a plasma membrane e-map reveals links between the eisosome...

A Plasma Membrane E-MAP Reveals Links Between the Eisosome, Sphingolipid Metabolism and Endosomal Trafficking Pablo S. Aguilar1,#, Florian Fröhlich2,#, Michael Rehman2,#, Mike Shales3,#, Igor Ulitsky4, Agustina Olivera-Couto1, Hannes Braberg3, Ron Shamir4, Peter Walter5, Matthias Mann6, Christer S. Ejsing7, Nevan J. Krogan3*, Tobias C. Walther2* 1 Institut Pasteur de Montevideo, Uruguay 2 Max Planck Institute of Biochemistry, Organelle Architecture and Dynamics, Martinsried, Germany 3 Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA 4 The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel 5 Department of Biochemistry and Biophysics, University of California and Howard Hughes Medical Institute, San Francisco, CA, USA 6 Max Planck Institute of Biochemistry, Proteomics and Signal Transduction, Martinsried, Germany 7. University of Southern Denmark, Department of Biochemistry and Molecular Biology, Odense, Denmark

# These authors, listed in alphabetical order, contributed equally * Correspondence to: Nevan Krogan Department of Cellular and Molecular Pharmacology University of California, San Francisco 1700 4th Street, Beyers Hall 208D San Francisco, CA 94158 USA [email protected] or Tobias C. Walther Max Planck Institute of Biochemistry Organelle Dynamics and Architecture Am Klopferspitz 18 82152 Martinsried/Munich Germany [email protected]

Nature Structural & Molecular Biology: doi:10.1038/nsmb.1829

False positive rate

True

pos

itive

rate

0 0.001 0.002 0.003 0.004

00.

050.

100.

150.

200.

250.

300.

150.

15

Supplementary Figure 1 - Receiver operating characteristic (ROC) curves gauging the power of pairwise genetic profile correlations to predict physical interactions between pairs of proteins. The predictive power of the plasma membrane E-MAP (blue) is comparable to that of previously published E-MAPs, focused on chromosome biology ( , red) and the early secretory pathway ( , green). The slope of the initial portion of the curve serves as a measure of the predictor's discriminatory power at its minimal false positive rate. Physical interaction definitions were collected from , imposing a threshold of PE score > 2.

