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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
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
[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
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
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
NAD+-dependent methylenetetrahydrofolate dehydrogenase 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
  1. *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