Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility

Area of Science:

• Virology
• Molecular Biology
• Biochemistry

Background:

• Rotaviruses package eleven segmented genomic RNAs using viral RNA chaperones.
• The rotavirus non-structural protein 2 (NSP2) is a key RNA chaperone involved in genome packaging.
• The global impact of RNA chaperones on the entire viral transcriptome remains poorly understood.

Purpose of the Study:

• To investigate the global effect of rotavirus NSP2 on the secondary structure of the viral transcriptome.
• To determine how NSP2 influences RNA flexibility and structure in the context of the complete viral RNA set.

Main Methods:

• Selective 2'-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) was employed.
• SHAPE-MaP was used to analyze rotavirus RNA secondary structure in the presence of varying NSP2 concentrations.

Main Results:

• NSP2 did not significantly alter SHAPE reactivities, contrary to its known in vitro helix-unwinding activity.
• Mutation rates revealed a 5-fold global increase in RNA flexibility with NSP2, particularly affecting stems.
• A normalization procedure in SHAPE data analysis can mask global RNA chaperone effects.

Conclusions:

• Rotavirus NSP2 increases RNA backbone flexibility globally in a concentration-dependent manner.
• This global flexibility increase, rather than direct helix unwinding, is a key mechanism for NSP2's role in RNA packaging.
• The study provides the first experimental secondary structure model of the rotavirus transcriptome influenced by NSP2.