Strains and media
A.nidulans NID191 (argB2, pyrG89, veA1, nkuA-trS::AFpyrG, IS1::PgpdA-TtrpC::argB) [18] and NID495 (argB2, pyrG89, veA1, nkuA-trS::AFpyrG, ΔimdA::argB::mpaF) were grown on Minimal Medium (MM) containing 1% glucose, 10 mM NaNO3, 1 × salt solution [19], and 2% agar for solid media. MM was supplemented with 10 mM uridine, 10 mM uracil, and 4 mM L-arginine when necessary. P. brevicompactum IBT 23078 was grown on Czapek yeast autolysate (CYA) agar at 25°C. CYA: 5.0 g/l Yeast extract (Difco); 15 g/l agar; 35 g/l Czapek Dox broth (Difco); 10 mg/l ZnSO4·7H2O; 5 mg/l CuSO4·5H2O. The pH of the medium was adjusted to 6.5 by using NaOH/HCl.
Generating expression construct
Amplification of DNA by PCR was performed using proof-reading PfuTurbo® Cx Hotstart polymerase (Stratagene) in 50 μl according to the manufacturer's instructions. The reaction mixtures were heated to 95°C for 2 min followed by 30 cycles at 95°C for 30 s, 58°C for 30 s, and 72°C for 3 min. A fragment containing the fungal selection marker argB was amplified from the expression vector pU1111 [18] with primers BGHA71 and BGHA72 and cloned into MfeI/SbfI digested expression vector pU0002 [18] resulting in construct pHC1. A 2689 bp fragment containing mpaF including mpaF promoter and terminator was amplified using primers BGHA125 and BGHA132 from P. brevicompactum IBT 23078 gDNA and cloned into the KpnI/AsiSI site of pHC1 resulting in pHC2. The flanking regions of imdA (AN10476, A. nidulans IMPDH) were amplified using primer pairs BGHA168/BGHA169 and BGHA170/BGHA171. pHC3 was created by USER cloning these fragments into pHC2 following the USER cloning method previously described [18, 20]. All plasmids were propagated in Escherichia coli strain DH5α. All primers used in this study are listed in Table 2.
A. nidulansstrain construction
Protoplasting and gene-targeting procedures were performed as described previously [21, 22]. 5 μg pHC3 was digested with NotI to liberate the gene targeting substrate, which was used for transformation of NID3 [23]. Transformants containing the desired gene targeting event were verified by PCR with primer-pairs BGHA98/BGHA256HC and BGHA255HC/BGHA225 using Taq-polymerase (Sigma-Aldrich) on genomic DNA obtained from streak purified transformants extracted using the FastDNA® SPIN for Soil Kit (MP Biomedicals, LLC).
MPA treatment of fungi
Spores from A. nidulans NID191 and A. nidulans NID495 were harvested. 10-fold dilution series was performed on freshly made MM-plates with 0, 5, 25, 100, 200 μg MPA/ml (Sigma). All plates contained 0.8% (v/v) methanol. Relative growth of the strains was assessed by visual inspection.
Degenerate PCR
An alignment with the DNA sequence (including introns) of the genes encoding P. brevicompactum IMPDH-B, A. nidulans IMPDH-A, P. chrysogenum IMPDH-A, P. chrysogenum IMPDH-B and Aspergillus fumigatus IMPDH-A was created by using ClustalW [24]. The ClustalW algorithm was accessed from the CLC DNA workbench 5 (CLC bio, http://www.clcbio.com/) with the following parameters: 'gap open cost = 20.0', 'gap extension cost = 1.0', and 'end gap cost = free'. The alignment was used to design degenerate primers to amplify either IMPDH-A like genes (BGHA236HC/BGHA246HC) or IMPDH-B like genes (BGHA240 HC/BGHA241 HC). The primer-set BGHA343/BGHA344 was used to amplify the β-tubulin sequence. Genomic DNA from P. brevicompactum IBT 23078 and four other fungi from Penicillium subgenus Penicillium were extracted using the FastDNA® SPIN for Soil Kit (MP Biomedicals, LLC). Touch-down PCR was carried out using Phusion polymerase (Finnzymes) and the following program. An initial denaturation cycle at 98°C for 2 min; followed by 35 cycles at 98°C for 30 s, an annealing step ranging from 61°C (first cycle) to 54°C (last cycle) for 30 s, and extension at 72°C for 45 s. PCR mixture was made according to the manufacture's instructions. PCR products generated by degenerate PCR were purified from agarose gels using illustra™ DNA and Gel band purification kit (GE Healthcare). Sequencing of purified PCR products was performed by StarSeq (Germany).
Cladistic analysis
BLASTx search was performed with standard settings: 'blastp algorithm', 'expect threshold = 10', 'word size = 3', 'max matches in query range = 0', 'matrix = BLOSUM62', 'gap open cost = 11', 'gap extension cost = 1', and no filters were used. Alignment of DNA coding regions were performed with ClustalW [24] as implemented in the CLC DNA workbench 5 (CLC bio, http://www.clcbio.com/) and by using the following parameters: 'gap open cost = 20.0', 'gap extension cost = 1.0', and 'end gap cost = free'. A cladogram was constructed with the same software using the neighbour-joining method and 1000 bootstrap replicates [25]. The DNA sequence of IMPDH and β-tubulin from selected fungi with sequenced genome were retrieved from NCBI. These included IMPDH sequence from A. nidulans [GenBank:ANIA_10476], Aspergillus terreus [GenBank:XM_001218149], Aspergillus niger [GenBank:XM_001391855], P. chrysogenum putative IMPDH-A coding gene, [GenBank:XM_002562313], putative IMPDH-B coding gene [GenBank:XM_002559146], P. marneffei [GenBank:XM_002151867]. β-tubulin sequences from A. nidulans [GenBank:XM_653694], A. terreus [GenBank:XM_001215409], A. niger [GenBank:XM_001392399], P. chrysogenum [GenBank:XM_002559715] and P. marneffei [GenBank:XM_002151381]. The MPA gene cluster sequence from P. brevicompactum, which contains the IMPDH-B sequence (mpaF) is available from GenBank under accession number [GenBank:HQ731031].
Protein alignment
Amino acid sequences were aligned with ClustalW [24] as implemented in the CLC DNA workbench 5 (CLC bio, http://www.clcbio.com/) by using the following parameters: 'gap open cost = 20.0', 'gap extension cost = 1.0', and 'end gap cost = free'.
Nucleotide sequence accession numbers
All sequences obtained via degenerate PCR were submitted to GenBank (Table 1). Penicillium bialowiezense β-tubulin [GenBank:JF302653], putative IMPDH-A coding gene [GenBank:JF302658], putative IMPDH-B coding gene [GenBank:JF302662], P. brevicompactum β-tubulin [GenBank:JF302653], imdA [GenBank:JF302657], Penicillium carneum β-tubulin [GenBank:JF302650], putative IMPDH-A coding gene [GenBank:JF302656], putative IMPDH-B coding gene [GenBank:JF302660], Penicillium paneum β-tubulin [GenBank:JF302651], putative IMPDH-A coding gene [GenBank:JF302654], putative IMPDH-B coding gene [GenBank:JF302661], Penicillium roqueforti β-tubulin [GenBank:JF302649], putative IMPDH-A coding gene [GenBank:JF302655], putative IMPDH-B coding gene [GenBank:JF302659].