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Table 2 Heterozygous mutations in genes involved in metabolisms

From: Genomic analysis of a riboflavin-overproducing Ashbya gossypii mutant isolated by disparity mutagenesis

Chromosome

Position

Wt seq.

MT seq

Quality

Mutation

Gene

Product

DNA changes

Protein changes

Read number

MT seq. Ratio

WT seq.

MT seq.

Glycolysis/Gluconeogenesis

 III

456,890

C

T

327.19

missense

AGOS_ACR056W

Phosphoglycerate mutase (AgGPM1)

c.374C > T

p.A125V

28

12

0.300

 IV

287,997

T

C

503.19

missense

AGOS_ADL237C

6-phosphofructo-2-kinase (AgPFK26)

c.1796A > G

p.D599G

24

18

0.429

 IV

1,362,124

A

T

725.19

missense

AGOS_ADR368W

Pyruvate kinase (AgPYK1)

c.1040A > T

p.K347M

21

23

0.523

 V

242,262

A

C

708.19

missense

AGOS_AEL208W

Alpha subunit of phosphofructokinase (AgPFK1)

c.2255A > C

p.K752T

27

23

0.460

 V

426,255

C

T

700.19

missense

AGOS_AEL106W

Fructose-2,6-bisphosphatase (AgFBP26)

c.103C > T

p.R35W

21

23

0.523

 VI

96,950

A

C

1088.19

missense

AGOS_AFL185W

Beta subunit of phosphofructokinase (AgPFK2)

c.1963A > C

p.N655H

35

37

0.514

 VI

97,509

AT

A

907.15

frameshift

AGOS_AFL185W

Beta subunit of phosphofructokinase (AgPFK2)

c.2526Tdel

p.Phe842fs

20

32

0.615

TCA cycle

 I

346,384

G

A

758.19

missense

AGOS_AAR004C

Citrate synthase (AgCIT1)

c.68C > T

p.T23M

18

25

0.581

 I

634,291

G

T

991.19

Nonsense

AGOS_AAR162C

Pyruvate carboxylase (AgPYC2)

c.3266c > A

p.S1089*

31

33

0.514

 I

634,669

A

T

836.19

missense

AGOS_AAR162C

Pyruvate carboxylase (AgPYC2)

c.2888 T > A

p.L963Q

21

26

0.553

 III

238,489

T

G

729.19

missense

AGOS_ACL065C

Iron-sulfur protein subunit of succinate dehydrogenase (AgSDH2)

c.697A > C

p.T233P

25

23

0.479

 III

238,962

G

A

1051.19

missense

AGOS_ACL065C

Iron-sulfur protein subunit of succinate dehydrogenase (AgSDH2)

c.224C > T

p.T75M

20

32

0.615

 III

451,903

G

A

879.19

missense

AGOS_ACR052W

Flavoprotein subunit of succinate dehydrogenase (AgSDH1)a

c.1132G > A

p.D378N

17

27

0.614

 IV

403,968

C

T

488.19

missense

AGOS_ADL164C

Malate dehydrogenase (AgMDH2)

c.196G > A

p.A66T

27

16

0.372

 IV

644,214

A

G

568.19

missense

AGOS_ADL032W

Aconitase (AgACO1)

c.1367A > G

p.D456G

10

16

0.615

 V

1,328,889

C

A

922.19

missense

AGOS_AER374C

Subunit of the mitochondrial alpha-ketoglutarate dehydrogenase (AgKGD1)

c.1837G > T

p.D613Y

27

27

0.5

 V

1,328,948

G

A

711.19

missense

AGOS_AER374C

Subunit of the mitochondrial alpha-ketoglutarate dehydrogenase (AgKGD1)

c.1778C > T

p.T593M

25

23

0.479

 VI

810,404

G

T

482.19

missense

AGOS_AFR207C

Subunit of succinate dehydrogenase (AgSDH3)

c.200C > A

p.S67Y

20

18

0.473

 VI

1,103,105

G

A

636.19

missense

AGOS_AFR367W

Fumarate reductase (AgOSM1)

c.622G > A

p.A208T

21

19

0.475

 VI

1,585,840

G

T

635.19

missense

AGOS_AFR629W

Aconitase (AgACO2)

