Journal of Cell Science Supplementary Material

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2 Fig. S1. Functional categorization of genes misregulated more than 2-fold in arv1 Δ, comparison with data from a previous study, and expression levels of suppressor and functionally related genes upon ARV1 deletion. (A and B) Genes up-regulated (A) (265 genes) or down-regulated (B) (173 genes) more than 2-fold (average change of three experiments) by ARV1 deletion were grouped into 7 functional classes based on the information in the literature and the Saccharomyces Genome Database (SGD). (C and D) Venn diagrams showed the number and overlap of genes that were up-regulated (C) or downregulated (D) more that 2-fold in this study and a previous study (Shechtman et al., 2011). Overlapping genes are listed, and the transcripts that had changes greater than 3-fold in arv1 Δ cells are indicated by underlines. (E and F) Suppressor gene DEP1 expression is significantly down-regulated upon ARV1 deletion. Average value and standard deviation (s.d.) of the relative expression levels of suppressor and functionally related genes; Rad3L histone deacetylase complex (E) and nonsense-mediated mrna decay (F) genes were obtained from three independent experiments. *P value for the t test < 0.05; **P < 0.01; ***P <

3 Fig. S2. Co-fitness of genes related to sphingolipid synthesis and telomere homeostasis. (A and B) Heterozygous co-fitness scores were retrieved from the Yeast Fitness Database ( and visualized as a heatmap. (B) Sphingolipid biosynthetic pathway in yeast. Metabolites and genes encoding enzymes and proteins involved in sphingolipid synthesis are indicated.

4 Fig. S3. Deletion of ARV1 does not cause telomeric silencing defect. Average value and standard deviation (s.d.) of the relative expression levels of subtelomeric genes were obtained from three independent experiments.

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6 Fig. S4. Expression levels of RiBi, RP genes and genes involved in control of RiBi and RP gene transcription in sur2δ, arv1 Δ, and arv1 Δ sur2δ mutants. (A-H) Average value of the relative expression levels of RiBi (220 genes), RP (110 genes) and all (6349 genes) genes was obtained from three independent experiments. The results were expressed as percentage of RiBi (A-D) or RP (E-H) and all genes with 0.05-fold difference in the relative expression levels. (I) Average value and standard deviation (s.d.) of the relative expression levels of genes were obtained from three independent experiments. *P value for the t test < 0.05; **P < 0.01; ***P <

7 Table S1. Yeast strains used in this study Strain (number or Genotype ORF) Source or Reference 1) Figure and Table Wild type RH1800 MATa his4 leu2 ura3 bar1 Zanolari et al., B lcb1-100 RH3809 MATa lcb1-100 his4 leu2 ura3 bar1; same as RH1800 but lcb1-100 Zanolari et al., B Wild type RH6082 MATa his3 leu2 trp1 ura3 lys2 bar1; same as RH1800 but HIS4 his3 trp1 lys2 Kajiwara et al., B, 2A, 4A-H, S1A, B, E, F, S3-S4, Tables S2-S10 arv1δ sur2δ FKY131 MATa arv1δ::leu2 sur2δ::leu2 his3 leu2 trp1 ura3 bar1; same as RH1800 but HIS4 his3 trp1 arv1δ sur2δ This study 4A-H, S1E, F, S3-S4, Table S4, Tables S9-10 arv1δ FKY137 MATa arv1δ::trp1 his3 leu2 trp1 ura3 lys2 bar1; same as RH1800 but HIS4 his3 trp1 lys2 arv1δ Kajiwara et al., B, 2A, 4A-H, S1A, B, E, F, S3-S4, Tables S2-S6 sur2δ FKY268 MATa sur2δ::leu2 his3 leu2 trp1 ura3 lys2 bar1; same as RH1800 but HIS4 his3 trp1 lys2 sur2δ This study 4A-H, S1E, F, S3-S4, Table S4, Tables S7-8 Wild type BY4742 MATα his3δ1 leu2δ0 ura3δ0 lys2δ0 Open biosystem, Inc 1C, 2A, 2C ebs1δ YDR206W MATα ebs1δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but ebs1δ Open biosystem, Inc 1C upf1δ YMR080C MATα upf1δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but upf1δ Open biosystem, Inc 1C, 2A dep1δ YAL013W MATα dep1δ::kanmx leu2δ0 ura3δ0 lys2δ0; same as BY4742 but dep1δ HIS3 Open biosystem, Inc 1C arv1δ YLR242C MATα arv1δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but arv1δ Open biosystem, Inc 1C, 2A tel1δ YBL088C MATα tel1δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but tel1δ Open biosystem, Inc 2A, 2C rif1δ YBR275C MATα rif1δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but rif1δ Open biosystem, Inc 2C est3δ YIL009C-A MATα est3δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but est3δ Open biosystem, Inc used for strain construction Wild type BY4741 MATa his3δ1 leu2δ0 ura3δ0 met15δ0; same as BY4742 but MATa met15δ0 LYS2 Open biosystem, Inc 2A arv1δ YLR242C MATa arv1δ::kanmx his3δ1 leu2δ0 ura3δ0 met15δ0; same as BY4741 but arv1δ Open biosystem, Inc 2A arv1δ FKY671 MATa arv1δ::leu2 his3δ1 leu2δ0 ura3δ0 met15δ0; same as BY4741 but arv1δ This study used for strain construction Wild type FKY1129 MATa his3δ1 leu2δ0 met15δ0 ura3δ0 lys2δ0; same as BY4741 but lys2δ0 Kajiwara et al., B, 3A, 5A, 7A-C

