TABLE 2:

Candidate genes on chromosome XIV. Continued

Systematic name	Standard name	Hit from UPRE::GFP screen? (Jonikas et al., 2009)	Z-score from 25°C HSE::GFP screen (Brandman et al., 2012)	SGD gene description
YNL148C	ALF1	Yes	0.59263	Alpha-tubulin folding protein; similar to mammalian cofactor B; Alf1p-GFP localizes to cytoplasmic microtubules; required for the folding of alpha-tubulin and may play an additional role in microtubule maintenance
YNL077W	APJ1	No	–0.011564	Hsp40 chaperone with a role in SUMO-mediated protein degradation; works in concert with Hsp70 and Hsp110 (Sse1p) to promote disaggregation of intranuclear protein inclusions; competes with Hsp104 in disaggregation, supporting turnover instead of refolding; member of DnaJ-like family, conserved across eukaryotes; overexpression interferes with propagation of the [Psi+] prion; forms nuclear foci upon DNA replication stress
YNL159C	ASI2	No	0.198189	Subunit of the INM Asi ubiquitin ligase complex; the Asi complex targets both misfolded proteins of the INMAD pathway and inner for ubiquitin-mediated degradation; acts with Asi1p and Asi3p to ensure the fidelity of SPS-sensor signaling by targeting latent unprocessed forms of Stp1p and Stp2p, maintaining the repressed state of gene expression in the absence of inducing amino acids
YNL008C	ASI3	No	–0.071735	Subunit of the INM Asi ubiquitin ligase complex; Asi complex targets both misfolded proteins of the INMAD pathway and regulators of sterol biosynthesis for ubiquitin-mediated degradation; acts with Asi1p and Asi2p to ensure the fidelity of SPS-sensor signaling by targeting latent unprocessed forms of Stp1p and Stp2p, maintaining the repressed state of gene expression in the absence of inducing amino acids
YNL242W	ATG2	No	0.171614	Peripheral membrane protein required for autophagic vesicle formation; also required for vesicle formation during pexophagy and the cytoplasm-to-vaucole targeting (Cvt) pathway; involved in Atg9p cycling between the phagophore assembly site and mitochondria; contains an APT1 domain that binds phosphatidylinositol-3-phosphate; essential for cell cycle progression from G2/M to G1 under nitrogen starvation; forms cytoplasmic foci upon DNA replication stress
YNR007C	ATG3	No	–0.16644	E2-like enzyme; involved in autophagy and cytoplasm-to-vacuole targeting (Cvt) pathway; plays a role in formation of Atg8p-phosphatidylethanolamine conjugates, which are involved in membrane dynamics during autophagy and Cvt; interaction with Atg8p regulated by acetylation by NuA4 histone acetyltransferase Esa1p while attenuation of Atg3 acetylation is mediated by histone deacetylase Rpd3p; Atg12p-Atg5p conjugate enhances E2 activity of Atg3p by rearranging its catalytic site
YNL223W	ATG4	No	0.287679	Conserved cysteine protease required for autophagy; cleaves Atg8p to a form required for autophagosome and Cvt vesicle generation
YNR051C	BRE5	Yes	–0.326932	Ubiquitin-protease cofactor; forms deubiquitination complex with Ubp3p that coregulates anterograde and retrograde transport between the ER and Golgi compartments, deubiquitinating COPII and COPI vesicle coat constituents, Sec23p and Sec27p; involved along with Ubp3p in the steady-state retention of Golgi membrane proteins, such as glycosyltransferases; null is sensitive to brefeldin A
YNL155W	CUZ1	No	0.275969	Protein with a role in the ubiquitin-proteasome pathway; interacts with ubiquitinated protein, Cdc48p, and the proteasomal regulatory particle; may protect cells from trivalent metalloid–induced proteotoxicity; contains a PACE promoter element and is coregulated with proteasome subunit genes; AN1-type zinc finger protein, with DHHC and ubiquitin-like domains (UBL); orthologue of ZFAND1, a human gene linked to cancer; protein abundance increases under DNA replication stress
