Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori

The genetic organization and sequence heterogeneity of the iceA locus of He licobacter pylori was studied, and the existence of two distinct gene famil ies, iceA1 and iceA2, at this locus was confirmed. iceA1 has significant se quence homology to nlaIIIR, encoding an endonuclease in Neisseria lactamica , but the similarity at the protein level is limited, due to frameshift mut ations of iceA1 in most H. pylori strains. In only five of the 19 iceA1 str ains studied, a full-length open reading frame (ORF), capable of encoding a 228 aa protein, with 52% homology to NlaIII was observed. The region upstr eam of iceA2 is highly variable in length, containing up to 15 copies of 8 bp tandem repeats, iceA2 can encode proteins of 24, 59, 94, or 129 amino ac ids, consisting of 14 and 10 aa domains, conserved in all iceA2 strains, fl anking 0, i, 2, or 3 copies of a 35 aa cassette. This 35 aa cassette consis ts of domains of 13, 16 and 6 aa, respectively. The 13 aa and 6 aa domains are highly conserved, but the 16 aa domain exists in two variants. In total , five distinct iceA2 subtypes were defined. Database searches did not reve al any homologous sequences. Recombinant IceA1 and IceA2 proteins were expr essed in Escherichia coli, confirming the predicted ORFs. Genotype-specific PCR primers permitted iceA genotyping in 318 (99.1%) of a worldwide collec tion of 321 H. pylori, strains. The conserved sizes of the amplification pr oducts confirmed the worldwide distribution of discrete variants of iceA1 a nd iceA2. (C) 2000 Elsevier Science B.V, All rights reserved.