scholarly journals Double Stranded RNA Binding Proteins in the Serum Contribute to Systemic RNAi across Phyla – Towards Finding the Missing Link in Achelata

2020 ◽  
Author(s):  
Thomas Banks ◽  
Tianfang Wang ◽  
Quinn Fitzgibbon ◽  
Gregory Smith ◽  
Tomer Ventura
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Limiting Factor ◽  
Mobility Shift ◽  
Double Stranded Rna ◽  
Dsrna Binding ◽  
Spiny Lobsters ◽  
Systemic Rnai ◽  
Gel Mobility Shift

RNA interference (RNAi) has become a widely utilised method to study gene function, yet despite this, many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi, and may be the limiting factor in RNAi capacity for species such as spiny lobsters where gene silencing is not functional. Incubating serum from a variety of species across phyla with dsRNA led to a gel mobility shift in species where systemic RNAi has been observed, with this response being absent in species where systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon, and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters, and better understanding the mechanisms of systemic RNAi in Crustacea, as well as across phyla.

scholarly journals Double-Stranded RNA Binding Proteins in Serum Contribute to Systemic RNAi Across Phyla—Towards Finding the Missing Link in Achelata

2020 ◽  
Vol 21 (18) ◽  
pp. 6967
Author(s):  
Thomas M. Banks ◽  
Tianfang Wang ◽  
Quinn P. Fitzgibbon ◽  
Gregory G. Smith ◽  
Tomer Ventura
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Limiting Factor ◽  
Mobility Shift ◽  
Double Stranded Rna ◽  
Dsrna Binding ◽  
Spiny Lobsters ◽  
Systemic Rnai ◽  
Gel Mobility Shift

RNA interference (RNAi) has become a widely utilized method for studying gene function, yet despite this many of the mechanisms surrounding RNAi remain elusive. The core RNAi machinery is relatively well understood, however many of the systemic mechanisms, particularly double-stranded RNA (dsRNA) transport, are not. Here, we demonstrate that dsRNA binding proteins in the serum contribute to systemic RNAi and may be the limiting factor in RNAi capacity for species such as spiny lobsters, where gene silencing is not functional. Incubating sera from a variety of species across phyla with dsRNA led to a gel mobility shift in species in which systemic RNAi has been observed, with this response being absent in species in which systemic RNAi has never been observed. Proteomic analysis suggested lipoproteins may be responsible for this phenomenon and may transport dsRNA to spread the RNAi signal systemically. Following this, we identified the same gel shift in the slipper lobster Thenus australiensis and subsequently silenced the insulin androgenic gland hormone, marking the first time RNAi has been performed in any lobster species. These results pave the way for inducing RNAi in spiny lobsters and for a better understanding of the mechanisms of systemic RNAi in Crustacea, as well as across phyla.

scholarly journals Exportin-5, a novel karyopherin, mediates nuclear export of double-stranded RNA binding proteins

2002 ◽  
Vol 156 (1) ◽  
pp. 53-64 ◽  
Author(s):  
Amy M. Brownawell ◽  
Ian G. Macara
Keyword(s):  
Nuclear Export ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Dependent Manner ◽  
Intact Cells ◽  
Double Stranded Rna ◽  
Permeabilized Cells ◽  
Dsrna Binding ◽  
Rna Export

We have identified a novel human karyopherin (Kap)β family member that is related to human Crm1 and the Saccharomyces cerevisiae protein, Msn5p/Kap142p. Like other known transport receptors, this Kap binds specifically to RanGTP, interacts with nucleoporins, and shuttles between the nuclear and cytoplasmic compartments. We report that interleukin enhancer binding factor (ILF)3, a double-stranded RNA binding protein, associates with this Kap in a RanGTP-dependent manner and that its double-stranded RNA binding domain (dsRBD) is the limiting sequence required for this interaction. Importantly, the Kap interacts with dsRBDs found in several other proteins and binding is blocked by double-stranded RNA. We find that the dsRBD of ILF3 functions as a novel nuclear export sequence (NES) in intact cells, and its ability to serve as an NES is dependent on the expression of the Kap. In digitonin-permeabilized cells, the Kap but not Crm1 stimulated nuclear export of ILF3. Based on the ability of this Kap to mediate the export of dsRNA binding proteins, we named the protein exportin-5. We propose that exportin-5 is not an RNA export factor but instead participates in the regulated translocation of dsRBD proteins to the cytoplasm where they interact with target mRNAs.

