Modular architecture and functional annotation of human RNA-binding proteins containing RNA recognition motif

GEMIN5 and neurodevelopmental diseases: From functional insights to disease perception

GEMIN5 is a predominantly cytoplasmic multifunctional protein, known to be involved in recognizing snRNAs through its WD40 repeats domain placed at the N-terminus. A dimerization domain in the middle region acts as a hub for protein-protein interaction, while a non-canonical RNA-binding site is placed towards the C-terminus. The singular organization of structural domains present in GEMIN5 enables this protein to perform multiple functions through its ability to interact with distinct partners, both RNAs and proteins. This protein exerts a different role in translation regulation depending on its physiological state, such that while GEMIN5 down-regulates global RNA translation, the C-terminal half of the protein promotes translation of its mRNA. Additionally, GEMIN5 is responsible for the preferential partitioning of mRNAs into polysomes. Besides selective translation, GEMIN5 forms part of distinct ribonucleoprotein complexes, reflecting the dynamic organization of macromolecular complexes in response to internal and external signals. In accordance with its contribution to fundamental cellular processes, recent reports described clinical loss of function mutants suggesting that GEMIN5 deficiency is detrimental to cell growth and survival. Remarkably, patients carrying GEMIN5 biallelic variants suffer from neurodevelopmental delay, hypotonia, and cerebellar ataxia. Molecular analyses of individual variants, which are defective in protein dimerization, display decreased levels of ribosome association, reinforcing the involvement of the protein in translation regulation. Importantly, the number of clinical variants and the phenotypic spectrum associated with GEMIN5 disorders is increasing as the knowledge of the protein functions and the pathways linked to its activity augments. Here we discuss relevant advances concerning the functional and structural features of GEMIN5 and its separate domains in RNA-binding, protein interactome, and translation regulation, and how these data can help to understand the involvement of protein malfunction in clinical variants found in patients developing neurodevelopmental disorders.

Effect of RNA-binding protein nuclear accommodation of mitochondria 8-FgNam8 on deoxynivalenol production and virulence of mycotoxigenic Fusarium graminearum

RNA-binding proteins (RBPs) are important regulators in RNA metabolism and gene expression in eukaryotes. Emerging studies support that RBPs play important roles in human development, metabolism and various diseases. However, the function of fungal RBPs is less identified and understood. The present study identifies an RBP FgNam8 which is U1 auxiliary component nuclear accommodation of mitochondria 8 (Nam8). The FgNam8 contains three RNA recognition motifs (RRM) and localizes to the cytoplasm and nucleus in F. graminearum. The ΔFgNam8 is reduced in vegetative growth and production of conidia. RNA-seq analyses show multiple RNA-associated biological processes and secondary metabolite biosynthesis pathways are altered in the ΔFgNam8. Furthermore, ΔFgNam8 is significantly reduced in deoxynivalenol (DON) production and virulence. More importantly, we verify the NDR (nuclear Dbf2-related) protein kinase FgCot1 interacts with FgNam8. Taken together, our results indicate that FgNam8 is important for the vegetative development, conidia production, DON production and virulence of F. graminearum, which may help to provide a candidate target for the treatment of Fusarium disease.

Stress granules: emerging players in neurodegenerative diseases

Stress granules (SGs) are membraneless organelles formed in the cellular cytoplasm under stressful conditions through liquid-liquid phase separation (LLPS). SG assembly can be both dependent and independent of the eIF2α pathway, whereas cellular protein quality control systems mediate SG disassembly. Chaperones and specific domains of RNA-binding proteins strongly contribute to the regulation SG dynamics. Chronic stress, arising in association with aging, may promote persistent SGs that are difficult to disassemble, thereby acting as a potential pathological nidus for protein aggregation in neurodegenerative diseases (NDDs). In this review, we discuss the dynamics of SGs and the factors involved with SG assembly and disassembly. We also highlight the relationship among LLPS, SGs, and the pathogenesis of different NDDs. More importantly, we summarize SG assembly-disassembly, which may be a double-edged sword in the pathophysiology of NDDs. This review aims to provide new insights into the biology and pathology of LLPS, SGs, and NDDs.

RRMScorer: A web server for predicting RNA recognition motif binding preferences

RRMScorer is a web server designed to predict RNA binding preferences for proteins containing RNA recognition motifs (RRMs), the most prevalent RNA binding domain in eukaryotes. By carefully analysing a dataset of 187 RRM-RNA structural complexes, we calculated residue-level binding scores using a probabilistic model derived from amino acid-nucleotide interaction propensities, which are the basis of RRMScorer. The server accepts protein sequences and optional RNA sequences as input, providing detailed outputs, including bar plots, sequence logos, and downloadable CSV/JSON files, to visualize and interpret RNA binding preferences. RRMScorer is particularly useful for studying the impact of single-point mutations and comparing binding preferences across multiple RRM domains. The web server, freely accessible at https://bio2byte.be/rrmscorer without login requirements, offers a user-friendly interface and integrates precomputed predictions for over 1400 RRM-containing proteins. With its ability to provide residue-level insights and accurate predictions, RRMScorer serves as a valuable tool for researchers exploring the functional landscape of RRM-RNA interactions.

