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PubMed2005

GC-compositional strand bias around transcription start sites in plants and fungi.

BACKGROUND: A GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residues, was recently reported near the transcription start sites (TSS) of Arabidopsis genes. However, it is unclear whether other eukaryotic species have equally prominent GC-skews, and the biological meaning of this trait remains unknown. RESULTS: Our study confirmed a significant GC-skew (C > G) in the TSS of Oryza sativa (rice) genes. The full-length cDNAs and genomic sequences from Arabidopsis and rice were compared using statistical analyses. Despite marked differences in the G+C content around the TSS in the two plants, the degrees of bias were almost identical. Although slight GC-skew peaks, including opposite skews (C < G), were detected around the TSS of genes in human and Drosophila, they were qualitatively and quantitatively different from those identified in plants. However, plant-like GC-skew in regions upstream of the translation initiation sites (TIS) in some fungi was identified following analyses of the expressed sequence tags and/or genomic sequences from other species. On the basis of our dataset, we estimated that > 70 and 68% of Arabidopsis and rice genes, respectively, had a strong GC-skew (> 0.33) in a 100-bp window (that is, the number of C residues was more than double the number of G residues in a +/-100-bp window around the TSS). The mean GC-skew value in the TSS of highly-expressed genes in Arabidopsis was significantly greater than that of genes with low expression levels. Many of the GC-skew peaks were preferentially located near the TSS, so we examined the potential value of GC-skew as an index for TSS identification. Our results confirm that the GC-skew can be used to assist the TSS prediction in plant genomes. CONCLUSION: The GC-skew (C > G) around the TSS is strictly conserved between monocot and eudicot plants (ie. angiosperms in general), and a similar skew has been observed in some fungi. Highly-expressed Arabidopsis genes had overall a more marked GC-skew in the TSS compared to genes with low expression levels. We therefore propose that the GC-skew around the TSS in some plants and fungi is related to transcription. It might be caused by mutations during transcription initiation or the frequent use of transcription factor-biding sites having a strand preference. In addition, GC-skew is a good candidate index for TSS prediction in plant genomes, where there is a lack of correlation among CpG islands and genes.

Arabidopsis↗

PubMed2006

Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae.

BACKGROUND: Secretion stress is caused by compromised folding, modification or transport of proteins in the secretory pathway. In fungi, induction of genes in response to secretion stress is mediated mainly by the unfolded protein response (UPR) pathway. This study aims at uncovering transcriptional responses occurring in the filamentous fungi Trichoderma reesei exposed to secretion stress and comparing these to those found in the yeast Saccharomyces cerevisiae. RESULTS: Chemostat cultures of T. reesei expressing human tissue plasminogen activator (tPA) and batch bioreactor cultures treated with dithiothreitol (DTT) to prevent correct protein folding were analysed with cDNA subtraction and cDNA-amplified fragment length polymorphism (AFLP) experiments. ESTs corresponding to 457 unique genes putatively induced under secretion stress were isolated and the expression pattern of 60 genes was confirmed by Northern analysis. Expression of these genes was also studied in a strain over-expressing inositol-requiring enzyme 1 (IREI) protein, a sensor for the UPR pathway. To compare the data with that of S. cerevisiae, published transcriptome profiling data on various stress responses in S. cerevisiae was reanalysed. The genes up-regulated in response to secretion stress included a large number of secretion related genes in both organisms. In addition, analysis of T. reesei revealed up regulation of the cpc1 transcription factor gene and nucleosomal genes. The induction of the cpcA and histone gene H4 were shown to be induced also in cultures of Aspergillus nidulans treated with DTT. CONCLUSION: Analysis of the genes induced under secretion stress has revealed novel features in the stress response in T. reesei and in filamentous fungi. We have demonstrated that in addition to the previously rather well characterised induction of genes for many ER proteins or secretion related proteins also other types of responses exist.

Amino Acids↗

PubMed2001

Induction and catabolite repression mechanisms of cellulase in fungi.

