Figure 8.

Non-coding RNAs (ncRNAs).(Left) Sum of transcriptional activities from all 15 replicates (pooled RNA-Seq data). Black arrows indicate genes and green arrows the identified ncRNAs. (Right) Log-transformed NPKM values of ncRNAs and adjacent genes for single samples. (A)Indep RNA BLi_r0086 is transcribed constitutively with a length of 156 nt and located between the genes of threonyl-tRNA synthetase (thrZ, BLi00234) and a hypothetical protein (BLi00235). Both adjacent genes are also transcribed constitutively, but are less abundant by four and three orders of magnitude, respectively. (B) The differentially expressed indep transcript BLi_r1424 is located between the gene of a hypothetical protein (BLi01936) and a pseudogene (yobN, BLi01938) with a length of 251 nt. The TSS could be confirmed by dRNA-Seq. In the three early conditions the BLi_r1424 transcription level is low, but NPKM values of more than 12,000 were recorded during the productive stages of the fermentation process. A direct transcriptional connection to the adjacent BLi01936 is not visible from the shown NPKM values. (C) BLi_r2390 antisense to ytvB (BLi03176) and yttB (BLi03177) is an example for long antisense ncRNAs. The A_misc RNA occurs only in the later stages of the fermentation process, parallel to a distinct increase in transcriptional activity of ytvB, but does not exceed it regarding the NPKM value. (D) One example suggesting a regulatory function of A_misc RNAs is BLi_r0253, oriented antisense to BLi00413. In the earliest stage the asRNA shows stronger transcription than the corresponding gene, but in all later stages the asRNA is only weakly transcribed. This might indicate a silencing effect in the exponential stage. (E)A_I RNA BLi_r1596 localized antisense to the gene of the sulfate permease CysP2 (BLi02153). The transcription of both, the ncRNA and the protein-coding gene, starts during the late stages of the fermentation process.