| Strain, strain background (Saccharomyces cerevisiae) |
YPH499 |
Standard laboratory strain |
In-house ID: 524 |
MATa, ade2-101, his3-D200, leu2-D1, ura3-52, trp1-D63, lys2-801 |
| Strain, strain background (Saccharomyces cerevisiae) |
BY4741 |
Standard laboratory strain |
In-house ID: 755 |
MATa, his3D1, leu2D0, met15D0, ura3D0 |
| Strain, strain background (Saccharomyces cerevisiae) |
Δhsp104
|
Euroscarf |
In-house ID: 1001 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
hsp42-GFP
|
Invitrogen |
In-house ID: 1005 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
Hsp42-BY4741
|
Provided by Dr. Bernd Bukau |
In-house ID: 1178 |
-His selection; Gal1 promoter |
| Strain, strain background (Saccharomyces cerevisiae) |
pam16WT
|
10.1038/nsmb735
|
In-house ID: 736 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
pam16-1
|
10.1038/nsmb735
|
In-house ID: 733 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
pam16-3
|
10.1038/nsmb735
|
In-house ID: 734 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
pam18WT
|
10.1083/jcb.200308004
|
In-house ID: 738 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
pam18-1
|
10.1083/jcb.200308004
|
In-house ID: 739 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
mia40WT
|
10.1038/sj.emboj.7600389
|
In-house ID: 398 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
mia40-3
|
10.1038/sj.emboj.7600389
|
In-house ID: 178 |
|
| Strain, strain background (Saccharomyces cerevisiae) |
mia40-4int
|
10.1083/jcb.200804095
|
In-house ID: 739 |
|
| Strain, strain background (Caenorhabditis elegans) |
Worms expressing GFP |
Caenorhabditis Genetics Center (CGC) |
RRID:WB-STRAIN:WBStrain00005101CL2122 dvIs15 [(pPD30.38) unc-54(vector) + (pCL26) mtl-2::GFP] |
Control strain for GM101 |
| Strain, strain background (Caenorhabditis elegans) |
Worms expressing Aβ and GFP |
Caenorhabditis Genetics Center (CGC) |
RRID:WB-STRAIN:WBStrain00007866GMC101 dvIs100 [punc-54::A-beta-1–42::unc-54–3'-UTR+ mtl-2p::GFP] |
|
| Strain, strain background (Caenorhabditis elegans) |
α-syn::YFP |
10.1371/journal.pgen.1000027
|
OW40 zgIs15 [punc-54::αsyn::YFP]IV |
|
| Strain, strain background (Caenorhabditis elegans) |
YFP |
10.1371/journal.pgen.1000027
|
OW450 rmIs126 [punc-54::YFP]V |
Control strain for OW40 |
| Strain, strain background (Caenorhabditis elegans) |
[pmyo-3::wrmScarlet+ pmyo::GFP] |
A strain generated in our laboratory |
ACH87: wacIs11 [pmyo-3::mGFP::SL2 gdp-2-wrmScarlet::unc-54-3´UTR, unc-119(+)] |
|
| Strain, strain background (Escherichia coli) |
HB101 |
Caenorhabditis Genetics Center (CGC) |
RRID:WB-STRAIN:WBStrain00041075HB101 |
E. coli strain used as a food source for worms |
| Strain, strain background (Escherichia coli) |
HT115(DE3) |
Caenorhabditis Genetics Center (CGC) |
RRID:WB-STRAIN:WBStrain00041074HT115(DE3) |
E. coli strain used as a food source for worms in RNAi experiments |
| Strain, strain background (Escherichia coli) |
OP50 |
Caenorhabditis Genetics Center (CGC) |
RRID:WB-STRAIN:WBStrain00041971OP50 |
E. coli strain used as a food source for worms |
| Antibody |
Anti-Rip1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Sod2 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Mdh1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Hsp60 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Pgk1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Tom70 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Ssa1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Ssb1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Ssc1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Rpl17 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Ccp1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Qcr8 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Qcr6 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Cox12 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Tom20 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Edg1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Cdc48 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Rpl5 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Dnj21 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Rpn1 (rabbit polyclonal) |
