Nucleocapsid protein preferentially binds the stem-loop of duplex/quadruplex hybrid that unfolds the quadruplex structure

2021 ◽  
Author(s):  
Yaping Sheng ◽  
Bei Cao ◽  
Mingxi Ou ◽  
Yu Wang ◽  
Siming Yuan ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Hybrid Structure ◽  
Stem Loop ◽  
Quadruplex Structure ◽  
Loop Region ◽  
Dynamic Fluctuation

HIV nucleocapsid protein unfolds the duplex/quadruplex hybrid structure by binding to the stem-loop region, which induces dynamic fluctuation of G-tetrad and K+ ejection.

scholarly journals MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

2020 ◽  
Vol 117 (38) ◽  
pp. 23982-23990 ◽  
Author(s):  
Shengjun Li ◽  
Mu Li ◽  
Kan Liu ◽  
Huimin Zhang ◽  
Shuxin Zhang ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Protein ◽  
Dual Role ◽  
Mirna Biogenesis ◽  
Core Component ◽  
Stem Loop ◽  
Loop Region ◽  
Nuclear Rna ◽  
Efficient Processing ◽  
The Stability

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels inmac5is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

scholarly journals Protein disulfide isomerase blocks CEBPA translation and is up-regulated during the unfolded protein response in AML

Blood ◽  
2011 ◽  
Vol 117 (22) ◽  
pp. 5931-5940 ◽  
Author(s):  
Simon Haefliger ◽  
Christiane Klebig ◽  
Kerstin Schaubitzer ◽  
Julian Schardt ◽  
Nikolai Timchenko ◽  
...  
Keyword(s):  
Er Stress ◽  
Unfolded Protein Response ◽  
Protein Disulfide Isomerase ◽  
Leukemic Cells ◽  
Stem Loop ◽  
Unfolded Protein ◽  
Loop Region ◽  
The Unfolded Protein Response ◽  
Protein Response ◽  
Protein Disulfide

Abstract Deregulation of the myeloid key transcription factor CEBPA is a common event in acute myeloid leukemia (AML). We previously reported that the chaperone calreticulin is activated in subgroups of AML patients and that calreticulin binds to the stem loop region of the CEBPA mRNA, thereby blocking CEBPA translation. In this study, we screened for additional CEBPA mRNA binding proteins and we identified protein disulfide isomerase (PDI), an endoplasmic reticulum (ER) resident protein, to bind to the CEBPA mRNA stem loop region. We found that forced PDI expression in myeloid leukemic cells in fact blocked CEBPA translation, but not transcription, whereas abolishing PDI function restored CEBPA protein. In addition, PDI protein displayed direct physical interaction with calreticulin. Induction of ER stress in leukemic HL60 and U937 cells activated PDI expression, thereby decreasing CEBPA protein levels. Finally, leukemic cells from 25.4% of all AML patients displayed activation of the unfolded protein response as a marker for ER stress, and these patients also expressed significantly higher PDI levels. Our results indicate a novel role of PDI as a member of the ER stress–associated complex mediating blocked CEBPA translation and thereby suppressing myeloid differentiation in AML patients with activated unfolded protein response (UPR).

scholarly journals An RNA Pseudoknot in the 3′ End of the Arterivirus Genome Has a Critical Role in Regulating Viral RNA Synthesis

2007 ◽  
Vol 81 (17) ◽  
pp. 9426-9436 ◽  
Author(s):  
Nancy Beerens ◽  
Eric J. Snijder
Keyword(s):  
Rna Synthesis ◽  
Critical Role ◽  
Equine Arteritis Virus ◽  
Viral Rna ◽  
Replicase Gene ◽  
Loop Structure ◽  
Minus Strand ◽  
Stem Loop ◽  
Loop Region ◽  
Stem Loop Structure

ABSTRACT In the life cycle of plus-strand RNA viruses, the genome initially serves as the template for both translation of the viral replicase gene and synthesis of minus-strand RNA and is ultimately packaged into progeny virions. These various processes must be properly balanced to ensure efficient viral proliferation. To achieve this, higher-order RNA structures near the termini of a variety of RNA virus genomes are thought to play a key role in regulating the specificity and efficiency of viral RNA synthesis. In this study, we have analyzed the signals for minus-strand RNA synthesis in the prototype of the arterivirus family, equine arteritis virus (EAV). Using site-directed mutagenesis and an EAV reverse genetics system, we have demonstrated that a stem-loop structure near the 3′ terminus of the EAV genome is required for RNA synthesis. We have also obtained evidence for an essential pseudoknot interaction between the loop region of this stem-loop structure and an upstream hairpin residing in the gene encoding the nucleocapsid protein. We propose that the formation of this pseudoknot interaction may constitute a molecular switch that could regulate the specificity or timing of viral RNA synthesis. This hypothesis is supported by the fact that phylogenetic analysis predicted the formation of similar pseudoknot interactions near the 3′ end of all known arterivirus genomes, suggesting that this interaction has been conserved in evolution.

