TABLE 1.

Bacterial strains and plasmids

Strain or plasmidGenotype or featuresReference or source
Strains
    Paracoccus alcaliphilus JCM 7364RRifr derivative of wild-type strain JCM 7364 10
    Paracoccus alkenifer DSM 11593RRifr derivative of wild-type strain DSM 11593 9
    Paracoccus aminophilus JCM 7686Wild type 79
    Paracoccus aminovorans JCM 7685RRifr derivative of wild-type strain JCM 7685 10
    Paracoccus denitrificans LDM 22.21RRifr derivative of wild-type strain LDM 22.21 11
    Paracoccus methylutens DM12RRifr derivative of wild-type strain DM12 10
    Paracoccus pantotrophus KL100Rifr derivative of wild-type strain DSM 11073 10
    Paracoccus solventivorans DSM 11592RRifr derivative of wild type strain DSM 11592 11
    Paracoccus thiocyanathus IAM 12816RRifr derivative of wild-type strain IAM 12816 10
    Paracoccus versutus UW225Rifr derivative of wild-type strain UW1 5
    Rhodobacter sphaeroides 2.4.1RRifr derivative of wild-type strain 2.4.1 11
    Agrobacterium tumefaciens GMI 9023Rifr 47
    Rhizobium leguminosarum 1062Strr 43
    Escherichia coli BR825 polA::Tn10 trp 55
    Escherichia coli DH5Δlac deoR thi1 relA1 supE44 endA1 gyrA96 recA1 hsdR17 Δ(argF lac)U169 Nalr M. Yarmolinski
    Escherichia coli EC16816 hsdR2 galK2 galT22 supE44; contains N15; source of the gp49-gp48 TA cassetteV. Rybchin
    Escherichia coli EDL933Wild-type enterohemorrhagic E. coli O157:H7 strain, source of the Z3230-Z3231 TA cassette 62
    Escherichia coli HW220K-12 derivative (CAG18439) containing SXT element of V. cholerae, source of the s045-s044 TA cassette 44
    Escherichia coli MC1000 araD 139 Δ(araABC-leu)7679 galU galK Δ(lac)X74 rpsL thi 21
    Escherichia coli SG22025Kmr, Δlac rcsA 166::aphA 50
    Escherichia coli SG22093Kmr Cmr, Δlac rcsA 166::aphA clpP 1::cat 50
    Escherichia coli SG22095Kmr Tcr, Δlac rcsA 166::aphA lon 146::tet 50
    Escherichia coli TG1 supE hsdΔ5 thi Δ(lac proAB) F′ (traD36 proAB + lacI q lacZΔM15)Laboratory collection
Plasmids
    pAMI2Natural plasmid (approx. 18.6 kb) of P. aminophilus JCM 7686 4
    pAMI204Kmr, mini-pAMI2This study
    pABW1Kmr, ori pMB1, mobilizable cloning vector, oriT RK2 6
    pMDB209pABW1 carrying a DNA region of pAMI2 present in pAMI204This study
    pMDB300pMDB209 with diminished region of pAMI204This study
    pABW1-REPpABW1 carrying REP module of pAMI2 (amplified by PCR with primers LLDKREP and RREPAMI) inserted into HindIII siteThis study
    pABW1-REP+PARpABW1 carrying REP and PAR modules of pAMI2 (amplified by PCR with primers LLDKREP and RLDKPAR) inserted into HindIII siteThis study
    pABW1-REP+PAR+TApABW1 carrying REP, PAR, and TA modules of pAMI2 (amplified by PCR with primers LLDKREP and RKILHIII) inserted into HindIII siteThis study
    pUC4KSource of kanamycin resistance cassette 81
    pBGS18Kmr, ori pMB1, cloning vector 73
    pBGS-AMIpBGS18 carrying tad-ata (amplified by PCR with primers LLDZ2547 and RLDZ3578) inserted into SmaI siteThis study
    pBGS-SXTpBGS18 carrying s044-s045 (amplified by PCR with primers LSXT and RSXT) inserted into SmaI siteThis study
    pBGS-N15pBGS18 carrying gp49-gp48 (amplified by PCR with primers LN15 and RN15) inserted into SmaI siteThis study
    pBGS-EDLpBGS18 carrying Z3230-Z3231 (amplified by PCR with primers LEDL and REDL) inserted into SmaI siteThis study
    pMUT1pBGS-AMI with mutated tad This study
    pMUT2pMUT1 with mutated ata This study
    pFH450Cmr, ori R1, ori bacteriophage P1, segregational stability test vector for E. coli 41
    pFH-AMIpFH450 carrying tad-ata This study
    pFH-SXTpFH450 carrying s045-s044This study
    pFH-N15pFH450 carrying gp49-gp48 This study
    pFH-EDLpFH450 carrying Z3230-Z3231This study
    pABW3Kmr, ori pMB1, ori pTAV1, oriT RK2, segregational stability test vector for Paracoccus spp. 8
    pABW3-AMIpABW3 carrying tad-ata This study
    pABW3-SXTpABW3 carrying s045-s044This study
    pABW3-N15pABW3 carrying gp49-gp48 This study
