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

Gaskell, Jill; Marty, Amber J.; Mozuch, Michael D.; Kersten, Philip J.; BonDurant, Sandra Splinter; Sabat, Grzegorz; Azarpira, Ali; Ralph, John; Skyba, Oleksandr; Mansfield, Shawn D.; Blanchette, Robert A.; Cullen, Dan

doi:10.1128/aem.01604-14

Cited by 30 publications

(31 citation statements)

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“…To date, genome-wide transcriptome studies of gene expression in P. chrysosporium and P. placenta have been conducted only after incubation for a single, predetermined growth period in submerged cultures supplemented with ground wood substrate, glu- cose, or microcrystalline cellulose (17,28,(33)(34)(35)(36)(37). Although these studies have contributed to our understanding of the transcriptional regulation and modulation of gene expression on woody substrates, they bear little resemblance to solid substrates, where accessibility to cell wall polymers likely influences transcript levels.…”

Section: Discussionmentioning

confidence: 99%

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

Skyba

Cullen

Douglas

et al. 2016

Appl Environ Microbiol

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Identification 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 (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus 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) in P. chrysosporium and P. 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 of P. chrysosporium and P. placenta are 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. In an attempt to reduce societal dependence on fossil fuels and consequently aid in the alleviation of associated economic and environmental concerns regarding the exploitation of petroleum reserves, biofuels derived from renewable and domestic sources have received extensive interest in recent years (1). The lignocellulosic biomass derived from plant cell walls is the most abundant global renewable carbon source (2), stemming from either agricultural or forestry residuals or from dedicated energy crops. While improvement in lignocellulosic feedstock for biofuel applications via advanced breeding or genetic engineering appears feasible and is critical for the future...

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Section: Discussionmentioning

confidence: 99%

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

Skyba

Cullen

Douglas

et al. 2016

Appl Environ Microbiol

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“…Initial work in this area employed quantitative reverse transcriptase PCR (RT-PCR) measurements of select transcripts and showed that ligninolytic peroxidases are highly expressed by P. chrysosporium on wood (17), but it did not address the overall coordination of lignin degradation. With the advent of the initial genome assembly and annotations (v1.0 and v2.1) (18), microarray-based transcriptome analysis allowed examination of transcript levels of P. chrysosporium genes during growth on ball-milled wood and in defined growth media (19)(20)(21)(22)(23). This approach provided useful insights but was limited to 10,048 v2.1 targets and complicated by the unpredictable manner in which the fungus responds to unnatural carbon sources in submerged basal salts medium.…”

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confidence: 99%

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Korripally

Hunt

Houtman

et al. 2015

Appl Environ Microbiol

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Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew Phanerochaete chrysosporium on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2 P. chrysosporium genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe 3؉ reduction, and oxidase-catalyzed H 2 O 2 production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis. T he biodegradation of lignocellulose requires the disruption of its lignin, which shields the metabolically assimilable polysaccharides in this recalcitrant natural composite. Although a variety of microorganisms can attack lignocellulose, white rot basidiomycetes are uniquely efficient at this process, cleaving the recalcitrant intermonomer linkages of lignin via extracellular oxidative mechanisms and mineralizing many of the resulting fragments to carbon dioxide (1). Considerable progress has been made in understanding this process in the extensively researched white rot fungus Phanerochaete chrysosporium, which expresses important components of its ligninolytic system in response to nutrient limitation as part of its secondary metabolism. Biochemical and genetic evidence points to an important role in P. chrysosporium for secreted lignin peroxidases (LiPs), manganese peroxidases (MnPs), and H 2 O 2 -producing oxidases, which are thought to work together to cleave lignin into low-molecular-weight fragments (2). However, many aspects of ligninolysis by P. chrysosporium remain poorly understood.First, uncertainty remains about the process of lignin depolymerization. White rot fungi remove lignin not only from the surface of the wood cel...

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“…Genes encoding various CAZymes such as cellobiohydrolases, endoglucanases, β-glucosidase, endoxylanases, endo glucanases and mannases were found to be expressed in control conditions and the same genes were downregulated in oak extractives 25. In 2014, Gaskell et al has performed gene expression studies on P. chrysosporium to understand the influence of Populus genotype (P717, 82 and 64 transgenic lines) on its gene expression (GSE52922) 27. Results from this study showed that genes coding for GH-6 (CBH2), AA-3 (CDH), AA9 (LPMO), GH5 (endoglucanases) were highly upregulated in P717.…”

Section: Resultsmentioning

confidence: 99%

“…Till date there are 6 Microarray, 1 RNA sequencing and 1 Long-SAGE (Serial Analysis for Gene Expression) studies based on P. chrysosporium, out of which we have analyzed the microarray and RNA sequencing studies to understand the cellulolytic and hemicellulolytic degradation mechanisms. Accession IDs of microarray datasets retrieved from NCBI GEO are GSE14734 23, 24, GSE14735 23, 24 GSE54542 25, GSE2794126, GSE52922 27, GSE69008 28 GSE6946129 details of these gene expression datasets were shown in the Table 1.…”

Section: Data Analysis Methodologymentioning

confidence: 99%

“…Growth medium used for GSE27941 consists of 0.5% of ball milled aspen and ball milled pine as the sole carbon source supplemented with HBM 26. Similarly, growth medium used for GSE52922 consisted Wiley milled chemically distinct wood substrates of Populus trichocarpa P717 (parental hybrid clone line) with 65 mol% of syringyl units and the two transgenic lines 64 and 82 with 94 and 85 mol % of syringyl units, supplemented with HBM 27. GSE69461 medium consists of microtomed tangential sections of Picea glauca (40mm long, 10mm wide and 40 mm thick with a dry weight of 7mg) covered with 90µl of agar supplemented with nitrogen mineral salt medium 29.…”

Section: Data Analysis Methodologymentioning

confidence: 99%

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Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation

Kameshwar

Qin

2017

Int. J. Biol. Sci.

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In literature, extensive studies have been conducted on popular wood degrading white rot fungus, Phanerochaete chrysosporium about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of P. chrysosporium gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, P. chrysosporium, on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of P. chrysosporium transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.

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

Cited by 30 publications

References 53 publications

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

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

Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood

Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation

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