Figure 5

Secondary structure prediction and experimental validation by Northern hybridizations of three selected sRNAs. For each of the three sRNA genes, the left column shows the sequence coverage profile derived from library 1 (grey color). The y- and x-axis represent coverage and sequence localization. Grey arrows represent flanking genes, white arrows represent the sRNAs and brown stem-loop structures represent Rho-independent terminators. The middle column displays Northern blot results of all tested conditions at time point of harvesting of C. glutamicum cells, respectively. Exp = Exponential phase (OD₆₀₀ 10), unstressed. Further conditions were heat, cold, diamide, NaCl, and H₂O₂ stresses, all applied for 15 minutes at an OD₆₀₀ 10. The right column presents the secondary structure with lowest minimum free energy (MFE). Structure, MFE and shape probabilities determined with RNAShapes [56]. Sequence code: blue, A; green, C; red, G; yellow, U. Validated intergenic sRNAs by Northern hybridizations are (a) cgb_03605 (6C RNA), (b) cgb_00105 and (c) cgb_20715.