Genome flexibility in Neisseria meningitidis

Abstract

Neisseria meningitidis usually lives as a commensal bacterium in the upper airways of humans. However, occasionally some strains can also cause life-threatening diseases such as sepsis and bacterial meningitis. Comparative genomics demonstrates that only very subtle genetic differences between carriage and disease strains might be responsible for the observed virulence differences and that N. meningitidis is, evolutionarily, a very recent species. Comparative genome sequencing also revealed a panoply of genetic mechanisms underlying its enormous genomic flexibility which also might affect the virulence of particular strains. From these studies, N. meningitidis emerges as a paradigm for organisms that use genome variability as an adaptation to changing and thus challenging environments.

Fig. 1

Annotated multiple whole-genome alignment using Mauve . For each genome, the order of locally collinear blocks (LCBs) is given as a series of coloured blocks with the putative origin of replication designated oriC being indicated by a black rectangle. LCBs identically present in the four genomes are given in the same colours and horizontally flipped LCBs identify chromosomal inversions with respect to the genome of α14-like the inversion designated Inv1 in the genome of Z2491. Gaps or white spaces in the LCB order image indicate regions not (identically) present in all four genomes such as different prophages (Φ), genomic islands (GI), islands of horizontal transfer (IHT), or a region duplicated only in strain MC58 (D). In addition, the 20 kb region that is inverted in the four disease isolates (Inv) and the position of the capsule gene locus (C) are also shown.

Fig. 2

Region upstream of the carA gene coding for the small subunit of the carbamoylphosphate synthase in the genomes of N. meningitidis Z2491 and α14. (A) Comparison of the corresponding region in Z2491 and α14. The NIME repeat regions (hatched boxes) flanking the pilC1 gene in Z2491 and the corresponding region in α14 are depicted in more detail in panels B, C, and D, respectively. Direct and inverted identical regions in both genomes are connected by red and blue lines and areas, respectively. (B) Repeat region between carA and pilC1, and (C) between pilC1 and NMA0611, respectively, in Z2491. dRS3 repeats are depicted by green arrows and the names of the RS repeats (blue coloured arrows) are given. A red arrow indicates a REP2 repeat upstream of pilC1. (D) Corresponding repeat region in α14. Asterisks indicate identical dRS3 repeats that might constitute the integration or deletion site for pilC1 and that are also target sites for the prophage Nf1 integrase. The orange arrow indicates a 28-bp region that is identical to the 3′ end of a silent pilS cassette (pilS4 in Z2491 and pilS2 in α14, respectively).

Fig. 3

Gene content comparisons based on bi-directional best hits in all-against-all BLASTP comparisons of the annotated coding sequences. (A) Distribution of different classes of genes amongst the different genomic compartments. Depicted is the partition of all genes from the species pan-genome (grey bar), genes having a low GC content and probably acquired via HGT (white bar), and the candidate virulence genes (black bar) into the core, dispensable and strain-specific genome. The core genome contains the genes that can be found in all strains, the dispensable genome contains the genes that are missing in at least one strain and the strain-specific genome comprises all the genes that can only be found in one strain. (B) For varying numbers of disease strains, the number of genes that are exclusively found in all disease strains and are absent in all carriage strains is plotted against the number of carriage strains compared.

Fig. 4

Capsule loci in different Neisseria species. The cps locus is flanked on either side by genes belonging to the neisserial core genome (coloured in white and dark grey, respectively). The five regions comprising the cps locus are depicted in different colours. Homologous genes are given identical colours according to the regions they belong to. In order to obtain an un-encapsulated and thus attenuated mutant strain of MC58, ermC coding for an erythromycin resistance gene has artificially been inserted into siaD_B and is thus not part of the cps locus. NMA0184 putatively coding for a TPR protein (COG0790) has not been described so far as part of region B. The genes coloured in dark green between regions A and D in MC58 and FAM18 and between regions B and D′ in α275, respectively, potentially code for proteins also involved in capsule synthesis. The genes coloured pink and light grey in strains α14 and N. lactamica, respectively, code for hypothetical proteins. In addition, the G + C plot for the capsule locus with Z2491 as reference is given.

Fig. 5

Hypothetical scenario of the evolution of encapsulated meningococcal strains from an unencapsulated common ancestor with N. gonorrhoeae and N. lactamica as suggested by whole-genome comparisons (neighbour net reconstruction based on genome rearrangement distances [74]). A yet unencapsulated ancestor of N. meningitidis might first have acquired IS1655 indicating the separation of N. meningitidis from other Neisseria species. At later time points the genes required for the production of a polysaccharide capsule (cps) were imported via HGT from other bacterial species, probably members of the Pasteurellaceae that also inhabit the nasopharynx of mammalian hosts.