A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation

Soszynska-Jozwiak, Marta; Michalak, Paula; Moss, William C.; Kierzek, Ryszard; Kierzek, Elżbieta

doi:10.1371/journal.pone.0141132

Cited by 15 publications

(26 citation statements)

References 48 publications

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“…Most previous ASOs for IAV were designed to target mRNA (e.g., AUG region of different segments [ 36–40 ], conserved region [ 41 ], or structures [ 42 ] in NP, or UTRs [ 43 , 44 ]). For IAV vRNA, only the conserved 5′ and 3′ ends forming the panhandle structure have been targeted [ 45 , 46 ].…”

Section: Discussionmentioning

confidence: 99%

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

Lenartowicz

Nogales

Kierzek

et al. 2016

Nucleic Acid Therapeutics

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Influenza A virus (IAV) affects 5%–10% of the world's population every year. Through genome changes, many IAV strains develop resistance to currently available anti-influenza therapeutics. Therefore, there is an urgent need to find new targets for therapeutics against this important human respiratory pathogen. In this study, 2′-O-methyl and locked nucleic acid antisense oligonucleotides (ASOs) were designed to target internal regions of influenza A/California/04/2009 (H1N1) genomic viral RNA segment 8 (vRNA8) based on a base-pairing model of vRNA8. Ten of 14 tested ASOs showed inhibition of viral replication in Madin-Darby canine kidney cells. The best five ASOs were 11–15 nucleotides long and showed inhibition ranging from 5- to 25-fold. In a cell viability assay they showed no cytotoxicity. The same five ASOs also showed no inhibition of influenza B/Brisbane/60/2008 (Victoria lineage), indicating that they are sequence specific for IAV. Moreover, combinations of ASOs slightly improved anti-influenza activity. These studies establish the accessibility of IAV vRNA for ASOs in regions other than the panhandle formed between the 5′ and 3′ ends. Thus, these regions can provide targets for the development of novel IAV antiviral approaches.

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Section: Discussionmentioning

confidence: 99%

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

Lenartowicz

Nogales

Kierzek

et al. 2016

Nucleic Acid Therapeutics

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“…Bioinformatics studies showed the possibility of conserved structures both in (+) and in (–) RNA strands 6 , 7 . Only several of these motifs have been examined experimentally, and very few have been studied in vivo 2 , 8 – 10 . Only for two entire viral genomic segments, 8 and 7, has secondary structure been determined 11 , 12 .…”

Section: Introductionmentioning

confidence: 99%

Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies

Soszynska-Jozwiak

Michalak

Moss

et al. 2017

Sci Rep

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Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region. Chemical mapping data combined with thermodynamic energy minimization were used in secondary structure prediction. Sequence/structure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conserved between influenza virus type A strains. Microarray mapping and RNase H cleavage identified accessible sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA. Antisense oligonucleotides were designed based on the secondary structure model and tested against influenza virus in cell culture. Inhibition of influenza virus proliferation was noticed, identifying good targets for antisense strategies. Effective target sites fall within two domains, which are conserved in sequence/structure indicating their importance to the virus.

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“…Some of the conserved structures in segments 7 and 8 were shown to affect splicing14. Conserved structures were also suggested to fold in several domains of segment 51516.…”

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confidence: 96%

Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes

Gultyaev

Spronken

Richard

et al. 2016

Sci Rep

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The influenza A virus genome consists of eight RNA segments. RNA structures within these segments and complementary (cRNA) and protein-coding mRNAs may play a role in virus replication. Here, conserved putative secondary structures that impose significant evolutionary constraints on the gene segment encoding the surface glycoprotein hemagglutinin (HA) were investigated using available sequence data on tens of thousands of virus strains. Structural constraints were identified by analysis of covariations of nucleotides suggested to be paired by structure prediction algorithms. The significance of covariations was estimated by mutual information calculations and tracing multiple covariation events during virus evolution. Covariation patterns demonstrated that structured domains in HA RNAs were mostly subtype-specific, whereas some structures were conserved in several subtypes. The influence of RNA folding on virus replication was studied by plaque assays of mutant viruses with disrupted structures. The results suggest that over the whole length of the HA segment there are local structured domains which contribute to the virus fitness but individually are not essential for the virus. Existence of subtype-specific structured regions in the segments of the influenza A virus genome is apparently an important factor in virus evolution and reassortment of its genes.

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A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation

Cited by 15 publications

References 48 publications

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

Antisense Oligonucleotides Targeting Influenza A Segment 8 Genomic RNA Inhibit Viral Replication

Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies

Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes

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