| 1. |
- Melin, Petter, et al.
(författare)
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Characterization of phiA, a gene essential for phialide development in Aspergillus nidulans
- 2003
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Ingår i: Fungal Genetics and Biology. - : Academic Press. - 1087-1845 .- 1096-0937. ; 40:3, s. 234-241
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Tidskriftsartikel (refereegranskat)abstract
- We have previously identified genes and proteins involved in the fungal response to the Streptomyces-produced antibiotics, bafilomycin 131 and concanamycin A, known inhibitors of V-ATPases. Using mRNA differential display we identified an Aspergillus nidulans gene with 30-fold up-regulated expression in the presence of bafilomycin. This gene, here denoted phiA, and its gene product, were further characterized by targeted gene disruption and immunohistochemistry. Phenotypically, the phiA mutation resulted in reduced growth and severely reduced sporulation. The abnormality could be traced to the phialides, which divided several times instead of forming a single flask-shaped cell. The importance of phiA for phialide and conidium development was supported by immunohistochemistry experiments that showed the protein to be mainly present in these two cell types. Attempts to relate phiA to inhibition of V-ATPases did not result in unambiguous conclusions, but suggest the possibility that changed expression of phiA is correlated with growth arrest caused by inhibited V-ATPases.
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| 2. |
- Andersen, M.R., et al.
(författare)
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Current status of systems biology in Aspergilli
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46:584-590, s. 180-190
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Tidskriftsartikel (refereegranskat)abstract
- Saccharomyces cerevisiae is a unicellular eukaryal microorganism that has traditionally been regarded either as a model system for investigating cellular physiology or as a cell factory for biotechnological use, for example for the production of fuels and commodity chemicals such as lactate or pharmaceuticals, including human insulin and HPV vaccines. Systems biology has recently gained momentum and has successfully been used for mapping complex regulatory networks and resolving the dynamics of signal transduction pathways. So far, yeast systems biology has mainly focused on the development of new methods and concepts. There are also some examples of the application of yeast systems biology for improving biotechnological processes. We discuss here how yeast systems biology could be used in elucidating fundamental cellular principles such as those relevant for the study of molecular mechanisms underlying complex human diseases, including the metabolic syndrome and ageing.
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| 3. |
- Brandström Durling, Mikael, et al.
(författare)
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Fungal cross-talk: an integrated approach to study distance communication
- 2021
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 148
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Tidskriftsartikel (refereegranskat)abstract
- Despite the interest on fungi as eukaryotic model systems, the molecular mechanisms regulating the fungal nonself-recognition at a distance have not been studied so far. This paper investigates the molecular mechanisms regulating the cross-talk at a distance between two filamentous fungi, Trichoderma gamsii and Fusarium graminearum which establish a mycoparasitic interaction where T. gamsii and F. graminearum play the roles of mycoparasite and prey, respectively. In the present work, we use an integrated approach involving dual culture tests, comparative genomics and transcriptomics to investigate the fungal interaction before contact ('sensing phase').Dual culture tests demonstrate that growth rate of F. graminearum accelerates in presence of T. gamsii at the sensing phase. T. gamsii up-regulates the expression of a ferric reductase involved in iron acquisition, while F. graminearum up-regulates the expression of genes coding for transmembrane transporters and killer toxins. At the same time, T. gamsii decreases the level of extracellular interaction by down-regulating genes coding for hydrolytic enzymes acting on fungal cell wall (chitinases).Given the importance of fungi as eukaryotic model systems and the ever-increasing genomic resources available, the integrated approach hereby presented can be applied to other interactions to deepen the knowledge on fungal communication at a distance.
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| 4. |
- Chen, Hongxin, et al.
(författare)
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A cerato-platanin-like protein HaCPL2 from Heterobasidion annosum sensu stricto induces cell death in Nicotiana tabacum and Pinus sylvestris
- 2015
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 84, s. 41-51
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Tidskriftsartikel (refereegranskat)abstract
- The cerato-platanin family is a group of small secreted cysteine-rich proteins exclusive for filamentous fungi. They have been shown to be involved in the interactions between fungi and plants. Functional characterization of members from this family has been performed mainly in Ascomycota, except Moniliophthora perniciosa. Our previous phylogenetic analysis revealed that recent gene duplication of cerato-platanins has occurred in Basidiomycota but not in Ascomycota, suggesting higher functional diversification of this protein family in Basidiomycota than in Ascomycota. In this study, we identified three cerato-platanin homologues from the basidiomycete conifer pathogen Heterobasidion annosum sensu stricto. Expression of the homologues under various conditions as well as their roles in the H. annosum s.s.-Pinus sylvestris (Scots pine) pathosystem was investigated. Results showed that HaCPL2 (ceratoplatanin-like protein 2) had the highest sequence similarity to cerato-platanin from Ceratocystis platani and hacpl2 was significantly induced during nutrient starvation and necrotrophic growth. The treatment with recombinant HaCPL2 induced cell death, phytoalexin production and defense gene expression in Nicotiana tabacum. Eliciting and cell death-inducing ability accompanied by retardation of apical root growth was also demonstrated in Scots pine seedlings. Our results suggest that HaCPL2 might contribute to the virulence of H. annosum s.s. by promoting plant cell death.
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| 5. |
- Coutinho, P. M., et al.
(författare)
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Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46:Suppl 1, s. S161-S169
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Tidskriftsartikel (refereegranskat)abstract
- The plant polysaccharide degradative potential of Aspergillus nidulans was analysed in detail and compared to that of Aspergillus niger and Aspergillus oryzae using a combination of bioinformatics, physiology and transcriptomics. Manual verification indicated that 28.4% of the A. nidulans ORFs analysed in this study do not contain a secretion signal, of which 40% may be secreted through a non-classical method. While significant differences were found between the species in the numbers of ORFs assigned to the relevant CAZy families, no significant difference was observed in growth on polysaccharides. Growth differences were observed between the Aspergilli and Podospora anserina, which has a more different genomic potential for polysaccharide degradation, suggesting that large genomic differences are required to cause growth differences oil polysaccharides, Differences were also detected between the Aspergilli in the presence Of putative regulatory sequences in the promoters of the ORFs Of this Study and correlation of the presence Of putative XlnR binding sites to induction by xylose was detected for A. niger. These data demonstrate differences at genome content, Substrate specificity of the enzymes and gene regulation in these three Aspergilli, which likely reflect their individual adaptation to their natural biotope. (C) 2008 Elsevier Inc. All rights reserved.
