Background: Neisseria gonorrhoeae (GC), the causative agent of the sexually transmitted infection gonorrhea, is a polyploid organism whose genetic content is highly fluid and can readily change through natural transformation or genomic reorganization. How the gonococcus retains its genomic organization, and how changes influence GC biology remains unclear.
Aims and Methods: We compared the genomic organization of 53 complete genomes from strains that were collected from geographically distinct locations over the past 20 years or more to assess the extent of chromosomal organizational diversity.
Results: Using rRNA gene locations, we observed significant heterogeneity of gonococcal genome organization. We performed a Mauve alignment on 53 GC strains and identified numerous large and small inversions and translocations. None of the strains examined possessed the same overall genomic organization. Although previous studies attributed genome reorganization to individual mobile elements, we noted that these elements share extensive sequence homology. Our findings demonstrate that mobile elements do not directly drive rearrangements but instead provide regions of high homology that facilitate homologous recombination. PCR analysis confirmed that the observed inversion and translocation events were genuine and remained stable for many generations. Most strains showed a consistent genomic organization near the origin of replication region, which was located roughly 180° opposite the putative replication terminus. However, some strains exhibited a markedly different arrangement, with this region positioned at approximately 270°: this genome arrangement was associated with a pronounced growth defect and altered gene expression profiles
Conclusions: The results demonstrate that large-scale genomic rearrangements in GC that arise through homologous recombination. These changes alter growth parameters that have significant biological and pathogenic consequences.