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Mobley HLT, Mendz GL, Hazell SL, editors. Helicobacter pylori: Physiology and Genetics. Washington (DC): ASM Press; 2001.

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Helicobacter pylori: Physiology and Genetics.

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Chapter 23Chromosomal Replication, Plasmid Replication, and Cell Division

and .

Department of Microbiology, Yamaguchi University School of Medicine, Ube, Yamaguchi, 755-8505, Japan

The study of chromosomal replication and cell division of bacteria has extended beyond Escherichia coli, and important insights have emerged recently from studies in other species, especially Bacillus subtilis and Caulobacter crescentus (55, 67). In contrast, there is still little information about cell division processes in Helicobacter pylori. Analyses of the complete genome sequences of H. pylori strains 26695 and J99 (2, 64) provide insights into the cell division mechanisms of this microorganism, a spiral-shaped gram-negative bacterium with a bundle of polar flagella. Many genes homologous to those involved in replication and cell division in E. coli are found in the H. pylori genome, suggesting similar basic mechanisms for both bacteria. Orthologs of some E. coli genes have not been identified in the H. pylori genome, suggesting differences in the cell proliferation machinery of both bacteria, which belong to different subdivisions of the Proteobacteria.

Cell division is coordinated with other cell cycle events such as genomic DNA synthesis that leads to chromosomal replication and partition, increase of cell mass, and cell expansion by cell wall synthesis. Thus, in this chapter the information about predicted genes related to chromosomal replication, plasmid replication, and cell division in H. pylori is reviewed, and a plausible replication machinery of the bacterium is discussed in light of our current understanding of bacterial organization and function of replication and cell division. The focus of the section on chromosomal replication is on the replication origin and genes of the replication complex, while division site, filamenting, and other related genes are discussed in the section on cell division.

Chromosomal Replication

Origin of Replication and dnaA

Unlike eukaryotes, prokaryotic cells have a single origin of replication (oriC), and chromosomal replication initiates bidirectionally from that origin to the termination site in a region of the chromosome diametrically opposed from the origin (4, 41). Tomb et al. (64) found no typical eubacterial origin of replication in H. pylori strain 26695, and arbitrarily they designated bp 1 the beginning of a repeat that produces translational stop codons in the three reading frames. Salzberg et al. analyzed the H. pylori genome utilizing a new skewed oligomer method (56). Searching for significantly skewed oligomers, they found RRTAGGGG (R, purine) the most skewed octamers, and identified a putative oriC between positions 1,566,000 and 1,640,000, and tentatively located it in the small open reading frame (ORF) HP1515, which is flanked by two converging genes (Fig. 1). The oriC region contains the gene HP1529 ortholog of dnaA, which encodes an initiator protein for DNA replication in E. coli, and the gene HP1523 ortholog of recG, which encodes an ATP-dependent DNA helicase for genetic recombination and DNA repair in E. coli. Several DnaA-box-like sequences of putative DnaA-binding sites are also present (68). A similar oriC region was found in the J99 genome containing JHP1417 (dnaA), JHP1412 (recG), and several DnaA-box like sequences (Fig. 1). The J99 oriC tentatively has been located in the untranslational region between JHP1408, which encodes a protein of unknown function, and JHP1409, which encodes a type II DNA modification enzyme/methyltransferase (17). Interestingly, the putative oriC sequences of strains 26695 and J99 are dissimilar, and adjacent genes in each of these strains, HP1517 and JHP1409, share no homology but encode a type II DNA modification enzyme. With the exception of dnaA, other typical origins of replication genes such as gidA, gidB, dnaN, and gyrB (68) are not found in the putative oriC region but are scattered throughout the genome.

Figure 1. Regions including the putative origin of replication (oriC) of H.

Figure 1

Regions including the putative origin of replication (oriC) of H. pylori 26695 and J99. Numbers at each end of the scale represent the position in nucleotides in the genome. Open boxes without gene names represent hypothetical genes with unknown functions. (more...)