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| 6. |
- Davydenko, Kateryna, et al.
(författare)
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Looking for relationships between the populations of Dothistroma septosporum in northern Europe and Asia
- 2018
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 110, s. 15-25
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Tidskriftsartikel (refereegranskat)abstract
- Dothistroma septosporum, a notorious pine needle pathogen with an unknown historical geographic origin and poorly known distribution pathways, is nowadays found almost in all areas inhabited by pines (Pinus spp.). The main aim of this study was to determine the relationship between North European and East Asian populations. In total, 238 Eurasian D. septosporum isolates from 11 countries, including 211 isolates from northern Europe, 16 isolates from Russian Far East and 11 isolates from Bhutan were analysed using 11 species-specific microsatellite and mating type markers. The most diverse populations were found in northern Europe, including the Baltic countries, Finland and European Russia. Notably, D. septosporum has not caused heavy damage to P. sylvestris in northern Europe, which may suggest a long co-existence of the host and the pathogen. No indication was obtained that the Russian Far East or Bhutan could be the indigenous area of D. septosporum, as the genetic diversity of the fungus there was low and evidence suggests gene flow from northern Europe to Russian Far East. On the western coast of Norway, a unique genetic pattern was observed, which differed from haplotypes dominating other Fennoscandian populations. As an agent of dothistroma needle blight, only D. septosporum was documented in northern Europe and Asia, while D. pini was found in Ukraine and Serbia.
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| 7. |
- Diéguez-Uribeondo, Javier, et al.
(författare)
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Phylogenetic relationships among plant and animal parasites, and saprotrophs in Aphanomyces (Oomycetes)
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 46:5, s. 365-376
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Tidskriftsartikel (refereegranskat)abstract
- Molecular phylogenetic relationships among 12 species of Aphanomyces de Bary (Oomycetes) were analyzed based on 108 ITS sequences of nuclear rDNA. Sequences used in the analyses belonged to the major species currently available in pure culture and GenBank. Bayesian, maximum likelihood, and maximum parsimony analyses support that Aphanomyces constitutes a monophyletic group. Three independent lineages were found: (i) plant parasitic, (ii) animal parasitic, and (iii) saprotrophic or opportunistic parasitic. Sexual reproduction appeared to be critical in plant parasites for survival in soil environments while asexual reproduction seemed to be advantageous for exploiting specialization in animal parasitism. Repeated zoospore emergence seems to be an advantageous property for both plant and animal parasitic modes of life. Growth in unspecific media was generally faster in saprotrophs compared with parasitic species. A number of strains and GenBank sequences were found to be misidentified. It was confirmed molecularly that Aphanomyces piscicida and Aphanomyces invadans appear to be conspecific, and found that Aphanomyces iridis and Aphanomyces euteiches are closely related, if not the same, species. This study has shown a clear evolutionary separation between Aphanomyces species that are plant parasites and those that parasitize animals. Saprotrophic or opportunistic species formed a separate evolutionary lineage except Aphanomyces stellatus whose evolutionary position has not yet been resolved.
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| 8. |
- Diéguez-Uribeondo, Javier, et al.
(författare)
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Re-evaluation of the enigmatic species complex Saprolegnia diclina-Saprolegnia parasitica based on morphological, physiological and molecular data
- 2007
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 44:7, s. 585-601
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships among isolates of the Saprolegnia diclina-Saprolegnia parasitica complex were investigated based on ITS rDNA sequences, and correlated with morphological and physiological characters. The isolates studied belong to five phylogenetically separate clades. The majority of presumed parasitic isolates, mostly isolated from fish lesions, fell within a clade that comprises isolates which has been variously named as S. diclina Type 1, S. parasitica, Saprolegnia salmonis or just as unnamed Saprolegnia sp. Presence of bundles of long-hooked hairs on secondary cysts, high frequency of retracted germination, and oogonia production at 7 degrees C (when occurring) were characteristic of this clade. A single isolate identified as S. diclina Type 2 clustered in a clade along with Saprolegnia ferax isolates. The isolates identified as S. diclina s. str. (S. diclina Type 3) distributed in two clades and appeared closely related to Saprolegnia multispora and to a number of Chilean isolates identified as Saprolegnia australis. The ITS sequences of clade I were almost identical even though the isolates were of diverse geographical origins and showed physiological and morphological differences and variations in their pathogenicity. This suggest these species reproduces clonally even in apparently sexually competent isolates. Adaptation to parasitism in Saprolegnia might have occurred at spore level by the development of long-hooked hairs to facilitate host attachment and selection of a retracting germination. The use of the name S. parasitica should be assigned to isolates of clade I that contained isolates forming cysts with bundles of long-hooked hairs.
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| 9. |
- Dubey, Mukesh, et al.
(författare)
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The glyoxylate cycle is involved in pleotropic phenotypes, antagonism and induction of plant defence responses in the fungal biocontrol agent Trichoderma atroviride
- 2013
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 58-59, s. 33-41
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Tidskriftsartikel (refereegranskat)abstract
- Isocitrate lyase (ICL), a signature enzyme of the glyoxylate cycle, is required for metabolism of non-fermentable carbon compounds like acetate or ethanol, and virulence in bacteria and fungi. In the present study, we investigate the role of the glyoxylate cycle in the fungal biocontrol agent Trichoderma atroviride by generating id deletion and complementation mutants. Phenotypic analyses of the deletion mutant Delta icl suggest that ICL is required for normal growth, conidial pigmentation and germination, and abiotic stress tolerance. The Delta icl strain display reduced antagonism towards Botrytis cinerea in plate confrontation assays. Secretion and sandwich assays further show that secreted factors are partly responsible for the reduced antagonism. Furthermore, in vitro root colonization assays shows that the Delta icl strain retains the ability to internally colonize Arabidopsis thaliana roots. However, the Delta icl strain has a reduced ability to induce systemic defence in A. thaliana leaves that results in reduced protection against B. cinerea. These data shows that ICL and the glyoxylate cycle are important for biocontrol traits in T. atroviride, including direct antagonism and induction of defence responses in plants.
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| 10. |
- Fugelstad, Johanna, et al.
