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Open accessJournal ArticleDOI: 10.1073/PNAS.2017381118

Intracellular pathways for lignin catabolism in white-rot fungi.

02 Mar 2021-Proceedings of the National Academy of Sciences of the United States of America (Proceedings of the National Academy of Sciences)-Vol. 118, Iss: 9
Abstract: 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 extensively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here, we employ 13C-isotope labeling, systems biology approaches, and in vitro enzyme assays to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel carbon from 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 establish a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts-a key step toward enabling a sustainable bioeconomy.

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Topics: Lignin (54%)
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Book ChapterDOI: 10.1016/BS.ABR.2021.05.007
01 Jan 2021-
Abstract: The major Grapevine Trunk Diseases (GTD) gather diseases associated with either one particular fungal species, e.g., eutypiose, or with fungal species complexes, e.g., Botryosphaeriae dieback. GTD-associated fungi are part of different fungal classes, depending on their substrate degradation mechanisms or on their lifestyles. They are identified in grapevine wood and they lead to wood typical symptoms. They are sometimes associated to foliar symptoms too, despite not found in aerial parts, probably acting through fungal toxins or through physiological disorders, such as non-functional wood vessels. Grapevine is a liana, and as such shows structural and chemical differences compared to forest tree wood. However, knowledge on wood-degrading fungi growing on tree wood can contribute to a better understanding of grapevine wood adaptation mechanisms to fungal attack. For example, wood density, xylem vessels size and number, or lignin content and composition can play a role in wood sensitivity to fungi. Also, some fungal detoxification mechanisms against wood extractibles are host-specific. In a first part of this chapter, structure and chemical composition of grapevine wood are described, pointing out properties that might play a role in fungal growth. In a second part, GTD main associated fungi and their known mechanisms for wood degradation or wood chemical detoxification are discussed. Extracellular and intracellular enzymatic and non-enzymatic mechanisms are considered. These mechanisms, well described for their role in fungal adaptation to tree wood, have been much less studied for GTD associated fungi. Further studies about those mechanisms would contribute to understand fungal adaptation to grapevine.

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4 Citations


Open accessJournal ArticleDOI: 10.1038/S42003-021-02401-W
15 Jul 2021-
Abstract: Fungal biotechnology is set to play a keystone role in the emerging bioeconomy, notably to address pollution issues arising from human activities. Because they preserve biological diversity, Biological Resource Centres are considered as critical infrastructures to support the development of biotechnological solutions. Here, we report the first large-scale phenotyping of more than 1,000 fungal strains with evaluation of their growth and degradation potential towards five industrial, human-designed and recalcitrant compounds, including two synthetic dyes, two lignocellulose-derived compounds and a synthetic plastic polymer. We draw a functional map over the phylogenetic diversity of Basidiomycota and Ascomycota , to guide the selection of fungal taxa to be tested for dedicated biotechnological applications. We evidence a functional diversity at all taxonomic ranks, including between strains of a same species. Beyond demonstrating the tremendous potential of filamentous fungi, our results pave the avenue for further functional exploration to solve the ever-growing issue of ecosystems pollution.

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2 Citations


Open accessJournal ArticleDOI: 10.3390/JOF7060426
Ander Peña1, Rashid Babiker1, Delphine Chaduli2, Anna Lipzen3  +14 moreInstitutions (4)
28 May 2021-Journal of Fungi
Abstract: Pleurotus eryngii is a grassland-inhabiting fungus of biotechnological interest due to its ability to colonize non-woody lignocellulosic material. Genomic, transcriptomic, exoproteomic, and metabolomic analyses were combined to explain the enzymatic aspects underlaying wheat-straw transformation. Up-regulated and constitutive glycoside-hydrolases, polysaccharide-lyases, and carbohydrate-esterases active on polysaccharides, laccases active on lignin, and a surprisingly high amount of constitutive/inducible aryl-alcohol oxidases (AAOs) constituted the suite of extracellular enzymes at early fungal growth. Higher enzyme diversity and abundance characterized the longer-term growth, with an array of oxidoreductases involved in depolymerization of both cellulose and lignin, which were often up-regulated since initial growth. These oxidative enzymes included lytic polysaccharide monooxygenases (LPMOs) acting on crystalline polysaccharides, cellobiose dehydrogenase involved in LPMO activation, and ligninolytic peroxidases (mainly manganese-oxidizing peroxidases), together with highly abundant H2O2-producing AAOs. Interestingly, some of the most relevant enzymes acting on polysaccharides were appended to a cellulose-binding module. This is potentially related to the non-woody habitat of P. eryngii (in contrast to the wood habitat of many basidiomycetes). Additionally, insights into the intracellular catabolism of aromatic compounds, which is a neglected area of study in lignin degradation by basidiomycetes, were also provided. The multiomic approach reveals that although non-woody decay does not result in dramatic modifications, as revealed by detailed 2D-NMR and other analyses, it implies activation of the complete set of hydrolytic and oxidative enzymes characterizing lignocellulose-decaying basidiomycetes.

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Topics: Cellobiose dehydrogenase (55%), Pleurotus eryngii (55%), Laccase (55%) ... show more

2 Citations


Journal ArticleDOI: 10.1016/J.BIORTECH.2021.125655
Abstract: Lignin is a wasted renewable source of biomass-derived value-added chemicals. However, due to its material resistance to degradation, it remains highly underutilized. In order to develop new, catalysed and more environment friendly reaction processes for lignin valorization, science has turned a selective concentrated attention to microbial enzymes. This present work looks at the enzymes involved with the main reference focus on the different elementary mechanisms of action/conversion rate kinetics. Pathways, like with laccases/peroxidases, employ radicals, which more readily result in polymerization than de-polymerization. The β-etherase system interaction of proteins targets β-O-4 ether covalent bond, which targets lower molecular weight product species. Enzymatic activity is influenced by a wide variety of different factors which need to be considered in order to obtain the best functionality and synthesis yields.