H. pylori genes homologous to E. coli genes involved in chromosomal replication are summarized in Table 1. The DnaA protein is essential for the initiation of chromosomal replication and is highly conserved among different bacteria (68). The predicted DnaA proteins of strains 26695 (457 amino acids) and J99 (458 amino acids) have 97.6% identity, while the overall identity between H. pylori and E. coli DnaA (468 amino acids) is only 35% (43). Bacterial DnaA sequences have a short N-terminal domain (domain I) with reasonable homology, a stretch of dissimilar amino acid sequences (domain II), and highly conserved domains III and IV. Domain III contains an ATP-binding site in its N-terminal region, and domain IV contains an amphipathic α-helix for membrane binding and a helix-turn-helix motif for DNA binding in the N-terminal and the C-terminal regions, respectively (19, 53, 58). H. pylori DnaA contains a highly conserved domain III with an ATP-binding site, and a less conserved domain IV with the putative sites for membrane binding and DNA binding.

Table 1. Proteins involved in chromosomal replication of E. coli and their homologs recognized in H. pyloria.

Table 1

Proteins involved in chromosomal replication of E. coli and their homologs recognized in H. pyloria.

Replication Machinery

The mechanism of chromosomal replication has been well studied in E. coli. DnaA, the ATP-binding protein with intrinsic ATPase activity, has a key role (28, 29). Other DNA-binding proteins and an RpoD-containing RNA polymerase that form an open complex are also involved in the replication of the chromosome. The rpoB gene of H. pylori encodes a large fusion polypeptide of the β (RpoB) and β′ (RpoC) subunits of E. coli (71). In E. coli DnaA associates with the cell membrane, possibly through the membrane-binding site in N-terminal domain IV (19, 46), and binds to a DnaA box within the oriC region to induce unwinding of DNA for initial melting (53, 58, 70). To initiate replication, DnaB, a replicative DNA helicase that polymerizes to encircle a DNA strand, is recruited by the aid of a loading factor DnaC. DnaG primase and a single-strand DNA-binding protein are also required, and a DNA gyrase encoded by gyrA and gyrB is employed to relieve the superhelical stress during elongation. All these genes with the exception of dnaC are present in the H. pylori genome (Table 1).

For elongation or replication of the chromosome, polymerase III, a replicative DNA polymerase, has a key role (30, 43). A dimeric complex of the polymerase III holoenzyme assembles at each replication fork that is clamped by the ring formed by the β subunit of polymerase III (34, 45). The γ complex of polymerase III consisting of the N-terminal portion of DnaX, HolB, HolA, HolC, and HolD is required for loading the β subunit (21). The polymerase III core enzyme consists of an α subunit (DnaE) with polymerase activity, an ϵ subunit (DnaQ) with proofreading exonuclease activity, and a θ subunit (HolE) (43). The τ subunit of polymerase III encoded by dnaX connects two core molecules to allow the simultaneous synthesis of both the leading and the lagging strands of DNA (5). The H. pylori genome has all the gene homologs for the genes encoding the polymerase III holoenzyme present in the genome of H. pylori, with the exception of the γ components HolA, HolC, and HolD (Table 1).

In addition to topoisomerase genes such as topA, gyrA, and gyrB, H. pylori has xerC and xerD homologs for XerCD resolvase, which is involved in the termination of chromosome replication in E. coli (see below) (24). Other genes such as HP0213/JHP0199 (gidA) and HP1063/JHP0362 (gidB) for glucose-inhibited division proteins A and B, respectively; HP1478/JHP1371 (rep) for DNA helicase; HP0387/JHP0994 (priA) for primosome protein n′; and HP1523/JHP1412 (recG) for DNA helicase are also present in the H. pylori genome (16). The products of recG and priA are involved in forming Holliday junctions from replication forks stalled at lesions in the DNA and restarting replication, respectively (42). Thus, almost all of the basic genes encoding proteins of the replication machinery are present in the H. pylori genome, suggesting that mechanisms similar to those of E. coli and other eubacteria operate in the chromosomal replication of H. pylori.

