Fungal relationships and structural identity of their ectomycorrhizae

Aproximately 5,000–6,000 fungal species form ectomyorrhizae (ECM), the symbiotic organs with roots of predominantly trees. The contributing fungi are not evenly distributed over the system of fungi. Within Basidiomycota exclusively Hymenomycetes and within Ascomycota exclusively Ascomycetes contribute to the symbiosis. Hymenomycetes play a big part, Ascomycetes a minor role; Zygomycetes only form exceptionally ECM. Responsible for ascomycetous ECM are mostly Pezizales with their hypogeous derivatives, whereas Boletales, Gomphales, Thelephorales, Amanitaceae, Cantharellaceae, Cortinariaceae, Russulaceae, and Tricholomataceae are the most important ectomycorrhizal relationships within Hymenomycetes. ECM, as transmitting organs between soil and roots, are transporting carbohydrates for growth of mycelium and fruitbodies from roots and have to satisfy the tree’s demand for water and nutrients. The latter task particularly influences the structure of ECM as nutrients are patchily distributed in the soil and saprotrophic as well as ectomycorrhizal fungi can act as strong competitors for nutrients. In focusing these requirements, ECM developed variously structured hyphal sheaths around the roots, the so-called mantles, and differently organized mycelium that emanates from the mantle, the so-called extramatrical mycelium. The mantles can be plectenchymatous consisting of loosely woven, differently arranged hyphae or they are densely packed, forming a pseudoparenchyma similar to the epidermis of leaves. The extramatrical mycelium grows either as simple scattered hyphae from the mantle into the soil or it can be united to undifferentiated rhizomorphs with a small reach or to highly organized root-like organs with vessel-like hyphae for efficient water and nutrient transport from distances of decimeters. Cystidia, sterile and variously shaped hyphal ends, possibly appropriate for preventing animal attack, in addition, can cover mantles and rhizomorphs. Although only a limited number of species could be considered, some general conclusions are possible.The genus Tuber forms needle-shaped cystidia and lacks rhizomorphs and clamps. Gomphales ECM are identified by rhizomorphs with ampullate inflations at septa of some hyphae and by oleoacanthocystidia or/and oleoacanthohyphae. Thelephoraceae reveal a great diversity of mantle structures and of extramatrical mycelium, with some additional optional characters, i.e., dark brown color, cystidia, blue granules, amyloid hyphae, or amyloid septa. Bankeraceae are mostly characterized by plectenchymatous mantles with star-like pattern and chlamydospores. Russulaceae possess smooth and hydrophilic ECM. Russula forms plectenchymatous mantles with knob-bearing cystidia, so-called russuloid cystidia, or pseudoparenchymatous mantles without cystidia. Lactarius lacks cystidia and shows laticifers within plectenchymatous or within pseudoparenchymatous mantles. The Boletales families Boletaceae, Gyroporaceae, Melanogastraceae, Paxillaceae, Rhizopogonaceae, Sclerodermataceae, and Suillaceae have the most advanced rhizomorph type, the so-called boletoid rhizomorphs, and reveal generally plectenchymatous mantles, frequently with ring-like patterns. Gomphidiaceae and Albatrellaceae provide cystidia, plectenchymatous mantles, and amyloidy; Gomphidiaceae are generally growing in ECM of Suillaceae and Rhizopogonaceae. Cortinariaceae reveal plectenchymatous mantles and undifferentiated or differentiated rhizomorphs or lack rhizomorphs at all. Cortinarius and Dermocybe are distinct by irregularly shaped, bent to tortuous ECM with many rhizomorphs, some growing over the mycorrhizal tip into the soil. Inocybe lacks rhizomorphs and its emanating hyphae are furnished by many secondary septa and prominent clamps with a hole. Rozites lacks rhizomorphs, too, and reveals a distinctly amyloid gelatinous mantle matrix. Descolea and Descomyces are covered by bolbitioid cystidia. Lastly, the genus Tricholoma forms plectenchymatous mantles and a high diversity of rhizomorphs. Some of the ectomycorrhizal features are used to hypothesize relationships at different taxonomic levels. These conclusions are compared with recently developed molecular hypotheses. Correspondence between the two types of hypotheses are evident, while some conflicts wait for a settlement.     

