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Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose

Overview of attention for article published in Biotechnology for Biofuels, September 2016
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Title
Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose
Published in
Biotechnology for Biofuels, September 2016
DOI 10.1186/s13068-016-0608-9
Pubmed ID
Authors

Jaana Kuuskeri, Mari Häkkinen, Pia Laine, Olli-Pekka Smolander, Fitsum Tamene, Sini Miettinen, Paula Nousiainen, Marianna Kemell, Petri Auvinen, Taina Lundell

Abstract

The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC-MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus' natural growth substrate. According to proteomics analyses, several CAZy oxidoreductase class-II peroxidases with glyoxal and alcohol oxidases were the most abundant proteins produced on wood together with enzymes important for cellulose utilization, such as GH7 and GH6 cellobiohydrolases. Transcriptome additionally displayed expression of multiple AA9 lytic polysaccharide monooxygenases indicative of oxidative cleavage of wood carbohydrate polymers. Large differences were observed for individual protein quantities at specific time points, with a tendency of enhanced production of specific peroxidases on the first 2 weeks of growth on wood. Among the 10 class-II peroxidases, new MnP1-long, characterized MnP2-long and LiP3 were produced in high protein abundances, while LiP2 and LiP1 were upregulated at highest level as transcripts on wood together with the oxidases and one acetyl xylan esterase, implying their necessity as primary enzymes to function against coniferous wood lignin to gain carbohydrate accessibility and fungal growth. Majority of the CAZy encoding transcripts upregulated on spruce wood represented activities against plant cell wall and were identified in the proteome, comprising main activities of white-rot decay. Our data indicate significant changes in carbohydrate-active enzyme expression during the six-week surveillance of P. radiata growing on wood. Response to wood substrate is seen already during the first weeks. The immediate oxidative enzyme action on lignin and wood cell walls is supported by detected lignin substructure sidechain cleavages, release of phenolic units, and visual changes in xylem cell wall ultrastructure. This study contributes to increasing knowledge on fungal genetics and lignocellulose bioconversion pathways, allowing us to head for systems biology, development of biofuel production, and industrial applications on plant biomass utilizing wood-decay fungi.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 110 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Iceland 1 <1%
France 1 <1%
Unknown 108 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 29 26%
Student > Master 15 14%
Researcher 12 11%
Student > Bachelor 10 9%
Student > Doctoral Student 9 8%
Other 19 17%
Unknown 16 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 41 37%
Biochemistry, Genetics and Molecular Biology 26 24%
Engineering 4 4%
Environmental Science 4 4%
Chemical Engineering 3 3%
Other 10 9%
Unknown 22 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 08 September 2016.
All research outputs
#7,217,921
of 8,348,788 outputs
Outputs from Biotechnology for Biofuels
#574
of 680 outputs
Outputs of similar age
#210,748
of 252,660 outputs
Outputs of similar age from Biotechnology for Biofuels
#15
of 17 outputs
Altmetric has tracked 8,348,788 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 680 research outputs from this source. They receive a mean Attention Score of 4.0. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 17 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.