Table II. Selected host proteins identified by MS localizing to purified D. discoideum LCVs harbouring either Lp02 or Δpentuple. Abbreviations: no acronym (N.A.), cytoplasm (CP), plasma membrane (PM), inner membrane (IM), early endosome (EE), late endosome (LE), lysosome (LS), recycling endosome (RE), autophagosome (AP), endoplasmic reticulum (ER), Golgi apparatus (GA), ER-Golgi intermediate compartment (ERGIC), Mitochondria (MC), nucleus (NC). Detection frequency was determined in three independent biological samples, taken 1 h post infection. Complete set of D. discoideum LCV proteins identified by LC-MS/MS is listed in the supplementary Tables S3, S4, and S5.

Gene	Classification		Accession number (detection frequency)		Ref.
	Product	Localization	Lp02	Δpentuple
Signalling
CapB	cAMP-binding protein 2			DDB_G0277501 (1)	(65)
Dcd2A	Neutral ceramidase A			DDB_G0293538 (1)	(65)
FttB	14-3-3 protein	CP		DDB_G0269138 (3)	(66)
KinX	Probable Ser/Thr-protein kinase KinX		DDB_G0283391 (1)		(65)
LkhA	Leukotriene hydrolase	CP	DDB_G0269148 (1)		(65, 67)
KsrA-1	3-ketodihydro-sphingosine reductase	ER		DDB_G0274015 (2)	(65)
Mdn1	Midasin	NC		DDB_G0295765 (1)	(65)
N.A.	Regulator complex LAMTOR3			DDB_G0274833 (1)	(65)
N.A.	RCC domain protein			DDB_G0292586 (1)	(65)
Nca2	Nuclear control of ATPase protein 2			DDB_G0267648 (1)	(65)
Nop58	Nucleolar protein	NC		DDB_G0268098 (1)	(65)
Nup98	Nuclear pore complex protein Nup98-Nup96	NC	DDB_G0291390 (1)		(65)
Nup107	Nucleoporin 107	NC	DDB_G0285579 (1)		(65)
Nup155	Nucleoporin 155	NC	DDB_G0291163 (1)		(65)
NxnA	Annexin A7		DDB_G0269160 (2)		(65)
Rap1	Ras GTPase	PM	DDB_G0291237 (1)		(68, 69)
Rpb3	RNA polymerase	NC		DDB_G0292244 (3)	(65)
Sac1	PI phosphatase Sac1	ER, PM	DDB_G0271630 (2)		(70)
UbqJ	Polyubiquitin J	CP, NC		DDB_G0269458 (3)	(65)
UbqF	Polyubiquitin F	CP, NC	DDB_G0289449 (3)		(65)
Vesicle trafficking
AbpD	Interaptin		DDB_G0287291 (1)		(71)
DlpA	Dynamin-like protein A	CP		DDB_G0268592 (1)	(65)
DymB	Dynamin B GTPase	CP		DDB_G0277851 (1)	(72)
NsfA	Vesicle-fusing ATPase	CP	DDB_G0276153 (1)		(73)
Rab1A	Ras-related protein Rab1A	ER, GA		DDB_G0283757 (3)	(65)
Rab11C	Rab11C	GA, RE	DDB_G0277101 (1)		(65)
Rab21	Rab21	EE		DDB_G0286553 (1)	(74, 75)
Rtnlc	Reticulon family protein	ER		DDB_G0293088 (3)	(76, 77)
Ssr1	TRAP protein	ER, PM	DDB_G0283497 (3)		(78)
Syn5	Syntaxin 5 t-SNARE	ER, GA		DDB_G0277565 (1)	(65)
Vamp7A	Vamp7A v-SNARE	PM, EE		DDB_G0284951 (1)	(65)
Vps45	Vacuolar protein	GA, PM	DDB_G0290213 (1)		(65)
Metabolism
AlrA	Aldose reductase A	CP		DDB_G0293850 (1)	(65)
Coq4	Ubiquinone biosynthesis protein Coq4			DDB_G0292620 (1)	(65)
Coq9	Ubiquinone biosynthesis protein Coq9			DDB_G0274457 (2)	(65)
Cox11	Cytochrome c oxidase assembly protein Cox11	MC		DDB_G0289353 (1)	(65)
CxgE	Cytochrome c oxidase subunit 7e			DDB_G0277837 (1)	(65)
EnoA	Enolase A	CP		DDB_G0283137 (1)	(65)
FdfT	Squalene synthase	ER, PM	DDB_G0292072 (1)		(65)
Gpi	Glucose 6-P isomerase	CP	DDB_G0283673 (1)		(65)
MasA	Malate synthase	CP	DDB_G0275887 (1)		(65)
Surf1	SURF1-like protein			DDB_G0274001 (3)	(79)
Transport
AbcG10	ABC transporter G family	PM	DDB_G0292986 (1)		(80)
McfS	Mitochondrial substrate carrier	CP, MC		DDB_G0290913 (2)	(81)
McsP	Mitochondrial substrate carrier	CP, MC		DDB_G0292034 (1)	(81)
Mfsd1	Major facilitator superfamily protein 1		DDB_G0289201 (1)		(65)
Timm9	Mitochondrial import IM translocase Tim9	MC		DDB_G0272931 (1)	(65)
Timm16	Mitochondrial import IM translocase Tim16	MC		DDB_G0282195 (1)	(65)
Timm17	Mitochondrial import IM translocase Tim17	MC		DDB_G0287627 (2)	(65)
Cytoskeleton/motor proteins
AbpC	Gelation factor	CP, PM		DDB_G0269100 (1)	(65)
Act1	Major actin	CP	DDB_G0274599 (3)		(65)
Act2	Major actin	CP		DDB_G0274133 (3)	(65)
ArcC	Actin-related protein	CP	DDB_G0283755 (1)		(65)
ArcD	Actin-related protein 2/3 compl. subunit 4	CP		DDB_G0269102 (2)	(65)
CtxA	Cortexillin	CP, PM	DDB_G0289483 (1)		(82)
LimE	LIM domain protein	CP, PM		DDB_G0279415 (2)	(83)
MlcR	Myosin regulatory light chain	CP	DDB_G0276077 (1)		(65)
TalB	Talin B	CP	DDB_G0287505 (1)		(65)
Miscellaneous
Cnrl	SET domain-containing protein			DDB_G0269768 (2)	(65)
DscA	Discoidin 1 subunit A	CP		DDB_G0273919 (3)	(65)
Kil1	Sulfotransferase	PM	DDB_G0267630 (1)		(84)
SodA	Superoxide dismutase	MC		DDB_G0267420 (1)	(85)