MPI für Infektionsbiologie / Department of Molecular Biology |
|Gain and loss of multiple genes during the evolution of Helicobacter pylori|
|Authors:||Gressmann, Helga; Linz, Bodo; Ghai, Rohit; Pleissner, Klaus-Peter; Schlapbach, Ralph; Yamaoka, Yoshio; Kraft, Christian; Suerbaum, Sebastian; Meyer, Thomas F.; Achtman, Mark|
|Date of Publication (YYYY-MM-DD):||2005-10|
|Title of Journal:||PLoS Genetics|
|Journal Abbrev.:||PLoS Genet.|
|Issue / Number:||4|
|Copyright:||PLoS Genetics is an open-access journal published by the nonprofit organization Public Library of Science.
All journal content, except where otherwise noted, is licensed under the Creative Commons Attribution License.
|Abstract / Description:||Sequence diversity and gene content distinguish most isolates of Helicobacter pylori. Even greater sequence differences differentiate distinct populations of H. pylori from different continents, but it was not clear whether these populations also differ in gene content. To address this question, we tested 56 globally representative strains of H. pylori and four strains of Helicobacter acinonychis with whole genome microarrays. Of the weighted average of 1,531 genes present in the two sequenced genomes, 25% are absent in at least one strain of H. pylori and 21% were absent or variable in H. acinonychis. We extrapolate that the core genome present in all isolates of H. pylori contains 1,111 genes. Variable genes tend to be small and possess unusual GC content; many of them have probably been imported by horizontal gene transfer. Phylogenetic trees based on the microarray data differ from those based on sequences of seven genes from the core genome. These discrepancies are due to homoplasies resulting from independent gene loss by deletion or recombination in multiple strains, which distort phylogenetic patterns. The patterns of these discrepancies versus population structure allow a reconstruction of the timing of the acquisition of variable genes within this species. Variable genes that are located within the cag pathogenicity island were apparently first acquired en bloc after speciation. In contrast, most other variable genes are of unknown function or encode restriction/modification enzymes, transposases, or outer membrane proteins. These seem to have been acquired prior to speciation of H. pylori and were subsequently lost by convergent evolution within individual strains. Thus, the use of microarrays can reveal patterns of gene gain or loss when examined within a phylogenetic context that is based on sequences of core genes.|
|Comment of the Author/Creator:||Acknowledgments
We are grateful to Jörg Angermann and Christiana Stamer for technical support, Martina Böhme for assistance with bioinformatics, and Michaela Dehio for designing primers. We gratefully acknowledge the permission of Stephan C. Schuster, Penn State University, to analyze the unpublished genome of strain Sheeba and the helpful comments of two anonymous reviewers. The work was supported by grants to SS, TFM, and MA from the German Federal Ministry for Education and Research (BMBF) in the framework of the competence center of the PathoGenoMik Network (Grant 03U213), NGFN-2 grant 01GS0401 to T. Chakraborty, and the Fonds der Chemischen Industrie to TFM
The authors have declared that no competing interests exist.
|External Publication Status:||published|
|Version Comment:||Automatic journal name synchronization|
|Communicated by:||Hilmar Fünning|
|Affiliations:||MPI für Infektionsbiologie/Department of Molecular Biology|
MPI für Infektionsbiologie/Core Facilities
|External Affiliations:||Univ Giessen, Inst Med Microbiol, Giessen, Germany.; Univ Zurich, ETH, Funct Genom Ctr, Zurich, Switzerland.; ME DeBakey Vet Affairs Med Ctr, Dept Med, Houston, TX USA.; Baylor Coll Med, Houston, TX 77030 USA.; Hannover Med Sch, Inst Med Mikrobiol & Krankenhaushyg, Hannover, Germany.|
|Identifiers:||ISI:000234714800002 [ID No:1] |
ISSN:1553-7390 [ID No:2]
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