TABLE S1. Primers used in this study
Primer name
NEW-VC2433-SacI#1
NEW -VC2433#2
NEW -VC2433#3
NEW -VC2433XbaI#4
Sequence
(given in 5’ to 3’ direction)
CGCGAGCTCAAATGACCTATCAACTGCAAGTGC
CTTGGCGACTTACTCGGGTGTGTGGTCTTGCGAAAT
ATCC
ACACCCGAGTAAGTCGCCAAGCACAGTAATGTGAA
AGCC
CGCTCTAGATAACCGCCTAATGAACTTCCGACC
R-XmaI-clpX
VC1879-up-EcoRI
VC1879-down-XmaI
XmaI-comEA for gfp
GCCGAATTCCCGGGCCGCCATGTCCCTATAATGCG
AC
CGGGACGTCAACGCTGCCCGAGATGCGCCGCG
GCCGATATCAGGCCTTCACACAGGAAACAGCTATG
ACC
GCCGGATCCGGGGATCCTCTAGAGTCAAAAGG
GCCGGATCCATCATGAACAATAAAACTGTCTGCTT
AC
GCCGGATCCTGCCAGTGTTACAACCAATTAACC
CTGGCGGGTGTGATCAGTGTGTTG
PGATAGACCCTCATTTTGGTTGTTG
GCGCCTAGGTCTAGAGCACAGCGAAACAGCTCAAT
CCCG
CTAAATCATCAATTCAATTAAGGTAAAACC
GCGAGGTGATCGAGTTCGTGCTGTACACAG
CCGTAGAATTCGTCCGGATGCTGTCATTTGGGTC
CCAAGAATTCGGCTTTCTTATCGAGTATTCCTGC
CCAACCCGGGTTCTCAATCCTAGAGATGTTGAATG
CCAAGAATTCTTTAAGACGCAACCAAGGTCACAAC
C
CCAACCCGGGAGAGCCATTATCCCTCTATAGTTTGA
TCG
CCAAGAATTCGCGAACAAGTGCGTCAGCAAGCC
CCAACCCGGGTACTCTCTCCGGATAGTCACTCTCAG
G
CCAAGAATTCAATCCGTAAACCGGACTCCTCTCG
CCAACCCGGGTCACTCAAGGTGTAAGCCTCGCGAT
AAC
CCAAGAATTCATACAGGCCAGCCAATCGAAGTGAT
TG
CCAACCCGGGTCGCTAACCTCTTAGCCTTTACTCAC
CCAAGAATTCAGCCATAATCATTTGGCTGGGCAG
CCAACCCGGGGAAAATTCATTAAACGGTTTATGCC
GTTGCCCGGGGATAGACCCTCATTTTGGTTGTTG
StuI-pilA for dsRed
GTTGAGGCCTCTAAATCATCAATTCAATTAAGG
araC-rev_XmaI
GCGCCCGGGATTCTGCAAACCCTATGCTACTCCG
AACCCGCGGCCGCTCCCGGCGGATTTGTCCTACTC
AGG
AATGTGCTGGGCAACGACTG
GAGCCAAAGTTACCTTGGCC
CTCTGTCTCTGGATATCGCG
F_GFP-EcoRI/SmaI
R_GFP-AatII
F_dsRed-EcoRV/StuI
R_dsRed-BamHI
F_KanR
R_KanR
F-[VC1917]-200-up
P-[VC1917] reverse
F_pilA-AvrII-XbaI
p(VC2423+99+STOP)
F-P[VC0047]
R-[VC0047]-EcoRI
F-EcoRI-[hapA]
R-XmaI-[hapA]
F-EcoRI-gyrA
R-XmaI-gyrA
F-EcoRI-recA
R-XmaI-recA
F-EcoRI-ftsH
R-XmaI-ftsH
F-EcoRI-clpX
pBADterm_bck_NotI
gyrA-157-fwd
gyrA_332_bwd
qRT_recA_fwd
Comments
PCR of flanking
regions of gene
VC2433 to create
knock-out plasmid
pGP704-28-SacBΔcpdA
PCR of promoterless
gfp gene
PCR of promoterless
dsRed gene
PCR of aph gene
PCR of comEA
promoter region
PCR of pilA promoter
region
PCR of VC0047-50
promoter region
PCR of hapA
promoter region
PCR of gyrA promoter
region
PCR of recA promoter
region
PCR of ftsH promoter
region
PCR of clpX promoter
region
PCR of comEC
promoter region
PCR of [PcomEA]-[PpilA]
(“promoterswapping”)
PCR fragment araCPBAD-tfoX-amplified
from pBAD-tfoX-stop
qRT-PCR for gyrA
transcription
qRT-PCR for recA
qRT_recA_bwd
qRT_ftsH_fwd
qRT_ftsH_bwd
qRT_clpX_fwd
qRT_clpX_bwd
NEW_pilA_283_fwd
NEW_pilA_453_bwd
comEA_50_fwd
comEA_224_bwd
comEC_1029_fwd
comEC_1186_bwd
pilM_218_fwd
pilM_415_bwd
VC0047-573-fwd
VC0047-742-bwd
dprA_115_fwd
dprA_309_bwd
dns_276_fwd
dns_443_bwd
GCATAAACCGGATCCAGTGC
TGGTCAAGGCCAGATTCAGG
TTGCTCTTCAGGAGGCGTAC
GTTCGCAAACTGATCGCAGG
CGGCTAGCACTTTTTTGGCG
ATTGCCCCAACAGCATCAGG
TGTTGCACCTGCAGTACAGC
CGACATTACCGTTACTGGCC
CCGTTGGCTTCTCGATAATCG
GGTCGCGATTGTTCTCTACC
CCAAATTGTACAGAACTGCCG
CGATAGCAATCCCGGATAGC
ACACTTGGAAGGTCGTCGTG
CGAGGTAGCACAGTATCAAC
GCTCCTCAAGATCGACTTCTG
ACGCCTAAGCAATGGTTGGC
AATAAACAGGACGGGAGGCG
GCAATGCTGGCAACAAGGTG
CCATAGGTGACGCCATCAAC
transcription
qRT-PCR for ftsH
transcription
qRT-PCR for clpX
transcription
qRT-PCR for pilA
transcription
qRT-PCR for comEA
transcription
qRT-PCR for comEC
transcription
qRT-PCR for pilM
transcription
qRT-PCR for
VC0047 transcription
qRT-PCR for dprA
transcription
qRT-PCR for dns
transcription