Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements

Abstract

Background: There are four widely used experimental strains of N. gonorrhoeae, one of which has been sequenced and used as the basis for the construction of a multi-strain, mutli-species pan-neisserial microarray. Although the N. gonorrhoeae population structure is thought to be less diverse than N. meningitidis, there are some recognized gene-complement differences between strains, including the 59 genes of the Gonococcal Genetic Island. In this study we have investigated the three experimental strains that have not been sequenced to determine the extent and nature of their similarities and differences.

Results: Using the Pan-Neisseria microarray, three commonly used gonococcal laboratory experimental strains were investigated (F62, MS11, & FA19). Genes absent from these strains, but present in strain FA1090, were assessed as is possible with typical microarrays. Due to the design of this microarray, additional genes were also identified. Differences were associated with Minimal Mobile Elements (MMEs) or known divergences. Genomotyping indicates the presence of genes previously only described in meningococci and shows the presence of the complete Gonococcal Genetic Island in N. gonorrhoeae strain FA19. Five new neisserial genes were identified through microarray genomotyping and subsequent sequencing of two divergent MMEs in N. gonorrhoeae strain MS11 and four MMEs in N. gonorrhoeae strain FA19. No differences were identified between N. gonorrhoeae strains FA1090 and F62, indicating that these strains are very similar.

Conclusion: This study shows extensive similarity between the experimental strains, associated with a varying number of strain-specific genes. This provides a framework for those working with these strains to refer to the available gonococcal genome sequence, and is the first detailed comparison of gene complements between gonococcal strains.

Figure 1

The MME flanked by ung and a hypothetical protein. This MME contains the 59 predicted coding regions of the Gonococcal Genetic Island (GGI) in N. gonorrhoeae strains MS11 and FA19, one hypothetical gene in N. gonorrhoeae strain FA1090 [16], a putative methylase and a hypothetical gene in N. meningitidis strains MC58 and Z2491 [29,30], and two hypothetical genes, piv, and a putative regulator in N. meningitidis strain FAM18. Similar genes are indicated in the same colour.

Figure 2

The MME flanked by nuoL and nuoM. This MME contains a hypothetical gene in N. gonorrhoeae strain FA1090 [16], short intergenic sequences in N. meningitidis strains MC58 [29] and FAM18, two hypothetical genes in N. meningitidis strain Z2491 [30], and four newly described neisserial genes of unknown function in N. gonorrhoeae strain MS11 (AY386266).

Figure 3

The MME flanked by a putative LPS biosynthesis gene and pglB. This MME contains two hypothetical genes in N. gonorrhoeae strain FA1090 [16], N. meningitidis strain Z2491 [30], and N. meningitidis strain FAM18; and a short intergenic region in N. meningitidis strain MC58 [29] and N. gonorrhoeae strain MS11 (AY386267). Similar genes are indicated in the same colour.

Figure 4

The MME flanked by nadC and xthA. This MME contains a hypothetical gene (NMB0397) in N. meningitidis strain MC58 [29]. This gene is disrupted in a different way in all other strains from which it has been sequenced. In N. meningitidis strain Z2491 [30], it is interrupted by a CREE, which also disrupts the next gene, in N. meningitidis strain FAM18 it is disrupted by a 61 bp indel that causes a frame-shift, in N. gonorrhoeae strain FA1090 [16] it is disrupted by a hypothetical gene, and in N. gonorrhoeae strain FA19 (AY386268) it is disrupted by a different CREE from that in this location in N. meningitidis strain Z2491. Similar genes or fragments thereof are indicated in the same colour.

Figure 5

The MME flanked by a pilin-related gene and an AzlC-related gene. This MME contains a hypothetical gene in N. gonorrhoeae strain FA1090 [16], a compound CREE structure in N. meningitidis strains MC58 [29], Z2491 [30], and FAM18, in which two nearly identical CREE flank a variable intergenic region composed largely of tandem repeats and which disrupts the 3' end of the AzlC-related gene, and a single CREE in N. gonorrhoeae strain FA19 (AY386269), where the 3' end of the AzlC-related gene is disrupted by other intergenic sequence.

Figure 6

The MME flanked by uvrA and a hypothetical gene. This MME contains a gene encoding a putative methylase and a hypothetical gene in N. gonorrhoeae strain FA1090 [16], three hypothetical genes in N. meningitidis strain Z2491 [30], two hypothetical genes in N. meningitidis strain FAM18, and one new neisserial gene of unknown function in N. gonorrhoeae strain FA19 (AY386270). This is the point of a chromosomal rearrangement in N. meningitidis strain MC58 [29].

Figure 7

The MME flanked by two hypothetical genes. This MME contains an intergenic sequence in N. gonorrhoeae strain FA1090 [16], and a hypothetical gene in N. meningitidis strain Z2491 [30]. In N. gonorrhoeae strain FA19 (AY386271) there is a homologue of the meningococcal CDS, which has been disrupted by a CREE 44 bp into the gene. The CREE in this location introduces a termination codon and generates a frame-shift. However, it also generates a potential promoter 5' of a potential ribosomal binding site and secondary initiation codon internal to NMA2121. This is the point of a chromosomal rearrangement in N. meningitidis strains MC58 [29] and FAM18. Similar genes are indicated in the same colour.