c.1894G > T

p.D632Y

36

24

0.400

 VII

1,652,466

A

G

970.19

missense

AGOS_AGR323C

E3-binding protein of pyruvate dehydrogenase (AgPDX1) a

c.677 T > C

p.L226P

16

28

0.636

 VI

681,082

C

T

624.19

missense

AGOS_AFR134C

Alpha subunit of succinyl-CoA ligase (AgLSC1)

c.193G > A

p.A65T

23

24

0.510

Mitochondria

 II

324,797

A

G

633.19

missense

AGOS_ABL038W

Mitochondrial aspartate aminotransferase (AgAAT1)

c.224A > G

p.D75G

20

19

0.487

 II

325,256

C

T

487.19

missense

AGOS_ABL038W

Mitochondrial aspartate aminotransferase (AgAAT1)

c.683C > T

p.T228M

25

18

0.419

 IV

532,772

C

A

1079.19

missense

AGOS_ADL087W

Cytochrome b reductase (AgCBR1)a

c.155C > A

p.T52N

25

34

0.576

 IV

1,458,400

G

T

559.19

missense

AGOS_ADR417W

Mitochondrial aldehyde dehydrogenase (AgALD4)

c.561G > T

p.W187C

21

17

0.447

 V

1,227,029

G

A

503.19

missense

AGOS_AER321W

Mitochondrial D-lactate dehydrogenase (AgDLD1) a

c.190G > A

p.A64T

11

15

0.577

 VI

899,775

G

A

668.19

missense

AGOS_AFR255W

Mitochondrial tRNA translation optimization 1 (MTO1) a

c.1423G > A

p.G475S

27

22

0.449

 VI

1,243,899

C

T

819.19

missense

AGOS_AFR447C

NADH:ubiquinone oxidoreductase (AgNDI1) a

c.943G > A

p.V315M

16

26

0.619

 VII

1,441,269

C

A

874.19

missense

AGOS_AGR196W

Glutathione-disulfide reductase (AgGLR1) a

c.1415C > A

p.S472Y

27

28

0.509

Riboflavin metabolism

 II

194,781

G

T

733.19

missense

AGOS_ABL109W

Riboflavin kinase (AgFMN1)

c.80G > T

p.S27I

20

22

0.524

 IV

182,017

G

A

687.19

missense

AGOS_ADL296C

GTP cyclohydrolase II (AgRIB1)

c.230C > T

p.P77L

23

23

0.500

Glycine, serine, threonine metabolism

 I

448,391

G

A

962.19

missense

AGOS_AAR059C

Threonine synthase (AgTHR4)

c.685C > T

p.R229W

19

29

0.604

 III

125,457

G

A

821.19

missense

AGOS_ACL130C

Phosphoserine phosphatase (AgSER2)

c.140C > T

p.A47V

28

27

0.491

 III

727,688

C

T

572.19

missense

AGOS_ACR215C

Serine hydroxymethyltransferase (AgSHM2)

c.593G > A

p.R198Q

24

20

0.455

 VII

1,057,290

T

C

592.19

missense

AGOS_AGR012C

Cystathionine beta-synthase (AgCYS4)

c.269A > G

p.K90R

16

19

0.543

 VII

1,446,998

A

G

720.19

missense

AGOS_AGR200W

Threonine aldolase (AgGLY1)

c.1088A > G

p.Y363C

14

20

0.588

Branched-chain amino acid metabolism

 I

305,862

G

A

960.19

missense

AGOS_AAL021W

Small subunit of acetohydroxyacid synthase (AgILV6)

c.140G > A

p.S47N

25

29

0.537

 I

305,877

G

A

923.19

missense

AGOS_AAL021W

Small subunit of acetohydroxyacid synthase (AgILV6)

c.155G > A

p.S52N

28

30

0.517

 I

306,395

G

T

711.19

missense

AGOS_AAL021W

Small subunit of acetohydroxyacid synthase (AgILV6)

c.673G > T

p.G225C

23

22

0.489

 II

729,493

G

A

1028.19

missense

AGOS_ABR174W

Branched-chain amino acid biosynthesis activator (AgLEU3)

c.704G > A

p.G235D

23

33

0.589

 II

730,278

G

A

915.19

missense

AGOS_ABR174W

Branched-chain amino acid biosynthesis activator (AgLEU3)

