Table 1 Bacterial strains and plasmids used in this study.

From: Comparative analysis reveals regulatory motifs at the ainS/ainR pheromone-signaling locus of Vibrio fischeri

Strain, plasmid, or oligonucleotide

Relevant characteristicsa

Source or reference

Strains

E. coli

CC118λpir

Δ(ara-leu) araD Δlac74 galE galK phoA20 thi-1 rpsE rpsB argE(Am) recA λpir

68

DH5α

F-φ80dlacZΔM15 ∆(lacZYA-argF)U169 deoR supE44 hsdR17 recA1 endA1 gyrA96 thi-1 relA1

63

DH5α λpir

DH5α lysogenized with λpir

64

JW1644-5

∆(araD-araB)567 ∆(lacZ4787(::rrnB-3)) λ- ∆(rnt-730::kanR) rph-1 F- ∆(rhaD-rhaB)568 hsd514

52

JW1793-1

∆(araD-araB)567 ∆(lacZ4787(::rrnB-3)) λ- ∆(rnd-729::kanR) rph-1 F- ∆(rhaD-rhaB)568 hsd514

51

JW3618-2

∆(araD-araB)567 ∆(lacZ4787(::rrnB-3)) λ- ∆(rph-749::kanR) rph-1 F- ∆(rhaD-rhaB)568 hsd514

51

JW5741-1

∆(araD-araB)567 ∆(lacZ4787(::rrnB-3)) λ- ∆(rnr-729::kanR) rph-1 F- ∆(rhaD-rhaB)568 hsd514

52

MG1655

F– λ– ilvG – rfb-50 rph-1

65

SK2595

araD139 galE15 galK16 Δ(ara-leu)7697 spoT1 λ- hsdR2 Δ(codB-lacI)3 mcrA0 relA1 rpsL150 mcrB9999 ∆(rnz-500::kanR) ∆(elaC500::kanR)

53

V. fischeri

DC22

C8-HSL bioreporter: ES114 ∆ainS ∆luxR-luxI, mutant luxR (MJ1-T33A, R67M, S116A, M135I), P luxI -luxCDABEG

24

DC43

ES114 ΔainS ΔluxI Pcon-luxR MJ1 P luxI -luxCDABEG

21

DJ01

ES114 ΔainS ΔluxI Pcon-luxR ES114 P luxI -luxCDABEG

21

ES114

Wild-type isolate from E. scolopes

36

JB18

ES114 litR::ermR

13

JHK003

ES114 ∆ainR

13

JHK007

ES114 ΔainS ΔluxIR P luxI -luxCDABEG

13

JHK045

ES114 ΔainS ΔluxI Pcon-luxR ES114 P luxI -luxCDABEG litR::ermR

This study

JHK046

ES114 ΔainS ΔluxIR P luxI -luxCDABEG litR::ermR

This study

JHK055

ES114 ainR trunc (Δ30-815)

This study

JHK056

ES114 ainR nat (Δ36-815)

