Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae

Maintenance of an anaerobic respiratory system in the obligate human pathogen, Neisseria gonorrhoeae, suggests that an anaerobic lifestyle may be important during the course of infection. However, at this point there have been no studies analyzing the complete gonococcal transcriptome response to anaerobiosis. Here we performed deep sequencing to compare the gonococcal transcriptomes of aerobic and anaerobically grown cells. We found that the anaerobic stimulon in gonococci was large, and that 198 chromosomal genes were found to be differentially expressed. We also observed a large induction of genes encoded within the cryptic plasmid, pJD1. Secondary analysis of genes found to be differentially expressed by RNA-seq using translational-lacZ fusions or RT-PCR demonstrated the RNA-seq results to be very reproducible. Surprisingly, many genes of prophage origin were induced anaerobically, as well as several transcriptional regulators previously unknown to be involved in anaerobic growth. We also confirmed expression and regulation of a small RNA, likely a functional equivalent of fnrS in the Enterobacteriaceae family. Several novel factors were identified to be anaerobically regulated, as well as a large number of hypothetical proteins were induced. Overall design: Two biological replicates of cells grown aerobically or anaerobically with nitrite were analyzed, for a total of four samples subject to SOLiD RNA sequencing.