c.1489G > A

p.A497T

22

26

0.542

 VI

12,855

C

A

543.19

missense

AGOS_AFL229W

2-isopropylmalate synthase (AgLEU4)

c.1051C > A

p.P351T

26

19

0.422

 VII

1,381,676

C

T

564.19

missense

AGOS_AGR169W

3-isopropylmalate dehydratase (LEU1)

c.226C > T

p.H76Y

12

17

0.586

 VII

1,382,933

T

C

745.19

missense

AGOS_AGR169W

3-isopropylmalate dehydratase (LEU1)

c.1483 T > C

p.S495P

26

25

0.490

Aromatic amino acid metabolism

 II

206,627

C

T

580.19

missense

AGOS_ABL102C

3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase (AgARO3)

c.935G > A

p.C312Y

28

18

0.391

 II

799,743

C

A

554.19

missense

AGOS_ABR209W

Anthranilate synthase (AgTRP2)

c.982C > A

p.L328I

15

16

0.516

 VI

1,313,765

T

A

750.19

missense

AGOS_AFR485C

Tryptophan synthase (AgTRP5)

c.1917A > T

p.Q639H

33

29

0.468

 VI

1,426,745

G

T

476.19

missense

AGOS_AFR548C

Aromatic aminotransferase I (AgARO8)

c.544C > A

p.P182T

29

16

0.356

 VII

1,157,861

G

A

690.19

missense

AGOS_AGR066W

Pentafunctional aromatic polypeptide (AgARO1)

c.3536G > A

p.R1179H

22

21

0.488

 VII

1,158,247

G

A

921.19

missense

AGOS_AGR066W

Pentafunctional aromatic polypeptide (AgARO1)

c.3922G > A

p.G1308S

29

31

0.517

Sulfur amino acid metabolism

 I

361,523

G

A

834.19

missense

AGOS_AAR010W

Transcriptional activator of sulfur metabolism (AgMET28)

c.719G > A

p.R240Q

28

25

0.472

 II

259,309

C

T

578.19

missense

AGOS_ABL077W

Beta subunit of sulfite reductase (AgMET5) a

c.3002C > T

p.A1001V

25

19

0.432

 II

804,448

C

T

685.19

missense

AGOS_ABR212C

Cobalamin-independent methionine synthase (AgMET6)

c.499G > A

p.G167S

25

23

0.479

 III

259,886

C

A

1053.19

missense

AGOS_ACL059C

Peroxisomal cystathionine beta-lyase (AgSTR3)

c.1210G > T

p.V404L

16

32

0.667

 III

585,577

C

A

547.19

missense

AGOS_ACR134W

Folylpolyglutamate synthetase (AgMET7)

c.1135C > A

p.L379M

25

17

0.405

 IV

646,485

G

A

838.19

missense

AGOS_ADL031W

O-acetyl homoserine-O-acetyl serine sulfhydrylase (AgMET17)

c.302G > A

p.G101D

23

26

0.531

 V

1,338,633

G

A

974.19

missense

AGOS_AER377C

Component of cytosolic iron-sulfur protein assembly machinery (AgMET18)

c.1061C > T

p.T354I

28

31

0.525

 VI

1,699,984

C

A

936.19

missense

AGOS_AFR682C

L-homoserine-O-acetyltransferase (AgMET2)

c.1045G > T

p.A349S

20

32

0.615

 VI

1,720,007

C

T

393.19

missense

AGOS_AFR692C

S-adenosylmethionine synthetase (AgSAM2)

c.731G > A

p.G244D

30

13

0.302

 VII

1,511,391

C

A

892.19

missense

AGOS_AGR237C

Alpha subunit of assimilatory sulfite reductase (AgMET10)

c.2268G > T

p.E756D

22

28

0.560

 VII

1,512,792

C

A

606.19

missense

AGOS_AGR237C

Alpha subunit of assimilatory sulfite reductase (AgMET10)

c.867G > T

p.E289D

27

22

0.449

 VII

1,685,571

G

A

715.19

missense

AGOS_AGR343W

Component of cytosolic iron-sulfur protein assembly (CIA) machinery

c.563G > A

p.R188H

24

21

0.467

Other amino acid metabolism

 III

169,882

C

T

367.19

missense

AGOS_ACL096W

Proline utilization transactivator (AgPUT3)

