The dynamic transcriptome of natural competence in Streptococcus suis

Streptococcus suis is a major pig pathogen as well as an emerging zoonotic pathogen. In a previous study (Zaccaria et al. Plos One DOI: 10.1371/journal.pone.0099394) we identified the natural pheromone-induced competence system of S. suis. To identify the mechanisms enabling competence, gene expression analysis of bacteria induced or not for competence, and in presence or absence of exogenous DNA, was assessed at 5, 15 and 45 minutes after pheromone addition. The transcriptomes showed how competence was induced and eventually shut down, and which metabolic pathways were repressed or induced when competence was active or shut down. In this experiment, S. suis bacteria were grown in THB, exposed to three different conditions and RNA was extracted at three different timepoints: 5, 15 and 45 minutes after the zer timepoint which was essentially the induction of competence. The three conditions were: bacteria were (i) either growing in THB with no other additions, or (ii) grown in THB in the presence of competence-inducing pheromone but without exogenously added DNA, or (iii) grown in presence of pheromone and exogenous DNA. RNA samples extracted from the bacteria were hybridised once per array. ----------------------------- The samples above refer to the raw array data shown in the Matrix worksheet. The corresponding biological comparisons and their statistics are shown in the separate worksheet, Array Results. The samples are as follows: Sample 1: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA Sample 2: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide (No DNA) Sample 3: suis WT O.D. 0.04 + DNA 45’ (No peptide) VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA Sample 4: suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + DNA 15’ (No peptide) Sample 5: suis WT O.D. 0.04 + Pep 15’ (no DNA) VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA Sample 6: suis WT O.D. 0.04 + DNA 15’ (No peptide) VS suis WT O.D. 0.04 + DNA 45’ (No peptide) Sample 7: suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA VS suis WT O.D. 0.04 + 15 minutes of incubation with competence peptide and DNA Sample 8: suis WT O.D. 0.04 + 5 minutes of incubation with competence peptide and DNA VS suis WT O.D. 0.04 + 45 minutes of incubation with the competence peptide and DNA