Custom made |
|
WB (1:500) |
| Antibody |
Anti-Hsp42 (rabbit polyclonal) |
Provided by Dr. Bernd Bukau |
|
WB (1:5000) |
| Antibody |
Anti-Hsp104(rabbit polyclonal) |
Enzo |
RRID:AB_11181448ADI-SPA-1040-F |
WB (1:1000) |
| Antibody |
Anti-GFP(mouse monoclonal) |
Sigma |
RRID:AB_39091311814460001 |
WB (1:1000) |
| Antibody |
anti-3-PGDH (rabbit polyclonal) |
Millipore |
RRID:AB_2783876ABS571
|
IF(1:1000), WB (1:1000) |
| Antibody |
Anti-beta amyloid 1–16 (mouse monoclonal) |
BioLegend |
RRID:AB_2564653803001 |
WB (1:1000) |
| Antibody |
Anti-Tubulin (mouse monoclonal) |
Sigma |
RRID:AB_477593T9026 |
WB (1:500) |
| Antibody |
Anti-mCherry (anti-wrmScarlet/RFP); (rabbit polyclonal) |
Abcam |
RRID:AB_2571870ab167453 |
WB (1:1000) |
| Antibody |
Anti-FLAG(mouse monoclonal) |
Sigma |
RRID:AB_262044F1804 |
IF (1:1000)WB (1:1000) |
| Antibody |
Alexa Fluor 568(goat anti-mouse) |
Invitrogen |
RRID:AB_144696A11031 |
IF (1:500) |
| Recombinant DNA reagent |
L4440 (control for RNAi in C. elegans) (plasmid) |
AddGene |
#1654 |
|
| Recombinant DNA reagent |
dnj-21 RNAi (plasmid) |
Recombinant DNA generated in our laboratory |
pMJS1 In-house ID: 435p |
Plasmid used for silencing of dnj-21
|
| Recombinant DNA reagent |
Hsp104-pFL46L (plasmid) |
10.1128/MCB.20.19.7220–7229.2000
|
|
Provided by Dr. Magdalena Boguta |
| Recombinant DNA reagent |
α-Syn WT-GFP (plasmid) |
10.1126/science.1090439
|
|
Provided by Dr. Tiago Outeiro |
| Recombinant DNA reagent |
α-Syn A53T-GFP (plasmid) |
10.1126/science.1090439
|
|
Provided by Dr. Tiago Outeiro |
| Recombinant DNA reagent |
Empty vector with FLAG-tag, pCup1 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh26 In-house ID: 435p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Cox8 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh17In-house ID: 481p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Atp2 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh18In-house ID: 482p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Cor1 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh19In-house ID: 484p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Mas1 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh20In-house ID: 485p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Qcr6 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh21In-house ID: 486p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Qcr8 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh22In-house ID: 487p |
See Supplementary file 3
|
| Recombinant DNA reagent |
pRip1 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh23In-house ID: 488p |
See Supplementary file 3
|
| Recombinant DNA reagent |
iRip1 (plasmid) |
RDNA generated in our laboratory |
pPCh24In-house ID: 489p |
See Supplementary file 3
|
| Recombinant DNA reagent |
mRip1 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh29In-house ID: 490p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Atp20 (plasmid) |
Recombinant DNA generated in our laboratory |
pPCh30In-house ID: 483p |
See Supplementary file 3
|
| Recombinant DNA reagent |
Cox12 (plasmid) |
Recombinant DNA generated in our laboratory10.1186/s12915-018-0536-1
|
pPB36.1In-house ID: 471p |
See Supplementary file 3
|
| Sequence-based reagent |
Primers |
This paper |
PCR primers |
See Supplementary file 2
|
| Commercial assay or kit |
RNeasy Mini Kit |
Qiagen |
74104 |
|
| Chemical compound, drug |
CCCP |
Sigma |
C2759 |
|
| Chemical compound, drug |
MG132 |
Enzo |
BML-PI102-0005 |
|
| Software, algorithm |
ZEN |
Zeiss |
ZEN 2012 SP5 FP3 (black) |
Confocal Microscopy Data Collection Software |
| Software, algorithm |
FastQC |
www.bioinformatics.babraham.ac.uk/projects/fastqc
|
RRID:SCR_014583
|
|
| Software, algorithm |
Salmon (v0.11.2) |
10.1038/nmeth.4197
|
RRID:SCR_017036
|
|
| Software, algorithm |
DESeq2 version 1.26.0 |
10.1186/s13059-014-0550-8
|
RRID:SCR_015687
|
|
| Other |
ProLong Diamond antifade mountant with DAPI |
Thermo Fisher Scientific |
P36962 |
|
