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.

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.

scholarly journals An mRNA silencing mechanism reliant on the cooperation between REGE-1/Regnase-1 and RLE-1/Roquin-1

2021 ◽  
Author(s):  
Daria Sobanska ◽  
Alicja A Komur ◽  
Agnieszka Chabowska-Kita ◽  
Julita Gumna ◽  
Pooja Kumari ◽  
...  
Keyword(s):  
Functional Relationship ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
The Other ◽  
Immune Homeostasis ◽  
C Elegans ◽  
Evolutionarily Conserved ◽  
Competing Models

Regnase-1 is an evolutionarily conserved endoribonuclease, degrading diverse mRNAs important, among others, for immune homeostasis, development, and cancer. There are two competing models of Regnase-1 mediated mRNA silencing. One model postulates that Regnase-1 works together with another RNA-binding protein, Roquin-1. The other model proposes that the two proteins function separately. Studying the C. elegans Regnase-1 ortholog, REGE-1, we have uncovered a functional relationship between REGE-1 and the nematode counterpart of Roquin-1, RLE-1. While REGE-1 and RLE-1 associate with mRNA independently of each other, both proteins are essential for mRNA silencing. Intriguingly, the functional interdependence between REGE-1 and RLE-1 is reminiscent of the proposed cooperation between mammalian Regnase-1 and Roquin-1, which may underlie a prototypic silencing mechanism involving both proteins.

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 Evolutionarily Conserved Polyadenosine RNA Binding Protein Nab2 Cooperates with Splicing Machinery To Regulate the Fate of Pre-mRNA

2016 ◽  
Vol 36 (21) ◽  
pp. 2697-2714 ◽  
Author(s):  
Sharon Soucek ◽  
Yi Zeng ◽  
Deepti L. Bellur ◽  
Megan Bergkessel ◽  
Kevin J. Morris ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Tail Length ◽  
Mrna Processing ◽  
Evolutionarily Conserved ◽  
Mrna Maturation

Numerous RNA binding proteins are deposited onto an mRNA transcript to modulate posttranscriptional processing events ensuring proper mRNA maturation. Defining the interplay between RNA binding proteins that couple mRNA biogenesis events is crucial for understanding how gene expression is regulated. To explore how RNA binding proteins control mRNA processing, we investigated a role for the evolutionarily conserved polyadenosine RNA binding protein, Nab2, in mRNA maturation within the nucleus. This study reveals thatnab2mutant cells accumulate intron-containing pre-mRNAin vivo. We extend this analysis to identify genetic interactions between mutant alleles ofnab2and genes encoding a splicing factor,MUD2, and RNA exosome,RRP6, within vivoconsequences of altered pre-mRNA splicing and poly(A) tail length control. As further evidence linking Nab2 proteins to splicing, an unbiased proteomic analysis of vertebrate Nab2, ZC3H14, identifies physical interactions with numerous components of the spliceosome. We validated the interaction between ZC3H14 and U2AF2/U2AF65. Taking all the findings into consideration, we present a model where Nab2/ZC3H14 interacts with spliceosome components to allow proper coupling of splicing with subsequent mRNA processing steps contributing to a kinetic proofreading step that allows properly processed mRNA to exit the nucleus and escape Rrp6-dependent degradation.

scholarly journals The evolutionarily conserved RNA binding protein SMOOTH is essential for maintaining normal muscle function

Fly ◽  
2009 ◽  
Vol 3 (4) ◽  
pp. 235-246 ◽  
Author(s):  
Isabelle Draper ◽  
Meg E. Tabaka ◽  
F. Rob Jackson ◽  
Robert N. Salomon ◽  
Alan Kopin
Keyword(s):  
Muscle Function ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Normal Muscle ◽  
Evolutionarily Conserved
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