MBE Advance Access published online on October 5, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm215
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Research Article |
The Repertoire of Minimal Mobile Elements in the Neisseria Species and Evidence That These are Involved in Horizontal Gene Transfer in Other Bacteria
1 Bacterial Pathogenesis and Functional Genomics Group, The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, UK. OX1 3RE
2 Computational Biology Research Group, University of Oxford, South Parks Road, Oxford, UK. OX1 3RE
* Corresponding author's current address – Lori A. S. Snyder. Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, UK. B15 2TT. Telephone: +44 121 414 8849. FAX: +44 121 414 8844. E-mail: l.a.snyder{at}bham.ac.uk
Received for publication July 2, 2007. Revision received September 25, 2007. Accepted for publication September 26, 2007.
In the Neisseria spp., natural competence for transformation and homologous recombination generate antigenic variants through creation of mosaic genes (such as opas) and through recombination with silent cassettes (such as pilE/pilS), and gene-complement diversity through the horizontal exchange of whole genes, or groups of genes, in Minimal Mobile Elements (MMEs). A MME is a region encompassing two conserved genes between which different whole-gene cassettes are found in different strains, which are chromosomally incorporated solely through the action of homologous recombination. Comparative analyses of the neisserial genome sequences identified 39 potential MME sites, the contents of which were investigated in 11 neisserial strains. 108 different MME regions were identified, 20 of which contain novel sequences and these contain 12 newly identified neisserial CDSs. Neisserial uptake signal sequences are associated with 38 of the 40 MMEs studied. In some sites, divergent dinucleotide signatures of the sequences between the flanking genes suggest relatively recent horizontal acquisition of some cassettes. The neisserial MMEs were used to interrogate all of the other available bacterial genome sequences, revealing frequent conservation of the flanking genes combined with the presence of different gene cassettes between them. In some cases, these sites can definitively be classified as MMEs in these other genera. These findings provide additional evidence for the MME model, indicate that MME-directed investigations are a good basis for the identification of novel strain-specific genes and differences within bacterial populations, and demonstrate that these elements are probably ubiquitously involved in genetic exchange, particularly in naturally competent bacteria.
Key Words: Horizontal gene acquisition • bacterial population diversity • Neisseria gonorrhoeae • Neisseria meningitidis • MME