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Table 3. Two hundred and eleven candidate membrane-associated ubiquitinated proteins

Cytoskeleton/cell wall/cytokinesis

Gene

TM domain

Localization

Description

ECM21*

No

Unknown

"ExtraCellular Mutant" protein of unknown function

CHS3

Yes

Plasma Membrane

Chitin synthase III

CHS2

Yes

Plasma Membrane

Chitin synthase II

ECM33

Yes

Plasma Membrane

"ExtraCellular Mutant" protein of unknown function

BUD3

Predicted

Bud Neck Membrane

Bud neck protein required for axial budding

SPO71

Predicted

Spore Wall

Protein involved in spore wall formation

SAC6

No

Actin Cytoskeleton

Actin filament bundling protein Fimbrin homolog

NUM1

No

Microtubule Cytoskeleton

Tubulin-binding protein required for G2 nucleus migration

RVS167

No

Actin Cytoskeleton

BAR adaptor protein; actin cytoskeleton regulator

ACT1

No

Actin Cytoskeleton

Actin

GSC2

Yes

Plasma Membrane

Beta-1,3-glucan synthase

SKN1

Yes

Golgi Membrane

Beta-1,6-glucan synthase (putative)

BGL2

No

Cell Wall

Cell wall endo-beta-1,3-glucanase

RHO3

No

Actin Cytoskeleton

Ras homolog; GTP-binding actin cytoskeleton regulator

BUD4

No

Bud Neck (Peripheral)

Bud neck protein required for axial budding

FKS1*

Yes

Plasma Membrane

Beta-1,3-glucan synthase

YLR422W

Predicted

Unknown Membrane

Protein of unknown function containing region of homology to mouse actin regulatory protein Dock2

GAS1

Yes

Plasma Membrane

1,3-Beta-Glucanosyltransferase

CHS1

Yes

Plasma Membrane

Chitin synthase I

HUA2

No

Actin Cytoskeleton

Putative role in assembly of cortical actin patches

KRE6

Yes

Golgi Membrane

Beta-1,6-glucan synthase (putative)

DNA Replication/Transcription

HTB2/HTB1*

No

Nucleus

Histone H2B

CDC47

No

Nucleus

MCM/P1 family member involved in DNA synthesis initiation

RPO21*

No

Nucleus

RNA polymerase II, largest subunit

CDC1

Predicted

Unknown Membrane

Protein that affects bud emergence, intrachromosomal recombination, and nuclear division

TRA1

No

Nucleus

Member SAGA histone acetyltransferase complex

IMP2

Predicted

Unknown Membrane

Transcription factor encoded by YIL154C; Regulates mitochondrial sugar utilization

MGA2

Yes

ER-Nuclear Membrane

ER-anchored OLE1 transcription factor

RNR2

No

Nucleus

Ribonucleotide reductase (small subunit)

