Metabolism and genetics of Helicobacter pylori: the genome era

The publication of the complete sequence of Helicobacter pylori 26695 in 19 97 and more recently that of strain J99 has provided new insight into the b iology of this organism. In this review, we attempt to analyze and interpre t the information provided by sequence annotations and to compare these dat a with those provided by experimental analyses. After a brief description o f the general features of the genomes of the two sequenced strains, the pri ncipal metabolic pathways are analyzed In particular, the enzymes encoded b y H. pylori involved in fermentative and oxidative metabolism, lipopolysacc haride biosynthesis, nucleotide biosynthesis, aerobic and anaerobic respira tion and iron and nitrogen assimilation are described, and the areas of con troversy between the experimental data and those provided by the sequence a nnotation are discussed. The role of urease, particularly in pH homeostasis , and other specialized mechanisms developed by the bacterium to maintain i ts internal pH are also considered. The replicational, transcriptional, and translational apparatuses are reviewed, as is the regulatory network. The numerous findings on the metabolism of the bacteria and the paucity of gene expression regulation systems are indicative of the high level of adaptati on to the human gastric environment. Arguments in favor of the diversity of H. pylori and molecular data reflecting possible mechanisms involved in th is diversity are presented. Finally, we compare the numerous experimental d ata on the colonization factors and those provided from the genome sequence annotation, in particular for genes involved in motility and adherence of the bacterium to the gastric tissue.