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Table 4 List of strains, plasmids and primers used in the present study

From: The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus

Strain, plasmid and primers

Genotype or phenotype

Serratia sp.

 LCN16 WT

WT resistant to ampicillin and erythromycin.

 LCN16 oxyR::int(614)

Knockout mutant of oxyR with group II intron inserted in the position 614; Resistant to gentamicin and kanamycin.

 LCN16 katA::int(808)

Knockout mutant of katA with group II intron inserted in the position 808; Resistant to gentamicin and kanamycin.

Escherichia coli

 DH5α

Competent cells (Sigma-Albrich)

Plasmids

 pAR1219

TargeTron vector with chloramphenicol resistant

 pAR1219-ΩGm

Constructed vector with gentamicin resistant gene aacC

 pACD4K-C

TargeTron vector; kanamicin RAM marker (for chromosomal insertion) and chloramphenicol resistance (plasmid propagation)

 pACD4K-C_oxyR

TargeTron vector with intron RNA retarget for oxyR gene

 pACD4K-C_kat

TargeTron vector with intron RNA retarget for kat gene

 pBK-miniTn7-ΩGm

Tn7 plasmid constructed with gentamicin resistant gene aacC

PCR Primers (5′-3′)

 aacC1_IfFor

CATACTCTTCCTTTTTCAATATTATTG

 aacC1_IfRev

TAACTGTCAGACCAAGTTTACTC

 oxyR_614|615 s-IBS

AAAAAAGCTTATAATTATCCTTAGGAAGCTGGTCAGTGCGCCCAGATAGGGTG

 oxyR_614|615 s-EBS1d

CAGATTGTACAAATGTGGTGATAACAGATAAGTCTGGTCACTTAACTTACCTTTCTTTGT

 oxyR_614|615 s-EBS2

TGAACGCAAGTTTCTAATTTCGATTCTTCCTCGATAGAGGAAAGTGTCT

 oxyR_KO_chkFor

CGTGGTCTGGAGGGAAACAA

 oxyR_KO_chkRev

CATAACGACTGCGCAATGGG

 katA_808|809a -IBS

AAAAAAGCTTATAATTATCCTTATAATCCGGATTTGTGCGCCCAGATAGGGTG

 katA_808|809a EBS1d

CAGATTGTACAAATGTGGTGATAACAGATAAGTCGGATTTGCTAACTTACCTTTCTTTGT

 katA_808|809a -EBS2

TGAACGCAAGTTTCTAATTTCGGTTGATTATCGATAGAGGAAAGTGTCT

 katA_KO_chkFor

GGTGAAGTTCCATTTCCGCTGC

 katA_KO_chkRev

GGGTTCACCGCTACCTGTTCAAC

RT-qPCR primers (5′-3′)

 gyrA_For

TTATCTCCCTGATTGTGCCA

 gyrA_Rev

CATTACGCTCGCTCACCTTA

 oxyR_For

TTTAGAGTACCTGGTCGCCTTG

 oxyF_Rev

ATCACACCCAGTTCGTCTTCC

 katA_For

CCAGATTATGCCTGAACACG

 katA_Rev

TGCAGTTCGAAGAAACCAAC

 katG_For

AGCGGTAAGCCAAATACACC

 katG_Rev

AATCGAAGTCAGGGTCCATC