Identification and Functional Analysis of Pheromone and Receptor Genes in the B3 Mating Locus of Pleurotus eryngii
et al. (2014) Identification and Functional Analysis of Pheromone and Receptor Genes in the B3 Mating Locus of
Pleurotus eryngii. PLoS ONE 9(8): e104693. doi:10.1371/journal.pone.0104693
Identification and Functional Analysis of Pheromone and Receptor Genes in the B3 Mating Locus of Pleurotus eryngii
Kyung-Hee Kim 0
Young Min Kang 0
Chak Han Im 0
Asjad Ali 0
Sun Young Kim 0
Hee-Jeong Je 0
Min-Keun Kim 0
Hyun Su Rho 0
Hyun Sook Lee 0
Won-Sik Kong 0
Jae-San Ryu 0
Stefanie Po ggeler, Georg-August-University of Go ttingen Institute of Microbiology & Genetics, Germany
0 1 Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services , Jinju , Republic of Korea, 2 Herbal Medicine Research Division, Korea Institute of Oriental Medicine (KIOM), Daejeon, Republic of Korea, 3 Department of Microbiology, Gyeongsang National University , Jinju , Republic of Korea, 4 Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration , Eumsung , Republic of Korea
Pleurotus eryngii has recently become a major cultivated mushroom; it uses tetrapolar heterothallism as a part of its reproductive process. Sexual development progresses only when the A and B mating types are compatible. Such mating incompatibility occasionally limits the efficiency of breeding programs in which crossing within loci-shared strains or backcrossing strategies are employed. Therefore, understanding the mating system in edible mushroom fungi will help provide a short cut in the development of new strains. We isolated and identified pheromone and receptor genes in the B3 locus of P. eryngii and performed a functional analysis of the genes in the mating process by transformation. A genomic DNA library was constructed to map the entire mating-type locus. The B3 locus was found to contain four pheromone precursor genes and four receptor genes. Remarkably, receptor PESTE3.3.1 has just 34 amino acid residues in its C-terminal cytoplasmic region; therefore, it seems likely to be a receptor-like gene. Real-time quantitative RT-PCR (real-time qRT-PCR) revealed that most pheromone and receptor genes showed significantly higher expression in monokaryotic cells than dikaryotic cells. The pheromone genes PEphb3.1 and PEphb3.3 and the receptor gene PESTE3.3.1 were transformed into P5 (A3B4). The transformants were mated with a tester strain (A4B4), and the progeny showed clamp connections and a normal fruiting body, which indicates the proposed role of these genes in mating and fruiting processes. This result also confirms that PESTE3.3.1 is a receptor gene. In this study, we identified pheromone and receptor genes in the B3 locus of P. eryngii and found that some of those genes appear to play a role in the mating and fruiting processes. These results might help elucidate the mechanism of fruiting differentiation and improve breeding efficiency.
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Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its
Supporting Information files.
Funding: This work was supported by a grant from the Next-Generation BioGreen 21 Program (No. PJ00821602014), Rural Development Administration,
Republic of Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This study was
designed and started by the corresponding author who is an employee of the GNARES. GNARES is a non-profit organization by the Gyeongnam government.
Competing Interests: The authors have declared that no competing interests exist.
Pleurotus eryngii is a white rotter of wood and the only species
of its genus that grows on the living stems and roots of umbellifers
[1]. Pleurotus sp. mushrooms have rapidly emerged as one of the
most popular cultivated edible mushrooms [2]. In particular, P.
eryngii, the king oyster mushroom, has recently become a major
cultivated mushroom in Korea, China, and Japan because of its
good taste, flavor, and nutritional factors. As the consumption of
P. eryngii increases, new strains need to be bred with improved
traits. However, mating incompatibility occasionally limits the
efficiency of breeding programs in which crossing within
locisharing strains or backcrossing strategies are employed. When a
specific strain is required to have a single useful trait such as
disease resistance, backcrossing is considered to be the best
method for introducing the trait into the recurrent parent. In a
backcross, however, only 25% of all possible combinations are
compatible in tetrapolar mushroom fungi. Therefore, a breeder
cannot evaluate the traits of incompatible hybrids. Although the
mating-type systems of several edible mushrooms have been
examined [3,4], most current knowledge has been derived from
studies of model mushrooms such as Schizophyllum commune and
Coprinopsis cinerea [5,6]. Thus, the mechanisms controlling the
mating system in P. eryngii require further examination to
improve the efficiency of P. eryngii breeding programs and to
address its basic biology.
