Analysis of New Functional Profiles of Protein Isoforms Yielded by Ds Exonization in Rice

Abstract

Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Exonization can enrich the complexity of transcriptomes and proteomes. Previously, we performed a genome-wide computational analysis of Ds exonization events in the monocot Oryza sativa (rice). The insertion patterns of Ds increased the number of transcripts and subsequent protein isoforms, which were determined as interior and C-terminal variants. In this study, these variants were scanned with the PROSITE database in order to identify new functional profiles (domains) that were referred to their reference proteins. The new profiles of the variants were expected to be beneficial for a selective advantage and more than 70% variants achieved this. The new functional profiles could be contributed by an exon–intron junction, an intron alone, an intron–TE junction, or a TE alone. A Ds-inserted intron may yield 167 new profiles on average, while some cases can yield thousands of new profiles, of which C-terminal variants were in major. Additionally, more than 90% of the TE-inserted genes were found to gain novel functional profiles in each intron via exonization. Therefore, new functional profiles yielded by the exonization may occur in many local regions of the reference protein.

A Deluge of Complex Repeats: The Solanum Genome

“…Exonization occurs due to the presence of splice-sites within the repetitive elements which are found overlapping with genes. There are many possible outcomes of exonization, most of which lead towards beneficial inclusion and fixation [ 96 , 97 ]. Exonization of repetitive elements and their impact on shaping the transcriptome of various species has been studied widely [ 48 , 55 , 98 – 100 ].…”

The Ds1 Transposon Provides Messages That Yield Unique Profiles of Protein Isoforms and Acts Synergistically With Ds to Enrich Proteome Complexity via Exonization

“…We have previously reported that Ds passively enriches proteome complexity in exonization by mainly adopting the messages of the flanking introns after Ds insertion sites. 13 However, by offering acceptors that create new A-variants and DA-variants, Ds1 is more actively involved in exonization, either through its message alone or together with its flanking intron/exon, allowing the building of various new functional protein variants. We also demonstrated that, although a few of the 11 possible exonizing patterns from that Ds1 inserting into a single site are very similar to each other, even differences of only a few amino acids are enough to result in a wide spectrum of new profiles among these isoforms.…”

“…We also performed a functional profile analysis based on the PROSITE database 12 and revealed the possibility of proteome enrichment by Ds exonization. 13 …”

“…We also performed a functional profile analysis based on the PROSITE database 12 and revealed the possibility of proteome enrichment by Ds exonization. 13 In this study, we investigated the behavior of Ds1 in exonization and compared it with that of Ds. A protocol similar to that used by Chien et al, 13 with some modifications (see "Materials and Methods" section), was applied to the Ds1exonized protein variants.…”

“…13 In this study, we investigated the behavior of Ds1 in exonization and compared it with that of Ds. A protocol similar to that used by Chien et al, 13 with some modifications (see "Materials and Methods" section), was applied to the Ds1exonized protein variants. We found that the Ds1-exonized messages with no more than 59 nucleotides were actively involved in creating diverse functional profiles.…”