Identification of genes differentially expressed in extraradical mycelium and ectomycorrhizal roots during Paxillus involutus-Betula pendula ectomycorrhizal symbiosis

The development of ectomycorrhizal symbiosis leads to drastic changes in gene expression in both partners. However, little is known about the spatial regulation of symbiosis-regulated genes. Using cDNA array profiling, we compared the levels of expression of fungal genes corresponding to approximately 1,200 expressed sequenced tags in the ectomycorrhizal root tips (ECM) and the connected extraradical mycelium (EM) for the Paxillus involutus-Betula pendula ectomycorrhizal association grown on peat in a microcosm system. Sixty-five unique genes were found to be differentially expressed in these two fungal compartments. In ECM, a gene coding for a putative phosphatidylserine decarboxylase (Psd) was up-regulated by 24-fold, while genes coding for urea (Dur3) and spermine (Tpo3) transporters were up-regulated 4.1- and 6.2-fold in EM. Moreover, urea was the major nitrogen compound found in EM by gas chromatography-mass spectrometry analysis. These results suggest that (i) there is a spatial difference in the patterns of fungal gene expression between ECM and EM, (ii) urea and polyamine transporters could facilitate the translocation of nitrogen compounds within the EM network, and (iii) fungal Psd may contribute to membrane remodeling during ectomycorrhiza formation.     

Identification of Genes Differentially Expressed in Extraradical Mycelium and Ectomycorrhizal Roots during Paxillus involutus-Betula pendula Ectomycorrhizal Symbiosis

The development of ectomycorrhizal symbiosis leads to drastic changes in gene expression in both partners. However, little is known about the spatial regulation of symbiosis-regulated genes. Using cDNA array profiling, we compared the levels of expression of fungal genes corresponding to approximately 1,200 expressed sequenced tags in the ectomycorrhizal root tips (ECM) and the connected extraradical mycelium (EM) for the Paxillus involutus-Betula pendula ectomycorrhizal association grown on peat in a microcosm system. Sixty-five unique genes were found to be differentially expressed in these two fungal compartments. In ECM, a gene coding for a putative phosphatidylserine decarboxylase (Psd) was up-regulated by 24-fold, while genes coding for urea (Dur3) and spermine (Tpo3) transporters were up-regulated 4.1- and 6.2-fold in EM. Moreover, urea was the major nitrogen compound found in EM by gas chromatography-mass spectrometry analysis. These results suggest that (i) there is a spatial difference in the patterns of fungal gene expression between ECM and EM, (ii) urea and polyamine transporters could facilitate the translocation of nitrogen compounds within the EM network, and (iii) fungal Psd may contribute to membrane remodeling during ectomycorrhiza formation.     

Persistence of ecto- and ectendomycorrhizal fungi associated with <Emphasis Type="Italic">Pinus montezumae</Emphasis> in experimental microcosms

Ectomycorrhizal (ECM) and ectendomycorrhizal fungal species associated with Pinus montezumae were recorded in 8 year-old trees established in microcosms and compared with those associated with 2 year-old trees, in order to determine their persistence over the long-term. Mycorrhizal root tips were morphologically and anatomically characterized and sequenced. The extension of extramatrical mycelium of ECM fungi with long exploration strategies was evaluated. In total, 11 mycorrhizal species were registered. Seven mycorrhizal species were detected on both 2 and 8 year-old pines: Atheliaceae sp., Rhizopogon aff. fallax, R. aff. occidentalis, Suillus pseudobrevipes, Tuber separans, Wilcoxina mikolae and Wilcoxina rehmii. One species, Thelephora terrestris, was exclusively associated with two year–old seedlings, while Cenococcum geophilum, Pezizaceae sp. and Pyrenomataceae sp. were exclusively found on 8 year-old trees. Atheliaceae sp. was the ECM fungal species that presented the most abundant mycelium. Finally, we report one new fungal species of Pezizaceae occurring as a symbiont of P. montezumae.     

Differential expression of oxidative stress and extracellular matrix remodeling genes in low- or high-dose-rate photon-irradiated skin

Changes in the expression of genes implicated in oxidative stress and in extracellular matrix (ECM) remodeling and selected protein expression profiles in mouse skin were examined after exposure to low-dose-rate or high-dose-rate photon irradiation. ICR mice received whole-body γ rays to total doses of 0, 0.25, 0.5 and 1 Gy at dose rates of 50 cGy/h or 50 cGy/min. Skin tissues were harvested for characterization at 4 h after irradiation. For oxidative stress after low-dose-rate exposure, 0.25, 0.5 and 1 Gy significantly altered 27, 23 and 25 genes, respectively, among 84 genes assessed (P < 0.05). At doses as low as 0.25 Gy, many genes responsible for regulating the production of reactive oxygen species (ROS) were significantly altered, with changes >2-fold compared to 0 Gy. For an ECM profile, 18-20 out of 84 genes were significantly up- or downregulated after low-dose-rate exposure. After high-dose-rate irradiation, of 84 genes associated with oxidative stress, 16, 22 and 22 genes were significantly affected after 0.25, 0.5 and 1 Gy, respectively. Compared to low-dose-rate radiation, high-dose-rate exposure resulted in different ECM gene expression profiles. The most striking changes after low-dose-rate or high-dose-rate exposure on ECM profiles were on genes encoding matrix metalloproteinases (MMPs), e.g., Mmp2 and Mmp15 for low dose rate and Mmp9 and Mmp11 for high dose rate. Immunostaining for MMP-2 and MMP-9 proteins showed radiation dose rate-dependent differences. These data revealed that exposure to low total doses with low-dose-rate or high-dose-rate photon radiation induced oxidative stress and ECM-associated alterations in gene expression profiles. The expression of many genes was differentially regulated by different total dose and/or dose-rate regimens.     

