scholarly journals Genome Recognition by MYC

2014 ◽  
Vol 4 (2) ◽  
pp. a014191-a014191 ◽  
Author(s):  
A. Sabo ◽  
B. Amati
Keyword(s):  
Genome Recognition

scholarly journals Multiple capsid protein binding sites mediate selective packaging of the alphavirus genomic RNA

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Rebecca S. Brown ◽  
Dimitrios G. Anastasakis ◽  
Markus Hafner ◽  
Margaret Kielian
Keyword(s):  
Capsid Protein ◽  
Binding Sites ◽  
Semliki Forest Virus ◽  
Virus Assembly ◽  
Genomic Rna ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Genome Recognition ◽  
Infected Cells

Abstract The alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, here we comprehensively define binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrate Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments show that PS is not required for production of infectious SFV or Chikungunya virus. Instead, we identify multiple Cp binding sites that are enriched on gRNA-specific regions and promote infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrate that budding causes discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site is maintained throughout virus assembly, and specifically binds and assembles with Cp into core-like particles in vitro. Together our data suggest a model for selective alphavirus genome recognition and assembly.

scholarly journals The Role of the Stem-Loop A RNA Promoter in Flavivirus Replication

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1107
Author(s):  
Kyung H. Choi
Keyword(s):  
Viral Genome ◽  
Rna Synthesis ◽  
Current Model ◽  
Viral Rna ◽  
Genome Replication ◽  
Stem Loop ◽  
Genome Recognition ◽  
Rna Genome ◽  
Long Stem ◽  
Rna Promoter

An essential challenge in the lifecycle of RNA viruses is identifying and replicating the viral genome amongst all the RNAs present in the host cell cytoplasm. Yet, how the viral polymerase selectively recognizes and copies the viral RNA genome is poorly understood. In flaviviruses, the 5′-end of the viral RNA genome contains a 70 nucleotide-long stem-loop, called stem-loop A (SLA), which functions as a promoter for genome replication. During replication, flaviviral polymerase NS5 specifically recognizes SLA to both initiate viral RNA synthesis and to methylate the 5′ guanine cap of the nascent RNA. While the sequences of this region vary between different flaviviruses, the three-way junction arrangement of secondary structures is conserved in SLA, suggesting that viruses recognize a common structural feature to replicate the viral genome rather than a particular sequence. To better understand the molecular basis of genome recognition by flaviviruses, we recently determined the crystal structures of flavivirus SLAs from dengue virus (DENV) and Zika virus (ZIKV). In this review, I will provide an overview of (1) flaviviral genome replication; (2) structures of viral SLA promoters and NS5 polymerases; and (3) and describe our current model of how NS5 polymerases specifically recognize the SLA at the 5′ terminus of the viral genome to initiate RNA synthesis at the 3′ terminus.

Stem-loop SL4 of the HIV-1 Ψ RNA packaging signal exhibits weak affinity for the nucleocapsid protein. structural studies and implications for genome recognition

2001 ◽  
Vol 314 (5) ◽  
pp. 961-970 ◽  
Author(s):  
Gaya K. Amarasinghe ◽  
Jing Zhou ◽  
Matthew Miskimon ◽  
Kalola J. Chancellor ◽  
Jasmine A. McDonald ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Structural Studies ◽  
Rna Packaging ◽  
Packaging Signal ◽  
Stem Loop ◽  
Genome Recognition ◽  
Rna Packaging Signal ◽  
Hiv 1

scholarly journals Multiple Capsid Protein Binding Sites Mediate Selective Packaging of the Alphavirus Genomic RNA

2020 ◽  
Author(s):  
Rebecca S. Brown ◽  
Dimitrios G. Anastasakis ◽  
Markus Hafner ◽  
Margaret Kielian
Keyword(s):  
Capsid Protein ◽  
Binding Sites ◽  
Semliki Forest Virus ◽  
Virus Assembly ◽  
Genomic Rna ◽  
Packaging Signal ◽  
Genome Packaging ◽  
Genome Recognition ◽  
Infected Cells

ABSTRACTThe alphavirus capsid protein (Cp) selectively packages genomic RNA (gRNA) into the viral nucleocapsid to produce infectious virus. Using photoactivatable ribonucleoside crosslinking and an innovative biotinylated Cp retrieval method, we comprehensively defined binding sites for Semliki Forest virus (SFV) Cp on the gRNA. While data in infected cells demonstrated Cp binding to the proposed genome packaging signal (PS), mutagenesis experiments showed that PS was not required for production of infectious SFV or Chikungunya virus. Instead, we identified multiple novel Cp binding sites that were enriched on gRNA-specific regions and promoted infectious SFV production and gRNA packaging. Comparisons of binding sites in cytoplasmic vs. viral nucleocapsids demonstrated that budding caused discrete changes in Cp-gRNA interactions. Notably, Cp’s top binding site was maintained throughout virus assembly, and specifically bound and assembled with Cp into core-like particles in vitro. Together our data suggest a new model for selective alphavirus genome recognition and assembly.

Single-step label-free hepatitis B virus detection by a piezoelectric biosensor

RSC Advances ◽  
2015 ◽  
Vol 5 (48) ◽  
pp. 38152-38158 ◽  
Author(s):  
Nicoletta Giamblanco ◽  
Sabrina Conoci ◽  
Dario Russo ◽  
Giovanni Marletta
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Virus Detection ◽  
Single Step ◽  
Label Free ◽  
B Virus ◽  
Genome Recognition

Probe densityvs.genome recognition selectivity.

scholarly journals Herpesvirus Genome Recognition Induced Acetylation of Nuclear IFI16 Is Essential for Its Cytoplasmic Translocation, Inflammasome and IFN-β Responses

2015 ◽  
Vol 11 (7) ◽  
pp. e1005019 ◽  
Author(s):  
Mairaj Ahmed Ansari ◽  
Sujoy Dutta ◽  
Mohanan Valiya Veettil ◽  
Dipanjan Dutta ◽  
Jawed Iqbal ◽  
...  
Keyword(s):  
Genome Recognition ◽  
Cytoplasmic Translocation ◽  
Herpesvirus Genome
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