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Evolution of a common structural core in the internal ribosome entry sites of picornavirus
1Laboratory of Mathematical Biology, Division of Cancer Biology Diagnosis and Centers, National Cancer Institute, NIH, Frederick, Maryland 21702, USA. shuyun@fcrfv1.ncifcrf.gov
Insights
Picornaviruses use internal ribosome entry sites (IRES) for translation. These IRES elements share a conserved structural core, suggesting a common evolutionary origin and function across the picornavirus family.
Area of Science:
- Molecular Biology
- Virology
- Evolutionary Biology
Background:
- Internal ribosome binding is a translational control mechanism observed in several picornaviruses, including poliovirus (PV) and human rhinoviruses (HRV).
- This process relies on cis-acting genetic elements known as internal ribosome entry sites (IRES), approximately 450 nucleotides in length, located in the 5'-untranslated region (5'UTR) of these viral genomes.
Purpose of the Study:
- To investigate the structural conservation of IRES elements across the picornavirus family.
- To understand the evolutionary implications of conserved IRES structures for viral translation.
Main Methods:
- Phylogenetic analysis of picornavirus 5' UTR sequences.
- RNA folding predictions to determine secondary and tertiary structures of IRES elements.
- Comparative analysis of IRES structures from diverse picornaviruses.
Main Results:
- Despite significant differences in primary sequence, IRES elements from various picornaviruses exhibit a conserved 3' structural core.
- This conserved core structure was identified as a general feature across the entire picornavirus family, including PV, HRV, encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV), and hepatitis A virus (HAV).
Conclusions:
- The conserved structural core in picornaviral IRES elements suggests a common evolutionary origin.
- The preservation of this core structure through gradual domain additions/deletions likely facilitates IRES utilization in specific host-cell environments, highlighting structural adaptability in viral evolution.
Abstract:
The translational control involving internal ribosome binding occurs in poliovirus (PV), human rhinoviruses (HRV), encephalomyocarditis virus (EMCV), foot-and-mouth disease virus (FMDV), and hepatitis A virus (HAV). Internal ribosome binding utilizes cis-acting genetic elements of approximately 450 nucleotides (nt) termed the internal ribosome entry sites (IRES) found in these picornaviral 5'-untranslated region (5'UTR). Although these IRES elements are quite different in their primary sequence, a similar folding structure with a conserved 3' structural core exists in the IRES. Phylogenetic analysis and RNA folding of the 5' UTR of picornaviruses, including PV types 1-3, coxsackievirus types A and B, swine vesicular disease virus, echoviruses, enteroviruses (human and bovine), HRV, HAV, EMCV, mengovirus, Theiler's murine encephalomyelitis viruses, FMDV, and equine rhinoviruses, indicates that the predicted conserved structural core is indeed a general structural feature for all members of the picornavirus family. The evolution of a common structural core likely occurred by the gradual addition or deletion of structural domains and elements to preserve a similar tertiary structure that facilitates the utilization of the IRES in specific host-cell environments.