Increasing Coverage of Proteome Identification of the Fruiting Body of Agaricus bisporus by Shotgun Proteomics

To increase coverage of protein identification of an fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged...

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Bibliographic Details
Published in:Foods 2020-05, Vol.9 (5), p.632
Main Authors: Ham, Tae-Ho, Lee, Yoonjung, Kwon, Soon-Wook, Jang, Myoung-Jun, Park, Youn-Jin, Lee, Joohyun
Format: Article
Language:English
Subjects:
Agaricus bisporus
Antioxidants
Biological activity
Biosynthesis
Chromatography
Coils
Encyclopedias
Food science
Fruit bodies
Gene expression
gene ontology
Genes
Genomes
Humidity
Identification
Mass spectrometry
Metabolites
Methods
Molecular weight
Mushrooms
Nucleotides
Peptides
Physicochemical properties
Proteins
Proteomes
Proteomics
Scientific imaging
Secondary metabolites
shotgun proteomics
Tyrosine
Ubiquitin
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Summary:To increase coverage of protein identification of an fruiting body, we analyzed the crude protein fraction of the fruiting body by using a shotgun proteomics approach where 7 MudPIT (Multi-Protein identification Technology) runs were conducted and the MS/MS spectra from the 7 MudPIT runs were merged. Overall, 3093 non-redundant proteins were identified to support the expression of those genes annotated in the genome database of . The physicochemical properties of the identified proteins, i.e., wide pI value range and molecular mass range, were indicative of unbiased protein identification. The relative quantification of the identified proteins revealed that K5XI50 (Aldedh domain-containing protein) and K5XEW1 (Ubiquitin-like domain-containing protein) were highly abundant in the fruiting body. Based on the information in the Uniprot (Universal Protein Resource) database for , only approximately 53% of the 3093 identified proteins have been functionally described and approximately 47% of the proteins remain uncharacterized. Gene Ontology analysis revealed that the majority of proteins were annotated with a biological process, and proteins associated with coiled-coil (12.8%) and nucleotide binding (8.21%) categories were dominant. The Kyoto Encyclopedia of Genes and Genome analysis revealed that proteins involved in biosynthesis of secondary metabolites and tyrosine metabolism were enriched in a fruiting body of , suggesting that the proteins are associated with antioxidant metabolites.
ISSN:2304-8158
2304-8158
DOI:10.3390/foods9050632