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Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins
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 structur...
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Published in: | Molecular biology reports 2019-02, Vol.46 (1), p.1413-1424 |
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creator | De Nova-Ocampo, Mónica Soliman, Mayra Cristina Espinosa-Hernández, Wendy Velez-del Valle, Cristina Salas-Benito, Juan Valdés-Flores, Jesús García-Morales, Lorena |
description | 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. |
doi_str_mv | 10.1007/s11033-018-4498-8 |
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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.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-018-4498-8</identifier><identifier>PMID: 30448895</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Arginine ; Base Sequence ; Binding Sites ; Biomedical and Life Sciences ; Children ; Computer Simulation ; Conserved sequence ; Gastroenteritis ; Histology ; Life Sciences ; Mamastrovirus - genetics ; Molecular modelling ; Morphology ; Nucleic Acid Conformation ; Nucleotide sequence ; Protein structure ; Proteins - metabolism ; Replication ; Review ; Ribonucleic acid ; RNA ; Secondary structure ; Serine ; Untranslated Regions - genetics</subject><ispartof>Molecular biology reports, 2019-02, Vol.46 (1), p.1413-1424</ispartof><rights>Springer Nature B.V. 2018</rights><rights>Molecular Biology Reports is a copyright of Springer, (2018). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c470t-c351a9d1c869265e06e5f28daadc055a14bf0a96adf93af09771d38bcfd9c18f3</citedby><cites>FETCH-LOGICAL-c470t-c351a9d1c869265e06e5f28daadc055a14bf0a96adf93af09771d38bcfd9c18f3</cites><orcidid>0000-0003-2688-4951 ; 0000-0002-4096-0079 ; 0000-0002-0750-7977 ; 0000-0002-2377-942X ; 0000-0003-1787-9229 ; 0000-0003-0254-7782 ; 0000-0002-6898-024X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30448895$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>De Nova-Ocampo, Mónica</creatorcontrib><creatorcontrib>Soliman, Mayra Cristina</creatorcontrib><creatorcontrib>Espinosa-Hernández, Wendy</creatorcontrib><creatorcontrib>Velez-del Valle, Cristina</creatorcontrib><creatorcontrib>Salas-Benito, Juan</creatorcontrib><creatorcontrib>Valdés-Flores, Jesús</creatorcontrib><creatorcontrib>García-Morales, Lorena</creatorcontrib><title>Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>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.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Arginine</subject><subject>Base Sequence</subject><subject>Binding Sites</subject><subject>Biomedical and Life Sciences</subject><subject>Children</subject><subject>Computer Simulation</subject><subject>Conserved sequence</subject><subject>Gastroenteritis</subject><subject>Histology</subject><subject>Life Sciences</subject><subject>Mamastrovirus - genetics</subject><subject>Molecular modelling</subject><subject>Morphology</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleotide sequence</subject><subject>Protein structure</subject><subject>Proteins - metabolism</subject><subject>Replication</subject><subject>Review</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Secondary structure</subject><subject>Serine</subject><subject>Untranslated Regions - 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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. 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subjects | Animal Anatomy Animal Biochemistry Arginine Base Sequence Binding Sites Biomedical and Life Sciences Children Computer Simulation Conserved sequence Gastroenteritis Histology Life Sciences Mamastrovirus - genetics Molecular modelling Morphology Nucleic Acid Conformation Nucleotide sequence Protein structure Proteins - metabolism Replication Review Ribonucleic acid RNA Secondary structure Serine Untranslated Regions - genetics |
title | Human astroviruses: in silico analysis of the untranslated region and putative binding sites of cellular proteins |
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