Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78

By Diego Martínez, L. Larrondo, N. Putnam, M. Gelpke, Katherine H. Huang, Jarrod Chapman, Kevin G. Helfenbein, Preethi Ramaiya, J. Detter, F. Larimer and 5 more. Nature Biotechnology, 2004

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White rot fungi efficiently degrade lignin, a complex aromatic polymer in wood that is among the most abundant natural materials on earth. These fungi use extracellular oxidative enzymes that are also able to transform related aromatic compounds found in explosive contaminants, pesticides and toxic waste. We have sequenced the 30-million base-pair genome of Phanerochaete chrysosporium strain RP78 using a whole genome shotgun approach. The P. chrysosporium genome reveals an impressive array of genes encoding secreted oxidases, peroxidases and hydrolytic enzymes that cooperate in wood decay. Analysis of the genome data will enhance our understanding of lignocellulose degradation, a pivotal process in the global carbon cycle, and provide a framework for further development of bioprocesses for biomass utilization, organopollutant degradation and fiber bleaching. This genome provides a high quality draft sequence of a basidiomycete, a major fungal phylum that includes important plant and animal pathogens.

Subfields: Biotechnology, Cell Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/14057d36553b4f3a0a17d382b8a0d33a64381335

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Citations in the corpus

Process Design and Economics for the Conversion of Lignocellulosic Biomass to Hydrocarbons: Dilute-Acid and Enzymatic Deconstruction of Biomass to Sugars and Biological Conversion of Sugars to Hydrocarbons (2013, background): “Regarding lignin removal or fractionation before or concomitantly with carbohydrate deconstruction, there are many processing options available for this type of work, including biological pretreatment [119-125], alkaline or acid-based pulping-like processes [120, 126], numerous Organosolv processes ”
Fueling the future with fungal genomics (2011, methodology): “As of this writing, complete genome sequences have been published for three wood-decaying Agaricomycotina, Phanerochaete chrysosporium, Postia placenta, and Schizophyllum commune (Martinez et al. 2004, 2009; Ohm et al. 2010).”
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005, background): “The reports on the genomes for Phanerochaete chrysosporium (Martinez et al. 2004) and M.”
Trichoderma: A significant fungus for agriculture and environment (2016, background): “T. reesei contains the smallest number of genes encoding enzymes responsible for plant cell wall degradation within Sordariomycetes (Martinez et al., 2008).”
Improved enzyme production by co-cultivation of Aspergillus niger and Aspergillus oryzae and with other fungi (2011, positive): “chrysosporium itself does not produce laccase (Martinez et al., 2004) and therefore the increase in laccase activity must be caused by stimulation of laccase production in A.”
MycoCosm portal: gearing up for 1000 fungal genomes (2013, background): “The first JGI fungal portal was created for the white rot fungus Phanerochaete chrysosporium in 2004 (2).”
Fungal enzyme sets for plant polysaccharide degradation (2011, background): “Annotation of carbohydrate-active enzymes has been done for many fungal genomes (Pel et al. 2007; Espagne et al. 2008; Battaglia et al. 2011; Ohm et al. 2010; Martinez et al. 2004; Martinez et al. 2008).”
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, background): “The first genomes of the white-rot fungus Phanerochaete chrysosporium and brown-rot fungus Postia placenta revealed a gene complement consistent with their respective modes of wood decay (22, 23).”
Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion (2009, background): “Appl Environ Microbiol 73(19):6241–6253.”
Lignin utilization: A review of lignin depolymerization from various aspects (2019, positive): “Previous studies indicated that even though with the limited amount or without the presence of laccase, the microbes are still able to degrade lignin [207,208].”