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 < 0.001.
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 (http://fitdb.stanford.edu/) and visualized as a heatmap. (B) Sphingolipid biosynthetic pathway in yeast. Metabolites and genes encoding enzymes and proteins involved in sphingolipid synthesis are indicated.
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.
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 < 0.001.
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., 2000 3B lcb1-100 RH3809 MATa lcb1-100 his4 leu2 ura3 bar1; same as RH1800 but lcb1-100 Zanolari et al., 2000 3B Wild type RH6082 MATa his3 leu2 trp1 ura3 lys2 bar1; same as RH1800 but HIS4 his3 trp1 lys2 Kajiwara et al., 2008 1B, 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., 2008 1B, 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., 2012 2B, 3A, 5A, 7A-C
arv1δ FKY1145 MATa arv1δ::leu2 his3δ1 leu2δ0 met15δ0 ura3δ0 lys2δ0; same as BY4741 but lys2δ0 arv1δ Kajiwara et al., 2012 2B, 5A, 7A-C yca1δ FKY1174 MATa yca1::leu2 his3δ1 leu2δ0 met15δ0 ura3δ0 lys2δ0; same as BY4741 but lys2δ0 yca1δ Kajiwara et al., 2012 7C arv1δ yca1δ FKY1372 MATα arv1δ::leu2 yca1::leu2 his3δ1 leu2δ0 ura3δ0; same as BY4742 but LYS2 arv1δ yca1δ Kajiwara et al., 2012 7C 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., 2003 2C, 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., 2008 2C, 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
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., 2004 2C gpi3-10 DL2829 MATα gpi3-10c ade2 lys2 Sobering et al., 2004 2C 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. 2000. Sphingoid base synthesis requirement for endocytosis in Saccharomyces cerevisiae. EMBO J. 19:2824-33. Kajiwara K, Watanabe R, Pichler H, Ihara K, Murakami S, Riezman H, Funato K. 2008. 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 19:2069-82. Kajiwara K, Muneoka T, Watanabe Y, Karashima T, Kitagaki H, Funato K. 2012. Perturbation of sphingolipid metabolism induces endoplasmic reticulum stress-mediated mitochondrial apoptosis in budding yeast. Mol Microbiol. 86:1246-61. Sobering AK, Watanabe R, Romeo MJ, Yan BC, Specht CA, Orlean P, Riezman H, Levin DE. 2004. Yeast Ras regulates the complex that catalyzes the first step in GPI-anchor biosynthesis at the ER. Cell 117:637-48. Umemura M, Okamoto M, Nakayama K, Sagane K, Tsukahara K, Hata K, Jigami Y. 2003. GWT1 gene is required for inositol acylation of glycosylphosphatidylinositol anchors in yeast. J Biol Chem 278:23639-47.
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 315.173 0.535887 0.615572 105.4415 148.3026 0.375641 other YMR011W HXT2 22.62742 12.99604 17.14838 17.59061 3.944409 0.004007 transport YLR194C 12.99604 9.849155 11.31371 11.3863 1.285735 0.000335 glycosylation and cell wall YLR121C YPS4 12.99604 8.574188 8.574188 10.04814 2.08448 0.00357 glycosylation and cell wall YJR129C 2.143547 25.99208 1.624505 9.920043 11.36662 0.329301 metabolism YJR032W CPR7 1.624505 3.24901 22.62742 9.166977 9.541046 0.292707 other YLR327C TMA10 12.99604 6.498019 2.462289 7.318782 4.339371 0.108538 protein synthesis YJL104W PAM16 1.866066 1.414214 16 6.42676 6.771816 0.320404 transport YOR134W BAG7 12.12573 3.24901 2.143547 5.83943 4.467939 0.200332 other YBR071W 6.498019 6.062866 3.732132 5.431006 1.21435 0.006697 unknown YBR056W-A 4.594793 4 6.062866 4.885887 0.866951 0.003172 unknown YPL141C FRK1 3.732132 8 2.639016 4.790383 2.313001 0.081358 cell cycle YNL141W AAH1 6.964405 3.482202 3.482202 4.642936 1.641526 0.034899 metabolism YPL061W ALD6 5.656854 5.656854 2.462289 4.591999 1.505933 0.02796 metabolism YNR066C 10.55606 2.297397 0.5 4.451153 4.378744 0.327461 unknown YKL165C MCD4 4 2.828427 6.498019 4.442149 1.530381 0.033507 glycosylation and cell wall YHR138C 4.594793 3.24901 5.278032 4.373945 0.842937 0.004801 transport YIR035C 8 1.319508 3.732132 4.350547 2.762133 0.161401 unknown YPL163C SVS1 5.656854 3.24901 4 4.301955 1.00592 0.009718 glycosylation and cell wall YKL216W URA1 6.062866 1.866066 4.924578 4.284503 1.772109 0.058728 metabolism YGR103W NOP7 2.143547 8 2.639016 4.260854 2.651701 0.157005 protein synthesis
YLR099C ICT1 4.594793 2.297397 4.924578 3.938923 1.168516 0.023652 metabolism YGR032W GSC2 3.732132 3.031433 4.924578 3.896048 0.781516 0.006338 glycosylation and cell wall YLR435W TSR2 3.031433 6.498019 2.143547 3.891 1.87874 0.095149 protein synthesis YOR236W DFR1 3.031433 4.924578 3.482202 3.812738 0.80744 0.007893 metabolism YMR305C SCW10 4.594793 3.031433 3.732132 3.78612 0.63938 0.00352 glycosylation and cell wall YDR055W PST1 3.732132 4.924578 2.639016 3.765242 0.93337 0.013809 glycosylation and cell wall YPL256C CLN2 4.924578 2.828427 3.482202 3.745069 0.875704 0.011394 cell cycle YLR172C DPH5 4.594793 4 2.462289 3.685694 0.898512 0.013401 protein synthesis YOR294W RRS1 5.656854 1.866066 3.482202 3.668374 1.553172 0.072009 protein synthesis YJL102W MEF2 3.031433 2.639016 5.278032 3.649494 1.162641 0.032195 protein synthesis YOL080C REX4 2 3.24901 5.656854 3.635288 1.517686 0.07002 protein synthesis YOL019W 4.594793 3.031433 3.031433 3.552553 0.736975 0.008054 unknown YNR009W NRM1 6.062866 2.828427 1.741101 3.544132 1.8355 0.121527 cell cycle YKL073W LHS1 2.639016 2.462289 5.278032 3.459779 1.287722 0.054016 other YGR213C RTA1 2.828427 3.24901 4.287094 3.454844 0.613027 0.004793 transport YPR006C ICL2 3.031433 3.24901 4 3.426814 0.414923 0.001166 metabolism YHR169W DBP8 4.594793 2.639016 3.031433 3.421747 0.844798 0.015424 protein synthesis YKR075C 4 3.482202 2.639016 3.373739 0.560888 0.003918 metabolism YLR414C PUN1 4 3.031433 3.031433 3.354289 0.456587 0.00188 glycosylation and cell wall YMR199W CLN1 4.594793 2.639016 2.828427 3.354079 0.880719 0.019435 cell cycle YNL044W YIP3 4.594793 2.639016 2.828427 3.354079 0.880719 0.019435 transport YNL289W PCL1 4.594793 3.031433 2.297397 3.307874 0.958061 0.02711 cell cycle YBR247C ENP1 3.482202 2.297397 4 3.259866 0.712643 0.010951 protein synthesis
