Extended Data Fig. 9: DE, gene, and protein expression analyses.
(a) Enrichment of the CAAAAA motif in DE genes compared to non-DE ones either globally (left, n = 3,649 genes) or at each time point studied (right, nEXP = 3,641, nSPO_9 = 3,636, n SPO_10.5 = 3,644, nSTAT = 3,642). For box plots, the middle line indicates the median value, boxes are 25th and 75th quartiles, and whiskers indicate 1.5 times the interquartile range. * P < 0.05, ** P < 10-2, *** P < 10-3 (one-sided Mann-Whitney-Wilcoxon rank sum test with continuity correction). (b) Time-course change in the expression of genes under the control of the specific sigma factors (σF, σE, σG, and σK) and master transcriptional activator Spo0A at both 9 and 10.5 h after sporulation induction (respectively n = 121 and n = 124 genes). (c) Representative immunoblot time-course (from n = 2 independent biological replicates with similar results) comparing the levels of the early sporulation proteins σF, SpoIIQ, σE, and SpoIVA in WT and ∆camA at 8, 10, 12, 14, and 16 h following induction of sporulation. (d) Western blot for TcdA for each C. difficile genotype. (e) RT-qPCR of spoVD and cwp17 genes (n = 3 independent biological replicates) of exponential and stationary phase liquid broth cultures. Data is presented as mean ± standard deviation. * P < 0.05, ** P < 10-2, two-tailed unpaired Student’s t-test.
