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Comparative analysis of four Campylobacterales

Nature Reviews Microbiology volume 2, pages 872–885 (2004)Cite this article

Key Points

The ε-proteobacteria is a large group of diverse bacteria that occupy many different ecological niches. Five complete genome sequences are now available for a particular order — the Campylobacterales — within this proteobacterial subgroup. This article focuses on the comparative analysis of these sequences, three of which are pathogens of humans (Helicobacter pylori 26695 and J99, and Campylobacter jejuni NCTC 11168), one pathogen of rodents (Helicobacter hepaticus ATCC 51449) and one of which is a commensal (Wolinella succinogenes DSM 1740). The following noteworthy features are discussed in depth in the article:

  • Wolinella succinogenes DSM 1740 has genomic islands and 'homologues' of virulence factors.

  • The comparison identifies species-specific clusters (SSCs) that cannot be detected by the classical approach, which only looks for deviation from the average GC-content and the traditional 'hallmarks' of genomic islands.

  • Many of the SSCs that were found are direct neighbours of virulence genes, suggesting they might be relevant for the bacteria–host interaction.

  • This class of bacteria seems to have had (and still has in H. pylori and C. jejuni) a particular high rate of recombination, as their co-linear gene order has been almost entirely lost, despite being closely related.

  • Phase-variable contingency genes were also found in Wolinella succinogenes DSM 1740, which underlines the fact that it too has an issue with the host's immune system.

Abstract

Comparative genome analysis can be used to identify species-specific genes and gene clusters, and analysis of these genes can give an insight into the mechanisms involved in a specific bacteria–host interaction. Comparative analysis can also provide important information on the genome dynamics and degree of recombination in a particular species. This article describes the comparative genome analysis of representatives of four different Campylobacterales species — two pathogens of humans, Helicobacter pylori and Campylobacter jejuni, as well as Helicobacter hepaticus, which is associated with liver cancer in rodents, and the non-pathogenic commensal species, Wolinella succinogenes.

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Figure 1: Comparative gene content analysis of sequenced ε-proteobacteria.
Figure 2: Functional classification of the genome inventory of sequenced ε-proteobacteria.
Figure 3: Species-specific and syntenic regions of sequenced ε-proteobacteria.
Figure 4: Genome-wide co-linearity analysis.
Figure 5: Visualization of intra- and interspecies recombinatorial events.
Figure 6: Microbial genomics and the study of bacterial pathogenicity.

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Acknowledgements

The authors would like to thank Ramkumar Nandakumar and Daniel Richter for assistance with the computation and graphics. This work was funded by the Max-Planck Society.

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  1. Mark Eppinger and Claudia Baar: These authors contributed equally to this work.

Authors and Affiliations

  1. Max-Planck-Institute for Developmental Biology, Genome Centre, Spemannstr. 35, Tübingen, 72076, Germany

    Mark Eppinger, Claudia Baar, Guenter Raddatz & Stephan C. Schuster

  2. ZBIT Zentrum für Bioinformatik, Tübingen University, Tübingen, 72076, Germany

    Daniel H. Huson

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DATABASES

Entrez

CagA

Campylobacter jejuni NCTC 11168

Chlamydia pneumoniae

Chlamydia trachomatis

cmeABC

Helicobacter hepaticus ATCC 51449

Helicobacter pylori 26695

Helicobacter pylori J99

pVir

Wolinella succinogenes DSM 1740

FURTHER INFORMATION

Stephan C. Schuster's laboratory

COG database

PyloriGene database

Helicobacter Foundation

REBASE

DOLOP

CAZy

Glossary

CHEMOLITHOTROPHIC

An organism that is capable of using CO, CO2 or carbonates as the sole source of carbon for cell biosynthesis, and that derives energy from the oxidation of reduced inorganic or organic compounds.

CHEMOORGANOTROPHIC

An organism that derives energy from organic sources in a light-independent manner.

ORTHOLOGUES

Homologous genes that originated through speciation.

FLEXIBLE GENOME

A bacterial chromosome represents a mosaic structure composed of ancestral DNA, the core genome, and the horizontally acquired flexible genome pool.

LOW-COMPLEXITY ZONES

Genomic regions with a high level of repetitiveness of distinct nucleotides.

SYNTENIC

A genomic region found in two organisms with a co-linear order of genes (or nucleotides). Syntenic regions are found in chromosomal or plasmid-encoded replicons.

PARALOGOUS

Homologous genes that originated by gene duplication

TWO-COMPONENT SIGNAL-TRANSDUCTION SYSTEMS

A signal-transduction system using two components — a histidine protein kinase (HPK) and a response regulator (RR) — to sense and respond to external stimuli. The HPK autophosphorylates at a histidyl residue following stimulation and transfers that phosphoryl group to a cognate RR at its aspartyl residue to induce a conformational change in the regulatory domain, which in turn activates an associated domain.

LEWISXY ANTIGENS

Fucosylated carbohydrate antigens usually found on the surface of eukaryotic cells. They are structurally related to the human ABH blood group system.

HOMOPOLYMERIC TRACTS

The simplest but most frequent low-complexity zones in prokaryotes are simple sequence repeats (SSR), which consist either of homopolymeric tracts or multimeric repeats. These genomic regions are prone to slippage and mispairing.

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Eppinger, M., Baar, C., Raddatz, G. et al. Comparative analysis of four Campylobacterales. Nat Rev Microbiol 2, 872–885 (2004). https://doi.org/10.1038/nrmicro1024

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