Table 1.

Bacterial strains, plasmids, and oligonucleotide primers utilized in this study and their relevant characteristics

Strain, plasmid, or oligonucleotide primerRelevant characteristicsa or nucleotide sequencebSource or reference
Bacterial strains
E. coli
  DH10BPlasmid-free strain used for cloning 9
  RW120 lexA+ recA +Δ(umuDC)595::cat 12
P. aeruginosa
  PAO1UVs, no detectable plasmidsA. M. Chakrabarty
P. fluorescens
  Pf5UVs,ina-negative 27
P. syringae pv. syringae
  B86-17UVr, containsrulAB on pB8617A 21
  GWS242As B86-17 but alsorulB::KmThis study
Plasmids
 pBluescript SK(+)Apr, cloning vectorStratagene
 pBSL86Source of Kmrcassette 1
 pCR2.1AprKmr, direct cloning vector for PCR productsInvitrogen
 pET-5aApr, source of Shine-Dalgarno sequencePromega
 pGem7zf−Apr, cloning vectorPromega
 pJB321Cbr, broad-host-range cloning vector 2
 pJQ200SKGmr sacB, suicide gene replacement vector 34
 pPROBE KI′Kmr, broad-host-range, inaZ reporter vectorS. E. Lindow
 pRK2013Helper plasmid for triparental matings 7
 pRW144Spr, 2.4-kb mucAB asBamHI in pGB2 12
 pRW154Spr, 2.8-kb umuDC asEcoRI in pGB2 12
 pB8617A rulAB +, native plasmid fromP. syringae pv. syringae B86-17This study
 pGWS1400.7-kb HindIII-PstI from pSM1 in pBluescript SK(+) 47
 pJJK16.4-kb rulAB as BamHI from pB8617A in pBluescript SK(+)This study
 pJJK51.7-kbmucAB as NdeI-BamHI from pRW144 in pET-5aThis study
 pJJK123.8-kb rulAB as partialEcoRI from pJJK1 in pGem7zf−This study
 pJJK151.2-kb Kmr cassette as HincII from pBSL86 in pJJK12 at blunt-ended BssHIIThis study
 pJJK164.4-kb rulA, rulB::Km as XbaI-BamHI in pJQ200SKThis study
 pJJK173.8-kb rulAB asXbaI-BamHI from pJJK12 in pJB321This study
 pJJK200.75-kb umuDC promoter asSphI-XbaI in pET-5aThis study
 pJJK211.7-kb rulAB asNdeI-BamHI from pJJK12 in pJJK20This study
 pJJK220.75-kb umuDC promoter asSphI-XbaI in pJJK5This study
 pJJK231.7-kb umuDC asNdeI-EcoRI from pRW154 in pET-5aThis study
 pJJK240.75-kb umuDC promoter asSphI-XbaI in pJJK23This study
 pJJK252.45-kb umuDC promoter + rulAB asSalI-BamHI in pJB321This study
 pJJK262.45-kb umuDC promoter + mucAB asSphI-BamHI in pJB321This study
 pJJK272.45-kb umuDC promoter + umuDC asSphI-EcoRI in pJB321This study
 pJJK401.1-kb rulAB promoter region in pCR2.1This study
 pJJK410.9-kb rulAB promoter as HindIII-EcoRI from pJJK40 in pPROBE KI′This study
Oligonucleotide primers
mucAB Nde 5′5′-GGAATTCCATATGAAGGTCGATATTTTTG-3′This study
mucAB Bam3′5′-GATCGGATCCTTATTTGATGGTGGCTATTGG-3′This study
rulAB Nde5′5′-GGAATTCCATATGAACGTCAAAATACTCGGGCGG-3′This study
 3′ rulB TAABamHI5′-GATCGGATCCTTACTTTACAACCCACAGCTG-3′This study
rul PX5′-GGATTGGGAAAACCGGCAGGG-3′This study
umuDC Nde5′5′-GATCCATATGTTGTTTATCAAGCCTGCGG-3′This study
umuDC Eco3′5′-GATCGAATTCTTATTTGACCCTCAGTAAATCAG-3′This study
umu Pro 5′SphI5′-GATCGCATGCGAGCAATTGCGTCGC-3′This study
umu Pro 3′5′-GTACTCTAGACTGCCTGAAGTTATACTG-3′This study
  • a Abbreviations: Ap, ampicillin; Cb, carbenicillin; Gm, gentamicin; Km, kanamycin; Sp, spectinomycin.

  • b Restriction sites incorporated in primers are underlined. GGATCC, BamHI; GAATTC,EcoRI; CATATG, NdeI; GAGCTC, SacI; GCATGC, SphI; TCTAGA, XbaI.