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Title: Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins

Abstract

Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteasesmore » and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. As a result, ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.« less

Authors:
 [1];  [2];  [2];  [1]
  1. Univ. de Lorraine, Vandoeuvre-les-Nancy (France); Institut National de la Recherche Agronomique, Champenoux (France)
  2. Institut National de la Recherche Agronomique, Champenoux (France)
Publication Date:
Research Org.:
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1241128
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ectomycorrhizal; saprotrophs; secretomics; small-secreted proteins; symbiosis; secretomes

Citation Formats

Pellegrin, Clement, Morin, Emmanuelle, Martin, Francis M., and Veneault-Fourrey, Claire. Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins. United States: N. p., 2015. Web. doi:10.3389/fmicb.2015.01278.
Pellegrin, Clement, Morin, Emmanuelle, Martin, Francis M., & Veneault-Fourrey, Claire. Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins. United States. doi:https://doi.org/10.3389/fmicb.2015.01278
Pellegrin, Clement, Morin, Emmanuelle, Martin, Francis M., and Veneault-Fourrey, Claire. Wed . "Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins". United States. doi:https://doi.org/10.3389/fmicb.2015.01278. https://www.osti.gov/servlets/purl/1241128.
@article{osti_1241128,
title = {Comparative analysis of secretomes from Ectomycorrhizal fungi with an emphasis on small-secreted proteins},
author = {Pellegrin, Clement and Morin, Emmanuelle and Martin, Francis M. and Veneault-Fourrey, Claire},
abstractNote = {Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. As a result, ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.},
doi = {10.3389/fmicb.2015.01278},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {11}
}

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