Cellulases are induced in most of fungi only when cellulose or an inducer exists. In Hypocrea jecorina and Penicillium purpurogenum, the respective inducers are sophorose and gentiobiose, which do not have beta-1,4 linkages though cellobiose, which has this linkage, is an inducer in other fungi. beta-Glucosidase, which catalyzes transglucosylation, is the key enzyme in converting cello-oligosaccharides to the inducers for cellulase induction in H. jecorina and P. purpurogenum. There are three states in the regulation of cellulase at the transcriptional level in fungi: expression at a basal level, mass secretion of cellulases induced by inducers, and glucose or catabolite repression. Expression at a basal level allows a small amount of cellulase to hydrolyze cellulose to soluble oligosaccharides or to an inducer if cellulose exists near the mycelia. Once the inducer enters the cell, it triggers full-scale transcription of the cellulase gene mediated by activator proteins and activating elements. After cellulose is degraded a large amount of glucose is liberated, which causes catabolite repression.

Journal Article↗

PubMed2000

Biosynthesis of abscisic acid by the non-mevalonate pathway in plants, and by the mevalonate pathway in fungi.

The biosynthetic pathways to abscisic acid (ABA) were investigated by feeding [1-(13)C]-D-glucose to cuttings from young tulip tree shoots and to two ABA-producing phytopathogenic fungi. 13C-NMR spectra of the ABA samples isolated showed that the carbons at 1, 5, 6, 4', 7' and 9' of ABA from the tulip tree were labeled with 13C, while the carbons at 2, 4, 6, 1', 3', 5', 7', 8' and 9' of ABA from the fungi were labeled with 13C. The former corresponds to C-1 and -5 of isopentenyl pyrophosphate, and the latter to C-2, -4 and -5 of isopentenyl pyrophosphate. This finding reveals that ABA was biosynthesized by the non-mevalonate pathway in the plant, and by the mevalonate pathway in the fungi. 13C-Labeled beta-carotene from the tulip tree showed that the positions of the labeled carbons were the same as those of ABA, being consistent with the biosynthesis of ABA via carotenoids. Lipiferolide of the tulip tree was also biosynthesized by the non-mevalonate pathway.

Abscisic Acid↗

PubMed2005

An overview of the CCAAT-box binding factor in filamentous fungi: assembly, nuclear translocation, and transcriptional enhancement.

Filamentous fungi are frequently used for the production of industrial enzymes, since they produce a variety of enzymes including polysaccharide-degrading enzymes. Among the many filamentous fungi, Aspergillus species, such as A. oryzae and A. niger, are known as strong producers of amylolytic enzymes. We have been studying on the regulatory mechanisms underlying the expression of A. oryzae amylolytic genes. Based on analyses using a hybrid model system of A. nidulans transformed by a gene encoding A. oryzae Taka-amylase A, the major amylase (taaG2), we have found that three factors, CCAAT-box binding protein, CreA, and AmyR, are involved in taaG2 gene expression and regulation. In this review, the focus is on the CCAAT-box binding protein of filamentous fungi. The assembly, nuclear translocation, and transcriptional enhancement mechanisms of the CCAAT-box binding protein are discussed.

Active Transport, Cell Nucleus↗

PubMed2003

Carbon-thirteen cross-polarization magic angle spinning nuclear magnetic resonance and Fourier transform infrared studies of thermally modified wood exposed to brown and soft rot fungi.

