Table 1 Bacterial strains and plasmids used in this study

Strains

 E. coli DH5α

Subcloning host

Our lab

 E. coli XL1-Blue

Subcloning host

Our lab

 L. lactis NZ9000

L. lactis MG1363 pepN::nisRK; commonly used host for NICE system

[43]

 L. lactis IL1403

The source of putative recombinase pi12

[27]

 E. faecalis ATCC14506

The source of recombinase RecT

Our lab

 Lb. plantarum WCFS1

The source of recombinase Lp_0641

[4]

 Lb. casei BL23

The source of recombinase LCABL_13050

[5]

 Lb. delbrueckii SDMCC050201

The source of putative recombinase phiJB_00020

[26]

Plasmids

 pLeiss:Sec:Nuc

L. lactis and E. coli shuttle cloning vector which contains PnisA promoter used for nisin controlled gene expression; Cm^r

[44]

 pTRKL₂

L. lactis and E. coli shuttle cloning vector which exists at low copy number in L. lactis; Erm^r

[45]

 pTRKH₂

L. lactis and E. coli shuttle cloning vector which exists at high copy number in L. lactis; Erm^r

[45]

 pCas9

Low copy number vector, expression of Cas9 nuclease, tracrRNA and crRNA in E. coli; Cm^r

[23]

 pKD46

λ Red recombinase expression vector; the source of recombinase Beta; Amp^r

[46]

 pTLCas9

Cas9, tracrRNA and crRNA cloning in pTRKL₂; Erm^r

This work

 pTHCas9

Cas9, tracrRNA and crRNA cloning in pTRKH₂; Erm^r

This work

 pTLCas9upp

pTLCas9 with a 20 bp spacer targeting the upp gene of L. lactis NZ9000; Erm^r

This work

 pTLCas9galk1

pTLCas9 with a 20 bp spacer targeting the galK gene of L. lactis NZ9000; Erm^r

This work

 pTLCas9hemN1

pTLCas9 with a 20 bp spacer targeting the hemN gene of L. lactis NZ9000; Erm^r

This work

 pTLCas9recA1

pTLCas9 with a 20 bp spacer targeting the recA gene of L. lactis NZ9000; Erm^r

This work

 pTLCas9noxD1

pTLCas9 with a 20 bp spacer targeting the noxD gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9galk1

pTHCas9 with a 20 bp spacer targeting the galK gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9hemN1

pTHCas9 with a 20 bp spacer targeting the hemN gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9recA1

pTHCas9 with a 20 bp spacer targeting the recA gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9noxD1

pTHCas9 with a 20 bp spacer targeting the noxD gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9galk2

pTHCas9 with a 25 bp spacer targeting the galK gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9hemN2

pTHCas9 with a 25 bp spacer targeting the hemN gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9recA2

pTHCas9 with a 25 bp spacer targeting the recA gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9noxD2

pTHCas9 with a 25 bp spacer targeting the noxD gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9galk3

pTHCas9 with a 30 bp spacer targeting the galK gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9hemN3

pTHCas9 with a 30 bp spacer targeting the hemN gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9recA3

pTHCas9 with a 30 bp spacer targeting the recA gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9noxD3

pTHCas9 with a 30 bp spacer targeting the noxD gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9upp

pTHCas9 with a 25 bp spacer targeting the upp gene of L. lactis NZ9000; Erm^r

This work

 pTHCas9galk

pTHCas9 with a 25 bp spacer targeting the galk gene of L. lactis NZ9000; Erm^r

This work

 pL-beta

λ Red beta cloning in pLeiss:Sec:Nuc; Cm^r

This work

 pL-RecT

RecT from E. faecalis ATCC14506 cloning in pLeiss:Sec:Nuc; Cm^r

This work

 pL-LC50

LCABL_13050 from Lb. casei BL23 cloning in pLeiss:Sec:Nuc; Cm^r

This work

 pL-Lp41

Lp_0641 from Lb. plantarum WCFS1 cloning in pLeiss:Sec:Nuc; Cm^r

This work

 pL-JB02

phiJB_00020 from Lb. delbrueckii SDMCC050201 cloning in pLeiss:Sec:Nuc; Cm^r

This work

 pL-pi12

pi12 from L. lactis IL1403 cloning in pLeiss:Sec:Nuc; Cm^r

This work