Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens

Background

Phellinus sulphurascens is a fungal pathogen that causes laminar root rot in conifers, one of the most damaging root diseases in western North America. Despite its importance as a forest pathogen, this fungus is still poorly studied at the genomic level. An understanding of the molecular events involved in establishment of the disease should help to develop new methods for control of this disease.

Results

We generated over 4600 expressed sequence tags from two cDNA libraries constructed using either mycelia grown on cellophane sheets and exposed to Douglas-fir roots or tissues from P. sulphurascens-infected Douglas-fir roots. A total of 890 unique genes were identified from the two libraries, and functional classification of 636 of these genes was possible using the Functional Catalogue (FunCat) annotation scheme. cDNAs were identified that encoded 79 potential virulence factors, including numerous genes implicated in virulence in a variety of phytopathogenic fungi. Many of these putative virulence factors were also among 82 genes identified as encoding putatively secreted proteins. The expression patterns of 86 selected fungal genes over 7 days of infection of Douglas-fir were examined using real-time PCR, and those significantly up-regulated included rhamnogalacturonan acetylesterase, 1,4-benzoquinone reductase, a cyclophilin, a glucoamylase, 3 hydrophobins, a lipase, a serine carboxypeptidase, a putative Ran-binding protein, and two unknown putatively secreted proteins called 1 J04 and 2 J12. Significantly down-regulated genes included a manganese-superoxide dismutase, two metalloproteases, and an unknown putatively secreted protein called Ps0058.

Conclusions

This first collection of Phellinus sulphurascens EST sequences and its annotation provide an important resource for future research aimed at understanding key virulence factors of this forest pathogen. We examined the expression patterns of numerous fungal genes with potential roles in virulence, and found a collection of functionally diverse genes that are significantly up- or down-regulated during infection of Douglas-fir seedling roots by P. sulphurascens.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-603) contains supplementary material, which is available to authorized users.     

Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum

Pairings between heterokaryons and homokaryons of Agaricomycete fungi (he-ho pairings) can lead to either heterokaryotization of the homokaryon or displacement of the homokaryotic nucleus through migration of nuclei from the heterokaryon into the homokaryon. In species of Agaricomycetes with multinucleate cells (>2 nuclei per cell), he-ho pairings could result in the stable or transient formation of a hypha with three genetically different nuclei (trikaryons). In this study, he-ho pairings were conducted using the multinucleate Agaricomycete Heterobasidion parviporum to determine whether trikaryons can be formed in the laboratory and whether nuclear genotype affects migration and heterokaryon formation. Nuclei were tracked by genotyping the heterokaryotic mycelium using nucleus-specific microsatellite markers. The data indicated that certain nuclear combinations were favored, and that nuclei from some strains had a higher rate of migration. A high percentage of trikaryons (19 %) displaying three microsatellite alleles per locus were identified among subcultures of the he-ho pairings. Using hyphal tip and conidial isolation, we verified that nuclei of three different mating types can inhabit the same mycelium, and one of the trikaryotic strains was judged to be semi-stable over multiple sub-culturing steps, with some hyphal tips that retained three alleles and others that reduced to two alleles per locus. These results demonstrate that nuclear competition and selection are possible outcomes of heterokaryon-homokaryon interactions in H. parviporum and confirm that ratios of component nuclei in heterokaryons are not strictly 1:1. The high rate of trikaryon formation in this study suggests that fungi with multinucleate cells may have the potential for greater genetic diversity and recombination relative to dikaryotic fungi.     

Changes in quality of Phellinus gilvus mushroom by different drying methods

This study was conducted to investigate the changes in characteristics of the Phellinus gilvus mushroom as influenced by drying methods after harvest. The lowest weight loss rate of P. gilvus mushroom was 75.8% with drying in the shade and 80% by dryer (60°C). The size loss rate of pileus was 19.3% of that in a hot air dryer (60°C). The hardness of dried material context using a hot air dryer (60°C) was the lowest (20 kg/cm²), and that by a dry oven (60°C) was the highest (457 kg/m²). For ΔE value, 4.9 of context and 2.6 of tubes using drying in the shade (20°C) were found to be the lowest. The survival rate of sarcoma 180 treated with P. gilvus dried in the sun was the lowest (51.8%), and this was considered the most effective method for antitumor activity against sarcoma 180.     

