scholarly journals Structural basis for RNA recognition by the N-terminal tandem RRM domains of human RBM45

2021 ◽  
Author(s):  
Xiaolei Chen ◽  
Zhongmei Yang ◽  
Wenfeng Wang ◽  
Kaiyue Qian ◽  
Mingjie Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Neural Development ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Structural Basis ◽  
Rna Recognition ◽  
Aromatic Residues ◽  
Frontotemporal Lobar Dementia ◽  
Lateral Sclerosis

Abstract RBM45 is an RNA-binding protein involved in neural development, whose aggregation is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). However, the mechanisms of RNA-binding and aggregation of RBM45 remain unelucidated. Here, we report the crystal structure of the N-terminal tandem RRM domains of human RBM45 in complex with single-stranded DNA (ssDNA). Our structural and biochemical results revealed that both the RRM1 and RRM2 of RBM45 recognized the GAC sequence of RNA/ssDNA. Two aromatic residues and an arginine residue in each RRM were critical for RNA-binding, and the interdomain linker was also involved in RNA-binding. Two RRMs formed a pair of antiparallel RNA-binding sites, indicating that the N-terminal tandem RRM domains of RBM45 bound separate GAC motifs in one RNA strand or GAC motifs in different RNA strands. Our findings will be helpful in the identification of physiologic targets of RBM45 and provide evidence for understanding the physiologic and pathologic functions of RBM45.

scholarly journals Structural basis of the zinc-induced cytoplasmic aggregation of the RNA-binding protein SFPQ

2020 ◽  
Vol 48 (6) ◽  
pp. 3356-3365 ◽  
Author(s):  
Jie Huang ◽  
Mitchell Ringuet ◽  
Andrew E Whitten ◽  
Sofia Caria ◽  
Yee Wa Lim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Cortical Neurons ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Zinc Binding ◽  
Structural Basis ◽  
Rna Biogenesis ◽  
Cytoplasmic Accumulation ◽  
Nucleocytoplasmic Distribution

Abstract SFPQ is a ubiquitous nuclear RNA-binding protein implicated in many aspects of RNA biogenesis. Importantly, nuclear depletion and cytoplasmic accumulation of SFPQ has been linked to neuropathological conditions such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS). Here, we describe a molecular mechanism by which SFPQ is mislocalized to the cytoplasm. We report an unexpected discovery of the infinite polymerization of SFPQ that is induced by zinc binding to the protein. The crystal structure of human SFPQ in complex with zinc at 1.94 Å resolution reveals intermolecular interactions between SFPQ molecules that are mediated by zinc. As anticipated from the crystal structure, the application of zinc to primary cortical neurons induced the cytoplasmic accumulation and aggregation of SFPQ. Mutagenesis of the three zinc-coordinating histidine residues resulted in a significant reduction in the zinc-binding affinity of SFPQ in solution and the zinc-induced cytoplasmic aggregation of SFPQ in cultured neurons. Taken together, we propose that dysregulation of zinc availability and/or localization in neuronal cells may represent a mechanism for the imbalance in the nucleocytoplasmic distribution of SFPQ, which is an emerging hallmark of neurodegenerative diseases including AD and ALS.

scholarly journals Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

2015 ◽  
Vol 49 ◽  
Author(s):  
Marianna Teplova ◽  
Thalia A. Farazi ◽  
Thomas Tuschl ◽  
Dinshaw J. Patel
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Hek293 Cells ◽  
Structural Basis ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Binding Studies ◽  
Muscle Plasticity ◽  
Rrm Domain

AbstractRNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. As anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo.

scholarly journals Myo-granules Connect Physiology and Pathophysiology

2019 ◽  
Vol 13 ◽  
pp. 117906951984215 ◽  
Author(s):  
Alicia A Cutler ◽  
Theodore Eugene Ewachiw ◽  
Giulia A Corbet ◽  
Roy Parker ◽  
Brad B Olwin
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Alzheimer Disease ◽  
Muscle Regeneration ◽  
Inclusion Body Myositis ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Neuromuscular Diseases ◽  
Normal Muscle ◽  
Frontotemporal Lobar Dementia ◽  
Lateral Sclerosis