1 2

3


–3.0 –1.5 0.0 1.5 3.0

S-scores

MYO5BNR1

BCK1 SYP1

BBC1SLA1

ARC18

SLT2 CAP1 EDE1

CLA4BEM3ABP1

CAP2

TWF1

BZZ1

RVS167SMY1

LCB4

LAG1

SUR2 SUR4

LCB3

LAC1

VPS17

VPS29

PEP8

VPS5

VPS35

DPL1

FEN1

TLG2 ARF1

SNC2

YPT31

PEP5 VPS8

VPS41 YPT7CCZ1

ERG5ERG3ERG2ERG6

PEX15PEX6PEX1

SSK1SSK22PBS2HOG1

COG6 COG5

COG8 COG7

BEM3EDE1BBC1TWF1CLA4SYP1SMY1SLT2

RVS167ARC18

ABP1CAP2MYO5BZZ1BCK1SLA1BNR1CAP1LAG1LCB4SUR2LAC1SUR4LCB3FEN1DPL1

VPS29PEP8

VPS35VPS17VPS5YPT7

VPS41PEP5CCZ1VPS8ARF1

YPT31TLG2SNC2ERG2ERG5ERG3ERG6SSK1

SSK22PBS2HOG1COG5COG6COG8COG7

PEX15PEX1PEX6ARL3SYS1CSG2SUR1

CDC50DRS2SRN2

MVB12MKS1RTG2RTG1RTG3MID1

CCH1APM3APL5VPS9

VPS21MON2ARL1TCB3TCB2

BE

M3

ED

E1

BB

C1

TWF1

CLA

4S

YP

1S

MY

1S

LT2

RV

S16

7A

RC

18A

BP

1C

AP

2M

YO

5B

ZZ1

BC

K1

SLA

1B

NR

1C

AP

1LA

G1

LCB

4S

UR

2LA

C1

SU

R4

LCB

3FE

N1

DP

L1V

PS

29P

EP

8V

PS

35V

PS

17V

PS

5Y

PT7

VP

S41

PE

P5

CC

Z1V

PS

8A

RF1

YP

T31

TLG

2S

NC

2E

RG

2E

RG

5E

RG

3E

RG

6S

SK

1S

SK

22P

BS

2H

OG

1C

OG

5C

OG

6C

OG

8C

OG

7P

EX

15P

EX

1P

EX

6A

RL3

SY

S1

CS

G2

SU

R1

CD

C50

DR

S2

SR

N2

MV

B12

MK

S1

RTG

2R

TG1

RTG

3M

ID1

CC

H1

AP

M3

AP

L5V

PS

9V

PS

21M

ON

2A

RL1

TCB

3TC

B2

Supplementary Figure 2 - Functional modules identified using the plasma mem-brane E-MAP data and protein-protein interactions. Modules were identified as described in . White lines separate modules, which are ordered by size. Missing values are in grey. The protein-protein interaction sub-network is shown next to each module with at least three genes.

