Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus
Abstract
Identification of proteins from proteolytic peptides or intact proteins plays an essential
role in proteomics. Researchers use search engines to match the acquired peptide sequences
to the target proteins. However, search engines depend on protein databases to provide
candidates for consideration. Alternative splicing (AS), the mechanism where the exon
of pre-mRNAs can be spliced and rearranged to generate distinct mRNA and therefore
protein variants, enable higher eukaryotic organisms, with only a limited number of
genes, to have the requisite complexity and diversity at the proteome level. Multiple
alternative isoforms from one gene often share common segments of sequences. However,
many protein databases only include a limited number of isoforms to keep minimal redundancy.
As a result, the database search might not identify a target protein even with high
quality tandem MS data and accurate intact precursor ion mass. We computationally
predicted an exhaustive list of putative isoforms of Aspergillus flavus proteins from
20 371 expressed sequence tags to investigate whether an alternative splicing protein
database can assign a greater proportion of mass spectrometry data. The newly constructed
AS database provided 9807 new alternatively spliced variants in addition to 12 832
previously annotated proteins. The searches of the existing tandem MS spectra data
set using the AS database identified 29 new proteins encoded by 26 genes. Nine fungal
genes appeared to have multiple protein isoforms. In addition to the discovery of
splice variants, AS database also showed potential to improve genome annotation. In
summary, the introduction of an alternative splicing database helps identify more
proteins and unveils more information about a proteome.
Type
Other articleSubject
mass spectrometryproteomics
alternative splicing
database
aspergillus flavus
cystathionine beta-synthase
tandem mass-spectrometry
identification
gene
sequence
genome
proteins
peptides
polymorphisms
biochemical research methods
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https://hdl.handle.net/10161/4113Published Version (Please cite this version)
10.1021/pr900602dCitation
Chang,Kung-Yen;Georgianna,D. Ryan;Heber,Steffen;Payne,Gary A.;Muddiman,David C.. 2010.
Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus.
Journal of Proteome Research 9(3): 1209-1217.
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