Diversity in the variable region of Helicobacter pylori cagA gene involves more than simple repetition of a 102-nucleotide sequence.

CagA, a product of cytotoxin-associated gene A cagA, is an important virulence-related antigen of Helicobacter pylori (HP). CagA varies in size from 128 kDa to about 140 kDa and this variation is believed to be generated by a 102-nucleotide (NT) repeat sequence in the so-called variable region of cagA. However, this explanation has not previously been tested by comparing the NT sequences of cagA derived from a number of different isolates of HP. In this study we first compared the size of PCR products obtained from 54 different isolates of HP with oligonucleotide primers designed to amplify a cagA fragment predicted to be at least 1059 NT, including the variable region of the gene. As expected, the size of the PCR products varied considerable, from 1110 to 1822 NT, but the majority (50 of 54) measured 1335 NT or less. The deduced amino acid (AA) sequences of 9 representative amplicons and 4 other known sequences were compared with the following result: Within the variable region of cagA there are actually two adjacent variable regions, which we label as proximal and distal. The proximal-variable region of CagA extends from a motif of 4 to 6 asparagine residues to a 7-AA repeat sequence (KIDQLNQ); the distal-variable region is confined between KIDQLNQ and a well-conserved duplicate, KIDNLNQ. Despite these shared features CagA of every HP strain examined to date has a variable region with a unique AA sequence.