SPT23

Yes

ER-Nuclear Membrane

ER-anchored OLE1 transcription factor

MET4

No

Nucleus

Transcription factor; Regulates sulfur assimilation pathway

RPB2

No

Nucleus

RNA polymerase II, second-largest subunit

Lipid/Ergosterol Metabolism/Modification

TSC13

Predicted

ER-Nuclear Membrane

Very-long-chain fatty acid (VLCFA) metabolism

LCB2

Yes

ER-Nuclear Membrane

Component of serine C-palmitoyltransferase; Sphingolipid biosynthesis

DPL1

Predicted

ER-Nuclear Membrane

Dihydrosphingosine-1-phosphate lyase; Sphingolipid metabolism

SUR2

Yes

ER-Nuclear Membrane

Sphingosine hydroxylase; Sphingolipid metabolism

SCS2

Yes

ER-Nuclear Membrane

Involved in regulation of INO1 expression

SCS3

Predicted

Unknown Membrane

Involved in inositol phospholipid biosynthesis

ERG25*

Yes

ER-Nuclear Membrane/Plasma Membrane

C-4 sterol methyl oxidase; Ergosterol biosynthesis

ERG1*

Yes

ER-Nuclear Membrane

Squalene monooxygenase; Ergosterol biosynthesis

ERG11

Predicted

ER-Nuclear Membrane

Cytochrome P450, lanosterol 14a-demethylase; Ergosterol biosynthesis

NCP1*

Yes

ER-Nuclear Membrane

NADP-cytochrome P450 reductase

ERG9

Yes

ER-Nuclear Membrane

Squalene synthetase; Ergosterol biosynthesis

INP51

Predicted

Unknown Membrane

Inositol polyphosphate-5-phosphatase

CBR1

Predicted

ER-Nuclear Membrane

NADH-cytochrome b5 reductase

TES1

Predicted

Peroxisomal Membrane

Acyl-CoA thioesterase; Fatty-acid oxidation

TOR2

No

Plasma Membrane/Vacuolar Membrane (Peripheral)

Putative phosphatidylinositol kinase involved in actin cytoskeleton, translation, and meiosis

SAC1

Yes

ER-Nuclear Membrane

Polyphosphoinositide phosphatase

YLL012W

Predicted

Unknown Membrane

Putative phosphatidylinositol-binding protein

ERG27

Predicted

ER-Nuclear Membrane

3-Keto sterol reductase; Ergosterol biosynthesis

STT4

No

Plasma Membrane

Phosphatidylinositol-4-kinase

YML125C

Predicted

Unknown Membrane

Protein with similarity to NADH-cytochrome b5 reductase

ERG5

Predicted

ER-Nuclear Membrane

Cytochrome P450, delta 22(23) sterol desaturase; Ergosterol biosynthesis

ERG2

Predicted

ER-Nuclear Membrane

Sterol C8-C7 isomerase; Ergosterol biosynthesis

SCS7

Predicted

ER-Nuclear Membrane

Ceramide hydroxylase; Very long chain fatty acid (VLCFA) metabolism

LCB1

Yes

ER-Nuclear Membrane

Component of serine C-palmitoyltransferase; Sphingolipid biosynthesis

Membrane transporter/permease/pump

Gene

TM Domain

Localization

Description

TAT1*

Yes

Plasma Membrane

Plasma membrane valine, leucine, isoleucine, and tyrosine transporter

PHO88

Predicted

Unknown Membrane

Involved in inorganic phosphate transport

SNQ2

Yes

Plasma Membrane

Plasma membrane drug-efflux pump

ENA5/ENA2/ENA1*

Yes

Plasma Membrane

Plasma membrane sodium pump

BAP3

Yes

Plasma Membrane

Plasma membrane branched-chain amino acid permease

DNF2

Yes

Plasma Membrane

Plasma membrane putative phospholipid transporter; "Flipase"

YDR119W

Predicted

Unknown Membrane

Putative multidrug resistance transporter

YCF1

Yes

Vacuolar Membrane

Vacuolar glutathione-conjugate transporter

HXT7

Yes

Plasma Membrane

Plasma membrane high-affinity hexose transporter

HXT3

Yes

Plasma Membrane

Plasma membrane low-affinity hexose transporter

ITR1*

Yes

Plasma Membrane

Plasma membrane myo-inositol permease

GNP1

Yes

Plasma Membrane

Plasma membrane glutamine permease

NPR2

Predicted

Unknown Membrane

Putative nitrogen permease regulator

PMC1

Yes

Vacuolar Membrane

Vacuolar calcium transporter

PMA1*

Yes

Plasma Membrane

Plasma membrane proton pump

HIP1

Yes

Plasma Membrane

Plasma membrane histidine permease

TNA1

Yes

Plasma Membrane

Plasma membrane nicotinic acid transporter

YOR1

Yes

Plasma Membrane

Plasma membrane multispecific organic anion transporter

YHR032W

Predicted

Unknown Membrane

Putative membrane transporter

HXT4*

Yes

Plasma Membrane

Plasma membrane moderate- to low-affinity hexose transporter

NEO1

Predicted

Unknown Membrane

Putative phospholipid transporter ; "Flipase"