Towards a more nuanced understanding of the relationship between sex-biased gene expression and rates of protein-coding sequence evolution

Genes that are differentially expressed between the sexes (sex-biased genes) are among the fastest evolving genes in animal genomes. The majority of sex-biased expression is attributable to genes that are primarily expressed in sex-limited reproductive tissues, and these reproductive genes are often rapidly evolving because of intra- and intersexual selection pressures. Additionally, studies of multiple taxa have revealed that genes with sex-biased expression are also expressed in a limited number of tissues. This is worth noting because narrowly expressed genes are known to evolve faster than broadly expressed genes. Therefore, it is not clear whether sex-biased genes are rapidly evolving because they have sexually dimorphic expression, because they are expressed in sex-limited reproductive tissues, or because they are narrowly expressed. To determine the extend to which other confounding variables can explain the rapid evolution of sex-biased genes, I analyzed the rates of evolution of sex-biased genes in Drosophila melanogaster and Mus musculus in light of tissue-specific measures of expression. I find that genes with sex-biased expression in somatic tissues shared by both sexes are often evolving faster than non-sex-biased genes, but this is best explained by the narrow expression profiles of sex-biased genes. Sex-biased genes in sex-limited tissues in D. melanogaster, however, evolve faster than other narrowly expressed genes. Therefore, the rapid evolution of sex-biased genes is limited only to those genes primarily expressed in sex-limited reproductive tissues.     

Nitrogen and phosphorus acquisition by the mycelium of the ectomycorrhizal fungus Paxillus involutus and its effect on host nutrition

The contribution of the extramatrical mycelium to N and P nutrition of mycorrhizal Norway spruce ( Picea abies (L.) Karst.) was investigated. Seedlings either inoculated with Paxillus involutus (Batsch) Fr. or non-mycorrhizal were grown in a two compartment sand culture system where hyphae were separated from roots by a 45 μm nylon net. Nutrient solution of the hyphal compartment contained either 1.8 m m NH₄⁺ and 0.18 m m H₂PO₄⁻ or no N and P. Aluminium added to the hyphal compartment as a tracer of mass flow was not detected in the plant compartment, indicating that measurements of N and P transfer by the mycelium were not biased by solute movement across the nylon net.
The addition of N and P to the hyphal compartment markedly increased dry weight, N and P concentration and N and P content of mycorrhizal plants. Calculating uptake from the difference in input and output of nutrient in solution confirmed a hyphal contribution of 73% and 76% to total N and P uptake, respectively. Hyphal growth was increased at the site of nutrient solution input.     

Beyond comparing means: the usefulness of analyzing interindividual variation in gene expression for identifying genes associated with cancer development

Identifying genes associated with cancer development is typically accomplished by comparing mean expression values in normal and tumor tissues, which identifies differentially expressed (DE) genes. Interindividual variation (IV) in gene expression is indirectly included in DE gene identification because given the same absolute differences in means, genes with lower variance tend to have lower p-values. We explored the direct use of IV in gene expression to identify candidate genes associated with cancer development. We focused on prostate (PCa) and lung (LC) cancers and compared IV in the expression level of genes shown to be cancer related with that in all other genes in the human genome. Compared with all those other genes, cancer-related genes tended to have greater IV in normal tissues and a greater increase in IV during the transition from normal to tumorous tissue. Genes without significantly different mean expression values between tumor and normal tissues but with greater IV in tumor than in normal tissue (note: the DE-based approach completely ignores those genes) had stronger associations with clinically important features like Gleason score in PCa or tumor histology in LC than all other genes were. Our results suggest that analyzing IV in gene expression level is useful in identifying novel candidate genes associated with cancer development.     

