Biology subjects

Anbo, H.

Publications and source records attributed to Anbo, H..

2 recordsLinked to original sources

bioRxiv2024

Longer Internal Exons Tend to Have More Tandem Repeats and Experience Insertions and Deletions More Frequently

Insertions and deletions (indels) in eukaryotic proteins are known to preferentially encode intrinsically disordered regions (IDRs), protein regions that by themselves do not form unique three-dimensional structures. As a previous investigation showed that long internal exons tend to encode IDRs in eukaryotes in general, we thought it worthwhile to analyze how indels alter internal exons and affect IDRs of the encoded proteins. For consideration of evolutionary roles indels play, we decided to select indels commonly observed in all variants ("fixed" indels) since indels in minor variants may represent transient aberrations in splicing. Here, by comparison of orthologous variants of closely related species together with those of outgroups, we identified fixed indels in the internal exons in four mammals and two flies. The fixed indels are nearly always nonframeshifting, short, and mostly encode IDRs. On average 51% of inserted and 40% of deleted residues are attributable to alterations in tandem repeats. Deletion tends to occur more frequently than insertion does and indels are generally more prevalent in long internal exons. Tandem repeats occur preferentially in long internal exons, indicating that their alterations account for the high frequency of indels in long internal exons. Also, since tandem repeats mostly encode IDRs, this finding at least partially explains the high incidence of IDRs in long internal exons. We propose that long internal exons had been produced in early eukaryotes mainly by repeat expansion that added IDRs to the encoded proteins but are experiencing frequent indels by alterations in tandem repeats.

bioinformatics↗

bioRxiv2022

Elongated exons encoding disordered regions expedited eukaryotic evolution

Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, while the typical eukaryotic protein is comprised of multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the "small bang" model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat-mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analysed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.

bioinformatics↗