Quantitative response of cell growth and polysaccharide biosynthesis by the medicinal mushroom Phellinus linteus to NaCl in the medium

The effect of NaCl on cell growth and polysaccharide biosynthesis in the medicinal mushroom Phellinus linteus was studied. With the increase of NaCl concentration between 1 g/l and 7 g/l in the culture medium, the cell growth and intracellular polysaccharide (IPS) accumulation were decreased; extracellular polysaccharide (EPS) concentration was enhanced, with an increase of NaCl concentration from 1 g/l to 3 g/l. Under the optimum NaCl concentration of 3 g/l, the maximum EPS and IPS production reached 2.2±0.15 g/l and 53.6±2.45 mg/g DW on day 12, which improved 32.27% and decreased 16.89% compared to the control, respectively. Both EPS and IPS showed new polysaccharide components by fractionation with DEAE-cellulose ion exchange chromatography compared to the control. The results presented in this study are considered helpful for further investigation on the diversity of polysaccharide biosynthesis of this medicinal fungus under NaCl environments.     

The pattern of zygotene and pachytene pairing in allotetraploid Aegilops species sharing the U genome

Allotetraploid Aegilops species sharing the U genome, Ae. columnaris (UUMM), Ae. ovata (UUMM), Ae. triaristata (UUMM), Ae. triuncialis (UUCC) and Ae. variabilis (UUSS), regularly form bivalents at metaphase I of meiosis. The pattern of zygotene and pachytene pairing was analyzed by whole-mount surface-spreading of synaptonemal complexes under the electron microscope. The data indicated that at the zygotene stage the chromosomes were almost exclusively associated as bivalents; only a few multivalents (7%) were observed. These observations are discussed in relation to mechanisms of diploidization of polyploid meiosis.     

The pattern of zygotene and pachytene pairing in allotetraploid Aegilops species sharing the D genome

Chromosome pairing behaviour of the allotetraploid Aegilops species sharing the D genome, Ae. crassa (DDMM), Ae. cylindrica (DDCC) and Ae. ventricosa (DDNN), was analyzed by electron microscopy in surfacespread prophase-I nuclei. Synaptonemal-complex analysis at zygotene and pachytene revealed that synapsis in the allotetraploids was mostly between homologous chromosomes, although a few multivalents were also formed. Only homologous bivalents were observed at metaphase-I. It is concluded that the mechanism controlling bivalent formation in these species acts mainly at zygotene by restricting pairing to homologous chromosomes, but also acts at pachytene by preventing chiasma formation in homoeologous associations. These observations are discussed in relation to mechanisms of diploidization of polyploid meiosis.     

Inhibition of cytochrome P450 isozymes in rat liver microsomes by polysaccharides derived from Phellinus linteus

Polysaccharides (0.5, 1 and 3 mg ml^–1) from cultured broth and mycelia of Phellinus linteus inhibited cytochrome P450 (CYP) 1A1, CYP 1A2, CYP 2B1, and CYP 2E1 activities in rat liver microsomes. The polysaccharides from the broth of Phellinus linteus grown with 5% (v/v) mulberry extract had highest inhibitory potency for CYP 1A1, 1A2 and 2B1 activities. The most potent inhibitor of CYP 2E1 activity were the polysaccharides from the broth of Phellinus linteusgrown with 10% (v/v) mulberry extract.     

Tumor-inhibitory and liver-protective effects of <Emphasis Type="Italic">Phellinus igniarius</Emphasis> extracellular polysaccharides

The tumor-inhibitory and liver-protective effects of crude extracellular polysaccharides (EPS) extracted from the liquid mycelial culture of the mushroom Phellinus igniarius were studied in mice. The mice were injected with murine sarcoma S180 and murine hepatoma H22. Crude EPS at 100, 200, 400 mg kg⁻¹ body weight was administered to EPS groups each day in the twelve consecutive days. The result showed that EPS 200 mg kg⁻¹ body weight significantly inhibited S180 and H22 at 65.0 and 46.3%, respectively. Moreover, EPS could not only keep the numbers of WBC, RBC, PLT and the concentration of HGB in a normal range, but also normalize the activities of AST, ALT and ALP. For example, in EPS-treated mice, AST significantly reduced with the percentage of A/G reverse in S180 (P < 0.05) and H22 (P < 0.01) when the mice took EPS 200 mg kg⁻¹ body weight. In conclusion, it was remarkable that P. igniarius EPS exhibited antitumor activity related to dosage and protected liver function by sustaining the blood routine as well as keeping the blood biochemical indexes normal.     

