Rev1.2 -9.9 kcal/mol 3-8 cycles

Starting deletion mutant

Rev1.1 -5.9 kcal/mol 3 cycles

Rev1.2 -9.9 kcal/mol 3-8 cycles

Figure 15-9 Evolutionary reconstruction of the deleted coat-protein initiator hairpin in MS2 RNA. A: At the sequence level and B: at the level of secondary structure. In the starting deletion mutant (bottom left) 19 nucleotides have been deleted and coat protein synthesis could no longer be detected. In Rev2.1 a specific 14 nucleotide duplication (bold italics) has occurred that restores both the initiator hairpin and the A-protein terminator hairpin as well as the Shine-Dalgarno (SD) sequence. Panel B shows that in Rev3.1 and Rev2.2 the terminator is further polished by replacing the GG mismatch by G U and G-C, respectively (black boxes). Rev2.3 acquires another 4 nucleotides that enlarges the distance between the two hairpins. In Rev 2.4, finally, the SD sequence is extended with one nucleotides and the distance between the hairpins is back to wild-type but for one nt. In Rev1.1, the SD sequence and the initiator hairpin are restored by a 6 nucleotides deletion. The terminator hairpin is sacrificed. In Rev1.2, the same A ! G substitution is selected as in Rev2.4 and Rev3.1. This change extends the SD sequence by one nucleotide. In panel A stop codon of the A-protein gene and start codon of the coat protein are shaded. The SD sequence is in bold and suppressor mutations are in lower-case. In panel B suppressor mutations are in black boxes. SD sequences and coat-start codon are boxed. Note that the starting mutant has two accidental base substitutions, three and six nucleotide 3' to the start codon.

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