YJL158C CIS3 4.287094 2.639016 2.828427 3.251512 0.736338 0.012406 glycosylation and cell wall YOL031C SIL1 2.462289 3.732132 3.482202 3.225541 0.549261 0.004593 other YLR292C SEC72 1.866066 2.143547 5.656854 3.222156 1.725315 0.142634 transport YGL253W HXK2 3.24901 2.297397 4 3.182135 0.696692 0.011426 metabolism YNL061W NOP2 4 2.462289 3.031433 3.164574 0.634788 0.008508 protein synthesis YPL057C SUR1 4 2.828427 2.639016 3.155814 0.601917 0.007155 metabolism YLR104W LCL2 3.24901 2.639016 3.482202 3.123409 0.355502 0.001076 unknown YJR159W SOR1 4.594793 2.639016 2 3.077936 1.10385 0.056262 metabolism YDR087C RRP1 3.732132 3.031433 2.462289 3.075285 0.519338 0.00483 protein synthesis YOL124C TRM11 3.732132 2 3.482202 3.071445 0.764466 0.018586 protein synthesis YJL073W JEM1 4 2.143547 3.031433 3.058327 0.758132 0.018466 other YBL054W TOD6 2.143547 1.741101 5.278032 3.054227 1.581028 0.140006 protein synthesis YKL001C MET14 2.462289 1.741101 4.924578 3.042656 1.362901 0.101392 metabolism YGR189C CRH1 4 2.828427 2.297397 3.041941 0.711293 0.015351 glycosylation and cell wall YKR013W PRY2 4 2.297397 2.828427 3.041941 0.711293 0.015351 transport YMR182C RGM1 4.287094 2.828427 2 3.038507 0.945445 0.038057 other YJR048W CYC1 2.462289 2 4.594793 3.019027 1.130105 0.064898 other YBR201W DER1 2.297397 2.462289 4.287094 3.015593 0.901603 0.034133 other YDR441C APT2 3.031433 2.462289 3.482202 2.991975 0.417312 0.002511 unknown YPL093W NOG1 4 2.143547 2.828427 2.990658 0.766526 0.021341 protein synthesis YDR034W-B 3.482202 3.482202 2 2.988135 0.698717 0.015812 unknown YPR139C VSP66 2.462289 3.24901 3.24901 2.986769 0.370864 0.001628 transport YDR519W FPR2 3.24901 2.639016 3.031433 2.973153 0.252416 0.000381 transport
YJL208C NUC1 3.031433 2.143547 3.732132 2.969037 0.650036 0.012809 other YBL039C URA7 3.482202 2.143547 3.24901 2.958253 0.583897 0.009018 metabolism YDL004W ATP16 2.639016 2.462289 3.732132 2.944479 0.561608 0.008064 other YER003C PMI40 3.482202 1.866066 3.482202 2.94349 0.761854 0.022604 glycosylation and cell wall YNL112W DBP2 3.482202 2.462289 2.828427 2.924306 0.421861 0.002972 protein synthesis YDR299W BFR2 2.828427 2.143547 3.732132 2.901369 0.650585 0.014457 transport YHR183W GND1 3.031433 2.143547 3.482202 2.885727 0.556131 0.008678 metabolism YPL266W DIM1 3.732132 2.462289 2.462289 2.88557 0.59861 0.011206 protein synthesis YMR290C HAS1 4 2.297397 2.297397 2.864931 0.802615 0.030329 protein synthesis YER126C NSA2 3.482202 2.462289 2.639016 2.861169 0.445024 0.004092 protein synthesis YLR243W GPN3 3.482202 2.639016 2.462289 2.861169 0.445024 0.004092 protein synthesis YDR400W URH1 2.462289 1.515717 4.594793 2.8576 1.287732 0.110937 metabolism YPL111W CAR1 4.924578 1.624505 2 2.849694 1.475151 0.150861 metabolism YLR126C 4 1.515717 3.031433 2.84905 1.022371 0.062789 unknown YJR077C MIR1 3.732132 1.741101 3.031433 2.834889 0.824631 0.034621 transport YLR103C CDC45 2.462289 4.287094 1.741101 2.830161 1.071453 0.073107 other YDL014W NOP1 3.031433 2.143547 3.24901 2.807997 0.47816 0.005896 protein synthesis YGR245C SDA1 3.482202 2.297397 2.639016 2.806205 0.497933 0.006839 protein synthesis YNL002C RLP7 3.031433 2.639016 2.639016 2.769822 0.184987 0.000173 protein synthesis YLR372W SUR4 3.732132 1.741101 2.828427 2.76722 0.813986 0.03728 metabolism YCR034W FEN1 2.828427 1.741101 3.732132 2.76722 0.813986 0.03728 metabolism YGR159C NSR1 3.24901 2 3.031433 2.760148 0.544795 0.010268 protein synthesis YJL034W KAR2 3.24901 2 3.031433 2.760148 0.544795 0.010268 transport
YIL158W AIM20 3.031433 3.24901 2 2.760148 0.544795 0.010268 unknown YAL007C ERP2 2.143547 1.515717 4.594793 2.751352 1.32847 0.135709 transport YOL007C CSI2 2.297397 3.24901 2.639016 2.728474 0.393611 0.003421 unknown YKL109W HAP4 2.828427 3.031433 2.297397 2.719086 0.309482 0.001419 other YNL064C YDJ1 3.24901 1.866066 3.031433 2.715503 0.607175 0.016188 other YLR040C AFB1 3.482202 3.031433 1.624505 2.712713 0.791179 0.037606 glycosylation and cell wall YER002W NOP16 3.732132 1.741101 2.639016 2.704083 0.814136 0.04155 protein synthesis YBR243C ALG7 2.828427 2.639016 2.639016 2.702153 0.089289 1.13E-05 glycosylation and cell wall YEL026W SNU13 3.24901 2.143547 2.639016 2.677191 0.45211 0.006313 protein synthesis YBR034C HMT1 3.24901 2.297397 2.462289 2.669565 0.415222 0.004723 protein synthesis YJL148W RPA34 2.828427 2.143547 3.031433 2.667802 0.379856 0.003423 protein synthesis YNR010W CSE2 2.639016 3.732132 1.624505 2.665218 0.860635 0.052102 protein synthesis YOR321W PMT3 1.866066 2.639016 3.482202 2.662428 0.659993 0.023539 glycosylation and cell wall YBR039W ATP3 2.639016 1.866066 3.482202 2.662428 0.659993 0.023539 other YIL131C FKH1 2.828427 2.462289 2.639016 2.643244 0.149505 0.0001 other YMR128W ECM16 2.639016 2.828427 2.462289 2.643244 0.149505 0.0001 protein synthesis YMR214W SCJ1 3.031433 1.414214 3.482202 2.642616 0.887892 0.059027 other YPR143W RRP15 3.732132 2.297397 1.866066 2.631865 0.797685 0.044423 protein synthesis YOR247W SRL1 3.482202 1.741101 2.639016 2.620773 0.710919 0.032153 glycosylation and cell wall YPL012W RRP12 3.24901 2.143547 2.462289 2.618282 0.464587 0.007895 protein synthesis YDL010W GRX6 3.24901 2.297397 2.297397 2.614601 0.448595 0.007031 metabolism YIR026C YVH1 2.828427 1.741101 3.24901 2.606179 0.635344 0.023267 other YKL163W PIR3 3.031433 2.143547 2.639016 2.604665 0.363291 0.003348 glycosylation and cell wall
