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

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.00134-16 ◽

2016 ◽

Vol 82 (14) ◽

pp. 4387-4400 ◽

Cited By ~ 21

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.

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

Applied and Environmental Microbiology ◽

10.1128/aem.00058-10 ◽

2010 ◽

Vol 76 (11) ◽

pp. 3599-3610 ◽

Cited By ~ 181

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.

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Transcriptomic Responses of Phanerochaete chrysosporium to Oak Acetonic Extracts: Focus on a New Glutathione Transferase

Applied and Environmental Microbiology ◽

10.1128/aem.02103-14 ◽

2014 ◽

Vol 80 (20) ◽

pp. 6316-6327 ◽

Cited By ~ 22

Author(s):

Anne Thuillier ◽

Kamel Chibani ◽

Gemma Belli ◽

Enrique Herrero ◽

Stéphane Dumarçay ◽

...

Keyword(s):

Phanerochaete Chrysosporium ◽

Glutathione Transferase ◽

Functional Characterization ◽

Wood Decay ◽

Wood Degradation ◽

Decay Fungi ◽

Toxic Compounds ◽

Content Type ◽

Wood Decay Fungi ◽

Detoxification Systems

ABSTRACTThe first steps of wood degradation by fungi lead to the release of toxic compounds known as extractives. To better understand how lignolytic fungi cope with the toxicity of these molecules, a transcriptomic analysis ofPhanerochaete chrysosporiumgenes was performed in the presence of oak acetonic extracts. It reveals that in complement to the extracellular machinery of degradation, intracellular antioxidant and detoxification systems contribute to the lignolytic capabilities of fungi, presumably by preventing cellular damages and maintaining fungal health. Focusing on these systems, a glutathione transferase (P. chrysosporiumGTT2.1 [PcGTT2.1]) has been selected for functional characterization. This enzyme, not characterized so far in basidiomycetes, has been classified first as a GTT2 compared to theSaccharomyces cerevisiaeisoform. However, a deeper analysis shows that the GTT2.1 isoform has evolved functionally to reduce lipid peroxidation by recognizing high-molecular-weight peroxides as substrates. Moreover, the GTT2.1 gene has been lost in some non-wood-decay fungi. This example suggests that the intracellular detoxification system evolved concomitantly with the extracellular ligninolytic machinery in relation to the capacity of fungi to degrade wood.

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

Holzforschung ◽

10.1515/hf.2004.124 ◽

2004 ◽

Vol 58 (6) ◽

pp. 682-687 ◽

Cited By ~ 14

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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Cupressus macrocarpa Heartwood Oil and its Bioactivity against some Wood Decay Fungi

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.485.413 ◽

2012 ◽

Vol 485 ◽

pp. 413-416 ◽

Cited By ~ 2

Author(s):

Li Jun Zhang ◽

Yuan Yuan Zhang ◽

Shu Jun Li ◽

J.J. Karchesy

Keyword(s):

Steam Distillation ◽

Wood Decay ◽

Irpex Lacteus ◽

Decay Fungi ◽

Filter Paper Disc ◽

Postia Placenta ◽

Fungal Activity ◽

Wood Decay Fungi ◽

Anti Fungal ◽

Paper Disc

Cupressus macrocarpa (Monterey cypress) heartwood has natural durability. The heartwood oil was prepared by steam distillation and its anti-fungal activity was tested against four wood decay fungi, i.e. Trametes versicolor, Irpex lacteus, Gloeophyllum trabeum, and Postia placenta with a filter paper disc method. The oil was active against all these fungi at the concentration of 8 mg.mL-1 or greater, but Postia placenta was the most difficult for the oil to inhibit. GC-MS was adopted to analyze the components of the heartwood oil. Two components, 4-terpineol and carvacrol were identified and carvacrol represented 94.428% of the oil. The oil had anti-fungal activity mostly because of carvacrol in the high content

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Detection and species discrimination using rDNA T-RFLP for identification of wood decay fungi

Holzforschung ◽

10.1515/hf.2005.111 ◽

2005 ◽

Vol 59 (6) ◽

pp. 696-702 ◽

Cited By ~ 15

Author(s):

Ulrika Råberg ◽

Nils O.S. Högberg ◽

Carl Johan Land

Keyword(s):

Fragment Length ◽

Point Mutations ◽

Wood Decay ◽

Species Discrimination ◽

Specific Sequence ◽

Decay Fungi ◽

Postia Placenta ◽

Coniophora Puteana ◽

Wood Decay Fungi ◽

Microscopic Evaluation

AbstractIn the present work PCR technology was used as a tool to detect the early stages of wood decay and was compared with microscopic evaluation. The wood decay fungiPostia placentaandConiophora puteanawere detectable in interior wood samples by terminal restriction fragment length polymorphism (T-RFLP) after 2weeks of incubation with monocultures, while microscopic detection of hyphae was not possible until after 7 weeks. A potential problem when fungal communities are studied with T-RFLPs of rDNA is that intra-specific variation complicates data analysis. In this work, we show that intra-specific sequence variation in the internal transcribed spacer of the rDNA inConiophora puteanaallows T-RFLP identification of this species. This is due to intra-specific variations in fragment length, in combination with the absence of point mutations in the selected restriction sites.