pH control strategy in a shaken minibioreactor for polysaccharide production by medicinal mushroom Phellinus linteus and its anti-hyperlipemia activity

A process at various pH values ranging from 4.5 to 7.5 for production of mycelia and extracellular polysaccharide (EPS) by P. linteus fermentation in pH-controlled shaken bioreactor was investigated. A two-stage pH control strategy in which pH value was kept at 6.5 for the first 24 h, and then switched to 4.5 was developed successfully to enhance simultaneously the cell growth and EPS production. The maximum cell density and EPS production reached 15.13 ± 0.1 g/l on day 6 and 6.74 ± 0.1 g/l on day 4, respectively. The anti- hyperlipemia effect of EPS and intracellular polysaccharide (IPS) extracted from mycelia were observed that both EPS and IPS can obviously reduce the serum triglyceride (TG), the blood cholesterol (TC) and serum low density lipoprotein (LDL) level, and increase the high density lipoprotein (HDL) level of the hyperlipemia mice. Polysaccharides from submerged cultivation of medicinal fungus P. linteus have favorable potency to develop anti-hyperlipermia drugs.     

Hypoglycemic effects of exopolysaccharides produced by mycelial cultures of two different mushrooms Tremella fuciformis and Phellinus baumii in ob/ob mice

The anti-diabetic activities of the exopolysaccharides (EPS) produced by submerged mycelial culture of two different mushrooms, Tremella fuciformis and Phellinus baumii, in ob/ob mice were investigated. All the animals were randomly divided into three groups with seven animals in each group: The control group received 0.9% NaCl solution; the diabetic groups were treated with EPS from T. fuciformis (Tf EPS) and P. baumii (Pb EPS) at the level of 200 mg/kg body weight using an oral zoned daily for 52 days. The plasma glucose levels in the EPS-fed mice were substantially reduced by about 52% (Tf EPS) and 32% (Pb EPS), respectively, as compared to control mice. The results of oral glucose tolerance test (OGTT) revealed that both EPS-fed groups significantly increased the glucose disposal after 52 days of EPS treatments. Furthermore, higher food efficiency ratios and reduced blood triglyceride levels were observed in the EPS-treated groups. Because peroxisome proliferator-activated receptor gamma (PPAR-γ) is indeed a key regulator of insulin action, we investigated the expression pattern of adipose tissue PPAR-γ messenger RNA (mRNA) and plasma levels of PPAR-γ. It was revealed that PPAR-γ was significantly activated in response to EPS treatments. The results suggested that both EPS exhibited considerable hypoglycemic effect and improved insulin sensitivity possibly through regulating PPAR-γ-mediated lipid metabolism. Our results indicated that two mushroom-derived EPS might be developed as potential oral hypoglycemic agents or functional foods for the management of non-insulin-dependent diabetes mellitus.     

Nuclear ribosomal ITS sequences and phylogeny in East AsianAconitum subgenusAconitum (Ranunculaceae), with special reference to extensive polymorphism in individual plants

Internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA) were used to examine the phylogeny of East Asian aconites. Individual aconites were discovered to contain as many as eight different ITS sequences after cloning and PCR-SSCP (single-stranded conformational polymorphisms) analysis. We identified eight putative ITS pseudogenes from four taxa with low predicted secondary structure stability and high substitution rates. Maximum likelihood (ML) and neighbor-joining (NJ) methods were used for phylogenetic reconstruction. The ITS trees agree with the previous chloroplast DNA (cpDNA) tree for the vast majority of the taxa. We found two East Asian clades in the ITS trees: 1) a clade with the Chinese diploid,Aconitum volubile and East Asian tetraploids, and 2) a clade of East Asian diploids and Siberian tetraploids. In the former clade, most tetraploid taxa appear to be polyphyletic; sequences from individual plants did not correspond to recognized taxonomic units. This indicates a recent divergence of the East Asian tetraploids.     

Laccase and Manganese Peroxidase Activities of Phellinus Robustus and Ganoderma Adspersum Grown on Food Industry Wastes in Submerged Fermentation

Phellinus robustus produced both laccase (700–4,000 U l⁻¹) and manganese peroxidase (MnP) (1,000–11,300 U l⁻¹) in fermentation of nine food wastes, whereas Ganoderma adspersum produced only laccase (600–34,000 U l⁻¹). Glucose provided high laccase and MnP activity of P. robustus but repressed enzyme production by G. adspersum. Ammonium sulphate and ammonium tartrate increased the P. robustus laccase yield (3-fold), whereas the accumulation of MnP was not enhanced by additional nitrogen.     