c.382C > T

p.R128W

26

14

0.350

 IV

98,235

C

A

727.19

missense

AGOS_ADL346W

Alpha-aminoadipate reductase (AgLYS2)

c.1648C > A

p.L550M

27

23

0.460

 VI

1,397,559

C

A

864.19

missense

AGOS_AFR534W

Small subunit of carbamoyl phosphate synthetase (AgCPA1)

c.976C > A

p.P326T

29

25

0.463

 VII

389,521

C

A

724.19

missense

AGOS_AGL165W

Proline oxidase (AgPUT1) a

c.104C > A

p.T35K

28

24

0.462

 VII

1,708,538

T

G

528.19

missense

AGOS_AGR357W

Asparaginase (AgASP1)

c.311 T > G

p.I104R

19

17

0.472

Purine, pyrimidine nulceotide metabolism

 I

558,677

G

A

532.19

missense

AGOS_AAR120C

Phosphoribosyl-glycinamide transformylase (AgADE8)

c.218C > T

p.T73I

16

16

0.500

 II

269,595

C

A

593.19

missense

AGOS_ABL070C

Xanthine-guanine phosphoribosyl transferase (AgXPT1)

c.232G > T

p.D78Y

29

22

0.431

 II

784,947

G

A

618.19

missense

AGOS_ABR204C

AMP deaminase (AgAMD1)

c.1553C > T

p.T518I

38

21

0.356

 III

132,857

C

A

773.19

missense

AGOS_ACL121C

Trifunctional C1-tetrahydrofolate synthase (AgADE3)

c.2067G > T

p.R689S

21

25

0.543

 III

214,069

A

T

441.19

missense

AGOS_ACL077C

Ribose-5-phosphate isomerase (AgRKI1)

c.17 T > A

p.I6N

29

17

0.370

 III

636,192

A

T

711.19

missense

AGOS_ACR160C

Nicotinate phosphoribosyltransferase (AgNPT1)

c.84 T > A

p.N28K

26

24

0.480

 III

654,234

C

T

690.19

missense

AGOS_ACR170C

Uridylate kinase (AgURA6)

c.152G > A

p.R51H

14

21

0.600

 III

715,325

G

T

697.19

missense

AGOS_ACR210C

Phosphoribosylaminoimidazole carboxylase (AgADE2)

C.926C > A

p.A309D

23

21

0.477

 III

832,220

C

T

957.19

missense

AGOS_ACR263C

Bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase (AgURA2)

c.2275G > A

p.E759K

19

31

0.620

 III

832,428

C

T

745.19

missense

AGOS_ACR263C

Bifunctional carbamoylphosphate synthetase/aspartate transcarbamylase (AgURA2)

c.2067G > A

p.M689I

27

23

0.460

 IV

580,072

G

T

461.19

missense

AGOS_ADL057W

Large subunit of ribonucleotide reductase (AgRNR1)

c.2520G > T

p.K840N

16

15

0.483

 V

792,520

T

C

1069.19

missense

AGOS_AER083C

5-phospho-ribosyl-1-pyrophosphate synthetase (AgPRS1)

c.488A > G

p.Q163R

24

33

0.578

 VI

896,312

A

T

502.19

missense

AGOS_AFR254C

Aminoimidazole ribotide synthetase and glycinamide ribotide synthetase (AgADE5,7)

c.1654 T > A

p.L552I

20

15

0.428

 VI

978,821

C

A

584.19

missense

AGOS_AFR297W

Myb-related transcription factor (AgBAS1)

c.905C > A

p.P302H

23

20

0.465

 VII

108,330

G

A

674.19

missense

AGOS_AGL320C

CTP synthase (AgURA7)

c.1361C > T

p.T454I

23

25

0.521

 VII

430,379

G

A

703.19

missense

AGOS_AGL146W

GTP cyclohydrolase (AgURC1)

c.1247G > A

p.G416D

27

21

0.438

 VII

1,072,826

T

C

377.19

missense

AGOS_AGR022C

Nicotinic acid mononucleotide adenylyltransferase (AgNMA1)

c.814A > G

p.T272A

26

13

0.333

Fatty acid metabolism

 I

564,702

G

A

769.19

missense

AGOS_AAR124C

Carnitine acetyl-CoA transferase (AgCAT2)

