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Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins

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Abstract

Human astrovirus (HAstV) constitutes a major cause of acute gastroenteritis in children. The viral 5′ and 3′ untranslated regions (UTR) have been involved in the regulation of several molecular mechanisms. However, in astrovirues have been less characterized. Here, we analyzed the secondary structures of the 5′ and 3′ UTR of HAstV, as well as their putative target sites that might be recognized by cellular factors. To our knowledge, this is the first bioinformatic analysis that predicts the HAstV 5′ UTR secondary structure. The analysis showed that both the UTR sequence and secondary structure are highly conserved in all HAstVs analyzed, suggesting their regulatory role of viral activities. Notably, the UTRs of HAstVs contain putative binding sites for the serine/arginine-rich factors SRSF2, SRSF5, SRSF6, SRSF3, and the multifunctional hnRNPE2 protein. More importantly, putative binding sites for PTB were localized in single-stranded RNA sequences, while hnRNPE2 sites were localized in double-stranded sequence of the HAstV 5′ and 3′ UTR structures. These analyses suggest that the combination of SRSF proteins, hnRNPE2 and PTB described here could be involved in the maintenance of the secondary structure of the HAstVs, possibly allowing the recruitment of the replication complex that selects and recruits viral RNA replication templates.

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Acknowledgements

We are grateful to Bert L. Semler (University of California, Irvine) for the pET22b-PCBP2 plasmid. This work was partly supported by Secretaría de Investigación y Posgrado (SIP) of Instituto Politécnico Nacional (IPN) Grants 20151007, 20160939, 20170853, 20180182 (M. De N-O.), and by Consejo Nacional de Ciencia y Tecnología (CONACyT) Grants 127557-M and 236104 (J.V.). M.C.S was a CONACyT (747789) and BEFI SIP-IPN (reg. 16783) fellowships recipient. M. De N-O., J.S.B. and L.G.M. received fellowships from Comisión de Operación y Fomento a las Actividades Académicas (COFAA), and M. De N-O, J.S.B received Estímulo al Desempeño de los Investigadores (EDI) from IPN. Additionally, M. De N-O, C.V.V., J.S.B and J.V. received fellowships Sistema Nacional de Investigadores (SNI) CONACyT.

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Authors and Affiliations

  1. ENMH, Programa Institucional de Biomedicina Molecular, Instituto Politécnico Nacional, Guillermo Massieu Helguera No. 239 Col. Fracc. La Escalera-Ticomán, 07320, Ciudad de Mexico, Mexico

    Mónica De Nova-Ocampo, Mayra Cristina Soliman, Wendy Espinosa-Hernández, Juan Salas-Benito & Lorena García-Morales

  2. Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del IPN, Avenida IPN 2508 Col. San Pedro Zacatenco, 07360, Ciudad de Mexico, Mexico

    Cristina Velez-del Valle

  3. Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, Avenida IPN 2508 Col. San Pedro Zacatenco, 07360, Ciudad de Mexico, Mexico

    Jesús Valdés-Flores

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  1. Mónica De Nova-Ocampo
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  2. Mayra Cristina Soliman
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Contributions

M. De N-O, C.V.V, J.S.B, J.V. and L.G.M., wrote the introduction, RNA structural analysis, comparison between the 5′ and 3′ UTR sections and the cellular protein interactions with other RNA viruses. M.C.S and W.E.H made the table containing the proteins that bind to the 5′ UTR and 3′ UTR respectively. M.C.S prepared the Figs. 1c, e, 2d and 3. All authors discussed the manuscript contents and agreed with this paper.

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Correspondence to Mónica De Nova-Ocampo.

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De Nova-Ocampo, M., Soliman, M.C., Espinosa-Hernández, W. et al. Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins. Mol Biol Rep 46, 1413–1424 (2019). https://doi.org/10.1007/s11033-018-4498-8

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