YJR015W

Predicted

Unknown Membrane

Potential multidrug resistance transporter

STE6

Yes

Plasma Membrane

Plasma membrane mating pheromone transporter

GAP1*

Yes

Plasma Membrane

Plasma membrane general amino acid permease

PTR2

Yes

Plasma Membrane

Plasma membrane peptide permease

BPT1

Yes

Vacuolar Membrane

Vacuolar glutathione-conjugate transporter

YBT1

Yes

Vacuolar Membrane

Vacuolar bile acid transporter

CCC1

Yes

Vacuolar Membrane

Vacuolar calcium/manganese/iron transporter

PHO84

Yes

Plasma Membrane

Plasma membrane high-affinity inorganic phosphate transporter

HXT2

Yes

Plasma Membrane

Plasma membrane high-affinity hexose transporter

YMR166C

Yes

Mitochondrial Membrane

Putative mitochondrial inner membrane transporter

RSN1

Predicted

Unknown Membrane

Possible membrane transporter

LYP1

Yes

Plasma Membrane

Plasma membrane high affinity lysine permease

SMF1

Yes

Plasma Membrane

Plasma membrane manganese transporter

PDR5*

Yes

Plasma Membrane

Plasma membrane multidrug resistance transporter

TPO4

Yes

Plasma Membrane/Vacuolar Membrane

Plasma membrane polyamine transporter

PMA2*

Yes

Plasma Membrane

Plasma membrane proton pump

PDR12

Yes

Plasma Membrane

Plasma membrane multidrug resistance transporter

DIP5

Yes

Plasma Membrane

Plasma membrane dicarboxylic amino acid permease

VMA13

No

Vacuolar Membrane (Peripheral)

Regulatory subunit of vacuolar proton pump (V-ATPase)

Protein glycosylation and lipid modification

PMT2

Predicted

ER-Nuclear Membrane

Mannosyltransferase responsible for initiation of O-linked glycosylation

WBP1

Yes

ER-Nuclear Membrane

Beta-subunit of oligosaccharyltransferase involved in N-linked glycosylation

GPI16

Yes

ER-Nuclear Membrane

Subunit of GPI transamidase

PMT4

Predicted

ER-Nuclear Membrane

Mannosyltransferase responsible for initiation of O-linked glycosylation

ALG9

Predicted

ER-Nuclear Membrane

Mannosyltransferase involved in N-linked glycosylation

ECM39

Predicted

ER-Nuclear Membrane

Alpha-1,6-mannosyltransferase involved in N-linked glycosylation

OST3

Yes

ER-Nuclear Membrane

Gamma-subunit of oligosaccharyltransferase involved in N-linked glycosylation

KTR1

Yes

Golgi Membrane

Alpha-1,2-mannosyltransferase involved in N- and O-linked glycosylation

DPM1

Predicted

ER-Nuclear Membrane

Dolichol-phosphate mannosyltransferase involved in N- and O-linked glycosylation; GPI anchor biosynthesis

Protein Synthesis/Folding/Translocation

Gene

TM Domain

Localization

Description

SSA1

No

Cytoplasm/Ribosome/Vacuolar Membrane (Peripheral)

Cytoplasmic chaperone and heat shock protein

PTH2*

No

Cytoplasm

Aminoacyl-tRNA hydrolase

RPL23A/RPL23B

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Large subunit ribosomal protein L23

TEF2/TEF1

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Ribosome-associated translation elongation factor EF-1 alpha

SSH1

Yes

ER-Nuclear Membrane

SEC61 homolog involved in co-translational pathway of protein transport

PDI1

No

ER Lumen

ER lumenal protein disulfide isomerase and oxidoreductase

MRH1

Yes

Plasma Membrane

Plasma membrane protein related to the Hsp30p chaperone and heat shock protein

EFT2/EFT1

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Ribosome-associated translation elongation factor EF-2

