Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

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The two major molecular chaperone families that mediate ATP-dependent protein folding and refolding are the heat shock proteins Hsp6Os (GroEL) and Hsp7Os (DnaK). Cip proteins, like chaperones, are highly conserved, present in all organisms, and contain ATP and polypeptide binding sites. We discovered that CipA, the ATPase component of the ATP-dependent ClpAP protease, is a molecular chaperone. CipA performs the ATP-dependent chaperone function of DnaK and DnaJ in the in vitro activation of the plasmid P1 RepA replication initiator protein. RepA is activated by the conversion of dimers to monomers. We show that CipA targets RepA for degradation by ClpP, demonstrating a direct link between the protein unfolding function of chaperones and proteolysis. In another chaperone assay, ClpA protects luciferase from irreversible heat inactivation but is unable to reactivate luciferase.Molecular chaperones interact with other proteins to mediate ATP-dependent protein folding, refolding, assembly, and disassembly of proteins. The Hsp7O chaperone system of Escherichia coli consists of the DnaK, DnaJ, and GrpE heat shock proteins. In vivo these three heat shock proteins function together in many cellular processes, as demonstrated by the observations that mutants in dnaK, dnaJ, and grpE have similar effects on DNA replication of E. coli, plasmids P1 and F and phage A, RNA synthesis, cell division, protein transport, regulation of the heat shock response, protection of enzymes from misfolding or aggregation during heat shock, and degradation of abnormal proteins (reviewed in ref.

DnaK is a major heat shock protein of Escherichia coli and the homolog of hsp7O in eukaryotes. We demonstrate the mechanism by which DnaK and another heat shock protein, DnaJ, render the plasmid P1 initiator RepA 100-fold more active for binding to the P1 origin of replication.