P. eryngii uses tetrapolar heterothallism as a part of its
reproductive process. In a tetrapolar system, genes in the A locus
encode a homeodomain transcription factor, whereas the B locus
encodes both peptide pheromones and receptors (for review, see
[7]). The structure of the B locus differs in different species. For
example, in Ustilago maydis, a single locus contains one receptor
and one pheromone, whereas S. commune possesses two
functionally independent sub-loci containing one receptor and
several pheromones [6]. In C. cinerea, a common structure is three
sub-groups, with one receptor and multiple pheromones in each
sub-group [5,8,9]. However, recent genome sequence reports have
shown that the matB locus is much more complex than previously
realized [4,10,11]. Some receptors referred to as receptor-like were
found at loci distinct from the known mating loci, and until now,
whether the receptor-like gene(s) had a role in the mating process
was unclear.
Previously, sixteen alleles at locus A and 15 alleles at locus B
were identified from the 12 strains of P. eryngii, and the
B3specific SCAR primers discriminating the B3 locus were
developed based on the RAPD (random amplified polymorphic
DNA)-derived sequence, which was specifically amplified from B3
locus-harboring strains [12]. In this study, we isolated the
matingtype B3 locus of P. eryngii using a PCR-based library screening
method with a specific marker. A physical gene map of the region
controlling mating type with both flanking regions is presented
here. The expression patterns of the pheromone and receptor
genes were analyzed in both monokaryotic and dikaryotic mycelia.
Functional analyses of the pheromone and receptor genes were
performed by Agrobacterium-based transformation. To the best of
our knowledge, this study is the first functional analysis of
pheromone and receptor genes in edible mushrooms.
Materials and Methods
Fungal strains and growth conditions
Two monokaryon strains, P5 and P6 (Table 1), were obtained
from the dikaryotic mushroom KNR2312 using de-dikaryotization
through protoplast homogenization [12] and has been deposited at
Korean Culture Center of Microorganisms as KCCM90103 (P5)
and KCCM90104 (P6). Cultured mycelia were obtained by
inoculating 34 pieces of 161 cm2 MCM (mushroom complete
medium: 0.2% peptone, 0.2% yeast extract, 2.0% glucose, 0.05%
MgSO4?7H2O, 0.05% K2HPO4, and 0.046% KH2PO4) agar with
mycelia in MCM broth, followed by incubation for 14 days at
25uC and 120 rpm. After incubation, the mycelia were filtered
with sterile Whatman filter paper No. 41 and lyophilized before
grinding with a sterile mortar. For long-term storage, strains were
cultivated on slant medium of MCM, filled with sterile mineral oil
(Sigma, St. Louis, MO, USA), and placed at 4uC until further use.
Fosmid library construction and screening
High-molecular-weight P6 DNA was purified using the
Neurospora SDS buffer method as described previously [13], with
minor modifications. First, 1 g of lyophilized mycelium powder
was added slowly to 10 mL of Neurospora SDS buffer (0.15 M
NaCl, 0.1 M EDTA, and 2% SDS, pH 9.5) in a 125-mL flask.
Second, 0.5 mL of 2 mg/mL proteinase K (Fermentas, Waltham,
MA, USA) solution was added, followed by incubation at 37uC for
up to 24 h with gentle agitation; 10 mL of sterile water was added
to the slurry, and the cellular debris was removed by centrifugation
at 15,3446 g. The supernatant was extracted 35 times with
phenol saturated with Tris-HCl (pH 8.0) and once with
watersaturated chloroform. DNA was precipitated by adding 2.5
volumes of absolute ethanol and removed with a sterile glass rod
into a 1.5-mL centrifuge tube. After briefly air-drying, 1 mL of
sterile TE buffer (10 mM Tris-EDTA, pH 8.0) containing 30 mg/
mL RNase A (Qiagen, Hilden, Germany) was added. After
incubation at 37uC for several hours with occasional mixing by
inversion, the genomic DNA (gDNA) solution was stored at 5uC
until use. The gDNA was used to construct a library using the
CopyControl Fosmid library production kit (Epicentre
Biotechnologies, Madison, WI, USA) according to the manufacturers
instructions.
Screening of clones harboring the mating-type region from the
fosmid library was conducted using direct PCR; 25 clones were
pooled in LB+chloramphenicol (12.5 mg/mL) using sterile
toothpicks, followed by incubation for 24 h at 37uC and 120 rpm.
Plasmid DNA was extracted with the GeneAll EXPREP plasmid
SV MINI Kit (GeneAll Biotechnology, Seoul, Korea) according to
the manufacturers protocol. The B3-specific SCAR primer set
(Table S1) was used to specifically amplify strains harboring the B3
locus. The thermal cycling reaction was conducted in 20-mL
volumes using GoTaq (Promega, Madison, WI, USA) in a Dyad
thermal cycler (Bio-Rad, Hercules, CA, USA) with the following
parameters: initial denaturation at 94uC for 4 min, followed by 35
cycles of denaturation at 94uC for 1 min, annealing at 65uC for
1 min, and extension at 72uC for 1 min 30 s. Two clones carrying
the B3 locus were isolated by further PCR with individual clones
displaying the SCAR marker band.
