Intracellular pathways for lignin catabolism in white-rot fungi.
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ABSTRACT:
SUBMITTER: Del Cerro C
PROVIDER: S-EPMC7936344 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.
2021-01-15 | GSE151629 | GEO
Project description:White-rot fungi (WRF), considered the most efficient organisms at degrading organic carbon in the biosphere, are found in plant cell wall lignin biopolymer. We employ multi-omics to demonstrate that Trametes versicolor and Gelatoporia subvermispora funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems.
2021-02-10 | PXD019839 | Pride
Project description:Intracellular pathways for lignin catabolism in white-rot fungi
| PRJNA636664 | ENA
Project description:We propose to elucidate new metabolic pathways in fungi - with a special focus on white rot fungi (WRF)- involved in the catabolism of lignin-derived aromatic compounds. Basidiomycete fungi, in particular WRF, are the most efficient organisms for the depolymerization and mineralization of lignin to CO2 and H2O in Nature and thus, WRF play a pivotal role in carbon cycling. Lignin depolymerization by WRF is mediated by the action of extracellular oxidative ligninolytic enzymes, such as laccases and peroxidases, alongside other secreted metabolites. This extracellular process has been studied for decades via analysis of lignin modifications, ligninolytic enzyme activity in fungal broths, enzyme isolation and characterization, and more recently through multi-omics analyses. Despite the massive research effort directed toward understanding how WRF depolymerize lignin, almost no attention has been dedicated to the elucidation of the intracellular metabolism of WRF in catabolizing lignin. In fact, whether or not WRF are able to catabolize lignin remains a matter of discussion and debate.
The work (proposal:https://doi.org/10.46936/10.25585/60001176) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-05-16 | MSV000094781 | MassIVE
Project description:We propose to elucidate new metabolic pathways in fungi - with a special focus on white rot fungi (WRF)- involved in the catabolism of lignin-derived aromatic compounds. Basidiomycete fungi, in particular WRF, are the most efficient organisms for the depolymerization and mineralization of lignin to CO2 and H2O in Nature and thus, WRF play a pivotal role in carbon cycling. Lignin depolymerization by WRF is mediated by the action of extracellular oxidative ligninolytic enzymes, such as laccases and peroxidases, alongside other secreted metabolites. This extracellular process has been studied for decades via analysis of lignin modifications, ligninolytic enzyme activity in fungal broths, enzyme isolation and characterization, and more recently through multi-omics analyses. Despite the massive research effort directed toward understanding how WRF depolymerize lignin, almost no attention has been dedicated to the elucidation of the intracellular metabolism of WRF in catabolizing lignin. In fact, whether or not WRF are able to catabolize lignin remains a matter of discussion and debate.
The work (proposal:https://doi.org/10.46936/10.25585/60001176) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-05-16 | MSV000094781 | GNPS
Project description:A comparison of sequenced Agaricomycotina genomes suggests that efficient degradation of wood lignin was associated with the appearance of secreted peroxidases with a solvent-exposed catalytic tryptophan. This hypothesis is experimentally demonstrated here by resurrecting ancestral fungal peroxidases, after sequence reconstruction from genomes of extant white-rot Polyporales, and evaluating their oxidative attack on the lignin polymer by state-of-the-art analytical techniques. Rapid stopped-flow estimation of the transient-state constants for the 2 successive one-electron transfers from lignin to the peroxide-activated enzyme (k 2app and k 3app ) showed a progressive increase during peroxidase evolution (up to 50-fold higher values for the rate-limiting k 3app ). The above agreed with 2-dimensional NMR analyses during steady-state treatments of hardwood lignin, showing that its degradation (estimated from the normalized aromatic signals of lignin units compared with a control) and syringyl-to-guaiacyl ratio increased with the enzyme evolutionary distance from the first peroxidase ancestor. More interestingly, the stopped-flow estimations of electron transfer rates also showed how the most recent peroxidase ancestors that already incorporated the exposed tryptophan into their molecular structure (as well as the extant lignin peroxidase) were comparatively more efficient at oxidizing hardwood (angiosperm) lignin, while the most ancestral "tryptophanless" enzymes were more efficient at abstracting electrons from softwood (conifer) lignin. A time calibration of the ancestry of Polyporales peroxidases localized the appearance of the first peroxidase with a solvent-exposed catalytic tryptophan to 194 ± 70 Mya, coincident with the diversification of angiosperm plants characterized by the appearance of dimethoxylated syringyl lignin units.
| S-EPMC6731631 | biostudies-literature
Project description:Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subvermispora, fungi lacking lignin peroxidase (LiP) activity. Amplification products were highly similar to previously described LiP genes. Using reverse transcription-coupled PCR a LiP-like cDNA clone was amplified from P. sordida RNA. In contrast, no evidence was obtained for transcription of C. subvermispora LiP genes.