8 arv1δ FKY1145 MATa arv1δ::leu2 his3δ1 leu2δ0 met15δ0 ura3δ0 lys2δ0; same as BY4741 but lys2δ0 arv1δ Kajiwara et al., B, 5A, 7A-C yca1δ FKY1174 MATa yca1::leu2 his3δ1 leu2δ0 met15δ0 ura3δ0 lys2δ0; same as BY4741 but lys2δ0 yca1δ Kajiwara et al., C arv1δ yca1δ FKY1372 MATα arv1δ::leu2 yca1::leu2 his3δ1 leu2δ0 ura3δ0; same as BY4742 but LYS2 arv1δ yca1δ Kajiwara et al., C arv1δ est3δ FKY3177 MATa arv1δ::leu2 est3δ::kanmx his3δ1 leu2δ0 ura3δ0 met15δ0; same as BY4741 but arv1δ est3δ This study 5C arv1δ FKY3178 MATα arv1δ::leu2 his3δ1 leu2δ0 ura3δ0 met15δ0 lys2δ0; same as BY4742 but lys2δ0 arv1δ This study 5C WT FKY3179 MATa his3δ1 leu2δ0 ura3δ0; same as BY4741 but MET15 This study 5C est3δ FKY3180 MATα est3δ::kanmx his3δ1 leu2δ0 ura3δ0 lys2δ0; same as BY4742 but est3δ This study 5C Wild type W303-1B MATα ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100 Umemura et al., C, 2D, 5B arv1δ FKY245 MATα arv1δ::leu2 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but arv1δ Kajiwara et al., C, 2D, 6A, 6B Wild type W303-1A MATa ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but MATa Umemura et al., 2003 used for strain construction exo1δ FKY1751 MATa exo1δ::ura3 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1A but exo1δ This study 6B mre11δ FKY1752 MATa mre11δ::ura3 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1A but mre11δ This study 6A Wild type FKY1784 MATa ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1A This study 6C arv1δ FKY1785 MATα arv1δ::leu2 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but arv1δ This study 6C mre11δ FKY1786 MATα mre11δ::ura3 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but mre11δ This study 6C arv1δ mre11δ FKY1787 MATa arv1δ::leu2 mre11δ::ura3 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as This study 6C W303-1A but arv1δ mre11δ arv1δ FKY1895 MATα arv1δ::trp1 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but arv1δ This study 5B arv1δ FKY2303 MATa arv1δ::leu2 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1A but arv1δ This study used for strain construction DDC2-GFP FKY3389 MATα DDC2-GFP::HIS ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but This study used for strain construction in wild-type DDC2-GFP::HIS DDC2-GFP FKY3423 MATα DDC2-GFP::HIS ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as W303-1B but This study 6D-E in wild-type DDC2-GFP::HIS

