Detection of new potential asRNAs in RNase Y and J1 mutants.

<p>(A) Structure and predicted degradation pathways of the S520 RNA antisense to <i>yknT</i>. ORFs are shown as large white arrows, transcripts as thin black arrows. Scissors indicate cleavage by RNase Y, ‘Pacman’ symbols represent 5′-3′ degradation by RNase J1. A short thick line indicates the position of the probe used. Pσ^B indicates the putative promoter and sigma factor for the regulatory RNA predicted by the DBTBS website (<a href="http://dbtbs.hgc.jp/" target="_blank">http://dbtbs.hgc.jp/</a>) and in agreement with the size detected by Northern blot. (B) Northern blot of total mRNA isolated at times after addition of rifampicin (rif) from wild-type and RNase J1 depleted (<i>Pspac-rnjA</i>−IPTG) and RNase J1 induced (<i>Pspac-rnjA</i>+IPTG) cells. The blot was probed with 5′-labeled oligo CCB857 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002520#pgen.1002520.s015" target="_blank">Table S6</a>) and reprobed with oligo HP246 against 5S rRNA. The half-life of the S520 transcript is given under the Northern blot. Migration positions of RNA markers are shown to the right of the blot. (C) Structure and predicted degradation pathway of the S276 RNA antisense to <i>yfkF</i>. Features as in panel (A). (D) Northern blot of total mRNA isolated at times after addition of rifampicin (rif) from wild-type and RNase Y depleted (<i>Pspac-rny</i>−IPTG) and RNase Y induced (<i>Pspac-rny</i>+IPTG) cells. The blot was probed with 5′-labeled oligo CCB859 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002520#pgen.1002520.s015" target="_blank">Table S6</a>) and reprobed with oligo HP246 against 5S rRNA. Description as in panel (B).