Table S1. Yeast Up-Regulated Genes Under Quinine Stress

Table S1. Yeast up-regulated genes under quinine stress.

Gene / Description / Fold
change
nutrient and energy metabolism
ACS1 / Acetyl-coA synthetase isoform which, along with Acs2p, is the nuclear source of acetyl-coA for histone acetylation / 2.0
ALD4 / Mitochondrial aldehyde dehydrogenase, required for growth on ethanol and conversion of acetaldehyde to acetate; activity is K+ dependent; utilizes NADP+ or NAD+ equally as coenzymes / 6.0
ALD6 / Cytosolic aldehyde dehydrogenase that is activated by Mg2+ and utilizes NADP+ as the preferred coenzyme; required for the conversion of acetaldehyde to acetate / 3.7
ASI2 / Integral inner nuclear membrane protein that acts with Asi1p and Asi3p to ensure the fidelity of SPS-sensor signalling by maintaining the dormant repressed state of gene expression in the absence of inducing signals / 2.2
ATG7 / Autophagy-related protein and dual specificity member of the E1 family of ubiquitin-activating enzymes; mediates the conjugation of Atg12p with Atg5p and Atg8p with phosphatidylethanolamine, required steps in autophagosome formation / 2.2
ATH1 / Vacuolar acid trehalase, required for trehalose utilization / 2.2
CIT3 / Citrate synthase, catalyzes the condensation of acetyl coenzyme A and oxaloacetate to form citrate, mitochondrial isozyme involved in the TCA cycle / 4.1
CRC1 / Mitochondrial inner membrane carnitine transporter, required for carnitine-dependent transport of acetyl-CoA from peroxisomes to mitochondria during fatty acid beta-oxidation / 6.3
FAA2 / Long chain fatty acyl-CoA synthetase; accepts a wider range of acyl chain lengths than Faa1p, preferring C9:0-C13:0; involved in the activation of endogenous pools of fatty acids / 3.5
GCV2 / P subunit of the mitochondrial glycine decarboxylase complex, required for the catabolism of glycine to 5,10-methylene-THF / 2.1
GDH2 / NAD+-dependent glutamate dehydrogenase, degrades glutamate to ammonia and alpha-ketoglutarate / 2.5
GLC3 / Glycogen branching enzyme, involved in glycogen accumulation / 3.0
GLG1 / Self-glucosylating initiator of glycogen synthesis, also glucosylates n-dodecyl-beta-D-maltoside / 3.4
GLK1 / Glucokinase, catalyzes the phosphorylation of glucose at C6 in the first irreversible step of glucose metabolism; one of three glucose phosphorylating enzymes; expression regulated by non-fermentable carbon sources / 2.9
GSY1 / Glycogen synthase with similarity to Gsy2p, the more highly expressed yeast homolog / 3.1
GUT2 / Mitochondrial glycerol-3-phosphate dehydrogenase / 4.5
ICL1 / Isocitrate lyase, catalyzes the formation of succinate and glyoxylate from isocitrate, a key reaction of the glyoxylate cycle / 4.3
NDI1 / NADH:ubiquinone oxidoreductase, transfers electrons from NADH to ubiquinone in the respiratory chain but does not pump protons, in contrast to the higher eukaryotic multisubunit respiratory complex I which is absent in S. cerevisiae / 3.3
PDH1 / Mitochondrial protein that participates in respiration, induced by diauxic shift / 6.5
PFK27 / 6-phosphofructo-2-kinase, has negligible fructose-2,6-bisphosphatase activity / 2.8
PYK2 / Pyruvate kinase that appears to be modulated by phosphorylation / 2.0
RPM2 / Multifunctional protein that is distributed to mitochondria, cytoplasmic processing bodies, and the nucleus; has roles in nuclear transcription, cytoplasmic and mitochondrial RNA processing, and mitochondrial translation / 3.7
SDH2 / Iron-sulfur protein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p), which couples the oxidation of succinate to the transfer of electrons to ubiquinone / 2.4
SUR1 / Probable catalytic subunit of a mannosylinositol phosphorylceramide synthase, forms a complex with probable regulatory subunit Csg2p; function in sphingolipid biosynthesis is overlapping with that of Csh1p / 2.4
YLR345W / Similar to 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase enzymes responsible for the metabolism of fructoso-2,6-bisphosphate; mRNA expression is repressed by the Rfx1p-Tup1p-Ssn6p repressor complex / 2.3
YPL113C / Glyoxylate reductase; acts on glyoxylate and hydroxypyruvate substrates / 4.1
regulation of metabolism
ADR1 / Carbon source-responsive zinc-finger transcription factor, required for transcription of the glucose-repressed genes, of peroxisomal protein genes, and of genes required for ethanol, glycerol, and fatty acid utilization / 4.1
CAT8 / Zinc cluster transcriptional activator necessary for derepression of a variety of genes under non-fermentative growth conditions, active after diauxic shift, binds carbon source responsive elements / 7.6
CSR2 / Nuclear protein with a potential regulatory role in utilization of galactose and nonfermentable carbon sources / 3.6
GAL4 / DNA-binding transcription factor required for the activation of the GAL genes in response to galactose / 2.2
