Spencer-Smith, Russell (2011) The origins and evolution of genomic rearrangements in 'Neisseria gonorrhoeae'. (MSc(R) thesis), Kingston University, .

Abstract

Alignments of the complete genome sequences of 'N. gonorrhoeae' strains FA 1090, NCCP11945 and TCDC-NG08107 show large variations in total genome length and chromosomal arrangement. Changes in genome length may be partially attributed to DNA uptake sequences (DUS), which are widespread throughout the 'N. gonorrhoeae' genome. DUS allows endogenous DNA to be exchanged between 'Neisseria' species, and also occur as inverted repeats (IR-DUS) which have been suggested previously to play a role in 'rho'-independent termination and attenuation. Current literature only describes IR-DUS where the DUS precedes the inverted DUS. Here we show that IR-DUS also occur in reverse order, and can potentially act as bi-directional terminators, and therefore affect coding sequences (CDS) on both DNA strands. This work also provides evidence that gaps in DUS density coincide with areas of DNA that are foreign in origin, such as the gonococcal genetic island and prophage CDSs. This could provide a useful indicator to the origins of DNA that contribute to the additional length seen in the NCCP11945 genome. The presence of five dsDNA lysogenic prophages and four ssDNA filamentous prophages play key roles in the genomic rearrangements seen between 'N. gonorrhoeae' strains. Previous theories have suggested that 'N. gonorrhoeae' filamentous prophage are mobilized and reintegrated via a circular intermediary requiring one copy of the ISNgo2 sequence. This work provides compelling 'in silico' evidence that these prophage require two copies of insertion sequence Ngo2 (ISNgo2) and function in much the same way as composite transposons, seen in other bacterial species. Flanking ISNgo2 associated with these prophage appear to have the capacity to mobilize large sections of genomic DNA. Unlike the filamentous prophage, lysogenic prophages do not appear to be complete or mobile. They do however appear to mediate chromosomal rearrangements via a previously undiscovered, repeat enclosed element, similar to the CREE elements also found in 'N. honorrhoeae'. These Spencer-Smith Repeat Enclosed Elements (SSREE) are found in lysogenic prophage NGO[phi]1, NGO[phi]2 and NGO[phi]3 and appear to have mediated a 700 kb inversion between NGO[phi]1 and NGO[phi]2. Stressful continuous culturing of 'N. gonorrhoeae' strain NCCP11945 has shown continued growth into the third day of culturing, growth upon media containing 128[mu]g/ml nalidixic acid and a 41[degrees]C upper temperature limit, with a 39[degrees]C limit for sustained passages. Pulsed field gel electrophoresis upon 'N. gonorrhoeae' strain NCCP11945 8 week cultures is shown to produce additional banding which may be the result of prophage mobilization and reintegration within this strain.

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