4


–3.0 –1.5 0.0 1.5 3.0

S-scores

MON2YPT31VPS17

ARL3SYS1

VPS13RIC1SFT2ARL1APM3ENT5SCS7SAC1SNC2SWA2

VPS29VPS35GET3APL5PEP8GOT1TPM1TLG2GET1VPS8GUP1EDE1BSP1SMY1HKR1

VPS27CHS6BNR1VPS9PEX6BEM3ERG4

PEX15CLA4SYP1PEX1SKN7

ARC18VPS64

FPS1ADH1

ECM33AKR1SLA1CAP1AIP1

BBC1TWF1

YLR408CYPT35PRM8ABP1SUR7CAP2GGA1MYO5BZZ1

YGL079WGIM4JSN1

MSB3YPT53RAS1

VPS21SYN8SRN2

YMR031CYPT52ENT3TAT1YPT7ARF3

MVB12CCZ1GPB2ARN2RAD1BRE4MID1SIP2

PBS2MRH1DUR3ARN1

JJJ1VPS33CHC1STD1ASG7

ASK10QDR3CRN1TOR1ATG8HXT2RSR1GAL2TGS1

YHL044WSKN1SSK1IPT1

LCB4YNL086W

ENT4HOG1CRZ1ERP1RAS2ATO3SUR1ARF1

COG5CDC50COG6PER1INP53GYL1DRS2ERG3PIB2

COG8COG7LRO1BUL1CIS3

GPA2YKL061W

PDR12YBP2CMP2MID2

GSC2MDG1CCH1BCH2KEM1RTG1MKS1ALP1

PEP12RTG2RTG3VAC8VPS5COG1FKS1

ROM2SUR2LEM3ERG5SUR4PKH3LCB3FEN1SEM1SHO1BOI1

ARK1WSC4

KIN2SPO14

EXG1ROM1TCB3TCB2LCB5

WSC3SIW14NCR1SST2PMA2TRE1NHA1MKK2INP51

PIL1COS10

YSR3EMP70

ERG6YDL012C

AIF1YEH2EHD3GEF1OSH2

FUI1HOR7

YBR016WPSR2YPS3MTL1SLI1

UBC5KIN1

ENB1LAG1

TSC10VPS4DPL1FAT1

SSU1GAP1YTA6SVL3GPB1SRO7

YAP1801CSG2ALR2

YOL019WPDR5TAT2PLB3

ROD1RSB1AKR2LSB5

RVS161RVS167

SAC6PMP3HSE1

YBR108WSES1STV1CHS1BRO1ISC1

SCH9QDR1

THI7YLR073C

CNA1YCK3WHI2ELM1RGD1

ATG18ERG2HAC1

SIT1YOR1

YGR266WYIR044C

ENT2FTR1

PEX11SSK22SMF1ERS1BIO5

HXT10PRM9DAL5GYP5SKM1GPR1GPG1SNQ2SNC1GCS1

SPS22YAP1802

IMH1

MO

N2

YP

T31

VP

S17

AR

L3S

YS

1V

PS

13R

IC1

SFT

2A

RL1

AP

M3

EN

T5S

CS

7S

AC

1S

NC

2S

WA

2V

PS

29V

PS

35G

ET3

AP

L5P

EP

8G

OT1

TPM

1TL

G2

GE

T1V

PS

8G

UP

1E

DE

1B

SP

1S

MY

1H

KR

1V

PS

27C

HS

6B

NR

1V

PS

9P

EX

6B

EM

3E

RG

4P

EX

15C

LA4

SY

P1

PE

X1

SK

N7

AR

C18

VP

S64

FPS

1A

DH

1E

CM

33A

KR

1S

LA1

CA

P1

AIP

1B

BC

1TW

F1Y

LR40

8CY

PT3

5P

RM

8A

BP

1S

UR

7C

AP

2G

GA

1M

YO

5B

ZZ1

YG

L079

WG

IM4

JSN

1M

SB

3Y

PT5

3R

AS

1V

PS

21S

YN

8S

RN

2Y

MR

031C

YP

T52

EN

T3TA

T1Y

PT7

AR

F3M

VB

12C

CZ1

GP

B2

AR

N2

RA

D1

BR

E4

MID

1S

IP2

PB

S2

MR

H1

DU

R3

AR

N1

JJJ1

VP

S33

CH

C1

STD

1A

SG

7A

SK

10Q

DR

3C

RN

1TO

R1

ATG

8H

XT2

RS

R1

GA

L2TG

S1

YH

L044

WS

KN

1S

SK

1IP

T1LC

B4

YN

L086

WE

NT4

HO

G1

CR

Z1E

RP

1R

AS

2AT

O3

SU

R1

AR

F1C

OG

5C

DC

50C

OG

6P

ER

1IN

P53

GY

L1D

RS

2E

RG

3P

IB2

CO

G8

CO

G7

LRO

1B

UL1

CIS

3G

PA2

YK

L061

WP

DR

12Y

BP

2C

MP

2M

ID2

GS

C2

MD

G1

CC

H1

BC

H2

KE

M1

RTG

1M

KS

1A

LP1

PE

P12

RTG

2R

TG3

VAC

8V

PS

5C

OG

1FK

S1

RO

M2

SU

R2

LEM

3E

RG

5S

UR

4P

KH

3LC

B3

FEN

1S

EM

1S

HO

1B

OI1

AR

K1

WS

C4

KIN

