scholarly journals Characterisation of Postia placenta colonisation during 36 weeks in acetylated southern yellow pine sapwood at three acetylation levels including genomic DNA and gene expression quantification of the fungus

Holzforschung ◽  
2016 ◽  
Vol 70 (11) ◽  
pp. 1055-1065 ◽  
Author(s):  
Gry Alfredsen ◽  
Annica Pilgård ◽  
Carl Gunnar Fossdal
Keyword(s):  
Decay Rate ◽  
Genomic Dna ◽  
Decay Fungi ◽  
Postia Placenta ◽  
Expression Of Genes ◽  
Gene Transcripts ◽  
Gene Expression Quantification ◽  
Pinus Spp ◽  
Decay Threshold ◽  
Southern Yellow Pine

Abstract One way to protect timber in service against basidiomycete deterioration is by means of acetylation via reaction with acetic anhydride. The reason why acetylated wood (WAc) is resistant against decay fungi is still not exactly understood. The aim of this study was to contribute to this field of science, and Postia placenta colonisation after 4, 12, 20, 28 and 36 weeks was observed at three acetylation levels of Pinus spp. sapwood. Mass loss (ML) and wood moisture content (MC) data reflected the acetylation levels. The initial equilibrium MC (EMC) proved to be a good indicator of subsequent ML. Genomic DNA quantification showed P. placenta colonisation in all samples, also in samples where no ML were detectable. The number of expressed gene transcripts was limited, but the findings supported the results of previous studies: WAc seems to have some resistance against oxidative mechanisms, which are part of the metabolism of P. placenta. This leads to a delay in decay initiation, a delay in expression of genes involved in enzymatic depolymerisation, and a slower decay rate. The magnitudes of these effects are presented for each acetylation level. The data also imply that there is no absolute decay threshold at high acetylation levels, but instead a significant delay of decay initiation and a slower decay rate.

scholarly journals Structure and expression of genes for surface proteins in Paramecium.

1983 ◽  
Vol 3 (3) ◽  
pp. 466-474 ◽  
Author(s):  
J D Forney ◽  
L M Epstein ◽  
L B Preer ◽  
B M Rudman ◽  
D J Widmayer ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Restriction Enzyme ◽  
Genomic Dna ◽  
Gene Dosage ◽  
Surface Proteins ◽  
Paramecium Tetraurelia ◽  
Complementary Sequences ◽  
Expression Of Genes ◽  
Inactive Genes ◽  
Polyadenylated Rnas

Surface proteins from 11 antigenic types of Paramecium tetraurelia vary in molecular weight from 251,000 to 308,000. The size of a series of polyadenylated RNAs obtained from these types were correlated with the sizes of the proteins and judged to be the mRNAs for the proteins. The mRNAs were used to identify genomic DNA clones containing complementary sequences. The gene for antigen A was present in one copy per genome, and the data suggest that extensive introns were absent. When restriction enzyme digests of DNA from cultures of paramecia with active and inactive genes were probed with portions of the cloned genes, no evidence for rearrangements or changes in gene dosage was found.

scholarly journals Significant Alteration of Gene Expression in Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium by Plant Species

2011 ◽  
Vol 77 (13) ◽  
pp. 4499-4507 ◽  
Author(s):  
Amber Vanden Wymelenberg ◽  
Jill Gaskell ◽  
Michael Mozuch ◽  
Sandra Splinter BonDurant ◽  
Grzegorz Sabat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbon Source ◽  
Phanerochaete Chrysosporium ◽  
Wood Decay ◽  
Hydrolytic Cleavage ◽  
Decay Fungi ◽  
Transcript Levels ◽  
Content Type ◽  
Postia Placenta ◽  
Wood Decay Fungi

ABSTRACTIdentification of specific genes and enzymes involved in conversion of lignocellulosics from an expanding number of potential feedstocks is of growing interest to bioenergy process development. The basidiomycetous wood decay fungiPhanerochaete chrysosporiumandPostia placentaare promising in this regard because they are able to utilize a wide range of simple and complex carbon compounds. However, systematic comparative studies with different woody substrates have not been reported. To address this issue, we examined gene expression of these fungi colonizing aspen (Populus grandidentata) and pine (Pinus strobus). Transcript levels of genes encoding extracellular glycoside hydrolases, thought to be important for hydrolytic cleavage of hemicelluloses and cellulose, showed little difference forP. placentacolonizing pine versus aspen as the sole carbon source. However, 164 genes exhibited significant differences in transcript accumulation for these substrates. Among these, 15 cytochrome P450s were upregulated in pine relative to aspen. Of 72P. placentaextracellular proteins identified unambiguously by mass spectrometry, 52 were detected while colonizing both substrates and 10 were identified in pine but not aspen cultures. Most of the 178P. chrysosporiumglycoside hydrolase genes showed similar transcript levels on both substrates, but 13 accumulated >2-fold higher levels on aspen than on pine. Of 118 confidently identified proteins, 31 were identified in both substrates and 57 were identified in pine but not aspen cultures. Thus,P. placentaandP. chrysosporiumgene expression patterns are influenced substantially by wood species. Such adaptations to the carbon source may also reflect fundamental differences in the mechanisms by which these fungi attack plant cell walls.

