Strain or plasmid / Relevant genotype or description / Reference or source
Strains
Escherichia coli
JM109 / recA1 endA1 gyrA96 thi-1 hsdR17(rK－mK＋) e14－(mcrA－) supE44 relA1 Δ (lac-proAB)/F'[traD36 proAB＋lac IqlacZΔM15] / Takara
DH5α / F－Φ80dlacZΔM15 Δ(lacZYA-argF)U169 deoRrecA1 endA1 hsdR17(rK－, mK＋) phoAsupE44 λ－thi-1 gyrA96 relA1 / Invitrogen
Bacteroides fragilis
YCH46 / Clinical isolate, parental strain for all deletion mutants / 1
TSRM0518 / YCH46 mutant with deletion of BF0518 / This study
TSRM0667 / YCH46 mutant with deletion of BF0667 / This study
TSRM1168 / YCH46 mutant with deletion of BF1168 / This study
TSRM1340 / YCH46 mutant with deletion of BF1340 / This study
TSRM1677 / YCH46 mutant with deletion of BF1677 / This study
TSRM1781 / YCH46 mutant with deletion of BF1781 / This study
TSRM1966 / YCH46 mutant with deletion of BF1966 / This study
TSRM2058 / YCH46 mutant with deletion of BF2058 / This study
TSRM2359 / YCH46 mutant with deletion of BF2359 / This study
TSRM2766 / YCH46 mutant with deletion of BF2766 / This study
TSRM3036 / YCH46 mutant with deletion of BF3036 / This study
TSRM3038 / YCH46 mutant with deletion of BF3038 / This study
TSRM3522 / YCH46 mutant with deletion of BF3522 / This study
TSRM4033 / YCH46 mutant with deletion of BF4033 / This study
TSRM4201 / YCH46 mutant with deletion of BF4201 / This study
TSRM4274 / YCH46 mutant with deletion of BF4274 / This study
TSRM4283 / YCH46 mutant with deletion of BF4283 / This study
TSRM4438 / YCH46 mutant with deletion of BF4438 / This study
TSRM4484 / YCH46 mutant with deletion of BF4484 / This study
SSRM2765 (Δmpi) / YCH46 mutant with deletion of BF2765 (mpi) / This study
RECAM1213 (ΔrecA) / YCH46 mutant with deletion of BF1213 (recA) / This study
Plasmids
pBluescript II KS / E. coli cloning vector; ApR / Stratagene
pACYC184 / E. coli cloning vector; TcR, CmR / Nipppon gene
pE5-2 / E. coli-Bacteroides shutle vector, elements for TcR in E. coli and EmR in Bacteroides lie within a 3.8-kb EcoR I fragment of Tn4351 / 2
pKK100 / Suicidal vector for Bacteroides, 3.8-kb Em/Tc resistance element amplified with primers EmTc-F2 and EmTc-R2 from pE5-2 cloned into the Xmn I site of pBluescript II KS / This study
pVAL-1 / E. coli-Bacteroides shutle vector; ApR TcR in E. coli, EmR in Bacteroides / 3
pVAL-Exp / Bacteroides expression vector, IS1224/cepA hybrid promoter (4), restriction sites (Nde I, Not I, Xba I and Sal I), and the transcription terminator of BF1719 cloned into the Nhe I/Nru I site of pVAL-1 / This study
pVAL0667 / BF0667 amplified with primers BF0667-NdeI and BF0667-SalI from BF strain YCH46 cloned into the Nde I/Sal I site of pVAL-Exp / This study
pKS0667(-) / BF0667 in a Sma I site of pBluescript II KS oriented oppositely to the lac promoter / This study
pKS0667(+) / BF0667 in a Sma I site of pBluescript II KS oriented same direction to the lac promoter / This study
pKSmpi(-) / BF2765 (mpi) in a Sma I site of pBluescript II KS oriented oppositely to the lac promoter / This study
pKSmpi(+) / BF2765 (mpi) in a Sma I site of pBluescript II KS oriented same direction to the lac promoter / This study
pRep1 / class II-1 invertible region in an EcoR V site of pACYC184 / This study
pRep2 / class II-2 invertible region in an EcoR V site of pACYC184 / This study
pRep3 / class II-3 invertible region in an EcoR V site of pACYC184 / This study
pRep4 / class II-4 invertible region in an EcoR V site of pACYC184 / This study
pRep5 / class II-5 invertible region in an EcoR V site of pACYC184 / This study
pRep6 / class II-6 invertible region in an EcoR V site of pACYC184 / This study
pRep7 / class II-7 invertible region in an EcoR V site of pACYC184 / This study
pRep8 / class II-8 invertible region in an EcoR V site of pACYC184 / This study
pRep9 / class II-9 invertible region in an EcoR V site of pACYC184 / This study
pRep10 / class II-10 invertible region in an EcoR V site of pACYC184 / This study
pRep11 / class V invertible region amplified with primers J1 and K2 from the TSRM0667 genomic DNA cloned into an EcoR V site of pACYC184 / This study
pRep12 / class VI invertible region in an EcoR V site of pACYC184 / This study
pRep13 / PS3 invertible promoter region in an EcoR V site of pACYC184 / This study
Abbreviations: Ap, ampicillin; Em, erythromycin; Tc, tetracycline.
- Kuwahara, T., M. R. Sarker, H. Ugai, S. Akimoto, S. M. Shaheduzzaman, H. Nakayama, T. Miki, and Y. Ohnishi. 2002. Physical and genetic map of the Bacteroides fragilis YCH46 chromosome. FEMS Microbiol. Lett. 207:193-197.
- Shoemaker, N. B., E. P. Guthrie, A. A. Salyers, and J.F.Gardner. 1985. Evidence that the clindamycin-erythromycin resistance gene of Bacteroides plasmid pBF4 is on a transposable element. J. Bacteriol. 162:626-632.
- Valentine, P. J., N. B. Shoemaker, and A. A. Salyers. 1988. Mobilization of Bacteroides plasmids by Bacteroides conjugal elements. J. Bacteriol. 170:1319-1324.
- Bayley, D. P., E. R. Rocha, and C. J. Smith. 2000. Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol. Lett. 193:149-154.