S1 Table: Sequence of DNA substrates used in EMSAs
DNA Substrate
Name
33-34 intergenic
region – Fig. 2
DNase
Footprinting
substrate – Fig. 3
Region 1 – Fig. 3
Region 2 – Fig. 3
Region 3 – Fig. 3
Region 4 – Fig. 3
Region 5 – Fig. 3
TIR-1 – Fig. 3
TIR-2 – Fig. 3
TIR-3 – Fig. 3
TIR-4 – Fig. 3
TIR-5 – Fig. 3
TIR-6 – Fig. 3
Mt-2 – Fig. 4
Mt-3 – Fig. 4
Mt-4 – Fig. 4
Mt-5 – Fig. 4
Mt-6 – Fig. 4
Mt-7 – Fig. 4
Mt-8 – Fig. 4
Mt-9 – Fig. 4
Mt-10 – Fig. 4
Mt-11 – Fig 4
Mt-12 – Fig. 4
Mt-13 – Fig. 4
O6-L – Fig. 7
O6-R – Fig. 7
O27-R – Fig 7
O27-L – Fig. 7
OR-R – Fig. 7
ORep-L – Fig 7
O55-L – Fig. 7
O55-R – Fig. 7
O61-R – Fig. 7
O61-L – Fig. 7
5-6 intergenic
region – Fig. 7
26-27 intergenic
Sequence/Primers used
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG (starts at position 29,228 in BPs genome)
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC (ends at position 29,593 in BPs genome)
Fwd: TACGAAtctagaACCGGCGATTGTATGTAC
Rev: AGCTCC aagcttGTGCACCAACATAGCGAC
AACCGTGCATATCGCGCAATACACTTGCGACATACCGGCAACGTTGAAACAATCACGTTG
AACCGTGCATATCGCGCAATACAAACATTGTATGGTTGAAACAATCACGTTGCACGTTGC
AACCGTGCATATCGCGCAATACAAACTTCGGGCGTTGAAACAATCACGTTGCACGTTGCA
AACCGTGCATATCGCGCAATACAAACGGCGCATGTTGAAACAATCACGTTGCACGTTGCA
AACCGTGCATATCGCGCAATAAATAGACGACATATGTCGCAAACGTTGAAACAATCACGT
ACCGGCGATTGTATGTACGTCTGTCGCGTACGCGCAATAT
CGCGCAATATCGCCGTTCGTCAACCGTTGCGAGCGGAAAC
GAGCGGAAACGGCACGGCGCGTTGATCCTGGCAAACCGTC
GCAAACCGTCGGTGGTAACGGATTGCGTGGCAAACGCAAA
CAAACGCAAAAGTTCGGGCGTGGCGCATTTTCCAATAGAC
TCCAATAGACGACATATGTCGCT
Fwd: TTGGTGCACATGACCCCAACCGAAAC
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: TTCGGGCGTGGCGCATTTTCCAATAGA
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: TGGCAAACCGTCGGTGGTAACGGAT
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: GTTCGTCAACCGTTGCGAGCGGAAA
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: ACATACCGGCGATTGTATGTACGTCTGTC
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: ACGAAAGCCTGCTCGGCGGGATC
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: GTTTCGGTTGGGGTCATGTGCACCAA
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: TCTATTGGAAAATGCGCCACGCCCGAA
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: ATCCGTTACCACCGACGGTTTGCCA
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: tttccGCTCGCAACGGTTGACGAAC
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: GACAGACGTACATACAATCGCCGGTATGT
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
Rev: GATCCCGCCGAGCAGGCTTTCGT
CACACACGACGCTTGCACCGCGACATATGTCGGTTTTGCAGACGTGCAGGTT
GCATTTTCCAATAGAGGACATATGCGGCTATGTTGGTGCACA
GCATCACGGACGCTGCTATCCGACATATGTCGTGGATGATCGGGATATGGCC
GCATTTTCCAATAGACCGCATATGTCGCTATGTTGGTGCACA
GCATTTTCCAATAGACGACATATGTCGCTATGTTGGTGCACA
TTCGGGCGTGGCGCATTTTCCAATAGACGACATCTATGTTGGTGCACATGACCCCAACCG
TCGGACATGGTGAACGCTTGCGACATATGTCGCCAATGTGTGCATCTTTGCA
GCATTTTCCAATAGATGACACTTGTCGCTATGTTGGTGCACA
GCATTTTCCAATAGACGACATATGTGCCTATGTTGGTGCACA
GCATTTTCCAATAGACGACATTCGCGCCTATGTTGGTGCACA
Fwd: AACGTAGCCACACACGACGCTTGC
Rev: ATTCGCCATGCTGCTTGCTCCCGGT
Fwd: TGCCGTGGCGCTGATTCTGAGGTAA
Rev: GCATCGGGAAGAAACGATCGGCCAT
region – Fig. 7
Fwd: TCCGGCCCATATCGAATGCTTGCGACAT
33-34 intergenic
Rev: CGGTTGGGGTCATGTGCACCAACAT
region (226bp) –
Fig. 7
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG
33-34 intergenic
Rev: GTGTAGTGATCGCTTCGGAATGTCATGC
region (366bp) –
Fig. 7
Fwd: CACGGGGTAGCGGCTGTTCGTCG
54-55 intergenic
Rev: TGCGGGTTCTGGCTGGTGGGGTC
region – Fig. 7
Fwd: GGCGAGTTCGACGCGCCCGT
60-61 intergenic
Rev: TGGCCTTGTTGGTGTCGCGTGGAG
region – Fig. 7
Fwd: GTTCTTCTTGCTTCAAACCAGCTTCAAGG (starts at position 29,228 in BPs genome)
RepressorRev: GTGTAGTGATCGCTTCGGAATGTCATGC (ends at position 29,593 in BPs genome)
insensitive BPs
mutants 33-34 intergenic
region – Fig. 9
CACCGACGCGACATATGTCGACTGACGACATATGTCGCAGCCTGG
2 half sites 5bp
apart – Fig. 8
CACCGACGAAGTGCCACGATACTGACGACATATGTCGCAGCCTGG
Left half site
ablated (5bp
apart) – Fig. 8
CACCGACGCGACATATGTCGACTGAAAGTGCCACGATCAGCCTGG
Right half site
ablated (5bp
apart) – Fig. 8
ACCGACGCGACATATGTCGACGCTTGACGACATATGTCGCAGCCT
2 half sites 8bp
apart – Fig. 8
CCGACGAAGTGCCACGATACGCTTGACGACATATGTCGCAGCCTG
Left half site
ablated (8bp
apart) – Fig. 8
CCGACGCGACATATGTCGACGCTTGAAAGTGCCACGATCAGCCTG
Right half site
ablated (8bp
apart) – Fig. 8
Sequences corresponding to operator half sites are underlined.
Bold type denotes non-phage sequences
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