Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms

Abstract

Alternative splicing of pre-mRNA generates two or more protein isoforms from a single gene, thereby contributing to protein diversity. Despite intensive efforts, an understanding of the protein structure-function implications of alternative splicing is still lacking. Intrinsic disorder, which is a lack of equilibrium 3D structure under physiological conditions, may provide this understanding. Intrinsic disorder is a common phenomenon, particularly in multicellular eukaryotes, and is responsible for important protein functions including regulation and signaling. We hypothesize that polypeptide segments affected by alternative splicing are most often intrinsically disordered such that alternative splicing enables functional and regulatory diversity while avoiding structural complications. We analyzed a set of 46 differentially spliced genes encoding experimentally characterized human proteins containing both structured and intrinsically disordered amino acid segments. We show that 81% of 75 alternatively spliced fragments in these proteins were associated with fully (57%) or partially (24%) disordered protein regions. Regions affected by alternative splicing were significantly biased toward encoding disordered residues, with a vanishingly small P value. A larger data set composed of 558 SwissProt proteins with known isoforms produced by 1,266 alternatively spliced fragments was characterized by applying the PONDR VSL1 disorder predictor. Results from prediction data are consistent with those obtained from experimental data, further supporting the proposed hypothesis. Associating alternative splicing with protein disorder enables the time-and tissue-specific modulation of protein function needed for cell differentiation and the evolution of multicellular organisms.evolution ͉ natively unfolded ͉ intrinsically unstructured ͉ protein structure T he splicing of pre-mRNA (1) was first described in 1977. Soon thereafter, Gilbert (2) coined the terms ''intron'' (intragenic region) and ''exon'' (expressed region) for the noncoding and coding regions, respectively. Alternative splicing occurs when different mRNAs are assembled from a single gene by joining exons in different ways. Alternative splicing is proposed to generate complexity in multicellular eukaryotes by increasing protein diversity, and thus proteome size, from a relatively small number of genes (3). Estimates indicate that between 35 and 60% of human genes yield protein isoforms by means of alternatively spliced (AS) mRNA (4). Furthermore, complexity in higher organisms is also brought about by signaling and regulatory networks that enable robustness (5). The importance of alternative splicing as a regulatory process (3, 6) has been highlighted by the high occurrence of such splicing in the pre-mRNAs of regulatory and signaling proteins (7).Alternative splicing can bolster organism complexity, not only by effectively increasing proteome size and regulatory and signaling network complexity, but also by doing so in a time-and tissue-specific manner, supporting ...

Resilience of death: intrinsic disorder in proteins involved in the programmed cell death

“…Both of these features are typical for IDPs/IDPRs. 24,27 These observations provide further support to the general conclusion of this study that intrinsic disorder is crucial for the regulation and control of all the PCD types. Here, proteins regulating necroptosis seem to be more disordered than protein involved in other types of the controlled cell death.…”

“…Functions of IDPs are further controlled by alternative splicing, which generates a set of protein isoforms with a highly diverse set of regulatory elements. 27 The complexity of the disorderbased interactomes is further increased due to the ability of a single IDPR to bind to multiple partners gaining potentially very different structures in the bound state. 28 Because of their critically important roles in regulation, signaling, and control pathways, misbehavior of IDPs is commonly associated with the pathogenesis of various diseases.…”

Exploring the binding diversity of intrinsically disordered proteins involved in one‐to‐many binding

“…83 Interestingly, of the human MoRFs studied here, 50% (4 of 8) are in exon regions that have been identified as included or excluded by alternative splicing. The discussion in the previous paragraph suggests that a concerted effort should be made to identify additional MoRFs that map to tissue-specific alternatively spliced regions and to identify their partners as well.…”

Alternative splicing and the evolution of phenotypic novelty

“…In addition, a gene's alternatively spliced regions are more likely to encode disordered regions of protein (i.e. which have multiple stable configurations) [73]. These regions may also experience stronger selection for functions related to binding-flexible sensors are more adaptable than rigid ones [74,75]-supporting an association of alternative splicing with the evolution of regulatory networks [76] (see [77] for a review of the regulatory circuits through which alternative splicing may act to regulate expression).…”