c.1736C > T

p.S579F

19

23

0.548

 IV

1,430,996

G

A

829.19

missense

AGOS_ADR403C

Oleate-activated transcription factor (AgOAF1 or AgPIP2)

c.1405C > T

p.R469C

22

26

0.542

 IV

1,436,329

G

T

757.19

missense

AGOS_ADR405C

Oleate-activated transcription factor (AgOAF1 or AgPIP2)

c.2170C > A

p.L724I

35

28

0.444

 IV

1,437,793

G

A

800.19

stop_gained

AGOS_ADR405C

Oleate-activated transcription factor (AgOAF1 or AgPIP2)

c.706C > T

p.Q236*

30

25

0.455

 IV

1,443,883

T

A

729.19

nonsense

AGOS_ADR408W

Acetyl-coA synthetase (AgACS1)

c.1128 T > A

p.Tyr376*

21

23

0.523

 V

794,683

T

C

631.19

missense

AGOS_AER085C

Beta subunit of fatty acid synthetase (AgFAS1) a

c.5837A > G

p.K1946R

23

19

0.452

 V

797,843

T

G

419.19

missense

AGOS_AER085C

Beta subunit of fatty acid synthetase (AgFAS1) a

c.2677A > C

p.K893Q

38

15

0.283

 V

797,858

C

A

1299.19

missense

AGOS_AER085C

Beta subunit of fatty acid synthetase (AgFAS1) a

c.2662G > T

p.D888Y

14

38

0.731

 VI

172,719

A

T

746.19

missense

AGOS_AFL138W

Alpha subunit of fatty acid synthetase (AgFAS2)

c.7A > T

p.M3L

19

26

0.578

 VI

175,856

C

A

656.19

missense

AGOS_AFL138W

Alpha subunit of fatty acid synthetase (AgFAS2)

c.3144C > A

p.F1048L

21

21

0.500

 VI

1,507,650

T

A

742.19

missense

AGOS_AFR592W

1-acyl-sn-glycerol-3-phosphate acyltransferase (AgSLC1)

c.832A > T

p.L278M

21

22

0.512

 VII

421,657

G

T

728.19

missense

AGOS_AGL148C

Acetyl-coA synthetase (AgACS2)

c.772C > A

p.Q258K

24

24

0.500

 VII

422,089

C

T

804.19

missense

AGOS_AGL148C

Acetyl-coA synthetase (AgACS2)

c.340G > A

p.A114T

25

26

0.510

 VII

913,244

C

A

553.19

missense

AGOS_AGL060W

3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase (AgFOX2)

c.814C > A

p.P272T

25

17

0.405

Heme biosynthesis

 I

380,486

A

C

573.19

missense

AGOS_AAR021W

Protoporphyrinogen oxidase (AgHEM14) a

c.617A > C

p.E206A

30

21

0.412

 II

203,080

T

C

1002.19

missense

AGOS_ABL104C

5-aminolevulinate synthase (AgHEM1)

c.1397A > G

p.E466G

18

31

0.633

 V

1,281,270

T

A

552.19

nonsense

AGOS_AER351W

Uroporphyrinogen-III synthase (AgHEM4)

c.762 T > A

p.Y254*

19

20

0.513

 VII

1,608,654

A

AG

453.15

frameshift

AGOS_AGR298C

S-adenosyl-L-methionine uroporphyrinogen III transmethylase (AgMET1)

c.1412dupC

p.A472fs

19

19

0.500

Other flavoprotein

 III

660,436

G

T

853.19

missense

AGOS_ACR175W

Sulfhydryl oxidase (AgERV2) a

c.441G > T

p.W147C

28

28

0.500

 IV

94,090

G

A

485.19

missense

AGOS_ADL348W

Endoplasmic oxidoreductin1 (AgERO1) a

c.386G > A

p.S129N

20

18

0.474

Folate metabolism

 VII

1,665,459

G

A

658.19

missense

AGOS_AGR330W

Aminodeoxychorismate lyase (AgABZ2)

c.208G > A

p.V70M

29

23

0.442

 VII

1,674,504

C

A

813.19

missense

AGOS_AGR335C

GTP-cyclohydrolase I (AgFOL2)

c.343G > T

p.D115Y

30

25

0.455

  1. These heterozygous mutations are a subset among all 1382 heterozygous mutations which are shown in Table S2
  2. aFlavoproteins
  3. *Translation stops here