RPS18A/RPS18B

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Small subunit ribosomal protein S18

PAB1

No

Nucleus/Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Poly(A)-binding protein

RPL1B/RPL1A

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Large subunit ribosomal protein L1

GCN1

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Translational activator of GCN4 in response to starvation

RPS20*

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Small subunit ribosomal protein S20

SEC11

Yes

ER-Nuclear Membrane

Signal sequence processing protein

KAR2

No

ER Lumen

ER lumenal heat shock protein required for protein translocation and nuclear fusion

SSA2

No

Cytoplasm/Ribosome/Vacuolar Membrane (Peripheral)

Cytoplasmic chaperone and heat shock protein

ERO1

No

ER-Nuclear Membrane (Lumenal Peripheral)

FAD-dependent oxidase of protein disulfide isomerase

SIS1

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Protein chaperone required for initiation of translation

RPL3

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Large subunit ribosomal protein L3

RPS7A

No

Cytoplasm/Ribosome/ER-Nuclear Membrane (Peripheral)

Small subunit ribosomal protein S7

HSP82

No

Cytoplasm

Cytoplasmic chaperone and heat shock protein

Ubiquitin/Proteasome Pathway

Gene

TM Domain

Localization

Description

Ubiquitin*

No

n/a

Ubiquitin

CDC48

No

Cytoplasm/Nucleus/ER-Nuclear Membrane (Peripheral)

AAA-ATPase required for ER-associated degradation, membrane fusion, and cell cycle progression

UFD2

Predicted

Unknown Membrane

Ubiquitin conjugating factor E4; Required for the assembly of multi-ubiquitin chains

TOM1

Predicted

Unknown Membrane

Protein required for the G2/M transition, has similarity to Rsp5p, a HECT-domain ubiquitin-protein ligase (E3 enzyme)

RPN3

No

Proteasome/ER-Nuclear Membrane (Peripheral)/Nucleus

Non-ATPase component of 26S proteasome complex, also functions in RNA polymerase II transcription elongation

PUP3

No

Proteasome/ER-Nuclear Membrane (Peripheral)/Nucleus

20S proteasome subunit beta3_sc

UBC6

Yes

ER-Nuclear Membrane

Ubiquitin-conjugating enzyme, anchored in the ER membrane with the catalytically active domain in cytoplasm

RSP5

No

Plasma Membrane/ER-Nuclear Membrane (Peripheral)

Essential HECT-domain ubiquitin-protein ligase (E3 enzyme)

DDI1*

No

Plasma Membrane (Peripheral)

Protein involved in ubiquitin-dependent protein degradation, binds to t- and v-SNARE complexes

PRE9*

No

Proteasome/ER-Nuclear Membrane (Peripheral)/Nucleus

20S proteasome subunit alpha3_sc

UBR1

Predicted

Unknown Membrane

Ubiquitin-protein ligase (N-recognin or E3 enzyme), involved in selection of substrates for the N-end rule pathway

RPN1

No

Proteasome/ER-Nuclear Membrane (Peripheral)/Nucleus

Non-ATPase component of the 26S proteasome complex, also functions in RNA polymerase II transcription elongation

SSM4

Yes

ER-Nuclear Membrane

E3 ubiquitin ligase of the endoplasmic reticulum

HRD3

Yes

ER-Nuclear Membrane

ER-membrane protein required for ER-associated degradation

CUE1

Yes

ER-Nuclear Membrane

ER-membrane protein required for ER-associated degradation (through ER-recruitment of the E2 ubiquitin conjugating enzyme)