Plasmid Replication

Clinical isolates of H. pylori have been reported to carry plasmids ranging in size from 1.5 to 40 kb (49, 57, 63). Three cryptic plasmids, pHPK225 (1.5 kb), pHPM180 (3.5 kb), and pHel1 (2.9 kb), have been completely sequenced (22, 32, 44). Plasmid pHPK225 has an ORF encoding a 25-kDa putative Rep protein with significant homology to a replication-initiation protein commonly found in small plasmids endogenous to gram-positive bacteria that replicate by the "rolling circle" mechanism, suggesting that this plasmid originated from a gram-positive microorganism (32). In contrast, pHPM180 and pHel1 have ORF encoding 54- and 65-kDa RepA proteins, respectively, which have a sequence identity of 88.5% and weak homology to the RepA protein of the E. coli plasmid pSC101 with the θ-type replicon (22, 44). Both the upstream regions of repA in pHPM180 and pHel1 have several copies of a 22-mer direct repeat sequence, called a DNA iteron, a feature typical of the ori of many bacterial plasmids. The repA sequence together with the iterons of pHPM180 and pHel1 are present in nearly all plasmids harbored in H. pylori strains, while the rep sequence in pHPK225 is rarely found (32), indicating that the θ-type replicon is predominant in H. pylori plasmids (22). On the basis of the pHel1 structure, the H. pylori–E. coli shuttle vectors pHe12 and pHe13 have been constructed with the replication origins of pHel1 and ColE1, as well as the oriT sequence from ColE1, to allow mobilization by conjugation (23).

Cell Division

Cell division of gram-negative bacteria proceeds through nucleoid segregation, partitioning of the cytoplasm into two compartments each containing a copy of the cell's genetic information, and invagination of the three layers of the cell envelope between the chromosome. The MukB homolog that serves as a motor for rapid DNA displacement in E. coli (47) is absent in H. pylori.

Fourteen homologs of E. coli cell division genes (39, 67) have been recognized in H. pylori (Table 2). After chromosome movement (partition), the GTP-binding protein FtsZ gathers in the center of the cell (midcell) and forms a Z ring in cooperation with other fts gene products. Then, ingrowth of the peptidoglycan layer for septation occurs by the action of PBP3 encoded by ftsI, and finally, the division of the cell is completed after cleavage of the peptidoglycan, although the enzyme involved in cell separation is not known. The location of cell division-related genes in the H. pylori 26695 genome is depicted in Fig. 2.

Table 2. Proteins involved in cell division of E. coli and their homologs identified in H. pylori strains 26695a and J99b.

Table 2

Proteins involved in cell division of E. coli and their homologs identified in H. pylori strains 26695a and J99b.

Figure 2. Localization of cell division-related genes on the H.

Figure 2

Localization of cell division-related genes on the H. pylori 26695 genome. Boxes with numbers below represent ORF of strain 26695. Horizontal arrows above the boxes represent the direction of transcription. Boxes are not drawn to scale and are separated (more...)

The min Genes for Determining the Division Site

For partitioning of the chromosome, a regulatory mechanism to determine the site of Z-ring formation is important. Without such system, cell division occurs at peripheral sites in addition to the midcell, producing chromosomeless minicells. Selection of the correct division site at midcell is controlled by the MinCDE system in E. coli. The MinCD complex is an inhibitor of cell division (12, 13, 27), while MinE competes with the MinCD complex and forms a ring at midcell prior to Z-ring formation (51). Thus, MinC- or MinD-deficient mutants as well as a MinE-overproducing mutant show abnormal cell division at the cell pole, resulting in the production of minicells. On the other hand, cell division is inhibited in a MinC-overproducing mutant, resulting in cell death (54). MinD associates with the membrane around the entire periphery of the cell in the absence of MinE, but it is recruited into a broad zone at one cell pole in the presence of MinE (26). A similar oscillatory behavior is seen on MinC that associates with MinD (52). In the H. pylori genome, orthologs of minD and minE have been identified, but an ortholog of MinC is absent. A survey of Min-encoding genes in sequenced bacterial genomes revealed that MinD is the most conserved of these proteins, whereas MinC and MinE are present in a small subset of genomes (55). The two division-determining genes minD and minE together with the dprA gene for natural transformation (3) form a cluster, possibly an operon, in H. pylori, suggesting that these genes are coordinately regulated in a cell cycle-dependent fashion (Fig. 2).

