Table 1 Bacterial strains and plasmids used in this study

Pseudomonas putida

P. putida RD8MR3

Wild type; isolated from rhizosphere of rice roots

[24]

P. putida RD8MR3PPRI

[16]

P. putida RD8MR3PPRR

pprR::Km of P. putida RD8MR3; Kmr

[16]

P. putida RD8MR3PPOR

ppoR::Km of P. putida RD8MR3, Kmr

This study

P. putida WCS358

Wild type; plant growth promoting strain from the rhizosphere of potato roots

[21]

P. putida WCS358PPOR

ppoR::Km of P. putida WCS358, Kmr

This study

P. putida M17

psrA178::Tn5 of P. putida WCS358, Kmr

[23]

P. putida MKO1

rpoS880::Tn5 of P. putida WCS358, Kmr

[22]

P. putida IBE1

gacA400::Tn5 of P. putida WCS358, Kmr

[17]

P. putida IBE2

ppuR1793::Tn5 of P. putida WCS358, Kmr

[17]

P. putida IBE3

rsaL1640::Tn5 of P. putida WCS358, Kmr

[17]

P. putida IBE5

ppuI::Km of P. putida WCS358, Kmr

This study

E. coli

E. coli M15(pRep4)

Derivative of E. coli K-12, containing pREP4 plasmid ensuring the production of high levels of lac repressor protein; Kmr

Qiagen

E. coli Dh5α

F'/endA1 hsdR17 supE44 thi-1 recA1 gyrA relA1 (lacZYA-argF)U169 deoR [80dlac(lacZ)M15recA1]

[26]

A. tumefaciens NTL4 (pZLR4)

A. tumefaciens NT1 derivative carrying a traG::lacZ reporter fusion

[34]

Plasmid

pRK2013

Tra+ Mob+ ColE1 replicon; Kmr

[31]

pMOSBlue i

Cloning vector, Ampr

Amersham-Pharmacia

pBBR mcs-5

Broad-host-range vector, Gmr

[29]

pBBRPpoR

pBBR mcs-5 with 749-bp XbaI-KpnI fragment containing ppoR, Gmr

This study

pBluescript KS

Cloning vector, Ampr

Stratagene

pQE30

Expression vector, Ampr

Qiagen

pQEPpoR

721-bp containing ppoR of P. putida KT2440 cloned as SphI-HindIII fragment in pQE30

This study

pMP220

Promoter probe vector, IncP1; Tcr

[28]

pPUI220

ppul promoter cloned in pMP220; Tcr

[17]

pPUR220

ppuR promoter cloned in pMP220; Tcr

[17]

pRSA220

rsaL promoter cloned in pMP220; Tcr

[17]

pPpoR1

ppoR promoter of P. putida RD8MR3 cloned in pMP220; Tcr

This study

pPpoR2

ppoR promoter of P. putida WCS358 cloned in pMP220; Tcr

This study

pMPpprIprom

Promoter of gene pprI cloned in pMP220 vector

[16]

pKNOCK-Km

Conjugative suicide vector; Kmr

[35]

pKNOCKppoR1

Internal fragment of P. putida RD8MR3 ppoR cloned into KpnI-XbaI sites of pKNOCK-Km

This study

pKNOCKppoR2

Internal fragment of P. putida WCS358 ppoR cloned into KpnI-XbaI sites of pKNOCK-Km

This study

pEXPPUIKm

pEXGm containing KpnI-SalI fragment of ppuI::Km

This study

pLAFRppoR

Cosmid clone containing P. putida RD8MR3 ppoR

[16]

pBS1

pBluescript KS carrying the 598-bp pcr product of the P. putida RD8MR3 ppoR promoter region

This study

pBS2

pBluescript KS carrying the 318-bp pcr product of the P. putida WCS358 ppoR promoter region

This study

pBS3

pBluescript KS carrying the 721-bp pcr product of the P. putida KT2440 complete ppoR gene

This study

pBS4

pBluescript KS carrying the 749-bp pcr product of the P. putida WCS358 complete ppoR gene

This study

pBS5

pBluescript KS carrying the HindIII subclone of pLAFRppoR that contains ppoR

This study

pBS6

pBluescript KS carrying the pKNOCK-Km insertion flanking sequences from P. putida WCS358PPOR genomic DNA

This study

pMOS1

pMOSBlue vector carrying 394-bp internal portion of P. putida RD8MR3 ppoR gene

This study

pMOS2

pMOSBlue vector carrying 385-bp internal portion of P. putida WCS358 ppoR gene

This study

pMOS3

pMOSBlue vector carrying pcr product of 358_PpoRf and 4648 degR primers

This study