TABLE 2.

Non-conservative mutations found in single-colony isolates obtained from serial transfer evolution experiments with S. cerevisiae CEN.PK113-7D on SMD variants lacking individual B vitamins^a

Gene mutated in evolution expt	Codon changeb	Amino acid change	Gene annotation
Pantothenate
IMS0733
AMN1	agC-agG	S67R	Antagonist of mitotic exit network protein 1
DAN4	aTc-aCc	I353T	Cell wall protein, delayed anaerobic 4
ERG3	Gct-Cct	A145P	Delta(7)-sterol 5(6)-desaturase, ergosterol biosynthesis 3
ERR3	ttG-ttT	L344F	Enolase-related protein 3
ISW2	tCa-tGa	S181Stop	ISWI chromatin-remodeling complex ATPase, imitation switch subfamily 2
IMS0734
CDC15	Aca-Gca	T262A	Cell division control protein 15
RPS14A	Cca-Tca	P94S	40S ribosomal protein S14-A
TUP1	gTg-gCg	V374A	General transcriptional corepressor
RRT6	gCg-gTg	A267V	Regulator of rRNA gene transcription protein 6
CEG1	gCa-gTa	A4V	mRNA-capping enzyme subunit alpha
SCY1	Cct-Tct	P42S	Protein kinase-like protein SCY1
PDX1	gCa-gTa	A208V	Pyruvate dehydrogenase complex protein X component
TRM5	gCg-gTg	A106V	tRNA [guanine(37)-N1]-methyltransferase
GEF1	aGa-aTa	R637I	Anion/proton exchange transporter, glycerol ethanol, ferric requiring 1
LIP2	gGc-gAc	G235D	Octanoyltransferase
HFA1	Aag-Gag	K1021E	Acetyl coenzyme A carboxylase, mitochondrial
UBP8	aGt-aCt	S149T	Ubiquitin carboxyl-terminal hydrolase 8
MGS1	Cca-Aca	P392T	DNA-dependent ATPase
CPT1	Gtg-Atg	V255M	Cholinephosphotransferase 1
SPE2	Gca-Aca	A278T	S-Adenosylmethionine decarboxylase proenzyme
GAL11	aTt-aAt	I541N	Mediator of RNA polymerase II transcription subunit 15
CUE5	Cca-Tca	P377S	Ubiquitin-binding protein
MIP1	Gca-Aca	A630T	DNA polymerase gamma
POC4	aGc-aTc	S7I	Proteasome chaperone 4
KAP120	tTg-tCg	L582S	Importin beta-like protein
KAP120	gAc-gGc	D850G	Importin beta-like protein
SEC16	Gca-Aca	A1015T	COPII coat assembly protein
IMS0735
TUP1	Cag-Tag	Q99Stop	General transcriptional corepressor
FMS1	Caa-Aaa	Q-33K	Polyamine oxidase
GAL11	Caa-Taa	Q383Stop	Mediator of RNA polymerase II transcription subunit 15
Pyridoxine
IMS0736
BAS1	cAa-cGa	Q152R	Myb-like DNA-binding protein, basal 1
ERG5	Aga-Gga	R529G	C-22 sterol desaturase, ergosterol biosynthesis 5
IMS0737
BAS1	Gat-Aat	D101N	Myb-like DNA-binding protein, basal 1
ERG5	Ggt-Tgt	G472C	C-22 sterol desaturase, ergosterol biosynthesis 5
IMS0738
GIP4	Tcc-Ccc	S464P	GLC7-interacting protein 4
AOS1	Gtg-Atg	V286M	DNA damage tolerance protein RHC31
ORC4	aGt-aAt	S160N	Origin recognition complex subunit 4
MSB1	Att-Ttt	I180F	Morphogenesis-related protein, multicopy suppression of a budding defect 1
GCR2	Gga-Aga	G5R	Glycolytic genes transcriptional activator, glycolysis regulation 2
VNX1	aCa-aTa	T490I	Low-affinity vacuolar monovalent cation/H+ antiporter
MMT1	gCt-gAt	A175D	Mitochondrial metal transporter 1
ISF1	Tat-Gat	Y220D	Increasing suppression factor 1
RPM2	Gcc-Acc	A1020T	Ribonuclease P protein component, mitochondrial
BAS1	Tca-Cca	S41P	Myb-like DNA-binding protein, basal 1
AAD14	agC-agA	S322R	Putative aryl-alcohol dehydrogenase AAD14