This study

JHK091

ES114 ΔluxI Pcon-luxR MJ1 P luxI -luxCDABEG litR::ermR

This study

JHK099

ES114 ΔainS ΔluxI Pcon-luxR MJ1 P luxI -luxCDABEG litR::ermR

This study

JHK114

ES114 ΔainR

This study

JHK115

ES114 ainR scar

This study

JHK119

ES114 ainR scar-repaired

This study

JHK120

ES114 ainR mut

This study

NL60

ES114 ∆ainS

23

NL63

ES114 ∆ainS luxI

13

Plasmids b

pCR-Blunt

PCR product cloning vector; ColE1 oriV kanR

Invitrogen

pCR-Blunt-II-TOPO

PCR product cloning vector; ColE1 oriV kanR

Invitrogen

pDJ01

Pcon-luxR ES114 P luxI -luxCDABEG ColE1, R6Kγ, oriT RP4, kanR, camR

21

pEVS104

Conjugative helper plasmid; R6Kγ oriT RP4 kanR

69

pEVS118

Suicide vector; R6Kγ, oriT RP4, camR

64

pEVS122

Suicide vector; R6Kγ, oriT RP4, ermR, lacZα

64

pHK12

P ainS -gfp P con -mCherry in pJLS27; pES213, R6Kγ oriT RP4 kanR, camR

70

pHK34

ainR trunc (Δ30-815) in pCR-Blunt; ColE1 oriV kanR

This study

pHK37

ainR trunc (Δ30-815) allele; ColE1 R6Kγ oriV oriT RP4 camR kanR

This study

pHK75

1500-bp ainR downstream in pEVS122; R6Kγ oriT RP4 ermR lacZα

This study

pHK76

ainR nat (Δ36-815) allele; R6Kγ oriT RP4 ermR lacZα

This study

pHK93

P ainS -ainR trunc (Δ36-815) in pCR-Blunt; ColE1 oriV kanR

This study

pHK94

P ainS -ainR nat (Δ30-815) in pCR-Blunt; ColE1 oriV kanR

This study

pHK95

P ainS -ainR in pCR-Blunt; ColE1 oriV kanR

This study

pHK102

P ainS -ainR trunc (Δ30-815) allele; ColE1 R6Kγ oriV oriT RP4 kanR camR

This study

pHK103

P ainS -ainR nat (Δ36-815) allele; ColE1 R6Kγ oriV oriT RP4 kanR camR

This study

pHK104

P ainS -ainR allele; ColE1 R6Kγ oriV oriT RP4 kanR camR

This study

pHK129

ainSR ClaI-NdeI fragment with mutated IR1 (ainR_IR_conAA) in pCR-Blunt; ColE1 oriV kanR

This study

pHK135

1,350-bp upstream of ainR in pCR-Blunt; ColE1 oriV kanR

This study

pHK136

∆ainR, 1,480-bp downstream ainR in pHK135; ColE1 oriV kanR

This study

pHK137

ainR scar in pHK136; ColE1 oriV kanR

This study

pHK138

∆ainR allele; ColE1 R6Kγ oriT RP4 kanR camR

This study

pHK139

ainR scar allele; ColE1 R6Kγ oriT RP4 kanR camR

This study

pHK152

ainR mut in pHK95; ColE1 oriV kanR

This study

pHK153

ainR mut allele; ColE1 R6Kγ oriT RP4 kanR camR

This study

pHK156

P ainS -gfp (truncated) P con -mCherry in pJLS27; pES213, R6Kγ oriT RP4 kanR, camR

This study

pJLS27

Promoterless gfp, P con -mCherry pES213, R6Kγ oriT RP4 kanR

26

pJLB95

litR::ermR (opposite) allele; ColE1 camR ermR

13

Oligonucleotides c

pr_HK01

GGATCTGGCTTTTAAAAAATGCATCATCTGC

This study

pr_HK02

CATCTAGATGACGATGAAGTACAGATATTGGTTTATGAAT

This study

pr_HK03

GGGGCATGCAGAACCAAGACCTGCTCGTGCTAA

70

pr_HK13

AGCGCCCAATACGCAAACC

This study

pr_HK14

CCGGCGTGTCAATAATATCACTCTGTACA

This study

pr_HK17.2

CATGGGATCCTAGAGAGCGGATAAAATACCCTACCCAA

This study

pr_HK27.3

CATGGGTACCAGAACCAAGACCTGCTCGTGCTAA

This study

pr_HK28.2

CATGGGATCCTAAGGGTTTACCTTTGTCCGCTCTCTA

This study

pr_HK40.1

CATGGGATCCATAAGTGGTTATAACACCGATAAAAAAATAGCC

This study

pr_HK41.4

CATGGCATGCTGAAGGTGCTTGCTATTACTGATCA

This study

pr_HK126

CATGGGATCCTGAAGGTGCTTGCTATTACTGATC

This study

pr_HK136

CATGGCTAGCTTAACTACTTTACCTAAAGTTTATTTAC

This study

pr_HK137

CATGGCTAGCTAACCACTTATCTACGACCT

This study

pr_HK144

AAAATAAGTATTCCAAATTTCCAA

This study

pr_HK146

AAAGTACTCATAACACCACTACC

This study

pr_NL28.3

GGGCCTAGGCATTTATATAAAACTCACTGA TTTCGAAGTTT

23

pr_NL29

GGGGCCTAGGTAACACCGATAAAAAAATAGCCAGAAC

23

pr_NL35

GAGTCCGTTAGCAAGGTCACACTTTGTTG

23

pr_NL63

GGGCCTAGGCTACTCTTTTATAAATTCATATTGCAGGTTTT

23

pr_NL89

AAATCTAAGGGTTTACCTTTGTCCGCTCTC

24

pr_NL108

GGCGGAACGATTGGAAATTTGGAATACTTATTTTCAACATC

24

pr_NL109

CAGTACTGCATTTCAAAAGACAACCAAAAACTTTGATAGCC

24

QO

CCAGTGAGCAGAGTGACG

72

QI

GAGGACTCGAGCTCAAGC

72

QT

CCAGTGAGCAGAGTGACGAGGACTCGAGCTCAAGCTTTTTTTTTTTTTTTTT

72

  1. aDrug resistance abbreviations used: camR, chloramphenicol resistance; ermR, erythromycin resistance; and kanR, kanamycin resistance (aph).
  2. bAll alleles cloned in this study are from V. fischeri strain ES114. Replication origin(s) of each vector are listed as R6Kγ, ColE1, oriV and/or pES213. Plasmids based on pES213 are stable and do not require antibiotic selection for maintenance.
  3. cAll oligonucleotides are shown 5′ to 3′. Restriction enzyme recognition sequences are underlined.
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