A hallmark of many neuromuscular diseases including Alzheimer disease, inclusion body myositis, amyotrophic lateral sclerosis, frontotemporal lobar dementia, and ocular pharyngeal muscular dystrophy is large cytoplasmic aggregates containing the RNA-binding protein, TDP-43. Despite acceptance that cytoplasmic TDP-43 aggregation is pathological, cytoplasmic TDP-43 assemblies form in healthy regenerating muscle. These recently discovered ribonucleoprotein assemblies, termed myo-granules, form in healthy muscle following injury and are readily cleared as the myofibers mature. The formation and dissolution of myo-granules during normal muscle regeneration suggests that these amyloid-like oligomers may be functional and that perturbations in myo-granule kinetics or composition may promote pathological aggregation.

scholarly journals Human DND1-RRM2 forms a non-canonical domain swapped dimer

2020 ◽  
Author(s):  
Pooja Kumari ◽  
Neel Sarovar Bhavesh
Keyword(s):  
Crystal Structure ◽  
Redox Regulation ◽  
Rna Binding ◽  
Md Simulations ◽  
Structural Basis ◽  
List Type ◽  
Rna Recognition ◽  
Dimer Formation ◽  
Rna Recognition Motifs ◽  
Recognition Motifs

SummaryHuman DND1 (Dead end protein homolog1) is an RNA binding protein. DND1 plays pivotal role in animal development and has been implicated in cancer. DND1 consists of two RNA recognition motifs (RRMs) in tandem and a double stranded RNA binding domain at the C terminal separated by 40 residues flexible linker. The conserved RNP site in the RRM1 domain helps in specific RNA recognition while the RNP sites in RRM2 are not well conserved. DND1 has been reported to be involved in inhibition of microRNA access to target mRNA and it also associate with CCR4-NOT complex that targets mRNA. In order to understand this intriguing contrasting molecular function, we have determined the 2.3 Å resolution crystal structure of the human DND1 RRM2 domain. The structure revealed an interesting non-canonical RRM fold that is maintained by the formation of a domain swapped dimer between β1 and β4 strands across two chains. The domain swapping is attributed by a hinge loop between α2 and β4 that helps in mediating a domain swap forming anti-parallel β sheets. We have delineated the structural basis of stable dimer formation using the residue level dynamics of protein explored by NMR spectroscopy and MD simulations. Our structural and dynamics studies demonstrate the molecular basis for the dimerization of the RRM2 domain and shed light on the possibility for this motif for interaction with other proteins which helps in transcription regulation.Graphical AbstractHighlightsFirst report of a domain swapped dimer formation by an RRM identified through crystal structure determination of the human DND1 RRM2 domain.RRM2 exhibit domain swapped dimerization attributed by hinge loop and disulfide bond formation.Dimer formation is under redox regulation.Major determinants of swapping were identified.DND1 RRM2 is not involved in RNA recognition.

Identification and expression analysis of Dazl homologue in Cynops cyanurus

Zygote ◽  
2021 ◽  
pp. 1-6
Author(s):  
Yinjiao Zhao ◽  
Ya Du ◽  
Qinglan Ge ◽  
Fang Yan ◽  
Shu Wei
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Studies ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Specific Expression ◽  
Recognition Motif ◽  
Deleted In Azoospermia ◽  
Specific Expression Pattern

Summary The Dazl (deleted in azoospermia-like) gene encodes an RNA-binding protein containing an RNA recognition motif (RRM) and a DAZ motif. Dazl is essential for gametogenesis in vertebrates. In this study, we report the cloning of Dazl cDNA from Cynops cyanurus. Ccdazl mRNA showed a germline-specific expression pattern as expected. Ccdazl expression gradually decreased during oogenesis, suggesting that it may be involved in oocyte development. Phylogenetic analysis revealed that the Ccdazl protein shares conserved motifs/domains with Dazl proteins from other species. Cloning of Ccdazl provides a new tool to carry out comparative studies of germ cell development in amphibians.

scholarly journals The Interplay of RNA Binding Proteins, Oxidative Stress and Mitochondrial Dysfunction in ALS

Antioxidants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 552
Author(s):  
Jasmine Harley ◽  
Benjamin E. Clarke ◽  
Rickie Patani
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Mitochondrial Dysfunction ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Therapeutic Strategies ◽  
Lateral Sclerosis

RNA binding proteins fulfil a wide number of roles in gene expression. Multiple mechanisms of RNA binding protein dysregulation have been implicated in the pathomechanisms of several neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Oxidative stress and mitochondrial dysfunction also play important roles in these diseases. In this review, we highlight the mechanistic interplay between RNA binding protein dysregulation, oxidative stress and mitochondrial dysfunction in ALS. We also discuss different potential therapeutic strategies targeting these pathways.

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