Characterization of the flamenco Region of the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 701-713 ◽  
Author(s):  
Valérie Robert ◽  
Nicole Prud’homme ◽  
Alexander Kim ◽  
Alain Bucheton ◽  
Alain Pélisson
Keyword(s):  
Genomic Dna ◽  
Distal Part ◽  
Rna Binding ◽  
Insertion Site ◽  
Endogenous Retrovirus ◽  
P Element ◽  
Insertion Point ◽  
Double Stranded Rna ◽  
Binding Domains

Abstract The flamenco gene, located at 20A1-3 in the β-heterochromatin of the Drosophila X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. As a first step to characterize this gene, ∼100 kb of genomic DNA flanking a P-element-induced mutation of flamenco was isolated. This DNA is located in a sequencing gap of the Celera Genomics project, i.e., one of those parts of the genome in which the “shotgun” sequence could not be assembled, probably because it contains long stretches of repetitive DNA, especially on the proximal side of the P insertion point. Deficiency mapping indicated that sequences required for the normal flamenco function are located >130 kb proximal to the insertion site. The distal part of the cloned DNA does, nevertheless, contain several unique sequences, including at least four different transcription units. Dip1, the closest one to the P-element insertion point, might be a good candidate for a gypsy regulator, since it putatively encodes a nuclear protein containing two double-stranded RNA-binding domains. However, transgenes containing dip1 genomic DNA were not able to rescue flamenco mutant flies. The possible nature of the missing flamenco sequences is discussed.

scholarly journals Conformational dynamics at microsecond timescale in the RNA-binding regions of dsRNA-binding domains

2019 ◽  
Author(s):  
H Paithankar ◽  
J Chugh
Keyword(s):  
Rna Binding ◽  
Conformational Dynamics ◽  
Relaxation Dispersion ◽  
Striking Similarity ◽  
Detailed Characterization ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Binding Regions ◽  
Rna Binding Domains

AbstractDouble-stranded RNA-binding domains (dsRBDs) are involved in a variety of biological functions via recognition and processing of dsRNAs. Though the primary substrate of the dsRBDs are dsRNAs with A-form helical geometry; they are known to interact with structurally diverse dsRNAs. Here, we have employed two model dsRBDs – TAR-RNA binding protein and Adenosine deaminase that acts on RNA – to understand the role of intrinsic protein dynamics in RNA binding. We have performed a detailed characterization of the residue-level dynamics by NMR spectroscopy for the two dsRBDs. While the dynamics profiles at the ps-ns timescale of the two dsRBDs were found to be different, a striking similarity was observed in the μs-ms timescale dynamics for both the dsRBDs. Motions at fast μs timescale (kex > 50000 s−1) were found to be present not only in the RNA-binding residues but also in some allosteric residues of the dsRBDs. We propose that this intrinsic μs timescale dynamics observed independently in two distinct dsRBDs allows them to undergo conformational rearrangement that may aid dsRBDs to target substrate dsRNA from the pool of structurally different RNAs in cellular environment.Statement of SignificanceThis study reports for the first time the detailed characterization of microsecond timescale dynamics observed in RNA-binding regions of two distinct double-stranded RNA-binding domains (dsRBDs) using NMR relaxation dispersion experiments. dsRBDs have been known to target topologically distinct dsRNAs. However, the mechanistic details of the structural adaptation of proteins is not fully understood. We propose that the presence of such dynamics may have large-scale implications in understanding the RNA recognition mechanisms by the dsRBDs.

scholarly journals RNA Helicase A Regulates the Replication of RNA Viruses

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 361
Author(s):  
Rui-Zhu Shi ◽  
Yuan-Qing Pan ◽  
Li Xing
Keyword(s):  
Virus Replication ◽  
Rna Binding ◽  
Rna Viruses ◽  
Rna Helicase ◽  
Rna Helicase A ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
N Terminus

The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

scholarly journals The Mutant Phenotype Associated With P-Element Alleles of the vestigial Locus in Drosophila melanogaster May Be Caused by a Readthrough Transcript Initiated at the P-Element Promoter

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1665-1672 ◽  
Author(s):  
Ross B Hodgetts ◽  
Sandra L O'Keefe
Keyword(s):  
Rna Secondary Structure ◽  
Insertion Site ◽  
Large Body ◽  
P Element ◽  
Wild Type ◽  
Subtle Difference ◽  
Pronounced Difference ◽  
Internal Repeat ◽  
Mutant Phenotypes

Abstract We report here the isolation of a new P-element-induced allele of the vestigial locus vg2a33, the molecular characterization of which allows us to propose a unifying explanation of the phenotypes of the large number of vestigial P-element alleles that now exists. The first P-element allele of vestigial to be isolated was vg21, which results in a very weak mutant wing phenotype that is suppressed in the P cytotype. By destabilizing vg2a33 in a dysgenic cross, we isolated the vg2a33 allele, which exhibits a moderate mutant wing phenotype and is not suppressed by the P cytotype. The new allele is characterized by a 46-bp deletion that removes the 3′-proximal copy of the 11-bp internal repeat from the P element of vg21. To understand how this subtle difference between the two alleles leads to a rather pronounced difference in their phenotypes, we mapped both the vg and P-element transcription units present in wild type and mutants. Using both 5′-RACE and S1 protection, we found that P-element transcription is initiated 19 bp farther upstream than previously thought. Using primer extension, the start of vg transcription was determined to lie 435 bp upstream of the longest cDNA recovered to date and upstream of the P-element insertion site. Our discovery that the P element is situated within the first vg exon has prompted a reassessment of the large body of genetic data on a series of alleles derived from vg21. Our current hypothesis to explain the degree of variation in the mutant phenotypes and their response to the P repressor invokes a critical RNA secondary structure in the vg transcript, the formation of which is hindered by a readthrough transcript initiated at the P-element promoter.