GIS1 / JmjC domain-containing histone demethylase; transcription factor involved in the expression of genes during nutrient limitation / 3.1
HAP4 / Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; provides the principal activation function of the complex / 3.0
MAL33 / MAL-activator protein, part of complex locus MAL3 / 10.6
other regulators
HAL1 / Cytoplasmic protein involved in halotolerance; decreases intracellular Na+ (via Ena1p) and increases intracellular K+ by decreasing efflux / 2.3
signal transduction
CMK1 / Calmodulin-dependent protein kinase; may play a role in stress response, many CA++/calmodulan dependent phosphorylation substrates demonstrated in vitro / 2.2
KIN82 / Putative serine/threonine protein kinase, most similar to cyclic nucleotide-dependent protein kinase subfamily and the protein kinase C subfamily / 2.8
MDG1 / Plasma membrane protein involved in G-protein mediated pheromone signaling pathway / 2.2
MTH1 / Negative regulator of the glucose-sensing signal transduction pathway, required for repression of transcription by Rgt1p; interacts with Rgt1p and the Snf3p and Rgt2p glucose sensors; phosphorylated by Yck1p, triggering Mth1p degradation / 9.0
SKS1 / Putative serine/threonine protein kinase; involved in the adaptation to low concentrations of glucose independent of the SNF3 regulated pathway / 3.0
SNF3 / Plasma membrane glucose sensor that regulates glucose transport; long cytoplasmic C-terminal tail is required for low glucose induction of hexose transporter genes HXT2 and HXT4 / 3.4
membrane transport
AGP2 / High affinity polyamine permease, preferentially uses spermidine over putrescine; expression is down-regulated by osmotic stress; plasma membrane carnitine transporter, also functions as a low-affinity amino acid permease / 2.6
AVT6 / Vacuolar transporter, exports aspartate and glutamate from the vacuole; member of a family of seven S. cerevisiae genes (AVT1-7) related to vesicular GABA-glycine transporters / 2.0
ENA2 / P-type ATPase sodium pump, involved in Na+ efflux to allow salt tolerance; likely not involved in Li+ efflux / 2.4
ENA5 / P-type ATPase sodium pump, involved in Na+ efflux to allow salt tolerance; likely not involved in Li+ efflux / 2.0
FUI1 / High affinity uridine permease, localized to the plasma membrane; not involved in uracil transport / 2.1
HXT2 / High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose / 2.1
HXT4 / High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose / 3.1
HXT6 / High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt7p, expressed at high basal levels relative to other HXTs, repression of expression by high glucose requires SNF3 / 2.0
HXT7 / High-affinity glucose transporter of the major facilitator superfamily, nearly identical to Hxt6p, expressed at high basal levels relative to other HXTs, expression repressed by high glucose levels / 2.0
JEN1 / Lactate transporter, required for uptake of lactate and pyruvate / 2.3
MAL11 / Maltose permease, inducible high-affinity maltose transporter (alpha-glucoside transporter) / 2.8
MAL31 / Maltose permease, high-affinity maltose transporter (alpha-glucoside transporter) / 3.1
MUP3 / Low affinity methionine permease / 2.0
PHO89 / Na+/Pi cotransporter, active in early growth phase; transcription regulated by inorganic phosphate concentrations and Pho4p / 8.6
SIT1 / Ferrioxamine B transporter, member of the ARN family of transporters that specifically recognize siderophore-iron chelates; transcription is induced during iron deprivation and diauxic shift; potentially phosphorylated by Cdc28p / 2.0
YFL054C / Putative channel-like protein; similar to Fps1p; mediates passive diffusion of glycerol in the presence of ethanol / 3.9
other
OM14 / Integral mitochondrial outer membrane protein; abundance is decreased in cells grown in glucose relative to other carbon sources / 3.2
SSH4 / Vacuolar protein that presumably functions within the endosomal-vacuolar trafficking pathway, affecting events that determine whether plasma membrane proteins are degraded or routed to the plasma membrane / 2.1
UBP11 / Ubiquitin-specific protease that cleaves ubiquitin from ubiquitinated proteins / 3.1
uncharacterized ORFs
ALT1 / Putative alanine transaminase (glutamyc pyruvic transaminase) / 2.2
BOP2 / Protein of unknown function, overproduction suppresses a pam1 slv3 double null mutation / 2.6
FMP43 / Putative protein of unknown function; The authentic, non-tagged protein was localized to mitochondria / 8.8
TMA10 / Protein of unknown function that associates with ribosomes / 12.7
YCL042W / Putative protein of unknown function; epitope-tagged protein localizes to the cytoplasm / 2.9
YER067W / Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus / 4.7
