Molecular signatures of silencing suppression degeneracy from a complex RNA virus.

As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we follo...

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Autores principales: Silvia Ambrós, Neus Gómez-Muñoz, Silvia Giménez-Santamarina, Javier Sánchez-Vicente, Josep Navarro-López, Fernando Martínez, José-Antonio Daròs, Guillermo Rodrigo
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Publicado: Public Library of Science (PLoS) 2021
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Acceso en línea:https://doaj.org/article/9824296705be40929eb35a6f70215df5
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spelling oai:doaj.org-article:9824296705be40929eb35a6f70215df52021-11-25T05:40:34ZMolecular signatures of silencing suppression degeneracy from a complex RNA virus.1553-734X1553-735810.1371/journal.pcbi.1009166https://doaj.org/article/9824296705be40929eb35a6f70215df52021-06-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009166https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA silencing suppressors, using an experimental system of transient expression in a model plant. The study was expanded by considering two different isolates of the virus, and some key interactions were confirmed by bimolecular fluorescence complementation assays. We found that p20 and p25 target a common set of plant proteins including chloroplastic proteins and translation factors. Moreover, we noted that even specific targets of each viral protein overlap in function. Notably, we identified argonaute proteins (key players in RNA silencing) as reliable targets of p20. Furthermore, we found that these viral proteins preferentially do not target hubs in the host protein interactome, but elements that can transfer information by bridging different parts of the interactome. Overall, our results demonstrate that two distinct proteins encoded in the same viral genome that overlap in function also overlap in their interactions with the cell proteome, thereby highlighting an overlooked connection from a degenerate viral system.Silvia AmbrósNeus Gómez-MuñozSilvia Giménez-SantamarinaJavier Sánchez-VicenteJosep Navarro-LópezFernando MartínezJosé-Antonio DaròsGuillermo RodrigoPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 6, p e1009166 (2021)
institution DOAJ
collection DOAJ
language EN
topic Biology (General)
QH301-705.5
spellingShingle Biology (General)
QH301-705.5
Silvia Ambrós
Neus Gómez-Muñoz
Silvia Giménez-Santamarina
Javier Sánchez-Vicente
Josep Navarro-López
Fernando Martínez
José-Antonio Daròs
Guillermo Rodrigo
Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
description As genomic architectures become more complex, they begin to accumulate degenerate and redundant elements. However, analyses of the molecular mechanisms underlying these genetic architecture features remain scarce, especially in compact but sufficiently complex genomes. In the present study, we followed a proteomic approach together with a computational network analysis to reveal molecular signatures of protein function degeneracy from a plant virus (as virus-host protein-protein interactions). We employed affinity purification coupled to mass spectrometry to detect several host factors interacting with two proteins of Citrus tristeza virus (p20 and p25) that are known to function as RNA silencing suppressors, using an experimental system of transient expression in a model plant. The study was expanded by considering two different isolates of the virus, and some key interactions were confirmed by bimolecular fluorescence complementation assays. We found that p20 and p25 target a common set of plant proteins including chloroplastic proteins and translation factors. Moreover, we noted that even specific targets of each viral protein overlap in function. Notably, we identified argonaute proteins (key players in RNA silencing) as reliable targets of p20. Furthermore, we found that these viral proteins preferentially do not target hubs in the host protein interactome, but elements that can transfer information by bridging different parts of the interactome. Overall, our results demonstrate that two distinct proteins encoded in the same viral genome that overlap in function also overlap in their interactions with the cell proteome, thereby highlighting an overlooked connection from a degenerate viral system.
format article
author Silvia Ambrós
Neus Gómez-Muñoz
Silvia Giménez-Santamarina
Javier Sánchez-Vicente
Josep Navarro-López
Fernando Martínez
José-Antonio Daròs
Guillermo Rodrigo
author_facet Silvia Ambrós
Neus Gómez-Muñoz
Silvia Giménez-Santamarina
Javier Sánchez-Vicente
Josep Navarro-López
Fernando Martínez
José-Antonio Daròs
Guillermo Rodrigo
author_sort Silvia Ambrós
title Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
title_short Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
title_full Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
title_fullStr Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
title_full_unstemmed Molecular signatures of silencing suppression degeneracy from a complex RNA virus.
title_sort molecular signatures of silencing suppression degeneracy from a complex rna virus.
publisher Public Library of Science (PLoS)
publishDate 2021
url https://doaj.org/article/9824296705be40929eb35a6f70215df5
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