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Table 3 Mutations in methanol-adapted P. pastoris clones

From: Implications of evolutionary engineering for growth and recombinant protein production in methanol-based growth media in the yeast Pichia pastoris

Strain

chr

Position

Type

Ref

Alt

Gene/locus

Effect

Y250 1c

chr. 1

1,477,448

SNP

G

A

Upstream of PAS_chr1-4_0035 (SPC110)

 

chr. 2

1,572,979

SNP

C

G

PAS_chr2-1_0445 (Zn_cluster)

G142 to R142

chr. 4

237,622

SNP

G

A

PAS_chr4_0821 (AOX1)

W190 to stop

chr. 4

1,574,048

SNP

G

A

PAS_chr4_0108 (YCT1) weak homology

A64 to T64

Y250 2c

chr. 2

1,573,676

SNP

G

T

PAS_chr2-1_0445 (Zn_cluster)

Upstream of gene

chr. 3

627,999

SNP

C

A

PAS_chr3_0836 (ECM22)

W95 to C95

Y250 3a

chr. 3

313,093

SNP

G

T

PAS_chr3_1001 (TUP1)

C285 to F285

chr. 3

628,000

SNP

C

A

PAS_chr3_0836 (ECM22)

W95 to L95

Y250 3c

chr. 2

2,100,561

SNP

C

T

PAS_chr2-1_0162 (SLN1)

R336 to K336

chr. 4

238,206

indel

AAGACAAGCC

A

PAS_chr4_0821 (AOX1)

3 amino acid deletion after E385

M250 1a

chr. 2

1,060,279

SNP

G

A

PAS_chr2-1_0701 (PKH3)

G354 to D354

chr. 3

384,863

SNP

C

T

PAS_chr3_0956 (RRP45)

G206 to D206

chr. 3

575,412

SNP

C

T

Downstream of PAS_chr3_1229 (SEC5) and downstream of PAS_chr3_0322 (tRNA-Thr7)

–

M250 2c

chr. 1

1,737,822

SNP

A

C

PAS_chr1-4_0181 (NMA1)

Q118 to H118

chr. 4

238,443

SNP

G

A

PAS_chr4_0821 (AOX1)

R464 to K464

M250 3b

chr. 3

1,260,818

SNP

G

A

PAS_chr3_0512 (PAH1)

C304 to Y304

chr. 4

238,309

SNP

C

G

PAS_chr4_0821 (AOX1)

F419 to L419

  1. Mutations were identified by WGS (Illumina mi-Seq). The type of mutation (Single nucleotide polymorphism—SNP or insertion/deletion—indel) as well as the DNA sequence of the ancestral strain (ref) and the sequence of the evolved clone (alt) is shown. Chromosomal position (chr) and nucleotide position on contigs is shown with respect to the P. pastoris CBS7435 reference sequence