Cargando…

Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA

The functionality of RNA is fully dependent on its structure. For the influenza A virus (IAV), there are confirmed structural motifs mediating processes which are important for the viral replication cycle, including genome assembly and viral packaging. Although the RNA of strains originating from di...

Descripción completa

Detalles Bibliográficos
Autores principales: Michalak, Paula, Piasecka, Julita, Szutkowska, Barbara, Kierzek, Ryszard, Biala, Ewa, Moss, Walter N., Kierzek, Elzbieta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8004953/
https://www.ncbi.nlm.nih.gov/pubmed/33810157
http://dx.doi.org/10.3390/v13030525
_version_ 1783672021814607872
author Michalak, Paula
Piasecka, Julita
Szutkowska, Barbara
Kierzek, Ryszard
Biala, Ewa
Moss, Walter N.
Kierzek, Elzbieta
author_facet Michalak, Paula
Piasecka, Julita
Szutkowska, Barbara
Kierzek, Ryszard
Biala, Ewa
Moss, Walter N.
Kierzek, Elzbieta
author_sort Michalak, Paula
collection PubMed
description The functionality of RNA is fully dependent on its structure. For the influenza A virus (IAV), there are confirmed structural motifs mediating processes which are important for the viral replication cycle, including genome assembly and viral packaging. Although the RNA of strains originating from distant IAV subtypes might fold differently, some structural motifs are conserved, and thus, are functionally important. Nowadays, NGS-based structure modeling is a source of new in vivo data helping to understand RNA biology. However, for accurate modeling of in vivo RNA structures, these high-throughput methods should be supported with other analyses facilitating data interpretation. In vitro RNA structural models complement such approaches and offer RNA structures based on experimental data obtained in a simplified environment, which are needed for proper optimization and analysis. Herein, we present the secondary structure of the influenza A virus segment 5 vRNA of A/California/04/2009 (H1N1) strain, based on experimental data from DMS chemical mapping and SHAPE using NMIA, supported by base-pairing probability calculations and bioinformatic analyses. A comparison of the available vRNA5 structures among distant IAV strains revealed that a number of motifs present in the A/California/04/2009 (H1N1) vRNA5 model are highly conserved despite sequence differences, located within previously identified packaging signals, and the formation of which in in virio conditions has been confirmed. These results support functional roles of the RNA secondary structure motifs, which may serve as candidates for universal RNA-targeting inhibitory methods.
format Online
Article
Text
id pubmed-8004953
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-80049532021-03-29 Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA Michalak, Paula Piasecka, Julita Szutkowska, Barbara Kierzek, Ryszard Biala, Ewa Moss, Walter N. Kierzek, Elzbieta Viruses Article The functionality of RNA is fully dependent on its structure. For the influenza A virus (IAV), there are confirmed structural motifs mediating processes which are important for the viral replication cycle, including genome assembly and viral packaging. Although the RNA of strains originating from distant IAV subtypes might fold differently, some structural motifs are conserved, and thus, are functionally important. Nowadays, NGS-based structure modeling is a source of new in vivo data helping to understand RNA biology. However, for accurate modeling of in vivo RNA structures, these high-throughput methods should be supported with other analyses facilitating data interpretation. In vitro RNA structural models complement such approaches and offer RNA structures based on experimental data obtained in a simplified environment, which are needed for proper optimization and analysis. Herein, we present the secondary structure of the influenza A virus segment 5 vRNA of A/California/04/2009 (H1N1) strain, based on experimental data from DMS chemical mapping and SHAPE using NMIA, supported by base-pairing probability calculations and bioinformatic analyses. A comparison of the available vRNA5 structures among distant IAV strains revealed that a number of motifs present in the A/California/04/2009 (H1N1) vRNA5 model are highly conserved despite sequence differences, located within previously identified packaging signals, and the formation of which in in virio conditions has been confirmed. These results support functional roles of the RNA secondary structure motifs, which may serve as candidates for universal RNA-targeting inhibitory methods. MDPI 2021-03-22 /pmc/articles/PMC8004953/ /pubmed/33810157 http://dx.doi.org/10.3390/v13030525 Text en © 2021 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 (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Michalak, Paula
Piasecka, Julita
Szutkowska, Barbara
Kierzek, Ryszard
Biala, Ewa
Moss, Walter N.
Kierzek, Elzbieta
Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title_full Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title_fullStr Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title_full_unstemmed Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title_short Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA
title_sort conserved structural motifs of two distant iav subtypes in genomic segment 5 rna
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8004953/
https://www.ncbi.nlm.nih.gov/pubmed/33810157
http://dx.doi.org/10.3390/v13030525
work_keys_str_mv AT michalakpaula conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT piaseckajulita conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT szutkowskabarbara conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT kierzekryszard conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT bialaewa conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT mosswaltern conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna
AT kierzekelzbieta conservedstructuralmotifsoftwodistantiavsubtypesingenomicsegment5rna