Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE26092 | GEO | 2010/12/25
SECONDARY ACCESSION(S): PRJNA135403
REPOSITORIES: GEO
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Project description:Cellulose from plant biomass is the largest renewable energy resource of carbon fixed from the atmosphere, which can be converted into fermentable sugars for production into ethanol. However, the cellulose present as lignocellulosic biomass is embedded in a hemicellulose and lignin matrix from which it needs to be extracted for efficient processing. Here, we show that expression of an Arabidopsis transcription factor SHINE (SHN) in rice, a model for the grasses, causes a 34% increase in cellulose and a 45% reduction in lignin content. Rice genotypes expressing the Arabidopsis SHN2 gene hereafter called rice AtSHN lines were used in this study. Progenies of three independent AtSHN lines were grown in controlled growth chambers. For all analyses, six plants were used for each of the two transgenic lines and WT. For total RNA isolation, rice leaf tissue of WT and AtSHN lines was used. Samples were hybridized to the rice Affymetrix GeneChip.
2010-12-25 | E-GEOD-26092 | biostudies-arrayexpress
Project description:Lignocellulosic biomass is composed of three major biopolymers: cellulose, hemicellulose and lignin. Although lignin has long been considered a waste product in biomass conversion efforts, its utilization has since been identified as critical to the economic viability of second-generation biofuel production. There is thus increasing interest in finding enzymes and enzyme cocktails which can efficiently deconstruct both the cellulose/hemicellulose and lignin components of lignocellulosic biomass. Analytical tools capable of quickly detecting both glycan and lignin deconstruction could are needed to support the development and characterization of efficient enzymes/enzyme cocktails.
2021-09-09 | PXD020215 | Pride
Project description:Plant biomass holds tremendous potential as a renewable feedstock in the production of biofuels and biochemicals. The effective co-utilization of the main components cellulose and hemicellulose in plant lignocellulose is critical to the economic viability of lignocellulosic biorefineries. Here, we found that the thermophilic cellulolytic fungi Myceliophthora thermophila can utilize cellulose and hemicellulose synchronously. To investigate the underlying molecular mechanisms, we firstly checked the soluble carbohydrate of the culture using plant biomass (corncob) as sole carbon source and revealed the presence of various oligosaccharides including cellodextrin and xylodextrin, both intracellularly and extracellularly in the cultures, in addition to glucose or xylose. Based on these, intracellular oligosaccharide metabolism was proposed and confirmed by identification of cellodextrin and xylodextrin metabolism pathway. Furthermore, sugar consumption assay showed that contrasting with synchronous utilization of mixed cello-/xylo-dextrin, the inhibition effect of glucose for the metabolism of xylose and cello-/xylo-dextrin exists in this fungus, suggesting Carbon Catabolite Repression (CCR) is largely avoided at the form of oligosaccharides. Transporter MtCDT-2 showing preference to xylobiose and the tolerance of cellobiose inhibition also helps to bypass metabolic inhibition. Finally, the expression of cellulase and hemicellulase genes, were found orthogonal induction by cellobiose/Avicel and xylobiose/xylan, which conferred the ability of the strain to synchronously utilize cellulose and hemicellulose. Taken together, the orthogonal oligosaccharide catabolic pathway in this fungus establishes the molecular basis for the synchronous utilization of cellulose and hemicellulose, which sheds new light on understanding the plant biomass degradation by fungi and provides alternative paradigm for development of lignocellulose biorefinery such as consolidated bioprocessing in the future.
2024-02-28 | GSE222371 | GEO
Project description:The common edible mushroom Agaricus bisporus is a basidiomycete that thrives on decaying plant material in the forests and grasslands of North America and Europe. It is adapted to forest litter and contributes to global carbon recycling, degrading cellulose, hemicellulose and lignin in plant biomass to oligomers and monomers. A. bisporus is also an edible mushroom that is widely cultivated and economically important. However, relatively little is known about how A. bisporus grows in this controlled environment and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were highly expressed during the spawning stage day 16 and had low expression during all the other growth stages which could indicate that lignin is not modified after the spawning stage. Our results also revealed differences in gene expression involved in cellulose and hemicellulose degradation between the first and second flushes. This could partially explain the reduction in the number of mushrooms during the second flush.
