A Systemic and Molecular Study of Subcellular Localization of SARS-CoV-2 Proteins

Abstract

Coronavirus possesses the largest RNA genome among all the RNA viruses. Its genome encodes about 29 proteins. Most of the viral proteins are non-structural proteins (NSP) except envelop (E), membrane (M), nucleocapsid (N) and Spike (S) proteins that constitute the viral nucleocapsid, envelop and surface. We have recently cloned all the 29 SARS-CoV-2 genes into vectors for their expressions in mammalian cells except NSP11 that has only 14 amino acids (aa). We are able to express all the 28 cloned SARS-CoV-2 genes in human cells to characterize their subcellular distributions. The proteins of SARS-CoV-2 are mostly cytoplasmic but some are both cytoplasmic and nuclear. Those punctate staining proteins were further investigated by immunofluorescent assay (IFA) using specific antibodies or by co-transfection with an organelle marker-expressing plasmid. As a result, we found that NSP15, ORF6, M and ORF7a are related to Golgi apparatus, and that ORF7b, ORF8 and ORF10 colocalize with endoplasmic reticulum (ER). Interestingly, ORF3a distributes in cell membrane, early endosome, endosome, late endosome and lysosome, which suggests that ORF3a might help the infected virus to usurp endosome and lysosome for viral use. Furthermore, we revealed that NSP13 colocalized with SC35, a protein standing for splicing compartments in the nucleus. Our studies for the first time visualized the subcellular locations of SARS-CoV-2 proteins and might provide novel insights into the viral proteins' biological functions.

SARS-CoV-2 Nsp14 activates NF-κB signaling and induces IL-8 upregulation

“…Nsp14 may manipulate IMPDH2 to increase the phosphorylation of IKKβ and IκBα to promote nuclear translocation and phosphorylation of p65 (24). In addition, we also noticed that Nsp14 partially localizes in the nuclei of cells (Fig 1C, D), similar to findings from other groups (51,52). Thus, Nsp14 may associate with and modify the host cellular RNAs via its exonuclease and methyltransferase activities.…”

Characterization and structural prediction of the putative ORF10 protein in SARS-CoV-2

“…A prior study found the ORF10 protein colocalized with accessory proteins 7b and 8 in the endoplasmic reticulum (ER); however, its role in the ER was not described. 47 In this case, the ORF10 protein may oligomerize and form a viroporin that associates with ER membranes as a means to assist in viral replication and/or processing of other viral proteins. Alternatively, the ORF10 protein could be interacting with another protein.…”

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

“…Information about what each study was investigating and how we determined the ORF referred to is provided in Supplementary Table 1 . ORF called “ORF3b” in study Recommended name Study type Studies (first author and citation) 22 codon ORF ORF3b Genome report (F. Wu et al, 2020a ) Empirical ( Konno et al, 2020b ; Lokugamage et al, 2020 ; Xia et al, 2020 ; Zhang et al, 2020 ) Review Sa Ribero et al (2020) 57 codon ORF ORF3d Genome Report Chan et al (2020) Empirical ( Banerjee et al, 2020 ; Gordon et al, 2020 ; Hachim et al, 2020 ; Hayn et al, 2020 ; Lam et al, 2020 ; Laurent et al, 2020 ; Samavarchi-Tehrani et al, 2020 n.d.; St-Germain et al, 2020 ) Laboratory resource - sequence clone collection (D.-K. Kim et al, 2020a ) Computational ( Michel et al, 2020 ; Pasquier and Robichon, 2020 ; Sadegh et al, 2020 ) Review ( Celik et al, 2020 ; Garofalo et al, 2020 ; Helmy et al, 2020 ; Taefehshokr et al, 2020 ; J. Wu et al, 2020b ; Yang et al, 2020 ; Yi et al, 2020 ; Yoshimoto, 2020 ; Zinzula, 20...…”