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Application of ATR-FTIR Spectroscopy to Compare the Cell Materials of Wood Decay Fungi with Wood Mould Fungi

International Journal of Spectroscopy ◽

10.1155/2015/521938 ◽

2015 ◽

Vol 2015 ◽

pp. 1-7 ◽

Cited By ~ 13

Author(s):

Barun Shankar Gupta ◽

Bjørn Petter Jelle ◽

Tao Gao

Keyword(s):

Fatty Acid ◽

Ftir Spectroscopy ◽

Wood Decay ◽

Principal Component ◽

Protein Band ◽

Band Ratio ◽

Decay Fungi ◽

Postia Placenta ◽

Wood Decay Fungi ◽

Standing Trees

Wood fungi create vast damage among standing trees and all types of wood materials. The objectives of this study are to (a) characterize the cell materials of two major wood decay fungi (Basidiomycota), namely, Trametes versicolor and Postia placenta, and (b) compare the cell materials of decay fungi with four wood mould fungi (Ascomycota), namely, Aureobasidium pullulans, Alternaria alternata, Cladosporium cladosporioides, and Ulocladium atrum. Fourier transform infrared (FTIR) spectroscopy is used to characterize the microbial cellular materials. The results showed that the IR bands for the fatty acid at ∼2900 cm−1 were different for the two-decay-fungi genre. Postia placenta shows more absorbance peaks at the fatty acid region. Band ratio indices for amide I and amide II from protein amino acids were higher for the mould fungi (Ascomycota) than the decay fungi (Basidiomycota). Similarly, the band ratio index calculated for the protein end methyl group was found to be higher for the mould fungi than the decay fungi. Mould fungi along with the decay fungi demonstrated a positive correlation (R2=0.75) between amide I and amide II indices. The three-component multivariate, principal component analysis showed a strong correlation of amide and protein band indices.

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The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

Microbiology Resource Announcements ◽

10.1128/mra.00778-19 ◽

2019 ◽

Vol 8 (34) ◽

Cited By ~ 1

Author(s):

Gordon Webster ◽

Alex J. Mullins ◽

Aimee S. Bettridge ◽

Cerith Jones ◽

Edward Cunningham-Oakes ◽

...

Keyword(s):

Plant Pathogens ◽

Novel Species ◽

Wood Decay ◽

Gene Clusters ◽

Antagonistic Activity ◽

Biosynthetic Gene Clusters ◽

Decay Fungi ◽

Content Type ◽

Wood Decay Fungi ◽

Novel Taxa

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters.

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Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium

Applied and Environmental Microbiology ◽

10.1128/aem.01604-14 ◽

2014 ◽

Vol 80 (18) ◽

pp. 5828-5835 ◽

Cited By ~ 22

Author(s):

Jill Gaskell ◽

Amber Marty ◽

Michael Mozuch ◽

Philip J. Kersten ◽

Sandra Splinter BonDurant ◽

...

Keyword(s):

Gene Expression ◽

Phanerochaete Chrysosporium ◽

Expression Patterns ◽

Hybrid Poplar ◽

Wood Decay ◽

Transcript Abundance ◽

Gene Expression Patterns ◽

Parental Line ◽

Content Type ◽

Liquid Chromatography Tandem Mass

ABSTRACTWe examined gene expression patterns in the lignin-degrading fungusPhanerochaete chrysosporiumwhen it colonizes hybrid poplar (Populus alba×tremula) and syringyl (S)-rich transgenic derivatives. A combination of microarrays and liquid chromatography-tandem mass spectrometry (LC-MS/MS) allowed detection of a total of 9,959 transcripts and 793 proteins. Comparisons ofP. chrysosporiumtranscript abundance in medium containing poplar or glucose as a sole carbon source showed 113 regulated genes, 11 of which were significantly higher (>2-fold,P< 0.05) in transgenic line 64 relative to the parental line. Possibly related to the very large amounts of syringyl (S) units in this transgenic tree (94 mol% S), several oxidoreductases were among the upregulated genes. Peptides corresponding to a total of 18 oxidoreductases were identified in medium consisting of biomass from line 64 or 82 (85 mol% S) but not in the parental clone (65 mol% S). These results demonstrate thatP. chrysosporiumgene expression patterns are substantially influenced by lignin composition.

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Syringyl-Rich Lignin Renders Poplars More Resistant to Degradation by Wood Decay Fungi

Applied and Environmental Microbiology ◽

10.1128/aem.03182-12 ◽

2013 ◽

Vol 79 (8) ◽

pp. 2560-2571 ◽

Cited By ~ 69

Author(s):

Oleksandr Skyba ◽

Carl J. Douglas ◽

Shawn D. Mansfield

Keyword(s):

Wood Decay ◽

Critical Factor ◽

Cell Types ◽

Transgenic Poplar ◽

Decay Fungi ◽

Content Type ◽

Monomer Composition ◽

Syringyl Lignin ◽

Wood Decay Fungi ◽

Cell Layers

ABSTRACTIn order to elucidate the effects of lignin composition on the resistance of wood to degradation by decay fungi, wood specimens from two transgenic poplar lines expressing anArabidopsisgene encoding ferulate 5-hydroxylase (F5H) driven by the cinnimate-4-hydroxylase promoter (C4H::F5H) that increased syringyl/guaiacyl (S/G) monolignol ratios relative to those in the untransformed control wood were incubated with six different wood decay fungi. Alterations in wood weight and chemical composition were monitored over the incubation period. The results showed that transgenic poplar lines extremely rich in syringyl lignin exhibited a drastically improved resistance to degradation by all decay fungi evaluated. Lignin monomer composition and its distribution among cell types and within different cell layers were the sole wood chemistry parameters determining wood durability. Since transgenic poplars with exceedingly high syringyl contents were recalcitrant to degradation, where wood durability is a critical factor, these genotypes may offer improved performance.

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