Microdistribution of copper in copper-ethanolamine (Cu-EA) treated southern yellow pine (Pinus spp.) related to density distribution

Holzforschung ◽  
2005 ◽  
Vol 59 (1) ◽  
pp. 82-89 ◽  
Author(s):  
Jinzhen Cao ◽  
D. Pascal Kamdem
Keyword(s):  
Cell Wall ◽  
Density Distribution ◽  
Cell Walls ◽  
Middle Lamella ◽  
Treated Wood ◽  
Yellow Pine ◽  
Using Data ◽  
Pinus Spp ◽  
Southern Yellow Pine ◽  
The Relationship

Abstract The relationship between copper absorption and density distribution in wood cell walls was investigated in this study. The density distribution on layer level was obtained from two approaches: (1) calculation by using data obtained from literature; (2) microdistribution of carbon and oxygen atoms in the wood cell. The microdistribution of carbon and oxygen in untreated southern yellow pine (Pinus spp.) sapwood, as well as copper in cell walls of copper-ethanolamine (Cu-EA) treated wood was determined by scanning electron microscopy coupled with energy dispersive X-ray analysis (SEM-EDXA). Both approaches for density distribution led to the same result: the density was higher in the compound middle lamella and cell corners than in the secondary wall. The concentration/intensity of Cu, C and O in the cell wall follow the same trend as the density distribution; suggesting that density may play a major role in SEM-EDXA study of the distribution of metal-containing wood preservatives within the wood cell wall.

scholarly journals Comparative Transcriptome and Secretome Analysis of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium

2010 ◽  
Vol 76 (11) ◽  
pp. 3599-3610 ◽  
Author(s):  
Amber Vanden Wymelenberg ◽  
Jill Gaskell ◽  
Michael Mozuch ◽  
Grzegorz Sabat ◽  
John Ralph ◽  
...  
Keyword(s):  
Phanerochaete Chrysosporium ◽  
Cellulose Degradation ◽  
Expression Patterns ◽  
Wood Decay ◽  
Brown Rot ◽  
White Rot ◽  
Glycosyl Hydrolases ◽  
Decay Fungi ◽  
Postia Placenta ◽  
Wood Decay Fungi

ABSTRACT Cellulose degradation by brown rot fungi, such as Postia placenta, is poorly understood relative to the phylogenetically related white rot basidiomycete, Phanerochaete chrysosporium. To elucidate the number, structure, and regulation of genes involved in lignocellulosic cell wall attack, secretome and transcriptome analyses were performed on both wood decay fungi cultured for 5 days in media containing ball-milled aspen or glucose as the sole carbon source. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), a total of 67 and 79 proteins were identified in the extracellular fluids of P. placenta and P. chrysosporium cultures, respectively. Viewed together with transcript profiles, P. chrysosporium employs an array of extracellular glycosyl hydrolases to simultaneously attack cellulose and hemicelluloses. In contrast, under these same conditions, P. placenta secretes an array of hemicellulases but few potential cellulases. The two species display distinct expression patterns for oxidoreductase-encoding genes. In P. placenta, these patterns are consistent with an extracellular Fenton system and include the upregulation of genes involved in iron acquisition, in the synthesis of low-molecular-weight quinones, and possibly in redox cycling reactions.

scholarly journals Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation

2016 ◽  
Vol 82 (14) ◽  
pp. 4387-4400 ◽  
Author(s):  
Oleksandr Skyba ◽  
Dan Cullen ◽  
Carl J. Douglas ◽  
Shawn D. Mansfield
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
White Rot Fungi ◽  
Wood Decay ◽  
White Rot ◽  
Decay Fungi ◽  
Content Type ◽  
Postia Placenta ◽  
Substrate Composition ◽  
Wood Decay Fungi

ABSTRACTIdentification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi,Rhodonia placenta(formerlyPostia placenta) andPhanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-oldPopulus trichocarpa(poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold,P< 0.05) inP. chrysosporiumandP. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold,P< 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles ofP. chrysosporiumandP. placentaare influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode “proteins of unknown function,” and determining their role in lignocellulose degradation presents opportunities and challenges for future research.IMPORTANCEThis study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.

scholarly journals Inferring the presence of aflatoxin-producingAspergillus flavusstrains using RNA sequencing and electronic probes as a transcriptomic screening tool

2018 ◽  
Author(s):  
Andres S. Espindola ◽  
William Schneider ◽  
Kitty F. Cardwell ◽  
Yisel Carrillo ◽  
Peter R. Hoyt ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Screening Tool ◽  
Aflatoxin Production ◽  
Specific Gene ◽  
Potato Dextrose Broth ◽  
Expression Of Genes ◽  
Bioinformatic Tool ◽  
Gene Transcripts ◽  
Nucleic Acid Analysis ◽  
Transcriptomic Level

