Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci USA

Los Alamos National Laboratory/Joint Genome Institute, P.O. Box 1663, Los Alamos, NM 87545, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 02/2009; 106(6):1954-1959. DOI: 10.1073/pnas.0809575106

ABSTRACT Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures.
Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying
genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular
glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes,
are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a
single putative β-1–4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles
were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated
during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially
involved in extracellular generation of Fe(II) and H2O2. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H2O2 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More
broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with
the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin
was lost.

Download full-text


Available from: Ursula Kües, Aug 16, 2015
  • Source
    • "As reviewed by Sun et al. [5] several strains of Aspergillus sp. has potential to produce RSDE. To explore the cellulose and lignocellulosic biomass hydrolysis potential and to investigate the abundance of lignocellulolytic enzymes, the proteomic analysis of secretome by biomass degrading microbes such as Thermobifida fusca [8], Trichoderma reesei [9] [10] [11], Phanerochaete chrysosporium [12] [13], Botrytis cinerea [14] [15], Postia placenta [16], Aspergillus niger [17] Fusarium graminearum [18] and many more have been documented . However, the post translational modifications (PTMs) of these proteins that could result in a huge impact on their functions have not been studied so far. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Aspergillus sp. plays an essential role in lignocellulosic biomass recycling and is also exploited as cell factories for the production of industrial enzymes. This study profiled the secretome of Aspergillus fumigatus when grown with cellulose, xylan and starch by high throughput quantitative proteomics using isobaric tags for relative and absolute quantification (iTRAQ). Post translational modifications (PTMs) of proteins play a critical role in protein functions. However, our understanding of the PTMs in secretory proteins is limited. Here, we present the identification of PTMs such as deamidation of secreted proteins of A. fumigatus. This study quantified diverse groups of extracellular secreted enzymes and their functional classification revealed cellulases and glycoside hydrolases (32.9%), amylases (0.9%), hemicellulases (16.2%), lignin degrading enzymes (8.1%), peptidases and proteases (11.7%), chitinases, lipases and phosphatases (7.6%), and proteins with unknown function (22.5%). The comparison of quantitative iTRAQ results revealed that cellulose and xylan stimulates expression of specific cellulases and hemicellulases, and their abundance level as a function of substrate. In-depth data analysis revealed deamidation as a major PTM of key cellulose hydrolyzing enzymes like endoglucanases, cellobiohydrolases and glucosidases. Hemicellulose degrading endo-1,4-beta-xylanase, monosidases, xylosidases, lignin degrading laccase, isoamyl alcohol oxidase and oxidoreductases were also found to be deamidated.
    Journal of Proteomics 02/2015; 119. DOI:10.1016/j.jprot.2015.02.007 · 3.93 Impact Factor
  • Source
    • "Particularly notable were the multiple genes encoding high-oxidation potential class-II peroxidases (PODs), which are in some cases known to help depolymerize lignin by generating reactive free radicals (Kirk and Farrell, 1987). The second wood-decaying fungus to be sequenced was the brown rot fungus Postia placenta (Martinez et al., 2009). This study made possible the comparison of the respective lignocellulosedegrading abilities of white and brown rot fungi by comparison to P. chrysosporium. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Woody plants convert the energy of the sun into lignocellulosic biomass, which is an abundant substrate for bioenergy production. Fungi, especially wood decayers from the class Agaricomycetes, have evolved ways to degrade lignocellulose into its monomeric constituents, and understanding this process may facilitate the development of biofuels. Over the past decade genomics has become a powerful tool to study the Agaricomycetes. In 2004 the first sequenced genome of the white rot fungus Phanerochaete chrysosporium revealed a rich catalog of lignocellulolytic enzymes. In the decade that followed the number of genomes of Agaricomycetes grew to more than 75 and revealed a diversity of wood-decaying strategies. New technologies for high-throughput functional genomics are now needed to further study these organisms.
    Fungal Genetics and Biology 11/2014; 72. DOI:10.1016/j.fgb.2014.05.001 · 3.26 Impact Factor
  • Source
    • "Important advances in the research on microbial decomposition obtained using (meta)genomics, (meta) transcriptomics and (meta)proteomics Decomposition by individual microorganisms Knowledge obtained using traditional methods Good knowledge of the gene content in model species and enzymes in focus, fragmentary knowledge for non-model species and proteins with putatively lower importance; limited studies on the transcriptomics and protein production by a few key model taxa; decomposition abilities of microbes not exhibiting saprotrophic lifestyle largely absent Advances made using modern molecular and analytical methods Complete knowledge of gene complement in the first genomes of model saprotrophic and symbiotic fungi Martin et al. (2008); Martinez et al. (2004) (2009) "
    [Show abstract] [Hide abstract]
    ABSTRACT: Molecular methods for the analysis of biomolecules have undergone rapid technological development in the last decade. The advent of next-generation sequencing methods and improvements in instrumental resolution enabled the analysis of complex transcriptome, proteome and metabolome data, as well as a detailed annotation of microbial genomes. The mechanisms of decomposition by model fungi have been described in unprecedented detail by the combination of genome sequencing, transcriptomics and proteomics. The increasing number of available genomes for fungi and bacteria shows that the genetic potential for decomposition of organic matter is widespread among taxonomically diverse microbial taxa, while expression studies document the importance of the regulation of expression in decomposition efficiency. Importantly, high-throughput methods of nucleic acid analysis used for the analysis of metagenomes and metatranscriptomes indicate the high diversity of decomposer communities in natural habitats and their taxonomic composition. Today, the metaproteomics of natural habitats is of interest. In combination with advanced analytical techniques to explore the products of decomposition and the accumulation of information on the genomes of environmentally relevant microorganisms, advanced methods in microbial ecophysiology should increase our understanding of the complex processes of organic matter transformation.
    Applied Microbiology and Biotechnology 01/2014; 98(4). DOI:10.1007/s00253-013-5457-x · 3.81 Impact Factor
Show more