YPL211W NIP7 4 1.624505 2.143547 2.589351 1.019739 0.092223 protein synthesis YIL096C BMT5 2.828427 2.297397 2.639016 2.58828 0.219741 0.000516 protein synthesis YBL107C MIX23 2.462289 2.462289 2.828427 2.584335 0.172599 0.000203 unknown YJR117W STE24 1.741101 2 4 2.580367 1.009381 0.091198 other YER043C SAH1 4 1.414214 2.297397 2.570537 1.073166 0.107273 metabolism YPR125W YLH47 2.297397 1.414214 4 2.570537 1.073166 0.107273 transport YNL175C NOP13 3.031433 1.624505 3.031433 2.562457 0.663232 0.029061 protein synthesis YIL103W DPH1 3.031433 2 2.639016 2.556816 0.425073 0.006609 other YAR002C ERP1 2.639016 2 3.031433 2.556816 0.425073 0.006609 transport YDL095W PMT1 2 1.624505 4 2.541502 1.042645 0.10473 glycosylation and cell wall YJL092W HPR5 2.297397 2.462289 2.828427 2.529371 0.221921 0.000621 other YAL023C PMT2 2.462289 1.624505 3.482202 2.522999 0.759616 0.047085 glycosylation and cell wall YOR239W ABP140 2.462289 2.639016 2.462289 2.521198 0.08331 1.34E-05 other YML130C ERO1 2.297397 1.515717 3.732132 2.515082 0.917847 0.079864 other YJL116C NCA3 4.287094 1.741101 1.515717 2.514637 1.256689 0.163492 other YDR399W HPT1 3.031433 2.639016 1.866066 2.512172 0.48414 0.011536 other YJR097W JJJ3 2.639016 1.866066 3.031433 2.512172 0.48414 0.011536 unknown YMR215W GAS3 3.482202 2.297397 1.741101 2.5069 0.726075 0.042598 glycosylation and cell wall YOR198C BFR1 1.624505 2.143547 3.732132 2.500061 0.896605 0.077153 other YLR300W EXG1 3.031433 2 2.462289 2.497907 0.421833 0.007376 glycosylation and cell wall YDL208W NHP2 3.031433 2 2.462289 2.497907 0.421833 0.007376 protein synthesis YNL151C RPC31 3.031433 2.462289 2 2.497907 0.421833 0.007376 protein synthesis YBL049W MOH1 2.143547 3.482202 1.866066 2.497272 0.705604 0.039906 unknown
YJL118W 3.031433 2.143547 2.297397 2.490792 0.387416 0.005536 unknown YBR162W YSY6 2.828427 2.297397 2.297397 2.474407 0.25033 0.001135 transport YDR492W ISH1 3.482202 1.624505 2.297397 2.468035 0.76794 0.053899 metabolism YPL127C HHO1 2.462289 2.639016 2.297397 2.466234 0.139493 0.000119 other YOR338W 2.462289 2.639016 2.297397 2.466234 0.139493 0.000119 unknown YBR106W PHO88 2.828427 1.741101 2.828427 2.465985 0.51257 0.015543 transport YBR078W ECM33 3.732132 1.515717 2.143547 2.463798 0.932754 0.090676 glycosylation and cell wall YHR043C DOG2 1.624505 2.462289 3.24901 2.445268 0.663311 0.036882 metabolism YPL267W ACM1 2.462289 2.828427 2 2.430239 0.338962 0.003961 cell cycle YJL153C INO1 2.828427 2.462289 2 2.430239 0.338962 0.003961 metabolism YAL040C CLN3 2.143547 2.297397 2.828427 2.423124 0.293395 0.002365 cell cycle YKR061W KTR2 2.143547 2.828427 2.297397 2.423124 0.293395 0.002365 glycosylation and cell wall YAL059W ECM1 2.828427 2.143547 2.297397 2.423124 0.293395 0.002365 transport YOR342C 2.297397 2.143547 2.828427 2.423124 0.293395 0.002365 unknown YER006W NUG1 1.741101 2.462289 3.031433 2.411608 0.527993 0.01942 protein synthesis YOL139C CDC33 2.297397 2.297397 2.639016 2.41127 0.161041 0.000244 protein synthesis YDR216W ADR1 2.297397 2.639016 2.297397 2.41127 0.161041 0.000244 other YOR101W RAS1 1.741101 2.639016 2.828427 2.402848 0.474272 0.013884 other YNL015W PBI2 2.828427 1.741101 2.639016 2.402848 0.474272 0.013884 other YLR367W RPS22B 2.828427 1.741101 2.639016 2.402848 0.474272 0.013884 protein synthesis YOL077C BRX1 2.828427 1.741101 2.639016 2.402848 0.474272 0.013884 protein synthesis YGL187C COX4 2.297397 1.866066 3.031433 2.398299 0.481079 0.014726 other YGL055W OLE1 3.031433 2 2.143547 2.39166 0.456168 0.012502 metabolism
YGR284C ERV29 1.624505 1.515717 4 2.380074 1.146321 0.163856 transport YHR143W RPC10 2.143547 1.741101 3.24901 2.377886 0.637512 0.037783 protein synthesis YGR200C ELP2 2.143547 2.828427 2.143547 2.37184 0.322856 0.003861 protein synthesis YBR029C CDS1 3.732132 1.741101 1.624505 2.365913 0.967235 0.116498 metabolism YBR069C VAP1 3.482202 1.741101 1.866066 2.363123 0.792951 0.071895 transport YNL333W SNZ2 2.639016 2.143547 2.297397 2.359986 0.20706 0.000747 other YCL054W SPB1 2.462289 2.297397 2.297397 2.352361 0.077731 1.62E-05 protein synthesis YGR146C ECL1 3.031433 1.866066 2.143547 2.347015 0.497038 0.018576 unknown YMR217W GUA1 3.24901 1.319508 2.462289 2.343602 0.792174 0.074466 metabolism YLR222C UTP13 2.297397 1.866066 2.828427 2.33063 0.393584 0.008768 protein synthesis YDL049C KNH1 2.639016 2.828427 1.515717 2.32772 0.579357 0.031645 glycosylation and cell wall YDR060W MAK21 2.828427 2.143547 2 2.323991 0.361472 0.006607 protein synthesis YGR145W ENP2 3.482202 1.741101 1.741101 2.321468 0.820763 0.085072 protein synthesis YKL009W MRT4 2.639016 2 2.297397 2.312138 0.261085 0.00207 protein synthesis YMR312W ELP6 2.297397 2.639016 2 2.312138 0.261085 0.00207 protein synthesis YHR170W NMD3 2.639016 2 2.297397 2.312138 0.261085 0.00207 transport YIL008W URM1 2.639016 2.143547 2.143547 2.308703 0.233566 0.001373 other YDL055C PSA1 2.462289 1.624505 2.828427 2.305074 0.503914 0.02153 glycosylation and cell wall YBR238C 1.624505 2.828427 2.462289 2.305074 0.503914 0.02153 other YML093W UTP14 2.828427 1.624505 2.462289 2.305074 0.503914 0.02153 protein synthesis YOR272W YTM1 3.24901 1.515717 2.143547 2.302758 0.716513 0.061893 protein synthesis YLR295C ATP14 1.866066 2 3.031433 2.299166 0.52067 0.024258 other YCL001W RER1 2.297397 2.297397 2.297397 2.297397 0 #DIV/0! transport
