Figure 5.

An abundant putative small RNA encoded in Cpn0332. (a) Visualization of sequencing reads of the CPn0332 locus. Grey bars represent untreated total RNA libraries and red bars represent libraries of RNA treated with TEX and thus are enriched for primary transcripts. The upper line shows sequence reads obtained from EBs and the lower those from RBs. Black bars show annotated genes and coordinates of the genome. A highly abundant transcript is co-transcribed with ltuB. It ends 18 nucleotides upstream of the annotated stop codon of CPn0332 and lacks an alternative ORF. (b) Northern blot analysis of the abundant transcript reveals several bands ranging from approximately 70 to 250 nucleotides. The probe binding site is marked by a vertical arrow in (b). (c) Alignment of the locus downstream of ltuB shows homology between all available Chlamydia genomes and the two C. trachomatis strains B and L2. The boxed area marks the start codon of the annotated gene CPn0332, which is not conserved. (d) The RNA consensus secondary structure estimated from the RNA sequence alignment in (c). The colors indicate the base pair probabilities. The accumulation of red collared base pairs indicates the high reliability of the estimated consensus structure. The free energy of the thermodynamic ensemble is -106.37 kcal/mol.