    pABW3-EDLpABW3 carrying Z3230-Z3231This study
    pCF430Tcr, ori RK2, oriT RK2, PBAD promoter 60
    pTOX-tadpCF430 carrying tad (amplified by PCR with primers TADL and TADR) inserted between PstI and XbaI sitesThis study
    pTOX-s045pCF430 carrying s045 (amplified by PCR with primers LTSXT and RTSXT) inserted between PstI and XbaI sitesThis study
    pTOX-gp49pCF430 carrying gp49 (amplified by PCR with primers LTN15 and RTN15) inserted between PstI and XbaI sitesThis study
    pTOX-Z3230pCF430 carrying Z3230 (amplified by PCR with primers LTEDL and RTEDL) inserted between PstI and XbaI sitesThis study
    pNDM220Apr, ori R1, pA1/O4/O3, lacI q 34
    pANTI-atapNDM220 carrying ata (amplified by PCR with primers 2LAAMIBH and 2RAAMIER) inserted between EcoRI and BamHI sitesThis study
    pANTI-s044pNDM220 carrying s044 (amplified by PCR with primers 2LASXTBH and 2RASXTER) inserted between EcoRI and BamHI sitesThis study
    pANTI-gp48pNDM220 carrying gp48 (amplified by PCR with primers LAN15BHI and RAN15ERI) inserted between EcoRI and BamHI sitesThis study
    pANTI-Z3231pNDM220 carrying Z3231 (amplified by PCR with primers LAEDLBHI and RAEDLERI) inserted between EcoRI and BamHI sites blunt ended with KlenowThis study
    pOU82Apr, ori R1, lacZYA 30
    pOU-SXTpOU82 carrying s045-s044This study
    pOU-N15pOU82 carrying gp49-gp48 This study
    pCM132Kmr, ori RK2, lacZ reporter gene fusion vector 56
    pCM-P1AMIpCM132 carrying P1 promoter of tad-ata This study
    pCM-P1SXTpCM132 carrying P1 promoter of s045-s044 (amplified by PCR with primers LP1SXT and RP1SXT2) inserted between EcoRI and BglII sitesThis study
    pCM-P1N15pCM132 carrying P1 promoter of gp49-gp48 (amplified by PCR with primers LP1N15 and RP1N15) inserted between EcoRI and BglII sitesThis study
    pCM-P1EDLpCM132 carrying P1 promoter of Z3230-Z3231 (amplified by PCR with primers LP1EDL2 and RP1EDL2) inserted between EcoRI and BglII sitesThis study
    pCM-P2AMIpCM132 carrying P2 promoter of tad-ata (amplified by PCR with primers LP2AMI and RP2AMI) inserted between EcoRI and BglII sitesThis study
    pCM-P2SXTpCM132 carrying P2 promoter of s045-s044 (amplified by PCR with primers LP2EDL and RP2EDL) inserted between EcoRI and BglII sitesThis study
    pCM-P2N15pCM132 carrying P2 promoter of gp49-gp48 (amplified by PCR with primers LP2N15 and RP2N15) inserted between EcoRI and BglII sitesThis study
    pCM-P2EDLpCM132 carrying P2 promoter of Z3230-Z3231 (amplified by PCR with primers LP2EDL and RP2EDL) inserted between EcoRI and BglII sitesThis study
    pRS551Kmr, ori pMB1, lacZ reporter gene fusion vector 71
    pRS-P1AMIpRS551 carrying P1 promoter of tad-ata This study
    pRS-P1SXTpRS551 carrying P1 promoter of s045-s044 (amplified by PCR with primers LP1SXT and RP1SXT2) inserted between EcoRI and BamHI sitesThis study
    pRS-P1N15pRS551 carrying P1 promoter of gp49-gp48 (amplified by PCR with primers LP1N15 and RP1N15) inserted between EcoRI and BamHI sitesThis study
    pRS-P1EDLpRS551 carrying P1 promoter of Z3230-Z3231 (amplified by PCR with primers LP1EDL2 and RP1EDL2) inserted between EcoRI and BamHI sitesThis study
    pRS-P2AMIpRS551 carrying P2 promoter of tad-ata (amplified by PCR with primers LP2AMI and RP2AMI) inserted between EcoRI and BamHI sitesThis study
    pRS-P2SXTpRS551 carrying P2 promoter of s045-s044 (amplified by PCR with primers LP2SXT and RP2SXT) inserted between EcoRI and BamHI sitesThis study
    pRS-P2N15pRS551 carrying P2 promoter of gp49-gp48 (amplified by PCR with primers LP2N15 and RP2N15) inserted between EcoRI and BamHI sitesThis study
    pRS-P2EDLpRS551 carrying P2 promoter of Z3230-Z3231 (amplified by PCR with primers LP2EDL and RP2EDL) inserted between EcoRI and BamHI sitesThis study
    pGEM-T EasyApr, cloning vectorPromega
    pBluescript II KSApr, cloning vectorStratagene
    pRK2013Kmr, helper plasmid carrying genes for conjugal transfer of RK2 27