AbstractE-probe Diagnostic for Nucleic acid Analysis (EDNA) is a bioinformatic tool originally developed to detect plant pathogens in metagenomic databases. However, enhancements made to EDNA increased its capacity to conduct hypothesis directed detection of specific gene targets present in transcriptomic databases. To target specific pathogenicity factors used by the pathogen to infect its host or other targets of interest, e-probes need to be developed for transcripts related to that function. In this study, EDNA transcriptomics (EDNAtran) was developed to detect the expression of genes related to aflatoxin production at the transcriptomic level. E-probes were designed from genes up-regulated duringA.flavusaflatoxin production. EDNAtran detected gene transcripts related to aflatoxin production in a transcriptomic database from corn, where aflatoxin was produced. The results were significantly different from e-probes being used in the transcriptomic database where aflatoxin was not produced (atoxigenic AF36 strain and toxigenic AF70 in Potato Dextrose Broth).

Differential Expression of a Putative Copper Homeostasis CutC Gene in Fibroporia radiculosa During Initial Decay of Copper-Treated Wood

2020 ◽  
Vol 70 (4) ◽  
pp. 469-475
Author(s):  
Katie M. Ohno ◽  
Amy B. Bishell ◽  
Glen R. Stanosz
Keyword(s):  
Differential Expression ◽  
Treated Wood ◽  
Wood Decay ◽  
Untreated Wood ◽  
Copper Homeostasis ◽  
Southern Pine ◽  
Decay Fungi ◽  
Wood Decay Fungi ◽  
Decay Test ◽  
Pinus Spp

Abstract Living organisms require copper for several cellular processes. Yet intracellular concentrations of copper must be regulated to avoid toxicity. Not much is known about mechanisms of copper regulation in wood decay fungi. However, one putative annotation for a copper homeostasis CutC gene (FIBRA_00129), found in other brown-rot wood decay fungi, has been annotated in Fibroporia radiculosa. The aim of this study was to evaluate wood mass loss and differential expression of FIBRA_00129 during initial decay of untreated and copper-treated wood by two copper-tolerant F. radiculosa isolates (FP-90848-T and L-9414-SP) compared with copper-sensitive Gloeophyllum trabeum. Untreated southern pine (Pinus spp.) and ammoniacal copper citrate treated southern pine at three concentrations (0.6%, 1.2%, and 2.4%) were used in a 4-week-long standard decay test. Results showed G. trabeum was unable to decay copper-treated wood while both F. radiculosa isolates successfully decayed southern pine at all copper concentrations. G. trabeum and F. radiculosa L-9414-SP showed no detectable FIBRA_00129 expression over the course of this study. F. radiculosa FP-90848-T showed greater FIBRA_00129 downregulation on copper-treated wood than on untreated wood (P = 0.003). Additionally, there was greater FIBRA_00129 downregulation in F. radiculosa FP-90848-T at week 3 compared with other weeks (P = 0.015). Future studies are needed to further evaluate FIBRA_00129 during the decay process to determine its potential role in copper-tolerance.

High-performance liquid chromatographic analysis of soluble and total oxalate in Ca- and Mg-amended liquid cultures of three wood decay fungi

Holzforschung ◽  
2004 ◽  
Vol 58 (6) ◽  
pp. 682-687 ◽  
Author(s):  
Jonathan S. Schilling ◽  
Jody Jellison
Keyword(s):  
High Performance ◽  
Wood Decay ◽  
Brown Rot ◽  
High Performance Liquid Chromatographic ◽  
White Rot ◽  
Fomitopsis Pinicola ◽  
Decay Fungi ◽  
Postia Placenta ◽  
Medium Components ◽  
Wood Decay Fungi

AbstractTwo brown-rot wood decay fungi,Fomitopsis pinicolaandMeruliporia incrassata, and the white-rot speciesPhanerochaete chrysosporiumwere grown for 4 weeks in liquid culture at 0.35, 0.70, 1.05, and 5.00 mM calcium (Ca) and 1.35 and 2.70 mM magnesium (Mg) concentrations. Soluble and total oxalate levels were quantified using a revised ion-exchange HPLC protocol developed specifically for resolving oxalate and other organic acid anions from medium components. Total oxalate concentrations in brown-rot filtrate were not significantly different among treatments; however, soluble oxalate decreased significantly with increasing Ca concentration. Higher Mg concentrations increased soluble oxalate levels only slightly. There was a significant decrease in medium pH at 5.00 mM Ca for all species, as well as an apparent increase in decarboxylation activity in brown-rot fungi. Total and soluble oxalate levels in the white-rot cultures were generally below detection for all treatments. The results show a significant influence of Ca on soluble oxalate concentrations not seen previously in the brown-rot speciesPostia placenta.

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