TABLE 1.
Strains and plasmids
| Bacterial strain or plasmid | Relevant feature(s) | Reference or source | |||
|---|---|---|---|---|---|
| H. pylori strains | |||||
| G27 | Clinical isolate | 50 | |||
| G25 | Clinical isolate | 50 | G46 | Clinical isolate | 50 |
| G50 | Clinical isolate | 50 | |||
| P76 | Spontaneous streptomycin-resistant derivative of mouse-adapted strain P49 | 15 | G27/HP165::km | ||
| G27 with a kanamycin resistance cassette replacing ORF HP165 | 5 | ||||
| G27/P1408-gfp | G27 with a fusion of the promoter region of ORF HP1408 to a promoterless gfp gene flanked by a kanamycin resistance cassette and replacing ORF HP1408 | This study | |||
| G27/P1408-gfpΔ165 | G27/HP165::km with a fusion of the promoter region of ORF HP1408 to a promoterless gfp gene flanked by a chloramphenicol resistance cassette and replacing ORF HP1408 | This study | |||
| G27/P166-gfp | G27 with a fusion of the promoter region of ORF HP166 to a promoterless gfp gene flanked by a kanamycin resistance cassette and replacing ORF HP1408 | This study | |||
| G27/P166Δ-gfp | G27 with a fusion of the 3′ truncated promoter region of ORF HP166 to a promoterless gfp gene flanked by a kanamycin resistance cassette and replacing ORF HP1408 | This study | |||
| G27/P166-gfpΔ165 | G27/HP165::km with a fusion of the promoter region of ORF HP166 to a promoterless gfp gene flanked by a chloramphenicol resistance cassette and replacing ORF HP1408 | This study | |||
| G27/P166Δ-gfpΔ165 | G27/HP165::km with a fusion of the 3′ truncated promoter region of ORF HP166 to a promoterless gfp gene flanked by a chloramphenicol resistance cassette and replacing ORF HP1408 | This study | |||
| G27/pHel-P120-gfp | G27 harboring pHel2 carrying a fusion of the promoter region of ORF HP120 to a promoterless gfp gene | This study | |||
| P76/Δ1408 | P76 with the regions located between the 23S rDNA loci and ORFs HP1413 and HP422 replaced by kanamycin and chloramphenicol resistance cassettes, respectively | This study | |||
| P76/Δ119 | P76 with the regions located between ORFs HP1186 to HP1189 and ORFs HP117 to HP121 replaced by kanamycin and chloramphenicol resistance cassettes, respectively | This study | |||
| E. coli strains | |||||
| DH5α | Strain used for high-efficiency transformation | Gibco | |||
| XL1-Blue | Strain used for high-efficiency transformation | Stratagene | |||
| M15 | Strain used for overproducing His6-HP166 | Qiagen | |||
| Plasmids | |||||
| pBluescript SK | Cloning vector | Stratagene | |||
| pSL1180 | Cloning vector | Pharmacia | |||
| pILL600 | Plasmid containing the kanamycin resistance cassette from C. coli | 24 | |||
| pDT2548 | Plasmid containing the chloramphenicol resistance gene from C. coli | 48 | |||
| pHel2 | Shuttle vector for H. pylori | 18 | |||
| pQE-166 | pQE30 expressing the His6-tagged response regulator HP166 | 5 | |||
| pLSV16gfp | Listeria-E. coli shuttle vector used as source of the promoterless gfp-mut2 gene | 8 | |||
| pGG1 | pBluescript SK carrying a 284-bp DraI fragment from H. pylori G27 with homology to the upstream region and part of the coding region of ORF HP1408 in H. pylori 26695 | This study | |||
| pGG2 | pBluescript SK carrying a 183-bp DraI fragment from H. pylori G27 with homology to the upstream region of ORF HP119 in H. pylori 26695 | This study | |||
| pGG3 | pBluescript SK carrying a 183-bp DraI fragment from H. pylori G27 with homology to the upstream region of ORF HP119 in H. pylori 26695 | This study | |||