Thermally modified wood has many technically interesting properties, such as increased dimensional stability, low equilibrium moisture content, and enhanced biological and weather resistance. This paper describes solid-state nuclear magnetic resonance (NMR) and Fourier transform infrared (FT-IR) spectroscopic studies on the decay of heat-treated and untreated pine (Pinus sylvestris) by brown (Poria placenta) and soft rot fungi. Both techniques combined with multivariate data analysis proved to be powerful tools for the study of wood degradation by fungi. When untreated pine was exposed to brown or soft rot fungi, a drastic decay of the cell wall polysaccharides was observed. Brown rot fungus degraded mainly hemicelluloses while soft rot fungus attacked cellulose more extensively. The aromatic region of 13C cross-polarization magic angle spinning (CPMAS) NMR spectra revealed that the structure of lignin was also altered. New carboxylic structures were formed as a consequence of the decay. The increased biological resistance of pine wood heat-treated at >220 degrees C was observed in the 13C CPMAS NMR and IR spectra.

Basidiomycota↗

PubMed2007

Risk factors for pulmonary Aspergillus terreus infection in patients with positive culture for filamentous fungi.

BACKGROUND: Invasive aspergillosis (IA) is a common fungal infection in immunocompromised patients and has a high mortality rate. Among patients with IA, Aspergillus terreus infections have become a growing concern in the past few years. OBJECTIVE: To determine the clinical risk factors for isolation of and respiratory infection by A terreus in patients with culture findings positive for filamentous fungi. METHODS: Cohort study of 505 consecutive isolates of filamentous fungi in 332 patients from one center. A terreus was present in 46 isolates from 40 patients (9.1%). Clinical histories were reviewed to identify the risk factors related to isolation of and infection by A terreus, which were grouped into three categories (ie, host factors, factors related to immunosuppression, and factors related to hospitalization), and were analyzed using a multiple logistic regression model. RESULTS: A total of 192 of 505 isolates studied (38%) were due to invasive respiratory infection. A total of 27 of 46 cultures (58.7%) that were positive for A terreus were due to invasive infection (odds ratio [OR], 2.53; 95% confidence interval [CI], 1.37 to 4.69; p = 0.034). The factors associated with invasive A terreus infection were prophylactic use of amphotericin B aerosols (OR, 27.8; 95% CI, 6.7 to 109.7; p = 0.001) and mechanical ventilation (OR, 3.3; 95% CI, 1.02 to 10.9; p = 0.04). Transplantation was associated with a lower risk of A terreus infection (OR, 0.2; 95% CI, 0.046 to 0.789; p = 0.02). CONCLUSIONS: In patients with culture findings positive for filamentous fungi, the prophylactic use of amphotericin B aerosols and mechanical ventilation are associated with a higher risk of A terreus infections. In these patients, transplantation is associated with a lower risk of isolation and respiratory infection by A terreus.

Administration, Inhalation↗

PubMed2000

Screening of potential antibiotic action of cellulolytic fungi.

Twenty different strains of filamentous fungi were initially selected for evaluation of cellulolytic activity using a single test in a simple mineral salts culture medium with filter paper as the only carbon source. Those fungi strains that were capable of completely breaking the filter paper strip within 4-8 d were assayed also for antimicrobial action, using Staphyloccocus aureus ATCC 6538P according to the so-called agar piece method. We screened three different strains with both capacities: the production of cellulolytic activity and antibiotic action. The experimental results suggest that the fungi Penicillium sp. F0PC01, Aspergillus sp. F0Q001, and Cephalosporium sp. F03800 have both capabilities because they grew rapidly on cellulose as the only carbon source and were able to produce an area of growth inhibition in S. aureus of approx 2.04, 1.57, and 2.39 cm, respectively, on agar plates using the agar piece method. Subsequently, the antibiotic production obtained with those cellulolytic strains was evaluated by submerged fermentation at the flask level, in a simple culture medium containing lactose without biosynthesis precursor, obtaining 3670, 2830, and 4060 antibiotic units/mL, referred to as penicillin G, whereas for cellulolytic activity, the results were 1.34, 1.81 and 0.57 FPU/mL, respectively.

Acremonium↗

PubMed1999

From edible to useful mushrooms--an attempt for the new economical assessment of large fungi.

