Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea

Dörnte, Bastian; Peng, Can; Fang, Zemin; Kamran, Aysha; Yulvizar, Cut; Kües, Ursula

doi:10.1186/s40694-020-00105-0

Table 1 Identification of gene functions in de novo purine biosynthesis, formation of folates and THF-mediated one-carbon metabolism in C. cinerea OK130

From: Selection markers for transformation of the sequenced reference monokaryon Okayama 7/#130 and homokaryon AmutBmut of Coprinopsis cinerea

Steps in de novo purine synthesis and interlinked processes		Enzyme
Steps in de novo purine synthesis and interlinked processes		Name, GenBank accession number		C. cinerea OK130
Substrate—product	Enzymatic function	E. coli	S. cerevisiae	Broad model, classic name	Chromosomal location in OK130*
PRPP to PRA	Glutamine amidophosphoribosyltransferase (GPAT)	PurF, CAA30971	Ade4, P04046	CC1G_01222T0, likely Ade2	Chr_2:1,228,139–1,230,457
PRA to GAR	Glycinamide ribonucleotide synthase (GARS)	PurD, CAA36213	N-terminal domain of bifunctional Ade5,7, NP_011280	CC1G_01782T0, N-terminal domain of bifunctional Ade8	Chr_1:2,548,109–2,550,858
GAR to FGAR	Phosphoribosylglycinamide formyltransferase (GART)	PurN, P08179	Ade8, NP_010696	CC1G_04353T0, potentially Ade4	Chr_1:715,850–716,603
GAR to FGAR	[Bacterial alternative: formate-dependent phosphoribosylglycinamide formyltransferase]	PurT, NP_416363	–	–	–
FGAR to FGAM	Phosphoribosylformylglycinamidine synthase (FGAMS)	PurL, THH53207	Ade6, NP_011575	CC1G_11804T0, potentially Ade4	Chr_6:3,409,097–3,413,188
FGAM to AIR	Aminoimidazole ribonucleotide synthase (AIRS)	PurM, THH44093	C-terminal domain of bifunctional Ade5,7, NP_011280	CC1G_01782T0, C-terminal domain of bifunctional Ade8	Chr_1:2,548,109–2,550,858
AIR to CAIR	5-(Carboxyamino)imidazole ribonucleotide synthase + 5-(carboxyamino)imidazole ribonucleotide mutase (AIR carboxylase)	PurK + PurE, NP_415055, NP_415056	Fused Ade2, P21264	CC1G_11091T0, fused Ade1	Chr_5:473,822–471,864
CAIR to SAICAR	Phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICARS)	PurC, NP_416971	Ade1, NP_009409	CC1G_05887T0	Chr_7:2,536,570–2,535,540
SAICAR to AICAR	Adenylosuccinate lyase	Bifunctional PurB, THI73349	Bifunctional Ade13, NP_013463	CC1G_08733T0, bifunctional Ade5	Chr_10:936,450–934,462
AICAR to FAICAR	AICAR transformylase	Bifunctional PurH, NP_418434	Bifunctional Ade16, NP_009409 or isoenzyme Ade17, NP_013839	CC1G_08365T0	Chr_7:2,467,163–2,464,958
FAICAR to IMP	IMP cyclohydrolase	Bifunctional PurH, NP_418434	Bifunctional Ade16, NP_009409 or isoenzyme Ade17, NP_013839	CC1G_08365T0	Chr_7:2,467,163–2,464,958
IMP to SAMP	Adenylosuccinate synthase	PurA, NP_418598	Ade12, NP_014179	CC1G_10072T0	Chr_2:407,487–405,875
SAMP to AMP	Adenylosuccinate lyase	Bifunctional PurB, THI73349	Bifunctional Ade13, NP_013463	CC1G_08733T0, bifunctional Ade5	Chr_10:936,450–934,462
GTP to DHNTP	GTP cyclohydrolase	FolE, NP_416658	Fol2, P51601	CC1G_14672T0	Chr_5:2,160,832–2,161,846
DHNTP and PABA to 7,8-DHP to DHF	Trifunctional dihydropteroate synthase/dihydrohydroxymethylpterin pyrophosphokinase/dihydroneopterin aldolase	FolB + FolK + FolP, NP_417530, 3IP0_A, NP_417644	Fused Fol1, NP_014143	CC1G_15556T0, fused	Chr_6:783,810–781,706
DHP to DHF	Dihydrofolate synthase/ folylpolyglutamate synthase	FolC, P08192	Fol3, NP_013831	CC1G_00421T0	Chr_2:3,461,586–3,463,459
DHP to DHF	Dihydrofolate synthase/ folylpolyglutamate synthase	FolC, P08192	Met7, NP_014884	CC1G_04850T0	Chr_5:1,857,755–1,855,944
DHF to THF	Dihydrofolate reductase	FolA, 4GH8_A	Dfr1, P07807	CC1G_012670T0, potentially Ade9	Chr_1:1,571,610–1,572,294
5,10-Methylene-THF to 10-formyl-THF	NADP-dependent methylentetrahydrofolate cyclohydrolase, methylenetetrahydrofolate dehydrogenase	Bifunctional FolD, 5O22_D	N-terminal domain of trifunctional Ade3, NP_011720	CC1G_13910T0, N-terminal domain of trifunctional enzyme	Chr_2:1,522,272–1,525,659
5,10-Methylene-THF to 10-formyl-THF	NAD⁺-dependent methylenetetrahydrofolate dehydrogenase	Bifunctional FolD, 5O22_D	Mtd1, Q02046	CC1G_01428T0	Chr_5:2,438,251–2,463,749
10-Formyl-THF to formate and THF	Formyltetrahydrofolate deformylase	PurU, THH46545	–	–	–
3-PHP to phosphoserine	O-Phospho-L-serine:2-oxoglutarate aminotransferase	SerC, THI65673	Ade9 = Ser1, NP_014827	CC1G_11497T0	Chr_2:2,589,569–2,588,293
L-serine to glycine + THF to 5,10-CH₂-THF	Glycine/serine hydroxymethyltransferase	SHMT, 3G6M_A	SHM2, NP_013159	CC1G_10328T0	Chr_6:1,087,903–1,089,686

