Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

Abstract

BackgroundThe genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally.ResultsNon-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent.ConclusionThe three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.

Genetic Distribution of Noncapsular Meningococcal Group B Vaccine Antigens in Neisseria lactamica

“…Intragenically directed PCRs indicated the genome-wide absence of fhbp alleles among all of the N. lactamica isolates. In the corresponding meningococcal fhbp locus, they each were found to possess nla18150 alleles for an unrelated putative opacity protein (31), and this gene was orientated in the opposite direction from that of fhbp. The nla18150 alleles possessed between 2 and Ն22 octanucleotide GCGTTCCT repeats within the open reading frame (the tract length of six isolates was indeterminate, owing to strand slippage during PCR, heterogeneous plate population, or both), which was shortly preceded by a homopolymeric A repeat tract of between four and six repeats.…”

“…One isolate (N. lactamica M02 241586) had an A-to-T substitution (corresponding to residue 698 in nla18150 of the N. lactamica isolate 020-06; GenBank accession no. NC_014752 [31]), creating a premature stop codon site 42 bp upstream from the prototypical stop codon.…”

“…Sequence analyses of the respective N. lactamica fhbp loci indicated that all of the isolates possessed alleles for a phase-variable putative opacity protein, NLA18150 (31), the function of which is currently unknown. This too was consistent with the published genomes.…”

“…KC480197 to KC480246. Alleles corresponding to nla18150 (31) were deposited in GenBank under the accession no. KC495573 to KC495616.…”

The Amino Acid Sequence of Neisseria lactamica PorB Surface-Exposed Loops Influences Toll-Like Receptor 2-Dependent Cell Activation

“…In Fig. 1A, loops 1, 4, 5, 6, 7, and 8 are shaded, and loops 2 and 3, involved in porin function, are boxed (3,11). The alignment revealed single substitutions or, in some cases, multiple residue substitutions in the sequence of PorB from commensal and pathogenic strains.…”