Fosmid sequencing and data analysis
To isolate fosmid DNA, a QIAprep 96 Turbo Miniprep kit
(Qiagen) was used. Two fosmids containing mating type-specific
regions were sequenced by the shotgun method. Purified DNA was
sheared into random fragments. After end repair and size
fractionation, a DNA fragment was ligated into pUC118/HincII
(Takara, Shiga, Japan) and then sequenced using the Big-Dye
cycle sequencing kit and an ABI3700 or 3730xl DNA analyzer
(Applied Biosystems, Foster City, CA, USA). Base calling, contig
assembly, and editing were conducted using the phred/phrap/
consed package (University of Washington, USA).
Genes in the mating type-specific region were identified using
DNAMAN (Lynnon Biosoft, Quebec, Canada) and FgeneSH
(Softberry, http://linux1.softberry.com/berry.phtml) with a C.
cinerea model; the BLASTX function of the NCBI database was
used to identify open reading frames (ORFs) and genes. ORFs
with small peptide sequences (10100 amino acids) were manually
curated to identify the CaaX motif in the C-terminus and were
compared with known sequences in the NCBI database using
BLAST to identify small genes such as those encoding
pheromones. Additionally, the characterization and identification of
putative mating-type genes were manually curated using the NCBI
BLASTX and Protein BLAST databases (USA). Transmembrane
motif analysis of receptor genes from P. eryngii and other receptor
sequences retrieved from GenBank were predicted using
PHOBIOUS (http://phobius.sbc.su.se/), HMMTOP (http://www.
enzim.hu/hmmtop/), and TMHMM (http://www.cbs.dtu.dk/
services/TMHMM/) software. Phylogenetic analysis was
performed according to a previous report [4]. The receptor sequences
of S. commune, P. djamor, C. cinerea, and U. maydis, available in
the NCBI GenBank database, were used with previously reported
accession numbers [14]. The receptor sequence of Laccaria bicolor
was obtained from a genome site at the Joint Genome Institute
(JGI: http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html)
according to an accession number listed in a previous report [15].
The U. maydis PRA2 was used as an out-group. Protein sequences
were aligned using ClustalW 1.64, and maximum likelihood
analyses were conducted to estimate phylogenetic relationships
using RAxML 7.04. Branch support was inferred from 1000
repetitions of nonparametric bootstrapping.
RNA extraction and cDNA synthesis
Total RNA from KNR2312 (dikaryon) and P6 (monokaryon) of
P. eryngii were extracted from lyophilized mycelia using modified
protocols for TRIzol (Invitrogen, Carlsbad, CA, USA) and the
dikaryon, P5 (A4B3)+P6 (A3B4)
Note (reference)a
aProtoclones were prepared from the homogenization of protoplast [12]; meiotic spores were derived from meiotic recombination.
doi:10.1371/journal.pone.0104693.t001
RNeasy Mini Kit (Qiagen). After extracting total RNA, the
RNase-Free DNase set (Qiagen) was used to eliminate gDNA
contamination. Both sets of RNA were evaluated for quantity and
quality using a NanoDrop Spectrophotometer ND-1000
(NanoDrop Technologies, Wilmington, DE, USA). The remaining
samples were flash-frozen in liquid nitrogen and stored at 270uC
until use. Then, the isolated RNA was transcribed into cDNA
using a reverse transcription system with oligo-dT primer
(Promega). The converted cDNA was used for both sequence
verification and gene expression analysis. Four putative
pheromone precursor genes and 4 receptor genes were amplified from
the P6 cDNA using specific primers (deposited with the cDNA
sequences in GenBank). PCR products purified from the gel using
the QIAquick PCR Purification Kit (Qiagen) were transformed
into Escherichia coli plasmids using the TOPO cloning kit for
sequencing (Invitrogen) and the pGEM-T Easy Vector (Promega).
Plasmids in transformed E. coli were isolated using Hybrid-Q
(GeneAll Biotechnology) and prepared for sequencing by the
GenoTech Company (GenoTech Corp., Daejeon, Korea). After
qualifying the cDNA sequences, the four pheromone and four
receptor gene sequences, along with their primers for
amplification, were deposited in GenBank under the following accession
numbers: KC879316 for PESTE3.3.1, KC879317 for
PESTE3.3.2, KC879318 for PESTE3.3.3, KC879319 for
PESTE3.3.4, KC879320 for PEphb3.1, KC879321 for
PEphb3.2, KC879322 for PEphb3.3 and KC879323 for
PEphb3.4.
Analysis of gene expression by real-time qRT-PCR
Real-time qRT-PCR (CFX96, Bio-Rad) was performed using
KNR2312 (dikaryon) and P6 (monokaryon) to quantify the
expression of the 4 receptor genes and the 4 pheromone genes.
The primer pairs used for real-time qRT-PCR amplification of the
internal fragments of these genes are listed in table S2. Synthesized
cDNA (100 ng/ul) was used as a template for real-time qRT-PCR.