(författare)
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Identification of the cellulose synthase genes from the Oomycete Saprolegnia monoica and effect of cellulose synthesis inhibitors on gene expression and enzyme activity
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 46:10, s. 759-767
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Tidskriftsartikel (refereegranskat)abstract
- Cellulose biosynthesis is a vital but yet poorly understood biochemical process in Oomycetes. Here, we report the identification and characterization of the cellulose synthase genes (CesA) from Saprolegnia monoica. Southern blot experiments revealed the occurrence of three CesA homologues in this species and phylogenetic analyses confirmed that Oomycete CesAs form a clade of their own. All gene products contained the D,D,D,QXXRW signature of most processive glycosyltransferases, including cellulose synthases. However, their N-terminal ends exhibited Oomycete-specific domains, i.e. Pleckstrin Homology domains, or conserved domains of an unknown function together with additional putative transmembrane domains. Mycelial growth was inhibited in the presence of the cellulose biosynthesis inhibitors 2,6-dichlorobenzonitrile or Congo Red. This inhibition was accompanied by a higher expression of all CesA genes in the mycelium and increased in vitro glucan synthase activities. Altogether, our data strongly suggest a direct involvement of the identified CesA genes in cellulose biosynthesis.
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| 11. |
- Ianiri, Giuseppe, et al.
(författare)
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Development of resources for the analysis of gene function in Pucciniomycotina red yeasts
- 2011
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 48:7, s. 685-695
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Tidskriftsartikel (refereegranskat)abstract
- The Pucciniomycotina is an important subphylum of basidiomycete fungi but with limited tools to analyze gene functions. Transformation protocols were established for a Sporobolomyces species (strain IAM 13481), the first Pucciniomycotina species with a completed draft genome sequence, to enable assessment of gene function through phenotypic characterization of mutant strains. Transformation markers were the URA3 and URA5 genes that enable selection and counter-selection based on uracil auxotrophy and resistance to 5-fluoroorotic acid. The wild type copies of these genes were cloned into plasmids that were used for transformation of Sporobolomyces sp. by both biolistic and Agrobacterium-mediated approaches. These resources have been deposited to be available from the Fungal Genetics Stock Center. To show that these techniques could be used to elucidate gene functions, the LEU1 gene was targeted for specific homologous replacement, and also demonstrating that this gene is required for the biosynthesis of leucine in basidiomycete fungi. T-DNA insertional mutants were isolated and further characterized, revealing insertions in genes that encode the homologs of Chs7, Erg3, Kre6, Kexl, Pik1, Sad 1, Ssu1 and Tlg1. Phenotypic analysis of these mutants reveals both conserved and divergent functions compared with other fungi. Some of these strains exhibit reduced resistance to detergents, the antifungal agent fluconazole or sodium sulfite, or lower recovery from heat stress. While there are current experimental limitations for Sporobolomyces sp. such as the lack of Mendelian genetics for conventional mating, these findings demonstrate the facile nature of at least one Pucciniomycotina species for genetic manipulation and the potential to develop these organisms into new models for understanding gene function and evolution in the fungi.
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| 12. |
- Johannesson, Henrik, et al.
(författare)
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Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii
- 2006
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 43:8, s. 545-559
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Tidskriftsartikel (refereegranskat)abstract
- Coccidioides posadasii is a dimorphic fungal pathogen that grows as a Wlamentous saprobe in the soil and as endosporulating spheruleswithin the host. To identify genes speciWc to the pathogenic phase of Co. posadasii, we carried out a large-scale study of gene expression intwo isolates of the species. From the sequenced Co. posadasii genome, we chose 1000 open reading frames to construct a 70-mer microarray.RNA was recovered from both isolates at three life-cycle phases: hyphae, presegmented spherules, and spherules releasing endospores.Comparative hybridizations were conducted in a circuit design, permitting comparison between both isolates at all three life-cyclephases, and among all life-cycle phases for each isolate. By using this approach, we identiWed 92 genes that were diVerentially expressedbetween pathogenic and saprobic phases in both fungal isolates, and 43 genes with consistent diVerential expression between the two parasiticdevelopmental phases. Genes with elevated expression in the pathogenic phases of both isolates included a number of genes thatwere involved in the response to environmental stress as well as in the metabolism of lipids. The latter observation is in agreement withprevious studies demonstrating that spherules contain a higher proportion of lipids than saprobic phase tissue. Intriguingly, we discoveredstatistically signiWcant and divergent levels of gene expression between the two isolates proWled for 64 genes. The results suggest thatincorporating more than one isolate in the experimental design oVers a means of categorizing the large collection of candidate genes thattranscriptional proWling typically identiWes into those that are strain-speciWc and those that characterize the entire species.
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| 13. |
- Kejžar, Anja, et al.
(författare)
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HwHog1 kinase activity is crucial for survival of Hortaea werneckii in extremely hyperosmolar environments.
- 2015
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Ingår i: Fungal genetics and biology : FG & B. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 74, s. 45-58
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Tidskriftsartikel (refereegranskat)abstract
- Although suggested, the involvement of the HOG pathway in adaptation processes in extremely halotolerant fungus Hortaea werneckii has never been specifically demonstrated. Here, we show that the H. werneckii HOG pathway is very robust, and that it includes two functionally redundant MAPK homologues, HwHog1A and HwHog1B, that show osmolyte-type-dependent phosphorylation. Inhibition of HwHog1 kinase activity with the ATP analogue BPTIP restricts H. werneckii colony growth at 3.0M NaCl, KCl and sorbitol, most likely due to restricted cell division. On the other hand, HwHog1-regulated transcription of a selected group of genes (HwSTL1, HwGUT2, HwOPI3, HwGDH1, HwUGP1, HwGPD1) is an osmolyte-specific process that is important for induction of gene transcription with high NaCl, for regulation of specific genes with high sorbitol, and has no role in KCl stressed cells. Survival of H. werneckii at moderate NaCl and KCl concentrations is not dependent on HwHog1 activity or the calcineurin pathway, and thus alternative mechanisms must exist. The HOG pathway described here is vital for the extreme osmotolerance of H. werneckii, and its regulation shows important differences from the homologue pathways characterised in other mesophilic and halotolerant fungi.
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| 14. |
- Klaubauf, Sylvia, 1981, et al.