YLR350W ORM2 2.639016 1.414214 2.828427 2.293886 0.62681 0.043275 metabolism YOR004W UTP23 3.24901 1.624505 2 2.291171 0.694425 0.058217 protein synthesis YEL042W GDA1 2.639016 1.741101 2.462289 2.280802 0.388386 0.009563 transport YML027W YOX1 2.828427 1.866066 2.143547 2.279347 0.404447 0.011045 cell cycle YNL062C GCD10 2.828427 1.866066 2.143547 2.279347 0.404447 0.011045 protein synthesis YDR529C QCR7 2.462289 1.319508 3.031433 2.271077 0.711849 0.064995 other YLR196W PWP1 2.462289 1.515717 2.828427 2.268811 0.553099 0.031548 protein synthesis YBR162C TOS1 2.639016 2.143547 2 2.260854 0.273747 0.002867 glycosylation and cell wall YER042W MXR1 2.639016 2 2.143547 2.260854 0.273747 0.002867 metabolism YIL064W SEE1 2.639016 2 2.143547 2.260854 0.273747 0.002867 protein synthesis YDL166C FAP7 3.031433 2 1.741101 2.257511 0.557359 0.033193 protein synthesis YPR135W CTF4 2.462289 2.297397 2 2.253229 0.191295 0.000755 other YBR294W SUL1 1.741101 1.741101 3.24901 2.243737 0.710835 0.06862 transport YMR131C RRB1 2.639016 1.624505 2.462289 2.241936 0.442511 0.016551 protein synthesis YDR083W RRP8 2.462289 2.639016 1.624505 2.241936 0.442511 0.016551 protein synthesis YBR135W CKS1 2.297397 1.741101 2.639016 2.225838 0.370048 0.009414 cell cycle YOR145C PNO1 2.639016 1.741101 2.297397 2.225838 0.370048 0.009414 protein synthesis YPL217C BMS1 2.639016 2.297397 1.741101 2.225838 0.370048 0.009414 protein synthesis YDR465C RMT2 2.828427 1.515717 2.297397 2.213847 0.539158 0.03341 metabolism YHR052W CIC1 2.828427 1.515717 2.297397 2.213847 0.539158 0.03341 other YGL120C PRP43 2.297397 1.515717 2.828427 2.213847 0.539158 0.03341 protein synthesis YDL181W INH1 2.462289 1.866066 2.297397 2.208584 0.251378 0.002444 other YOR274W MOD5 2.297397 1.866066 2.462289 2.208584 0.251378 0.002444 protein synthesis
YKR024C DBP7 2.462289 2.297397 1.866066 2.208584 0.251378 0.002444 protein synthesis YCL043C PDI1 2.143547 1.624505 2.828427 2.198826 0.493051 0.026328 other YGL078C DBP3 2.828427 1.624505 2.143547 2.198826 0.493051 0.026328 protein synthesis YJR118C ILM1 2.143547 2.143547 2.297397 2.19483 0.072525 2.01E-05 other YML033W SRC1 2.143547 2.143547 2.297397 2.19483 0.072525 2.01E-05 other YLR050C 2 1.741101 2.828427 2.189843 0.463753 0.022191 unknown YPL239W YAR1 2.639016 1.624505 2.297397 2.186972 0.421468 0.016363 protein synthesis YPL149W APG5 2.639016 2.297397 1.624505 2.186972 0.421468 0.016363 transport YPL248C GAL4 2.462289 2.297397 1.741101 2.166929 0.308539 0.005891 other YCR028C RIM1 2.297397 1.741101 2.462289 2.166929 0.308539 0.005891 other YOL022C TSR4 2.828427 2.143547 1.515717 2.162564 0.536081 0.037405 other YHR179W OYE2 2 2 2.462289 2.154096 0.217925 0.0017 metabolism YAL053W FLC2 2 2 2.462289 2.154096 0.217925 0.0017 transport YDR297W SUR2 2.828427 1.624505 2 2.150977 0.50296 0.031785 metabolism YLR175W CBF5 2.462289 1.148698 2.828427 2.146471 0.721192 0.087824 protein synthesis YPL052W OAZ1 1.741101 2.828427 1.866066 2.145198 0.485802 0.029003 other YDR502C SAM2 2.462289 1.319508 2.639016 2.140271 0.584834 0.050989 metabolism YPL106C SSE1 2.462289 1.319508 2.639016 2.140271 0.584834 0.050989 other YER064C VHR2 2.462289 1.319508 2.639016 2.140271 0.584834 0.050989 protein synthesis YNL300W TOS6 2.828427 1.414214 2.143547 2.128729 0.577445 0.050623 glycosylation and cell wall YNL283C WSC2 2.639016 2 1.741101 2.126706 0.377362 0.013451 glycosylation and cell wall YPR183W DPM1 2.297397 1.414214 2.639016 2.116875 0.516059 0.037633 glycosylation and cell wall YOR021C SFM1 2.297397 1.414214 2.639016 2.116875 0.516059 0.037633 protein synthesis
YJL173C RFA3 2.462289 1.741101 2.143547 2.115646 0.295084 0.005898 other YKL084W HOT13 2.297397 1.741101 2.297397 2.111965 0.26224 0.003891 other YML081C ATP18 2.297397 1.741101 2.297397 2.111965 0.26224 0.003891 other YJL091C GWT1 1.866066 2 2.462289 2.109452 0.255415 0.003561 glycosylation and cell wall YPR137W RRP9 1.866066 2.462289 2 2.109452 0.255415 0.003561 protein synthesis YGL080W FMP37 1.741101 1.741101 2.828427 2.103543 0.51257 0.038224 transport YFL037W TUB2 2.297397 1.866066 2.143547 2.102337 0.178485 0.000947 other YOR078W BUD21 2.297397 2.143547 1.866066 2.102337 0.178485 0.000947 protein synthesis YLR120C YPS1 2.143547 1.515717 2.639016 2.099426 0.459645 0.027717 glycosylation and cell wall YHR152W SPO12 2 2 2.297397 2.099132 0.140194 0.000376 other YLR168C MSF1' 2.143547 2 2.143547 2.095698 0.067669 2.15E-05 metabolism YIL162W SUC2 1.515717 2.297397 2.462289 2.091801 0.412878 0.020126 metabolism YKL143W LTV1 2.639016 1.319508 2.297397 2.085307 0.559173 0.051646 other YJR092W BUD4 2.639016 1.741101 1.866066 2.082061 0.397117 0.018249 other YNL259C ATX1 2.462289 1.624505 2.143547 2.07678 0.345267 0.011596 transport YBL042C FUI1 1.624505 2.297397 2.297397 2.073099 0.317204 0.008748 transport YGR079W 2.462289 2 1.741101 2.067797 0.298301 0.007169 unknown YNL113W RPC19 2.462289 1.866066 1.866066 2.064807 0.281062 0.005855 protein synthesis YDR309C GIC2 2.297397 2.143547 1.741101 2.060682 0.234544 0.003069 other YBR154C RPB5 2.143547 1.741101 2.297397 2.060682 0.234544 0.003069 protein synthesis YNL110C NOP15 2.297397 1.741101 2.143547 2.060682 0.234544 0.003069 protein synthesis YMR295C 2.143547 1.741101 2.297397 2.060682 0.234544 0.003069 unknown YGR014W MSB2 1.866066 2 2.297397 2.054488 0.180256 0.001165 other