Real-time qRT-PCR was run as a duplex, in which one duplex
partner was used as the internal standard gene (18S rRNA of P.
eryngii), with the accession number FJ572254. The other duplex
partner was one of the 4 pheromone genes or 4 receptor genes.
The Rotor-Gene Q (QIAGEN, Hilden, Germany) was used for
the reaction as follows: an initial step at 95uC for 5 min, followed
by 39 cycles at 95uC for 5 s and 62uC for 10 s. One microlitre of
cDNA was amplified in a 25.0 ml reaction using Rotor-Gene
SYBR Green PCR kit master mix (Qiagen) with each primer at a
final concentration of 500 nmol/l. The Ct value of each gene was
normalized for differences in the amount of total cDNA in the
reaction using the 18S rRNA of P. eryngii as an internal standard
control. The normalized values for the pheromones and receptors
were then calibrated to the value for the monokaryon (P6), which
was assigned a value of 1, by the standard curve method using the
Rotor-Gene software (QIAGEN). All assays were performed in
triplicate. The statistical analysis of the gene expression was
performed by one-way analysis of variance (ANOVA) and Tukeys
test (alpha = 0.05) using the SAS program (SAS 9.1, SAS Institute
Inc., Cary, NC, USA).
Agrobacterium-mediated transformation
Genomic fragments containing a 1-kb upstream fragment for
the promoter and a 0.7-kb downstream fragment for the
terminator of two pheromone genes (PEphb3.1 and PEphb3.3)
and one receptor gene (PESTE3.3.1) were ligated into the Sal I
site of the pBGgHg binary vector carrying the hygromycin B
resistance gene (hph) [16]. Although this vector has the Agaricus
bisporus gpdII promoter for expression, we adapted each genes
own promoter and terminator. Recombinant pPEphb3.1,
pPEphb3.3 and pPESTE3.3.1 were introduced into
Agrobacterium tumefaciens AGL-1 and transformed into P. eryngii P5 as
described previously [17], with minor modifications.
Agrobacterium induction medium (IM) culture and mycelium (harvested from
colonies grown on MCM and homogenized for 30 s) culture
(100 mL each) were co-cultivated, followed by treatment with
sonication for 3 min and vacuum for 30 min, and then inoculated
overnight at 25uC in darkness.
Putative transgenic lines showing hygromycin resistance were
confirmed by PCR using specific primers (Table S1) as described
previously [17]. The SSR45 primer set showing co-dominant
polymorphism on KNR2312, P5 and P6 [18] was used to confirm
the monokaryon or dikaryon (hybrid) P5 transformants.
Test crossing and fruiting
To verify the biologically active transformed genes,
transformants were crossed with monokaryotic tester strains harboring 4
different mating types (Table 1). Crosses between monokaryotic
cultures were performed by placing actively growing mycelial
plugs approximately 1 cm apart in the center of a Petri dish of
MCM [12]. The mycelia were screened for clamp connections
under 406 magnification at the growing boundary lines of either
side of the interacting strains. Fruiting tests for all crosses were
performed as described by Ryu et al. [12].
Isolation and sequence analysis of the mating
type-specific region
The B3 mating-type locus was isolated using PCR amplification
with the B3-specific SCAR primer sets from a genomic library
(more than 8,850 fosmid clones) constructed from KNR2312.
DNA inserts of P. eryngii in cPE932-22 and cPE1462-8 were
subcloned and sequenced using the shotgun method. Only the
subclones containing 24 kb of DNA were sequenced in the
forward and reverse directions using universal sequencing primers.
The sequence data were edited, aligned, and merged using
software. The sequence sizes in cPE932-22 and cPE1462-8 were
40.4 kb and 32.7 kb, respectively, and the total size of the
sequences in the two clones was approximately 60 kb, excluding
overlapping sequences. The SCAR marker [12] is located at the
center of the locus (Figure 1), where the sequences from the two
clones overlapped; thus, the two fosmid clones likely covered the
complete B3 locus.
Identification of the pheromone and pheromone
receptor genes on the B3 locus
ORFs and their putative functions were identified in the entire
60-kb B3 locus using BLASTX and FgeneSH (Softberry). A
physical map of the B3 locus is shown in Figure 1. The four
pheromone and four receptor genes in the B3 locus of KNR2312
spanned less than 12 kb. To verify the existence of subloci in
KNR2312, flanking sequences were subjected to TBLASTX and
contained additional open reading frames, but none of the
encoded proteins showed sequence similarity to known
pheromone or receptor genes (Table 2). However, we did not exclude th
possibility that there are B3 subloci in KNR232 even though there
was no non-parental B locus in the 98 meiotic monokaryons from
KNR2312 (12).