Characterization of Viral Double-Stranded RNA-Binding Proteins

Methods ◽  
1998 ◽  
Vol 15 (3) ◽  
pp. 225-232 ◽  
Author(s):  
Bertram L. Jacobs ◽  
Jeffrey O. Langland ◽  
Teresa Brandt
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Double Stranded Rna

scholarly journals Identification of cis Elements Directing Termination of Yeast Nonpolyadenylated snoRNA Transcripts

2004 ◽  
Vol 24 (14) ◽  
pp. 6241-6252 ◽  
Author(s):  
Kristina L. Carroll ◽  
Dennis A. Pradhan ◽  
Josh A. Granek ◽  
Neil D. Clarke ◽  
Jeffry L. Corden
Keyword(s):  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Large Degree ◽  
Sequence Motifs ◽  
Mobility Shift ◽  
Nascent Transcript ◽  
Pol Ii ◽  
Gel Mobility Shift

ABSTRACT RNA polymerase II (Pol II) termination is triggered by sequences present in the nascent transcript. Termination of pre-mRNA transcription is coupled to recognition of cis-acting sequences that direct cleavage and polyadenylation of the pre-mRNA. Termination of nonpolyadenylated [non-poly(A)] Pol II transcripts in Saccharomyces cerevisiae requires the RNA-binding proteins Nrd1 and Nab3. We have used a mutational strategy to characterize non-poly(A) termination elements downstream of the SNR13 and SNR47 snoRNA genes. This approach detected two common RNA sequence motifs, GUA[AG] and UCUU. The first motif corresponds to the known Nrd1-binding site, which we have verified here by gel mobility shift assays. We also show that Nab3 protein binds specifically to RNA containing the UCUU motif. Taken together, our data suggest that Nrd1 and Nab3 binding sites play a significant role in defining non-poly(A) terminators. As is the case with poly(A) terminators, there is no strong consensus for non-poly(A) terminators, and the arrangement of Nrd1p and Nab3p binding sites varies considerably. In addition, the organization of these sequences is not strongly conserved among even closely related yeasts. This indicates a large degree of genetic variability. Despite this variability, we were able to use a computational model to show that the binding sites for Nrd1 and Nab3 can identify genes for which transcription termination is mediated by these proteins.

Double-stranded RNA-binding Proteins and the Control of Protein Synthesis and Cell Growth

2001 ◽  
Vol 66 (0) ◽  
pp. 485-498 ◽  
Author(s):  
L.M. PARKER ◽  
I. FIERRO-MONTI ◽  
T.W. REICHMAN ◽  
S. GUNNERY ◽  
M.B. MATHEWS
Keyword(s):  
Protein Synthesis ◽  
Cell Growth ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Double Stranded Rna

scholarly journals Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins

Biochemistry ◽  
2014 ◽  
Vol 53 (21) ◽  
pp. 3457-3466 ◽  
Author(s):  
Lela Vuković ◽  
Hye Ran Koh ◽  
Sua Myong ◽  
Klaus Schulten
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Substrate Recognition ◽  
Double Stranded Rna

scholarly journals Know Thyself: RIG-I-Like Receptor Sensing of DNA Virus Infection

2019 ◽  
Vol 93 (23) ◽  
Author(s):  
Yang Zhao ◽  
John Karijolich
Keyword(s):  
Virus Infection ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Virus ◽  
Intrinsic Immunity ◽  
Dna Virus ◽  
Double Stranded Rna ◽  
Recent Advances

ABSTRACT The RIG-I-like receptors (RLRs) are double-stranded RNA-binding proteins that play a role in initiating and modulating cell intrinsic immunity through the recognition of RNA features typically absent from the host transcriptome. While they are initially characterized in the context of RNA virus infection, evidence has now accumulated establishing the role of RLRs in DNA virus infection. Here, we review recent advances in the RLR-mediated restriction of DNA virus infection with an emphasis on the RLR ligands sensed.

scholarly journals Dynamic profiling of double-stranded RNA binding proteins

2015 ◽  
Vol 43 (15) ◽  
pp. 7566-7576 ◽  
Author(s):  
Xinlei Wang ◽  
Lela Vukovic ◽  
Hye Ran Koh ◽  
Klaus Schulten ◽  
Sua Myong
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Double Stranded Rna ◽  
Dynamic Profiling
Sign in / Sign up

Export Citation Format

Share Document