9 DDC2-GFP FKY3424 MATa DDC2-GFP::HIS arv1δ::leu2 ade2-1 his3-11,15 leu2-3, -112 trp1-1 ura3-1 can1-100; same as This study 6D-E in arv1δ W303-1A but arv1δ DDC2-GFP::HIS gpi2-7b DL2828 MATα gpi2-7b ade2 ura3 his4 Sobering et al., C gpi3-10 DL2829 MATα gpi3-10c ade2 lys2 Sobering et al., C gpi2-7b FKY2353 MATα gpi2-7b ade2 ura3 his This study 2D gpi3-10 FKY2362 MATα gpi3-10c ade2 leu2 trp1 ura3 his This study 2D 1) References: Zanolari B, Friant S, Funato K, Sütterlin C, Stevenson BJ, Riezman H Sphingoid base synthesis requirement for endocytosis in Saccharomyces cerevisiae. EMBO J. 19: Kajiwara K, Watanabe R, Pichler H, Ihara K, Murakami S, Riezman H, Funato K Yeast ARV1 is required for efficient delivery of an early GPI intermediate to the first mannosyltransferase during GPI assembly and controls lipid flow from the endoplasmic reticulum. Mol Biol Cell 19: Kajiwara K, Muneoka T, Watanabe Y, Karashima T, Kitagaki H, Funato K Perturbation of sphingolipid metabolism induces endoplasmic reticulum stress-mediated mitochondrial apoptosis in budding yeast. Mol Microbiol. 86: Sobering AK, Watanabe R, Romeo MJ, Yan BC, Specht CA, Orlean P, Riezman H, Levin DE Yeast Ras regulates the complex that catalyzes the first step in GPI-anchor biosynthesis at the ER. Cell 117: Umemura M, Okamoto M, Nakayama K, Sagane K, Tsukahara K, Hata K, Jigami Y GWT1 gene is required for inositol acylation of glycosylphosphatidylinositol anchors in yeast. J Biol Chem 278:

10 Table S2. Genes whose transcripts are increased greater than 2-fold in arv1δmutant (vs WT). Genes fold (Exp. 1.) fold (Exp. 2.) fold (Exp. 3.) average SD p-value categorization YLL067C other YMR011W HXT transport YLR194C glycosylation and cell wall YLR121C YPS glycosylation and cell wall YJR129C metabolism YJR032W CPR other YLR327C TMA protein synthesis YJL104W PAM transport YOR134W BAG other YBR071W unknown YBR056W-A unknown YPL141C FRK cell cycle YNL141W AAH metabolism YPL061W ALD metabolism YNR066C unknown YKL165C MCD glycosylation and cell wall YHR138C transport YIR035C unknown YPL163C SVS glycosylation and cell wall YKL216W URA metabolism YGR103W NOP protein synthesis

11 YLR099C ICT metabolism YGR032W GSC glycosylation and cell wall YLR435W TSR protein synthesis YOR236W DFR metabolism YMR305C SCW glycosylation and cell wall YDR055W PST glycosylation and cell wall YPL256C CLN cell cycle YLR172C DPH protein synthesis YOR294W RRS protein synthesis YJL102W MEF protein synthesis YOL080C REX protein synthesis YOL019W unknown YNR009W NRM cell cycle YKL073W LHS other YGR213C RTA transport YPR006C ICL metabolism YHR169W DBP protein synthesis YKR075C metabolism YLR414C PUN glycosylation and cell wall YMR199W CLN cell cycle YNL044W YIP transport YNL289W PCL cell cycle YBR247C ENP protein synthesis

12 YJL158C CIS glycosylation and cell wall YOL031C SIL other YLR292C SEC transport YGL253W HXK metabolism YNL061W NOP protein synthesis YPL057C SUR metabolism YLR104W LCL unknown YJR159W SOR metabolism YDR087C RRP protein synthesis YOL124C TRM protein synthesis YJL073W JEM other YBL054W TOD protein synthesis YKL001C MET metabolism YGR189C CRH glycosylation and cell wall YKR013W PRY transport YMR182C RGM other YJR048W CYC other YBR201W DER other YDR441C APT unknown YPL093W NOG protein synthesis YDR034W-B unknown YPR139C VSP transport YDR519W FPR transport

13 YJL208C NUC other YBL039C URA metabolism YDL004W ATP other YER003C PMI glycosylation and cell wall YNL112W DBP protein synthesis YDR299W BFR transport YHR183W GND metabolism YPL266W DIM protein synthesis YMR290C HAS protein synthesis YER126C NSA protein synthesis YLR243W GPN protein synthesis YDR400W URH metabolism YPL111W CAR metabolism YLR126C unknown YJR077C MIR transport YLR103C CDC other YDL014W NOP protein synthesis YGR245C SDA protein synthesis YNL002C RLP protein synthesis YLR372W SUR metabolism YCR034W FEN metabolism YGR159C NSR protein synthesis YJL034W KAR transport