The CLA4, AKOR1, and AKOR2 genes, which are located
next to or near the B mating locus in Pleurotus djamor [14], were
not identified at 226.3 to +21.7 kb relative to the B3 region
(Table 2). Instead, cytochrome P450 (CYP) and reverse
transcriptase-RNase H-integrase (pol) was identified upstream of the B3
region.
All receptors contain a 7-transmembrane (TM) motif with
varying amino acid lengths: 328 for PESTE3.3.1, 420 for
PESTE3.3.2, 558 for PESTE3.3.3, and 470 amino acids for
PESTE3.3.4. Alignment analysis revealed that the identities
between PESTE3.3.1 and PESTE3.3.2 were 64.8% (full length)
and 83.4% (compared with the truncated PESTE3.3.2 [326 amino
acids], which did not include the non-corresponding C-terminal
sequence of PESTE3.3.1). Comparison analysis showed that the
C-terminal cytoplasmic domains varied in length across the genus,
species, and even within a locus. PESTE3.3.1 has only 34 amino
acid residues in its C-terminal cytoplasmic domain (Table S3). The
C-terminal cytoplasmic domain of S. commune was relatively long
(326344 amino acids), whereas those of U. maydis and Lentinus
edodes were 54 and 2635 amino acids long, respectively.
Using maximum likelihood algorithms, the molecular
phylogenetic analysis of receptors from P. eryngii and several mushroom
fungi, which are available in GenBank (http://www.ncbi.nlm.nih.
gov/genbank/), showed that two distinct clades were grouped with
basal STE-like proteins such as U. maydis PRA2 (Figure 2). Clade
2 was roughly sub-divided into 3 groups, with not all having strong
bootstrap support (.80). PESTE3.3.1 and PESTE3.3.2 are part of
clade 2, which were similar to P. ostreatus D330 STE3-1 and P.
eryngii D625 STE3, whereas PESTE3.3.3 belongs to clade 1 with
L. bicolor LbSTE3.2 and C. cinerea RCB2.42. PESTE3.3.4
belonged with the receptors of clade 1 along with the orthologous
C. cinerea RCB2.43 and S. commune BAR8. Sub-clusters
containing P. eryngii receptors possessed a known mating-type
gene, indicating that the receptor genes from P. eryngii likely
evolved from the common ancestor of the known mating genes. In
particular, L. edodes receptors were found in a basal position in
every subgroup of clade, suggesting that the sequences of L. edodes
receptors are most likely closer to the ancestral gene than the other
receptor pheromone sequences in clade 2.
Fungal pheromone genes are sufficiently different to not
hybridize with other genes, but they share consensus sequences
in the C-terminal end of the protein precursors, the CaaX motif in
C. cinerea and the CXXX motif (CVCH, CVRG, CVVA) in S.
commune [9]. CaaX is conserved for post-translational
modification in most pheromones; therefore, it can be used to identify the
clade of the pheromone. We translated all possible peptides and
evaluated the CaaX sequence at the C-terminal end. In the P.
ribosomal large subunit pseudouridine synthase F
[Flavobacteria bacterium BBFL7] (ZP_01201616.1)
responsible for the synthesis of pseudouridine
from uracil-2604 in 23S ribosomal RNA
DNA/RNA polymerase, partial [Trametes versicolor
FP-101664 SS1] (EIW61623.1)
reverse transcriptase-RNase H-integrase
[Tricholoma matsutake] (BAA78625.1)
conserved hypothetical protein [Trichophyton
verrucosum HKI 0517] (XP_003018684.1)
O-methyltransferase [Punctularia strigosozonata
HHB-11173 SS5] (EIN06883.1)
fungal mating-type pheromone [Coprinopsis
cinerea okayama7#130] (XP_002910434.1)
B mating type pheromone precursor [Ceriporiopsis
subvermispora B] (EMD35227.1)
putative pheromone receptor
[Flammulina velutipes] (AGG68705.1)
fungal mating-type pheromone [Coprinopsis
cinerea okayama7#130] (XP_00183497.1)
putative pheromone receptor
[Flammulina velutipes] (AGG68705.1)
hypothetical fungal pheromone GPCR, STE3-type
[Postia placenta Mad-698-R] (XP_002471247.1)
lipopeptide mating pheromone precursor bap3-1
[Schizophyllum commune H4-8] (XP_003028251.1)
pheromone receptor Rcb2 B43 [Coprinopsis
cinerea okayama7#130] (XP_002910431.1)
catalysis of the oxidation of organic substances
catalysis of the transfer of a methyl group to the
oxygen atom of an acceptor molecule
catalysis of the endonucleolytic cleavage into
nucleoside 39-phosphates and
39phosphooligonucleotides ending in Gp with
29,39cyclic phosphate intermediates.
mating type-specific peptide pheromone
mating type-specific peptide pheromone
mating type-specific G-protein-coupled receptor
mating type-specific peptide pheromone
mating type-specific G-protein-coupled receptor
mating type-specific G-protein-coupled receptor
mating type-specific peptide pheromone
mating type-specific G-protein-coupled receptor
hypothetical protein SERLA73DRAFT_78193 [Serpula unknown
lacrymans var. lacrymans S7.3] (EGN93817.1)
UbiA prenyltransferase [Saprospira grandis str.
