Nuclear translocation of the SARS-CoV-2 spike protein and spike protein mRNA

A recent study by American researchers has shown nuclear translocation of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) spike (S) protein and S protein messenger ribonucleic acid (mRNA) in SARS-CoV-2-infected cells. The translocation of the S protein mRNA appeared to be assisted by the S protein, which contains the novel NLS motif that is unique among human pathogenic beta-coronaviruses.

SARS-CoV-2 is highly pathogenic and more transmissible than SARS-CoV or MERS-CoV. These coronaviruses contain positive-strand RNA genome. The different subgenomic RNAs encode four conserved structural proteins, spike, envelope, membrane, nucleocapsid, and several accessory proteins. The S protein appears to be a major pathogenic factor that contributes to the unique pathogenesis of SARS-CoV-2. The S protein is composed of an S1 subunit and an S2 subunit, separated by host cell proteases. The receptor-binding domain in the S1 subunit is responsible for attachment to host cells. The S protein interacts not only with angiotensin-converting enzyme 2 (ACE2) receptors, but also with several other host receptors.

One of the controversies regarding the natural origin of SARS-CoV-2 is that its S gene has multiple novel sequence insertions. Recent data have revealed several genomic features of SARS-CoV-2, including new sequence insertions and enhanced N protein nuclear localization signal (NLS) that is believed to be responsible for the unique pathogenesis of this coronavirus.

About the study

The objective of this study was to determine whether the SARS-CoV-2 S protein and the S protein mRNA translocate in the nucleus of the airway epithelium infected with SARS-CoV-2, which is an appropriate lung model for in vitro investigation of respiratory virus infection. The cells were subjected to immunohistochemistry analysis and were examined by confocal microscopy.

The results showed that the S protein translocated into the nucleus in the SARS-CoV-2-infected airway epithelium. In addition, the S protein mRNA colocalization image analysis with nuclear staining showed that the S protein mRNA translocated into the nucleus. The S protein mRNA nuclear translocation was mediated by the S protein because the S protein mRNA nuclear translocation was always associated with the S protein.

The S protein is a surface transmembrane type 1 glycoprotein, but, it has been predicted to be translocated into the nucleus due to the novel NLS motif “PRRARSV”, which is absent from the S protein of other human pathogenic beta-coronaviruses. The novel sequence insertion resides at the S1/S2 boundary of the S protein and constitutes a functional NLS motif “PRRARSV”. It may supersede the importance of previously proposed polybasic furin cleavage site “RRAR”, which may contribute to increased serin protease-driven entry of SARS-CoV-2 and is implicated in broader tropism and/or enhanced viral transmissibility compared to SARS-CoV.

NLS-driven S protein nuclear translocation is a novel pathogenic feature of SARS-CoV-2 infection compared to other pathogenic beta-coronaviruses, and may contribute to the evasion of the host immune response.

The authors concluded that the identification of novel features in the S protein gene sequence, its expression and subcellular localization may shed light on the unique pathogenesis of SARS-CoV-2 compared to other pathogenic beta-coronaviruses, particularly SARS-CoV and MERS-CoV.

The results of the study have been published in the scientific journal Frontiers in Microbiology. Sattar S. et al. Nuclear translocation of spike mRNA and protein is a novel feature of SARS-CoV-2. Front Microbiol 2023; 14: 1073789.