CUE5

Predicted

Unknown Membrane

Member of the CUE domain family, which bind ubiquitin-conjugating enzymes

Vesicle Transport/Protein Trafficking

YAL048C

Predicted

Unknown Membrane

Protein of unknown function involved in the secretory pathway

ERP1

Yes

Transport Vesicle Membrane

Component of COPII-coated vesicles

COP1

No

Transport Vesicle Membrane (Peripheral)

Coatomer (COPI) complex alpha chain of secretory pathway vesicles required for retrograde Golgi to ER transport

GSG1

No

Transport Vesicle Membrane (Peripheral)

TRAPP-complex protein involved in vesicular transport from the ER to the Golgi and Golgi trafficking

SEC27

No

Transport Vesicle Membrane (Peripheral)

Coatomer (COPI) complex beta' chain of secretory pathway vesicles, required for retrograde Golgi to ER transport

EMP24

Yes

Transport Vesicle Membrane

Component of COPII-coated vesicles possibly involved in cargo sorting

GGA2

No

Golgi Membrane (Peripheral)

Protein involved in trafficking of proteins between the trans-Golgi network and the vacuole

GVP36

No

Transport Vesicle Membrane (Peripheral)

Putative Golgi-vesicle protein

YKT6

Yes

Transport Vesicle Membrane

Synaptobrevin (v-SNARE) homolog essential for ER-Golgi transport

VPS13

No

Transport Vesicle Membrane (Peripheral)

Protein involved in vacuolar sorting

SEL1

Predicted

Unknown Membrane

Protein involved in secretory pathway

GSF2

Yes

ER-Nuclear Membrane

Protein required for secretion of Hxt1p glucose transporter

SSO2

Yes

Transport Vesicle Membrane

Syntaxin homolog (t-SNARE) involved in vesicle transport from Golgi to plasma membrane

VTI1

Yes

Transport Vesicle Membrane

Synaptobrevin (v-SNARE) homolog required for cis-Golgi trafficking and involved in Golgi to prevacuole trafficking

CVT19

No

Perivacuolar Preautophagosomal Structure

Protein involved in cytoplasm to vacuole targeting (CVT) pathway

YOR086C

Predicted

Unknown Membrane

C2-domain containing protein homologous to mouse synaptotagmin 7, which is involved in synaptic vesicle fusion

NCE102

Yes

ER-Nuclear Membrane

Involved in secretion of proteins that lack classical secretory signal sequences

Other

GDH3

No

Cytoplasm

Glutamate dehydrogenase (NADP+); Glutamate biosynthesis

IRA1

Yes

Plasma Membrane

Plasma membrane Ras GTPase activator (GAP)

FZO1

Yes

Mitochondrial Membrane

Transmembrane GTPase required for mitochondrial fusion and maintenance of mitochondrial DNA

RNQ1

No

Cytoplasm

[RNQ+] prion

NUP84

No

NPC/ER-Nuclear Membrane (Peripheral)

Nuclear pore complex subunit

GLY1*

No

Cytoplasm

Threonine aldolase; Glycine biosynthesis

STE2

Yes

Plasma Membrane

Plasma membrane alpha-factor pheromone receptor

YFR006W*

Predicted

Unknown Membrane

Putative Xaa-Pro aminopeptidase

NUP145

No

NPC/ER-Nuclear Membrane (Peripheral)

Nuclear pore complex subunit

LSB1*

No

Cytoplasm

LAs17 Binding protein; Contains SH3 domain

ENO2

No

Cytoplasm

Enolase 2; Glycolysis

VTC4

Yes

Vacuolar Membrane

Subunit of VTC complex required for vacuolar membrane fusion, involved in vacuolar polyphosphate accumulation

CPS1

Yes

Vacuolar Membrane

Vacuolar carboxypeptidase yscS

STE24

Yes

ER-Nuclear Membrane

ER-localized zinc-metalloprotease that processes a-factor pheromone

PSR2

No

Plasma Membrane (Peripheral)