Lewin](YP_005323559.1)
hypothetical protein SERLA73DRAFT_172732 [Serpula unknown
lacrymans var. lacrymans S7.3] (EGN92622.1)
hypothetical protein SERLA73DRAFT_190801 [Serpula unknown
lacrymans var. lacrymans S7.3] (EGN92621.1)
reverse transcriptase-RNase H-integrase
[Tricholoma matsutake] (BAA78625.1)
aThe expected value (E) indicates the number of hits one can expect to see by chance in GenBank similarity searches. Under Homolog, the species form with the
lowest E-value hit or the value closest to zero is given in brackets, followed by the GenBank accession number in parentheses.
doi:10.1371/journal.pone.0104693.t002
eryngii B3 locus, four pheromone precursors were identified using
DNAMAN (Lynnon Biosoft, Cambridge, UK) and BLASTP. A
BLASTP search showed that each pheromone precursor has a
similar precursor, including C. cinerea phb3.2 in B43
(XP_002910434.1) for PEphb1.1, the Ceriporiopsis subvermispora
B mating-type pheromone precursor (EMD35227.1) for
PEphb3.2, C. cinerea fungal mating-type pheromone
(XP_001834397.1) for PEphb3.3, and phb3 in the B5 locus in
C. cinerea (AAQ96360.1) for PEphb3.4. The 4 pheromone
precursors contain 5761 amino acids and have a cysteine residue
at the 4th site from the C-terminus. During post-translational
modification, 3 amino acid residues at the C-terminus are
removed, and a 4th cysteine residue is farnesylated. Mature
pheromones were 915 amino acids in length [8,21] in the B3
locus; the mature pheromone size was assumed to be 12 to 13
amino acids based on the consensus sequences for the excision site
(Figure 3). Additional consensus sequences were found at the ER
or TR at the 915th sites from the C-terminus and at a proline at
Figure 2. Phylogenetic relationships of the fungal pheromone receptor protein sequences. CC: C. cinerea; SC: S. commune. rcb1, rcb2, and
rcb3 from C. cinerea; Ba and Bb from S. commune; PDSTE3.3 from P. djamor; PESTE3-like from P. eryngii; and LBSTE3-like from L. bicolor. The GenBank
accession numbers of the receptors analyzed here are shown in Table 2 and were previously reported [14], except the following; L. edodes SUP2 B2
rcb2: AER51012.1; V. volvacea ste3.1: JX982139.1; V. volvacea ste3.2: JX982140.1; V. volvacea ste3.3: JX982141.1; V. volvacea ste3.4: JX982142.1; F.
velutipes W23 ste3.2: KC208605.1; F. velutipes W23 ste3.4: KC208611.1; F. velutipes KACC42780 ste3.1: HQ630590.1; and F. velutipes KACC42780 ste3.2:
HQ630591.1.
doi:10.1371/journal.pone.0104693.g002
the 24 and aspartate/asparagine at 22 relative to the cutting site.
These conserved sites were recognized by processing molecules
[9]. Sequences are typically more diverse across a genus and
species than within a species. The cDNA sequences of the
pheromone and receptor genes were deposited in GenBank with
the primers used for their amplification.
Gene expression of the pheromone receptor and
pheromone genes in monokaryons and dikaryons
Real-time qRT-PCR was performed with KNR2312 (dikaryon)
and P6 (monokaryon) to quantify the expression of the 4
pheromone precursor genes and the 4 receptor genes. Gene
expression was normalized to 18S rRNA expression and calibrated
to the assigned value of 1 by the standard curve method (Qiagen).
The transcription level of the receptor genes was significantly
higher (95% confidence interval) in the monokaryon (P6) (3.812.2
fold) than in the dikaryon (KNR2312), except for PESTE3.3.2
(Figure 4a, Table S4). The expression patterns of the pheromone
precursor genes were similar to those of the receptor genes,
ranging from 1.531.4 fold (Figure 4b, Table S4). In particular,
PESTE3.3.4 and PEphb3.2 showed the most significantly
different expression pattern between monokaryotic and dikaryotic
mycelia.