*Assigning classical linkage groups [50,51,52] and adenine auxotrophies [49, 50] to the new chromosome classification in OK130 sorted after sequence length [20]: Chromosome 1 = classical linkage group I with A mating type locus, ade8 (with function prior to AIR ring closure [49]) and, 9 cM away from the A mating type locus, ade9 [51, 52] which appears to function as a regulatory enzyme rather than within the direct de novo pathway of purine biosynthesis [49] and might therefore be a dihydrofolate reductase gene for THF production located 752 kb downstream to A43β (recombination rate is then 83 kb/cM) with potential cross-pathway effects between de novo purine biosynthesis and THF-mediated C1, histidine and methionine metabolisms [42, 46]. A gene with potential GART function (step 3 in de novo purine biosynthesis) as one candidate for the unmapped gene ade4 functioning in the pathway prior to imidazole ring closure [49, 52] is present 1932 kb downstream of A43β, closer to the telomere. Chromosome 2 = classical linkage group III with trp1, trp3, ade2 (with function prior to AIR ring closure [49]) and ade12 (0.2 cM apart from ade2 [52] = an estimated distance of 5.6 to 6.6 kb [20, 33] which could point to CC1G_01221T0 for S-adenosylmethionine synthase at position Chr_2:1,226,385–1,227,850 or CC1G_01223T0 for diadenosine polyphosphate hydrolase and related proteins of the histidine triad (HIT) family at position Chr_2: 1,231,397–1,230,670 as potential candidates for ade12). Chromosome 3 = classical linkage group G with trp2 [51, 52], pcc1 [33], and, 16 cM distal to trp2 [51, 52], ade3 unidentified here with a function prior to AIR ring closure [49]. Chromosome 5 = classical linkage group IV with ade1 with CAIR synthase function [49]. Chromosome 6 (with a gene for a FGAMS function as another ade4 candidate) and chromosome 7 = classical linkage groups unclear. Chromosome 10 = classical linkage group II with B mating type locus, the bifunctional ade5 with adenylosuccinate lyase function [49], ad/his-1 and ad/his-2 which are likely ade5 alleles with cross-pathway effects on histidine biosynthesis via effects of the regulatory metabolite AICAR [46, 49]. Classical linkage groups V and VI with ade6 and an ad/met locus, respectively [51, 52] = new chromosome numbers unclear

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