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 Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures

2021 ◽  
Author(s):  
Christine Roden ◽  
Yifan Dai ◽  
Ian Seim ◽  
Myungwoon Lee ◽  
Rachel Sealfon ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Structure ◽  
Nucleocapsid Protein ◽  
Rna Binding ◽  
Genome Packaging ◽  
Rna Motifs ◽  
Double Stranded Rna ◽  
N Protein ◽  
Binding Domains

Betacoronavirus SARS-CoV-2 infections caused the global Covid-19 pandemic. The nucleocapsid protein (N-protein) is required for multiple steps in the betacoronavirus replication cycle. SARS-CoV-2-N-protein is known to undergo liquid-liquid phase separation (LLPS) with specific RNAs at particular temperatures to form condensates. We show that N-protein recognizes at least two separate and distinct RNA motifs, both of which require double-stranded RNA (dsRNA) for LLPS. These motifs are separately recognized by N-protein's two RNA binding domains (RBDs). Addition of dsRNA accelerates and modifies N-protein LLPS in vitro and in cells and controls the temperature condensates form. The abundance of dsRNA tunes N-protein-mediated translational repression and may confer a switch from translation to genome packaging. Thus, N-protein's two RBDs interact with separate dsRNA motifs, and these interactions impart distinct droplet properties that can support multiple viral functions. These experiments demonstrate a paradigm of how RNA structure can control the properties of biomolecular condensates.

scholarly journals Double-stranded RNA-activated protein kinase PKR of fishes and amphibians: Varying the number of double-stranded RNA binding domains and lineage-specific duplications

BMC Biology ◽  
2008 ◽  
Vol 6 (1) ◽  
Author(s):  
Stefan Rothenburg ◽  
Nikolaus Deigendesch ◽  
Madhusudan Dey ◽  
Thomas E Dever ◽  
Loubna Tazi
Keyword(s):  
Protein Kinase ◽  
Rna Binding ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Rna Binding Domains

scholarly journals RNA-Regulated Interaction of Transportin-1 and Exportin-5 with the Double-Stranded RNA-Binding Domain Regulates Nucleocytoplasmic Shuttling of ADAR1

2009 ◽  
Vol 29 (6) ◽  
pp. 1487-1497 ◽  
Author(s):  
Jutta Fritz ◽  
Alexander Strehblow ◽  
Andreas Taschner ◽  
Sandy Schopoff ◽  
Pawel Pasierbek ◽  
...  
Keyword(s):  
Nuclear Export ◽  
Rna Binding ◽  
Nuclear Export Signal ◽  
Nucleocytoplasmic Transport ◽  
Nucleocytoplasmic Shuttling ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Dsrna Binding ◽  
Localization Signal ◽  
Editing Enzyme

ABSTRACT Double-stranded RNA (dsRNA)-binding proteins interact with substrate RNAs via dsRNA-binding domains (dsRBDs). Several proteins harboring these domains exhibit nucleocytoplasmic shuttling and possibly remain associated with their substrate RNAs bound in the nucleus during nuclear export. In the human RNA-editing enzyme ADAR1-c, the nuclear localization signal overlaps the third dsRBD, while the corresponding import factor is unknown. The protein also lacks a clear nuclear export signal but shuttles between the nucleus and the cytoplasm. Here we identify transportin-1 as the import receptor for ADAR1. Interestingly, dsRNA binding interferes with transportin-1 binding. At the same time, each of the dsRBDs in ADAR1 interacts with the export factor exportin-5. RNA binding stimulates this interaction but is not a prerequisite. Thus, our data demonstrate a role for some dsRBDs as RNA-sensitive nucleocytoplasmic transport signals. dsRBD3 in ADAR1 can mediate nuclear import, while interaction of all dsRBDs might control nuclear export. This finding may have implications for other proteins containing dsRBDs and suggests a selective nuclear export mechanism for substrates interacting with these proteins.

scholarly journals Recognition of viral RNA stem-loops by the tandem double-stranded RNA binding domains of PKR

RNA ◽  
2013 ◽  
Vol 19 (3) ◽  
pp. 333-344 ◽  
Author(s):  
E. Dzananovic ◽  
T. R. Patel ◽  
S. Deo ◽  
K. McEleney ◽  
J. Stetefeld ◽  
...  
Keyword(s):  
Rna Binding ◽  
Viral Rna ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Rna Binding Domains

scholarly journals The N-Terminal Double-Stranded RNA Binding Domains of Arabidopsis HYPONASTIC LEAVES1 Are Sufficient for Pre-MicroRNA Processing

2007 ◽  
Vol 19 (3) ◽  
pp. 914-925 ◽  
Author(s):  
Feijie Wu ◽  
Lin Yu ◽  
Wenguang Cao ◽  
Yanfei Mao ◽  
Zhongyuan Liu ◽  
...  
Keyword(s):  
Rna Binding ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Microrna Processing ◽  
Rna Binding Domains

scholarly journals RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence

2012 ◽  
Author(s):  
Grégoire Masliah ◽  
Pierre Barraud ◽  
Frédéric H. -T. Allain
Keyword(s):  
Rna Binding ◽  
Rna Recognition ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
Rna Binding Domains
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