The fts Genes for Septum Formation

Ten fts (filamenting temperature-sensitive) homologs are present in H. pylori (Table 2). There are 13 fts genes of E. coli, and comparisons of bacterial genome sequences show that the ftsZ homologs, with marked degrees of sequence conservation, are present in almost all eubacterial and archaeal species that have been examined (55). Among the Fts proteins the second most conserved is FtsA, although it is not as widespread as FtsZ. Homologs of other E. coli division proteins are present in other bacteria in smaller and variable subsets. For example, FtsI, FtsK, and FtsW commonly are found in H. pylori, B. subtilis, Borrelia burgdorferi, and Treponema pallidum (55).

FtsZ plays a key regulatory and structural role during cell division. It self-assembles by its tubulin signature motif (GGGTGTG) to form a ring structure on the inner face of the cytoplasmic membrane at the division site and remains at the leading edge of the invagination septum (6, 37, 61). In addition, FtsZ is required for the recruitment of the essential cell division proteins FtsA and ZipA to the septal ring by binding with the C-terminal core domain (40). FtsA in turn may serve as a molecular bridge between the FtsZ ring and the other cell division proteins in the membrane or periplasm.

The ratios of FtsA to FtsZ in the cytoplasm seem to be important to initiate cell division (10, 16). In E. coli, the ftsQ-ftsA operon is followed by ftsZ, and several promoters are identified in the coding regions of ftsQ and ftsA. A two-component regulatory system, RcsC/RcsB, is involved in the regulation of these promoters (9). Since the organization of the ftsA and ftsZ genes in E. coli is conserved in H. pylori (Fig. 2), it is possible to hypothesize that one of the two-component regulatory systems recognized in the H. pylori genome, HP0244-HP0703 (flgR) and HP0165-HP0166, is involved in the regulation (7).

FtsW is an integral membrane protein that plays an important role in Z-ring stability (8, 31), and FtsI (penicillin-binding protein 3) is a transpeptidase required for the final step of peptidoglycan synthesis in the septum (11). E. coli FtsL, FtsN, and FtsQ proteins have some role in cell division, possibly at the final step by associating with FtsI in the inner membrane (1), but no homologs have been identified in H. pylori (Table 2). Also absent from the genome is the integral membrane protein ZipA, which interacts with FtsZ at an early stage.

FtsH belongs to the protein family of ATPase associated with diverse cellular activities (35). Two ftsH genes, HP0286 (JHP0271) and HP1069 (JHP0356), have been identified in H. pylori. The protein encoded by HP1069 is essential for proliferation of H. pylori (20) and is well conserved in most bacteria, whereas the FtsH encoded by HP0286 is less conserved. E. coli FtsH is an ATP-dependent zinc protease with a membrane-spanning segment in the N terminus. This protein is known to degrade SecY, the F0 subunit of ATPase, heat shock transcription factor sigma 32, and EnvA (LpxC), a key enzyme for lipid A biosynthesis (48).

In E. coli, the genes ftsY, ftsE, and ftsX are organized in a single operon and transcribed in the same direction; in H. pylori the genes ftsE and ftsX, but not ftsY, form a cluster (Fig. 2). FtsY belongs to the family of "signal recognition particle (SRP)-type GTPases." SRP is a ribonucleoprotein particle that binds to short nascent polypeptides, exposing a hydrophobic targeting signal just outside the ribosome that is released by the action of the receptor FtsY in a GTP-dependent process, so that the nascent chain can enter the membrane (15, 38, 65, 66). FtsE and FtsX of E. coli form a complex in the inner membrane that bears the characteristics of an ATP-binding cassette (ABC)-type transporter (14). A mutant lacking functional FtsE has filamentous growth and is only viable on high-salt medium, indicating a role for FtsE in cell division and/or salt transport.

