REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
1.4 nm gold-conjugated fragment antigen-binding (Fab) goat antibody to mouse IgG	Nanoprobe	A24921
Goat anti-mouse AlexaFluor 488	Invitrogen	A11029
Donkey anti-mouse AlexaFluor 594	Invitrogen	A21203
Goat anti-rabbit AlexaFluor 488	Invitrogen	A11034
Donkey anti-rabbit AlexaFluor 594	Invitrogen	A21207
Mouse monoclonal anti-actin-HRP	Santa Cruz	sc-47778-HRP
Mouse monoclonal anti-ATP5B	Santa Cruz	sc-166462
Mouse monoclonal anti-ATP5B	Millipore	MAB3494
Mouse monoclonal anti-FLAG M2-HRP	Sigma	A8592
Mouse monoclonal anti-GFP	Abcam	AB1218
Mouse monoclonal anti-Myc	Santa Cruz	sc-56634
Mouse monoclonal anti-NBR1	Santa Cruz	sc-130380
Mouse monoclonal ant-OPA1	BD Biosciences	612606
Mouse monoclonal anti-Parkin	Cell Signaling Technology	4211
Mouse monoclonal anti-PHB1	Santa Cruz	sc-377037
Mouse monoclonal anti-PHB2	Santa Cruz	sc-133094
Mouse monoclonal anti-TIM50	Santa Cruz	sc-393678
Mouse monoclonal anti-TOMM20	Santa Cruz	sc-17764
Mouse monoclonal anti-TOMM70	Santa Cruz	sc-390545
Mouse monoclonal anti-WIPI2	Abcam	ab105459
Rabbit polyclonal anti-ATG7	Sigma	A2856
Rabbit polyclonal anti-GABARAP	Novus Biologicals	NBP1-71771
Rabbit polyclonal anti-GATE-16	Millipore	ABC24
Rabbit polyclonal anti-HA	Santa Cruz	sc-805
Rabbit polyclonal anti-HSP60	Santa Cruz	sc-13966
Rabbit polyclonal anti-LC3B	Novus Biologicals	NB100-2220
Rabbit polyclonal anti-PHB1	ThermoFisher	PA5-19556
Rabbit polyclonal anti-PHB2	ThermoFisher	PA5-14133
Rabbit polyclonal anti-TOMM20	Santa Cruz	sc-11415
Rabbit polyclonal anti-ULK1	Novus	NBP2-29922
Chemicals, Peptides, and Recombinant Proteins
Strep-Tactin Sepharose	IBA Lifesciences	2-1201-004
Anti–FLAG M2 affinity gel	Sigma	A2220
MitoTracker Red (CMXRos)	Invitrogen	M7512
CellMask Deep Red	ThermoFisher	C10046
ProLong Diamond Antifade Mountant with DAPI	Invitrogen	P36971
Oligomycin	Sigma	75351
Antimycin	Sigma	A8674
Epoxomicin	Sigma	E3652
Lactacystin	Sigma	L6785
Critical Commercial Assays
QProteome mitochondria isolation kit	QIAGEN	37612
HQ silver enhancement kit	Nanoprobe	2012
Experimental Models: Cell Lines
Phb2flox/flox murine embryonic fibroblasts	Thomas Langer	N/A
Phb2+/+ murine embryonic fibroblasts	Thomas Langer	N/A
Phb2flox/flox/Parkin MEFs	This paper	N/A
HeLa/Control cells	This paper	N/A
HeLa/Parkin cells	This paper	N/A
HeLa/Parkin/Flag.StrepII-LC3 cells	This paper	N/A
HeLa/Parkin/GFP-LC3	This paper	N/A
Experimental Models: Organisms/Strains
E. coli: BL21 (DE3)	Invitrogen	C600003
E. coli: OP50	Caenorhabditis Genetics Center	RRID: WB_OP50
E. coli: HT115 (DE3)	Caenorhabditis Genetics Center	RRID: WB_HT115(DE3)
C. elegans: wild-type Bristol strain N2	Caenorhabditis Genetics Center	N/A
C. elegans: LB138: him-8(e1489) IV; uaDf5/+	Caenorhabditis Genetics Center	RRID: WB_LB138
C. elegans: CB3844: fem-3(e2006) IV	Caenorhabditis Genetics Center	RRID: WB_CB3844
Recombinant DNA
pIRES-hyg3	Clontech	631620
pIRES-hyg3-Parkin	This paper	N/A
pLV-Cre	Pfeifer et al., 2001	Addgene: 38248
pLenti-IRES-Neo-PHB1	This paper	N/A
pLenti-IRES-Puro-PHB2	This paper	N/A
pLenti-IRES-Puro-PHB2 mLIR2	This paper	N/A
psPAX2	Didier Trono	Addgene: 12260
pMD2.g	Didier Trono	Addgene: 12259
pGEX-4T-1	GE healthcare	28-9545-49
ppSUMO-StrepII	This study	N/A
pIRES-Neo-Flag.StrepII	This study	N/A
L4440	Andrew Fire	Addgene: 1654
L4440-atg-7	Julie Ahringer	WormBase: sjj_M7.5
L4440-phb-2	Julie Ahringer	WormBase: sjj_T24H7.1
Sequence-Based Reagents
Dicer-substrate siRNA: NC1 negative control	Integrated DNA Technologies	51-01-14-03
5′-CGUUAAUCGCGUAUAAUACGCGUAT-3′	Integrated DNA Technologies	51-01-14-03
3′-CAGCAAUUAGCGCAUAUUAUGCGCAUA-5′	Integrated DNA Technologies	51-01-14-03
Dicer-substrate siRNA: PHB2 #1	Integrated DNA Technologies	N/A
5′-GUGAUUUCCUACAGUGUUGUUCCCT-3′;	Integrated DNA Technologies	N/A
3′-GUCACTAAAGGAUGUCACAACAAGGGA-5	Integrated DNA Technologies	N/A
Dicer-substrate siRNA: PHB2 #2	Integrated DNA Technologies	N/A
5′-AGAUAAACACCAACCCAGGAAUUCT-3′;	Integrated DNA Technologies	N/A
3′-CCUCUAUUUGUGGUUGGGUCCUUAAGA-5′	Integrated DNA Technologies	N/A
Dicer-substrate siRNA: PHB2 #3	Integrated DNA Technologies	N/A
5′-AGAUUCGAGCAGCCCAGAAUAUCTC-3′;	Integrated DNA Technologies	N/A
3′-GUUCUAAGCUCGUCGGGUCUUAUAGAG-5′	Integrated DNA Technologies	N/A
Primer: U1-F	Liau et al., 2007	N/A
5′-CCATCCGTGCTAGAAGACAA-3′	Liau et al., 2007	N/A
Primer: Cemt1A-R	Liau et al., 2007	N/A
5′-CTTCTACAGTGCATTGACCTAGTC-3′	Liau et al., 2007	N/A
Primer: Cemt5012-F	Liau et al., 2007	N/A
5′-TTGGTGTTACAGGGGCAACA-3′	Liau et al., 2007	N/A
Software and Algorithms
Imaris version 8.2	Bitplane	N/A
Deltavision softWoRx software	GE healthcare	N/A