. 2018 Mar 9;7:e32110. doi: 10.7554/eLife.32110

Table 2. Predicted gene function: Mutants with decreased lipid accumulation.

Predicted functions for genes for which mutants were high-confidence candidates for decreased lipid accumulation (enrichment scores clustered in LA6 - LA8, Figure 5).

	Gene ID	Short name	Annotation from	Description	Cluster	Enrichment
	Gene ID	Short name	Annotation from	Description	Cluster	BD	FACS
tRNA thiolation
	RTO4_10764	NCS2	S. cerevisiae	tRNA 2-thiolation protein	LA7	0.5	−2.3
	RTO4_12817	NCS6	S. cerevisiae	tRNA 2-thiolation protein	LA7	0.7	−2.6
	RTO4_14918	ELP2	S. cerevisiae	Elongator complex protein	LA7	0.7	−1.2
	RTO4_14716	IKI3	S. cerevisiae	Elongator complex protein	LA7	0.4	−1.1
	RTO4_11341	UBA4	S. cerevisiae	Adenylyltransferase and sulfurtransferase	LA7	0.6	−2.6

G Protein Switches
†	RTO4_15198	Rab6	H. sapiens	GTPase	LA6	−1.3	−1.6
	RTO4_14622	RGP1	H. sapiens	Guanine nucleotide exchange factor	LA6	−1.4	−1.5

Kinases and Phosphatases
	RTO4_10698	VHS1	S. cerevisiae	Kinase	LA6	0.8	−3.7
	RTO4_16375	HRK1	S. cerevisiae	Kinase	LA6	0.4	−2.2
*	RTO4_11453	GLC7	S. cerevisiae	Kinase	LA8	−1.2	−0.9
	RTO4_16810	KIN1	S. cerevisiae	Kinase	LA6	0.1	−1.1
	RTO4_10025	SAT4	S. cerevisiae	Kinase	LA7	1.6	−3.6
	RTO4_13327	ATG1	S. cerevisiae	Kinase	LA6	0.1	−2.5
	RTO4_14907	SCH9	S. cerevisiae	Kinase	LA6	−0.6	−2.0
	RTO4_14906	kinase-like	S. cerevisiae	Kinase	LA6	−0.3	−1.8
	RTO4_13290	YAK1	S. cerevisiae	Kinase	LA8	−1.1	−0.9
	RTO4_11732	PPH3	S. cerevisiae	Phosphatase 4 catalytic subunit	LA6	0.9	−3.6
	RTO4_12586	PSY2	S. cerevisiae	Phosphatase 4 regulatory subunit	LA6	0.2	−1.2
	RTO4_16463	PTC7-like	S. cerevisiae	Phosphatase	LA6	0.1	−2.0

Autophagy
	RTO4_13327	ATG1	S. cerevisiae	Kinase	LA6	0.1	−2.5
	RTO4_13598	ATG2	S. cerevisiae	Membrane protein	LA6	−0.6	−3.4
	RTO4_12968	ATG3	S. cerevisiae	Ubiquitin-like-conjugating enzyme	LA6	−0.8	−4.5
	RTO4_13496	ATG4	S. cerevisiae	Cysteine protease	LA6	−0.1	−2.3
	RTO4_11901	ATG7	S. cerevisiae	Ubiquitin-like modifier-activating enzyme	LA6	−0.8	−4.2
	RTO4_13543	ATG8	S. cerevisiae	Ubiquitin-like protein	LA6	−1.0	−4.2
	RTO4_11326	ATG9	S. cerevisiae	Membrane protein	LA6	0.0	−1.3
	RTO4_9008	ATG14	S. cerevisiae	Autophagy-specific subunit of PtdIns3P-kinase complex	LA6	0.0	−5.0
	RTO4_16723	ATG18	S. cerevisiae	Phosphoinositide binding protein	LA6	−0.9	−5.8

