TABLE 1.

Genes deletions that phenocopy nhx1Δ

The viable single gene deletion yeast collection was screened for growth sensitivity to four nhx1Δ phenotypes: 15 μg/ml hygromycin B (HygB), pH 2.7, 800 mm KCl, and 800 mm NaCl. Gene deletions showing sensitivity to at least three of these four conditions after 19 h growth are listed according to their annotated function. GEF, guanine nucleotide exchange factor; WASP, Wiskott-Aldrich syndrome protein; PtdIns(3,5)P₂, phosphatidylinositol 3,5-bisphosphate.

Gene	Function	HygB	pH 2.7	KCl	NaCl
MVB formation (three)
BRO1	Recruits deubiquitylase Doa4 to endosome, regulates membrane scission	+		+	+
VPS4	AAA-ATPase, ESCRT-III disassembly	+	+	+
VPS36	ESCRT-II subunit, Ub-dependent protein sorting	+	+	+
Vacuole fusion (four)
MON1	GEF for vacuole Rab GTPase Ypt7		+	+	+
VAM7	SNAP25 ortholog, Q-SNARE	+	+		+
VPS41	Ypt7 effector, component of HOPS	+		+	+
YPT7	Vacuole Rab GTPase		+	+	+
Endosome trafficking and fusion (six)
PEP7/VAC1	Ortholog of mammalian EEA1	+	+	+
RCY1	Effector for Rab GTPases Ypt31 and Ypt32	+	+	+	+
SYS1	Arl3 receptor on Golgi, multicopy suppressor of ypt6Δ	+		+	+
VPS1	Dynamin-like, possible role in membrane fission	+	+		+
VPS9	GEF for endosomal Rab GTPase Vps21	+	+	+
VPS35	Component of retromer	+	+	+
Actin cytoskeleton (three)
LAS17/BEE1	WASP ortholog, Arp2/3-mediated actin nucleation	+	+	+	+
SAC6	Fimbrin ortholog, actin filament stability	+		+	+
VRP1	Verprolin (WIP ortholog) binds WASP to remodel actin		+	+	+
Membrane lipid distribution (three)
OPI1	Transcription factor, pH-sensitive regulation of phospholipid biosynthesis genes		+	+	+
SAC3	PtdIns(3,5)P2 phosphatase required for endocytic trafficking		+	+	+
ERG24	Ergosterol biosynthesis	+	+		+
Cell signaling (four)
ARG82	Inositol polyphosphate multikinase		+	+	+
CNB1	Calcineurin B		+	+	+
REF2	Regulator of Glc7 protein phosphatase I, involved in cation homeostasis		+	+	+
STE11	MEK kinase (MAPKKK)		+	+	+
Other (11)
DHH1	Cytoplasmic DEx(D/H) box helicase	+	+	+
HSP31	Possible chaperone and cysteine protease		+	+	+
NST1	Unknown function, mediates salt stress	+		+	+
OCT1	Mitochondrial intermediate (metallo)peptidase	+		+	+
PDB1	Pyruvate dehydrogenase β-subunit	+		+	+
RAI1	Activator of exoribonuclease Rat1	+		+	+
SPT20	Subunit of SAGA transcriptional regulation complex	+	+	+
UIP5	Unknown function, putative U box ubiquitin ligase	+		+	+
VPH2	Required for V-ATPase activity	+	+	+
YDR455C	Dubious ORF, overlaps NHX1*	+	+	+
YEL007W	Unknown function, C. albicans ortholog mediates white opaque switching		+	+	+