RRT6 / Putative protein of unknown function, contains two putative transmembrane spans, shows no significant homology to any other known protein sequence / 2.2
RMR1 / Protein required for meiotic recombination and gene conversion; deletion mutant results in reduced PIS1 expression and has growth defects on non-fermentable carbon sources and on minimal media; GFP-fusion protein localizes to both the cytoplasm and the nucleus / 2.1
YGR031W / Putative protein of unknown function; The authentic, non-tagged protein was localized to mitochondria / 2.2
CLD1 / Mitochondrial cardiolipin-specific phospholipase; functions upstream of Taz1p to generate monolyso-cardiolipin; transcription increases upon genotoxic stress; involved in restricting Ty1 transposition; has homology to mammalian CGI-58 / 2.4
YJL185C / Putative protein of unknown function; mRNA is weakly cell cycle regulated, peaking in G2 phase / 2.1
REE1 / Cytoplasmic protein of unknown function; expression induced by calcium shortage and via the copper sensing transciption factor Mac1p during conditions of copper deficiency; mRNA is cell cycle regulated, peaking in G1 phase / 2.2
YKL123W / Dubious open reading frame, unlikely to encode a protein; partially overlaps the verified gene SSH4 / 2.3
YKL171W / Putative protein of unknown function; predicted protein kinase; implicated in proteasome function; epitope-tagged protein localizes to the cytoplasm / 2.2
YKR075C / Protein of unknown function; similar to YOR062Cp and Reg1p; expression regulated by glucose and Rgt1p; GFP-fusion protein is induced in response to the DNA-damaging agent MMS / 4.1
YLR122C / Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data; partially overlaps the dubious ORF YLR123C / 2.1
YLR149C / Hypothetical ORF / 3.4
YMR103C / Dubious open reading frame unlikely to encode a protein, based on available experimental and comparative sequence data / 3.7
YMR291W / Putative kinase of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus / 3.6
YNL144C / Putative protein of unknown function; the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies / 3.5
YPR196W / Putative maltose activator / 4.1

Table S2. Yeast down–regulated genes under quinine stress.

Gene / Description / Fold change
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
ALB1 / Shuttling pre-60S factor; involved in the biogenesis of ribosomal large subunit / -2.2
CGR1 / Protein involved in nucleolar integrity and processing of the pre-rRNA for the 60S ribosome subunit; transcript is induced in response to cytotoxic stress but not genotoxic stress / -2.3
DBP8 / Putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit / -2.3
DUS3 / Dihydrouridine synthase, member of a widespread family of conserved proteins including Smm1p, Dus1p, and Dus4p / -2.0
ENP1 / Protein associated with U3 and U14 snoRNAs, required for pre-rRNA processing and 40S ribosomal subunit synthesis / -2.1
ENP2 / Essential nucleolar protein of unknown function; contains WD repeats, interacts with Mpp10p and Bfr2p, and has homology to Spb1p / -2.1
FAF1 / Protein required for pre-rRNA processing and 40S ribosomal subunit assembly / -2.9
FAL1 / Nucleolar protein required for maturation of 18S rRNA, member of the eIF4A subfamily of DEAD-box ATP-dependent RNA helicases / -2.5
HCA4 / Putative nucleolar DEAD box RNA helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis / -2.2
KRR1 / Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit / -2.1
LRP1 / Substrate-specific nuclear cofactor for exosome activity in the processing of stable RNAs; homolog of mammalian nuclear matrix protein C1D, which is involved in regulation of DNA repair and recombination / -2.2
LTV1 / Component of the GSE complex, which is required for proper sorting of amino acid permease Gap1p; required for ribosomal small subunit export from nucleus; required for growth at low temperature / -2.4
MAK5 / Essential nucleolar protein, putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits / -2.1
MPP10 / Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability / -2.0
NOP12 / Nucleolar protein, required for pre-25S rRNA processing; contains an RNA recognition motif (RRM) / -2.0
NOP14 / Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA / -2.1
NOP4 / Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs / -2.2
NOP53 / Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p / -2.1
NOP7 / Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles / -2.1
PXR1 / Essential protein involved in rRNA and snoRNA maturation; competes with TLC1 RNA for binding to Est2p, suggesting a role in regulation of telomerase / -2.1
REX4 / Putative RNA exonuclease possibly involved in pre-rRNA processing and ribosome assembly / -2.7
RNT1 / RNAase III; cleaves a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end / -2.1
RPA34 / RNA polymerase I subunit A34.5 / -2.2