Limits...
Proteome exploration to provide a resource for the investigation of Ganoderma lucidum.

Yu GJ, Yin YL, Yu WH, Liu W, Jin YX, Shrestha A, Yang Q, Ye XD, Sun H - PLoS ONE (2015)

Bottom Line: Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies.Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity.In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.

ABSTRACT
Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with "binding", "catalytic activity", and "hydrolase activity" having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

Show MeSH
GO annotation of the G. lucidum proteome.(A) GO annotation of the total identified 803 proteins. GO annotations for 470 proteins were classified into 36 GO sub-categories. The results were summarized in three main GO categories: cellular component, molecular function and biological process. The left y-axis indicates the number of proteins in a sub-category. The right y-axis indicates the percentage of a specific sub-category of proteins in that main category. (B) GO annotation of the 61 wood-degrading proteins. GO annotations for 43 out of the 61 proteins were classified into 12 GO sub-categories. One protein could be annotated into more than one GO term.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4355618&req=5

pone.0119439.g004: GO annotation of the G. lucidum proteome.(A) GO annotation of the total identified 803 proteins. GO annotations for 470 proteins were classified into 36 GO sub-categories. The results were summarized in three main GO categories: cellular component, molecular function and biological process. The left y-axis indicates the number of proteins in a sub-category. The right y-axis indicates the percentage of a specific sub-category of proteins in that main category. (B) GO annotation of the 61 wood-degrading proteins. GO annotations for 43 out of the 61 proteins were classified into 12 GO sub-categories. One protein could be annotated into more than one GO term.

Mentions: A total of 470 proteins were annotated across the GO sub-categories (S2 Table) and classified into 36 functional groups with 6 involved in cellular component, 16 in molecular function and 14 in biological processe (Fig. 4A). Among these GO classifications, ‘binding’ (275 proteins, 58.5%), ‘catalytic activity’ (337, 71.7%), ‘hydrolase activity’ (170, 36.2%), ‘cellular process’ (169, 36%), ‘metabolic process’ (324, 68.9%), and ‘primary metabolic process’ (242, 51.5) were dominant. In contrast, a small number of proteins were assigned to ‘membrane-enclosed lumen’ (2 proteins, 0.4%), ‘molecular transducer activity’ (1, 0.2%), and ‘multicellular organismal process’ (1, 0.2%).


Proteome exploration to provide a resource for the investigation of Ganoderma lucidum.

Yu GJ, Yin YL, Yu WH, Liu W, Jin YX, Shrestha A, Yang Q, Ye XD, Sun H - PLoS ONE (2015)

GO annotation of the G. lucidum proteome.(A) GO annotation of the total identified 803 proteins. GO annotations for 470 proteins were classified into 36 GO sub-categories. The results were summarized in three main GO categories: cellular component, molecular function and biological process. The left y-axis indicates the number of proteins in a sub-category. The right y-axis indicates the percentage of a specific sub-category of proteins in that main category. (B) GO annotation of the 61 wood-degrading proteins. GO annotations for 43 out of the 61 proteins were classified into 12 GO sub-categories. One protein could be annotated into more than one GO term.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4355618&req=5

pone.0119439.g004: GO annotation of the G. lucidum proteome.(A) GO annotation of the total identified 803 proteins. GO annotations for 470 proteins were classified into 36 GO sub-categories. The results were summarized in three main GO categories: cellular component, molecular function and biological process. The left y-axis indicates the number of proteins in a sub-category. The right y-axis indicates the percentage of a specific sub-category of proteins in that main category. (B) GO annotation of the 61 wood-degrading proteins. GO annotations for 43 out of the 61 proteins were classified into 12 GO sub-categories. One protein could be annotated into more than one GO term.
Mentions: A total of 470 proteins were annotated across the GO sub-categories (S2 Table) and classified into 36 functional groups with 6 involved in cellular component, 16 in molecular function and 14 in biological processe (Fig. 4A). Among these GO classifications, ‘binding’ (275 proteins, 58.5%), ‘catalytic activity’ (337, 71.7%), ‘hydrolase activity’ (170, 36.2%), ‘cellular process’ (169, 36%), ‘metabolic process’ (324, 68.9%), and ‘primary metabolic process’ (242, 51.5) were dominant. In contrast, a small number of proteins were assigned to ‘membrane-enclosed lumen’ (2 proteins, 0.4%), ‘molecular transducer activity’ (1, 0.2%), and ‘multicellular organismal process’ (1, 0.2%).

Bottom Line: Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies.Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity.In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.

ABSTRACT
Ganoderma lucidum is a basidiomycete white rot fungus that has been used for medicinal purposes worldwide. Although information concerning its genome and transcriptome has recently been reported, relatively little information is available for G. lucidum at the proteomic level. In this study, protein fractions from G. lucidum at three developmental stages (16-day mycelia, and fruiting bodies at 60 and 90 days) were prepared and subjected to LC-MS/MS analysis. A search against the G. lucidum genome database identified 803 proteins. Among these proteins, 61 lignocellulose degrading proteins were detected, most of which (49 proteins) were found in the 90-day fruiting bodies. Fourteen TCA-cycle related proteins, 17 peptidases, two argonaute-like proteins, and two immunomodulatory proteins were also detected. A majority (470) of the 803 proteins had GO annotations and were classified into 36 GO terms, with "binding", "catalytic activity", and "hydrolase activity" having high percentages. Additionally, 357 out of the 803 proteins were assigned to at least one COG functional category and grouped into 22 COG classifications. Based on the results from the proteomic and sequence alignment analyses, a potentially new immunomodulatory protein (GL18769) was expressed and shown to have high immunomodulatory activity. In this study, proteomic and biochemical analyses of G. lucidum were performed for the first time, revealing that proteins from this fungus can play significant bioactive roles and providing a new foundation for the further functional investigations that this fungus merits.

Show MeSH