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Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging

Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which i...

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Autores principales: Boon, Priscilla L. S., Martins, Ana S., Lim, Xin Ni, Enguita, Francisco J., Santos, Nuno C., Bond, Peter J., Wan, Yue, Martins, Ivo C., Huber, Roland G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179140/
https://www.ncbi.nlm.nih.gov/pubmed/37175867
http://dx.doi.org/10.3390/ijms24098158
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author Boon, Priscilla L. S.
Martins, Ana S.
Lim, Xin Ni
Enguita, Francisco J.
Santos, Nuno C.
Bond, Peter J.
Wan, Yue
Martins, Ivo C.
Huber, Roland G.
author_facet Boon, Priscilla L. S.
Martins, Ana S.
Lim, Xin Ni
Enguita, Francisco J.
Santos, Nuno C.
Bond, Peter J.
Wan, Yue
Martins, Ivo C.
Huber, Roland G.
author_sort Boon, Priscilla L. S.
collection PubMed
description Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2′-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA–RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses.
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spelling pubmed-101791402023-05-13 Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging Boon, Priscilla L. S. Martins, Ana S. Lim, Xin Ni Enguita, Francisco J. Santos, Nuno C. Bond, Peter J. Wan, Yue Martins, Ivo C. Huber, Roland G. Int J Mol Sci Article Dengue virus (DENV) is a single-stranded (+)-sense RNA virus that infects humans and mosquitoes, posing a significant health risk in tropical and subtropical regions. Mature virions are composed of an icosahedral shell of envelope (E) and membrane (M) proteins circumscribing a lipid bilayer, which in turn contains a complex of the approximately 11 kb genomic RNA with capsid (C) proteins. Whereas the structure of the envelope is clearly defined, the structure of the packaged genome in complex with C proteins remains elusive. Here, we investigated the interactions of C proteins with viral RNA, in solution and inside mature virions, via footprinting and cross-linking experiments. We demonstrated that C protein interaction with DENV genomes saturates at an RNA:C protein ratio below 1:250. Moreover, we also showed that the length of the RNA genome interaction sites varies, in a multimodal distribution, consistent with the C protein binding to each RNA site mostly in singlets or pairs (and, in some instances, higher numbers). We showed that interaction sites are preferentially sites with low base pairing, as previously measured by 2′-acetylation analyzed by primer extension (SHAPE) reactivity indicating structuredness. We found a clear association pattern emerged: RNA-C protein binding sites are strongly associated with long-range RNA–RNA interaction sites, particularly inside virions. This, in turn, explains the need for C protein in viral genome packaging: the protein has a chief role in coordinating these key interactions, promoting proper packaging of viral RNA. Such sites are, thus, highly consequential for viral assembly, and, as such, may be targeted in future drug development strategies against these and related viruses. MDPI 2023-05-02 /pmc/articles/PMC10179140/ /pubmed/37175867 http://dx.doi.org/10.3390/ijms24098158 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Boon, Priscilla L. S.
Martins, Ana S.
Lim, Xin Ni
Enguita, Francisco J.
Santos, Nuno C.
Bond, Peter J.
Wan, Yue
Martins, Ivo C.
Huber, Roland G.
Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title_full Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title_fullStr Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title_full_unstemmed Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title_short Dengue Virus Capsid Protein Facilitates Genome Compaction and Packaging
title_sort dengue virus capsid protein facilitates genome compaction and packaging
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179140/
https://www.ncbi.nlm.nih.gov/pubmed/37175867
http://dx.doi.org/10.3390/ijms24098158
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