Influence of carbon source on wood decay-associated gene expression in sequential hyphal zones of the brown rot fungus Gloeophyllum trabeum

2021 ◽  
Author(s):  
Kiwamu Umezawa ◽  
Shuji Itakura
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Carbon Source ◽  
Glycoside Hydrolase ◽  
Degradation Mechanism ◽  
Enzymatic Saccharification ◽  
Brown Rot ◽  
Gloeophyllum Trabeum ◽  
Brown Rot Fungi ◽  
Brown Rot Fungus

Abstract Brown rot fungi show a two-step wood degradation mechanism comprising oxidative radical-based and enzymatic saccharification systems. Recent studies have demonstrated that the brown rot fungus Rhodonia placenta expresses oxidoreductase genes ahead of glycoside hydrolase genes and spatially protects the saccharification enzymes from oxidative damage of the oxidoreductase reactions. This study aimed to assess the generality of the spatial gene regulation of these genes in other brown rot fungi and examine the effects of carbon source on the gene regulation. Gene expression analysis was performed on 14 oxidoreductase and glycoside hydrolase genes in the brown rot fungus Gloeophyllum trabeum, directionally grown on wood, sawdust-agar, and glucose-agar wafers. In G. trabeum, both oxidoreductase and glycoside hydrolase genes were expressed at higher levels in sections behind the wafers. The upregulation of glycoside hydrolase genes was significantly higher in woody substrates than in glucose, whereas the oxidoreductase gene expression was not affected by substrates.

scholarly journals Transcriptome analysis of the brown rot fungus Gloeophyllum trabeum during lignocellulose degradation

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243984
Author(s):  
Kiwamu Umezawa ◽  
Mai Niikura ◽  
Yuka Kojima ◽  
Barry Goodell ◽  
Makoto Yoshida
Keyword(s):  
Degradation Mechanism ◽  
Enzymatic Saccharification ◽  
Japanese Cedar ◽  
Brown Rot ◽  
Terpene Synthase ◽  
Lignocellulose Degradation ◽  
Substrate Selectivity ◽  
Gloeophyllum Trabeum ◽  
Wood Degradation ◽  
Brown Rot Fungi

Brown rot fungi have great potential in biorefinery wood conversion systems because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Comparison to the gene expression on glucose, 1,129 genes were upregulated on cellulose and 1,516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included glycoside hyrolase family 12 (GH12), GH131, carbohydrate esterase family 1 (CE1), auxiliary activities family 3 subfamily 1 (AA3_1), AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these gene products in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.

scholarly journals A Lytic Polysaccharide Monooxygenase with Broad Xyloglucan Specificity from the Brown-Rot Fungus Gloeophyllum trabeum and Its Action on Cellulose-Xyloglucan Complexes

2016 ◽  
Vol 82 (22) ◽  
pp. 6557-6572 ◽  
Author(s):  
Yuka Kojima ◽  
Anikó Várnai ◽  
Takuya Ishida ◽  
Naoki Sunagawa ◽  
Dejan M. Petrovic ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dynamic Viscosity ◽  
Brown Rot ◽  
Primary Cell Wall ◽  
Gloeophyllum Trabeum ◽  
Lytic Polysaccharide Monooxygenase ◽  
Content Type ◽  
Brown Rot Fungus ◽  
Sensitive Method ◽  
Polysaccharide Monooxygenase

