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Distinct structural elements and internal entry of ribosomes in mRNA3 encoded by infectious bronchitis virus
S Y Le1, N Sonenberg, J V Maizel
1Laboratory of Mathematical Biology, National Cancer Institute, NIH, Frederick, Maryland 21702.
Abstract:
Infectious bronchitis virus (IBV) mRNA3 encodes three small proteins, 3a, 3b, and 3c, at its 5' end. Recently, it was demonstrated that initiation of protein 3c is dependent on the upstream sequence. Monte Carlo simulations of RNA folding in this tricistronic mRNA3 indicate that a highly significant folding region occurs prior to the initiator AUG of 3c. The unusual folding region (UFR) of 265 nucleotides (nt) contains the coding sequences of proteins 3a and 3b. Details of the structural analyses show that five highly significant RNA stem-loops in the UFR can be modeled into a compact superstructure by the interaction of two predicted pseudoknot structures. The folded superstructure comprising nt 44 to 330, with additional 22 nt downstream from this UFR, is suggested to serve as a ribosome landing pad (or an internal ribosomal entry site) in the cap-independent translation of the 3c of IBV. Intriguingly, the proposed structural motif of this coronavirus shares structural features similar to those proposed in a number of picornavirus mRNAs. Based on the common structural features, a plausible base pairing model between mRNA3 and 18 S rRNA is suggested, which is consistent with a general mechanism for regulation of internal initiation described in many picornaviruses.
Insights
Infectious bronchitis virus (IBV) mRNA3 utilizes an unusual folding region (UFR) to facilitate cap-independent translation of protein 3c. This structured RNA element acts as a ribosome landing pad, similar to mechanisms in picornaviruses.
Area of Science:
- Virology
- Molecular Biology
- Structural Biology
Background:
- Infectious bronchitis virus (IBV) mRNA3 encodes proteins 3a, 3b, and 3c.
- Protein 3c translation initiation is dependent on upstream sequences.
- IBV is a significant pathogen in poultry.
Purpose of the Study:
- To investigate the structural basis for cap-independent translation of IBV protein 3c.
- To elucidate the role of the unusual folding region (UFR) in mRNA3.
- To compare structural motifs with other viral mRNAs.
Main Methods:
- Monte Carlo simulations of RNA folding.
- Detailed structural analyses of RNA stem-loops and pseudoknots.
- Comparative analysis of viral mRNA structures.
Main Results:
- A highly significant RNA folding region (UFR) was identified in mRNA3 prior to the 3c initiator AUG.
- Five stem-loops within the UFR form a compact superstructure via pseudoknot interactions.
- This superstructure is proposed to function as a ribosome landing pad for 3c translation.
- Structural similarities were found between IBV mRNA3 and picornavirus mRNAs.
Conclusions:
- The folded superstructure in IBV mRNA3 facilitates cap-independent translation of protein 3c.
- This mechanism shares features with internal ribosomal entry site (IRES) elements in other viruses.
- A potential base-pairing model between IBV mRNA3 and 18S rRNA suggests a conserved translation regulation strategy.