(författare)
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Similar is not the same: Differences in the function of the (hemi-)cellulolytic regulator XlnR (Xlr1/Xyr1) in filamentous fungi
- 2014
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Ingår i: Fungal Genetics and Biology. - 1096-0937 .- 1087-1845. ; 72, s. 73-81
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Tidskriftsartikel (refereegranskat)abstract
- The transcriptional activator XlnR (Xlr1/Xyr1) is a major regulator in fungal xylan and cellulose degradation as well as in the utilization of d-xylose via the pentose catabolic pathway. XlnR homologs are commonly found in filamentous ascomycetes and often assumed to have the same function in different fungi. However, a comparison of the saprobe Aspergillus niger and the plant pathogen Magnaporthe oryzae showed different phenotypes for deletion strains of XlnR. In this study wild type and xlnR/xlr1/xyr1 mutants of five fungi were compared: Fusarium graminearum, M. oryzae, Trichoderma reesei, A. niger and Aspergillus nidulans. Growth profiling on relevant substrates and a detailed analysis of the secretome as well as extracellular enzyme activities demonstrated a common role of this regulator in activating genes encoding the main xylanolytic enzymes. However, large differences were found in the set of genes that is controlled by XlnR in the different species, resulting in the production of different extracellular enzyme spectra by these fungi. This comparison emphasizes the functional diversity of a fine-tuned (hemi-)cellulolytic regulatory system in filamentous fungi, which might be related to the adaptation of fungi to their specific biotopes. Data are available via ProteomeXchange with identifier PXD001190.
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| 15. |
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| 16. |
- Melin, Petter
(författare)
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The decarboxylation of the weak-acid preservative, sorbic acid, is encoded by linked genes in Aspergillus spp.
- 2010
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 47, s. 683-692
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Tidskriftsartikel (refereegranskat)abstract
- The ability to resist anti-microbial compounds is of key evolutionary benefit to microorganisms. Aspergillus has previously been shown to require the activity of a phenylacrylic acid decarboxylase (encoded by padA1) for the decarboxylation of the weak-acid preservative sorbic acid (2,4-hexadienoic acid) to 1,3-pentadiene. It is now shown that this decarboxylation process also requires the activity of a putative 4-hydroxybenzoic acid (3-octaprenyl-4-hydroxybenzoic acid) decarboxylase, encoded by a gene termed ohbA1, and a putative transcription factor, sorbic acid decarboxylase regulator, encoded by sdrA. The padA1, ohbA1 and sdrA genes are in close proximity to each other on chromosome 6 in the A. niger genome, and further bioinformatic analysis revealed conserved synteny at this locus in several Aspergillus species and other ascomycete fungi indicating clustering of metabolic function. This cluster is absent from the genomes of A. fumigatus and A. clavatus and, as a consequence, neither species is capable of decarboxylating sorbic acid. (C) 2010 Elsevier Inc. All rights reserved.
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| 17. |
- Mierke, Friederike, 1992, et al.
(författare)
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Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates
- 2023
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 166
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Tidskriftsartikel (refereegranskat)abstract
- Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of the recently isolated P. hubeiensis BOT-O strain was sequenced using MinION long-read sequencing and resulted in the most contiguous P. hubeiensis assembly to date with 18.95 Mb in 31 contigs. Using transcriptome data as experimental support, we generated the first mRNA-supported P. hubeiensis genome annotation and identified 6540 genes. 80% of the predicted genes were assigned functional annotations based on protein homology to other yeasts. Based on the annotation, key metabolic pathways in BOT-O were reconstructed, including pathways for storage lipids, mannosylerythritol lipids and xylose assimilation. BOT-O was confirmed to consume glucose and xylose at equal rates, but during mixed glucose-xylose cultivation glucose was found to be taken up faster. Differential expression analysis revealed that only a total of 122 genes were significantly differentially expressed at a cut-off of |log2 fold change| ≥ 2 when comparing cultivation on xylose with glucose, during exponential growth and during nitrogen-starvation. Of these 122 genes, a core-set of 24 genes was identified that were differentially expressed at all time points. Nitrogen-starvation resulted in a larger transcriptional effect, with a total of 1179 genes with significant expression changes at the designated fold change cut-off compared with exponential growth on either glucose or xylose.
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| 18. |
- Nieuwenhuis, Bart P. S., et al.
(författare)
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On the asymmetry of mating in natural populations of the mushroom fungus Schizophyllum commune
- 2013
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 56, s. 25-32
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Tidskriftsartikel (refereegranskat)abstract
- Before a mycelium of a mushroom-forming basidiomycete develops mushrooms, the monokaryotic mycelium needs to become fertilized. Although the mechanistic details of mating in mushrooms have been studied thoroughly in laboratory research, very little is known on mating patterns in nature. In this study, we performed fine-scale analyses of three populations of Schizophyllum commune from their natural substrate (i.e. dead beech branches). From the three branches, 24, 12, and 24 fruiting bodies were isolated and for each mushroom, the origins of its nuclei and cytoplasm were reconstructed using DNA markers. Nuclear genotypes were determined using sequencing data and mating types, and mitochondrial haplotypes using SNP markers. From these combined data we reconstructed colonization and mating patterns of the mycelia. On each branch, we found multiple dikaryons (3, 3, and 8, respectively); in two instances one nuclear haplotype was shared between two dikaryons and in two other cases a nuclear haplotype was shared between three dikaryons. Each dikaryon always had a single mitochondrial haplotype. These findings indicate that mating usually is not symmetrical and that a monokaryon is most likely fertilized by a small monokaryon, a spore or a dikaryon. Sharing of nuclear haplotype between different dikaryons resulted either from multiple fertilizations of a single monokaryon, if the dikaryons had identical mitochondrial haplotypes, or, if the dikaryons had different mitochondria] haplotypes, most likely from secondary matings between a monokaryon and a dikaryon (Buller phenomenon). We conclude that mating in S. commune between same-sized monokaryons with reciprocal migration, as generally described in textbooks, is rare in nature. We discuss the implications of non-symmetric mating for basidiomycete evolution.
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| 19. |
- Oliw, Ernst H., 1948-
(författare)
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Diversity of the manganese lipoxygenase gene family - A mini-review
- 2022
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Ingår i: Fungal Genetics and Biology. - : Elsevier. - 1087-1845 .- 1096-0937. ; 163
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Forskningsöversikt (refereegranskat)abstract
- Analyses of fungal genomes of escalate from biological and evolutionary investigations. The biochemical analyses of putative enzymes will inevitably lag behind and only a selection will be characterized. Plant-pathogenic fungi secrete manganese-lipoxygenases (MnLOX), which oxidize unsaturated fatty acids to hydroperoxides to support infection. Six MnLOX have been characterized so far including the 3D structures of these enzymes of the Rice blast and the Take-all fungi. The goal was to use this information to evaluate MnLOX-related gene transcripts to find informative specimens for further studies. Phylogenetic analysis, determinants of catalytic activities, and the C-terminal amino acid sequences divided 54 transcripts into three major subfamilies. The six MnLOX belonged to the same "prototype" subfamily with conserved residues in catalytic determinants and Cterminal sequences. The second subfamily retained the secretion mechanism, presumably necessary for uptake of Mn2+, but differed in catalytic determinants and by cysteine replacement of an invariant Leu residue for positioning ("clamping") of fatty acids. The third subfamily contrasted with alanine in the Gly/Ala switch for regiospecific oxidation and a minority contained unprecedented C-terminal sequences or lacked secretion signals. With these exceptions, biochemical analyses of transcripts of the three subfamilies appear to have reasonable prospects to find active enzymes.