ABSTRACTFungi secrete a set of glycoside hydrolases and lytic polysaccharide monooxygenases (LPMOs) to degrade plant polysaccharides. Brown-rot fungi, such asGloeophyllum trabeum, tend to have few LPMOs, and information on these enzymes is scarce. The genome ofG. trabeumencodes four auxiliary activity 9 (AA9) LPMOs (GtLPMO9s), whose coding sequences were amplified from cDNA. Due to alternative splicing, two variants ofGtLPMO9A seem to be produced, a single-domain variant,GtLPMO9A-1, and a longer variant,GtLPMO9A-2, which contains a C-terminal domain comprising approximately 55 residues without a predicted function. We have overexpressed the phylogenetically distinctGtLPMO9A-2 inPichia pastorisand investigated its properties. Standard analyses using high-performance anion-exchange chromatography–pulsed amperometric detection (HPAEC-PAD) and mass spectrometry (MS) showed thatGtLPMO9A-2 is active on cellulose, carboxymethyl cellulose, and xyloglucan. Importantly, compared to other known xyloglucan-active LPMOs,GtLPMO9A-2 has broad specificity, cleaving at any position along the β-glucan backbone of xyloglucan, regardless of substitutions. Using dynamic viscosity measurements to compare the hemicellulolytic action ofGtLPMO9A-2 to that of a well-characterized hemicellulolytic LPMO,NcLPMO9C fromNeurospora crassarevealed thatGtLPMO9A-2 is more efficient in depolymerizing xyloglucan. These measurements also revealed minor activity on glucomannan that could not be detected by the analysis of soluble products by HPAEC-PAD and MS and that was lower than the activity ofNcLPMO9C. Experiments with copolymeric substrates showed an inhibitory effect of hemicellulose coating on cellulolytic LPMO activity and did not reveal additional activities ofGtLPMO9A-2. These results provide insight into the LPMO potential ofG. trabeumand provide a novel sensitive method, a measurement of dynamic viscosity, for monitoring LPMO activity.IMPORTANCECurrently, there are only a few methods available to analyze end products of lytic polysaccharide monooxygenase (LPMO) activity, the most common ones being liquid chromatography and mass spectrometry. Here, we present an alternative and sensitive method based on measurement of dynamic viscosity for real-time continuous monitoring of LPMO activity in the presence of water-soluble hemicelluloses, such as xyloglucan. We have used both these novel and existing analytical methods to characterize a xyloglucan-active LPMO from a brown-rot fungus. This enzyme,GtLPMO9A-2, differs from previously characterized LPMOs in having broad substrate specificity, enabling almost random cleavage of the xyloglucan backbone.GtLPMO9A-2 acts preferentially on free xyloglucan, suggesting a preference for xyloglucan chains that tether cellulose fibers together. The xyloglucan-degrading potential ofGtLPMO9A-2 suggests a role in decreasing wood strength at the initial stage of brown rot through degradation of the primary cell wall.

De Novo Synthesis of 4,5-Dimethoxycatechol and 2,5-Dimethoxyhydroquinone by the Brown Rot FungusGloeophyllum trabeum

1999 ◽  
Vol 65 (2) ◽  
pp. 674-679 ◽  
Author(s):  
Andrzej Paszczynski ◽  
Ronald Crawford ◽  
David Funk ◽  
Barry Goodell
Keyword(s):  
Mass Spectrometry ◽  
Methylene Chloride ◽  
De Novo ◽  
Brown Rot ◽  
Gas Chromatography Mass Spectrometry ◽  
Gloeophyllum Trabeum ◽  
De Novo Synthesis ◽  
Brown Rot Fungus ◽  
Synthetic Standard ◽  
Brown Rot Decay

ABSTRACT The new dimethoxycatechol 4,5-dimethoxy-1,2-benzenediol (DMC) and the new dimethoxyhydroquinone 2,5-dimethoxy-1,4-benzenediol (DMH) were isolated from stationary cultures of the brown rot fungusGloeophyllum trabeum growing on a glucose mineral medium protected from light. The structure was elucidated by gas chromatography-mass spectrometry through comparison to a synthetic standard. Further confirmation was obtained by forming a dimethoxyoxazole derivative by condensation of DMC with methylene chloride and through examination of methylated derivatives. DMC and DMH may serve as ferric chelators, oxygen-reducing agents, and redox-cycling molecules, which would include functioning as electron transport carriers to Fenton’s reactions. Thus, they appear to be important components of the brown rot decay system of the fungus.

scholarly journals Gene Regulation Shifts Shed Light on Fungal Adaption in Plant Biomass Decomposers

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
Jiwei Zhang ◽  
Kevin A. T. Silverstein ◽  
Jesus David Castaño ◽  
Melania Figueroa ◽  
Jonathan S. Schilling
Keyword(s):  
Reactive Oxygen Species ◽  
Gene Regulation ◽  
Plant Biomass ◽  
Reactive Oxygen ◽  
Brown Rot ◽  
Comparative Transcriptomics ◽  
White Rot ◽  
Ecological Niches ◽  
Oxygen Species ◽  
Brown Rot Fungi