Protein-RNA Docking Benchmark v3.0 Integrated With Binding Affinity

We introduce an updated non-redundant protein-RNA docking benchmark version 3.0 (PRDBv3.0) containing 197 test cases curated from 288 unique protein-RNA complexes available in the Protein Data Bank until July 2024. Among these, 27 are unbound-unbound (UU) type where both the binding partners are available in their unbound states, 160 are unbound-bound (UB) type where only the protein is available in unbound state and remaining 10 are bound-unbound (BU) type where only the RNA is available in unbound state. The benchmark is categorized into three classes based on the conformational flexibility of the protein interface: 117 rigid-body (R) complexes with minimal structural changes, 41 semi-flexible (S) complexes showing moderate conformational changes and 29 full-flexible (F) complexes with significant conformational changes. The current benchmark represents a 62% increase in the number of test cases compared to its previous version. Binding affinity (Kd) values for a subset of 105 protein-RNA complexes from PRDBv3.0 are catalogued along with additional experimental details to develop a comprehensive protein-RNA affinity benchmark. Moreover, a total of 255 unique RNA-binding domains, present in RNA-binding proteins, are also catalogued in this updated benchmark. PRDBv3.0 will facilitate the evaluation of both rigid-body and flexible docking methods as well as the methods that aim to predict binding affinity. The updated benchmark is freely available at http://www.csb.iitkgp.ac.in/applications/PRDBv3/PRDBv3.php.

Deep mutational scanning of the Trypanosoma brucei developmental regulator RBP6 reveals an essential disordered region influenced by positive residues

To regain infectivity, Trypanosoma brucei, the pathogen causing Human and Animal African trypanosomiasis, undergoes a complex developmental program within the tsetse fly known as metacyclogenesis. RNA-binding protein 6 (RBP6) is a potent orchestrator of this process, however, an understanding of its functionally important domains and their mutational constraints is lacking. Here, we perform deep mutational scanning of the entire RBP6 primary structure. Expression of libraries containing all single-point variants of RBP6 in non-infectious procyclic forms and subsequent purification of infectious metacyclics supports the existence of an RNA-recognition motif (RRM) and reveal an N-terminal intrinsically disordered region (N-IDR). In contrast to the RRM, the N-IDR is more tolerant to substitutions; however, a handful of positions contain a third of all deleterious mutations found in the N-IDR. Introduction of positively charged residues in the N-IDR dramatically alters the normal metacyclogenesis pattern. Our results reveal an essential N-IDR, possibly playing a regulatory role, and an RRM likely involved in protein-RNA interactions.

Structural, biological, and biomedical implications of mRNA interactions with the master regulator HuR

Human antigen R (HuR) is a ubiquitously expressed RNA-binding protein (RBP) that has been implicated in a vast range of biological processes including stress response, angiogenesis, cell proliferation, and differentiation. Dysregulation of HuR has been linked to a number of pathological disorders including vascular disease, inflammation, and cancers such as those of the breast and colon. Like many RBPs, HuR is composed of multiple RNA-recognition motif (RRM) domains; however, HuR and the three other members of the Hu family (HuB, HuC, and HuD) possess a unique structural composition with two RRMs separated from a third C-terminal RRM by a long, unstructured hinge region. While there has been extensive research on the role of HuR in cellular, molecular, and developmental biology, there are fewer structural and biochemical studies of HuR and many questions still remain about the molecular mechanisms of HuR. In this review, we endeavor to synthesize existing HuR research spanning the last three decades in order to define known mechanistic roles of each domain, highlight remaining uncertainties, and provide a backdrop for ongoing research into the chemistry and biology of HuR and similar multi-RRM containing proteins.

Insights into the Mode and Mechanism of Interactions Between RNA and RNA-Binding Proteins

Both RNA and protein play important roles in the process of gene expression and regulation, and it has been widely discussed that the interactions between RNA and protein affect gene transcription, translation efficiency, and post-translational modification. As an important class of proteins, RNA-binding proteins bind to RNA and affect gene expression in various ways. Here, we review the structural and functional properties of RNA-binding proteins and illustrate the specific modes of interactions between RNA and RNA-binding proteins and describe the involvement of some representative RNA-binding protein families in this network of action. Furthermore, we also explore the association that exists between RNA-binding proteins and the onset of diseases, as well as their potential in terms of serving as a therapeutic tool for the treatment of diseases. The in-depth exploration of the interactions between RNA and RNA-binding proteins reveals the dynamic process of gene expression and regulation, as well as offering valuable insights to advance the progress in the dissection of disease mechanisms and research and discovery of drugs, which promote the development of molecular biology.

