Severe acute respiratory syndrome coronavirus 2 may exploit human transcription factors involved in retinoic acid and interferon-mediated response: a hypothesis supported by an in silico analysis

Abstract

The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19), resulting in acute respiratory disease, is a worldwide emergency. Because recently it has been found that SARS-CoV is dependent on host transcription factors (TF) to express the viral genes, efforts are required to understand the molecular interplay between virus and host response. By bioinformatic analysis, we investigated human TF that can bind the SARS-CoV-2 sequence and can be involved in viral transcription. In particular, we analysed the key role of TF involved in interferon (IFN) response. We found that several TF could be induced by the IFN antiviral response, specifically some induced by IFN-stimulated gene factor 3 (ISGF3) and by unphosphorylated ISGF3, which were found to promote the transcription of several viral open reading frame. Moreover, we found 22 TF binding sites present only in the sequence of virus infecting humans but not bat coronavirus RaTG13. The 22 TF are involved in IFN, retinoic acid signalling and regulation of transcription by RNA polymerase II, thus facilitating its own replication cycle. This mechanism, by competition, may steal the human TF involved in these processes, explaining SARS-CoV-2's disruption of IFN-I signalling in host cells and the mechanism of the SARS retinoic acid depletion syndrome leading to the cytokine storm. We identified three TF binding sites present exclusively in the Brazilian SARS-CoV-2 P.1 variant that may explain the higher severity of the respiratory syndrome. These data shed light on SARS-CoV-2 dependence from the host transcription machinery associated with IFN response and strengthen our knowledge of the virus's transcription and replicative activity, thus paving the way for new targets for drug design and therapeutic approaches.

Keywords: ISGF3; Interferon regulatory factors; SARS-CoV-2; retinoic acid.

Fig. 1

Schematic overview of genome, genes and proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). (A) SARS-CoV-2 genome comprises positive-sense, single-stranded RNA (ssRNA) genome 27 to 32 kb in size. The 5′ terminus (translated from first ORF1a and ORF1b) encodes two large polyproteins, pp1a and pp1ab, which are proteolytically cleaved into 16 nonstructural proteins (NSPs), including papain-like protease (PLpro), 3C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp). An additional 9 to 12 open reading frames (ORFs) are encoded through transcription of nested set of subgenomic RNAs. The 3′ terminus encodes structural proteins, including envelope glycoproteins spike (S), envelope (E), membrane (M) and nucleocapsid (N). (B) Percentage distribution of transcription factor (TF) binding sites in different genomic regions of SARS-CoV-2, as follows: ORF1ab, open reading frame 1ab; S, protein S; ORF3a, open reading frame 3a; E, protein E; M, protein M; ORF6, open reading frame 6; ORF7a, open reading frame 7a; ORF7b, open reading frame 7b; ORF8, open reading frame 8; N, protein N; ORF10, open reading frame 10.

Fig. 2

Interferon-stimulated gene factor 3 (ISGF3)-induced and unphosphorylated ISGF3 (U-ISGF3)-induced transcription factors (TF) with binding sites present in different genomic regions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as follows: (1) ORF1ab, open reading frame 1ab; S, protein S. (3) ORF3a, open reading frame 3a; E, protein E; M, protein M. (6) ORF6, open reading frame 6. (7) ORF7a, open reading frame 7a. (8) ORF7b, open reading frame 7b. (9) ORF8, open reading frame 8; N, protein N. (11) ORF10, open reading frame 10.

Fig. 3

Polymorphisms affecting transcription factor (TF) binding sites in P.1 Brazilian severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant. (A) Mutation 26150 T/C causes formation of binding site for SPEDEF TF in P.1 sequence. (B, C) Mutation 6320 A/G leads to enrichment for binding sites of GRHL1 and TFCP2 TF.

Fig. 4

Network analysis of transcription factors (TF) exclusively binding genomic region of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from humans. Twenty-two TF formed a significant network (p 8.27e-13) showing their involvement in retinoic acid signalling through direct binding of retinoic acid receptor RXR-alpha gene by NR1H3, KLF5, THRB and PAX6 TF and indirect binding of remaining TF.