Plasma membrane associated phosphatase required for sodium stress response

PDC1

No

Cytoplasm

Pyruvate decarboxylase isozyme 1; Ethanol fermentation, pyruvate metabolism

FRE1

Yes

Plasma Membrane

Ferric (and cupric) reductase; Facilitates iron uptake

ALO1

Predicted

Mitochondrial Membrane

D-arabinino-1,4-lactone oxidase; D-erythroascorbic acid biosynthesis

MKT1

Predicted

Unknown Membrane

Protein involved in propagation of M2 dsRNA satellite of L-A virus

AAH1

No

Cytoplasm

Adenine deaminase; Adenine catabolism

ASI2

Predicted

Unknown Membrane

Involved in regulation of amino acid permease gene expression

MAM3

Predicted

Unknown Membrane

Hemolysin-like protein required for normal mitochondrial structure

YOR256C

Predicted

Plasma Membrane

Putative plasma membrane protein with similarity to human NAALAD2, which is a glutamate carboxypeptidase

GDH1

No

Cytoplasm

Glutamate dehydrogenase (NADP+); Glutamate biosynthesis

GLN1*

No

Cytoplasm

Glutamine synthetase; Glutamine biosynthesis

Unknown

YAR028W*

Predicted

ER-Nuclear Membrane

Members of duplicated family of subtelomerically encoded COS proteins of unknown function

YBR005W

Predicted

Mitochondrial Membrane

Putative mitochondrial protein of unknown function

AKL1

Predicted

Unknown Membrane

Serine/threonine protein kinase of unknown function

COS2* (+others)

Predicted

ER-Nuclear membrane

Member of duplicated family of subtelomerically encoded COS proteins of unknown function

SNA4

Yes

Vacuolar Membrane

Vacuolar membrane protein of unknown function

YRF1-1 (+others)

Predicted

Unknown Membrane

Duplicated family of subtelomerically encoded YRF proteins of unknown function

WWM1

Predicted

Unknown Membrane

Protein of unknown function; Interacts with metacaspase (Mca1p)

YGR130C

No

Cytoplasm

Protein of unknown function

YHL010C*

Predicted

Unknown Membrane

Protein of unknown function; Displays NLS binding activity

YHR131C

No

Unknown

PH-domain containing protein of unknown function

YIL108W

Predicted

Unknown Membrane

Protein of unknown function

YJL084C

No

Cytoplasm

Arrestin(S-antigen)-domain containing protein of unknown function

SNA3*

Yes

Vacuolar Membrane

Vacuolar membrane protein of unknown function

YJR088C

Predicted

Unknown Membrane

Protein of unknown function

JSN1

Predicted

Unknown Membrane

PUF(mRNA binding)-domain containing protein of unknown function

YET1*

Yes

ER-Nuclear Membrane

ER membrane protein of unknown function

YKL100C

Predicted

Unknown Membrane

Protein of unknown function

SSH4

Predicted

Unknown Membrane

Protein of unknown function; Confers resistance to leflunomide upon overproduction

YKR021W

No

Cytoplasm

Arrestin(S-antigen)-domain containing protein of unknown function

YLR413W

Predicted

Unknown Membrane

Protein of unknown function

YLR414C*

Predicted

Unknown Membrane

Protein of unknown function

USA1

Predicted

Unknown Membrane

Protein of unknown function; Interacts with the mRNA splicing factor Snp1p

YML072C

Predicted

Unknown Membrane

C2-domain containing protein of unknown function

YMR160W

Predicted

Unknown Membrane

Protein of unknown function

YMR209C

Predicted

Unknown Membrane

Protein of unknown function

YNL058C

Predicted

Unknown Membrane

Protein of unknown function

YOR164C

No

Cytoplasm

Protein of unknown function

YOR322C*

Predicted

Unknown Membrane

Protein of unknown function

TM, transmembrane; ER, endoplasmic reticulum.

*Indicates identified ubiquitination site. Shading indicates candidate ER-associated degradation (ERAD) substrates.





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