2S

PO

14E

XG

1R

OM

1TC

B3

TCB

2LC

B5

WS

C3

SIW

14N

CR

1S

ST2

PM

A2

TRE

1N

HA

1M

KK

2IN

P51

PIL

1C

OS

10Y

SR

3E

MP

70E

RG

6Y

DL0

12C

AIF

1Y

EH

2E

HD

3G

EF1

OS

H2

FUI1

HO

R7

YB

R01

6WP

SR

2Y

PS

3M

TL1

SLI

1U

BC

5K

IN1

EN

B1

LAG

1TS

C10

VP

S4

DP

L1FA

T1S

SU

1G

AP

1Y

TA6

SV

L3G

PB

1S

RO

7YA

P18

01C

SG

2A

LR2

YO

L019

WP

DR

5TA

T2P

LB3

RO

D1

RS

B1

AK

R2

LSB

5R

VS

161

RV

S16

7S

AC

6P

MP

3H

SE

1Y

BR

108W

SE

S1

STV

1C

HS

1B

RO

1IS

C1

SC

H9

QD

R1

THI7

YLR

073C

CN

A1

YC

K3

WH

I2E

LM1

RG

D1

ATG

18E

RG

2H

AC

1S

IT1

YO

R1

YG

R26

6WY

IR04

4CE

NT2

FTR

1P

EX

11S

SK

22S

MF1

ER

S1

BIO

5H

XT1

0P

RM

9D

AL5

GY

P5

SK

M1

GP

R1

GP

G1

SN

Q2

SN

C1

GC

S1

SP

S22

YAP

1802

IMH

1

Supplementary Figure 3 - Functional modules identified using the plasma membrane E-MAP data for pairs without PPIs. Modules were identified as described in , but without requiring PPI network connectivity. White lines separate modules, which are ordered by size. Missing values are in grey. The PIL1-EMP70 module is marked by a red bar.

4


Supplementary Figure 4 - Map of type I TGMs in the plasma membrane E-MAP. Overview of all Type I TGMs found in the plasma membrane E-MAP. PIL1, YMR031c and EMP70 are highlighted in red.


Emp70-GFP mergeVps5-RFPmars

FM4-64 Emp70-GFP merge

a

b

Supplementary Figure 5 - Emp70 localization in respect to endosomes. (a) Strains expressing Emp70-GFP and Vps5-RFPmars from the endogenous locus were imaged by confocal microscopy. Representative images are shown. (b) FM4-64 uptake experiment was performed at 16°C and representative confocal midsections are shown. Bar = 2.5 µm.


Module # Gene symbols ORFs 1 CLA4,ABP1 YNL298W,YCR088W 2 EDE1,SYP1,SLA1 YBL047C,YCR030C,YBL007C 3 SLT2,BCK1 YHR030C,YJL095W 4 CAP1,CAP2 YKL007W,YIL034C 5 RTG3,RTG1 YBL103C,YOL067C 6 ENT3,GGA2,ENT5 YJR125C,YHR108W,YDR153C 7 PEX15,PEX6 YOL044W,YNL329C 8 GET1,GEF1,GET3 YGL020C,YJR040W,YDL100C 9 SYS1,ARL3 YJL004C,YPL051W

10 IMH1,MON2,ARL1 YLR309C,YNL297C,YBR164C 11 SNC2,TLG2 YOR327C,YOL018C 12 VPS17,VPS35,PEP8,VPS29 YOR132W,YJL154C,YJL053W,YHR012W 13 VPS41,APM3,APL5 YDR080W,YBR288C,YPL195W 14 COG8,COG7,COG5,COG6 YML071C,YGL005C,YNL051W,YNL041C 15 VPS21,VPS9 YOR089C,YML097C 16 HOG1,SSK22,SSK1,PBS2 YLR113W,YCR073C,YLR006C,YJL128C

17 TSC10,DPL1,SUR2,LAC1, LCB3,SUR4,LAG1

YBR265W,YDR294C,YDR297W,YKL008C,YJL134W,YLR372W,YHL003C

18 ERG5,ERG3,ERG2 YMR015C,YLR056W,YMR202W Supplementary Table 3 - List of modules with PPIs found in the plasma membrane EMAP.


