Transcriptomes of ?relAspoT and ?dksA mutants of Haemophilus ducreyi in mid-log, transition, and stationary phase

To better understand the role of the (p)ppGpp-mediated stringent response in control of H. ducreyi virulence determinants, here we defined genes potentially regulated by either (p)ppGpp or DksA by using RNA-seq. We were able to show that loss of either (p)ppGpp or DksA resulted in dysregulation of multiple genes including several known virulence determinants. We also show that loss of (p)ppGpp or DksA resulted in differential expression of putative H. ducreyi small RNAs. Overall design: RNA of Haemophilus ducreyi wildtype, relAspoT and dksA mutants were collected at mid-log, transition, and stationary phases of growth, in quadruplicate using stranded RNA -seq.