FAS1	gaA-gaT	E1829D	Fatty acid synthase subunit beta
BEM2	Aac-Cac	N792H	GTPase-activating protein, bud emergence 2/IPL2
APL1	gGt-gTt	G6V	AP-2 complex subunit beta
DPB11	agG-agT	R699S	DNA replication regulator, DNA polymerase B (II) 11
LSB6	Aca-Gca	T458A	Phosphatidylinositol 4-kinase, las seventeen binding protein 6
EFG1	aAa-aGa	K188R	rRNA-processing protein, exit from G1 1
CCH1	atG-atA	M828I	Calcium-channel protein 1
RNR4	Gca-Tca	A210S	Ribonucleoside-diphosphate reductase small chain 2
GCD2	tTa-tCa	L472S	Translation initiation factor eIF-2B subunit delta
YHR219W	aAt-aGt	N61S	Putative uncharacterized protein YHR219W
CDC37	Gcc-Tcc	A275S	Hsp90 cochaperone, cell division cycle 37
SRP101	Gca-Aca	A75T	Signal recognition particle receptor subunit alpha homolog
ADE8	Gca-Aca	A142T	Phosphoribosylglycinamide formyltransferase
AIM9	gCa-gTa	A23V	Altered inheritance of mitochondria protein 9, mitochondrial
UTP20	tAt-tGt	Y1492C	U3 small nucleolar RNA-associated protein 20
RIF1	aGc-aTc	S1516I	Telomere length regulator protein, RAP1-interacting factor 1
PHO87	Gtc-Atc	V482I	Inorganic phosphate transporter
MAK21	tTg-tCg	L413S	Ribosome biogenesis protein, maintenance of killer 21
YDL176W	tCa-tAa	S186-Stop	Uncharacterized protein YDL176W
Thiamine
IMS0747
MAL12	Gtt-Ctt	V305L	Alpha-glucosidase, maltose fermentation 12
CNB1	ttA-ttT	L82F	Calcineurin subunit B
PRP16	aAa-aGa	K112R	Pre-mRNA-splicing factor ATP-dependent RNA helicase
ERR3	ttG-ttT	L447F	Enolase-related protein 3
IMS0748
PMR1	tCc-tAc	S104Y	Calcium-transporting ATPase 1
FRE2	aCt-aGt	T110S	Ferric/cupric reductase transmembrane component 2
IMS0749
YEL074W	cAc-cCc	H66P	Putative UPF0320 protein YEL074W
CNB1	ttA-ttC	L82F	Calcineurin subunit B
MSC1	Gtt-Att	V309I	Meiotic sister chromatid recombination protein 1
ERR3	ttG-ttT	L447F	Enolase-related protein 3
pABA
IMS0727
ABZ1	cGt-cAt	R593H	Aminodeoxychorismate synthase
IMS0728
ARO7	tTa-tCa	L205S	Chorismate mutase
NUP57	tCc-tTc	S396F	Nucleoporin 57
IMS0729
ABZ1	cGt-cAt	R593H	Aminodeoxychorismate synthase
HST2	ttG-ttT	L102F	NAD-dependent protein deacetylase, homolog of SIR two 2
Inositol
IMS0730
YFR045W	Gcc-Acc	A65T	Putative mitochondrial transport protein
IMS0732
YFR045W	Gcc-Acc	A65T	Uncharacterized mitochondrial carrier
Nicotinic acid
IMS0724
RPG1	Ggt-Tgt	G294C	Eukaryotic translation initiation factor 3 subunit A
PMR1	Ggt-Agt	G694S	Calcium-transporting ATPase 1
IMS0725
MTO1	atG-atT	M356I	Mitochondrial translation optimization protein 1
VTH2	Cca-Tca	P708S	Putative membrane glycoprotein, VPS10 homolog 2
VTH2	gTT-gCC	V478A	Putative membrane glycoprotein, VPS10 homolog 2
VTH2	TtT-GtG	F477V	Putative membrane glycoprotein, VPS10 homolog 2

^aMutations that were chosen for subsequent reverse engineering experiments are shown in boldface font. S. cerevisiae strains IMS0731 and IMS0726 evolved for fast myo-inositol- and nicotinic acid-independent growth, respectively, did not reveal non-conservative mutations and were not included in the table.

^bUppercase letters indicate the mutations.