N. gonorrhoeae encodes an anaerobically induced small RNA. (A) A schematic representation of the location of the fnrS coding region is given, with genes colored in grey encoded on the positive strand, and genes colored in black encoded on the negative strand (according to the NCBI annotation). Above the fnrS gene schematic, raw RNA-seq data from .wig files are plotted. The base count is representative of the number of times each base in the transcript was mapped by a 50 bp RNA sequence read from Replicate 1 (normalized to take into account slight differences in total mapped reads between the two samples). Blue bars represent aerobic base reads and red bars represent anaerobic base reads. A prediction of the -10 element and class-II FNR binding site is given to the left of the fnrS gene. The chromosomal location of the predicted transcriptional start site, in parenthesis under the +1, is reported. (B) The lowest energy structure of the fnrS transcript as predicted by the Mfold program http://mfold.rna.albany.edu/ is displayed. (C) The β-galactosidase activity of an fnrS::lacZ transcriptional fusion is presented as the mean + SD of 16 determinations (p < 0.001).