Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Oct;9(10):1266-74.
doi: 10.4161/rna.22081. Epub 2012 Sep 20.

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus

Andrey Chursov  1 , Sebastian J Kopetzky, Ignaty Leshchiner, Ivan Kondofersky, Fabian J Theis, Dmitrij Frishman, Alexander Shneider
Affiliations

Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus

Andrey Chursov et al. RNA Biol. 2012 Oct.

Abstract

For decades, cold-adapted, temperature-sensitive (ca/ts) strains of influenza A virus have been used as live attenuated vaccines. Due to their great public health importance it is crucial to understand the molecular mechanism(s) of cold adaptation and temperature sensitivity that are currently unknown. For instance, secondary RNA structures play important roles in influenza biology. Thus, we hypothesized that a relatively minor change in temperature (32-39°C) can lead to perturbations in influenza RNA structures and, that these structural perturbations may be different for mRNAs of the wild type (wt) and ca/ts strains. To test this hypothesis, we developed a novel in silico method that enables assessing whether two related RNA molecules would undergo (dis)similar structural perturbations upon temperature change. The proposed method allows identifying those areas within an RNA chain where dissimilarities of RNA secondary structures at two different temperatures are particularly pronounced, without knowing particular RNA shapes at either temperature. We identified such areas in the NS2, PA, PB2 and NP mRNAs. However, these areas are not identical for the wt and ca/ts mutants. Differences in temperature-induced structural changes of wt and ca/ts mRNA structures may constitute a yet unappreciated molecular mechanism of the cold adaptation/temperature sensitivity phenomena.

Keywords: RNA; influenza; structure; temperature; vaccine.

PubMed Disclaimer

Figures

None
Figure 1. Comparison of significantly changing positions between the PA mRNA of Len/wt (upper 7 rows) and Len/17/ca (lower 7 rows). Each row corresponds to a difference vector v32–33, …, v32–39 containing changes of base pairing probabilities between 32°C and a particular higher temperature. Positions in which base paring probabilities significantly change with temperature elevation in both sequences and those where these changes only affect one of the phenotypes are marked blue and orange, respectively. Only the first 40 bases of each sequence are shown; position numbers of the coding sequence are indicated at the top of the alignment.
None
Figure 2. Distributions of significantly changing positions along the PB2 mRNAs of Arb/wt and Arb/ca. A sliding window of size 20 was moved in steps of 1 position over the vector v32–39 and the percentage of significantly changing positions in the window was calculated for each possible starting position. The resulting density plots are depicted in Figure 2A and Figure 2C. Location of clusters of significantly changing positions identified by the DBSCAN algorithm are depicted in Figure 2B and Figure 2D with gray color. Synonymous and non-synonymous mutations are depicted in Figure 2B and Figure 2D with red and blue vertical lines, respectively.
None
Figure 3. The histogram of differences of the probability values of nucleotides to be in a double-stranded conformation for PB1 Arb/wt upon temperature change between 32°C and 39°C. The vector of probabilities for 32°C was subtracted from the vector for 39°C.
None
Figure 4. Density of significantly changing positions in determined clusters vs. length. (A) Clusters that occur only in wt mRNAs but are not statistically significant (37). (B) Clusters occurring in both wt and ca/ts mRNAs (126). (C) Clusters that occur only in ca/ts mutants but are not statistically significant (45). (D) Statistically significant clusters (9 of them occur only in ca/ts mutants and 1 of them occurs only in wt mRNA). Different colors show different numbers of clusters that have identical values of length and density. Black, one cluster; red, two clusters; green, three clusters; blue, four clusters.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Stöhr K, Kieny MP, Wood D. Influenza pandemic vaccines: how to ensure a low-cost, low-dose option. Nat Rev Microbiol. 2006;4:565–6. doi: 10.1038/nrmicro1482. - DOI - PubMed
    1. Belsey MJ, de Lima B, Pavlou AK, Savopoulos JW. Influenza vaccines. Nat Rev Drug Discov. 2006;5:183–4. doi: 10.1038/nrd1988. - DOI - PubMed
    1. Ilyinskii PO, Thoidis G, Shneider AM. Development of a vaccine against pandemic influenza viruses: current status and perspectives. Int Rev Immunol. 2008;27:392–426. doi: 10.1080/08830180802295765. - DOI - PubMed
    1. Song H, Nieto GR, Perez DR. A new generation of modified live-attenuated avian influenza viruses using a two-strategy combination as potential vaccine candidates. J Virol. 2007;81:9238–48. doi: 10.1128/JVI.00893-07. - DOI - PMC - PubMed
    1. Falcón AM, Marión RM, Zürcher T, Gómez P, Portela A, Nieto A, et al. Defective RNA replication and late gene expression in temperature-sensitive influenza viruses expressing deleted forms of the NS1 protein. J Virol. 2004;78:3880–8. doi: 10.1128/JVI.78.8.3880-3888.2004. - DOI - PMC - PubMed

Publication types

LinkOut - more resources