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Forest Products Laboratory
One Gifford Pinchot Drive
Madison, WI 53726-2398
Phone: (608) 231-9200
Fax: (608) 231-9592


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Institute for Microbial and Biochemical Techology

Project Title :  Optimizing lignocellulose-degrading fungi for bioprocessing and bioconversion of wood requires understanding the functional genomics of fung
Project Number : FPL-4712-4B
Status : NEW
Start Date : 10-01-2012
End Date : 09-30-2019

View the 23 publications associated with this project.

Daniel CullenPrincipal Investigator:
Daniel Cullen

Non Technical Summary
Wood (lignocellulose) is one of the most abundant carbon pools in terrestrial ecosystems. Decomposition of wood is a critical component of the carbon cycle, impacts soil productivity, and has the potential to be exploited in the production of biofuels and other green technologies. Two broad functional classes of wood decay chemistries are known, termed white rot and brown rot. White rot fungi are capable of degrading all components of plant cell walls, including the highly recalcitrant lignin fraction, which other microorganisms cannot attack. Brown rot fungi modify but do not appreciably remove lignin, which remains as a polymeric residue following removal of cellulose and hemicellulose. Brown rot residues are highly resistant to further decay and contribute to the carbon pool in humic soils, particularly in cool-temperate and boreal, conifer-dominated ecosystems. The factors controlling establishment of fungal communities in fire-disturbed forest ecosystems are poorly understood, and these investigations address this uncertainty.Most species of wood-decaying fungi have characteristic substrate ranges, generally exhibiting a preference for either conifers or hardwoods. Brown rot species have been shown to preferentially decay conifer wood, although some attack hardwoods. Some wood-decaying fungi are able to attack living trees or colonize freshly-cut sapwood, while others decay only dead trees. Colonization of freshly cut pine is key to bioprocess development and exemplified by Phlebiopsis gigantea.There have been multiple studies of gene expression in the model species Phanerochaete chrysosporium (white rot) and Postia placenta (brown rot) on media containing glucose, cellulose or single wood species, but there have been few side-by-side comparisons of gene expression on different wood species and on transgenic feedstocks. In short, the mechanisms of substrate specificity are obscure. Addressing this uncertainty is a major thrust of research within this problem area. Ultimately, understanding the mechanisms that enable wood decay fungi to colonize particular woody feedstocks will provide insight into the functioning of forest ecosystems, and guide selection of taxa for emerging bioprocesses such as energy-related bioconversions and organopollutant degradation.

Objectives Summary
The central objective of this research is to elucidate the processes and enzymes involved in the deconstruction of woody plant cell wall polymers including cellulose, hemicellulose and the more recalcitrant lignin. Complex interactions between wood inhabiting fungi, rapidly growing litter decomposers, and those forming mycorrhizal and pathogenic associations undoubtedly play a pivotal role in nutrient cycling, carbon sequestration and forest health. The nonspecific nature and extraordinary oxidation potential of fungal enzymes has long attracted interest for potential industrial applications such as biological pulping of paper, fiber bleaching, and remediation of organopollutants including pesticides, polyaromatic hydrocarbons, PCBs and other halogenated aromatics (including dioxins), certain textile dyes, and an array of hydrocarbons associated with the wood preservation industry. The underlying genetics and physiology of these important microbes have been poorly understood, but intensive worldwide research has recently begun to focus on sequencing the genomes of wood decay fungi. In large part, these efforts have sought to identify new enzymes and biochemical processes suitable for the efficient conversion of lignocellulose to small molecular weight, high value products. Analyses of several genomes have now been published, and dozens more are in progress. These efforts have revealed impressive genetic diversity and provided important clues about mechanisms of lignocellulose conversion. To date, however, relatively few studies have unambiguously identified key genes, and the absence of systematic functional analyses has become a critical barrier to the development of efficient bioprocesses. Addressing these issues, detailed investigations of gene function are underway. Results will benefit emerging biotechnologies and will advance understanding of carbon cycling in forest ecosystems.

Approach Summary
Using state-of-the-art experimental tools, this research will identify and characterize key genetic systems controlling the degradation of lignin and related aromatic hydrocarbons, cellulose, and hemicellulose. Emphasis is on extracellular oxidative systems. High throughput structural and functional genomic investigations are employed and, because of the scale and cost of such investigations, national and international collaborative efforts are expected to continue. Successful completion of research will require the combined resources of FPL, industrial and university collaborators.General methods and expected outcomes include: 1. Through functional genomics investigations, elucidate the major metabolic pathways controlling extracellular oxidative enzyme systems. Heterologously express proteins to assist functional characterizations. Emphasis is on model systems such as Phanerochaete chrysosporium, Ceriporiopsis subvermispora and Postia placenta.2. Through collaborative efforts, facilitate the completion and public release of fungal genomes directly related to lignocellulose deconstruction. These include a wide range of wood decaying and litter decomposing fungi.3. Toward the goal of expanding biomass feedstocks, identify the key enzyme systems needed for ‘deconstructing’ multiple forestry species including various conifers, hardwoods, and transgenic material. Much effort will focus on logdgepole pine from overstocked Western forests.4. Using Southern Yellow Pine as a model system, elucidate the mechanisms of extractive metabolism during colonization by the lignin-degrading fungus, Phlebiopisis gigantea.5. Under field conditions, determine the physiological interactions between wood decay, litter decomposition and mycorrhizal fungi. These environmental ‘metagenomic’ studies focus on logdgepole pine in Western stands following catastrophic fires.6. Communicate research through high impact, peer-reviewed publications, through presentation at scientific conferences, and through consultations with industrial, academic, government partners.

Publications associated with this Project

Publication YearTitleDate Posted
2013A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus09/05/13
2014Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood12/22/14
2014Chapter 3: Wood Decay09/16/14
2013Chapter 5: Organopollutant Degradation by Wood Decay Basidiomycetes11/18/14
2020Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus09/04/20
2017Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB1209/06/17
2016Draft genome sequence of the white-rot fungus Obba rivulosa 3A-209/29/16
2019Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi10/01/19
2014Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi09/17/14
2016Gene expression patterns of wood decay fungi Postia placenta and Phanerochaete chrysosporium are influenced by wood substrate composition during degradation09/22/16
2016Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution10/06/17
2012Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche11/06/12
2013Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay09/09/14
2016Heterologous production and characterization of two glyoxal oxidases from Pycnoporus cinnabarinus09/22/16
2014Influence of Populus Genotype on Gene Expression by the Wood Decay Fungus Phanerochaete chrysosporium09/17/14
2020Mechanism of extractive degradation by Phlebiopsis gigantea09/30/20
2018Multi-omic analyses of extensively decayed Pinus contorta reveal expression of a diverse array of lignocellulose-degrading enzymes10/02/18
2015Prospects and challenges for fungal metatranscriptomics of complex communities02/11/15
2016Prospects for bioprocess development based on recent genome advances in lignocellulose degrading basidiomycetes09/29/16
2018Substrate-specific differential gene expression and RNA editing in the brown rot fungus Fomitopsis pinicola09/28/18
2014Temporal Alterations in the Secretome of the Selective Ligninolytic Fungus Ceriporipsis subvermispora during growth on Aspen Wood Reveal this Organism's Strategy for Degrading Lighnocellulose09/17/14
2019The foliar endophyte Phialocephala scopiformis DAOMC 229536 proteome when grown on wood used as the sole carbon source10/01/19
2016Transcriptome and secretome analyses of the wood decay fungus Wolfiporia cocos support alternative mechanisms of lignocellulose conversion09/22/16

Project Summaries last modified: 08-22-2018