FIG. 6.
Interaction between loop 1 (L1) of the 3′ UTR pseudoknot (PK) and the 3′ end of the genome. (A) Refinement of the complete structure of the MHV 3′ UTR, incorporating base pairing of the 3′ end of the genome with both pseudoknot loop 1 and the region downstream of pseudoknot stem 2 (S2); other abbreviations are the same as those used in Fig. 1. Arrows indicate points at which truncations were introduced in the previously characterized ΔHVR2 deletion mutant (19) and in a new mutant, the ΔHVR3 mutant. (B) Phylogenetic conservation of the loop 1-3′-end interaction among all group 2 coronaviruses. GenBank accession numbers for the sequences shown, other than those given in the legend to Fig. 4, are as follows: HCoV-OC43, human coronavirus strain OC43, AF523847; and bat coronavirus (BatCoV) strains HKU4, HKU5, and HKU9, respectively, EF065505, EF065509, and EF065513. (C) Detailed view of the complete 164-nt 3′ UTR of the ΔHVR3 mutant. Broken lines represent alternative base pairings either for the bottom stem segment of the bulged stem-loop or for pseudoknot stem 1. Nucleotides of the tetraloop introduced between positions 29 and 171 are circled. Nucleotide numbering is from the first base at the 3′ end of the genome, excluding poly(A), and the N-gene stop codon is boxed.