14 YIL158W AIM unknown YAL007C ERP transport YOL007C CSI unknown YKL109W HAP other YNL064C YDJ other YLR040C AFB glycosylation and cell wall YER002W NOP protein synthesis YBR243C ALG E-05 glycosylation and cell wall YEL026W SNU protein synthesis YBR034C HMT protein synthesis YJL148W RPA protein synthesis YNR010W CSE protein synthesis YOR321W PMT glycosylation and cell wall YBR039W ATP other YIL131C FKH other YMR128W ECM protein synthesis YMR214W SCJ other YPR143W RRP protein synthesis YOR247W SRL glycosylation and cell wall YPL012W RRP protein synthesis YDL010W GRX metabolism YIR026C YVH other YKL163W PIR glycosylation and cell wall

15 YPL211W NIP protein synthesis YIL096C BMT protein synthesis YBL107C MIX unknown YJR117W STE other YER043C SAH metabolism YPR125W YLH transport YNL175C NOP protein synthesis YIL103W DPH other YAR002C ERP transport YDL095W PMT glycosylation and cell wall YJL092W HPR other YAL023C PMT glycosylation and cell wall YOR239W ABP E-05 other YML130C ERO other YJL116C NCA other YDR399W HPT other YJR097W JJJ unknown YMR215W GAS glycosylation and cell wall YOR198C BFR other YLR300W EXG glycosylation and cell wall YDL208W NHP protein synthesis YNL151C RPC protein synthesis YBL049W MOH unknown

16 YJL118W unknown YBR162W YSY transport YDR492W ISH metabolism YPL127C HHO other YOR338W unknown YBR106W PHO transport YBR078W ECM glycosylation and cell wall YHR043C DOG metabolism YPL267W ACM cell cycle YJL153C INO metabolism YAL040C CLN cell cycle YKR061W KTR glycosylation and cell wall YAL059W ECM transport YOR342C unknown YER006W NUG protein synthesis YOL139C CDC protein synthesis YDR216W ADR other YOR101W RAS other YNL015W PBI other YLR367W RPS22B protein synthesis YOL077C BRX protein synthesis YGL187C COX other YGL055W OLE metabolism

17 YGR284C ERV transport YHR143W RPC protein synthesis YGR200C ELP protein synthesis YBR029C CDS metabolism YBR069C VAP transport YNL333W SNZ other YCL054W SPB E-05 protein synthesis YGR146C ECL unknown YMR217W GUA metabolism YLR222C UTP protein synthesis YDL049C KNH glycosylation and cell wall YDR060W MAK protein synthesis YGR145W ENP protein synthesis YKL009W MRT protein synthesis YMR312W ELP protein synthesis YHR170W NMD transport YIL008W URM other YDL055C PSA glycosylation and cell wall YBR238C other YML093W UTP protein synthesis YOR272W YTM protein synthesis YLR295C ATP other YCL001W RER #DIV/0! transport

18 YLR350W ORM metabolism YOR004W UTP protein synthesis YEL042W GDA transport YML027W YOX cell cycle YNL062C GCD protein synthesis YDR529C QCR other YLR196W PWP protein synthesis YBR162C TOS glycosylation and cell wall YER042W MXR metabolism YIL064W SEE protein synthesis YDL166C FAP protein synthesis YPR135W CTF other YBR294W SUL transport YMR131C RRB protein synthesis YDR083W RRP protein synthesis YBR135W CKS cell cycle YOR145C PNO protein synthesis YPL217C BMS protein synthesis YDR465C RMT metabolism YHR052W CIC other YGL120C PRP protein synthesis YDL181W INH other YOR274W MOD protein synthesis

19 YKR024C DBP protein synthesis YCL043C PDI other YGL078C DBP protein synthesis YJR118C ILM E-05 other YML033W SRC E-05 other YLR050C unknown YPL239W YAR protein synthesis YPL149W APG transport YPL248C GAL other YCR028C RIM other YOL022C TSR other YHR179W OYE metabolism YAL053W FLC transport YDR297W SUR metabolism YLR175W CBF protein synthesis YPL052W OAZ other YDR502C SAM metabolism YPL106C SSE other YER064C VHR protein synthesis YNL300W TOS glycosylation and cell wall YNL283C WSC glycosylation and cell wall YPR183W DPM glycosylation and cell wall YOR021C SFM protein synthesis

