No abstract

DNA motifs at several informative loci in more than 500 strains of Helicobacter pylori from five continents were studied by PCR and sequencing to gain insights into the evolution of this gastric pathogen. Five types of deletion, insertion, and substitution motifs were found at the right end of the H. pylori cag pathogenicity island. Of the three most common motifs, type I predominated in Spaniards, native Peruvians, and Guatemalan Ladinos (mixed Amerindian-European ancestry) and also in native Africans and U.S. residents; type II predominated among Japanese and Chinese; and type III predominated in Indians from Calcutta. Sequences in the cagA gene and in vacAm1 type alleles of the vacuolating cytotoxin gene (vacA) of strains from native Peruvians were also more like those from Spaniards than those from Asians. These indications of relatedness of Latin American and Spanish strains, despite the closer genetic relatedness of Amerindian and Asian people themselves, lead us to suggest that H. pylori may have been brought to the New World by European conquerors and colonists about 500 years ago. This thinking, in turn, suggests that H. pylori infection might have become widespread in people quite recently in human evolution.Helicobacter pylori is a microaerophilic bacterium with the extraordinary ability to establish infections in human stomachs that can last for years or decades, despite immune and inflammatory responses and normal turnover of the gastric epithelium and overlying mucin layer in which it resides. It is carried by more than half of all people worldwide and has attracted great attention as a major cause of peptic ulcer disease and an early risk factor for gastric cancer, one of the most frequently lethal of malignancies worldwide (for reviews see references 23, 48, and 60).

We report the identification and functional analysis of nine genes from Gram-positive and Gram-negative bacteria and their phages that are similar to lambda () bet or Escherichia coli recT. Beta and RecT are single-strand DNA annealing proteins, referred to here as recombinases. Each of the nine other genes when expressed in E. coli carries out oligonucleotide-mediated recombination. To our knowledge, this is the first study showing single-strand recombinase activity from diverse bacteria. Similar to bet and recT, most of these other recombinases were found to be associated with putative exonuclease genes. Beta and RecT in conjunction with their cognate exonucleases carry out recombination of linear doublestrand DNA. Among four of these foreign recombinase/exonuclease pairs tested for recombination with double-strand DNA, three had activity, albeit barely detectable. Thus, although these recombinases can function in E. coli to catalyze oligonucleotide recombination, the double-strand DNA recombination activities with their exonuclease partners were inefficient. This study also demonstrated that Gam, by inhibiting host RecBCD nuclease activity, helps to improve the efficiency of Red-mediated recombination with linear double-strand DNA, but Gam is not absolutely essential. Thus, in other bacterial species where Gam analogs have not been identified, double-strand DNA recombination may still work in the absence of a Gam-like function. We anticipate that at least some of the recombineering systems studied here will potentiate oligonucleotide and double-strand DNA-mediated recombineering in their native or related bacteria.bacteriophage lambda ͉ Beta ͉ oligonucleotide recombination ͉ RecT ͉ ssDNA annealing proteins R ecombineering is a simple and efficient way to engineer DNA molecules in vivo without the in vitro use of restriction enzymes and DNA ligase (1, 2). In Escherichia coli, it allows genetic modifications, from point mutations to substitutions and deletions. Recombineering is mediated by phage-derived proteins, either the Red proteins of phage (1-3) or RecET from the Rac prophage of E. coli (4), which are particularly efficient in catalyzing homologous recombination between short (Ϸ50 bp) homology segments. The Red recombination functions are encoded by three adjacent genes, gam, bet and exo, in the pL operon (1). RecET functions are encoded by two adjacent genes, recE and recT, present on the cryptic lambdoid Rac prophage found in the genome of many E. coli K-12 strains (5). A variety of studies have concluded that the Exo/Beta and RecE/RecT protein pairs are functionally equivalent although not related at the sequence level (6, 7). Exo and RecE are 5Ј-3Ј exonucleases that degrade the 5Ј ends of linear duplex DNA, creating 3Ј single-strand (ss) DNA overhangs (8, 9). Beta and RecT are single-strand annealing proteins that bind to these ssDNA overhangs and pair them with complementary ssDNA targets (10-12). Gam inhibits two potent host nucleases, RecBCD and SbcCD (13,14), thereby preventing the degradation o...