In vitro evidence for RNA binding properties of the coat protein of prunus necrotic ringspot ilarvirus and their comparison to related and unrelated viruses

1999 ◽  
Vol 144 (4) ◽  
pp. 797-803 ◽  
Author(s):  
V. Pallás ◽  
J. A. Sánchez-Navarro ◽  
J. Díez
Keyword(s):  
Coat Protein ◽  
Rna Binding ◽  
Binding Properties

Detection and in vitro studies of Cucurbita maxima phloem serpin-1 RNA-binding properties

Biochimie ◽  
2020 ◽  
Vol 170 ◽  
pp. 118-127 ◽  
Author(s):  
Eugeny A. Tolstyko ◽  
Alexander A. Lezzhov ◽  
Anna V. Pankratenko ◽  
Marina V. Serebryakova ◽  
Andrey G. Solovyev ◽  
...  
Keyword(s):  
Rna Binding ◽  
In Vitro Studies ◽  
Cucurbita Maxima ◽  
Binding Properties

scholarly journals General and Target-Specific RNA Binding Properties of Epstein-Barr Virus SM Posttranscriptional Regulatory Protein

2009 ◽  
Vol 83 (22) ◽  
pp. 11635-11644 ◽  
Author(s):  
Zhao Han ◽  
Dinesh Verma ◽  
Chelsey Hilscher ◽  
Dirk P. Dittmer ◽  
Sankar Swaminathan
Keyword(s):  
Gene Expression ◽  
Nuclear Export ◽  
Epstein Barr Virus ◽  
Rna Binding ◽  
Regulatory Protein ◽  
Lytic Cycle ◽  
Binding Properties ◽  
Barr Virus ◽  
Epstein Barr

ABSTRACT Epstein-Barr virus (EBV) SM protein is an essential nuclear shuttling protein expressed by EBV early during the lytic phase of replication. SM acts to increase EBV lytic gene expression by binding EBV mRNAs and enhancing accumulation of the majority of EBV lytic cycle mRNAs. SM increases target mRNA stability and nuclear export, in addition to modulating RNA splicing. SM and its homologs in other herpesvirus have been hypothesized to function in part by binding viral RNAs and recruiting cellular export factors. Although activation of gene expression by SM is gene specific, it is unknown whether SM binds to mRNA in a specific manner or whether its RNA binding is target independent. SM-mRNA complexes were isolated from EBV-infected B-lymphocyte cell lines induced to permit lytic EBV replication, and a quantitative measurement of mRNAs corresponding to all known EBV open reading frames was performed by real-time quantitative reverse transcription-PCR. The results showed that although SM has broad RNA binding properties, there is a clear hierarchy of affinities among EBV mRNAs with respect to SM complex formation. In vitro binding assays with two of the most highly SM-associated transcripts suggested that SM binds preferentially to specific sequences or structures present in noncoding regions of some EBV mRNAs. Furthermore, the presence of these sequences conferred responsiveness to SM. These data are consistent with a mechanism of action similar to that of hnRNPs, which exert sequence-specific effects on gene expression despite having multiple degenerate consensus binding sites common to a large number of RNAs.

scholarly journals Multifunctional Roles for the N-Terminal Basic Motif of Alfalfa mosaic virus Coat Protein: Nucleolar/Cytoplasmic Shuttling, Modulation of RNA-Binding Activity, and Virion Formation

2012 ◽  
Vol 25 (8) ◽  
pp. 1093-1103 ◽  
Author(s):  
Mari Carmen Herranz ◽  
Vicente Pallas ◽  
Frederic Aparicio
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
Nuclear Export ◽  
Rna Binding ◽  
Nuclear Export Signal ◽  
Alfalfa Mosaic Virus ◽  
Binding Activity ◽  
Systemic Movement ◽  
Virion Formation

In addition to virion formation, the coat protein (CP) of Alfalfa mosaic virus (AMV) is involved in the regulation of replication and translation of viral RNAs, and in cell-to-cell and systemic movement of the virus. An intriguing feature of the AMV CP is its nuclear and nucleolar accumulation. Here, we identify an N-terminal lysine-rich nucleolar localization signal (NoLS) in the AMV CP required to both enter the nucleus and accumulate in the nucleolus of infected cells, and a C-terminal leucine-rich domain which might function as a nuclear export signal. Moreover, we demonstrate that AMV CP interacts with importin-α, a component of the classical nuclear import pathway. A mutant AMV RNA 3 unable to target the nucleolus exhibited reduced plus-strand RNA synthesis and cell-to-cell spread. Moreover, virion formation and systemic movement were completely abolished in plants infected with this mutant. In vitro analysis demonstrated that specific lysine residues within the NoLS are also involved in modulating CP-RNA binding and CP dimerization, suggesting that the NoLS represents a multifunctional domain within the AMV CP. The observation that nuclear and nucleolar import signals mask RNA-binding properties of AMV CP, essential for viral replication and translation, supports a model in which viral expression is carefully modulated by a cytoplasmic/nuclear balance of CP accumulation.

scholarly journals Induction of Particle Polymorphism by Cucumber Necrosis Virus Coat Protein Mutants In Vivo

2007 ◽  
Vol 82 (3) ◽  
pp. 1547-1557 ◽  
Author(s):  
Kishore Kakani ◽  
Ron Reade ◽  
Umesh Katpally ◽  
Thomas Smith ◽  
D'Ann Rochon
Keyword(s):  
Coat Protein ◽  
Rna Binding ◽  
In Planta ◽  
Necrosis Virus ◽  
Protein Mutants ◽  
Cucumber Necrosis Virus ◽  
Virus Coat ◽  
R Domain

