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Infection and Immunity, July 2000, p. 4155-4168, Vol. 68, No. 7
0019-9567/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Comparative Genomics of Helicobacter pylori: Analysis of the Outer Membrane Protein Families

Richard A. Alm,1,* James Bina,2,dagger Beth M. Andrews,1 Peter Doig,1 Robert E. W. Hancock,2 and Trevor J. Trust1

Infection Discovery AstraZeneca R & D Boston, Waltham, Massachusetts 02451,1 and Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z32

Received 11 January 2000/Returned for modification 17 March 2000/Accepted 4 April 2000

The two complete genomic sequences of Helicobacter pylori J99 and 26695 were used to compare the paralogous families (related genes within one genome, likely to have related function) of genes predicted to encode outer membrane proteins which were present in each strain. We identified five paralogous gene families ranging in size from 3 to 33 members; two of these families contained members specific for either H. pylori J99 or H. pylori 26695. Most orthologous protein pairs (equivalent genes between two genomes, same function) shared considerable identity between the two strains. The unusual set of outer membrane proteins and the specialized outer membrane may be a reflection of the adaptation of H. pylori to the unique gastric environment where it is found. One subfamily of proteins, which contains both channel-forming and adhesin molecules, is extremely highly related at the sequence level and has likely arisen due to ancestral gene duplication. In addition, the largest paralogous family contained two essentially identical pairs of genes in both strains. The presence and genomic organization of these two pairs of duplicated genes were analyzed in a panel of independent H. pylori isolates. While one pair was present in every strain examined, one allele of the other pair appeared partially deleted in several isolates.

* Corresponding author. Mailing address: Infection Discovery AstraZeneca R & D Boston, 35 Gatehouse Dr., Waltham, MA 02451. Phone: (781) 839-4000. Fax: (781) 839-4570. E-mail: richard.alm{at}astrazeneca.com.

dagger Present address: Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115.

Infection and Immunity, July 2000, p. 4155-4168, Vol. 68, No. 7
0019-9567/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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