The Repertoire of Minimal Mobile Elements in the Neisseria Species and Evidence That These Are Involved in Horizontal Gene Transfer in Other Bacteria

Abstract

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). An MME is a region encompassing 2 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. One hundred and eight different MME regions were identified, 20 of which contain novel sequences and these contain 12 newly identified neisserial coding sequences. 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.

Homologous Recombination Drives Both Sequence Diversity and Gene Content Variation in Neisseria meningitidis

“…Among the nine regions, only the glnD-guaB region (fig. 2 H ) has been previously identified (Snyder et al 2007).

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“…Homologous recombination at the conserved flanking genes would account for this phenomenon whereby gene organization was identical between distantly related genomes but different between the closely related ST60 genomes. These regions displayed characteristics of minimal mobile elements, which were defined as variable regions among the closest relatives in sequence composition and gene content between specific conserved flanking genes (Saunders and Snyder 2002; Snyder et al 2007). Among the nine regions, only the glnD-guaB region (fig.…”

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence

“…Of the 1450 single-copy orthologous genes used for transcriptomic comparisons 30 differed in the presence of putative mobile genetic elements within their 200 bp upstream regions (Additional file 2: S1). These comprised various so called minimal mobile elements [63, 64] as well Correia repeats and Correia repeat enclosed elements which have previously been shown to affect gene expression in a polar manner [65–67]. However, this class of genes was not enriched for genes differently expressed in at least one ex vivo condition.…”

The Genetics of Neisseria Species

“…An MME is a cassette flanked by protein-encoding genes whose contents differ between strains or species. The cassettes can be exchanged and incorporated by homologous recombination in the conserved flanking regions (138,158). In this manner, a rare insertion event originally independent of homology can spread throughout a population, especially in naturally competent bacteria.…”