YNL001W	DOM34	No	-–.374767	Protein that facilitates ribosomal subunit dissociation; Dom34-Hbs1 complex and Rli1p have roles in dissociating inactive ribosomes to facilitate translation restart, particularly ribosomes stalled in 3′ UTRs; required for RNA cleavage in no-go decay, but reports conflict on endonuclease activity; pelota orthologue; protein abundance increases in response to DNA replication stress; DOM34 has a paralogue, YCL001W-B, that arose from the whole-genome duplication
YNL080C	EOS1	Yes	1.454465	Protein involved in N-glycosylation; deletion mutation confers sensitivity to oxidative stress and shows synthetic lethality with mutations in the spindle checkpoint genes BUB3 and MAD1; YNL080C is not an essential gene
YNL281W	HCH1	No	0.288015	Heat shock protein regulator; binds to Hsp90p and may stimulate ATPase activity; originally identified as a high-copy-number suppressor of a HSP90 loss-of-function mutation; role in regulating Hsp90 inhibitor drug sensitivity; GFP-fusion protein localizes to the cytoplasm and nucleus; protein abundance increases in response to DNA replication stress
YNL227C	JJJ1	Yes	–0.24319	Cochaperone that stimulates the ATPase activity of Ssa1p; required for a late step of ribosome biogenesis; associated with the cytosolic large ribosomal subunit; contains a J-domain; mutation causes defects in fluid-phase endocytosis
YNL123W	NMA111	No	–0.143379	Serine protease and general molecular chaperone; cleaves Roq1p, which modifies the substrate specificity of the Ubr1p Ub-ligase, promoting the stress-induced homeostatically regulated protein degradation (SHRED) of misfolded and native ER-membrane and cytosolic proteins; chaperone activity involved in the heat stress response; promotes apoptosis through proteolysis of Bir1p; role in lipid homeostasis; mammalian Omi/HtrA2 serine protease family member
YNL149C	PGA2	N/a	N/a	Essential protein required for maturation of Gas1p and Pho8p; involved in protein trafficking; GFP-fusion protein localizes to the ER and YFP-fusion protein to the nuclear envelope-ER network; null mutants have a cell separation defect
YNL097C	PHO23	Yes	–0.899301	Component of the Rpd3L histone deacetylase complex; involved in transcriptional regulation of PHO5; affects termination of snoRNAs and cryptic unstable transcripts (CUTs); C-terminus shares significant sequence identity with the human candidate tumor suppressor p33-ING1 and its isoform ING3
YNL206C	RTT106	Yes	1.472194	Histone chaperone; involved in regulation of chromatin structure in both transcribed and silenced chromosomal regions; affects transcriptional elongation; has a role in regulation of Ty1 transposition; interacts physically and functionally with Chromatin Assembly Factor-1 (CAF-1)
YNL007C	SIS1	n/a	0.391894	Type II HSP40 cochaperone that interacts with the HSP70 protein Ssa1p; shuttles between cytosol and nucleus; mediates delivery of misfolded proteins into the nucleus for degradation; involved in proteasomal degradation of misfolded cytosolic proteins; protein abundance increases in response to DNA replication stress; polyQ aggregates sequester Sis1p and interfere with clearance of misfolded proteins; similar to bacterial DnaJ proteins and mammalian DnaJB1
YNL209W	SSB2	No	0.211499	Cytoplasmic ATPase that is a ribosome-associated molecular chaperone; functions with J-protein partner Zuo1p; may be involved in the folding of newly synthesized polypeptide chains; member of the HSP70 family; SSB2 has a paralogue, SSB1, that arose from the whole-genome duplication
YNL064C	YDJ1	No	1.879207	Type I HSP40 cochaperone; involved in regulation of HSP90 and HSP70 functions; acts as an adaptor that helps Rsp5p recognize cytosolic misfolded proteins for ubiquitination after heat shock; critical for determining cell size at Start as a function of growth rate; involved in protein translocation across membranes; member of the DnaJ family; chimeric protein in which the human p58IPK J domain replaces yeast Ydj1p J domain can complement yeast ydj1 mutant