TY - JOUR
T1 - Structure of the 5= untranslated region of enteroviral genomic RNA
AU - Mahmud, Bejan
AU - Horn, Christopher M.
AU - Tapprich, William E.
N1 - Funding Information:
This research was made possible by grants from the National Center for Research Resources (5P20RR016469) and the National Institute for General Medical Science (NIGMS) (8P20GM103427), a component of the National Institutes of Health (NIH).
Publisher Copyright:
Copyright © 2019 Mahmud et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Enteroviral RNA genomes share a long, highly structured 5= untranslated region (5= UTR) containing a type I internal ribosome entry site (IRES). The 5= UTR is composed of stably folded RNA domains connected by unstructured RNA regions. Proper folding and functioning of the 5= UTR underlies the efficiency of viral replication and also determines viral virulence. We have characterized the structure of 5= UTR genomic RNA from coxsackievirus B3 using selective 2=-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical probes in solution. Our results revealed novel structural features, including realignment of major domains, newly identified long-range interactions, and an intrinsically disordered connecting region. Together, these newly identified features contribute to a model for enteroviral 5= UTRs with type I IRES elements that links structure to function during the hierarchical processes directed by genomic RNA during viral infection. IMPORTANCE Enterovirus infections are responsible for human diseases, including myocarditis, pancreatitis, acute flaccid paralysis, and poliomyelitis. The virulence of these viruses depends on efficient recognition of the RNA genome by a large family of host proteins and protein synthesis factors, which in turn relies on the three-dimensional folding of the first 750 nucleotides of the molecule. Structural information about this region of the genome, called the 5= untranslated region (5= UTR), is needed to assist in the process of vaccine and antiviral development. This work presents a model for the structure of the enteroviral 5= UTR. The model includes an RNA element called an intrinsically disordered RNA region (IDRR). Intrinsically disordered proteins (IDPs) are well known, but correlates in RNA have not been proposed. The proposed IDRR is a 20-nucleotide region, long known for its functional importance, where structural flexibility helps explain recognition by factors controlling multiple functional states.
AB - Enteroviral RNA genomes share a long, highly structured 5= untranslated region (5= UTR) containing a type I internal ribosome entry site (IRES). The 5= UTR is composed of stably folded RNA domains connected by unstructured RNA regions. Proper folding and functioning of the 5= UTR underlies the efficiency of viral replication and also determines viral virulence. We have characterized the structure of 5= UTR genomic RNA from coxsackievirus B3 using selective 2=-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical probes in solution. Our results revealed novel structural features, including realignment of major domains, newly identified long-range interactions, and an intrinsically disordered connecting region. Together, these newly identified features contribute to a model for enteroviral 5= UTRs with type I IRES elements that links structure to function during the hierarchical processes directed by genomic RNA during viral infection. IMPORTANCE Enterovirus infections are responsible for human diseases, including myocarditis, pancreatitis, acute flaccid paralysis, and poliomyelitis. The virulence of these viruses depends on efficient recognition of the RNA genome by a large family of host proteins and protein synthesis factors, which in turn relies on the three-dimensional folding of the first 750 nucleotides of the molecule. Structural information about this region of the genome, called the 5= untranslated region (5= UTR), is needed to assist in the process of vaccine and antiviral development. This work presents a model for the structure of the enteroviral 5= UTR. The model includes an RNA element called an intrinsically disordered RNA region (IDRR). Intrinsically disordered proteins (IDPs) are well known, but correlates in RNA have not been proposed. The proposed IDRR is a 20-nucleotide region, long known for its functional importance, where structural flexibility helps explain recognition by factors controlling multiple functional states.
KW - 5' untranslated region
KW - Coxsackievirus B3
KW - Internal ribosome entry site
KW - RNA structure
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U2 - 10.1128/JVI.01288-19
DO - 10.1128/JVI.01288-19
M3 - Article
C2 - 31534036
AN - SCOPUS:85074965450
SN - 0022-538X
VL - 9
JO - Journal of virology
JF - Journal of virology
IS - 23
M1 - e01288-19
ER -