scholarly journals U6atac snRNA stem-loop interacts with U12 p65 RNA binding protein and is functionally interchangeable with the U12 apical stem-loop III

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Jagjit Singh ◽  
Kavleen Sikand ◽  
Heike Conrad ◽  
Cindy L. Will ◽  
Anton A. Komar ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Stem Loop

scholarly journals Bovine Coronavirus Nonstructural Protein 1 (p28) Is an RNA Binding Protein That Binds Terminal Genomic cis-Replication Elements

2009 ◽  
Vol 83 (12) ◽  
pp. 6087-6097 ◽  
Author(s):  
Kortney M. Gustin ◽  
Bo-Jhih Guan ◽  
Agnieszka Dziduszko ◽  
David A. Brian
Keyword(s):  
Rna Binding ◽  
Nonstructural Protein ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Coding Region ◽  
Bovine Coronavirus ◽  
Stem Loop ◽  
Nonstructural Protein 1 ◽  
Gel Shift ◽  
Rna Levels

ABSTRACT Nonstructural protein 1 (nsp1), a 28-kDa protein in the bovine coronavirus (BCoV) and closely related mouse hepatitis coronavirus, is the first protein cleaved from the open reading frame 1 (ORF 1) polyprotein product of genome translation. Recently, a 30-nucleotide (nt) cis-replication stem-loop VI (SLVI) has been mapped at nt 101 to 130 within a 288-nt 5′-terminal segment of the 738-nt nsp1 cistron in a BCoV defective interfering (DI) RNA. Since a similar nsp1 coding region appears in all characterized groups 1 and 2 coronavirus DI RNAs and must be translated in cis for BCoV DI RNA replication, we hypothesized that nsp1 might regulate ORF 1 expression by binding this intra-nsp1 cistronic element. Here, we (i) establish by mutation analysis that the 72-nt intracistronic SLV immediately upstream of SLVI is also a DI RNA cis-replication signal, (ii) show by gel shift and UV-cross-linking analyses that cellular proteins of ∼60 and 100 kDa, but not viral proteins, bind SLV and SLVI, (SLV-VI) and (iii) demonstrate by gel shift analysis that nsp1 purified from Escherichia coli does not bind SLV-VI but does bind three 5′ untranslated region (UTR)- and one 3′ UTR-located cis-replication SLs. Notably, nsp1 specifically binds SLIII and its flanking sequences in the 5′ UTR with ∼2.5 μM affinity. Additionally, under conditions enabling expression of nsp1 from DI RNA-encoded subgenomic mRNA, DI RNA levels were greatly reduced, but there was only a slight transient reduction in viral RNA levels. These results together indicate that nsp1 is an RNA-binding protein that may function to regulate viral genome translation or replication but not by binding SLV-VI within its own coding region.

The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1

1993 ◽  
Vol 13 (1) ◽  
pp. 703-710
Author(s):  
D P Toczyski ◽  
J A Steitz
Keyword(s):  
Fusion Protein ◽  
Small Rna ◽  
Epstein Barr Virus ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Glutathione S Transferase ◽  
Stem Loop ◽  
Barr Virus ◽  
Epstein Barr

EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-EAP antibodies demonstrate that EAP binds a stem-loop structure (stem-loop 3) of EBER 1. Since bacterially expressed glutathione S-transferase-EAP fusion protein binds EBER 1, we conclude that EAP binding is independent of any other cellular or viral protein. Detailed mutational analyses of stem-loop 3 suggest that EAP recognizes the majority of the nucleotides in this hairpin, interacting with both single-stranded and double-stranded regions in a sequence-specific manner. Binding studies utilizing EBER 1 deletion mutants suggest that there may also be a second, weaker EAP-binding site on stem-loop 4 of EBER 1. These data and the fact that stem-loop 3 represents the most highly conserved region between EBER 1 and HVP 1 suggest that EAP binding is a critical aspect of EBER 1 and HVP 1 function.

scholarly journals The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1.