Ubiquitination and Proteolysis
†	RTO4_16672	PRB1	S. cerevisiae	Vacuolar proteinase	LA6	−0.2	−1.7
	RTO4_15345	SIS1	S. cerevisiae	Protein chaperone	LA6	−0.4	−1.2
	RTO4_10423	RMD5	S. cerevisiae	GID complex E3 ubiquitin ligase	LA6	−0.4	−2.0
	RTO4_11737	GID8	H. sapiens	GID complex member	LA6	−0.1	−1.5
	RTO4_9816	LONRF1	H. sapiens	E3 ubiquitin ligase	LA6	−0.5	−4.5
	RTO4_15320	USP48	H. sapiens	Ubiquitin carboxyl-terminal hydrolase	LA6	0.0	−1.2
	RTO4_9600	COPS3	H. sapiens	COP9 signalosome complex subunit	LA1	1.4	0.6
	RTO4_11569	GPS1	H. sapiens	COP9 signalosome complex subunit	LA6	0.7	−2.1
Triacylglyceride Synthesis
†	RTO4_12154	GPD1	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−1.7	−4.0
	RTO4_11043	BCSL2-like	H. sapiens	Seipin	LA6	−0.8	−2.9
	RTO4_16460	DGA1	H. sapiens	Diacylglycerol acyltransferase	LA6	−0.7	−4.0
	RTO4_14597	ACS1	S. cerevisiae	Acetyl-CoA synthetase	LA8	−1.7	−1.0
	RTO4_10182	YEF1	S. cerevisiae	NAD+/NADH kinase	LA6	−0.1	−1.6
‡	RTO4_11039	GUT2	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−0.2	−1.1

Lipid Droplet Associated
	RTO4_16381	PLIN1-like	S. cerevisiae	Perilipin	LA6	−1.7	−4.3
‡	RTO4_11039	GUT2	S. cerevisiae	Glycerol-3-phosphate dehydrogenase	LA6	−0.2	−1.1
	RTO4_15372	EGH1	S. cerevisiae	Steryl-beta-glucosidase	LA6	0.7	−2.5
	RTO4_13614	RIP1	S. cerevisiae	Mitochondrial complex III iron-sulfur protein	LA6	−0.5	−2.8
	RTO4_11043	BCSL2-like	H. sapiens	Seipin	LA6	−0.8	−2.9
	RTO4_16460	DGA1	H. sapiens	Diacylglycerol acyltransferase	LA6	−0.7	−4.0

Protein Modification
	RTO4_12670	B3GALT1-like	H. sapiens	Beta-1,3-Galactosyltransferase	LA6	−0.9	−3.1

Protein Trafficking
†	RTO4_15198	Rab6	H. sapiens	GTPase	LA6	−1.3	−1.6

Other ER/Golgi Proteins
	RTO4_8838	DNAJC4	H. sapiens	DnaJ family chaperone	LA6	−0.8	−1.3
	RTO4_13971	DNAJC3	H. sapiens	DnaJ family chaperone	LA6	−1.1	−2.2

Gene Expression
	RTO4_11333	KLF18-like	H. sapiens	Transcription factor	LA6	−0.2	−1.1
	RTO4_15641	SKN7	S. cerevisiae	Transcription factor	LA6	0.9	−2.9
	RTO4_14676	LHX5-like	H. sapiens	Transcription factor	LA6	−0.2	−2.8
	RTO4_11891	HAP2	S. cerevisiae	Transcription factor	LA6	−0.8	−2.4
	RTO4_12420	OPI1-like	S. cerevisiae	Transcription factor	LA6	0.0	−3.7
	RTO4_14100	HAPX	C. neoformans	Transcription factor	LA8	−1.2	−1.7
	RTO4_13255	SGF73	S. cerevisiae	SAGA-associated factor	LA6	0.4	−1.5

Methylcitrate Cycle
	RTO4_14162	ICL2	S. cerevisiae	2-methylisocitrate lyase	LA6	−0.3	−1.8
	RTO4_12642	PDH1	S. cerevisiae	2-methylcitrate dehydratase	LA6	−0.1	−1.7

Electron Transport and Redox Balancing
	RTO4_11165	CBP4	S. cerevisiae	Mitochondrial complex III assembly factor	LA6	−0.4	−2.5
	RTO4_13614	RIP1	S. cerevisiae	Mitochondrial complex III iron-sulfur protein	LA6	−0.5	−2.8
	RTO4_13902	AFG1	S. cerevisiae	Mitochondrial complex IV assembly factor	LA6	−0.3	−1.3
‡	RTO4_10010	NDUFS4	H. sapiens	Mitochondrial complex I accessory factor	LA8	−1.3	−0.1
	RTO4_13925	NDUFAF3	H. sapiens	Mitochondrial complex I assembly factor	LA8	−1.0	−1.6

