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

## TL;DR

This study identifies a human protein that helps SARS-CoV-2 replicate by influencing a key viral RNA process.

## Contribution

SLBP is newly identified as a host factor promoting SARS-CoV-2 replication via -1 programmed ribosomal frameshifting.

## Key findings

- SLBP overexpression increases frameshifting and viral replication in SARS-CoV-2.
- SLBP binds directly to the -1 PRF RNA, particularly the stem loop 3 region.
- SLBP deletions alter host factor interactions around the -1 PRF RNA.

## Abstract

The -1 programmed ribosomal frameshifting (-1 PRF) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for keeping the balance between pp1a and pp1ab polyproteins. To date, the host factors influencing this process remain poorly understood. Using RNA pull-down assays combined with mass spectrometry screening, we discovered five host proteins interacting with -1 PRF RNA, including Stem Loop Binding Protein (SLBP). Our findings revealed that SLBP overexpression enhanced frameshifting and promoted viral replication. Moreover, the interaction between SLBP and -1 PRF RNA was predicted using the PrismNet deep learning tool, which calculated a high binding probability of 0.922. Using Electrophoretic Mobility Shift Assays (EMSAs) and RNA pull down assays, our findings demonstrated SLBP’s direct binding to the SARS-CoV-2 genome, with preferential affinity for the stem loop 3 region of the -1 PRF RNA. Using smFISH assays, we further confirmed their physical colocalization. The role of SLBP in promoting frameshifting was verified using an in vitro translation system. Further investigation showed that SLBP deletions reshaped the host factor pattern around -1 PRF RNA, diminishing interactions with FUBP3 and RPS3A while enhancing RPL10A binding. Together, our findings identify SLBP as a host protein that promotes SARS-CoV-2 frameshifting, highlighting its potential as a druggable target for COVID-19.