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| 20. |
- Oliw, Ernst H., 1948-
(författare)
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Fatty acid dioxygenase-cytochrome P450 fusion enzymes of filamentous fungal pathogens
- 2021
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Ingår i: Fungal Genetics and Biology. - : Elsevier. - 1087-1845 .- 1096-0937. ; 157
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Tidskriftsartikel (refereegranskat)abstract
- Oxylipins designate oxygenated unsaturated C18 fatty acids. Many filamentous fungi pathogens contain dioxygenases (DOX) in oxylipin biosynthesis with homology to human cyclooxygenases. They contain a DOX domain, which is often fused to a functional cytochrome P450 at the C-terminal end. A Tyr radical in the DOX domain initiates dioxygenation of linoleic acid by hydrogen abstraction with formation of 8-, 9-, or 10-hydroperoxy metabolites. The P450 domains can catalyze heterolytic cleavage of 8- and 10-hydroperoxides with oxidation of the heme thiolate iron for hydroxylation at C-5, C-7, C-9, or C-11 and for epoxidation of the 12Z double bond; thus displaying linoleate diol synthase (LDS) and epoxy alcohol synthase (EAS) activities. LSD activities are present in the rice blast pathogen Magnaporthe oryzae, Botrytis cinerea causing grey mold and the black scurf pathogen Rhizoctonia solani. 10R-DOX-EAS has been found in M. oryzae and Fusarium oxysporum. The P450 domains may also catalyze homolytic cleavage of 8- and 9-hydroperoxy fatty acids and dehydration to produce epoxides with an adjacent double bond, i.e., allene oxides, thus displaying 8- and 9-DOX-allene oxide synthases (AOS). F. oxysporum, F. graminearum, and R. solani express 9S-DOX-AOS and Zymoseptoria tritici 8S-and 9R-DOXAOS. Homologues are present in endemic human-pathogenic fungi with extensive studies in Aspergillus fumigatus, A. flavus (also a plant pathogen) as well as the genetic model A. nidulans. 8R-and 10R-DOX appear to bind fatty acids "headfirst" in the active site, whereas 9S-DOX binds them "tail first" in analogy with cyclooxygenases. The biological relevance of 8R-DOX-5,8-LDS (also designated PpoA) was first discovered in relation to sporulation of A. nidulans and recently for development and programmed hyphal branching of A. fumigatus. Gene deletion DOXAOS homologues in F. verticillioides, A. flavus, and A. nidulans alters, inter alia, mycotoxin production, sporulation, and gene expression.
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| 21. |
- Padamsee, Mahajabeen, et al.
(författare)
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The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction
- 2012
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 49:3, s. 217-226
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Tidskriftsartikel (refereegranskat)abstract
- Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identified 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebi to colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is confirmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were identified although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic.
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| 22. |
- Peciulyte, Ausra, 1986, et al.
(författare)
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Morphology and enzyme production of Trichoderma reesei Rut C-30 are affected by the physical and structural characteristics of cellulosic substrates
- 2014
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 72, s. 64-72
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Tidskriftsartikel (refereegranskat)abstract
- The industrial production of cellulolytic enzymes is dominated by the filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina). In order to develop optimal enzymatic cocktail, it is of importance to understand the natural regulation of the enzyme profile as response to the growth substrate. The influence of the complexity of cellulose on enzyme production by the microorganisms is not understood. In the present study we attempted to understand how different physical and structural properties of cellulose-rich substrates affected the levels and profiles of extracellular enzymes produced by T. reesei. Enzyme production by T. reesei Rut C-30 was studied in submerged cultures on five different cellulose-rich substrates, namely, commercial cellulose Avicel (R) and industrial-like cellulosic pulp substrates which consist mainly of cellulose, but also contain residual hemicellulose and lignin. In order to evaluate the hydrolysis of the substrates by the fungal enzymes, the spatial polymer distributions were characterised by cross-polarisation magic angle spinning carbon-13 nuclear magnetic resonance (CP/MAS C-13-NMR) in combination with spectral fitting. Proteins in culture supernatants at early and late stages of enzyme production were labeled by Tandem Mass Tags (TMT) and protein profiles were analysed by liquid chromatography-tandem mass spectrometry. The data have been deposited to the ProteomeXchange with identifier PXD001304. In total 124 proteins were identified and quantified in the culture supernatants, including cellulases, hemicellulases, other glycoside hydrolases, lignin-degrading enzymes, auxiliary activity 9 (AA9) family (formerly GH61), supporting activities of proteins and enzymes acting on cellulose, proteases, intracellular proteins and several hypothetical proteins. Surprisingly, substantial differences in the enzyme profiles were found even though there were minor differences in the chemical composition between the cellulose-rich substrates.
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| 23. |
- Schnürer, Johan, 1957-, et al.
(författare)
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Fungal volatiles as indicators of food and feeds spoilage
- 1999
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Ingår i: Fungal Genetics and Biology. - : Academic Press. - 1087-1845 .- 1096-0937. ; 27:2-3, s. 209-217
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Forskningsöversikt (refereegranskat)abstract
- Fungal growth leads to spoilage of food and animal feeds and to formation of mycotoxins and potentially allergenic spores. Fungi produce volatile compounds, during both primary and secondary metabolism, which can be used for detection and identification. Fungal volatiles from mainly Aspergillus, Fusarium, and Penicillium have been characterized with gas chromatography, mass spectrometry, and sensory analysis. Common volatiles are 2-methyl-1-propanol, 3-methyl-1-butanol, 1-octen-3-ol, 3-octanone, 3-methylfuran, ethyl acetate, and the malodorous 2-methyl-isoborneol and geosmin. Volatile sesquiterpenes can be used for taxonomic classification and species identification in Penicillium, as well as to indicate mycotoxin formation in Fusarium and Aspergillus. Developments in sensor technology have led to the construction of "electronic noses" (volatile compound mappers). Exposure of different nonspecific sensors to volatile compounds produces characteristic electrical signals. These are collected by a computer and processed by multivariate statistical methods or in an artificial neural network (ANN). Such systems can grade cereal grain with regard to presence of molds as efficiently as sensory panels evaluating grain odor. Volatile compound mapping can also be used to predict levels of ergosterol and fungal colony-forming units in grain. Further developments should make it possible to detect individual fungal species as well as the degree of mycotoxin contamination of food and animal feeds.
