Important message offered by Ds1 transposon for yielding unique profiles of protein isoforms to enrich proteome complexity via exonization
Date Issued
2015
Date
2015
Author(s)
Hsu, Lung-Hsin
Abstract
An intronic transposable elements (TE) which provides splice site may lead to alternative splicing or exonization. For a sigle insertion event, Ds1 transposon could offer 3 splice donors and 2 splice acceptors (yield 11 transcripts and protein isoforms) while Ds element could offer the maximum of 4 splice donors (yield 4 transcripts and protein isoforms). Previous studies show that both of Ds and Ds1 exonization could increase transcripts’ and proteins’ sequence diversity by incorporating the intron sequences with different reading frame. This study aims to analyze how the exonized sequence diversity contributes to protein functional complexity. First, the functional profiles of all simulated exonized isoforms and the references were scanned according to PROSITE database. Compared with the reference proteins, a Ds1-inserted intron may yield 228 new profiles on average, while a Ds-inserted intron may yield only 152 new profiles on average. To prevent overestimating the diversity of added profiles, we analyzed the new functional profiles among the orthologous exonized protein isoforms which spliced using the third donor site (D3) versus the first one (D1) with the same reading frame. The analysis of protein orthologs yielded by using donor/acceptor sites of D1A2, D2A1 and D3A2 is conducted likewise. Though differ in the presence or absence merely 2 to 7 additional amino aciDs, the new profiles of protein orthologs remain diversified. In brief, the simulation results imply that Ds1 transposon offers message important for yielding unique profiles of protein isoforms in rice genome. To access the simulated results, 49 maize genes which contain Ds-like sequence are investigated to test previous result in rice. The annotation and transcripts of these genes indicate that 44 Ds-like element insert to intron and most of them make a part of intron. Besides, 3 Ds-like elements insert to exon regions and 2 Ds-like elements insert to untranslated regions. One Ds-like elements which insert to the 5th intron of GRMZM2G085600 resulted in exonized transcripts and yielding 2 new functional profiles. We analyze the exonized messages offered from Ds1 for yielding unique profiles according the simulation in rice, compare with the results of Ds and find an actual example in maize. Based on our research, exonization could be considered one of the reasons in the evolution of plant proteome complexity.
Subjects
Ds1 transposon
alternative splicing
exonization
nonsense-mediated decay pathway
protein function profile
Type
thesis
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