Module # Gene symbols ORFs

1 INP52,ERG3,ERG2 YNL106C,YLR056W,YMR202W

2 SRO77,FUI1,SHO1,BOI2,RGD1 YBL106C,YBL042C,YER118C,YER114C,YBR260C

3 MYO3,YCK3,YAP1801,TOR2 YKL129C,YER123W,YHR161C,YKL203C

4 GYP5,PRM9,DAL5 YPL249C,YAR031W,YJR152W

5 AIP1,BNR1,IST2,ECM33,YBR108W, CLA4,HSE1,ABP1,PMP3,MYO5

YMR092C,YIL159W,YBR086C,YBR078W,YBR108W, YNL298W,YHL002W,YCR088W,YDR276C,YMR109W

6 YOL019W,SRN2,INP54,FTH1,VPS4, ATG21,GUP1,VPS27

YOL019W,YLR119W,YOL065C,YBR207W,YPR173C, YPL100W,YGL084C,YNR006W

7 FIG4,LEM3 YNL325C,YNL323W

8 SPO14,SNC1 YKR031C,YAL030W

9 EDE1,SLT2,CAP1,BBC1,CHS6,ARC18, CAP2,SLA1,SMY1,MID2,BCK1

YBL047C,YHR030C,YKL007W,YJL020C,YJL099W, YLR370C,YIL034C,YBL007C,YKL079W,YLR332W, YJL095W

10 FPS1,VPS41,SIT1,RTG3,CCZ1,SAC6, RTG1,VAC8,MKS1,WHI2,SST2,MID1

YLL043W,YDR080W,YEL065W,YBL103C,YBR131W, YDR129C,YOL067C,YEL013W,YNL076W,YOR043W, YLR452C,YNL291C

11 DUR3,GGA2,SKM1,WSC4,WSC3, YPT53,ARN1,ARN2

YHL016C,YHR108W,YOL113W,YHL028W,YOL105C, YNL093W,YHL040C,YHL047C

12 CRN1,SRO7,YNL208W,SIP2,RAS2, YDC1

YLR429W,YPR032W,YNL208W,YGL208W,YNL098C, YPL087W

13 BCH1,YPT52,SYN8,RGT2 YMR237W,YKR014C,YAL014C,YDL138W

14 PEX15,BSP1,PEX6,RSR1 YOL044W,YPR171W,YNL329C,YGR152C

15 KIN2,JSN1,SSK22,YDR357C, HUA2,YNL086W,YPT35,PRM8

YLR096W,YJR091C,YCR073C,YDR357C,YOR284W, YNL086W,YHR105W,YGL053W

16 SFK1,BZZ1,SNQ2 YKL051W,YHR114W,YDR011W

17 YKL061W,OSH2,YDL012C,AIF1, GEF1,ALP1,SKN7,YEH2

YKL061W,YDL019C,YDL012C,YNR074C,YJR040W, YNL270C,YHR206W,YLR020C

18

VPS17,ENT3,GOT1,APM3,SAC1, VPS21,MON2,GET1,LCB5,CSG2, VPS29,GET3,VPS9,TLG2,SFT2, SNC2,VPS35,RCY1,SWA2,CUP5, PEP8,VPS8,TPM1,APL5

YOR132W,YJR125C,YMR292W,YBR288C,YKL212W, YOR089C,YNL297C,YGL020C,YLR260W,YBR036C, YHR012W,YDL100C,YML097C,YOL018C,YBL102W, YOR327C,YJL154C,YJL204C,YDR320C,YEL027W, YJL053W,YAL002W,YNL079C,YPL195W

19

HOG1,IMH1,SYS1,ELM1,COG8,CCH1, IPT1,ENT5,ARL1,COG5,COG6,SUR1, ARL3,TCB2,PIB2,ATO3,COG7,INP53, GSC2,CRZ1

YLR113W,YLR309C,YJL004C,YKL048C,YML071C, YGR217W,YDR072C,YDR153C,YBR164C,YNL051W, YNL041C,YPL057C,YPL051W,YNL087W,YGL023C, YDR384C,YGL005C,YOR109W,YGR032W,YNL027W