| pSL-gfp1409 | pSL1180 containing the promoterless gfp-mut2 gene and a 504-bp DNA fragment derived from ORF HP1409 | This study | |||
| pSL-P1408-gfp/km | pSL1180 carrying the kanamycin resistance cassette flanked by a fusion of a 287-bp DNA fragment derived from the promoter region of ORF HP1408 to the gfp-mut2 gene and a 504-bp DNA fragment derived from ORF HP1409 | This study | |||
| pSL-P1408-gfp/cm | pSL1180 carrying the chloramphenicol resistance cassette flanked by a fusion of a 287-bp DNA fragment derived from the promoter region of ORF HP1408 to the gfp-mut2 gene and a 504-bp DNA fragment derived from ORF HP1409 | This study | |||
| pSL-P166-gfp/km | pSL1180 containing a 543-bp DNA fragment from the 23S rDNA locus, a 153-bp DNA fragment comprising the promoter region of ORF HP166 which is fused to the gfp-mut2 gene, the kanamycin resistance cassette, and a 504-bp DNA fragment derived from ORF HP1409 | This study | |||
| pSL-P166Δ-gfp/km | Same as pSL-166-gfp/km except that there is a 36-bp deletion in the 3′ part of the promoter region of ORF HP166 | This study | |||
| pSL-P166-gfp/cm | pSL1180 containing a 543-bp DNA fragment from the 23S rDNA locus, a 153-bp DNA fragment comprising the promoter region of ORF HP166 which is fused to the gfp-mut2 gene, the chloramphenicol resistance cassette, and a 504-bp DNA fragment derived from ORF HP1409 | This study | |||
| pSL-P166Δ-gfp/cm | Same as pSL-166-gfp/cm except that there is a 36-bp deletion in the 3′ part of the promoter region of ORF HP166 | This study | |||
| pHel-P120-gfp | pHel2 carrying a 612-bp DNA fragment derived from the upstream region of ORF HP120 and fused to the gfp-mut2 gene | This study | |||
| pSL-1413:km:23S | pSL1180 containing a 506-bp DNA fragment derived from ORF HP1413 and a 543-bp DNA fragment derived from the 23S rDNA locus flanking the kanamycin resistance cassette | This study | |||
| pSL-422:cm:23S | pSL1180 containing a 539-bp DNA fragment derived from ORF HP422 and a 543-bp DNA fragment derived from the 23S rDNA locus flanking the chloramphenicol resistance cassette | This study | |||
| Bacterial strain or plasmid | Relevant feature(s) | Reference or source | |||
| pSL-1186:km:1189 | pSL1180 containing a 595-bp DNA fragment derived from ORF HP1186 and a 521-bp DNA fragment derived from ORF HP1189 flanking the kanamycin resistance cassette | This study | |||
| pSL-117:cm:121 | pSL1180 containing a 494-bp DNA fragment derived from ORF HP117 and a 499-bp DNA fragment derived from ORF HP121 flanking the chloramphenicol resistance cassette | This study | |||
| pSL-166PE | pSL1180 containing a 549-bp DNA fragment from H. pylori G27 comprising the promoter region and part of the coding DNA of ORF HP166 | This study | |||
| pSL-119PE1 | pSL1180 containing a 783-bp DNA fragment from H. pylori G27 with similarity to the promoter and part of the coding region of ORF HP119 in H. pylori 26695 | This study | |||
| pSL-119PE2 | pSL1180 containing a 700-bp DNA fragment from H. pylori G27 with similarity to the promoter and part of the coding region of ORF HP119 in H. pylori 26695 | This study | |||
| pSL-1408f | pSL1180 containing a 360-bp BamHI-EcoRI fragment derived from the P1408-gfp fusion in pSL-1408-gfp/km | This study | |||
| pSL-119f | pSL1180 containing a 298-bp BamHI-EcoRI fragment derived from the promoter region of ORF HP119 cloned in pSL-119PE1 | This study | |||
| pSL-166f | pSL1180 containing a 308-bp BamHI-EcoRI fragment comprising the promoter region and part of the coding DNA of ORF HP166 | This study |