The role of the motile tubular vacuole system in mycorrhizal fungi

Mycorrhizal fungi, to be effective for the plant, must be able to transfer mineral nutrient elements from sites of uptake at hyphal tips across various distances to the exchange region in the mycorrhiza. Vacuoles are likely to be important in this transport, since they contain elements of nutritional significance in abundance. In tip cells of hyphae of most fungi –- known to include three ectomycorrhizal basidiomycetes, an ericoid mycobiont, and two arbuscular mycorrhizal fungi –- the vacuoles form a motile tubular reticulum. The vacuoles are most active in hyphal tips, but non-motile vacuoles at a distance from the tip can be induced to become motile by environmental changes. Neither the tubular vacuolar reticulum nor its contents are properly preserved by conventional fixation and embedding. Vacuolar tubules are readily shown in vivo with fluorescent tracers, throughout the extramatrical mycelium and in outer hyphae of the sheath in eucalypt mycorrhizas synthesised with Pisolithus sp., but they have proved harder to label in field-collected ectomycorrhizas and ericoid mycorrhizas. Freeze-substitution does preserve the structure of vacuoles and vacuolar tubules, and careful anhydrous techniques allow them to be microanalysed, indicating high content of K and P in vacuoles of hyphal tips, and also in sheath and Hartig net of ectomycorrhizas. Vacuoles contain polyphosphate in diffuse, non-granular form. Polyphosphate is present right up to the tip region of hyphae as well as in sheath and Hartig net: thus important mineral nutrient elements are present at both ends of the long hyphal transport pathway. Exactly what happens in between, however, remains to be elucidated.     

生物信息学分析筛选结直肠癌靶基因及评估预后价值

为寻找与结直肠癌发展和预后相关的潜在关键基因及信号通路.从美国国立信息中心NCBI的GEO数据库获得结直肠癌基因表达数据集GSE106582,通过PCA对样本进行分组,利用GEO2R进行综合分析,筛选结直肠癌与癌旁对照组的差异表达基因;通过DAVID在线工具对差异表达基因进行GO本体分析和KEGG通路富集分析,初步分析...     

Expression of the nitrate transporter nrt2 gene from the symbiotic basidiomycete Hebeloma cylindrosporum is affected by host plant and carbon sources

Although the function of the extramatrical mycelium of ectomycorrhizal fungi is considered essential for the acquisition of nitrogen by forest trees, gene regulation in this fungal compartment is poorly characterized. In this study, the expression of the nitrate transporter gene nrt2 from the ectomycorrhizal basidiomycete Hebeloma cylindrosporum was shown to be regulated by plant host and carbon sources. In the presence of a low fructose concentration, nrt2 expression could not be detected in the free-living mycelium but was high in the extramatrical symbiotic mycelium associated to the host plant Pinus pinaster. In the absence of nitrogen or in the presence of nitrate, high sugar concentrations in the medium were able to enhance nrt2 expression. Nevertheless, in the presence of high fructose concentration, high ammonium concentration still completely repressed nrt2 expression indicating that the nitrogen repression overrides sugar stimulation. This is the first report revealing an effect of host plant and of carbon sources on the expression of a fungal nitrate transporter-encoding gene.     

The expression of GintPT, the phosphate transporter of Rhizophagus irregularis, depends on the symbiotic status and phosphate availability

The development of mutualistic interactions with arbuscular mycorrhizal (AM) fungi is one of the most important adaptation of terrestrial plants to face mineral nutrition requirements. As an essential plant nutrient, phosphorus uptake is acknowledged as a major benefit of the AM symbiosis, but the molecular mechanisms of its transport as inorganic phosphate (Pi) from the soil to root cells via AM fungi remain poorly known. Here we monitored the expression profile of the high-affinity phosphate transporter (PT) gene (GintPT) of Rhizophagus irregularis (DAOM 197198) in fungal structures (spores, extraradical mycelium and arbuscules), under different Pi availability, and in respect to plant connection. GintPT resulted constitutively expressed along the major steps of the fungal life cycle and the connection with the host plant was crucial to warrant GintPT high expression levels in the extraradical mycelium. The influence of Pi availability on gene expression of the fungal GintPT and the Medicago truncatula symbiosis-specific Pi transporter (MtPT4) was examined by qRT-PCR assay on microdissected arbusculated cells. The expression profiles of both genes revealed that these transporters are sensitive to changing Pi conditions: we observed that MtPT4 mRNA abundance is higher at 320 than at 32 μM suggesting that the flow towards the plant requires high concentrations. Taken on the whole, the findings highlight novel traits for the functioning of the GintPT gene and offer a molecular scenario to the models describing nutrient transfers as a cooperation between the mycorrhizal partners.     

Insights from the clustering of microarray data associated with the heart disease

Heart failure (HF) is the major of cause of mortality and morbidity in the developed world. Gene expression profiles of animal model of heart failure have been used in number of studies to understand human cardiac disease. In this study, statistical methods of analysing microarray data on cardiac tissues from dogs with pacing induced HF were used to identify differentially expressed genes between normal and two abnormal tissues. The unsupervised techniques principal component analysis (PCA) and cluster analysis were explored to distinguish between three different groups of 12 arrays and to separate the genes which are up regulated in different conditions among 23912 genes in heart failure canines'' microarray data. It was found that out of 23912 genes, 1802 genes were differentially expressed in the three groups at 5% level of significance and 496 genes were differentially expressed at 1% level of significance using one way analysis of variance (ANOVA). The genes clustered using PCA and clustering analysis were explored in the paper to understand HF and a small number of differentially expressed genes related to HF were identified.