HIV-1 Nucleocapsid Protein NCp7 and Its RNA Stem Loop 3 Partner: Rotational Dynamics of Spin-Labeled RNA Stem Loop 3†

Biochemistry ◽  
2008 ◽  
Vol 47 (38) ◽  
pp. 10099-10110 ◽  
Author(s):  
Xiangmei Xi ◽  
Yan Sun ◽  
Christine B. Karim ◽  
Vladimir M. Grigoryants ◽  
Charles P. Scholes
Keyword(s):  
Nucleocapsid Protein ◽  
Rotational Dynamics ◽  
Stem Loop ◽  
Labeled Rna ◽  
Hiv 1

scholarly journals Human ERAL1 is a mitochondrial RNA chaperone involved in the assembly of the 28S small mitochondrial ribosomal subunit

2010 ◽  
Vol 430 (3) ◽  
pp. 551-558 ◽  
Author(s):  
Sven Dennerlein ◽  
Agata Rozanska ◽  
Mateusz Wydro ◽  
Zofia M. A. Chrzanowska-Lightowlers ◽  
Robert N. Lightowlers
Keyword(s):  
16S Rrna ◽  
Cellular Localization ◽  
Mitochondrial Protein ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
Mitochondrial Rna ◽  
Rna Chaperone ◽  
Stem Loop ◽  
Loop Region

The bacterial Ras-like protein Era has been reported previously to bind 16S rRNA within the 30S ribosomal subunit and to play a crucial role in ribosome assembly. An orthologue of this essential GTPase ERAL1 (Era G-protein-like 1) exists in higher eukaryotes and although its exact molecular function and cellular localization is unknown, its absence has been linked to apoptosis. In the present study we show that human ERAL1 is a mitochondrial protein important for the formation of the 28S small mitoribosomal subunit. We also show that ERAL1 binds in vivo to the rRNA component of the small subunit [12S mt (mitochondrial)-rRNA]. Bacterial Era associates with a 3′ unstructured nonanucleotide immediately downstream of the terminal stem–loop (helix 45) of 16S rRNA. This site contains an AUCA sequence highly conserved across all domains of life, immediately upstream of the anti-Shine–Dalgarno sequence, which is conserved in bacteria. Strikingly, this entire region is absent from 12S mt-rRNA. We have mapped the ERAL1-binding site to a 33 nucleotide section delineating the 3′ terminal stem–loop region of 12S mt-rRNA. This loop contains two adenine residues that are reported to be dimethylated on mitoribosome maturation. Furthermore, and also in contrast with the bacterial orthologue, loss of ERAL1 leads to rapid decay of nascent 12S mt-rRNA, consistent with a role as a mitochondrial RNA chaperone. Finally, whereas depletion of ERAL1 leads to apoptosis, cell death occurs prior to any appreciable loss of mitochondrial protein synthesis or reduction in the stability of mitochondrial mRNA.

scholarly journals A Novel SARS-CoV-2 Viral Sequence Bioinformatic Pipeline Has Found Genetic Evidence That the Viral 3′ Untranslated Region (UTR) Is Evolving and Generating Increased Viral Diversity

2021 ◽  
Vol 12 ◽  
Author(s):  
Carlos Farkas ◽  
Andy Mella ◽  
Maxime Turgeon ◽  
Jody J. Haigh
Keyword(s):  
Stop Codon ◽  
Low Frequency ◽  
Variant Calling ◽  
Viral Diversity ◽  
Stem Loop ◽  
Bioinformatic Pipeline ◽  
Host Immune Responses ◽  
Sequencing Errors ◽  
Bioinformatic Tools ◽  
Loop Region