20 YJL173C RFA other YKL084W HOT other YML081C ATP other YJL091C GWT glycosylation and cell wall YPR137W RRP protein synthesis YGL080W FMP transport YFL037W TUB other YOR078W BUD protein synthesis YLR120C YPS glycosylation and cell wall YHR152W SPO other YLR168C MSF1' E-05 metabolism YIL162W SUC metabolism YKL143W LTV other YJR092W BUD other YNL259C ATX transport YBL042C FUI transport YGR079W unknown YNL113W RPC protein synthesis YDR309C GIC other YBR154C RPB protein synthesis YNL110C NOP protein synthesis YMR295C unknown YGR014W MSB other

21 YLR294C unknown YFL045C SEC glycosylation and cell wall YER133W GLC other YER154W OXA other YOL107W unknown YMR238W DFG glycosylation and cell wall YOR281C PLP other YGR037C ACB transport YPR166C MRP other YJR072C NPA other YLR449W FPR other YMR145C NDE other YAL003W EFB protein synthesis YLR054C OSW other

22 Table S3. Genes whose transcripts are decreased greater than 2-fold in arv1δmutant (vs WT) Genes fold (Exp. 1.) fold (Exp. 2.) fold (Exp. 3.) average SD p-value categorization YLR242C ARV E-10 glycosylation and cell wall YIL113W SDP E-05 other YLR452C SST E-06 other YOR186W unknown YHR022C unknown YGR087C PDC E-05 metabolism YDL222C FMP E-05 metabolism YMR320W unknown YJL213W E-05 protein synthesis YOR202W HIS metabolism YML123C PHO transport YMR096W SNZ metabolism YPL265W DIP transport YGL255W ZRT transport YIL119C RPI other YMR189W GCV metabolism YBR147W RTC transport YCL026C-A AGP E-06 metabolism YNL194C metabolism YOR203W unknown YOR100C CRC transport

23 YPL017C IRC metabolism YOR377W ATF metabolism YMR095C SNO metabolism YDR019C GCV metabolism YAR029W unknown YIL015W BAR E-05 other YGR088W CTT metabolism YCR061W E-05 unknown YDL223C HBT E-05 other YMR262W unknown YIL009C EST other YLR130C ZRT transport YMR250W GAD metabolism YNR014W unknown YLR164W SHH unknown YNL004W HRB E-05 transport YER066W RRT unknown YER024W YAT metabolism YJR039W unknown YOL153C unknown YGR230W BNS E-05 unknown YIL164C NIT metabolism YOL158C ENB transport

24 YKR058W GLG glycosylation and cell wall YLR122C unknown YDL170W UGA other YLR348C DIC transport YAL028W FRT unknown YEL039C CYC other YHR137W ARO metabolism YGR248W SOL metabolism YIL165C unknown YIL077C unknown YIR041W PAU unknown YKL091C SFH metabolism YMR303C ADH E-05 metabolism YFR015C GSY metabolism YJR036C HUL other YOL116W MSN other YGL259W YPS glycosylation and cell wall YMR210W metabolism YIL111W COX5B other YMR105C PGM metabolism YLR177W unknown YGL117W unknown YIL059C unknown

25 YGL116W CDC cell cycle YER039C-A unknown YGL237C HAP other YCR104W PAU other YBL086C unknown YDR408C ADE E-05 metabolism YIL114C POR E-05 transport YLR258W GSY metabolism YKR080W MTD metabolism YER035W EDC E-07 protein synthesis YMR195W ICY unknown YKL103C LAP metabolism YDR380W ARO metabolism YLR251W SYM metabolism YBR001C NTH metabolism YOR221C MCT unknown YOR173W DCS other YPL247C unknown YDR461W MFA other YFR017C IGD metabolism YMR120C ADE E-07 metabolism YEL011W GLC metabolism YJR021C REC E-05 other

