Table 1 Summary of statistically enriched genes identified in compound selections.

From: Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance

Gene

Description

NG

NC

Compounds

p-value

YRM1

Zn2-Cys6 zinc-finger transcription factor

52

13

See Supplementary Data 4

3.53 × 10−116

YRR1

Zn2-Cys6 zinc-finger transcription factor

48

12

See Supplementary Data 4

2.51 × 10−105

PMA1

Plasma membrane P2-type H + -ATPase

15

5

GNF-Pf-445, Hygromycin B, KAE609, Wortmannin, GNF-Pf-3891

3.00 × 10−24

BUL1

Ubiquitin-binding component of the Rsp5p E3-ubiquitin ligase complex

14

11

See Supplementary Data 4

3.92 × 10−22

PDE2

High-affinity cyclic AMP phosphodiesterase

13

2

MMV000570, MMV007181

4.76 × 10−20

TPO1

Polyamine transporter of the major facilitator superfamily

12

5

GNF-Pf-4283, MMV006389, CBR410, CBR572, TCMDC-124263

5.34 × 10−18

ANY1

Putative protein of unknown function

11

5

Amitriptyline, MMV019017, Clomipramine, MMV396736, Sertraline

5.51 × 10−16

BAP2

High-affinity leucine permease

10

6

GNF-Pf-3703, GNF-Pf-3815, GNF-Pf-5129, GNF-Pf-5468, MMV006389

5.19 × 10−14

SIP3

Putative sterol transfer protein

8

3

GNF-Pf-445, Lomerizine, Loratidine

3.38 × 10−10

INP53

Polyphosphatidylinositol phosphatase

8

1

MMV000442

3.38 × 10−10

AFT1

Transcription factor involved in iron utilization

7

3

MMV085203, MMV1007245, CBR868

2.28 × 10−8

PDR1

Transcription factor that regulates the pleiotropic drug response

7

7

DDD01027481, Doxorubicin, MMV000442, MMV007224, MMV667491, CBR668, CBR110

2.28 × 10−8

ERG9

Farnesyl-diphosphate farnesyl transferase

7

2

AN7973, MMV1078458

2.28 × 10−8

YAP1

Basic leucine zipper (bZIP) transcription factor

6

4

Cycloheximide, GNF-Pf-4739, DDD01027481, MMV001246

1.34 × 10−6

TOP2

Topoisomerase II

6

1

Etoposide

1.34 × 10−6

HXT3

Low-affinity glucose transporter of the major facilitator superfamily

6

3

Amitriptyline, DDD01035522, GNF-Pf-445

1.34 × 10−6

ERG11

Lanosterol 14-alpha-demethylase

6

2

MMV001239, CBR499

1.34 × 10−6

FUR1

Uracil phosphoribosyltransferase

6

1

Flucytosine

1.34 × 10−6

CCR4

Component of the CCR4-NOT transcriptional complex

5

4

GNF-Pf-2823, GNF-Pf-4583, MMV403679, CBR868

6.76 × 10−5

ERG3

C-5 sterol desaturase

5

2

Miconazole, Posaconazole

6.76 × 10−5

FKS1

Catalytic subunit of 1,3-beta-D-glucan synthase

5

4

DDD01027481, CBR113, CBR668, CBR110

6.76 × 10−5

CDC60

Cytosolic leucyl-tRNA synthetase

5

2

CBR668, Tavaborole

 

ROX1

Heme-dependent repressor of hypoxic genes;

5

3

Loratadine, MMV665909, TCMDC-124263

6.76 × 10−5

PDR3

Transcriptional activator of the pleiotropic drug-resistance network

5

3

Lapatinib, MMV665794, CBR110

6.76 × 10−5

OSH3

Member of an oxysterol-binding protein family

5

1

Posaconazole

6.76 × 10−5

CSG2

Endoplasmic reticulum membrane protein

4

2

GNF-Pf-1618, KAAA726

4.76 × 10−2

ELO2

Fatty acid elongase

4

2

Doxorubicin, MMV667491

4.76 × 10−2

TUP1

General repressor of transcription

4

1

Diethylstilbestrol

 

RPO21

RNA polymerase II largest subunit B220

4

4

Lapatinib, MMV007181, MMV1469689, CBR110

4.76 × 10−2

SUR2

Sphinganine C4-hydroxylase

4

1

MMV667491

4.76 × 10−2

VMA16

Subunit c” of the vacuolar ATPase

4

4

Lapatinib, MMV019017, MMV396736, MMV665882

4.76 × 10−2

PAN1

Part of actin cytoskeleton-regulatory complex Pan1p-Sla1p-End3p

4

2

Hygromycin B, KAE609

4.76 × 10−2

  1. 32 genes contained at least four independently selected coding mutations, the significance threshold for number of mutations occurring in a gene at a rate not expected by chance across the dataset. Bonferroni-corrected p-values were calculated using the hypergeometric mean function (number of successes in sample = number of times gene was identified as mutated; sample size = total number of genes mutated in dataset (731); successes in population = number of independent selections (355); population size = number of genes in yeast genome multiplied by 355) followed by Bonferroni-correction using number of independent selections.For a complete list of genes and mutations identified across the study, refer to Supplementary Data 4.
  2. NG number of times gene was identified as mutated in independent evolution experiments, NC number of compounds.