ABSTRACT Fungi dominate the recycling of carbon sequestered in woody biomass. This process of organic turnover was first evolved among “white rot” fungi that degrade lignin to access carbohydrates and later evolved multiple times toward more efficient strategies to selectively target carbohydrates—“brown rot.” The brown rot adaption was often explained by mechanisms to deploy reactive oxygen species (ROS) to oxidatively attack wood structures. However, its genetic basis remains unclear, especially in the context of gene contractions of conventional carbohydrate-active enzymes (CAZYs) relative to white rot ancestors. Here, we hypothesized that these apparent gains in brown rot efficiency despite gene losses were due, in part, to upregulation of the retained genes. We applied comparative transcriptomics to multiple species of both rot types grown across a wood wafer to create a gradient of progressive decay and to enable tracking temporal gene expression. Dozens of “decay-stage-dependent” ortho-genes were isolated, narrowing a pool of candidate genes with time-dependent regulation unique to brown rot fungi. A broad comparison of the expression timing of CAZY families indicated a temporal regulatory shift of lignocellulose-oxidizing genes toward early stages in brown rot compared to white rot, enabling the segregation of oxidative treatment ahead of hydrolysis. These key brown rot ROS-generating genes with iron ion binding functions were isolated. Moreover, transcription energy was shifted to be invested on the retained GHs in brown rot fungi to strengthen carbohydrate conversion. Collectively, these results support the hypothesis that gene regulation shifts played a pivotal role in brown rot adaptation. IMPORTANCE Fungi dominate the turnover of wood, Earth’s largest pool of aboveground terrestrial carbon. Fungi first evolved this capacity by degrading lignin to access and hydrolyze embedded carbohydrates (white rot). Multiple lineages, however, adapted faster reactive oxygen species (ROS) pretreatments to loosen lignocellulose and selectively extract sugars (brown rot). This brown rot “shortcut” often coincided with losses (>60%) of conventional lignocellulolytic genes, implying that ROS adaptations supplanted conventional pathways. We used comparative transcriptomics to further pursue brown rot adaptations, which illuminated the clear temporal expression shift of ROS genes, as well as the shift toward synthesizing more GHs in brown rot relative to white rot. These imply that gene regulatory shifts, not simply ROS innovations, were key to brown rot fungal evolution. These results not only reveal an important biological shift among these unique fungi, but they may also illuminate a trait that restricts brown rot fungi to certain ecological niches.

Enzymatic saccharification of biologically pretreated Pinus densiflora using enzymes from brown rot fungi

2008 ◽  
Vol 106 (2) ◽  
pp. 162-167 ◽  
Author(s):  
Jae-Won Lee ◽  
Ho-Yong Kim ◽  
Bon-Wook Koo ◽  
Don-Ha Choi ◽  
Mi Kwon ◽  
...  
Keyword(s):  
Pinus Densiflora ◽  
Enzymatic Saccharification ◽  
Brown Rot ◽  
Brown Rot Fungi

Changes of EPR Spectra of Wood Impregnated with Copper-Based Preservatives during Exposure to Several Wood-Rotting Fungi

Holzforschung ◽  
2002 ◽  
Vol 56 (3) ◽  
pp. 229-238 ◽  
Author(s):  
M. Humar ◽  
M. Petrič ◽  
F. Pohleven ◽  
M. Šentjurc ◽  
P. Kalan
Keyword(s):  
Schizophyllum Commune ◽  
White Rot Fungi ◽  
Brown Rot ◽  
White Rot ◽  
Gloeophyllum Trabeum ◽  
Nutrient Media ◽  
Paramagnetic Resonance ◽  
Copper Oxalate ◽  
Brown Rot Fungi ◽  
Electron Paramagnetic

SummaryThe tolerance of various fungi against copper was examined. For this purpose, we impregnated Norway spruce (Picea abies) specimens with two different aqueous solutions: copper(II) octanoate with ethanolamine or copper(II) sulfate (cCu= 1.0 × 10−2mol/l). Impregnated and unimpregnated test specimens were then exposed to brown rot fungiAntrodia vaillantiiandGloeophyllum trabeumor to white-rot fungiSchizophyllum communeandTrametes versicolor. After 2, 4, 6 and 12 weeks of exposure Electron Paramagnetic Resonance, Atomic Absorption Spectroscopy and mass loss measurements were performed. The results indicate thatA. vaillantii, G. trabeumandT. versicolortransform copper(II) sulfate in wood into non-soluble, and therefore non-toxic, copper oxalate. The intensity of this reaction depends on the amount of excreted oxalic acid and was the highest forA. vaillantiiand the lowest forT. versicolor. In the presence of ethanolamine, formation of insoluble copper oxalate was not possible and therefore, decay could not proceed. The major portion of copper remained in the wood and only minor amounts were in some cases translocated into nutrient media.

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