FtsK of E. coli contributes to chromosome resolution and cell division with its C-terminal and N-terminal regions, respectively (18, 69). Chromosome dimers are generated by recombination between circular sister chromosomes. Resolution of dimers occurs at the dif site located at an opposite position of the origin of replication, and it is effected through a system involving the XerC, XerD, and FtsK (50). At the time of cell division, the terminus region of the chromosome localizes near the division plane. Dimer resolution of the chromosome followed by cell separation may be achieved by an integral process with the recombinases, FtsK, and other cell division proteins involved in septum formation.

Other Cell Division-Related Genes

The product of the E. coli fic (filamentation induced by cAMP) gene is involved in a regulatory mechanism of cell division via folate metabolism (33), and its expression is controlled by a stationary sigma factor σs encoded by rpoS (25). H. pylori has an fic gene homolog, but it may be regulated differently since this bacterium has no rpoS homolog. In the genome of H. pylori, genes encoding only the three sigma factors σD, σF, and σN have been identified. No consensus motifs for binding σF and σN are found in the upstream region of the H. pylori fic gene (36, 59, 60), suggesting that σD may contribute to the expression of this gene.

A new cell division-related gene cdrA has been reported in H. pylori (62). No obvious homolog for CdrA has been identified in E. coli, but its N-terminal region has some homology to E. coli FtsK. In the exponential-growth phase, a cdrA-disrupted mutant shows higher growth and forms short curved rods, while the wild-type strain shows a relatively slower growth and forms long slender rods (Fig. 3). Under high-salt conditions, the restrained growth of the wild type is more obvious, with multinuclear filaments formed, whereas the cdrA-disrupted mutant has a normal shape (62). In the stationary phase, the wild-type strain forms coccoids with low colony-forming ability, whereas the cdrA-disrupted mutant retains short rod morphology with high colony-forming ability. Taken together, these observations imply that the crdA gene has a suppressive role in the cell division of H. pylori.

Figure 3. H.

Figure 3

H. pylori HPK5 (wild type, left) and HPKT510 (cdrA-disrupted mutant, right) micrographs. 4′, 6′-diamidino-2-phenylindole (DAP)-stained micrographs (A) and shadowed electron micrographs (B) of H. pylori HPK5 (wild type) and HPKT510 (cdrA (more...)

Summary and Perspectives

Chromosomal replication and cell division of bacteria are well-organized and coordinately regulated processes operated by a complex genetic machinery. Dysfunction or deletion of even a single component leads to disordered and abnormal cell growth and eventual cell death. H. pylori seems to possess almost all the components known to be involved in chromosomal replication and cell division in E. coli. These results are unexpected, considering that the doubling time of H. pylori in vitro, and possibly in vivo, is very slow relative to that of E. coli. The slow growth of H. pylori may be attributable to its limited translation machinery, since it has only two copies of rRNA genes, compared to seven copies in E. coli. Another factor limiting the bacterium's ability to proliferate is the lack of biosynthetic pathways where many different nutrients are required. A scattered distribution of DnaA-box elements in the putative oriC region of H. pylori also may result in an inefficient initiation of replication.

The presence in H. pylori of genes orthologous to those involved in cell division in E. coli does not imply necessarily that the proteins are expressed at the same rates as in E. coli. There are surprisingly few factors controlling gene expression in H. pylori; only genes encoding σD, σF, and σN RNA polymerase sigma factors are present, stress-response sigma factors such as σH and σS are absent (64), and regulatory genes that activate or suppress transcription also are scarce. It is possible that H. pylori did not develop a stress-response system to replicate and survive under a wide range of environmental conditions, but instead, the microorganism has adapted to survive in a restricted ecological niche.

As a causative agent of a slow infection, H. pylori might have developed a unique system to suppress cell division and restrain proliferation. It can be hypothesized that CdrA is a suppressor of cell division involved in such growth limitation. This assumption is based on the observations. of the division rate and morphology of the cdrA mutant compared to those of the wild type (Fig. 3). Further studies on the replication and cell division machinery are required to clarify the mechanism of proliferation of H. pylori that causes chronic and persistent infection in the stomach.


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