Comparative and transcriptional analysis of the predicted secretome in the lignocellulose-degrading basidiomycete fungus Pleurotus ostreatus.
Fungi interact with their environment by secreting proteins to obtain nutrients, elicit responses and modify their surroundings. Because the set of proteins secreted by a fungus is related to its lifestyle, it should be possible to use it as a tool to predict fungal lifestyle. To test this hypothesis, we bioinformatically identified 538 and 554 secretable proteins in the monokaryotic strains PC9 and PC15 of the white rot basidiomycete Pleurotus ostreatus. Functional annotation revealed unknown functions (37.2%), glycosyl hydrolases (26.5%) and redox enzymes (11.5%) as the main groups in the two strains. When these results were combined with RNA-seq analyses, we found that the relative importance of each group was different in different strains and culture conditions and the relevance of the unknown function proteins was enhanced. Only a few genes were actively expressed in a given culture condition in expanded multigene families, suggesting that family expansi on could increase adaptive opportunities rather than activity under a specific culture condition. Finally, we used the set of P. ostreatus secreted proteins as a query to search their counterparts in other fungal genomes and found that the secretome profiles cluster the tested basidiomycetes into lifestyle rather than phylogenetic groups.
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.
Manuel
M
Alfaro
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.
Raúl
R
Castanera
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.|Genome Analysis Platform, CIC bioGUNE & CIBERehd, Bizkaia Technology Park, Derio, 48160, Spain.
José L
JL
Lavín
US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
Igor V
IV
Grigoriev
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.
José A
JA
Oguiza
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.
Lucía
L
Ramírez
Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, Pamplona, 31006, Spain.
Antonio G
AG
Pisabarro
D005656:Fungal Proteins / Q000378:metabolism*; D016681:Genome, Fungal; D008031:Lignin / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D020076:Pleurotus / Q000201:enzymology / Q000378:metabolism*
D005656:Fungal Proteins; C036909:lignocellulose; D008031:Lignin