Analysis of differential gene expression in Streptococcus sanguinis wild type and ssaACB deletion mutant strains before and after adjustment of the pH from 7.4 to 6.2.

The purpose of this study was to determine what genes were differentially expressed in a Streptococcus sanguinis mutant deleted for the SsaACB manganese transporter, which underwent growth arrest upon shifting the pH to 6.2 with HCl vs. its wild-type parent, SK36, which continued to grow normally. The WT and mutant strain, JFP169, were grown in a fermenter with minimal aeration in BHI broth. RNA-seq was used to compare gene expression from samples taken 20 minutes prior to addition of HCl to samples taken 10, 25, and 50 min after addition. Samples were treated to deplete ribosomal RNA, then sequenced on a MiSeq sequencer, producing paired-end 75-base reads. Sequences were trimmed and filtered and expression levels determined using the DE-Seq module in the Geneious Prime program. Overall design: Expression was compared at four time points, one 20 min prior to adjustment of the pH to 6.2 and the other three at 10, 25, and 50 min after pH adjustment. Four biological replicates were analyzed for each time point.