Function of pheromones and pheromone receptors in
the fruiting process
The transgenic monokaryon P5 was developed using two
pheromone genes and one pheromone receptor gene by
Figure 3. Alignment of the pheromone precursor amino acid sequences. The processed pheromone sequences are underlined, and the
putative C-terminal doublets (ER) are shown. The GenBank accession number of the C. cinerea okayama 7 pheromone is XP_001834397.1, and that of
Ceriporiopsis subvermispora B is EMD35227.1.
doi:10.1371/journal.pone.0104693.g003
Agrobacterium-mediated transformation. Twelve transformants of
P5phb31, 16 of P5phb33 and 3 of P5STE331 were screened using
hygromycin selection medium and were confirmed by PCR with
hph-specific primers. PCR with the SSR45 primer set produced
one single band identical to that of P5, indicating the
monokaryotic nature of the transformants (Figure 5a). Clamp connections
were observed in dikaryon crosses between three transformants
and KNR2312-2 (A4B4) (Figure 5b and 5c (3)(5)), whereas
crosses between transformants and monokaryons (A3B3 or A3B4)
could not develop clamp connections due to incompatible
combinations (Figure 5b). The control combination of P5 and
the tester strain (A4B3) possessed clamp connections (Figure 5c
(1)), whereas the transformant containing the pBGgHg vector was
unable to form clamp connections when crossed with the A4B4
tester strain (Figure 5c (2)) due to incompatibility at the A locus.
The positive control developed the clamp connections within a
week, whereas the transformed monokaryons required 3040 days
after the two mycelia contacted. Moreover, the density of the
clamp connections was 2.5 times higher in transformed
monokaryons than in the wild-type strain (Figure 5c). Nonetheless, on
the basis of our results, the transformed pheromone and receptor
genes appear to play a role in the clamp connection process.
All combined dikaryons, including the positive and negative
control strains, were fruited in sawdust medium. Only compatible
combinations showed fruiting bodies similar to those of the
positive strain (Figure 5c). The dikaryons P5phb316KNR2312-2
and P5STE3316KNR2312-2 showed full fruiting bodies, whereas
those of P5phb336KNR2312-2 did not fully differentiate and had
primordia without caps. All fruiting bodies were relatively small
and delayed (more than 25 days) compared with KNR2312 (18
days, data not shown).
Structure of the B3 locus
Mating-type genes show extraordinarily diverse sequences; thus,
using sequence-based methods to isolate whole mating-type genes
is difficult. Although whole genome sequencing has been
widespread and most of the genes of interest are available in
online databases, the pheromone and receptor genes have distinct
sequences in each strain. Alternatively, genomic subtraction and
positional cloning using mitochondria intermediate peptidase
(MIP), CLA4, putative multidrug transporter (mfs1), and PAB1
have been employed to isolate the mating region [5,8,14,22].
Additionally, marker genes are sometimes located too far from the
B mating region to isolate the entire sequence of interest [14].
Recently, we identified mating-type alleles in the A and B loci and
developed SCAR primers specific to the B3 locus. Moreover, the
SCAR marker, shown to be located in the middle of the B3 locus,
was amplified in AxB3 monokaryons from in 100 monokaryons
[12]. We isolated the B3 mating region and identified a variety of
genes, including mating-type genes, by sequence analysis using
Fgenesh, BLASTX, and manual curation. The B3 locus of P.
eryngii possesses one more receptor (four receptors) than the
typical B locus in C. cinerea (three receptors). In S. commune, the
B locus is divided into two subloci, Ba and Bb [19,20], whereas in
C. cinerea, only a single B locus is present. More than three
pheromone genes at the B locus have been reported in C. cinerea,
Flammulina velutipes, and L. bicolor. In most of these cases, unlike
the B3 locus of P. eryngii, extra receptors (other than the three
functional receptors) that did not co-segregate with the mating
type were located outside the locus and were considered to be
impaired remnants of duplications [4,15]. According to the
phylogenetic analysis, PESTE3.3.1 and PESTE3.3.2 appear to
be very closely related (Figure 2), and the sequence identity (64.8%
between intact sequences and 83.4% between truncated and intact
sequences) suggests that these two proteins were most likely
duplicated later than any other receptors in the B3 locus. The
expression of the receptor and pheromone genes was supported by
real-time qRT-PCR data. However, due to the short length of the
C-terminal cytoplasmic residues, PESTE3.3.1 seems likely to be a
receptor-like gene. Whether such gene types play a role in the
interaction between the receptor and downstream molecules
remains unclear. Although P5-STE3.3.16KNR2312-2 showed
sparse clamp connections and late fruiting compared with the
positive control (P56KNR2312-6), it produced similar fruiting
bodies to that of the positive control, indicating that a receptor
with short C-terminal cytoplasmic residues could play a role in the
fruiting process. In the case of S. commune, the B-dependent
mating reaction was limited and produced an abnormal fruiting
body after the shortening of the intracellular C-terminus [23]. In
contrast, the truncation of the C-terminal intracellular region of
the S. commune receptors has not been observed to affect signal
transduction [2426]. Furthermore, this short cytoplasmic region
was found in not only P. eryngii but also other mushrooms such as
U. maydis and L. edodes (Table S3). In addition to the C-terminal
tail, multiple sites including the intracellular loop domains in
7TM are thought to be involved in mating-type specificity
[24,25,27]. Further analysis is required to determine how the
length of the cytoplasmic domain of the receptor functions in the
mating process. Novel pheromone-receptor interactions
presumably evolved through gene duplications of the prototype STE3-like
gene and the pheromone gene and subsequent mutation of the
duplicated genes (for review see [28]). Because single- or
doubleamino acid substitutions in receptors or pheromones can
significantly alter interaction specificity [29], PESTE3.3.1 could
be a candidate for new mating specificity.
