Intrinsically Disordered Proteins Link Alternative Splicing and Post-translational Modifications to Complex Cell Signaling and Regulation

Abstract

Intrinsically disordered proteins and regions (IDPs and IDRs) lack well-defined tertiary structures, yet carry out various important cellular functions, especially those associated with cell signaling and regulation. In eukaryotes, IDPs and IDRs contain the preferred loci for both alternative splicing (AS) and many post-translational modifications (PTMs). Furthermore, AS and/or PTMs at these loci generally alter the signaling outcomes associated with these IDPs or IDRs, where the functional cooperation of these three features is named the IDP-AS-PTM toolkit. However, the prevalence of such functional modulations remains unknown. Also, the signal-altering mechanisms by which AS, and PTMs modulate function and the extent to which AS and PTMs collaborate in their signaling modulations have not been well defined for particular protein examples. Here we focus on three important signaling and regulatory IDR-containing protein families in humans, namely, G protein-coupled receptors (GPCRs), which are transmembrane proteins; the nuclear factors of activated T cells (NFATs), which are transcription factors; and the Src family kinases (SFKs), which are signaling enzymes. The goals here are to determine how AS and PTMs individually alter the outcomes of the signaling carried out by the various IDRs and to determine whether AS and PTMs work together to bring about differential cellular responses. We also present data indicating that a wide range of other signaling IDPs or IDRs undergo both AS- and PTM-based modifications, suggesting that they, too, likely take advantage of signal outcome modulations that result from collaboration between these two events. Hence, we propose that the widespread cooperation of IDPs, AS and/or PTMs provides an IDP-AS-PTM toolkit and substantially contributes to the vast complexity of eukaryotic cell signaling systems.

Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding

“…Removal of the auto‐inhibition segments by AS will switch the proteins into active states or increase the binding affinities for other molecules. Consequently, removing disordered segments containing different functional or signaling elements allows for rewiring the cellular signaling pathways …”

“…In a comprehensive bioinformatics study carried out by Xie et al, a positive correlation between the functional annotation of the SwissProt database and the predicted intrinsic disorder has been found. Generally, IDPs/IDRs are enriched in proteins involved in signaling and regulatory functions, including transcription regulation, cell cycle, mRNA processing, scaffolding, and apoptosis . Consequently, dysregulation of IDPs/IDRs are associated with a variety of human diseases .…”

Presence and structure‐activity relationship of intrinsically disordered regions across mucins

“…In addition to splice events, numerous structural modifications of mucins drive protein–protein interactions which serve as a key to their oncogenic role in cancer progression . The flexibility of IDRs facilitates access to enzymes involved in PTM and the ability of an IDR to interact with target proteins is dramatically altered by the presence of these PTMs . Our findings show a high degree of overlap between the PhosphoSitePlus curated phosphorylation sites found in D 2 P 2 and IDRs, throughout the mucin protein family.…”

“…This also correlates with observed site‐specific and context‐dependent signaling of mucins under normal physiological as well as pathological conditions (eg, MUC5AC deleterious effects in pancreatic cancer and its protective role in the lung epithelium). Specific tissues or cell types are able to rewire/remodel protein pathways and gene expression patterns ( via transcription factors) through changes in PTMs and alternative splicing, which are impacted by the presence, prevalence, and size of IDRs . Mucins exhibit a high level of alternative splicing thus warranting further investigation into the effect of disorder on splicing events and impact on PTMs.…”

“…Though IDRs have been implicated in PTMs for years, a concept of an IDR-PTM-AS (alternative splicing) toolkit has recently been proposed. 94 This toolkit allows for a single protein-coding gene to produce multiple disparate functional units, predicated in tissue or cell-specific manner. This also correlates with observed site-specific and context-dependent signaling of mucins under normal physiological as well as pathological conditions (eg, MUC5AC deleterious effects in pancreatic cancer 95 and its protective role in the lung epithelium 96 ).…”