Figure 5

RNA structures affecting translation at T4-related phage TIRs. Panel A shows stem-loop regions that inhibit translation from early transcripts containing gene e. a) Phages are grouped if they have identical TIR regions. Other phages with e leaders identical to T4 include: T4T, T2, T6, RB18, RB26, RB32 and RB51. Those having gene e but no apparent RNA structure in the TIR: Aeh1, 44RR, 25, 31 & FelixO1. Phages examined but with no apparent gene e: RB16, RB43, RB49, phi-1, syn9, S-PM2, PSSM2, PSSM4, 65, 133, KVP40, nt-1, acj009, acj61. b) Gene e TIR nucleotides are marked with asterisks. Arrows mark the stems of the likely structures, which was demonstrated for T4 [98]. T4 bases noted with + are the mapped 5' transcript ends from the upstream late promoter (TATAAATA; shaded). Sequences were obtained from GenBank or the T4-type phage browser at http://phage.ggc.edu/. c) RNA folding and ΔG values were by the method of M. Zuker (http://mfold.rna.albany.edu/). Panel B shows the conserved stem at the gene 25 TIR of approximately 30 T-even related phages. Nucleotides of the TIR are indicated with an asterisk, with less conserved adjacent nucleotides noted with N. Panel B was derived from the data of [109].