YLR294C 2 1.866066 2.297397 2.054488 0.180256 0.001165 unknown YFL045C SEC53 2 1.515717 2.639016 2.051577 0.460033 0.031893 glycosylation and cell wall YER133W GLC7 1.515717 2.639016 2 2.051577 0.460033 0.031893 other YER154W OXA1 1.515717 2.143547 2.462289 2.040517 0.393244 0.020086 other YOL107W 2.143547 2.462289 1.515717 2.040517 0.393244 0.020086 unknown YMR238W DFG5 2 1.624505 2.462289 2.028931 0.342635 0.013191 glycosylation and cell wall YOR281C PLP2 1.624505 2 2.462289 2.028931 0.342635 0.013191 other YGR037C ACB1 2 1.624505 2.462289 2.028931 0.342635 0.013191 transport YPR166C MRP2 1.741101 1.866066 2.462289 2.023152 0.31468 0.010045 other YJR072C NPA3 2.462289 1.741101 1.866066 2.023152 0.31468 0.010045 other YLR449W FPR4 2.297397 1.741101 2 2.012833 0.227288 0.003241 other YMR145C NDE1 2.297397 2 1.741101 2.012833 0.227288 0.003241 other YAL003W EFB1 2.143547 1.741101 2.143547 2.009398 0.189715 0.00167 protein synthesis YLR054C OSW2 1.866066 2 2.143547 2.003204 0.113304 0.000234 other
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 ARV1 0.054409 0.058315 0.0625 0.058408 0.025453 2.27E-10 glycosylation and cell wall YIL113W SDP1 0.066986 0.176777 0.038473 0.094079 0.06577 2.77E-05 other YLR452C SST2 0.125 0.189465 0.108819 0.141094 0.068138 4.04E-06 other YOR186W 0.233258 0.307786 0.011049 0.184031 0.13515 0.00079 unknown YHR022C 0.125 0.353553 0.082469 0.187008 0.131091 0.000643 unknown YGR087C PDC6 0.233258 0.094732 0.233258 0.187083 0.098796 6.11E-05 metabolism YDL222C FMP45 0.108819 0.203063 0.25 0.187294 0.095719 4.01E-05 metabolism YMR320W 0.164938 0.307786 0.143587 0.205437 0.10908 0.000103 unknown YJL213W 0.189465 0.287175 0.143587 0.206742 0.103457 4.78E-05 protein synthesis YOR202W HIS3 0.203063 0.378929 0.041235 0.207742 0.149515 0.001248 metabolism YML123C PHO84 0.435275 0.088388 0.133972 0.219212 0.163634 0.001999 transport YMR096W SNZ1 0.378929 0.189465 0.108819 0.225738 0.138448 0.000639 metabolism YPL265W DIP5 0.353553 0.233258 0.125 0.237271 0.130734 0.00032 transport YGL255W ZRT1 0.435275 0.164938 0.153893 0.251369 0.156671 0.001241 transport YIL119C RPI1 0.287175 0.435275 0.033493 0.251981 0.180411 0.003103 other YMR189W GCV2 0.329877 0.329877 0.108819 0.256191 0.143006 0.000542 metabolism YBR147W RTC2 0.353553 0.378929 0.041235 0.257906 0.173658 0.002398 transport YCL026C-A AGP1 0.233258 0.233258 0.307786 0.258101 0.115829 7.49E-06 metabolism YNL194C 0.203063 0.378929 0.203063 0.261685 0.134144 0.000229 metabolism YOR203W 0.217638 0.535887 0.041235 0.26492 0.211146 0.007087 unknown YOR100C CRC1 0.267943 0.378929 0.164938 0.270604 0.139487 0.000295 transport
YPL017C IRC15 0.217638 0.435275 0.164938 0.272617 0.155576 0.000923 metabolism YOR377W ATF1 0.25 0.406126 0.164938 0.273688 0.146719 0.000504 metabolism YMR095C SNO1 0.378929 0.307786 0.143587 0.276768 0.147128 0.000487 metabolism YDR019C GCV1 0.353553 0.406126 0.094732 0.284804 0.170593 0.001751 metabolism YAR029W 0.217638 0.406126 0.25 0.291255 0.144861 0.000261 unknown YIL015W BAR1 0.307786 0.353553 0.217638 0.292992 0.135967 5.97E-05 other YGR088W CTT1 0.25 0.466516 0.164938 0.293818 0.168153 0.001411 metabolism YCR061W 0.307786 0.233258 0.353553 0.298199 0.136075 3.67E-05 unknown YDL223C HBT1 0.267943 0.378929 0.25 0.298958 0.138551 6.42E-05 other YMR262W 0.287175 0.435275 0.176777 0.299742 0.158927 0.000728 unknown YIL009C EST3 0.307786 0.435275 0.164938 0.302667 0.162239 0.000869 other YLR130C ZRT2 0.353553 0.353553 0.217638 0.308248 0.144549 0.000107 transport YMR250W GAD1 0.307786 0.466516 0.164938 0.31308 0.172504 0.001398 metabolism YNR014W 0.353553 0.535887 0.054409 0.314617 0.21933 0.00814 unknown YLR164W SHH4 0.378929 0.535887 0.041235 0.318683 0.225806 0.009528 unknown YNL004W HRB1 0.329877 0.378929 0.25 0.319602 0.145841 5.47E-05 transport YER066W RRT13 0.189465 0.615572 0.153893 0.319643 0.228376 0.010129 unknown YER024W YAT2 0.378929 0.435275 0.153893 0.322699 0.174951 0.001402 metabolism YJR039W 0.233258 0.535887 0.203063 0.324069 0.191391 0.003132 unknown YOL153C 0.233258 0.535887 0.203063 0.324069 0.191391 0.003132 unknown YGR230W BNS1 0.267943 0.378929 0.329877 0.325583 0.146364 3.04E-05 unknown YIL164C NIT1 0.466516 0.435275 0.076947 0.326246 0.208291 0.005726 metabolism YOL158C ENB1 0.378929 0.406126 0.203063 0.329373 0.162531 0.000459 transport
