The Role of Protein Post-Translational Modifications in Protein-RNA Interactions and RNP Assemblies

Editorial

04 January 2022

Editorial: The Role of Protein Post-Translational Modifications in Protein-RNA Interactions and RNP Assemblies

Roberto Giambruno

Ewa A. Grzybowska

Nicolas L. Fawzi

and

Dorothee Dormann

3,207 views

5 citations

Editors

Roberto Giambruno

National Research Council (CNR)

Dorothee Dormann

Johannes Gutenberg University Mainz

Nicolas Lux Fawzi

Brown University

Ewa Anna Grzybowska

Maria Sklodowska-Curie National Research Institute of Oncology

Impact

Original Research

19 October 2021

Phosphorylation Regulates CIRBP Arginine Methylation, Transportin-1 Binding and Liquid-Liquid Phase Separation

Aneta J. Lenard

, 6 more and

Tobias Madl

7,137 views

21 citations

$Dynamics of RBP-RNA interactions in dependence of PRMT pharmacological modulation. (A) Supervised clustering analysis of the quantitative OOPS proteomics data. Supervised clustering analysis of differential protein expression or differential RNA-binding after MS023 and GSK591 treatment normalized on DMSO led to the identification of four representative clusters: Cluster 1 and Cluster 2 contain proteins with Log2 SILAC ratio MS023/DMSO +1 and +1.5, respectively, only in the interface fraction; Cluster 3 and Cluster 4 contains proteins overall not significantly modulated in the interface, with Cluster 4 displaying a mild decrease in the interface upon GSK591 (−0.3 Log2 SILAC ratios). (B) Scatter plot representation of the normalized Log2 SILAC ratio in MS023-treated condition. Scatter plot of the Log2 MS023/DMSO SILAC ratio of interface proteins, normalized on the respective protein SILAC ratio in the WCE, in FWD versus REV experiment. Dashed lines indicate μ±σ of the respective SILAC protein ratio distributions; proteins up- or down-regulated are displayed in red and blue, respectively. (C) Scatter-plot representation of the normalized Log2 SILAC ratio in GSK591 treated condition. The scatter plot displays the Log2 GSK591/DMSO SILAC ratio of interface proteins, normalized on the respective SILAC ratio in the WCE in FWD versus REV experiment. Dashed lines indicate μ±σ of the respective SILAC protein ratio distributions; proteins down-regulated are displayed in blue.$

Original Research

07 September 2021

Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach

Marianna Maniaci

, 2 more and

Tiziana Bonaldi

5,897 views

11 citations

Review

05 July 2021

Post-Translational Modifications Modulate Proteinopathies of TDP-43, FUS and hnRNP-A/B in Amyotrophic Lateral Sclerosis

Stefania Farina

, 3 more and

Sofia Francia

10,118 views

23 citations

Molecular effects of arginine methylation in T. brucei and L. major. (A), Protein arginine methyltranferases (PRMTs) from types I, II and III are able to generate monomethylarginine (MMA) by transfering the methyl group from S-adenosylmethionine to the terminal nitrogen atom of arginine residues. While type III PRMTs only produce monomethylated products, type I PRMTs catalyze a second round of methylation at the same atom, generating asymmetrically dimethylated arginine (aDMA), whereas type II PRMTs add another methyl group to the adjacent terminal nitrogen, forming symmetric dimethylarginine (sDMA). The inset table contains the gene IDs of PRMT genes found in the genome of T. brucei and L. major. (B), Schematic representation of how methylation affects the capability of RBP16 to form macromolecular complexes containing proteins (gray) and RNA (red line) in T. brucei. The RBP16 intrinsically disordered RGG domain is methylated by TbPRMT1 on Arg78 and Arg85, whereas Arg93 is (potentially) methylated by either or both TbPRMT5 and TbPRMT7 (left). In its methylated state, RBP16 can associate with other proteins (5S complex) or with proteins and RNA (11S complex). A non-methylatable version of RBP16 is still able to associate with RNA but loses the capability to form multiprotein complexes. Non-methylated arginines are represented by gray circles and methylated arginines by red circles. (C), Representation of the methylation mediated by L. major PRMT7 on Alba3. Alba3 interacts with Alba1 and δ-amastin transcripts. Methylated Alba3 has a stronger association with δ-amastin transcripts and protects the RNA from degradation. The ability of Alba3 to bind δ-amastin is reduced upon LmjPRMT7-knockout, which reduces the half-life of the transcripts from approximately 4 h to around 1 h. *PRMT3 is currently known as PRMT1PRO in T. brucei; despite its similarity to mammalian PRMT3, TbPRMT3 misses key residues for PRMT activity, and is rather a prozyme for the catalytic TbPRMT1, which was thus renamed to TbPRMT1ENZ.

Mini Review

11 June 2021

Arginine Methyltransferases as Regulators of RNA-Binding Protein Activities in Pathogenic Kinetoplastids

Gustavo D. Campagnaro

, 3 more and

Pegine B. Walrad

4,234 views

8 citations

RIC-like assays and biases involved in quantifying RBP-RNA interactions. In RIC-like experiments, in vivo RBP-RNA interactions are stabilized by UV cross-linking. RNAs are isolated and the bound proteome is quantified with shotgun proteomics. We identify here four biases in the interpretation of RBP-RNA quantification results: RNA isolation (1), UV cross-linking (2), RBP occupancy (3), and indirect effects on RNA binding (4).