An unprecedented amount of SARS-CoV-2 sequencing has been performed, however, novel bioinformatic tools to cope with and process these large datasets is needed. Here, we have devised a bioinformatic pipeline that inputs SARS-CoV-2 genome sequencing in FASTA/FASTQ format and outputs a single Variant Calling Format file that can be processed to obtain variant annotations and perform downstream population genetic testing. As proof of concept, we have analyzed over 229,000 SARS-CoV-2 viral sequences up until November 30, 2020. We have identified over 39,000 variants worldwide with increased polymorphisms, spanning the ORF3a gene as well as the 3′ untranslated (UTR) regions, specifically in the conserved stem loop region of SARS-CoV-2 which is accumulating greater observed viral diversity relative to chance variation. Our analysis pipeline has also discovered the existence of SARS-CoV-2 hypermutation with low frequency (less than in 2% of genomes) likely arising through host immune responses and not due to sequencing errors. Among annotated non-sense variants with a population frequency over 1%, recurrent inactivation of the ORF8 gene was found. This was found to be present in the newly identified B.1.1.7 SARS-CoV-2 lineage that originated in the United Kingdom. Almost all VOC-containing genomes possess one stop codon in ORF8 gene (Q27∗), however, 13% of these genomes also contains another stop codon (K68∗), suggesting that ORF8 loss does not interfere with SARS-CoV-2 spread and may play a role in its increased virulence. We have developed this computational pipeline to assist researchers in the rapid analysis and characterization of SARS-CoV-2 variation.

scholarly journals Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

2020 ◽  
Author(s):  
Diego Rivera Gelsinger ◽  
Rahul Reddy ◽  
Kathleen Whittington ◽  
Sara Debic ◽  
Jocelyne DiRuggiero
Keyword(s):  
Oxidative Stress ◽  
Malic Enzyme ◽  
Tricarboxylic Acid Cycle ◽  
Redox Homeostasis ◽  
Fine Tuning ◽  
Oxidative Decarboxylation ◽  
Seed Region ◽  
Stem Loop ◽  
Loop Region ◽  
Rna Interaction

ABSTRACTHaloarchaea are highly resistant to oxidative stress, however, a comprehensive understanding of the processes regulating this remarkable response is lacking. Oxidative stress-responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms have not been elucidated. Using a combination of high throughput and reverse molecular genetic approaches, we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, named Small RNA in Haloferax Oxidative Stress (SHOxi). SHOxi was predicted to form a stable secondary structure with a conserved stem-loop region as the potential binding site for trans-targets. NAD-dependent malic enzyme mRNA, identified as a putative target of SHOxi, interacted directly with a putative “seed” region within the predicted stem loop of SHOxi. Malic enzyme is an enzyme of the tricarboxylic acid cycle that catalyzes the oxidative decarboxylation of malate into pyruvate using NAD+ as a cofactor. The destabilization of malic enzyme mRNA, and the decrease in the NAD+/NADH ratio, resulting from the direct RNA-RNA interaction between SHOxi and its trans-target was essential for the survival of H. volcanii to oxidative stress. These findings indicate that SHOxi likely regulates redox homeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. SHOxi-mediated regulation provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.

scholarly journals Integrating NMR and simulations reveals motions in the UUCG tetraloop

2020 ◽  
Vol 48 (11) ◽  
pp. 5839-5848 ◽  
Author(s):  
Sandro Bottaro ◽  
Parker J Nichols ◽  
Beat Vögeli ◽  
Michele Parrinello ◽  
Kresten Lindorff-Larsen
Keyword(s):  
Experimental Data ◽  
Three Dimensional ◽  
Machine Learning Techniques ◽  
Dimensional Structure ◽  
Stable Conformation ◽  
Stem Loop ◽  
Loop Region ◽  
Simple Model System ◽  
Nuclear Overhauser ◽  
Dynamics Simulations

Abstract We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem–loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements data allowed us to characterize two distinct states of this molecule. The most stable conformation corresponds to the consensus three-dimensional structure. The second state is characterized by the absence of the peculiar non-Watson–Crick interactions in the loop region. By using machine learning techniques we identify a set of experimental measurements that are most sensitive to the presence of non-native states. We find that although our MD ensemble, as well as the consensus UUCG tetraloop structures, are in good agreement with experiments, there are remaining discrepancies. Together, our results show that (i) the MD simulation overstabilize a non-native loop conformation, (ii) eNOE data support its presence with a population of ≈10% and (iii) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop.

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