein of the cortical actin cytoskeleton
YDR129C	SAC6	1.8	Fimbrin, actin-bundling protein; cooperates with Scp1p in the organization of the actin cytoskeleton
YNL044W	YIP3	1.7	Protein localized to COPII vesicles, proposed to be involved in ER to Golgi transport
YGR261C	APL6	1.7	Beta3-like subunit of the yeast AP-3 complex
YEL013W	VAC8	1.7	Phosphorylated and palmitoylated vacuolar membrane protein, required for cytoplasm-to-vacuole targeting
YPR139C	VPS66	1.6	Cytoplasmic protein of unknown function involved in vacuolar protein sorting
YFR051C	RET2	1.6	Delta subunit of the coatomer complex (COPI), which coats Golgi-derived transport vesicles
YFL039C	ACT1	1.6	Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions
YER143W	DDI1	1.5	DNA damage-inducible v-SNARE binding protein, contains a ubiquitin-associated (UBA) domain
YBR080C	SEC18	1.5	ATPase required for vesicular transport between ER and Golgi
YML048W	GSF2	1.5	ER localized integral membrane protein that may promote secretion of certain hexose transporters
YKR001C	VPS1	1.5	Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization
YCR009C	RVS161	1.5	Amphiphysin-like lipid raft protein; regulates polarization of the actin cytoskeleton, endocytosis, cell polarity
YPR029C	APL4	1.5	Gamma-adaptin, large subunit of the clathrin-associated protein (AP-1) complex