YKR058W GLG1 0.353553 0.535887 0.101532 0.330324 0.210343 0.006013 glycosylation and cell wall YLR122C 0.535887 0.378929 0.082469 0.332428 0.217324 0.007377 unknown YDL170W UGA3 0.435275 0.466516 0.101532 0.334441 0.20356 0.004687 other YLR348C DIC1 0.406126 0.353553 0.25 0.33656 0.156185 0.000133 transport YAL028W FRT2 0.203063 0.574349 0.233258 0.33689 0.206251 0.00509 unknown YEL039C CYC7 0.25 0.574349 0.189465 0.337938 0.206954 0.005188 other YHR137W ARO9 0.153893 0.574349 0.287175 0.338472 0.211105 0.005955 metabolism YGR248W SOL4 0.287175 0.5 0.233258 0.340144 0.177875 0.001261 metabolism YIL165C 0.466516 0.466516 0.088388 0.340474 0.213461 0.006373 unknown YIL077C 0.329877 0.5 0.203063 0.344313 0.18256 0.001591 unknown YIR041W PAU15 0.233258 0.5 0.307786 0.347015 0.179024 0.001195 unknown YKL091C SFH1 0.329877 0.466516 0.25 0.348798 0.169722 0.000501 metabolism YMR303C ADH2 0.406126 0.378929 0.287175 0.35741 0.160916 5.78E-05 metabolism YFR015C GSY1 0.287175 0.5 0.287175 0.358116 0.177751 0.000827 metabolism YJR036C HUL4 0.267943 0.574349 0.233258 0.358517 0.204253 0.004081 other YOL116W MSN1 0.307786 0.5 0.267943 0.358576 0.178345 0.000861 other YGL259W YPS5 0.287175 0.574349 0.217638 0.35972 0.205283 0.00422 glycosylation and cell wall YMR210W 0.329877 0.5 0.25 0.359959 0.180129 0.000969 metabolism YIL111W COX5B 0.307786 0.615572 0.164938 0.362766 0.226257 0.008694 other YMR105C PGM2 0.329877 0.5 0.267943 0.36594 0.179799 0.000795 metabolism YLR177W 0.329877 0.5 0.267943 0.36594 0.179799 0.000795 unknown YGL117W 0.406126 0.574349 0.125 0.368492 0.226341 0.008536 unknown YIL059C 0.329877 0.615572 0.164938 0.370129 0.227328 0.008743 unknown
YGL116W CDC20 0.435275 0.435275 0.25 0.373517 0.17855 0.000532 cell cycle YER039C-A 0.406126 0.466516 0.25 0.374214 0.180274 0.000632 unknown YGL237C HAP2 0.435275 0.406126 0.287175 0.376192 0.172084 0.000161 other YCR104W PAU3 0.267943 0.535887 0.329877 0.377902 0.191353 0.001545 other YBL086C 0.329877 0.5 0.307786 0.379221 0.180265 0.000516 unknown YDR408C ADE8 0.406126 0.406126 0.329877 0.38071 0.167765 1.68E-05 metabolism YIL114C POR2 0.329877 0.435275 0.378929 0.38136 0.169293 3.47E-05 transport YLR258W GSY2 0.378929 0.535887 0.233258 0.382691 0.197264 0.002118 metabolism YKR080W MTD1 0.5 0.353553 0.307786 0.387113 0.18204 0.000453 metabolism YER035W EDC2 0.406126 0.378929 0.378929 0.387995 0.168373 2.88E-07 protein synthesis YMR195W ICY1 0.466516 0.615572 0.082469 0.388186 0.25706 0.01826 unknown YKL103C LAP4 0.535887 0.466516 0.164938 0.389114 0.218715 0.005826 metabolism YDR380W ARO10 0.203063 0.615572 0.353553 0.39073 0.224531 0.007205 metabolism YLR251W SYM1 0.307786 0.615572 0.25 0.391119 0.219071 0.005821 metabolism YBR001C NTH2 0.406126 0.535887 0.233258 0.391757 0.200753 0.002265 metabolism YOR221C MCT1 0.378929 0.466516 0.329877 0.391774 0.176563 0.000109 unknown YOR173W DCS2 0.378929 0.659754 0.143587 0.39409 0.25002 0.015334 other YPL247C 0.353553 0.5 0.329877 0.394477 0.18282 0.00034 unknown YDR461W MFA1 0.5 0.307786 0.378929 0.395572 0.184558 0.000421 other YFR017C IGD1 0.435275 0.466516 0.287175 0.396322 0.1845 0.0004 metabolism YMR120C ADE17 0.378929 0.406126 0.406126 0.397061 0.17229 3.06E-07 metabolism YEL011W GLC3 0.329877 0.659754 0.203063 0.397565 0.239635 0.011457 metabolism YJR021C REC107 0.435275 0.353553 0.406126 0.398318 0.174946 1.48E-05 other
YOL048C RRT8 0.353553 0.574349 0.267943 0.398615 0.205645 0.002748 glycosylation and cell wall YMR135C GID8 0.353553 0.615572 0.233258 0.400795 0.221871 0.00605 metabolism YKL209C STE6 0.435275 0.535887 0.233258 0.401473 0.205178 0.002544 transport YHR155W YSP1 0.406126 0.535887 0.267943 0.403319 0.198688 0.001521 other YER096W SHC1 0.329877 0.615572 0.287175 0.410875 0.218161 0.004638 other YHL035C VMR1 0.287175 0.615572 0.329877 0.410875 0.218161 0.004638 transport YGL032C AGA2 0.466516 0.5 0.267943 0.411487 0.199034 0.001247 glycosylation and cell wall YNR058W BIO3 0.406126 0.615572 0.217638 0.413112 0.227621 0.00695 metabolism YMR031C EIS1 0.406126 0.615572 0.217638 0.413112 0.227621 0.00695 other YHL044W 0.307786 0.615572 0.329877 0.417745 0.217848 0.004195 unknown YDR530C APA2 0.435275 0.466516 0.353553 0.418448 0.185829 6.6E-05 metabolism YGL039W 0.267943 0.435275 0.574349 0.425856 0.213945 0.00292 metabolism YMR313C TGL3 0.406126 0.466516 0.406126 0.426256 0.186214 9.02E-06 metabolism YDL182W LYS20 0.757858 0.435275 0.088388 0.427174 0.300438 0.041415 metabolism YDR074W TPS2 0.378929 0.5 0.406126 0.428352 0.190843 9.89E-05 metabolism YHR080C 0.406126 0.5 0.378929 0.428352 0.190843 9.89E-05 unknown YLR241W 0.307786 0.574349 0.406126 0.42942 0.208952 0.001842 unknown YJL210W PEX2 0.435275 0.5 0.353553 0.42961 0.193129 0.000176 transport YFL026W STE2 0.466516 0.535887 0.287175 0.429859 0.20708 0.001535 other YGL085W LCL3 0.435275 0.574349 0.287175 0.432266 0.212949 0.002381 unknown YMR258C ROY1 0.329877 0.574349 0.406126 0.436784 0.208793 0.001458 transport YBR077C SLM4 0.435275 0.659754 0.217638 0.437556 0.245628 0.01163 other YDR100W TVP15 0.466516 0.5 0.353553 0.440023 0.198111 0.000226 transport