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| 24. |
- Stenlid, Jan
(författare)
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Gene expression associated with vegetative incompatibility in Amylostereum areolatum
- 2011
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 48, s. 1034-1043
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Tidskriftsartikel (refereegranskat)abstract
- In filamentous fungi, vegetative compatibility among individuals of the same species is determined by the genes encoded at the heterokaryon incompatibility (het) loci. The hyphae of genetically similar individuals that share the same allelic specificities at their het loci are able to fuse and intermingle, while different allelic specificities at the her loci result in cell death of the interacting hyphae. In this study, suppression subtractive hybridization (SSH) followed by pyrosequencing and quantitative reverse transcription PCR were used to identify genes that are selectively expressed when vegetatively incompatible individuals of Amylostereum areolatum interact. The SSH library contained genes associated with various cellular processes, including cell-cell adhesion, stress and defence responses, as well as cell death. Some of the transcripts encoded proteins that were previously implicated in the stress and defence responses associated with vegetative incompatibility. Other transcripts encoded proteins known to be associated with programmed cell death, but have not previously been linked with vegetative incompatibility. Results of this study have considerably increased our knowledge of the processes underlying vegetative incompatibility in Basidiomycetes in general and A. areolatum in particular. (C) 2011 Elsevier Inc. All rights reserved.
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| 25. |
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| 26. |
- Strandberg, Rebecka, 1982-, et al.
(författare)
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Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora
- 2010
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 47:10, s. 869-878
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we investigated the genealogies of genes important for sexual identity, i.e. mating-type (mat) and pheromone-receptor (pre) genes, among heterothallic and peudohomothallic taxa of Neurospora. The resulting genealogies were compared with the species phylogeny derived from non-coding sequences. We found conflicting topologies between the reproductive genealogies and the species phylogeny, and these conflicts were supported by both node support analyses and likelihood tests on the relative fit of datasets to alternative phylogenetic hypotheses. We argue that reproductive genes are more permeable to gene flow, i.e. are more often introgressed between species of Neurospora, than other parts of the genome. Certain conflicts between the species phylogeny and both mat genealogies were observed, suggesting that the two mating-type idiomorphs were selectively introgressed into a species from a single ancestral source. Taken together, the results presented here highlight complex evolutionary trajectories of reproductive genes in the fungal kingdom, which may be of importance for reproductive behavior in natural populations.
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| 27. |
- Tzelepis, Georgios, et al.
(författare)
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Functional analysis of glycoside hydrolase family 18 and 20 genes in Neurospora crassa
- 2012
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 49, s. 717-730
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Tidskriftsartikel (refereegranskat)abstract
- Glycoside hydrolase family 18 contains hydrolytic enzymes with chitinase or endo-N-acetyl-beta-D-glucosaminidase (ENGase) activity, while glycoside hydrolase family 20 contains enzymes with beta-N-acetylhexosaminidase (NAGase) activity. Chitinases and NAGases are involved in chitin degradation. Chitinases are phylogenetically divided into three main groups (A, B and C), each further divided into subgroups. In this study, we investigated the functional role of 10 Neurospora crassa genes that encode chitinases, 2 genes that encode ENGases and 1 gene that encode a NAGase, using gene deletion and gene expression techniques. No phenotypic effects were detected for any of the studied group A chitinase gene deletions. Deletion of the B group member chit-1 resulted in reduced growth rate compared with the wild type (WT) strain. In combination with the presence of a predicted glycosylphosphatidylinositol anchor motif in the C-terminal of chit-1, indicating cell wall localization, these data suggest a role in cell wall remodeling during hyphal growth for chit-1. Deletion of the ENGase gene gh18-10 resulted in reduced growth rate compared with WT, increased conidiation, and increased abiotic stress tolerance. In addition, Delta gh18-10 strains displayed lower secretion of extracellular proteins compared to WT and reduced levels of extracellular protease activity. The connection between gh18-10 ENGase activity and the endoplasmic reticulum associated protein degradation process, a stringent quality control of glycoprotein maturation, is discussed. N. crassa group C chitinase genes gh18-6 and gh18-8 were both induced during fungal fungal interactions. However, gh18-6 was only induced during interspecific interactions, while gh18-8 displayed the highest induction levels during self self interactions. These results provide new information on functional differentiation of fungal chitinases. (C) 2012 Elsevier Inc. All rights reserved.
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| 28. |
- Tzelepis, Georgios, et al.
(författare)
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Functional analysis of the C-II subgroup killer toxin-like chitinases in the filamentous ascomycete Aspergillus nidulans
- 2014
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 64, s. 58-66
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Tidskriftsartikel (refereegranskat)abstract
- Chitinases are hydrolytic enzymes responsible for chitin polymer degradation. Fungal chitinases belong exclusively to glycoside hydrolases family 18 and they are categorized into three phylogenetic groups (A, B and C), which are further divided into subgroups (A-II to A-V, B-I to B-V and C-I to C-II). Subgroup C chitinases display similarity with the alpha/beta-subunit of the zymocin yeast killer toxin produced by Kluyveromyces lactis, suggesting a role of these enzymes in fungal-fungal interactions. In this study, we investigated the regulation and function of 4 Aspergillus nidulans subgroup C-II killer toxin-like chitinases by quantitative PCR and by constructing gene deletion strains. Our results showed that all 4 genes were highly induced during interactions with Botrytis cinerea and Rhizoctonia solani, compared to self-interactions. In addition, chiC2-2 and chiC2-3 were also induced during contact with Fusarium sporotrichoides, while none of these genes were induced during interactions with Phytophthora niederhauserii. In contrast, no difference in expression levels were observed between growth on glucose-rich media compared with media containing colloidal chitin, while all genes were repressed during growth on R. solani cell wall material. Phenotypic analysis of chitinase gene deletion strains revealed that B. cinerea biomass was significantly higher in culture filtrate derived from the Delta chiC2-2 strain compared to biomasses grown in media derived from A. nidulans wild type or the other chitinase gene deletion strains. The analysis also showed that all chitinase gene deletion strains displayed increased biomass production in liquid cultures, and altered response to abiotic stress. In summary, our gene expression data suggest the involvement of A. nidulans subgroup C-II chitinases in fungal-fungal interactions, which is further proven for ChiC2-2. In addition, lacking any of the 4 chitinases influenced the growth of A. nidulans. (C) 2013 Elsevier Inc. All rights reserved.
