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Postgenomic taxonomy of human ureaplasmas – a case study based on multiple gene sequences

Centre for Infectious Diseases and Microbiology (CIDM), Institute of Clinical Pathology and Medical Research (ICPMR), Westmead, New South Wales, Australia

Correspondence
Gwendolyn L. Gilbert
lyng{at}icpmr.wsahs.nsw.gov.au

In 2000, the full genome sequence of Ureaplasma parvum (previously known as Ureaplasma urealyticum) serovar 3 was released. In 2002, after prolonged debate, it was agreed that the former U. urealyticum should be divided into two species – U. parvum and U. urealyticum. To provide additional support for this decision and improve our understanding of the relationship between these two species, the authors studied four ‘core’ genes or gene clusters in ATCC reference strains of all 14 serovars of U. parvum and U. urealyticum. These ‘core’ regions were the rRNA gene clusters, the EF-Tu genes (tuf), urease gene clusters and multiple-banded antigen genes (mba). The known U. parvum genome sequences (GenBank accession no. NC_002162) were used as reference. DNA insertions and deletions (indels) were found in all of the gene regions studied, except tuf, but they were found only between, not within, the two species. An incidental finding was that there was inter-copy heterogeneity for rRNA gene cluster sequences. Sequence analysis (sequence heterogeneity and especially indels) of all four selected targets consistently supported the separation of human ureaplasmas into two species. Except for multiple-banded antigen, there was less heterogeneity in amino acid sequences of proteins, between species, than in the nucleic acid sequences of the corresponding genes. The degrees of heterogeneity at the 5' end of the species-specific regions of multiple-banded antigen were almost identical for both amino acid and nucleotide sequences. Analysis of the authors' results provided an interesting case study to help resolve some common problems in the use of sequence data to infer phylogenetic relationships and support taxonomic changes. It is recommended that, to avoid confusion, the new nomenclature be used for human ureaplasmas in future publications.

The GenBank/EMBL/DDBJ accession numbers for the sequences described in this article are: rRNA gene cluster, AF272599–AF272604, AF073446–AF073459, AF059322–AF059335 and AF272605–AF272630; tuf, AF270758–AF270770; urease gene clusters, AF085720–AF085733; mba, AF055358–AF055367 and AF056982–AF056984.

Comparisons of two U. parvum serovar 3 rRNA operons (Fig. A), U. urealyticum serovar 8 and U. parvum serovar 3 rRNA operon 1 and operon 2 DNA sequences (Fig. B), U. urealyticum serovars 8 and 13 and U. parvum serovar 3 EF-Tu gene (tuf) DNA and amino acid sequences (Fig. C), and U. urealyticum serovar 8 (upper line) and U. parvum serovar 3 (lower line) urease gene cluster sequences (Fig. D), and a comparison of interspecies heterogeneity of DNA and amino acid sequences of the urease gene clusters of U. parvum and U. urealyticum (Table A) are available as supplementary material in IJSEM Online.

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