| S-EPMC168048 | biostudies-other
Project description:Indigenous white-rot fungal isolates Schizophyllum commune, Phanerochaete chrysosporium, Ganoderma racenaceum, and Lentinus squarrosulus, demonstrating the ability to depolymerize lignin of the crop residues, were studied for their potential to produce ligninolytic enzymes using modified production media under conditions of limiting and excess nitrogen for higher enzymatic expressions. Secretome-rich media on the investigation confirmed the successful production of lignin-depolymerizing enzymes, viz. laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase. Production of laccases and peroxidases was statistically significant in nitrogen-limiting media with and without the substrate, across all white-rot fungal cultures at 95% confidence interval. Nitrogen-limiting media with the substrate on analysis extracellularly expressed 99.27 U of laccase and 68.48 U of manganese peroxidase in Schizophyllum commune, while 195.14 U of lignin peroxidase was produced by Phanerochaete chrysosporium. Lentinus squarrosulus expressed 455.34 U of laccase and 357.13 U of versatile peroxidase with 250.09 U of laccase and 206.95 U of manganese peroxidase produced by Ganoderma racenaceum for every milliliter of the media used. Nitrogen-limiting media triggered the production of laccase during the initial stages of growth while the expression of peroxidases was predominant at a later stage. Also, this media evinced increased enzymatic yields with low biomass content compared to nitrogen-excess conditions. The extant study confirmed the positive influence of nitrogen-limiting media in the efficient production of ligninolytic enzymes and their suggestive degradation potential for environmental pollutants, making these enzymes a safe, clean alternative to the use of chemicals and the media to be effective for large-scale production of ligninolytic enzymes. IMPORTANCE Lignin on account of its high abundance, complex polymeric structure, and biochemical properties is identified as a promising candidate in renewable energy and bioproduct manufacturing. However, depolymerization of lignin remains a major challenge in lignin utilization, entailing the employment of harsh treatments representing not only an environmental concern but also a waste of economic potential. Developing an alternative green technology to minimize this impact is imperative. Methods using enzymes to depolymerize lignin are the focus of recent studies. Current research work emphasized the efficient expression of the major lignin-depolymerizing enzymes: laccases, lignin peroxidases, manganese peroxidases, and versatile peroxidases from native isolates of white-rot fungus for several biotechnological applications as well as treatment of crop residues for use as ruminant feed in improving productivity. The importance of nitrogen in augmenting the expression of lignin-depolymerizing enzymes and providing a media recipe for the cost-effective production of ligninolytic enzymes is highlighted.
| S-EPMC10581151 | biostudies-literature
Project description:There is increasing concern about tire wear compounds (TWCs) in surface water and stormwater as evidence grows on their toxicity and widespread detection in the environment. Because TWCs are prevalent in stormwater, there is a need to understand fate and treatment options including biotransformation in green infrastructure (e.g., bioretention). Particularly, fungal biotransformation is not well-studied in a stormwater context despite the known ability of certain fungi to remove recalcitrant contaminants. Here, we report the first study on fungal biotransformation of the TWCs acetanilide and hexamethoxymethylmelamine (HMMM). We found that the model white rot fungus, Trametes versicolor, removed 81.9% and 69.6% of acetanilide and HMMM, respectively, with no significant sorption to biomass. The bicyclic amine 1,3-diphenylguanidine was not removed. Additionally, we identified novel TWC metabolites using semi-untargeted metabolomics via high-resolution mass spectrometry. Key metabolites include multiple isomers of HMMM biotransformation products, melamine as a possible "dead-end" product of HMMM (verified with an authentic standard), and a glutamine-conjugated product of acetanilide. These metabolites have implications for environmental toxicity and treatment. Our discovery of the first fungal glutamine-conjugated product highlights the need to investigate amino acid conjugation as an important pathway in biotransformation of contaminants, with implications in other fields including natural products discovery.
| S-EPMC9100321 | biostudies-literature
Project description:The degradation of lignocellulose by fungi, especially white-rot fungi, contributes a lot to carbon cycle, bio-fuel production, and many other bio-based applications. However, the existing enzymatic and non-enzymatic degradation mechanisms cannot be unequivocally supported by in vitro simulation experiment, meaning that additional mechanisms might exist. Right now, it is still very difficult to discover new mechanisms with traditional forward genetic approaches. To disclose novel lignin degradation mechanisms in white-rot fungi, a series of fusants from wide cross by protoplast fusion between Pleurotus ostreatus, a well-known lignin-degrading fungus, and Saccharomyces cerevisiae, a well-known model organism unable to degrade lignocellulose, was investigated regarding their abilities to degrade lignin. By analyzing the activity of traditional lignin-degrading enzyme, the ability to utilize pure lignin compounds and degrade corn stalk, a fusant D1-P was screened out and proved not to contain well-recognized lignin-degrading enzyme genes by whole-genome sequencing. Further investigation with two-dimension nuclear magnetic resonance (NMR) shows that D1-P was found to be able to degrade the main lignin structure β-O-4 linkage, leading to reduced level of this structure like that of the wild-type strain P. ostreatus after a 30-day semi-solid fermentation. It was also found that D1-P shows a degradation preference to β-O-4 linkage in Aβ(S)-threo. Therefore, wide cross between white-rot fungi and S. cerevisiae provides a powerful tool to uncover novel lignocellulose degradation mechanism that will contribute to green utilization of lignocellulose to produce bio-fuel and related bio-based refinery.
| S-EPMC9310788 | biostudies-literature