According to the stand of the modern applied mycological research the most commonly used term "edible mushroom" does not express all significant aspects large fungi can be used for. Additionally to bioconversion for food and animal feed production there are at least three other fields where large fungi may also get economical relevance: for establishing of ectomycorrhiza, for medical application and for soil decontamination including environmental engineering. This new situation justifies the introduction of a new, all-embracing designation for large fungi. The term "useful mushroom" will be suggested. The various options of the use of mushrooms will be introduced and briefly discussed in this paper.

Agaricales↗

PubMed2006

Pathogenicity of three formulations of entomopathogenic fungi for control of adult Haematobia irritans (Diptera: Muscidae).

Powder formulations of three species of entomopathogenic fungi were evaluated for their pathogenic effect upon adult horn flies, Hematobia irritans (L.) (Diptera: Muscidae). Flies were treated with conidia and blastospores of the entomopathogenic fungi Beauveria bassiana (Bals.) Vuill. (strain GHA), Metarhizium anisopliae (Metschnikoff) Sorokin (strain ESCI), and Paecilomyces fimosoroseus (Wize) Brown & Smith (strain ARSEF 3581) in the laboratory. At 4 d postexposure, flies treated with B. bassiana had an average of 98.4% mortality versus 43.5% from treatment with M. anisopliae and 13.0% from treatment with P. fiimosoroseus. At 7 d postexposure, flies treated with B. bassiana had an average of 100.0% mortality compared with 73.0% from treatment with M. anisopliae and 33.3% from treatment with P.fumosoroseus. Mean lethal time (LT50) was 2.70, 4.98, and 7.97 d for B. bassiana, M. anisopliae, and P. fiumosoroseus, respectively. Entomopathogenic fungi such as B. bassiana and M. anisopliae may have the potential for controlling populations of horn flies. These studies indicate that B. bassiana and M. anisopliae were not only pathogenic to adult horn flies, but they caused mortality in a short time.

Animals↗

PubMed2004

Description, distribution, activity and phylogenetic relationship of ribosome-inactivating proteins in plants, fungi and bacteria.

Ribosome-Inactivating Proteins (RIPs) are enzymes that trigger the catalytic inactivation of ribosomes and other substrates. They are present in a large number of plants and have been found also in fungi, algae and bacteria. RIPs are currently classified as type 1, those formed by a single polypeptide chain with the enzymatic activity, and type 2, those formed by 2 types of chains, i.e. A chains equivalent to a type 1 RIPs and B chains with lectin activity. Type 2 RIPs usually contain the formulae A-B, (A-B)2 and less frequent (A-B)4 and polymeric forms of type 2 RIPs lectins. RIPs are broadly distributed in plants, and are present also in fungi, bacteria, at least in one alga; recently RIP-type activity has been described in mammalian tissues. The highest number of RIPs has been found in Caryophyllaceae, Sambucaceae, Cucurbitaceae, Euphorbiaceae, Phytolaccaceae and Poaceae. However there are no systematic screening studies to allow generalisations about occurrence. The most known activity of RIPs is the translational inhibitory activity, which seems a consequence of a N-glycosidase on the 28 S rRNA of the eukaryotic ribosome that triggers the split of the A(4324) (or an equivalent base in other ribosomes), which is key for translation. This activity seems to be part of a general adenine polynucleotide glycosylase able to act on several substrates other than ribosomes, such as tRNA, mRNA, viral RNA and DNA. Other enzymatic activities found in RIPs are lipase, chitinase and superoxide dismutase. RIPs are phylogenetically related. In general RIPs from close families share good amino acid homologies. Type 1 RIPs and the A chains of type 2 RIPs from Magnoliopsida (dicotyledons) are closely related. RIPs from Liliopsida (monocotyledons) are at the same time closely related and distant from Magnoliopsida. Concerning the biological roles played by RIPs there are several hypotheses, but the current belief is that they could play significant roles in the antipathogenic (viruses and fungi), stress and senescence responses. In addition, roles as antifeedant and storage proteins have been also proposed. Future research will approach the potential biological roles played by RIPs and their use as toxic effectors in the construction of immunotoxins and conjugates for target therapy.

