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. 2020 Oct 19;9(10):2322. doi: 10.3390/cells9102322

Figure 1.

Figure 1

Alterations of BCoV genome structures under persistent infection. (A) Schematic diagram of the BCoV genome structure. (B) Cis-acting RNA elements SLs I-III at the 5′-proximal region of the BCoV genome. The core sequences of the leader (CS-L; UCUAAAC) in the transcription regulatory sequence (TRS) are shaded in gray. ΔG: free energy. (C–F) Altered SL I structure caused by nt mutations (indicated in red) at the 5′ terminus of the BCoV genome during persistent infection. The nt deletion is indicated with a red dot. (G) Altered SL III structure due to mutation at nt 73 (indicated in red). The core sequences of the leader (CS-L; UCUAAAC) in the TRS are shaded in gray. (H) Poly(A) tail length at the 3′ terminus of the BCoV genome at different times of acute and persistent infection. Inf.: infection. (I) Upper panel: Illustration of core sequences of leader TRS (TRS-L) and body TRSs (TRS-B) TRS1, TRS2 and TRS3 in the BCoV genome employed for the synthesis of sgmRNA 12.7. Lower panel: The structure of the synthesized sgmRNA 12.7 with TRS2 (Wt-sgmRNA 12.7) or TRS1 (p95-sgmRNA 12.7). (J) Location of the mutated aa in the BCoV genome (except for nsp16 and S protein) during persistence. Wt (48 h): Viral RNA collected from fresh HRT-18 infected with wt BCoV at 48 hpi. Wt (95 d): Viral RNA collected from HRT-18 cells after 95 d of persistent infection with wt BCoV. (K) Linear schematic of nsp16 showing the positions of the conserved catalytic tetrad (K-D-K-E) and identified aa alterations during persistence. The aa deletion is indicated with a dash. (L) Linear schematic of BCoV S protein with subunits S1 (domains A–D) and S2 (FP, HR1 and HR2) showing the positions of the aa alterations identified during persistence. The residue numbering is based on the BCoV Mebus strain spike protein (GenBank: U00735) with domain boundaries based on the HCoV-OC43 S structure [33]. 32K: 32 kDa protein, HE: hemagglutinin/esterase, S: spike protein, 12.7: 12.7 kDa protein, E: envelope protein, M: membrane protein, N: nucleocapsid protein, FP: fusion peptide, HR1: heptad repeat 1, HR2: heptad repeat 2.