Amino Acid Biosynthesis
†	RTO4_12302	CPA2	S. cerevisiae	Large subunit of carbamoyl phosphate synthetase	LA6	−0.4	−2.4

Glucose and Energy Metabolism
	RTO4_10423	RMD5	S. cerevisiae	GID complex E3 ubiquitin ligase	LA6	−0.4	−2.0
	RTO4_11737	GID8	H. sapiens	GID complex member	LA6	−0.1	−1.5
	RTO4_12034	TPS2	S. cerevisiae	Trehalose 6-phosphate synthase	LA6	0.0	−3.8
*	RTO4_10264	GLK1	S. cerevisiae	Hexokinase	LA7	2.1	−2.0
Transporters
†	RTO4_12909	OAT1	C. neoformans	Nucleobase transporter	LA6	−0.2	−1.1
	RTO4_11397	COT1	S. cerevisiae	Vacuolar zinc transporter	LA6	−0.2	−1.1
	RTO4_11924	SNF3	S. cerevisiae	Plasma membrane low glucose sensor	LA6	0.0	−2.8

Other
	RTO4_12512	cry	N. crassa	Blue-light photoreceptor cryptochrome	LA7	0.6	−1.6
	RTO4_14974			Steroidogenesis/phosphatidylcholine transfer domain	LA6	−0.3	−1.2
	RTO4_15889	MAEA	H. sapiens	EMP macrophage erythroblast attacher	LA6	−0.1	−1.7
	RTO4_16287	CDD1	S. cerevisiae	Cytidine deaminase	LA6	0.3	−2.3
	RTO4_15247	WDR26	H. sapiens	WD repeat protein	LA6	−0.9	−1.3
	RTO4_8764	MGS1	S. cerevisiae	DNA-dependent ATPase and ssDNA annealing protein	LA6	0.2	−1.2

Unknown
	RTO4_10431			Protein of unknown function	LA6	0.7	−1.6
	RTO4_8973			Protein of unknown function	LA8	−0.2	−1.1
	RTO4_13195			Protein of unknown function	LA6	−0.2	−1.1
	RTO4_10367			Protein of unknown function	LA6	−0.1	−1.3
	RTO4_10102			Protein of unknown function	LA6	−0.3	−1.2
	RTO4_14926			Protein of unknown function	LA6	0.2	−1.7
	RTO4_12045			Protein of unknown function	LA6	0.0	−1.5
	RTO4_13600			Protein of unknown function	LA6	−0.3	−1.3
	RTO4_10976			Protein of unknown function	LA6	−0.2	−1.5
	RTO4_9970	LDB17	S. cerevisiae	Protein of unknown function	LA8	−1.3	−0.5
	RTO4_13435			Protein of unknown function	LA7	0.2	−2.0
	RTO4_9692			Protein of unknown function	LA6	−0.5	−1.4
	RTO4_15521			Protein of unknown function	LA6	0.2	−2.2
	RTO4_8769			Protein of unknown function	LA6	−0.5	−1.6
	RTO4_8770			Protein of unknown function	LA6	−0.5	−1.9
	RTO4_11259			Protein of unknown function	LA7	0.7	−3.3
	RTO4_9490			Protein of unknown function	LA6	−0.6	−2.4
	RTO4_15520			Protein of unknown function	LA6	−0.5	−2.5
	RTO4_8771			Protein of unknown function	LA6	−0.6	−2.5
	RTO4_13452			Protein of unknown function	LA6	−1.3	−4.0
	RTO4_15211			Protein of unknown function	LA8	−1.1	−1.5

Cellular processes grouped as in Figure 6. BD: Enrichment score from buoyant density separation. FACS: Enrichment score from fluorescence activated cell sorting.

Protein abundance under nitrogen limitation: * increased; † increased 10-fold or more; ‡ decreased; § decreased 10-fold or more (Zhu et al., 2012).