26 YOL048C RRT glycosylation and cell wall YMR135C GID metabolism YKL209C STE transport YHR155W YSP other YER096W SHC other YHL035C VMR transport YGL032C AGA glycosylation and cell wall YNR058W BIO metabolism YMR031C EIS other YHL044W unknown YDR530C APA E-05 metabolism YGL039W metabolism YMR313C TGL E-06 metabolism YDL182W LYS metabolism YDR074W TPS E-05 metabolism YHR080C E-05 unknown YLR241W unknown YJL210W PEX transport YFL026W STE other YGL085W LCL unknown YMR258C ROY transport YBR077C SLM other YDR100W TVP transport

27 YJL222W VTH transport YKL224C PAU unknown YOR044W IRC unknown YGL154C LYS metabolism YML116W ATR transport YGR281W YOR transport YLR193C UPS transport YJR046W TAH other YOL119C MCH transport YIL036W CST other YJL196C ELO metabolism YCL008C STP transport YKR091W SRL other YKR051W unknown YHL047C ARN transport YNL045W metabolism YJR025C BNA metabolism YPL264C unknown YCR005C CIT E-07 metabolism YGR131W FHN E-07 other YGL010W unknown YBR047W FMP unknown YKL035W UGP E-05 glycosylation and cell wall

28 YOR128C ADE E-05 metabolism YOR228C MCP E-05 metabolism YOR390W FEX transport YJL164C SRA other YPL004C LSP other YKL033W-A unknown YER039C HVG unknown YAL060W BDH metabolism YNL145W MFA other YAL061W BDH metabolism YDL054C MCH transport YJR127C ZMS other YPL224C MMT transport YBR145W ADH metabolism YBR068C BAP transport YOL133W HRT other YFR020W unknown YAL044C GCV metabolism YLL028W TPO transport YNL042W BOP E-05 unknown YLL060C GTT E-05 metabolism YKL132C RMA metabolism YNL251C NRD protein synthesis

29 YDR007W TRP metabolism YPL003W ULA other YJL142C IRC unknown YER180C ISC other YJR059W PTK other YLR152C unknown YKR089C TGL metabolism YHR016C YSC other YIR016W unknown YHR122W CIA other YMR171C EAR transport YKL211C TRP metabolism YJL200C ACO metabolism YHR195W NVJ other YIL152W unknown

30 Table S4. Number of genes whose transcripts are affected greater than 2-fold or 3-fold in deletion mutants Number of genes whose transcripts are increased by in sur2δ in arv1δ in arv1δsur2δ >2-fold >3-fold Number of genes whose transcripts are decreased by in sur2δ in arv1δ in arv1δsur2δ >2-fold >3-fold

31 Table S5. Open reading frames (ORFs) whose transcripts are increased by >3-fold in arv1δ ORF Gene Relative expression Function Average s.d (n=3) Transporter and vesicular transport YGR213C RTA ** putative transporter involved in 7-aminocholesterol resistance YHR138C ** putative protein of unknown function that has similarity to Pbi2p YJL104W PAM ns essential components of the import motor of mitochondrial preprotein translocase YKR013W PRY * sterol binding protein involved in the export of acetylated sterols YLR292C SEC ns non-essential subunit of Sec63 complex YMR011W HXT ** high-affinity glucose transporter YNL044W YIP *** protein localized to COPII vesicles and interacts with members of the Rab GTPase family and Yip1p Metabolism YGL253W HXK * hexokinase isoenzyme 2 YJR129C ns predicted S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family YJR159W SOR ns sorbitol dehydrogenase YKL001C MET ns adenylylsulfate kinase YKL216W URA ns dihydroorotate dehydrogenase YKR075C ** protein of unknown function that has similarity to YOR062Cp and Reg1p/Hex2p YLR099C ICT * lysophosphatidic acid acyltransferase YNL141W AAH * adenine deaminase YOR236W DFR ** dihydrofolate reductase YPL061W ALD * cytosolic aldehyde dehydrogenase