ABSTRACT The Cucumber necrosis virus (CNV) particle is a T=3 icosahedron consisting of 180 identical coat protein (CP) subunits. Plants infected with wild-type CNV accumulate a high number of T=3 particles, but other particle forms have not been observed. Particle polymorphism in several T=3 icosahedral viruses has been observed in vitro following the removal of an extended N-terminal region of the CP subunit. In the case of CNV, we have recently described the structure of T=1 particles that accumulate in planta during infection by a CNV mutant (R1+2) in which a large portion of the N-terminal RNA binding domain (R-domain) has been deleted. In this report we further describe properties of this mutant and other CP mutants that produce polymorphic particles. The T=1 particles produced by R1+2 mutants were found to encapsidate a 1.9-kb RNA species as well as smaller RNA species that are similar to previously described CNV defective interfering RNAs. Other R-domain mutants were found to encapsidate a range of specifically sized less-than-full-length CNV RNAs. Mutation of a conserved proline residue in the arm domain near its junction with the shell domain also influenced T=1 particle formation. The proportion of polymorphic particles increased when the mutation was incorporated into R-domain deletion mutants. Our results suggest that both the R-domain and the arm play important roles in the formation of T=3 particles. In addition, the encapsidation of specific CNV RNA species by individual mutants indicates that the R-domain plays a role in the nature of CNV RNA encapsidated in particles.

scholarly journals Potato virus X RNA-mediated assembly of single-tailed ternary ‘coat protein–RNA–movement protein’ complexes

2006 ◽  
Vol 87 (9) ◽  
pp. 2731-2740 ◽  
Author(s):  
O. V. Karpova ◽  
O. V. Zayakina ◽  
M. V. Arkhipenko ◽  
E. V. Sheval ◽  
O. I. Kiselyova ◽  
...  
Keyword(s):  
Coat Protein ◽  
Potato Virus ◽  
Rna Binding ◽  
Movement Protein ◽  
Infected Plant ◽  
Potato Virus X ◽  
Translation System ◽  
Transport Form

Different models have been proposed for the nature of the potexvirus transport form that moves from cell to cell over the infected plant: (i) genomic RNA moves as native virions; or (ii) in vitro-assembled non-virion ribonucleoprotein (RNP) complexes consisting of viral RNA, coat protein (CP) and movement protein (MP), termed TGBp1, serve as the transport form in vivo. As the structure of these RNPs has not been elucidated, the products assembled in vitro from potato virus X (PVX) RNA, CP and TGBp1 were characterized. The complexes appeared as single-tailed particles (STPs) with a helical, head-like structure composed of CP subunits located at the 5′-proximal region of PVX RNA; the TGBp1 was bound to the terminal CP molecules of the head. Remarkably, no particular non-virion RNP complexes were observed. These data suggest that the CP–RNA interactions resulting in head formation prevailed over TGBp1–RNA binding upon STP assembly from RNA, CP and TGBp1. STPs could be assembled from the 5′ end of PVX RNA and CP in the absence of TGBp1. The translational ability of STPs was characterized in a cell-free translation system. STPs lacking TGBp1 were entirely non-translatable; however, they were rendered translatable by binding of TGBp1 to the end of the head. It is suggested that the RNA-mediated assembly of STPs proceeds via two steps. Firstly, non-translatable CP–RNA STPs are produced, due to encapsidation of the 5′-terminal region. Secondly, the TGBp1 molecules bind to the end of a polar head, resulting in conversion of the STPs into a translatable form.

Determinants of ELAV gene-specific regulation

2010 ◽  
Vol 38 (4) ◽  
pp. 1122-1124 ◽  
Author(s):  
Matthias Soller ◽  
Min Li ◽  
Irmgard U. Haussmann
Keyword(s):  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Properties ◽  
Cellular Environment ◽  
Hu Proteins ◽  
Specific Regulation ◽  
Abnormal Visual ◽  
Major Target

How RNA-binding proteins recognize their complement of targets in a complex cellular environment remains poorly understood. Sequence degeneracy and redundancy of short motifs at genomic scales have mostly eluded predictions of specific target genes for gene-specific ELAV (embryonic lethal abnormal visual system)/Hu proteins that bind ubiquitous AU-rich motifs. Using the genetic tools of Drosophila, we have analysed binding properties of ELAV in vitro and ELAV-dependent regulation of its major target ewg (erect wing) in neurons. These studies reveal that an integral part of ELAV gene-specific regulation involves combinatorial binding to variably spaced short U-rich motifs on an extensive binding site.

scholarly journals Protein–protein- and protein–RNA-binding properties of the movement protein and VP25 coat protein of Apple latent spherical virus

Virology ◽  
2006 ◽  
Vol 352 (1) ◽  
pp. 178-187 ◽  
Author(s):  
Masamichi Isogai ◽  
Kentaro Watanabe ◽  
Yusuke Uchidate ◽  
Nobuyuki Yoshikawa
Keyword(s):  
Coat Protein ◽  
Rna Binding ◽  
Movement Protein ◽  
Binding Properties ◽  
Apple Latent Spherical Virus

scholarly journals In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule

2020 ◽  
Vol 48 (4) ◽  
pp. 1669-1680 ◽  
Author(s):  
Sougata Dey ◽  
Jonathan T Sczepanski
Keyword(s):  
In Vitro Selection ◽  
Rna Binding ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
Binding Properties ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Selection Of

Abstract The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.

scholarly journals RNA-Binding Properties and Translation Repression In Vitro by Germ Cell-Specific MSY2 Protein1

2002 ◽  
Vol 67 (4) ◽  
pp. 1093-1098 ◽  
Author(s):  
Junying Yu ◽  
Norman B. Hecht ◽  
Richard M. Schultz
Keyword(s):  
Germ Cell ◽  
Rna Binding ◽  
Binding Properties ◽  
Translation Repression
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