REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
AlexaFluor 488 anti-cytochrome c (clone 6H2.B4)	BioLegend	Cat# 612308; RRID:AB_2565240
Phospho-S6 Ribosomal Protein (S235/S236) XP rabbit (clone D57.2.2E) (Alexa Fluor 647 Conjugate)	Cell Signaling Technology	Cat# 4851; RRID:AB_10695457
S6 Ribosomal Protein (clone 54D2) Mouse mAb (Alexa Fluor 647 Conjugate)	Cell Signaling Technology	Cat# 5548; RRID:AB_10707322
Goat IgG anti-human Galectin-8	R&D Systems	Cat# AF1305; RRID:AB_2137229
Donkey anti-goat IgG (H+L), Alexa Fluor 488	Thermo Fisher Scientific	Cat# A-11055; RRID:AB_2534102
Optical-bottom tissue culture plates
96-well (half area) black plate with transparent bottom	Greiner Bio-One	Cat# 675090
VisiPlate 24-well black plate with clear bottom	Perkin Elmer	Cat# 1450–606
6-well No. 1.5 coverslip, 20 mm glass diameter, uncoated plate	MatTek	Cat# P06G-1.5-20-F
24-well No. 1.5 coverslip, 13 mm glass diameter, uncoated plate	MatTek	Cat# P24G-1.5-13-F
Bacterial and virus strains
M. marinum M strain transformed with pmsp12::BFP2	Takaki et al., 2013	Derivative of ATCC # BAA-535
M. marinum M strain transformed with pmsp12::mWasabi	Takaki et al., 2013	Derivative of ATCC # BAA-535
M. marinum M strain transformed with pmsp12::tdTomato	Takaki et al., 2013	Derivative of ATCC # BAA-535
M. marinum M strain transformed with pmsp12::tdKatushka2	Takaki et al., 2013	Derivative of ATCC # BAA-535
ΔESX1 M. marinum M strain transformed with pmsp12::tdTomato	Pagán et al., 2015	Derivative of ATCC # BAA-535
ΔmmpL7 M.marinum M strain transformed with pmsp12::tdTomato	Cambier et al., 2014b	Derivative of ATCC # BAA-535
Δerp M. marinum M strain transformed with pmsp12::tdTomato	Takaki et al., 2013	Derivative of ATCC # BAA-535
marP::Tn M. marinum M strain transformed with pmsp12::tdTomato	Levitte et al., 2016	Derivative of ATCC # BAA-535
ΔesxA M. marinum M strain transformed with pmsp12::tdTomato	Osman et al., 2022	Derivative of ATCC # BAA-535
ΔesxA M. marinum M strain transformed with ::esxAWT	Osman et al., 2022	Derivative of ATCC # BAA-535
ΔesxA M. marinum M strain transformed with ::esxAM83I	Osman et al., 2022	Derivative of ATCC # BAA-535
ΔesxA M. marinum M strain transformed with ::esxAM93T	Osman et al., 2022	Derivative of ATCC # BAA-535
M. tuberculosis ΔleuDΔpanCD mc2 6206 transformed with pmsp12::tdTomato	Roca et al., 2019	N/A
Chemicals, peptides, and recombinant proteins
BD Difco Middlebrook 7H9 broth (dehydrated)	Fisher Scientific	Cat# DF0713-17-9
Middlebrook 7H10 agar base	Sigma-Aldrich	Cat# M0303
L-leucine	Sigma-Aldrich	Cat# L8000; CAS: 61-90-5
Calcium pantothenate	Sigma-Aldrich	Cat# C8731; CAS: 137-08-6
Remel OADC Enrichment	Fisher Scientific	Cat# 11903262
RPMI 1640 medium	Sigma-Aldrich	Cat# R7509
Gibco Phenol-free RPMI	Thermo-Fisher	Cat# 11835030
XF DMEM, pH 7.4	Agilent	Cat# 103575-100
Instant Ocean Salt	ZM Systems	N/A
PTU (1-phenyl-2-thiourea)	Sigma-Aldrich	Cat# P7629; CAS: 103-85-5
Tango Buffer (10x)	Thermo Fisher	Cat# BY5
Phenol Red Sodium Salt	Sigma-Aldrich	Cat# P5530; CAS: 34487-61-1
Pronase	Sigma-Aldrich	Cat# P5147; CAS:9036-06-0