Oligomerization regulates the interaction of Gemin5 with members of the SMN complex and the translation machinery

RNA-binding proteins are multifunctional molecules impacting on multiple steps of gene regulation. Gemin5 was initially identified as a member of the survival of motor neurons (SMN) complex. The protein is organized in structural and functional domains, including a WD40 repeats domain at the N-terminal region, a tetratricopeptide repeat (TPR) dimerization module at the central region, and a non-canonical RNA-binding site at the C-terminal end. The TPR module allows the recruitment of the endogenous Gemin5 protein in living cells and the assembly of a dimer in vitro. However, the biological relevance of Gemin5 oligomerization is not known. Here we interrogated the Gemin5 interactome focusing on oligomerization-dependent or independent regions. We show that the interactors associated with oligomerization-proficient domains were primarily annotated to ribosome, splicing, translation regulation, SMN complex, and RNA stability. The presence of distinct Gemin5 protein regions in polysomes highlighted differences in translation regulation based on their oligomerization capacity. Furthermore, the association with native ribosomes and negative regulation of translation was strictly dependent on both the WD40 repeats domain and the TPR dimerization moiety, while binding with the majority of the interacting proteins, including SMN, Gemin2, and Gemin4, was determined by the dimerization module. The loss of oligomerization did not perturb the predominant cytoplasmic localization of Gemin5, reinforcing the cytoplasmic functions of this essential protein. Our work highlights a distinctive role of the Gemin5 domains for its functions in the interaction with members of the SMN complex, ribosome association, and RBP interactome.

Analysis of the inter-domain orientation of tandem RRM domains with diverse linkers: connecting experimental with AlphaFold2 predicted models

The RNA recognition motif (RRM) is the most prevalent RNA binding domain in eukaryotes and is involved in most RNA metabolism processes. Single RRM domains have a limited RNA specificity and affinity and tend to be accompanied by other RNA binding domains, frequently additional RRMs that contribute to an avidity effect. Within multi-RRM proteins, the most common arrangement are tandem RRMs, with two domains connected by a variable linker. Despite their prevalence, little is known about the features that lead to specific arrangements, and especially the role of the connecting linker. In this work, we present a novel and robust way to investigate the relative domain orientation in multi-domain proteins using inter-domain vectors referenced to a stable secondary structure element. We apply this method to tandem RRM domains and cluster experimental tandem RRM structures according to their inter-domain and linker-domain contacts, and report how this correlates with their orientation. By extending our analysis to AlphaFold2 predicted structures, with particular attention to the inter-domain predicted aligned error, we identify new orientations not reported experimentally. Our analysis provides novel insights across a range of tandem RRM orientations that may help for the design of proteins with a specific RNA binding mode.

Protein-based delivery systems for RNA delivery

RNA-based therapeutics have emerged as promising approaches to modulate gene expression and generate therapeutic proteins or antigens capable of inducing immune responses to treat a variety of diseases, such as infectious diseases, cancers, immunologic disorders, and genetic disorders. However, the efficient delivery of RNA molecules into cells poses significant challenges due to their large molecular weight, negative charge, and susceptibility to degradation by RNase enzymes. To overcome these obstacles, viral and non-viral vectors have been developed, including lipid nanoparticles, viral vectors, proteins, dendritic macromolecules, among others. Among these carriers, protein-based delivery systems have garnered considerable attention due to their potential to address specific issues associated with nanoparticle-based systems, such as liver accumulation and immunogenicity. This review provides an overview of currently marketed RNA drugs, underscores the significance of RNA delivery vector development, delineates the essential characteristics of an ideal RNA delivery vector, and introduces existing protein carriers for RNA delivery. By offering valuable insights, this review aims to serve as a reference for the future development of protein-based delivery vectors for RNA therapeutics.

Efficient mapping of RNA-binding residues in RNA-binding proteins using local sequence features of binding site residues in protein-RNA complexes

Protein-RNA interactions play vital roles in plethora of biological processes such as regulation of gene expression, protein synthesis, mRNA processing and biogenesis. Identification of RNA-binding residues (RBRs) in proteins is essential to understand RNA-mediated protein functioning, to perform site-directed mutagenesis and to develop novel targeted drug therapies. Moreover, the extensive gap between sequence and structural data restricts the identification of binding sites in unsolved structures. However, efficient use of computational methods demanding only sequence to identify binding residues can bridge this huge sequence-structure gap. In this study, we have extensively studied protein-RNA interface in known RNA-binding proteins (RBPs). We find that the interface is highly enriched in basic and polar residues with Gly being the most common interface neighbor. We investigated several amino acid features and developed a method to predict putative RBRs from amino acid sequence. We have implemented balanced random forest (BRF) classifier with local residue features of protein sequences for prediction. With 5-fold cross-validations, the sequence pattern derived dipeptide composition based BRF model (DCP-BRF) resulted in an accuracy of 87.9%, specificity of 88.8%, sensitivity of 82.2%, Mathew's correlation coefficient of 0.60 and AUC of 0.93, performing better than few existing methods. We further validated our prediction model on known human RBPs through RBR prediction and could map ~54% of them. Further, knowledge of binding site preferences obtained from computational predictions combined with experimental validations of potential RNA binding sites can enhance our understanding of protein-RNA interactions. This may serve to accelerate investigations on functional roles of many novel RBPs.