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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.

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COG annotation of the total identified 803 proteins.COG annotations for 357 proteins were grouped into 22 categories. The left y-axis indicates the number of proteins in a particular category. The right y-axis indicates the percentage of a specific category of proteins in that main category.
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pone.0119439.g005: COG annotation of the total identified 803 proteins.COG annotations for 357 proteins were grouped into 22 categories. The left y-axis indicates the number of proteins in a particular category. The right y-axis indicates the percentage of a specific category of proteins in that main category.

Mentions: To further evaluate the effectiveness of our annotation process and the accuracy of our proteome analysis, we searched the identified proteins against COG classifications. A total of 357 proteins were assigned to at least one COG functional category, grouped into 22 classifications (Fig. 5 and S3 Table). Of the 22 COG categories, ‘General function prediction only’ (14.52%) contained the most proteins, followed by ‘Carbohydrate transport and metabolism’ (13.58%), ‘Amino acid transport and metabolism’ (11.71%), and ‘Energy production and conversion’ (9.6%). These COG classifications are consistent with the results described above (Table 1) in which many wood-degrading proteins were detected in our proteome. A few proteins related to ‘Intracellular trafficking, secretion, and vesicular transport’ (0.47%), ‘Cytoskeleton’ (0.7%), ‘Nucleotide transport and metabolism’ (0.7%), and ‘RNA processing and modification’ (0.7%) were found. These annotations provide new resources for further exploring this macrofungus.


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)

COG annotation of the total identified 803 proteins.COG annotations for 357 proteins were grouped into 22 categories. The left y-axis indicates the number of proteins in a particular category. The right y-axis indicates the percentage of a specific category of proteins in that main category.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0119439.g005: COG annotation of the total identified 803 proteins.COG annotations for 357 proteins were grouped into 22 categories. The left y-axis indicates the number of proteins in a particular category. The right y-axis indicates the percentage of a specific category of proteins in that main category.
Mentions: To further evaluate the effectiveness of our annotation process and the accuracy of our proteome analysis, we searched the identified proteins against COG classifications. A total of 357 proteins were assigned to at least one COG functional category, grouped into 22 classifications (Fig. 5 and S3 Table). Of the 22 COG categories, ‘General function prediction only’ (14.52%) contained the most proteins, followed by ‘Carbohydrate transport and metabolism’ (13.58%), ‘Amino acid transport and metabolism’ (11.71%), and ‘Energy production and conversion’ (9.6%). These COG classifications are consistent with the results described above (Table 1) in which many wood-degrading proteins were detected in our proteome. A few proteins related to ‘Intracellular trafficking, secretion, and vesicular transport’ (0.47%), ‘Cytoskeleton’ (0.7%), ‘Nucleotide transport and metabolism’ (0.7%), and ‘RNA processing and modification’ (0.7%) were found. These annotations provide new resources for further exploring this macrofungus.

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