Elimination of SpyCIM1 alters global transcription patterns.

<p>RNA was isolated from SF370SmR or CEM1Δ4 at the onset of logarithmic growth (Early Log) or immediately before the cells entered stationary phase (Late Log); the cells were either grown at 37°C (<b>panel A</b>) or 39°C (<b>panel B</b>). Samples were then analyzed by RNA sequencing (RNA-Seq). In the ratio of gene expression from SF370SmR compared to CEM1Δ4 for values greater than 3 or less than -3 are plotted against the corresponding gene identification number from the SF370SmR annotation [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145884#pone.0145884.ref001" target="_blank">1</a>]. The MMR operon showed that no difference in expression was observed between the strains during early log phase but that the transcription of these genes was inhibited in SF370SmR at late log phase, in agreement with previous studies [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145884#pone.0145884.ref015" target="_blank">15</a>]; an expanded view of this region is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145884#pone.0145884.s003" target="_blank">S3 Fig</a>. Notable genes whose expression was altered in SF370SmR or CEM1Δ4 are identified. The ticks on the X-axis mark every 500 genes. Legend: Act–acetate CoA-transferase operon; <i>act</i>–acetyltransferase Spy154; <i>adhA</i>–alcohol dehydrogenase; <i>citM</i>—Mg2+/citrate complex transporter; <i>cspR</i> - 23S rRNA methyltransferase; CT- conserved transmembrane protein Spy0169; <i>dap</i>—diaminopimelate epimerase; <i>emm1</i> –M protein; <i>glfP</i>—glycerol uptake facilitator; <i>grab</i>—protein G-like alpha2-macroglobulin-binding protein; <i>has</i>–hyaluronic acid capsule operon; His–histidine catabolism operon; Hyp–gene encoding a protein of unknown function; <i>lctO</i>–lactate oxidase; MFS–uncharacterized major facilitator family protein (Spy1392); MMR–MMR operon; ϕMTP–phage major tail protein; <i>norA</i>—antibiotic resistance protein NorA; Nuc–nucleotide interconversions operon; <i>pbuG</i>—guanine-hypoxanthine permease; <i>pncA</i>—pyrazinamidase/nicotinamidase; <i>prtS</i>—cell envelope proteinase PrtS; PTS—mannose/fructose PTS system operon; <i>pur</i>–purine biosynthesis operon; sclA—collagen-like surface protein SclA; <i>slo</i>–streptolysin O operon; SpyCIM1 –phage-like CI. The identification of the SpyCIM1 genes is described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145884#pone.0145884.s001" target="_blank">S1 Fig</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145884#pone.0145884.s005" target="_blank">S1 Table</a>.