Expanded subgenomic mRNA transcriptome and coding capacity of a nidovirus

Area of Science:

• Virology
• Molecular Biology
• Genomics

Background:

• Nidovirales order viruses express structural proteins via subgenomic mRNAs (sg mRNAs) from nested sets.
• Previously, only nine transcription regulatory sequences (TRSs) were identified for Simian hemorrhagic fever virus (SHFV).

Purpose of the Study:

• To comprehensively identify functional TRSs in SHFV.
• To characterize the diversity and function of SHFV sg mRNAs and their regulatory elements.
• To investigate the expanded coding capacity of SHFV.

Main Methods:

• Utilized next-generation sequencing to identify SHFV TRSs in infected MA104 cells and macaque macrophages.
• Analyzed sg mRNA abundance and leader-body junction sequences.
• Employed mass spectrometry to detect viral proteins and mutations in an infectious clone to assess ORF function.

Main Results:

• Identified 96 functional SHFV body TRSs, significantly more than previously known.
• Found that sg mRNA abundance was consistent across cell types and time.
• Discovered multiple TRSs for most 3' ORFs, alternative sources for nonstructural proteins, and novel sg mRNAs encoding unreported ORFs, expanding SHFV's coding capacity.

Conclusions:

• SHFV possesses a complex transcriptional regulatory mechanism with numerous functional TRSs.
• The virus exhibits an expanded coding capacity through alternative ORFs and sg mRNA usage.
• These findings may be characteristic of other viruses within the Nidovirales order.