32 YPL057C SUR1/CSG ** catalytic subunit of a mannosylinositol phosphorylceramide synthase YPR006C ICL ** 2-methylisocitrate lyase Cell cycle YMR199W CLN * G1 cyclin involved in regulation of the cell cycle YNL289W PCL * Pho85 cyclin of the Pcl1,2-like subfamily YNR009W NRM ns MBF (Mbp1-Swi6)-associated transcriptional corepressor YPL141C FRK ns putative protein kinase that has similarity to kin4p YPL256C CLN * G1 cyclin involved in regulation of the cell cycle Stress response and protein folding YBR201W DER * ER membrane protein that promotes export of misfolded polypeptides YJL073W JEM * DnaJ-like chaperone YJR032W CPR ns peptidyl-prolyl cis-trans isomerase (cyclophilin) that contributes to chaperone activity (Hsp70 co-chaperones) YKL073W LHS ns molecular chaperone of the endoplasmic reticulum lumen that is involved in polypeptide translocation and folding YOL031C SIL ** nucleotide exchange factor for the endoplasmic reticulum lumenal Hsp70 chaperone Kar2p Protein synthesis YBL054W TOD ns PAC motif binding protein involved in rrna and ribosome biogenesis YBR247C ENP * protein required for pre-rrna processing and 40S ribosomal subunit synthesis YDR087C RRP ** nucleolar protein necessary for biogenesis of 60S ribosomal subunits and processing of pre-rrnas to mature rrnas YGR103W NOP ns nucleolar protein involved in rrna processing and 60S ribosomal subunit biogenesis

33 YHR169W DBP * putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit YJL102W MEF * mitochondrial elongation factor involved in translational elongation YLR172C DPH * methyltransferase required for synthesis of diphthamide YLR327C TMA ns proteins associated with ribosomal complexes YLR435W TSR ns protein with a potential role in pre-rrna processing YNL061W NOP ** probable RNA m(5)c methyltransferase essential for processing and maturation of 27S pre-rrna YOL080C REX ns putative RNA exonuclease involved in pre-rrna processing and ribosome assembly YOL124C TRM * catalytic subunit of adomet-dependent trna methyltransferase complex YOR294W RRS ns essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit Protein glycosylation, GPI-anchoed protein, cell and spore wall protein YDR055W PST * cell wall protein that contains a putative GPI-attachment site YGR032W GSC ** catalytic component of 1,3-beta-D-glucan synthase involved in formation of the inner layer of the spore wall YGR189C CRH * chitin transglycosylase YJL158C CIS * mannose-containing glycoprotein constituent of the cell wall YKL165C MCD * mannose-ethanolamine phosphotransferase involved in GPI anchor synthesis YLR121C YPS ** aspartic protease attached to the plasma membrane via a GPI anchor YLR194C NCW *** structural constituent of the cell wall YLR414C PUN ** plasma membrane protein with a role in cell wall integrity YMR305C SCW ** cell-wall glucanase/transglucosidase important for cell-wall stability YPL163C SVS ** cell wall and vacuolar protein of unknown function required for wild-type resistance to vanadate

34 Other YJR048W CYC ns cytochrome c, isoform 1 YLL067C ns putative Y' element ATP-dependent helicase YMR182C RGM * putative zinc finger DNA binding transcription factor YOR134W BAG ns Rho GTPase activating protein that has a role in actin cytoskeleton organization and control of cell wall synthesis Unknown YBR056W-A ** putative protein of unknown function YBR071W ** putative protein of unknown function YIR035C ns putative cytoplasmic protein of unknown function YLR104W LCL ** putative protein of unknown function and null mutant is deficient in amounts of cell wall mannosylphosphate YNR066C ns putative membrane-localized protein of unknown function YOL019W ** protein of unknown function

35 Table S6. Open reading frames (ORFs) whose transcripts are decreased by >3-fold in arv1δ ORF Gene Relative expression p-value Function Average s.d (n=3) YLR242C ARV *** Transporter and vesicular transport YBR147W RCT ** putative vacuolar membrane transporter for cationic amino acids YGL255W ZRT ** high-affinity zinc transporter YLR130C ZRT *** low-affinity zinc transporter YML123C PHO ** high-affinity inorganic phosphate transporter YNL004W HRB *** poly(a+) RNA-binding protein involved in the export of mrnas from the nucleus to the cytoplasm YOL158C ENB *** ferric enterobactin transporter YOR100C CRC *** mitochondrial carnitine transporter YPL265W DIP *** dicarboxylic amino acid transporter Metabolism YCL026C-A FRM *** type II nitroreductase YDL222C FMP *** integral membrane protein required for maintaining sphingolipid content YDR019C GCV ** glycine decarboxylase complex T subunit YER024W YAT ** carnitine acetyltransferase YGR087C PDC *** pyruvate decarboxylase isozyme YGR088W CTT ** cytosolic catalase T YIL164C NIT ** member of the nitrilase branch of the nitrilase superfamily YKR058W GLG ** glycogenin glucosyltransferase