Gene expression of the pheromone receptor and
pheromone genes in monokaryons and dikaryons
Few studies have been conducted to analyze the expression of
mating-type genes in mushroom fungi. Monokaryon and
dikaryon fungal states show different expression levels of the A
and B loci genes. Richardson et al. observed constitutive
expression of the A locus genes to a similar extent in both
monokaryons and dikaryons of C. cinereus [30]. In another
study [23], a different expression pattern was observed for the
receptor and pheromone genes of S. commune; at 12 h
(midpoint of massive dikaryosis) after mating, both genes were highly
expressed compared with the initial stage; at 72 h (end of
massive dikaryosis), the pheromone genes were expressed at
2fold higher levels than in the monokaryotic state, whereas the
receptor genes were expressed at similar levels in the
monokaryotic and dikaryotic states. The truncated pheromone was
expressed at a lower level in the dikaryon. In the present study,
comparative expression of the receptors and pheromone
precursor genes revealed that most pheromone precursor genes
were highly expressed in the monokaryons compared with the
dikaryons (Figure 4), indicating that the fungal monokaryon
status requires additional mate-specific pheromone and receptor
genes for a monokaryonmonokaryon interaction to generate a
dikaryon. The roles of pheromone perception in Saccharomyces
cerevisiae have been described previously in mate attraction and
the formation of shmoo cells that grow towards their mating
partner [31]. Similarly, in Neurospora crassa, pheromones and
receptors were involved in the chemotropic polarized growth of
female-specific hyphae (trichogynes) toward male cells of the
compatible mating type [32,33]. A dikaryon does not require
this attraction towards a compatible gamete. Before the mating
process, sufficient amounts of the pheromones and receptors are
required because the opposite mating type can only be met
randomly.
Function of pheromones and pheromone receptors in
the fruiting process
Fungal transformation, especially in edible mushrooms, is not
easily achieved, although some methods have been developed
[34,35]. We adapted Agrobacterium-mediated transformation,
thus succeeding in the isolation of several transformants. The
dikaryons from crosses between transformants (A3B4::PEphb3.1,
A3B4::PEphb3.3, A3B4::PESTE3.3.1) and a monokaryotic
tester strain (A4B4) demonstrated clamp connections, suggesting
that the transgenic genes most likely produced compatible
combinations with the tester strain. Although clamp connections
were formed more slowly and sparsely in the transgenic dikaryons
than in the positive control (Figure 5c), the transgenic dikaryons
showed full fruiting bodies, except P5phb336KNR2312-2, which
indicated the requirement for more components of the normal
process. This result is consistent with a previous report [23], in
which malformed fruiting bodies and spores were observed in the
transgenic dikaryons. The small and delayed fruiting bodies were
likely caused by selfing depression.
Supporting Information
Table S1 Primers for the isolation of the B3 locus and
the confirmation of transformation and expression. List
of specific primer sets for the isolation of the B3 locus from the
gDNA library, the confirmation of transgenic mycelia and the
amplification of pheromone and receptor gDNAs with their
promoter and terminator sequences.
(DOCX)
Table S2 Primers for real-time qRT-PCR (SYBR Green)
in this study. List of specific primer sets for real-time qRT-PCR
to address the expression profiles of the pheromone and receptor
genes in mono- and dikaryotic mycelia.
(DOCX)
Table S3 A predicted transmembrane motif of the
pheromone receptors. The table lists the transmembrane
motifs of fungal pheromone receptors from P. eryngii B3 and
other mushroom fungi. a All have GenBank accession numbers,
except LbSTE3.2 from JGI (http://genome.jgi-psf.org/Lacbi2/
Lacbi2.home.html), b A transmembrane motif was predicted using
PHOBIOUS, HMMTOP, and TMHMM, as described in the
methods. c P. eryngii, d L. bicolor, e P. djamor, f S. commune, g U.
maydis, h C. cinerea, i L. edodes.
(DOCX)
We thank to Dr. Young-Jin Park and Ms. Hui-Yeon Yun Sim for helpful
comments and suggestions.
Conceived and designed the experiments: J-SR M-KK YMK. Performed
the experiments: J-SR K-HK YMK. Analyzed the data: J-SR YMK SYK
CHI M-KK H-JJ. Contributed reagents/materials/analysis tools: AA
HSR WSK HSL H-JJ. Contributed to the writing of the manuscript: J-SR
YMK AA H-SR.
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