t44 is an r5′UTR. (A) An Artemis window showing expression of the t44 sRNA (pink box) as the 5′ UTR of genes VS_2353 and VS_2352. The read cluster corresponding to the 5′-UTR part of the transcript (t44) is highlighted in salmon. (Yellow boxes) ARNold prediction of Rho-independent transcription terminators (see Materials and Methods). (Blue boxes) Annotated CDS. The orange line underneath indicates the position of the oligonucleotide probe used for the Northern blot. (B) Northern blot of t44. Total RNA samples were prepared from different time points during growth of V. splendidus in marine salt medium at 20°C and submitted to electrophoresis on an agarose gel before transfer to a Hybond N+ membrane. The culture OD600 for each sample is indicated above each lane. The membrane was hybridized with a [γ-32P]ATP-labeled oligonucleotide probe (Supplemental Table S2; Panel A for the position of the probe). The approximate size of the bands (determined by comparison with the position of RNA markers of known size) is indicated on the left.