Tricaine (ethyl 3-amonobenzoate, methanesulfonic acid salt)	Fisher Scientific	Cat# 10743661; CAS: 886-86-2
TopVision Low Melt Agarose	Thermo Fisher	Cat# R0801
Rapamycin	Sigma-Aldrich	Cat# R0395; CAS: 53123-88-9
Torin1	Cambridge Bioscience	Cat# CAY10997; CAS: 1222998-36-8
Nifedipine	Cambridge Bioscience	Cat# N3228; CAS: 21829-25-4
Diltiazem HCl	Cambridge Bioscience	Cat# D3447; CAS: 33286-22-5
2DG (2-deoxy-D-glucose)	Sigma-Aldrich	Cat# D8375; CAS: 154-17-6
UK5099	Cambridge Bioscience	Cat# B1952; CAS: 56396-35-1
Digitonin	Acros	Cat# 407565000 CAS: 11024-24-1
Prazosin HCl	Sigma-Aldrich	Cat#: P7791; CAS: 19237-84-4
PMA (Phorbol 12-myristate 13-acetate)	Sigma-Aldrich	Cat#: P1585; CAS: 16561-29-8
Accutase	Sigma-Aldrich	Cat#: A6964
Paraformaldehyde, 16% w/v	Alfa Aesar	Cat# 11490570
Acridine Orange (2% solution in H20)	Sigma-Aldrich	Cat# A9231; CAS: 65-61-2
MitoTracker Red CM-H2Xros	Thermo Fisher	Cat# M7513
eBioscience Fixable Viability Dye eFluor 660	Thermo Fisher	Cat# 65-0864-14
Tetramethylrhodamine, ethyl ester	Abcam	Cat# ab113852
SYTOX Green Nucleic Acid Stain	Thermo Fisher	Cat# S7020
AMPure XP beads for PCR Purification	Beckman Coulter	Cat# A63881
Precision Melt Supermix	BioRad	Cat# 172-5112
KASP V4.0 2X Master Mix	LGC Biosearch	Cat# KBS-1016-002
Mammalian Cell Lysis Buffer 5x	Abcam	Cat# ab179835
Alt-R Sp Cas9 Nuclease V3	IDT	1081058
Critical commercial assays
Gibson Assembly Cloning Kit	New England BioLabs	Cat# E5510S
mMessage mMachine T7 Transcription Kit	Thermo Fisher	Cat# AM1344
Seahorse XFp Glycolytic Rate Assay Kit	Agilent	Cat# 103346-100
Seahorse XFp Mito Stress Test Kit	Agilent	Cat#103015-100
ATP Assay Kit (Colorimetric/Fluorometric)	Abcam	Cat# ab83355
Glucose-6-Phosphate Dehydrogenase Activity Assay Kit (Fluorometric)	Abcam	Cat# ab176722
Experimental models: Cell lines
THP-1	ATCC	Cat# TIB-202, RRID:CVCL_0006
Experimental models: Organisms/strains
Zebrafish (Danio rerio): wild type AB strain	University of Cambridge	ZDB-GENO-960809-7
Zebrafish: TL strain	University of Cambridge	ZDB-GENO-990623-2
Zebrafish: WIK strain	University of Washington	ZDB-GENO-010531-2
Zebrafish: Tg(mpeg1:YFP)w200	Roca and Ramakrishnan, 2013	ZDB-ALT-130130-3
Zebrafish: Tg(mpeg1:Brainbow)w201	Pagán et al., 2015	ZDB-ALT-150512-3
Zebrafish: Tg(mfap4:tdTomato-CAAX)xt6	Walton et al., 2015	ZDB-ALT-160122-3
Zebrafish: Tg(ubib:secA5-YFP)cu34	This work	N/A
Zebrafish: Tg(CMV:EGFP-map1lc3b)zf155	He et al., 2009	ZDB-ALT-091029-2
Zebrafish: Tg(lysC:EGFP)nz117	Hall et al., 2007	ZDB-ALT-071109-2
Zebrafish: Tg(cd41:GFP)	Lin et al., 2005	N/A
Zebrafish: pycardw216	Matty et al., 2019	ZDB-ALT-191009-1
Zebrafish: mtorfh178	This work	N/A
Zebrafish: mtorsa16755	Wellcome Trust Sanger Institute	ZDB-ALT-131217-12934
Zebrafish: rptorsa11537	Wellcome Trust Sanger Institute	ZDB-ALT-130530-177
Zebrafish: rictorasa15967	Wellcome Trust Sanger Institute	ZDB-ALT-130411-4494
Zebrafish: rictorbsa18403	Wellcome Trust Sanger Institute	ZDB-ALT-131217-14421
Zebrafish: atg12sa42684	Wellcome Trust Sanger Institute	ZDB-ALT-160601-8392
Zebrafish: casp9sa11164	Wellcome Trust Sanger Institute	ZDB-ALT-130411-1023