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| 29. |
- Van Der Nest, Magriet, et al.
(författare)
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Distribution and evolution of het gene homologs in the basidiomycota
- 2014
-
Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 64, s. 45-57
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Tidskriftsartikel (refereegranskat)abstract
- In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi. (C) 2013 Elsevier Inc. All rights reserved.
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| 30. |
- Van Der Nest, Magriet, et al.
(författare)
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Gene expression associated with intersterility in Heterobasidion
- 2014
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 73, s. 104-119
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Tidskriftsartikel (refereegranskat)abstract
- Intersterility (IS) is thought to prevent mating compatibility between homokaryons that belong to different species. Although IS in Heterobasidion is regulated by the genes located at the IS loci, it is not yet known how the IS genes influence sexual compatibility and heterokaryon formation. To increase our understanding of the molecular events underlying IS, we studied mRNA abundance changes during IS compatible and incompatible interactions over time. The clustering of the transcripts into expression profiles, followed by the application of Gene Ontology (GO) enrichment pathway analysis of each of the clusters, allowed inference of biological processes participating in IS. These analyses identified events involved in mating and sexual development (i.e., linked with IS compatibility), which included processes associated with cell-cell adhesion and recognition, cell cycle control and signal transduction. We also identified events potentially involved in overriding mating between individuals belonging to different species (i.e., linked with IS incompatibility), which included reactive oxygen species (ROS) production, responses to stress (especially to oxidative stress), signal transduction and metabolic biosynthesis. Our findings thus enabled detection and characterization of gene expression changes associated with IS in Heterobasidion, as well as identification of important processes and pathways associated with this phenomenon. Overall, the results of this study increase current knowledge regarding the molecular mechanisms underpinning IS in Heterobasidion and allowed for the establishment of a vital baseline for further studies. (C) 2014 Elsevier Inc. All rights reserved.
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| 31. |
- Wang, Zheng, et al.
(författare)
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Sex-specific gene expression during asexual development of Neurospora crassa
- 2012
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 49:7, s. 533-543
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Tidskriftsartikel (refereegranskat)abstract
- The impact of loci that determine sexual identity upon the asexual, dominant stage of fungal life history has been well studied. To investigate their impact, expression differences between strains of different mating type during asexual development were assayed, with RNA sampled from otherwise largely isogenic mat A and mat a strains of Neurospora crassa at early, middle, and late clonal stages of development. We observed significant differences in overall gene expression between mating types across clonal development, especially at late development stages. The expression levels of mating-type genes and pheromone genes were assayed by reverse transcription and quantitative PCR, revealing expression of pheromone and receptor genes in strains of both mating types in all development stages, and revealing that mating type (mat) genes were increasingly expressed over the course of asexual development. Interestingly, among differentially expressed genes, the mat A genotype more frequently exhibited a higher expression level than mat a, and demonstrated greater transcriptional regulatory dynamism. Significant up-regulation of expression was observed for many late light-responsive genes at late asexual development stages. Further investigation of the impact of light and the roles of light response genes in asexual development of both mating types are warranted.
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| 32. |
- Whittle, Carrie A., et al.
(författare)
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Consequences of reproductive mode on genome evolution in fungi
- 2011
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845 .- 1096-0937. ; 48:7, s. 661-667
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Forskningsöversikt (refereegranskat)abstract
- An organism's reproductive mode is believed to be a major factor driving its genome evolution. In theory, sexual inbreeding and asexuality are associated with lower effective recombination levels and smaller effective population sizes than sexual outbreeding, giving rise to reduced selection efficiency and genetic hitchhiking. This, in turn, is predicted to result in the accumulation of deleterious mutations and other genomic changes, for example the accumulation of repetitive elements. Empirical data from plants and animals supporting/refuting these theories are sparse and have yielded few conclusive results. A growing body of data from the fungal kingdom, wherein reproductive behavior varies extensively within and among taxonomic groups, has provided new insights into the role of mating systems (e.g., homothallism, heterothallism, pseudohomothallism) and asexuality, on genome evolution. Herein, we briefly review the theoretical relationships between reproductive mode and genome evolution and give examples of empirical data on the topic derived to date from plants and animals. We subsequently focus on the available data from fungi, which suggest that reproductive mode alters the rates and patterns of genome evolution in these organisms, e.g., protein evolution, mutation rate, codon usage, frequency of genome rearrangements and repetitive elements, and variation in chromosome size.
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| 33. |
- Wortman, J. R., et al.
(författare)
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The 2008 update of the Aspergillus nidulans genome annotation: A community effort
- 2009
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1096-0937 .- 1087-1845. ; 46, s. S2-S13
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Tidskriftsartikel (refereegranskat)abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. (C) 2009 Elsevier Inc. All rights reserved.
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| 34. |
- Balogh, Johanna, et al.
(författare)
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Deletion of a lectin gene does not affect the phenotype of the nematode-trapping fungus Arthrobotrys oligospora
- 2003
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Ingår i: Fungal Genetics and Biology. - 1087-1845. ; 39:2, s. 128-135
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Tidskriftsartikel (refereegranskat)abstract
- A number of filamentous fungi are known to produce high levels of saline-soluble and low-molecular-mass lectins. The function of these proteins are not clear but it has been proposed that they are involved in storage of nutrients, development, recognition of other organisms, and defense reactions. A gene encoding such a lectin (AOL) was deleted in the nematode-trapping fungus Arthrobotrys oligospora by homologous recombination. The deletion mutants did not express any hemagglutinating activity or protein cross-reacting with AOL antibodies. There were no significant differences between the DeltaAOL and wild-type strains in spore (conidia) germination, saprophytic growth, and pathogenicity. Furthermore, there was no significant difference in the growth and reproduction of collembolan feeding on the various strains of A. oligospora. Thus either the previous proposed functions of AOL are not correct, or the fungus can compensate for the absence of the lectin by expressing other proteins with similar function(s) as AOL. (C) 2003 Published by Elsevier Science (USA).
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| 35. |
- Le Quéré, Antoine, et al.
(författare)
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Size and complexity of the nuclear genome of the ectomycorrhizal fungus Paxillus involutus.
