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. 2002 Feb;184(4):992–1002. doi: 10.1128/jb.184.4.992-1002.2002

FIG. 1.

FIG. 1.

IS element maps. (A) Structures of ISs of H. pylori. ISHp608 is 1,833 bp long, making it slightly smaller than its three other known H. pylori relatives (size range, 1,888 to 2,028 bp [18, 19]). Boxes represent ORFs: those with the same shading pattern are related at the protein level (range of 28 to 36% amino acid sequence identities). orfA sizes are 156, 148, 139, and 218 codons and orfB sizes are 384, 427, 446, and 420 codons in ISHp608, IS605, IS606, and IS607, respectively. orfA and orfB overlap by 10 codons in ISHp608, which is reminiscent of the arrangement in IS607 (nine-codon overlap). Distances from left and right ends to the 5" end of orfA and 3" end of orfB in a representative ISHp608 are 171 bp and 75 bp, respectively (accession no. AF357224). GenBank accession nos. for IS605, IS606, and IS607 are AC000108, U95957, and AF189015, respectively. (B) Positions of oligonucleotide primers, the subtractive clone that led to the discovery of ISHp608, and mutations generated in ISHp608. The locations and orientations of PCR and sequencing primers are denoted by arrowheads; these primers are described in detail in Table 1. Primers 1 and 20 are specific to sequences in jhp0924 (an ORF in strain J99 [4]) located to the left and right of ISHp608, respectively, in strain PeCan2A. ∗ and ∗∗ identify primers specific for ISHp608 types 2 and 3, respectively (defined in Results). Subtractive clone D7 is a 242-bp AluI fragment from strain PeCan18B that begins approximately 30 to 34 bp from the left end of ISHp608 copy 2. cam#2, cam#3, cam#4, and cam#5 represent mutant derivatives of ISHp608 from strain PeCan2A that contain the cam (resistance gene) cassette inserted into (cam#4 and cam#5) or replacing (cam#2 and cam#3) particular ISHp608 sequences. In cam#4 (A+B+), cam was inserted just downstream of orfB and 68 bp from the rightmost end of ISHp608 (generated with primers 8 and 18); in cam#2 (A−B+), 154 bp of orfA sequence was replaced by the cam gene (generated with primers 2 and 12); in cam#3 (A+B−), 948 bp of orfB sequence was replaced by cam (generated with primers 4 and 16); in cam#5 (A+B+), cam was inserted just 22 bp from the ISHp608 right end, within a 22-bp direct repeat (putative transposase binding site) (generated with primers 9 and 19), as detailed in Results.