2015-09-23 | GSE65800 | GEO
Project description:The common edible mushroom Agaricus bisporus is a basidiomycete that thrives on decaying plant material in the forests and grasslands of North America and Europe. It is adapted to forest litter and contributes to global carbon recycling, degrading cellulose, hemicellulose and lignin in plant biomass to oligomers and monomers. A. bisporus is also an edible mushroom that is widely cultivated and economically important. However, relatively little is known about how A. bisporus grows in this controlled environment and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were highly expressed during the spawning stage day 16 and had low expression during all the other growth stages which could indicate that lignin is not modified after the spawning stage. Our results also revealed differences in gene expression involved in cellulose and hemicellulose degradation between the first and second flushes. This could partially explain the reduction in the number of mushrooms during the second flush. This study compares the gene expression of A. bisporus A15 at different stages of its life cycle using the controlled environment of indoor commercial cultivation. The samples were taken at the spawning stage, primordial stage, first flush, after first flush, second flush and after second flush, respectively
2015-09-23 | E-GEOD-65800 | biostudies-arrayexpress
Project description:The common edible mushroom Agaricus bisporus is a basidiomycete that thrives on decaying plant material in the forests and grasslands of North America and Europe. It is adapted to forest litter and contributes to global carbon recycling, depolymerizing cellulose, hemicellulose and lignin in plant biomass. A. bisporus is also an edible mushroom that is widely cultivated and economically important. However, relatively little is known about how A. bisporus grows in this controlled environment in commercial production facilities and utilizes its substrate. Using transcriptomics and proteomics, we showed that changes in plant biomass degradation by A. bisporus occur throughout its life cycle. Ligninolytic genes were highly expressed during the spawning stage day 16 and had low expression during all the other growth stages which could indicate that lignin is not modified after the spawning stage. Our results also revealed differences in gene expression involved in cellulose and hemicellulose degradation between the first and second flushes. This could partially explain the reduction in the number of mushrooms during the second flush.
2015-08-05 | PXD001817 | Pride
Project description:Evidence shows that bacteria contribute actively to the decomposition of cellulose and hemicellulose in forest soil; however, their role in this process is still unclear. Here we performed the screening and identification of bacteria showing potential cellulolytic activity from litter and organic soil of a temperate oak forest. The genomes of three cellulolytic isolates previously described as abundant in this ecosystem were sequenced and their proteomes were characterized during the growth on plant biomass and on microcrystalline cellulose. Pedobacter and Mucilaginibacter showed complex enzymatic systems containing highly diverse carbohydrate-active enzymes for the degradation of cellulose and hemicellulose, which were functionally redundant for endoglucanases, -glucosidases, endoxylanases, -xylosidases, mannosidases and carbohydrate-binding modules. Luteibacter did not express any glycosyl hydrolases traditionally recognized as cellulases. Instead, cellulose decomposition was likely performed by an expressed GH23 family protein containing a cellulose-binding domain. Interestingly, the presence of plant lignocellulose as well as crystalline cellulose both trigger the production of a wide set of hydrolytic proteins including cellulases, hemicellulases and other glycosyl hydrolases. Our findings highlight the extensive and unexplored structural diversity of enzymatic systems in cellulolytic soil bacteria and indicate the roles of multiple abundant bacterial taxa in the decomposition of cellulose and other plant polysaccharides.
2016-05-02 | PXD003844 | Pride
Project description:The search for new enzymes and microbial strains to degrade plant biomass is one of the most important strategies for improving the conversion processes in the production of environment-friendly chemicals and biofuels. In this study, we report a new Paenibacillus isolate, O199, which showed the highest efficiency for cellulose deconstruction in a screen of environmental isolates. Here, we provide a detailed description of the complex multi-component O199 enzymatic system involved in the degradation of lignocellulose. We examined the genome and the proteome of O199 grown on complex lignocellulose (wheat straw) and on microcrystalline cellulose. The genome contained 476 genes with domains assigned to carbohydrate-active enzyme (CAZyme) families, including 100 genes coding for glycosyl hydrolases (GHs) putatively involved in cellulose and hemicellulose degradation. Moreover, 31% of these CAZymes were expressed on cellulose and 29% on wheat straw. Proteomic analyses also revealed a complex and complete set of enzymes for deconstruction of cellulose (at least 22 proteins, including 4 endocellulases, 2 exocellulases, 2 cellobiohydrolases and 2 -glucosidases) and hemicellulose (at least 28 proteins, including 5 endoxylanases, 1 -xylosidase, 2 xyloglucanases, 2 endomannanases, 2 licheninases and 1 endo--1,3(4)-glucanase). Most of these proteins were secreted extracellularly and had numerous carbohydrate-binding domains (CBMs). In addition, O199 also secreted a high number of substrate-binding proteins (SBPs), including at least 42 proteins binding carbohydrates. Interestingly, both plant lignocellulose and crystalline cellulose triggered the production of a wide array of hydrolytic proteins, including cellulases, hemicellulases and other GHs. Our data provide an in-depth analysis of the complex and complete set of enzymes and accessory non-catalytic proteins—GHs, CBMs, transporters, and SBPs—implicated in the high cellulolytic capacity shown by this bacterial strain. The large diversity of hydrolytic enzymes and the extracellular secretion of most of them supports the use of Paenibacillus O199 as a candidate for second-generation technologies using paper or lignocellulosic agricultural wastes.
2016-04-26 | PXD003970 | Pride
Project description:The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors.
2018-02-13 | GSE96828 | GEO
Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.
2010-05-18 | E-GEOD-13977 | biostudies-arrayexpress