Tra2 protein biology and mechanisms of splicing control

2014 ◽  
Vol 42 (4) ◽  
pp. 1152-1158 ◽  
Author(s):  
Andrew Best ◽  
Caroline Dalgliesh ◽  
Mahsa Kheirollahi-Kouhestani ◽  
Marina Danilenko ◽  
Ingrid Ehrmann ◽  
...  
Keyword(s):  
Sex Determination ◽  
Brain Development ◽  
Present Article ◽  
Mrna Splicing ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Recognition Motif ◽  
Rs Domains

Tra2 proteins regulate pre-mRNA splicing in vertebrates and invertebrates, and are involved in important processes ranging from brain development in mice to sex determination in fruitflies. In structure Tra2 proteins contain two RS domains (domains enriched in arginine and serine residues) flanking a central RRM (RNA recognition motif). Understanding the mechanisms of how Tra2 proteins work to control splicing is one of the key requirements to understand their biology. In the present article, we review what is known about how Tra2 proteins regulate splicing decisions in mammals and fruitflies.

scholarly journals Rbm38 Reduces the Transcription Elongation Defect of the SMEK2 Gene Caused by Splicing Deficiency

2020 ◽  
Vol 21 (22) ◽  
pp. 8799
Author(s):  
Shintaro Muraoka ◽  
Kazuhiro Fukumura ◽  
Megumi Hayashi ◽  
Naoyuki Kataoka ◽  
Akila Mayeda ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Rna Binding ◽  
Transcription Elongation ◽  
Rna Binding Protein ◽  
Mrna Splicing ◽  
Eukaryotic Cells ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Control Mechanisms ◽  
Recognition Motif

Pre-mRNA splicing is an essential mechanism for ensuring integrity of the transcriptome in eukaryotes. Therefore, splicing deficiency might cause a decrease in functional proteins and the production of nonfunctional, aberrant proteins. To prevent the production of such aberrant proteins, eukaryotic cells have several mRNA quality control mechanisms. In addition to the known mechanisms, we previously found that transcription elongation is attenuated to prevent the accumulation of pre-mRNA under splicing-deficient conditions. However, the detailed molecular mechanism behind the defect in transcription elongation remains unknown. Here, we showed that the RNA binding protein Rbm38 reduced the transcription elongation defect of the SMEK2 gene caused by splicing deficiency. This reduction was shown to require the N- and C-terminal regions of Rbm38, along with an important role being played by the RNA-recognition motif of Rbm38. These findings advance our understanding of the molecular mechanism of the transcription elongation defect caused by splicing deficiency.

A novel rice dull gene, LowAC1, encodes an RNA recognition motif protein affecting Waxy pre-mRNA splicing

2021 ◽  
Vol 162 ◽  
pp. 100-109
Author(s):  
Hidenari Igarashi ◽  
Hiroyuki Ito ◽  
Toru Shimada ◽  
Dong-Jin Kang ◽  
Shigeki Hamada
Keyword(s):  
Mrna Splicing ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Recognition Motif

scholarly journals Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 273
Author(s):  
Yoshita Srivastava ◽  
Rachel Bonn-Breach ◽  
Sai Shashank Chavali ◽  
Geoffrey M. Lippa ◽  
Jermaine L. Jenkins ◽  
...  
Keyword(s):  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Molecular Replacement ◽  
Hydrophobic Core ◽  
Anomalous Diffraction ◽  
Recognition Motif ◽  
Determination Process ◽  
Experimental Phasing ◽  
Crystal Contacts ◽  
Apical Loop

RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.

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 A Small Cyclic β‐Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b

ChemBioChem ◽  
2019 ◽  
Vol 20 (7) ◽  
pp. 931-939 ◽  
Author(s):  
Yi‐Ting Sun ◽  
Matthew D. Shortridge ◽  
Gabriele Varani
Keyword(s):  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Peptide Mimics ◽  
Recognition Motif

scholarly journals The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Kathleen L McCann ◽  
Takamasa Teramoto ◽  
Jun Zhang ◽  
Traci M Tanaka Hall ◽  
Susan J Baserga
Keyword(s):  
Protein Interactions ◽  
Molecular Basis ◽  
Large Subunit ◽  
Ribosomal Subunit ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Rrna Processing ◽  
Protein Protein Interactions ◽  
Recognition Motif ◽  
Processing Defects

ANE syndrome is a ribosomopathy caused by a mutation in an RNA recognition motif of RBM28, a nucleolar protein conserved to yeast (Nop4). While patients with ANE syndrome have fewer mature ribosomes, it is unclear how this mutation disrupts ribosome assembly. Here we use yeast as a model system and show that the mutation confers growth and pre-rRNA processing defects. Recently, we found that Nop4 is a hub protein in the nucleolar large subunit (LSU) processome interactome. Here we demonstrate that the ANE syndrome mutation disrupts Nop4’s hub function by abrogating several of Nop4’s protein-protein interactions. Circular dichroism and NMR demonstrate that the ANE syndrome mutation in RRM3 of human RBM28 disrupts domain folding. We conclude that the ANE syndrome mutation generates defective protein folding which abrogates protein-protein interactions and causes faulty pre-LSU rRNA processing, thus revealing one aspect of the molecular basis of this human disease.

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