Table 1.

Bacterial strains and plasmids used in this study

Bacterial strains or plasmidCharacteristicsaReference(s) or source
Strains
E. coli
  DH5αFφ80dlacZΔM15 endA1 recA1 hsdR17(rK mK +)supE44 thi-1 gyrA96Δ(lacZYA-argF)U169 55
  S17-1Pro r m+ recA, integrated RP4-Tet::Mu-Kan::Tn7, Mob+ 57
  1830(pJB4JI)Met-63 Pro-22 Kmr Nmr, Tn5 donor8
A. tumefaciens
  NT1Derivative of strain C58 cured of pTiC5859
  NTM4Tn5-induced mutant of NT1 deficient in TraR/AAI-mediated activation of tragenesThis study
  NTM5Tn5-induced mutant of NT1 deficient in TraR/AAI-mediated activation of tragenesThis study
  NTM6Tn5-induced mutant of NT1 deficient in TraR/AAI-mediated activation of tragenesThis study
  NTM7Tn5-induced mutant of NT1 deficient in TraR/AAI-mediated activation of tragenesThis study
  A136Derivative of NT1 resistant to rifampin and nalixic acid, Rifr Nalr 59
  A136(miaA) miaA::Tn5mutant of A136, deficient in VirA/VirG-mediated activation ofvir genes28
  C58C1RSTi plasmid-cured C58, recipient strain for Ti plasmid conjugation, RifrStrr 21
Plasmids
 pBluescript SK(+)Cloning vector, Apr Stratagene
 pRK415Broad-host-range cloning vector, InP1α Tcr 36
 pMGmSource of gentamicin resistance cassette, Apr Gmr 46
 pBBR1MCS-5Broad-host-range cloning vector, unknown Inc group, Gmr 39
 pTiC58ΔaccR Derivative of pTiC58 with a deletion in the accR gene, Trac 5, 6
 pDCKI41Derivative of pTiC58ΔaccR with a lacZ fusion totraG, TraR reporter strain, TraCbr 32
 pKPK12Derivative of pTiC58ΔaccR with a lacZ fusion totraR, Tra Kmr 53
 pKMI41Derivative of pDCKI41 with an nptII cassette inserted into the traM gene, KmrCbr 32
 pYPQ lac promoter region of pZLQ (43) cloned by PCR into pBBR1MCS-5 as anSstI-KpnI fragmentOur collection
 pPLE2-25pDSK519 carrying a fragment from pTiC58 with a regulated trbE::lacZ fusion, IncQ Kmr Cbr 41
 pRK415GIIIpRK415 with a gentamicin cassette cloned into the unique XmnI site as a 1.7-kb end-blunted EcoRI-SphI fragment, IncP1α Tcr Gmr This study
 pRK415GIIIE33 EcoRI fragment 33 of pTiC58 containing traR cloned into pRK415GIIIThis study
 pRKL17Ca. 8-kb BglII fragment containing atrbE::lacZ fusion from pPLE2-25 cloned into pRK415GIIIE33, IncP1α Tcr Gmr This study
 pYDH208::lacZ #6 mocE::lacZfusion in pYDH208, IncP1α Tcr Cbr 31, 38
 pSOM303::lacZ #39 recA::lacZfusion cloned in pRK290, IncP1α Tcr Cbr 23
 pZL5E33 EcoRI fragment 33 of pTiC58 containingtraR cloned into pBBR1MCS-5, Gmr This study
 pTiA6pinF::lacZ pinF::lacZ(virH::lacZ) fusion in pTiA628, 35
 pSM358 virE::lacZ fusion from pTiA6 cloned into pVK101, IncP1α AprKmr 58
 pZLQ9Cosmid clone of the NT1 genome in pCP13/B that complements the mutation in NTM7, Tcr This study
 pZLQ10Cosmid clone of the NT1 genome in pCP13/B that complements the mutation in NTM7, Tcr This study
 pZLB1111-kb SalI fragment from pZLQ10 cloned into pBluescript SK(+)This study
 pZLR1111-kb SalI fragment from pZLB11 cloned into pRK415GIIIThis study
 pZLB77-kb SalI-BglII fragment from pZLB11 cloned into pBluescript SK(+)This study
 pZLG77-kbXbaI-BglII fragment from pZLB7 cloned into pRK415GIIIThis study
 pZLE2.72.7-kb EcoRI fragment from pZLB7 cloned into pBluescript SK(+)This study
 pZLE2522.7-kb EcoRI fragment from pZLB7 cloned into pRK415GIIIThis study
 pZLE253Same as pZLE252, but the fragment is cloned in the opposite orientationThis study
 pZLP1611.6-kb PstI fragment containing thernd gene cloned into pRK415GIII and oriented correctly with respect to the lac promoter of the vectorThis study
 pZLP162Same as pZLP162, but the insert is oriented in the opposite directionThis study
 pZLmeP12-kbNdeI-BamHI fragment from pZLQ10 containing theycaD homolog and 1 kb of downstream DNA cloned into pYPQThis study
 pZlmeP1.9Same as pZlmeP1, but the insert is oriented in the opposite directionThis study
 pZL41Tn5-tagged EcoRI fragment from NTM4 cloned into pBluescript SK(+)This study
 pZL51Tn5-tagged EcoRI fragment from NTM5 cloned into pBluescript SK(+)This study
 pBSM62Tn5-tagged EcoRI fragment from NTM6 cloned into pBluescript SK(+)This study
 pBSM72Tn5-tagged EcoRI fragment from NTM7 cloned into pBluescript SK(+)This study
 pZLK63.8-kbSalI-EcoRI fragment from pBSM62 cloned into pBluescript SK(+)This study
 pZLA63.2-kbSalI-EcoRI fragment from pBSM62 cloned into pBluescript SK(+)This study
 pZLK74.8-kbSalI-EcoRI fragment from pBSM62 cloned into pBluescript SK(+)This study
 pZLA73.6-kbSalI-EcoRI fragment from pBSM62 cloned into pBluescript SK(+)This study
 pDB14 E. coli rndgene cloned in pUC1862
 pZLD14 E. coli rnd gene from pDB14 cloned as a 1.4-kb EcoRI-BamHI fragment into pRK415GIIIThis study
  • a Abbreviations: Apr, ampicillin resistance; Cbr, carbenicillin resistance; Cmr, chloramphenicol resistance; Gmr, gentamicin resistance; Kmr, kanamycin resistance; Nalr, naladixic acid resistance; Rifr, rifampin resistance; Spcr, spectinomycin resistance; Strr, streptomycin resistance; Tcr, tetracycline resistance; Trac, transfer constitutive.