Inhibition of cytochrome P450 isozymes and ornithine decarboxylase activities by polysaccharides from soybeans fermented with Phellinus igniarius or Agrocybe cylindracea

Polysaccharides (5, 10, 25, 50 and 100 microg ml(-1)) from soybeans and soybeans fermented with Phellinus igniarius or Agrocybe cylindracea inhibited cytochrome P450 1A1, cytochrome P450 1A2 and cytochrome P450 2B1 activities in rat liver microsomes. The polysaccharides (5, 10 and 25 microg ml(-1)) also suppressed 12-O-tetradecanoylphorbol-13-acetate-induced ornithine decarboxylase activity. The most potent inhibitors of cytochrome P450 isozymes and ornithine decarboxylase activities were the polysaccharides from soybeans fermented with Agrocybe cylindracea.     

Bioconversion of starch processing waste to Phellinus linteus mycelium in solid-state cultivation

The objective of the experiment was to use starch processing waste as an alternative growth medium for cultivation of mycelia of the mushroom Phellinus linteus and to find an optimum condition under solid-state cultivation. Response surface analysis along with a central composite design was successfully applied to approximate the simultaneous effects of the substrate concentration (16-36 g l(-1)), pH (4.5-6.5), and temperature (25-35 degrees C) on the mycelial growth rate. In the model, pH and temperature significantly affected the mycelial growth but substrate concentration did not. The optimal substrate concentration, pH, and temperature for maximizing growth rate of P. linteus mycelia were found to be 16.5 g l(-1), pH 6.0, and 29.7 degrees C, respectively. Subsequent verification of these levels agreed with model predictions and the maximum mycelial growth rate at these conditions was 6.1 +/- 0.8 mm day(-1). Therefore, the results of the experiments suggest that starch processing waste could be utilized as a growth substrate for the cultivation of the mushroom mycelia of P. linteus, enhancing the usefulness of this byproduct of the starch manufacturing industry. This approach is likely to be useful for establishing similar parameters for the cultivation of other fungi.     

Distinguishing between metabolically active and inactive roots by combined staining with 2,3,5-triphenyltetrazolium chloride and image colour analysis

The objective of the present work was to develop a method to distinguish between metabolically inactive and active parts of plant roots. White clover (Trifolium repens L.) roots were stained with 2,3,5-triphenyltetrazolium chloride (TTC) followed by root colour classification with an interactive scanner-based image analysis programme (WinRHIZO). Roots inactivated by boiling were unstained and pale brown, whereas fresh samples with predominantly metabolically active roots turned dark red, red or pale red after staining. A small amount of very young, presumable active roots (0.8% of total active root length) failed to stain red with TTC. The colour analysis of inactive and active roots was based on four colour classes for boiled roots and seven classes for fresh roots, respectively, as defined upon visual examination of images. Pixel colours falling outside the defined classes were allocated to the nearest defined class – an option that increased objectivity and stability and reduced the required number of colour classes. For the fresh white clover roots, 75–86% of the total root length was determined as active, while 3–7% of the boiled roots fell into the same category. The percentage of total root length measured by WinRHIZO that was identified as metabolically active was linearly correlated with the percentage of fresh roots in mixtures of fresh and boiled roots (R²=0.99). Colour classes chosen à priori from one experiment could be used to distinguish fairly satisfactorily between active and inactive roots of another white clover cultivar grown under other conditions, but failed to classify activity in ryegrass (Lolium multiflorum Lam.) root samples. In the latter case, colour classes needed to be re-defined in order to produce reliable data. Our work shows that WinRHIZOs colour identification sub-module provides a new promising tool to classify root activity as identified after staining with TTC, but colour classes must be carefully evaluated on every new occasion.     