Zebrafish: sting1sa35634	Wellcome Trust Sanger Institute	ZDB-ALT-160601-4021
Zebrafish: g6pdsa24272	Wellcome Trust Sanger Institute	ZDB-ALT-161003-11894
Oligonucleotides
mtorfh178 forward primer for genotyping by HRMA 5’-TCACAGTATCAGATCTTCATTCCTATGGT-3’	This paper	N/A
mtorfh178 reverse primer for genotyping by HRMA 5’-ACATCATAGCGCTGGTGATTGAT-3’	This work	N/A
mtorsa16755 forward primer for genotyping by HRMA 5’-TGACTACAGCACCAGCGAGA-3’	This work	N/A
mtorsa16755 reverse primer for genotyping by HRMA 5’-ATGGTGTGGTGATTGGACAG-3’	This work	N/A
Alt-R crRNA Dr.Cas9.NDUFAF1.1.AA 5’-TGGAACAGACCCGTGTCGTG-3’	IDT	N/A
Alt-R crRNA Dr.Cas9.NDUFAF1.1.AB 5’-TATCGAGTCTCTCCATCACG-3’	IDT	N/A
Alt-R crRNA Dr.Cas9.NDUFAF1.1.AC 5’-GGTCCCATACAGCAAACACG-3’	IDT	N/A
Alt-R crRNA Dr.Cas9.NDUFAF1.1.AD 5’-CGTGTGTCTGGAGGCTGACC-3’	IDT	N/A
Alt-R CRISPR-Cas9 tracrRNA	IDT	1073191
Forward primer for genotyping ndufaf1 AA mutagenesis by HRMA 5’-AGAGCACATGCTGGAACAGA-3’	This work	N/A
Reverse primer for genotyping ndufaf1 AA mutagenesis by HRMA 5’-TGTTTTTGCCCAGACTGACA-3’	This work	N/A
Forward primer for genotyping ndufaf1 AB, AC mutagenesis by HRMA 5’-CGCAGTGTGGCTTATGTCAG-3’	This work	N/A
Reverse primer for genotyping ndufaf1 AB, AC mutagenesis by HRMA 5’-TTGGAGCGCATAGAGCAGTA-3’	This work	N/A
Forward primer for genotyping ndufaf1 AD mutagenesis by HRMA 5’-AGGAGCAAGTTTGAGCGAGA-3’	This work	N/A
Reverse primer for genotyping ndufaf1 AD mutagenesis by HRMA 5’-AAGCCAAAGTGCTTCCTGAC-3’	This work	N/A
pDestTol2pA2_ubi:EGFP forward primer for vector fragment amplification for Gibson Assembly 5’-GGCGGTGGAAGATCTGGG-3’	This work	N/A
pDestTol2pA2_ubi:EGFP reverse primer for vector fragment amplification for Gibson Assembly 5’-GGTCCAGCCTGCTTTTTTG-3’	This work	N/A
secA5-YFP forward primer for insert fragment amplification for Gibson Assembly 5’-aaagcaggctggaccATGCATAAGGTTTTGCTG-3’	This work	N/A
secA5-YFP reverse primer for insert fragment amplification for Gibson Assembly 5’-agatcttccaccgccGATGAATTAATTCGAGCTCC-3’	This work	N/A
ubb:secA5 joint sequence forward primer to validate assembled product 5’-TCGTTTAACATGGGAGAAGTGC-3’	This work	N/A
ubb:secA5 joint sequence reverse primer to validate assembled product 5’-AGCCTTTCATAGCCTTCCGA-3’	This work	N/A
YFP-SV40pA joint sequence forward primer to validate assembled product 5’-CTGTACAAGTAAAGCGGCCG-3’	This work	N/A
YFP-SV40pA joint sequence reverse primer to validate assembled product 5’-GTAAAACGACGGCCAGTGAA-3’	This work	N/A
Recombinant DNA
T7-TPase	Khattak et al., 2014	RRID:Addgene_51818
pDestTol2pA2_ubi:EGFP	Mosimann et al., 2011	RRID:Addgene_27323
pBH-UAS-secA5-YFP	van Ham et al., 2010	RRID:Addgene_32359
pTol2-ubb:secA5-YFP	This work	N/A
Software and algorithms
NIS Elements (5.21)	Nikon	N/A
IMARIS (8.2) and IMARIS for Cell Biologists (9.1)	Bitplane	N/A
FlowJo 10	TreeStar	N/A
Prism (versions 7 and 9)	GraphPad	N/A
ImageJ	https://imagej.nih.gov/ij/	N/A
Fluorescent Pixel Count Macro (Image J)	Takaki et al., 2013	N/A
AssayR	Wills et al., 2017	N/A
MetaboAnalyst 5.0	Pang et al., 2021	N/A
Photoshop CS6	Adobe	N/A
Illustrator CS6	Adobe	N/A