Bacterial Proteins↗

PubMed1996

An apparatus (Georgiou-Petri dish) for growing fungi and other microorganisms on liquid media in a Petri dish.

This work describes a new apparatus for growing fungi and other microorganisms on liquid nutrient media in a Petri dish. The apparatus is composed of a net supporting a cellophane membrane stretched between an outer and an inner ring that is placed inside a Petri dish. This modification of the standard Petri dish offers many advantages for studying growth, metabolism, differentiation, and other aspects of fungi in liquid cultures with minimal waste of expensive chemicals. Monitoring of excreted or absorbed substances by the fungi, the aseptic transfer of undisturbed fungal colonies from dish to dish, and harvesting are made easier, using this apparatus.

Ascomycota↗

PubMedDate not supplied

Phylogenetics and evolution of nematode-trapping fungi (Orbiliales) estimated from nuclear and protein coding genes.

The systematic classification of nematode-trapping fungi is redefined based on phylogenies inferred from sequence analyses of 28S rDNA, 5.8S rDNA and beta-tubulin genes. Molecular data were analyzed with maximum parsimony, maximum likelihood and Bayesian analysis. An emended generic concept of nematode-trapping fungi is provided. Arthrobotrys is characterized by adhesive networks, Dactylellina by adhesive knobs, and Drechslerella by constricting-rings. Phylogenetic placement of taxa characterized by stalked adhesive knobs and non-constricting rings also is confirmed in Dactylellina. Species that produce unstalked adhesive knobs that grow out to form loops are transferred from Gamsylella to Dactylellina, and those that produce unstalked adhesive knobs that grow out to form networks are transferred from Gamsylella to Arthrobotrys. Gamsylella as currently circumscribed cannot be treated as a valid genus. A hypothesis for the evolution of trapping-devices is presented based on multiple gene data and morphological studies. Predatory and nonpredatory fungi appear to have been derived from nonpredatory members of Orbilia. The adhesive knob is considered to be the ancestral type of trapping device from which constricting rings and networks were derived via two pathways. In the first pathway adhesive knobs retained their adhesive material forming simple two-dimension networks, eventually forming complex three-dimension networks. In the second pathway adhesive knobs lost their adhesive materials, with their ends meeting to form nonconstricting rings and they in turn formed constricting rings with three inflated-cells.

Animals↗

PubMed2005

Nonpathogenic, environmental fungi induce activation and degranulation of human eosinophils.

Eosinophils and their products are probably important in the pathophysiology of allergic diseases, such as bronchial asthma, and in host immunity to certain organisms. An association between environmental fungal exposure and asthma has been long recognized clinically. Although products of microorganisms (e.g., lipopolysaccharides) directly activate certain inflammatory cells (e.g., macrophages), the mechanism(s) that triggers eosinophil degranulation is unknown. In this study we investigated whether human eosinophils have an innate immune response to certain fungal organisms. We incubated human eosinophils with extracts from seven environmental airborne fungi (Alternaria alternata, Aspergillus versicolor, Bipolaris sorokiniana, Candida albicans, Cladosporium herbarum, Curvularia spicifera, and Penicillium notatum). Alternaria and Penicillium induced calcium-dependent exocytosis (e.g., eosinophil-derived neurotoxin release) in eosinophils from normal individuals. Alternaria also strongly induced other activation events in eosinophils, including increases in intracellular calcium concentration, cell surface expression of CD63 and CD11b, and production of IL-8. Other fungi did not induce eosinophil degranulation, and Alternaria did not induce neutrophil activation, suggesting specificity for fungal species and cell type. The Alternaria-induced eosinophil degranulation was pertussis toxin sensitive and desensitized by preincubating cells with G protein-coupled receptor agonists, platelet-activating factor, or FMLP. The eosinophil-stimulating activity in Alternaria extract was highly heat labile and had an M(r) of approximately 60 kDa. Thus, eosinophils, but not neutrophils, possess G protein-dependent cellular activation machinery that directly responds to an Alternaria protein product(s). This innate response by eosinophils to certain environmental fungi may be important in host defense and in the exacerbation of inflammation in asthma and allergic diseases.