20 YLR073C,SMF1,YPS3 YLR073C,YOL122C,YLR121C

21 TSC10,DPL1,SUR2,LCB3,SUR4,FAT1, LAG1

YBR265W,YDR294C,YDR297W,YJL134W, YLR372W,YBR041W,YHL003C

22 PMP1,ERS1,HXT10,NHA1,HSP30 YCR024C-A,YCR075C,YFL011W,YLR138W,YCR021C

23 HSP12,PSR1,SCP1 YFL014W,YLL010C,YOR367W

24 ROD1,RSB1,PEP12,STD1,AKR2 YOR018W,YOR049C,YOR036W,YOR047C,YOR034C

25 YPL150W,STV1,STL1,TWF1 YPL150W,YMR054W,YDR536W,YGR080W

26 YSR3,INP51,SUR7,PIL1,ERG6,EMP70 YKR053C,YIL002C,YML052W,YGR086C,YML008C, YLR083C

27 YMR086W,WSC2,LCB4,ERP1 YMR086W,YNL283C,YOR171C, YAR002C-A

28 MDG1,SKN1,YIR044C YNL173C,YGR143W,YIR044C

29 GGA1,TOR1,GAP1,HOR7,SSK1 YDR358W,YJR066W,YKR039W,YMR251W-A,YLR006C

Supplementary Table 4 - List of modules without PPIs found in the plasma membrane E-MAP.


PM E-MAP

(this study) ESP E-MAP (Schuldiner et al., 2005, 2)

E-MAP size (genes) 374 423 Number of modules 19 16 Genes in module (% of the E-MAP)

14% 22.4% PPI-based modules

% of modules enriched with GO “biological process” set (FDR<0.01)

63% 79.4%

Number of modules 29 36 Genes in module (% of the E-MAP)

72.4% 62.5% Modules identified without using PPIs

% of modules enriched with GO “biological process” set (FDR<0.01)

19.4% 23.2%

% of GO “biological process” sets enriched in at least one module

23.2% 23.0%

Supplementary Table 5 - Comparison of modules detected in the plasma membrane (PM) E-MAP and ESP E-MAP 2. Lipid lass (Normalized by levels in wild-type BY4742) WT sur2Δ sur4Δ lcb3Δ csg2Δ rom2Δ

rom2Δ sur2Δ

rom2Δ lcb3Δ

rom2Δ csg2Δ

LCB 1 65.78 270.22 16.60 0.97 100.40 409.41 14.07 261.34Cer 1 0.84 0.49 0.80 0.81 0.30 0.20 1.09 0.32IPC 1 0.19 0.96 0.77 2.48 0.64 0.10 0.86 1.03MIPC 1 3.80 0.00 1.26 0.00 1.10 0.78 2.10 0.00M(IP)2C 1 1.81 0.16 0.63 0.04 0.67 0.81 1.06 0.03PA 1 1.03 1.61 0.64 0.75 1.12 0.98 1.09 1.55PS 1 0.88 0.26 0.89 0.76 0.75 0.64 0.80 0.38PE 1 1.07 0.73 1.18 1.06 0.73 0.54 1.12 0.64PC 1 0.80 0.71 0.74 0.85 0.66 0.60 0.81 0.69PI 1 1.00 1.11 1.12 1.06 1.07 1.14 1.03 1.10DAG 1 0.89 0.73 0.72 0.89 0.72 0.58 0.82 0.74TAG 1 1.24 1.30 1.42 1.28 1.87 1.53 1.31 1.49SE 1 0.84 3.06 0.84 1.43 1.11 1.89 1.18 1.96

Abbreviations: PC (phosphatidylcholine), PE (phosphatidylethanolamine), PA (phosphatidic acid),

PS (phosphatidylserine), PI (phosphatidylinositol) DAG (diacylglycerol), TAG (triacylglycerol), SE (sterol ester) Cer (ceramide), LCB (long-chain base), IPC (inositolphosphoceramide), MIPC (mannosyl-inositolphosphoceramide), M(IP)2C (mannosyl-diinositolphosphoceramide)

Supplementary Table 6 - Lipidomic data for rom2Δ and mutants in the sphingolipid synthesis pathway as shown in Figure 8b


