Effect of extension of the terminator stem of sgrS on transcription termination. (A) DNA sequences of sgrS-S-rplLT and sgrS-S-LS1-rplLT. The sequence corresponding to the sgrS-S is shown as regular letters, whereas the terminator sequence derived from the rplL is shown as italic letters. The inverted repeat sequences are indicated by horizontal arrows. Nucleotides are numbered from the site corresponding to the 5′ end of sgrS-S. The inserted sequences to stabilize the terminator stem are shown as bold letters. (B) The predicted secondary structures and the thermodynamic stabilities (ΔG, kcal/mol) of terminator RNA hairpins without poly(U) sequence were determined according to the Mfold program (Zuker 2003). (C) Analysis of transcription termination. TM772 (ΔsgrS Δhfq) cells harboring indicated plasmids were grown in LB medium. At A600 = 0.6, 0.02% arabinose was added and incubation was continued for 5 min. Total RNAs were prepared, and 10 or 0.25 µg of RNA samples was subjected to Northern blotting using the SgrS-S probe and tmRNA probe, respectively.