Perspective

13 May 2021

Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking

Carlos H. Vieira-Vieira

and

Matthias Selbach

5,477 views

22 citations

SUMOylation of PRP3 promotes U4/U6U5 tri-snRNP formation. (A) The human PRP3 protein, as a component of the U4/U6 di-snRNP, is a SUMOylation target and promotes U4/U6U5 tri-snRNP formation to convert the A complex into the active B complex by interacting with U2 and U5 thereby promoting the splicing process. (B) After mutation of the relevant lysine residues into arginine, the SUMO-deficient PRP3 fails to co-precipitate U2 and U5 snRNAs resulting in hampered U4/U6U5 tri-snRNP assembly and shows diminished recruitment to splice sites indicating that SUMOylation of PRP3 promotes U4/U6U5 tri-snRNP formation.

Mini Review

07 May 2021

SUMO: Glue or Solvent for Phase-Separated Ribonucleoprotein Complexes and Molecular Condensates?

Jan Keiten-Schmitz

, 3 more and

Stefan Müller

10,116 views

53 citations

Mini Review

27 April 2021

Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation

Alejandro Velázquez-Cruz

, 3 more and

Irene Díaz-Moreno

Examples of PTM-mediated regulation of RBPs. (A) KSRP can shuttle between nucleus (N) and cytoplasm (C) to perform specific functions in each compartment. However, phosphorylation at Ser193 by Akt1, stimulated by growth factors, promotes the translocation of KSRP to the nucleus, whereas hypoxia-induced SUMOylation at Lys83 leads to its nuclear export (Díaz-Moreno et al., 2009; Yuan et al., 2017). (B) Phosphorylation of TIA-1 by FASTK improves its ability to recruit the U1 snRNP spliceosomal complex to the 5′ splice site region of the Fas receptor pre-mRNA exon 6. The resulting mature mRNA will express mFas, which plays an important role in the extrinsic apoptosis signaling pathways. In contrast, splicing of Fas receptor in the presence of unphosphorylated TIA-1 results in exon 6 skipping and the synthesis of sFas, that blocks apoptosis (Förch et al., 2002; Izquierdo and Valcárcel, 2007). (C) Under standard conditions, hnRNP K is targeted by the E3 Ub-ligase HDM2 for proteasomal degradation. Nonetheless, DNA damage triggers ATM-dependent phosphorylation of hnRNP K at Ser121, Thr174, Thr390, and Thr440, thus lowering its turnover rate. In addition, phosphorylated hnRNP K stimulates p53-mediated p21 gene expression, which causes cell cycle arrest (Moumen et al., 2005, 2013).

Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.

15,638 views

58 citations

Diagram of the major cellular functions of hnRNP A1. (A) Nuclear hnRNP A1 can regulate transcriptional expression by either promoter regulation, or by binding and sequestering transcription factors (TF; orange circles). (B) hnRNP A1 can also regulate telomeric elongation and capping either via telomerase binding and activation, direct 3’ telomeric end binding, or by aiding in the binding of Shelterin complex proteins. The results of these interactions are to prevent NHEJ and telomere degradation. (C) Pre-mRNA splicing is a major component of hnRNP A1 nuclear function, and its binding can result in the formation of various mRNA isoforms from a single pre-mRNA transcript. (D) mRNA transport from the nucleus to the cytoplasm has been shown to be a major function of hnRNP A1, where hnRNP A1 directs mRNA to ribosomes for cap-dependen translation. (E) In addition to directing mRNA to ribosomes for cap-dependent mRNA translation in the cytoplasm, hnRNP A1 can also bind to IRES elements within mRNA and influence cap-independent translational activation or inhibition. (F) hnRNP A1 has been shown to influence the nuclear formation of pre-miRNAs from pri-miRNAs. While the exact mechanism of how hnRNPA1 affects this pathway is unknown, it is theorized that hnRNP A1 may influence Drosha (yellow circle) binding to pri-miRNA.

Review

12 April 2021

A Comprehensive Analysis of the Role of hnRNP A1 Function and Dysfunction in the Pathogenesis of Neurodegenerative Disease

Joseph P. Clarke

, 2 more and

Michael C. Levin

Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a member of the hnRNP family of conserved proteins that is involved in RNA transcription, pre-mRNA splicing, mRNA transport, protein translation, microRNA processing, telomere maintenance and the regulation of transcription factor activity. HnRNP A1 is ubiquitously, yet differentially, expressed in many cell types, and due to post-translational modifications, can vary in its molecular function. While a plethora of knowledge is known about the function and dysfunction of hnRNP A1 in diseases other than neurodegenerative disease (e.g., cancer), numerous studies in amyotrophic lateral sclerosis, frontotemporal lobar degeneration, multiple sclerosis, spinal muscular atrophy, Alzheimer’s disease, and Huntington’s disease have found that the dysregulation of hnRNP A1 may contribute to disease pathogenesis. How hnRNP A1 mechanistically contributes to these diseases, and whether mutations and/or altered post-translational modifications contribute to pathogenesis, however, is currently under investigation. The aim of this comprehensive review is to first describe the background of hnRNP A1, including its structure, biological functions in RNA metabolism and the post-translational modifications known to modify its function. With this knowledge, the review then describes the influence of hnRNP A1 in neurodegenerative disease, and how its dysfunction may contribute the pathogenesis.

17,594 views

85 citations