1993 ◽  
Vol 13 (1) ◽  
pp. 703-710 ◽  
Author(s):  
D P Toczyski ◽  
J A Steitz
Keyword(s):  
Fusion Protein ◽  
Small Rna ◽  
Epstein Barr Virus ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Glutathione S Transferase ◽  
Stem Loop ◽  
Barr Virus ◽  
Epstein Barr

EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-EAP antibodies demonstrate that EAP binds a stem-loop structure (stem-loop 3) of EBER 1. Since bacterially expressed glutathione S-transferase-EAP fusion protein binds EBER 1, we conclude that EAP binding is independent of any other cellular or viral protein. Detailed mutational analyses of stem-loop 3 suggest that EAP recognizes the majority of the nucleotides in this hairpin, interacting with both single-stranded and double-stranded regions in a sequence-specific manner. Binding studies utilizing EBER 1 deletion mutants suggest that there may also be a second, weaker EAP-binding site on stem-loop 4 of EBER 1. These data and the fact that stem-loop 3 represents the most highly conserved region between EBER 1 and HVP 1 suggest that EAP binding is a critical aspect of EBER 1 and HVP 1 function.

Interaction of 68–kDa TAR RNA-binding protein and other cellular proteins with rpion protein-RNA stem-loop

1995 ◽  
Vol 1 (5-6) ◽  
pp. 391-398 ◽  
Author(s):  
Ute Scheffer ◽  
Takashi Okamoto ◽  
Jock MS Forrest ◽  
Peter G Rytik ◽  
Werner EG Müller ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cellular Proteins ◽  
Stem Loop ◽  
Tar Rna

scholarly journals DDX56 Binds to Chikungunya Virus RNA To Control Infection

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Frances Taschuk ◽  
Iulia Tapescu ◽  
Ryan H. Moy ◽  
Sara Cherry
Keyword(s):  
Chikungunya Virus ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Immune Defense ◽  
Genomic Rna ◽  
Stem Loop ◽  
Evolutionarily Conserved ◽  
Alphavirus Infection ◽  
Viral Genomic Rna

ABSTRACT DEAD box RNA helicases regulate diverse facets of RNA biology. Proteins of this family carry out essential cellular functions, and emerging literature is revealing additional roles in immune defense. Using RNA interference screening, we identified an evolutionarily conserved antiviral role for the helicase DDX56 against the alphavirus Sindbis virus (SINV), a mosquito-transmitted pathogen that infects humans. Depletion of DDX56 enhanced infection in Drosophila and human cells. Furthermore, we found that DDX56 also controls the emerging alphavirus chikungunya virus (CHIKV) through an interferon-independent mechanism. Using cross-linking immunoprecipitation (CLIP-Seq), we identified a predicted stem-loop on the viral genomic RNA bound by DDX56. Mechanistically, we found that DDX56 levels increase in the cytoplasm during CHIKV infection. In the cytoplasm, DDX56 impacts the earliest step in the viral replication cycle by binding and destabilizing the incoming viral genomic RNA, thereby attenuating infection. Thus, DDX56 is a conserved antiviral RNA binding protein that controls alphavirus infection. IMPORTANCE Arthropod-borne viruses are diverse pathogens and include the emerging virus chikungunya virus, which is associated with human disease. Through genetic screening, we found that the conserved RNA binding protein DDX56 is antiviral against chikungunya virus in insects and humans. DDX56 relocalizes from the nucleus to the cytoplasm, where it binds to a stem-loop in the viral genome and destabilizes incoming genomes. Thus, DDX56 is an evolutionarily conserved antiviral factor that controls alphavirus infection.

235: The RNA-Binding Protein IMP3: A Novel Molecular Marker Predicts Progression of Superficial (TA and T1) Urothelial Carcinomas of Bladder

2007 ◽  
Vol 177 (4S) ◽  
pp. 78-79
Author(s):  
Lioudmila Sitnikova ◽  
Gary Mendese ◽  
Qin Lui ◽  
Bruce A. Woda ◽  
Di Lu ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Urothelial Carcinomas

Author response for "Inhibition of osteoclastogenesis by the RNA‐binding protein QKI5: a novel approach to protect from bone resorption"

2019 ◽  
Author(s):  
Benjamin Rauwel ◽  
Yannick Degboe ◽  
Katy Diallo ◽  
Souraya Sayegh ◽  
Michel Baron ◽  
...  
Keyword(s):  
Bone Resorption ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Author Response ◽  
Novel Approach

The RNA-binding protein Musashi-2 (MSI2) controls mRNA processing and translational regulation via interactions with SFPQ and PIWIL1 during mammalian spermatogenesis

2014 ◽  
Author(s):  
Jessie M Sutherland ◽  
Alexander P Sobinoff ◽  
Kate Redgrove ◽  
Tara-Lynne Davidson ◽  
Nicole A Siddall ◽  
...  
Keyword(s):  
Translational Regulation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mrna Processing
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