YJL222W VTH2 0.329877 0.615572 0.378929 0.441459 0.219568 0.003183 transport YKL224C PAU16 0.329877 0.615572 0.378929 0.441459 0.219568 0.003183 unknown YOR044W IRC23 0.574349 0.574349 0.176777 0.441825 0.25089 0.013566 unknown YGL154C LYS5 0.435275 0.659754 0.233258 0.442762 0.243958 0.010626 metabolism YML116W ATR1 0.5 0.615572 0.217638 0.444403 0.240797 0.009302 transport YGR281W YOR1 0.353553 0.574349 0.406126 0.444676 0.20911 0.00113 transport YLR193C UPS1 0.615572 0.435275 0.287175 0.446007 0.225437 0.004301 transport YJR046W TAH11 0.307786 0.535887 0.5 0.447891 0.212452 0.00146 other YOL119C MCH4 0.535887 0.707107 0.101532 0.448175 0.293916 0.037594 transport YIL036W CST6 0.406126 0.535887 0.406126 0.44938 0.201669 0.000219 other YJL196C ELO1 0.615572 0.466516 0.267943 0.450011 0.230605 0.005462 metabolism YCL008C STP22 0.435275 0.535887 0.378929 0.45003 0.202818 0.000278 transport YKR091W SRL3 0.329877 0.615572 0.406126 0.450525 0.221358 0.003002 other YKR051W 0.5 0.5 0.353553 0.451184 0.204312 0.000357 unknown YHL047C ARN2 0.353553 0.535887 0.466516 0.451986 0.206251 0.000499 transport YNL045W 0.435275 0.615572 0.307786 0.452878 0.22453 0.003593 metabolism YJR025C BNA1 0.659754 0.466516 0.233258 0.453176 0.24761 0.011378 metabolism YPL264C 0.574349 0.615572 0.176777 0.455566 0.26129 0.017667 unknown YCR005C CIT2 0.466516 0.466516 0.435275 0.456103 0.19791 8.04E-07 metabolism YGR131W FHN1 0.466516 0.435275 0.466516 0.456103 0.19791 8.04E-07 other YGL010W 0.329877 0.659754 0.378929 0.456187 0.234223 0.006121 unknown YBR047W FMP23 0.535887 0.615572 0.217638 0.456366 0.247418 0.011056 unknown YKL035W UGP1 0.5 0.435275 0.435275 0.45685 0.199579 1.48E-05 glycosylation and cell wall
YOR128C ADE2 0.435275 0.435275 0.5 0.45685 0.199579 1.48E-05 metabolism YOR228C MCP1 0.5 0.435275 0.435275 0.45685 0.199579 1.48E-05 metabolism YOR390W FEX1 0.466516 0.574349 0.329877 0.456914 0.215986 0.001548 transport YJL164C SRA3 0.378929 0.615572 0.378929 0.45781 0.220525 0.002347 other YPL004C LSP1 0.5 0.5 0.378929 0.459643 0.205077 0.00018 other YKL033W-A 0.615572 0.435275 0.329877 0.460241 0.223949 0.002938 unknown YER039C HVG1 0.406126 0.707107 0.267943 0.460392 0.254863 0.014121 unknown YAL060W BDH1 0.406126 0.574349 0.406126 0.462201 0.211594 0.000661 metabolism YNL145W MFA2 0.615572 0.466516 0.307786 0.463292 0.228233 0.00379 other YAL061W BDH2 0.535887 0.574349 0.287175 0.465803 0.229854 0.00404 metabolism YDL054C MCH1 0.535887 0.615572 0.25 0.467153 0.243712 0.008642 transport YJR127C ZMS1 0.5 0.615572 0.287175 0.467582 0.23424 0.005205 other YPL224C MMT2 0.353553 0.615572 0.435275 0.468134 0.223779 0.00235 transport YBR145W ADH5 0.707107 0.535887 0.164938 0.469311 0.282317 0.029473 metabolism YBR068C BAP2 0.615572 0.615572 0.189465 0.473536 0.268897 0.020716 transport YOL133W HRT1 0.5 0.615572 0.307786 0.474453 0.23301 0.004247 other YFR020W 0.435275 0.659754 0.329877 0.474969 0.237681 0.005702 unknown YAL044C GCV3 0.615572 0.435275 0.378929 0.476592 0.224118 0.00184 metabolism YLL028W TPO1 0.435275 0.615572 0.378929 0.476592 0.224118 0.00184 transport YNL042W BOP3 0.435275 0.5 0.5 0.478425 0.208843 1.74E-05 unknown YLL060C GTT2 0.466516 0.535887 0.435275 0.479226 0.210682 6.24E-05 metabolism YKL132C RMA1 0.535887 0.574349 0.329877 0.480038 0.2277 0.002376 metabolism YNL251C NRD1 0.535887 0.5 0.406126 0.480671 0.213461 0.000178 protein synthesis
YDR007W TRP1 0.435275 0.574349 0.435275 0.481633 0.216144 0.000364 metabolism YPL003W ULA1 0.329877 0.615572 0.5 0.481816 0.232065 0.003351 other YJL142C IRC9 0.5 0.659754 0.287175 0.48231 0.247156 0.008667 unknown YER180C ISC10 0.406126 0.574349 0.466516 0.482331 0.217375 0.000461 other YJR059W PTK2 0.406126 0.615572 0.435275 0.485658 0.225077 0.001421 other YLR152C 0.574349 0.707107 0.176777 0.486078 0.287018 0.032111 unknown YKR089C TGL4 0.5 0.615572 0.353553 0.489709 0.231488 0.002538 metabolism YHR016C YSC84 0.329877 0.707107 0.435275 0.490753 0.253178 0.010564 other YIR016W 0.535887 0.535887 0.406126 0.492633 0.219796 0.000302 unknown YHR122W CIA2 0.574349 0.574349 0.329877 0.492858 0.235598 0.003395 other YMR171C EAR1 0.5 0.574349 0.406126 0.493492 0.221847 0.000482 transport YKL211C TRP3 0.615572 0.535887 0.329877 0.493779 0.237873 0.00401 metabolism YJL200C ACO2 0.707107 0.574349 0.203063 0.49484 0.282914 0.028595 metabolism YHR195W NVJ1 0.5 0.615572 0.378929 0.498167 0.231372 0.001829 other YIL152W 0.5 0.615572 0.378929 0.498167 0.231372 0.001829 unknown
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 3 265 296 >3-fold 1 62 118 Number of genes whose transcripts are decreased by in sur2δ in arv1δ in arv1δsur2δ >2-fold 13 173 600 >3-fold 1 45 243
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 RTA1 3.45 0.75 ** putative transporter involved in 7-aminocholesterol resistance YHR138C 4.37 1.03 ** putative protein of unknown function that has similarity to Pbi2p YJL104W PAM16 6.43 8.29 ns essential components of the import motor of mitochondrial preprotein translocase YKR013W PRY2 3.04 0.71 * sterol binding protein involved in the export of acetylated sterols YLR292C SEC72 3.22 1.73 ns non-essential subunit of Sec63 complex YMR011W HXT2 17.59 4.83 ** high-affinity glucose transporter YNL044W YIP3 3.66 0.38 *** protein localized to COPII vesicles and interacts with members of the Rab GTPase family and Yip1p Metabolism YGL253W HXK2 3.18 0.85 * hexokinase isoenzyme 2 YJR129C 9.92 13.92 ns predicted S-adenosylmethionine-dependent methyltransferase of the seven beta-strand family YJR159W SOR1 3.08 1.10 ns sorbitol dehydrogenase YKL001C MET14 3.04 1.36 ns adenylylsulfate kinase YKL216W URA1 4.28 2.17 ns dihydroorotate dehydrogenase YKR075C 3.37 0.69 ** protein of unknown function that has similarity to YOR062Cp and Reg1p/Hex2p YLR099C ICT1 3.94 1.43 * lysophosphatidic acid acyltransferase YNL141W AAH1 4.64 2.01 * adenine deaminase YOR236W DFR1 3.81 0.99 ** dihydrofolate reductase YPL061W ALD6 4.59 1.84 * cytosolic aldehyde dehydrogenase
