Identification of DNA uptake sequences in 'Neisseria gonorrhoeae' that are intrinsic transcriptional terminators using bioinformatics supported by RNA-seq

'Neisseria gonorrhoeae' is the causative agent of the sexually transmitted disease gonorrhoea. It is naturally competent for transformation and DNA uptake sequences (DUS) are widespread throughout the 'N. gonorrhoeae' genome. DUS allow endogenous DNA to be exchanged between 'Neisseria' species, and also occur as inverted repeats (IR-DUS). Here we show that IR-DUS occur both where the DUS precedes the inverted DUS and also in reverse order. Due to the position of IR-DUS downstream of genes and operons, it has anecdotally been believed that these act as transcriptional terminators, forming hairpin structures. Due to their structure, IR-DUS can potentially act as bi-directional 'rho'-independent transcriptional terminators, therefore affecting transcription on both DNA strands. Using both bioinformatics predictions and experimental evidence, we demonstrate which IR-DUS across the gonococcal genome are transcriptional terminators and in which direction, identifying the sequence features characteristic of these.