Alternaria↗

PubMed2005

Survey of nematophagous fungi in South Africa.

Three hundred and eighty-four samples of leaf litter, soil, faeces from domestic and game animals, compost and aqueous cultures of infective nematode larvae contaminated with unidentified fungi were plated out on water agar, baited with pure infective larvae of Haemonchus contortus, incubated and examined for the presence of nematophagous fungi. Duddingtonia flagrans was isolated from five samples, and 73 samples were positive for other nematophagous fungi.

Animals↗

PubMed1997

Keratinophilic fungi from coats of wild boars in Italy.

Hair samples were collected from wild boars (Sus scrofa) in Italy to determine the presence of keratinophilic fungi. Eleven (5%) of 211 boars had fungi: two (1%) had Trichophyton mentagrophytes, five (2%) had T. terrestre, two (1%) had Chrysosporium keratinophilum, one (0.5%) had Chrysosporium tropicum, and one (0.5%) had both C. keratinophilum and T. terrestre. These are the first recorded isolations of C. keratinophilum, C. tropicum, and T. terrestre from wild boars. Based on the low prevalence of keratinophilic fungi, wild boars probably are not of special epizootological interest for dermatophytic infections.

Animals↗

PubMed1999

Influence of fowl uropygial gland and its secretory lipid components on the growth of skin surface fungi of fowl.

Fungal species, which were shown to colonize consistently on the skin surface of the breast region of adult (1 year old) white leghorn fowl, were identified as Aspergillus sydowii, A. tamarii, A. rugulosus and Absidia corymbifera. Of these, A. sydowii and A. tamarii were the dominant forms. Two species of fungi, namely, Aspergillus niger and Scopulariopsis brevicaulis were shown to be present in the cultures of the scrubbings from breast skin surface after 60 days of captivity of the fowls. Extirpation of the uropygial gland resulted in encouragement of the in vitro population growth of all species of fungi except that of A. rugulosus. The effect was found to be very conspicuous for A. sydowii and A. tamarii, particularly after 60 days of gland removal. Addition of total lipids and the wax diester component of free-flowing uropygial secretion as 0.2% suspension in Sabouraud's agar medium of individual fungal isolates caused marked suppression of the population growth of A. sydowii, A. tamarii, Absidia corymbifera and to some extent of S. brevicaulis. Other components of secretory lipids, such as wax alcohols (2,3-alkane-diols), wax acids, triglycerides and hydrocarbons (including squalene) when supplemented separately to culture medium of individual fungi at identical concentration, were also shown to cause inhibition of the growth of most of fungal species at different degrees.

Absidia↗

PubMed2000

Molecular signaling in pathogenicity and host recognition in smut fungi taking Karnal bunt as a model system.

Karnal bunt of wheat, incited by a phytopathogen Tilletia indica (Syn. Neovossia indica) is a floret infecting disease. In the floral tissues fungus proliferates and produces massive amount of black spores. In smut fungi, belonging to order Ustilaginales, communication between cells is necessary to regulate growth, differentiation and monokaryotic to dikaryotic transition during pathogenic and sexual development. Neighbouring cells are able to communicate with each other by direct cell to cell contact through plasma membrane bound signaling molecules or through formation of gap junctions and alternatively through secretion of chemical signals if cells are some distance away. Current research efforts toward understanding of pathogenic and sexual development in phytopathogenic fungi, offer a number of opportunities. These include the analysis of molecular signal(s) for direct contribution of sexual interactions to ability of smut and bunt pathogens to cause disease. These efforts will provide not only to explore the mechanisms of pathogenesis, but also to enhance knowledge of basic cellular biology of an economically important group of fungi.

Cell Communication↗