Stem loop binding protein promotes SARS-CoV-2 replication via -1 programmed ribosomal frameshifting

Area of Science:

• Virology
• Molecular Biology
• Host-Pathogen Interactions

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) relies on -1 programmed ribosomal frameshifting (-1 PRF) for polyprotein synthesis.
• Host factors regulating SARS-CoV-2 -1 PRF remain largely unidentified, limiting therapeutic strategies.

Purpose of the Study:

• To identify host proteins that interact with SARS-CoV-2 -1 PRF RNA.
• To investigate the role of identified host proteins in viral replication and frameshifting.
• To explore potential therapeutic targets for COVID-19.

Main Methods:

• RNA pull-down assays coupled with mass spectrometry to identify interacting host proteins.
• Deep learning prediction (PrismNet) for RNA-protein binding probability.
• Electrophoretic Mobility Shift Assays (EMSAs) and RNA pull-down assays to confirm direct binding.
• Small fluorescent microscopy in situ hybridization (smFISH) for colocalization studies.
• In vitro translation systems to assess frameshifting efficiency.

Main Results:

• Five host proteins, including Stem Loop Binding Protein (SLBP), were identified interacting with -1 PRF RNA.
• SLBP directly binds to the SARS-CoV-2 -1 PRF RNA, particularly the stem loop 3 region.
• SLBP overexpression enhances -1 PRF and promotes viral replication.
• SLBP influences the binding of other host factors (FUBP3, RPS3A, RPL10A) to the -1 PRF RNA region.

Conclusions:

• Stem Loop Binding Protein (SLBP) is a novel host factor that promotes SARS-CoV-2 -1 PRF.
• SLBP's interaction with viral RNA is crucial for efficient viral replication.
• SLBP represents a potential druggable target for developing novel COVID-19 therapeutics.