Endomembrane remodeling in SARS-CoV-2 infection

Abstract

During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the viral proteins intimately interact with host factors to remodel the endomembrane system at various steps of the viral lifecycle. The entry of SARS-CoV-2 can be mediated by endocytosis-mediated internalization. Virus-containing endosomes then fuse with lysosomes, in which the viral S protein is cleaved to trigger membrane fusion. Double-membrane vesicles generated from the ER serve as platforms for viral replication and transcription. Virions are assembled at the ER-Golgi intermediate compartment and released through the secretory pathway and/or lysosome-mediated exocytosis. In this review, we will focus on how SARS-CoV-2 viral proteins collaborate with host factors to remodel the endomembrane system for viral entry, replication, assembly and egress. We will also describe how viral proteins hijack the host cell surveillance system-the autophagic degradation pathway-to evade destruction and benefit virus production. Finally, potential antiviral therapies targeting the host cell endomembrane system will be discussed.

Keywords: Autophagy; Coronavirus; DMV; Endocytosis; SARS-CoV-2.

Fig. 1

The SARS-CoV-2 infection cycle SARS-CoV-2 virions attach to the host cell through the interaction between viral spike (S) protein and the plasma membrane receptor ACE2. The cell-surface protease TMPRSS2 mediates the cleavage of S protein, which further triggers fusion of the viral envelope with the plasma membrane and subsequent entry of viral genomic RNA. SARS-CoV-2 can also enter into the host cell by the endocytosis pathway, in which S protein is cleaved by lysosomal cysteine proteases (cathepsins; CTSB and CTSL). The viral positive-strand (+) RNA genome is translated to polyproteins PP1a and PP1ab, which are further processed into 16 non-structural proteins (NSP1-16). NSPs participate in the formation of viral transcription replication complexes (RTCs) in DMVs to facilitate viral RNA synthesis and processing. The DMVs serve as a platform for RNA synthesis and the storage of negative-stranded templates/double-stranded viral RNAs. Nascent viral RNA is transported to the ERGIC or single-membrane vesicles (SMVs) for assembly. Viral particles egress through the secretory pathway and/or the lysosomal exocytosis pathway.

Fig. 2

The entry of SARS-CoV-2 SARS-CoV-2 enters into the host cell through direct membrane fusion or the endocytosis pathway. After the S protein binds to ACE2, a site is revealed in the S2 subunit which can be recognized and cleaved by the cell surface-localized protease TMPRSS2. TMPRSS2 cleavage leads to dramatic conformational changes of the S protein and shedding of the S1 subunit. This exposes the S2 fusion peptide, which induces the fusion of viral and host plasma membranes so that the viral genomic RNA is released into the host cell. When TMPRSS2 is absent, ACE2-bound virions are internalized through endocytosis. Upon fusion of the virion-containing endosomes with late endosomes/lysosomes, S protein is cleaved by CTSB/CTSL. The exposed S2 fusion peptide facilitates fusion of the viral membrane with the endocytic vesicle and release of the viral genome.

Fig. 3

DMV formation in SARS-CoV-2-infected cells At the initial step of biogenesis of double-membrane vesicles (DMVs), viral nonstructural proteins NSP3 and NSP4 interact to induce pairing of ER membranes. This is facilitated by the ER transmembrane protein TMEM41B. Upon interaction, NSP3 is distributed on the side of the ER which will become the cytoplasmic face of the DMV, while NSP4 is mainly located on the side of the ER which will become the luminal face of the DMV. The segregation of NSP3/4 occurs via unknown mechanisms. NSP3/4 interaction and segregation promote membrane curving and protrusion of DMVs from the ER, which is probably regulated by VMP1-modulated PS distribution. In most DMVs, the outer membranes are connected to the ER, while some DMVs undergo membrane fission and are free-floating. The nascent viral RNAs are transported to the cytosol through membrane-spanning DMV pores, which contain NSP3.

Fig. 4

Modulation of autophagy by the SARS-CoV-2 viral proteins The SARS-CoV-2 viral proteins intersect with the autophagy pathway at multiple steps. SARS-CoV-2 promotes autophagosome initiation but blocks maturation of autophagosomes into degradative autolysosomes. SARS-CoV-2 ORF8 and NSP13 interact with MHC-I and TBK1, respectively, and promote their autophagic degradation to protect SARS-CoV-2-infected cells from immune attack. The NSP6 protein impairs autophagosome formation and also prevents lysosome acidification to inhibit autophagic degradation. SARS-CoV-2 ORF3a sequesters the HOPS component VPS39 to prevent the fusion of autophagosomes/amphisomes and lysosomes. NSP15 blocks autophagy induction, while ORF7a causes lysosome deacidification and thus inhibits auto-lysosomal degradation. M and E also inhibit the formation of acidified autolysosomes. Host factors which are both involved in autophagy and essential for SARS-CoV-2 replication are listed in the grey boxes.