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Topics: Laccase (54%)

2 Citations


Open accessJournal ArticleDOI: 10.1126/SCIADV.ABG4585
Chenggu Cai1, Zhaoxian Xu1, Huarong Zhou1, Sitong Chen1  +1 moreInstitutions (1)
03 Sep 2021-Science Advances
Abstract: Converting lignin components into a single product is a promising way to upgrade lignin. Here, an efficient biocatalyst was developed to selectively produce gallate from lignin components by integr...

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Topics: Gallate (57%), Demethylation (53%), Hydroxylation (52%)

1 Citations


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70 results found


Open accessJournal ArticleDOI: 10.1093/NAR/GKY1106
Abstract: The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.

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Topics: Information repository (53%)

3,828 Citations


Open accessJournal ArticleDOI: 10.1038/NATURE10386
06 Oct 2011-Nature
Abstract: Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

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Topics: Soil organic matter (62%), Soil carbon (56%)

3,486 Citations


Journal ArticleDOI: 10.1021/CR900354U
10 Mar 2010-Chemical Reviews
Abstract: Biomass is an important feedstock for the renewable production of fuels, chemicals, and energy. As of 2005, over 3% of the total energy consumption in the United States was supplied by biomass, and it recently surpassed hydroelectric energy as the largest domestic source of renewable energy. Similarly, the European Union received 66.1% of its renewable energy from biomass, which thus surpassed the total combined contribution from hydropower, wind power, geothermal energy, and solar power. In addition to energy, the production of chemicals from biomass is also essential; indeed, the only renewable source of liquid transportation fuels is currently obtained from biomass.

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Topics: Renewable fuels (67%), Renewable energy (67%), Alternative energy (66%) ... show more

3,137 Citations


Journal ArticleDOI: 10.1126/SCIENCE.1246843
16 May 2014-Science
Abstract: Background Lignin, nature’s dominant aromatic polymer, is found in most terrestrial plants in the approximate range of 15 to 40% dry weight and provides structural integrity. Traditionally, most large-scale industrial processes that use plant polysaccharides have burned lignin to generate the power needed to productively transform biomass. The advent of biorefineries that convert cellulosic biomass into liquid transportation fuels will generate substantially more lignin than necessary to power the operation, and therefore efforts are underway to transform it to value-added products. Production of biofuels from cellulosic biomass requires separation of large quantities of the aromatic polymer lignin. In planta genetic engineering, enhanced extraction methods, and a deeper understanding of the structure of lignin are yielding promising opportunities for efficient conversion of this renewable resource to carbon fibers, polymers, commodity chemicals, and fuels. [Credit: Oak Ridge National Laboratory, U.S. Department of Energy] Advances Bioengineering to modify lignin structure and/or incorporate atypical components has shown promise toward facilitating recovery and chemical transformation of lignin under biorefinery conditions. The flexibility in lignin monomer composition has proven useful for enhancing extraction efficiency. Both the mining of genetic variants in native populations of bioenergy crops and direct genetic manipulation of biosynthesis pathways have produced lignin feedstocks with unique properties for coproduct development. Advances in analytical chemistry and computational modeling detail the structure of the modified lignin and direct bioengineering strategies for targeted properties. Refinement of biomass pretreatment technologies has further facilitated lignin recovery and enables catalytic modifications for desired chemical and physical properties. Outlook Potential high-value products from isolated lignin include low-cost carbon fiber, engineering plastics and thermoplastic elastomers, polymeric foams and membranes, and a variety of fuels and chemicals all currently sourced from petroleum. These lignin coproducts must be low cost and perform as well as petroleum-derived counterparts. Each product stream has its own distinct challenges. Development of renewable lignin-based polymers requires improved processing technologies coupled to tailored bioenergy crops incorporating lignin with the desired chemical and physical properties. For fuels and chemicals, multiple strategies have emerged for lignin depolymerization and upgrading, including thermochemical treatments and homogeneous and heterogeneous catalysis. The multifunctional nature of lignin has historically yielded multiple product streams, which require extensive separation and purification procedures, but engineering plant feedstocks for greater structural homogeneity and tailored functionality reduces this challenge.

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Topics: Biorefinery (54%), Lignin (52%), Commodity chemicals (51%) ... show more

2,324 Citations


Journal ArticleDOI: 10.1016/J.COPBIO.2005.08.009
Abstract: Biologically mediated processes seem promising for energy conversion, in particular for the conversion of lignocellulosic biomass into fuels. Although processes featuring a step dedicated to the production of cellulase enzymes have been the focus of most research efforts to date, consolidated bioprocessing (CBP)--featuring cellulase production, cellulose hydrolysis and fermentation in one step--is an alternative approach with outstanding potential. Progress in developing CBP-enabling microorganisms is being made through two strategies: engineering naturally occurring cellulolytic microorganisms to improve product-related properties, such as yield and titer, and engineering non-cellulolytic organisms that exhibit high product yields and titers to express a heterologous cellulase system enabling cellulose utilization. Recent studies of the fundamental principles of microbial cellulose utilization support the feasibility of CBP.

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Topics: Cellulase (61%), Lignocellulosic biomass (54%), Cellulosic ethanol (53%) ... show more

1,334 Citations


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