TABLE 2.

Oligonucleotides used in this study

Primer	Sequence (5′→3′)	Use and/or source
oMC44	5′-CTAGCTGCTCCTATGTCTCACATC-3′	69
oMC45	5′-CCAGTCTCTCCTGGATCAACTA-3′	69
oMC112	5′-GGCAAATGTAAGATTTCGTACTCA-3′	tcdB (CD0660) qPCR, 28
oMC113	5′-TCGACTACAGTATTCTCTGAC-3′	tcdB (CD0660) qPCR, 28
oMC189	5′-TGCCTCTTGTAAAGAGTATAGCA-3′	sigD (CD0266) qPCR, 24
oMC190	5′-GCATCAATCAATCCAATGACTCCAC-3′	sigD (CD0266) qPCR, 24
oMC331	5′-CTCAAAGCGCAATAAATCTAGGAGC-3′	spo0A (CD1214) qPCR, 28
oMC332	5′-TTGAGTCTCTTGAACTGGTCTAGG-3′	spo0A (CD1214) qPCR, 28
oMC333	5′-AGTAAGGGTATGGGCAAAGTATTACA-3′	CD1579 qPCR, 24
oMC334	5′-CCACTTCATTTGAGAACAACTCTTTG-3′	CD1579 qPCR, 24
oMC335	5′-ACTTGTAAGAAGTGCTGAAGGTGGTA-3′	CD1492 qPCR, 24
oMC336	5′-GTCATATCGACCAAATCACTTGAAACAC-3′	CD1492 qPCR, 24
oMC337	5′-CAGGAATTTGTGACTATCTGGGAAATGG-3′	CD2492 qPCR, 24
oMC338	5′-TCCCATTTGCCTTTATTTGAACTTGA-3′	CD2492 qPCR, 24
oMC339	5′-GGGCAAATATACTTCCTCCTCCAT-3′	sigE (CD2643) qPCR, 28
oMC340	5′-TGACTTTACACTTTCATCTGTTTCTAGC-3′	sigE (CD2643) qPCR, 28
oMC355	5′-CTGTTGGAATATCTAGGCGATAAGC-3′	rstA (CD3668) qPCR, 24
oMC356	5′-TGGTCCTCAGCCTTGTTTAATTC-3′	rstA (CD3668) qPCR, 24
oMC365	5′-GGAAGTAACTGTTGCCAGAGAAGA-3′	sigF (CD0772) qPCR, 28
oMC366	5′-CGCTCCTAACTAGACCTAAATTGC-3′	sigF (CD0772) qPCR, 28
oMC547	5′-TGGATAGGTGGAGAAGTCAGT-3′	tcdA qPCR (CD0663), 28
oMC548	5′-GCTGTAATGCTTCAGTGGTAGA-3′	tcdA qPCR (CD0663), 28
oMC569/tcdRqF	5′-AGCAAGAAATAACTCAGTAGATGATT-3′	tcdR qPCR (CD0659), 40
oMC570/tcdRqR	5′-TTATTAAATCTGTTTCTCCCTCTTCA-3′	tcdR qPCR (CD0659), 40
oMC897	5′-GCCATGGATCCTTGGAAGAATTGTGGTAACATATTTATAG-3′	CD1492 cloning
oMC898	5′-GATGCCTGCAGACGCATCAAATACAACTAAAGTAATAAA-3′	CD1492 cloning
oMC911	5′-GCGCGGCCGCGAGTAGGAAATCTGGCTTAT-3′	CD1492 deletion construct
oMC912	5′-ACAACTAAAGCACTTCTTCATTTTTATATAGTTTTACC-3′	CD1492 deletion construct
oMC913	5′-TGAAGAAGTGCTTTAGTTGTATTTGATGCGTTTTA-3′	CD1492 deletion construct
oMC914	5′-GCGCGGCCGCCAGCCTTGTCATTTTTTAGATTG-3′	CD1492 deletion construct
fliCqF	5′-TACAAGTTGGAGCAAGTTATGGAAC-3′	40
fliCqR	5′-GTTGTTATACCAGCTGAAGCCATTA-3′	40