- 2002
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Ingår i: Fungal Genetics and Biology. - 1087-1845. ; 36:3, s. 234-241
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Tidskriftsartikel (refereegranskat)abstract
- The basidiomycete Paxillus involutus is forming ectomycorrhizal symbiosis with a broad range of forest trees. Reassociation kinetics on P. involutus nuclear DNA indicated a haploid genome size of 23Mb including 11% of repetitive DNA. A similar genome size (20Mb) was estimated by genomic reconstruction analysis using three single copy genes. To assess the gene density in the P. involutus genome, a cosmid containing a 33-kb fragment of genomic DNA was sequenced and used to identify putative open reading frames (ORFs). Twelve potential ORFs were predicted, eight displayed significant sequence similarities to known proteins found in other organisms and notably, several homologues to the Podospora anserina vegetative incompatibility protein (HetE1) were found. By extrapolation, we estimate the total number of genes in the P. involutus haploid genome to approximately 7700.
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| 36. |
- Floudas, Dimitrios, et al.
(författare)
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Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii
- 2015
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 76, s. 78-92
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Tidskriftsartikel (refereegranskat)abstract
- Wood decay mechanisms in Agaricomycotina have been traditionally separated in two categories termed white and brown rot. Recently the accuracy of such a dichotomy has been questioned. Here, we present the genome sequences of the white-rot fungus Cylindrobasidium torrendii and the brown-rot fungus Fistulina hepatica both members of Agaricales, combining comparative genomics and wood decay experiments. C torrendii is closely related to the white-rot root pathogen Armillaria mellea, while F. hepatica is related to Schizophyllum commune, which has been reported to cause white rot. Our results suggest that C torrendii and S. commune are intermediate between white-rot and brown-rot fungi, but at the same time they show characteristics of decay that resembles soft rot. Both species cause weak wood decay and degrade all wood components but leave the middle lamella intact. Their gene content related to lignin degradation is reduced, similar to brown-rot fungi, but both have maintained a rich array of genes related to carbohydrate degradation, similar to white-rot fungi. These characteristics appear to have evolved from white-rot ancestors with stronger ligninolytic ability. F. hepatica shows characteristics of brown rot both in terms of wood decay genes found in its genome and the decay that it causes. However, genes related to cellulose degradation are still present, which is a plesiomorphic characteristic shared with its white-rot ancestors. Four wood degradation-related genes, homologs of which are frequently lost in brown-rot fungi, show signs of pseudogenization in the genome of F. hepatica. These results suggest that transition toward a brown-rot lifestyle could be an ongoing process in F. hepatica. Our results reinforce the idea that wood decay mechanisms are more diverse than initially thought and that the dichotomous separation of wood decay mechanisms in Agaricomycotina into white rot and brown rot should be revisited. (C) 2015 Elsevier Inc. All rights reserved.
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| 37. |
- Tikhonov, VE, et al.
(författare)
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Purification and characterization of chitinases from the nematophagous fungi Verticillium chlamydosporium and v. suchlasporium
- 2002
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 35:1, s. 67-78
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Tidskriftsartikel (refereegranskat)abstract
- Culture filtrates of the nematophagous fungi Verticillium chlamydosporium and V. suchlasporium growing on colloidal chitin showed increasing chitinolytic activity and production of two (32- and 43-kDa) main proteins. Maximum activity was found 18-20 days after inoculation, but V. suchlasporium always displayed higher activity. Zymography of such filtrates on carboxymethyl-chitin-Remazol brilliant violet 5R/acrylamide gels showed five bands of substrate degradation for V. suchlasporium and three for V. chlamydosporium. Filtrates with maximum activity were chromatographed on macroporous cross-linked chitin affinity matrix, showing a peak of main (50-60%) activity, which only contained a 43-kDa protein for both fungi. Zymography and colloidal chitin degradation showed that it was a single endochitinase (CHl43) with optimum pH range of 5.2-5.7. The main isoforms had pis of 7.6 for V. suchlasporium and 7.9 for V. chlamydosporium. Eggs of the nematode Globodera pallida treated with CHl43 and the serine protease P32 from V. suchlasporium alone or in combination showed surface damage in comparison with controls when examined by scanning electron microscopy. (C) 2002 Elsevier Science (USA).
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| 38. |
- Wasserstrom, Lisa, et al.
(författare)
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Fungal model systems and the elucidation of pathogenicity determinants
- 2014
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 70, s. 42-67
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Tidskriftsartikel (refereegranskat)abstract
- Fungi have the capacity to cause devastating diseases of both plants and animals, causing significant harvest losses that threaten food security and human mycoses with high mortality rates. As a consequence, there is a critical need to promote development of new antifungal drugs, which requires a comprehensive molecular knowledge of fungal pathogenesis. In this review, we critically evaluate current knowledge of seven fungal organisms used as major research models for fungal pathogenesis. These include pathogens of both animals and plants; Ashbya gossypii, Aspergillus fumigatus, Candida albicans, Fusarium oxysporum, Magnaporthe oryzae, Ustilago maydis and Zymoseptoria tritici. We present key insights into the virulence mechanisms deployed by each species and a comparative overview of key insights obtained from genomic analysis. We then consider current trends and future challenges associated with the study of fungal pathogenicity.
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| 39. |
- Wirsel, SGR, et al.
(författare)
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Four or more species of Cladosporium sympatrically colonize Phragmites australis
- 2002
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Ingår i: Fungal Genetics and Biology. - : Elsevier BV. - 1087-1845. ; 35:2, s. 99-113
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Tidskriftsartikel (refereegranskat)abstract
- A collection of Cladosporium has been recovered from common reed growing at Lake Constance (Germany). High-resolution cryo-scanning electron microscopy revealed that Cladosporium isolates from reed are diverse. Morphologically, we distinguished three species, viz. C. herbarum, C. oxysporum, and Cladosporium sp. Internal transcribed spacer (ITS) sequence analysis supported these results and, moreover, separated the most common species, C. oxysporum, into two subclades. Two additional phylogenies were generated to gain support for this finding. The first, differentiating fungi by their capacities to metabolize different carbon sources, showed correlation with morphology. The second, based on actin gene sequences, showed the same overall topology as that of the ITS tree, but resulted in a higher resolution indicating the existence of four or more species of Cladosporium on reed. A nested PCR assay targeting variable sequences within actin introns indicated that these four species sympatrically colonize reed. There was no evidence for mutual exclusion on or within the host or specialization for host habitats or organs.
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