Carex, subgenus Carex (Cyperaceae) – A phylogenetic approach using ITS sequences

To evaluate the sectional classification in Carex, subgenus Carex, the ITS region of 117 species belonging to 32 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. In our analyses (1) species of subgenus Indocarex appear as a statistically well supported group within subgenus Carex. (2) The representatives of sections Vesicariae, Hirtae, Pseudocypereae, Ceratocystis, Spirostachyae, Bicolores, Paniceae, Trachychlaenae, Scirpinae, Atratae and Albae group in statistically supported clades with higher support in MCMC than in NJ. (3) C. rariflora clusters with representatives of section Limosae, however only weakly supported. (4) Taxa of section Phacocystis are divided in two statistically supported subclusters that are closely related to a core group of section Hymenochlaenae. (5) Species of sections Montanae, Pachystylae, Digitatae, Phacocystis, Rhomboidales, Careyanae and Frigidae are segregated into two or more clusters each. (6) Five species of section Frigidae cluster together, whereas the seven others are in scattered positions. Based on these results, delimitation of sections is discussed.     

Genetic structure of <Emphasis Type="Italic">Tuber mesentericum</Emphasis> Vitt. based on polymorphisms at the ribosomal DNA ITS

Tuber mesentericum fruit bodies are in increasing demand on the food market and are an important economic resource for southern Italy, their major production area. Because molecular studies on this truffle species are very scarce, we analyzed ITS1 and ITS2 nucleotide variability of 126 ascocarps of T. mesentericum collected in different European areas, mainly southern Italy. The results of haplotype distribution, analysis of molecular variance, and spatial analysis of molecular variance analyses show strong genetic structuring of the samples collected in the different geographic areas, confirmed by parsimony and distance analyses. In particular, the Italian samples seem to be a well-distinguished group.     

云南重楼ITS序列单核苷酸多态性与甾体皂苷特征的相关性分析

为了解云南重楼(Paris polyphylla var. yunnanensis) ITS序列的单核苷酸多态性(SNP)特征与其甾体皂苷构成特征的相关性,并探讨其对药材质量稳定性的影响,利用MegAlign软件对37份云南重楼样本的ITS序列进行对比,根据SNP位点进行分型;采用HPLC法测定7种甾体皂苷成分(重楼皂苷Ⅰ、Ⅱ、Ⅴ、Ⅵ、Ⅶ、H和薯蓣皂苷);用SPSS 25.0软件和SIMCA-P 15.0软件对各基因型甾体皂苷构成特征进行统计分析。结果表明,云南重楼ITS序列存在40个双等位多态性位点,其中碱基转换32个,碱基颠换8个,根据SNP特征可划分为2类基因型YN-I和YN-II。6种甾体皂苷(重楼皂苷Ⅰ、Ⅱ、Ⅵ、Ⅶ、H、薯蓣皂苷)在云南重楼广泛分布,而重楼皂苷Ⅴ稀少。YN-I和YN-II的药典指标成分总含量分别为1.070%和0.93%,样本合格率分别为68.42%和77.78%;YN-I的甾体皂苷总含量为1.65%,YN-II为1.32%。方差分析表明,2类基因型的甾体皂苷特征存在一定程度的区别,但药典指标成分无显著差异,药材应该具有等效性。聚类分析和主成分分析表明,YN-Ⅰ的离散度更高,YN-Ⅱ的聚集度更好,表明YN-II的药材质量更加稳定,植株个体的甾体皂苷合成和累积差异更小,YN-II的SNP特征对云南重楼良种选育的分子遗传标记筛选具有重要意义。     

Fungal occurrence,disease incidence and severity,and yield of maize symptomatic for seedling disease in Mississippi

A study was conducted in Mississippi from 1995 to 1997 comparing soil rhizosphere fungi isolated from Pioneer 3167 hybrid maize (Zea mays L.) planted on Brooksville silty clay and Memphis silt loam soils. Maize seedlings were collected over four sampling dates from conventional and no-tillage plots. Eleven fungal genera consisting of nineteen species were isolated from these plants; Trichoderma spp. were most frequently isolated, followed by Fusarium spp. The highest disease incidence occurred in tilled plots of the latest planting date on Brooksville silty clay when samples were collected 17 days after planting. Root disease was most severe in 1996 from seedlings planted on the last planting date in tilled plots sampled 17 days after planting. Yields were significantly (P ≤ 0.05) higher on Brooksville silty clay soil than on Memphis silt loam in both 1995 and 1996. Yields were highest from no-tillage plots and from maize planted on the earliest date. There was a significant correlation between incidence of root infection and disease severity. There was no correlation between the incidence of root infection and yield or between disease severity and yield at either location. This revised version was published online in June 2006 with corrections to the Cover Date.