Strain Genotype Reference

TWY1194 Mat a KEX2-RFPmars::NATR, EMP70-GFP::KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1044 Mat a EMP70-GFP::KANR SNF7-RFPmars::NATR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1063 Mat a EMP70-GFP::KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY871 Mat α EMP70-GFP::KANR, LSP1-RFPmars::NATR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1319 Mat a YLR413w-RFPmars::NATR, EMP70-gfp::KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1320 Mat a YLR413w-RFPmars:.NATR, EMP70-gfp::KANR, pil1Δ::KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1195 Mat a KEX2-GFP::KANR, emp70Δ::NATR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY138 Mat a ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1360 Mat a emp70Δ::NATR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1223 Mat a vps1Δ::HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1230 Mat a tmn1Δ::NATR tmn2Δ::HPHR tmn3Δ::HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1183 Mat a VPS5-RFPmars::NATR, EMP70-GFP::KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

Mat α his3Δ1; leu2Δ0; met15Δ0; ura3Δ0; can1Δ::MATaPr-HIS3; lyp1Δ::MATαPr-LEU2 Fiedler et al., 2009

TWY1770 Mat a rom2Δ::KANR csg2Δ::NATR his3Δ1; leu2Δ0; met15Δ0; ura3Δ0; can1Δ::MATaPr-HIS3; lyp1Δ::MATαPr-LEU2 This study

TWY1771 Mat a rom2Δ::KANR sur2Δ::NATR his3Δ1; leu2Δ0; met15Δ0; ura3Δ0; can1Δ::MATaPr-HIS3; lyp1Δ::MATαPr-LEU2 This study

TWY1772 Mat a rom2Δ::KANR lcb3Δ::NATR his3Δ1; leu2Δ0; met15Δ0; ura3Δ0; can1Δ::MATaPr-HIS3; lyp1Δ::MATαPr-LEU2 This study

Mat α lcb3Δ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 Mat α sur4Δ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 Mat α csg2Δ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 Mat α rom2Δ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 Mat α sur2Δ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 TWY1122 Mat a PIL1-TEV-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY70 Mat a his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Walther et al., 2006 TWY790 Mat a pil1Δ::NATR LSP1-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY791 Mat a pil1Δ::NATR YMR031C-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY726 Mat a PIL1-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY787 Mat α ymr031cΔ::KANR PIL1-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY788 Mat α ymr031cΔ::KANR LSP1-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study Mat α ymr031cΔ::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 Winzeler et al., 1999 TWY743 Mat a YMR031C-GFP::HIS PIL1-RFPmars::KANR his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY727 Mat a YMR031C-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY786 Mat a Lsp1-GFP::HIS his3Δ1; leu2Δ0; ura3Δ0; lys2Δ0 This study TWY637 Mat a LSP1-TAP::KANR his3Δ1; leu2Δ0; ura3Δ0; met15Δ0 This study TWY642 Mat a YMR031C-TAP::KANR his3Δ1; leu2Δ0; ura3Δ0; met15Δ0 This study TWY450 Mat α pil1Δ :: KANR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1184 Mat a tmn2Δ :: HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1182 Mat α tmn3Δ :: HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1207 Mat α emp70Δ :: NATR, tmn3Δ :: HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1206 Mat a emp70Δ:: NATR, tmn2Δ :: HPHR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study TWY1814 Mat a tmn2Δ :: HPHR, tmn3Δ::NATR ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100 This study

TWY1064 Mat a EMP70-GFP :: KANR, LSP1-RFPcherry::HIS ura3-1 trp1-1 leu2 his3-11,15 ade2-1 can1-100

This study

Supplementary Table 7- List of strains used in this study


Supplementary Material References 1. Collins, S.R. et al. Functional dissection of protein complexes involved in yeast

chromosome biology using a genetic interaction map. Nature 446, 806-10 (2007).

2. Schuldiner, M. et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123, 507-19 (2005).

3. Collins, S.R. et al. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics 6, 439-50 (2007).

4. Ulitsky, I., Shlomi, T., Kupiec, M. & Shamir, R. From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. Mol Syst Biol 4, 209 (2008).


a plasma membrane e-map reveals links between the eisosome...

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