YPL057C SUR1/CSG1 3.16 0.74 ** catalytic subunit of a mannosylinositol phosphorylceramide synthase YPR006C ICL2 3.43 0.51 ** 2-methylisocitrate lyase Cell cycle YMR199W CLN1 3.35 1.08 * G1 cyclin involved in regulation of the cell cycle YNL289W PCL1 3.31 1.17 * Pho85 cyclin of the Pcl1,2-like subfamily YNR009W NRM1 3.54 2.25 ns MBF (Mbp1-Swi6)-associated transcriptional corepressor YPL141C FRK1 4.79 2.83 ns putative protein kinase that has similarity to kin4p YPL256C CLN2 3.75 1.07 * G1 cyclin involved in regulation of the cell cycle Stress response and protein folding YBR201W DER1 3.02 0.90 * ER membrane protein that promotes export of misfolded polypeptides YJL073W JEM1 3.06 0.76 * DnaJ-like chaperone YJR032W CPR7 9.17 11.69 ns peptidyl-prolyl cis-trans isomerase (cyclophilin) that contributes to chaperone activity (Hsp70 co-chaperones) YKL073W LHS1 3.46 1.58 ns molecular chaperone of the endoplasmic reticulum lumen that is involved in polypeptide translocation and folding YOL031C SIL1 3.23 0.67 ** nucleotide exchange factor for the endoplasmic reticulum lumenal Hsp70 chaperone Kar2p Protein synthesis YBL054W TOD6 3.05 1.58 ns PAC motif binding protein involved in rrna and ribosome biogenesis YBR247C ENP1 3.26 0.87 * protein required for pre-rrna processing and 40S ribosomal subunit synthesis YDR087C RRP1 3.08 0.64 ** nucleolar protein necessary for biogenesis of 60S ribosomal subunits and processing of pre-rrnas to mature rrnas YGR103W NOP7 4.26 3.25 ns nucleolar protein involved in rrna processing and 60S ribosomal subunit biogenesis
YHR169W DBP8 3.42 1.03 * putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit YJL102W MEF2 3.65 1.42 * mitochondrial elongation factor involved in translational elongation YLR172C DPH5 3.69 1.10 * methyltransferase required for synthesis of diphthamide YLR327C TMA10 7.32 5.31 ns proteins associated with ribosomal complexes YLR435W TSR2 3.89 2.30 ns protein with a potential role in pre-rrna processing YNL061W NOP2 3.16 0.78 ** probable RNA m(5)c methyltransferase essential for processing and maturation of 27S pre-rrna YOL080C REX4 3.64 1.86 ns putative RNA exonuclease involved in pre-rrna processing and ribosome assembly YOL124C TRM11 3.07 0.76 * catalytic subunit of adomet-dependent trna methyltransferase complex YOR294W RRS1 3.67 1.90 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 PST1 3.77 1.14 * cell wall protein that contains a putative GPI-attachment site YGR032W GSC2 3.90 0.96 ** catalytic component of 1,3-beta-D-glucan synthase involved in formation of the inner layer of the spore wall YGR189C CRH1 3.04 0.71 * chitin transglycosylase YJL158C CIS3 3.25 0.90 * mannose-containing glycoprotein constituent of the cell wall YKL165C MCD4 4.44 1.87 * mannose-ethanolamine phosphotransferase involved in GPI anchor synthesis YLR121C YPS4 10.05 2.55 ** aspartic protease attached to the plasma membrane via a GPI anchor YLR194C NCW2 11.39 1.57 *** structural constituent of the cell wall YLR414C PUN1 3.35 0.56 ** plasma membrane protein with a role in cell wall integrity YMR305C SCW10 3.79 0.78 ** cell-wall glucanase/transglucosidase important for cell-wall stability YPL163C SVS1 4.30 1.23 ** cell wall and vacuolar protein of unknown function required for wild-type resistance to vanadate
Other YJR048W CYC1 3.02 1.13 ns cytochrome c, isoform 1 YLL067C 105.44 181.63 ns putative Y' element ATP-dependent helicase YMR182C RGM1 3.04 0.95 * putative zinc finger DNA binding transcription factor YOR134W BAG7 5.84 5.47 ns Rho GTPase activating protein that has a role in actin cytoskeleton organization and control of cell wall synthesis Unknown YBR056W-A 4.89 1.06 ** putative protein of unknown function YBR071W 5.43 1.49 ** putative protein of unknown function YIR035C 4.35 3.38 ns putative cytoplasmic protein of unknown function YLR104W LCL2 3.12 0.44 ** putative protein of unknown function and null mutant is deficient in amounts of cell wall mannosylphosphate YNR066C 4.45 4.37 ns putative membrane-localized protein of unknown function YOL019W 3.55 0.90 ** protein of unknown function
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 ARV1 0.06 0.00 *** Transporter and vesicular transport YBR147W RCT2 0.26 0.19 ** putative vacuolar membrane transporter for cationic amino acids YGL255W ZRT1 0.25 0.16 ** high-affinity zinc transporter YLR130C ZRT2 0.31 0.08 *** low-affinity zinc transporter YML123C PHO84 0.22 0.19 ** high-affinity inorganic phosphate transporter YNL004W HRB1 0.32 0.07 *** poly(a+) RNA-binding protein involved in the export of mrnas from the nucleus to the cytoplasm YOL158C ENB1 0.33 0.11 *** ferric enterobactin transporter YOR100C CRC1 0.27 0.11 *** mitochondrial carnitine transporter YPL265W DIP5 0.24 0.11 *** dicarboxylic amino acid transporter Metabolism YCL026C-A FRM2 0.26 0.04 *** type II nitroreductase YDL222C FMP45 0.19 0.07 *** integral membrane protein required for maintaining sphingolipid content YDR019C GCV1 0.28 0.17 ** glycine decarboxylase complex T subunit YER024W YAT2 0.32 0.15 ** carnitine acetyltransferase YGR087C PDC6 0.19 0.08 *** pyruvate decarboxylase isozyme YGR088W CTT1 0.29 0.16 ** cytosolic catalase T YIL164C NIT1 0.33 0.22 ** member of the nitrilase branch of the nitrilase superfamily YKR058W GLG1 0.33 0.22 ** glycogenin glucosyltransferase