Repeat‐associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58

Abstract

Phase variation, mediated through variation in the length of simple sequence repeats, is recognized as an important mechanism for controlling the expression of factors involved in bacterial virulence. Phase variation is associated with most of the currently recognized virulence determinants of Neisseria meningitidis. Based upon the complete genome sequence of the N. meningitidis serogroup B strain MC58, we have identified tracts of potentially unstable simple sequence repeats and their potential functional significance determined on the basis of sequence context. Of the 65 potentially phase variable genes identified, only 13 were previously recognized. Comparison with the sequences from the other two pathogenic Neisseria sequencing projects shows differences in the length of the repeats in 36 of the 65 genes identified, including 25 of those not previously known to be phase variable. Six genes that did not have differences in the length of the repeat instead had polymorphisms such that the gene would not be expected to be phase variable in at least one of the other strains. A further 12 candidates did not have homologues in either of the other two genome sequences. The large proportion of these genes that are associated with frameshifts and with differences in repeat length between the neisserial genome sequences is further corroborative evidence that they are phase variable. The number of potentially phase variable genes is substantially greater than for any other species studied to date, and would allow N. meningitidis to generate a very large repertoire of phenotypes through expression of these genes in different combinations. Novel phase variable candidates identified in the strain MC58 genome sequence include a spectrum of genes encoding glycosyltransferases, toxin related products, and metabolic activities as well as several restriction/modification and bacteriocin‐related genes and a number of open reading frames (ORFs) for which the function is currently unknown. This suggests that the potential role of phase variation in mediating bacterium–host interactions is much greater than has been appreciated to date. Analysis of the distribution of homopolymeric tract lengths indicates that this species has sequence‐specific mutational biases that favour the instability of sequences associated with phase variation.

Autotransported Serine Protease A of Neisseria meningitidis : an Immunogenic, Surface-Exposed Outer Membrane, and Secreted Protein

“…The gonococcal aspA gene, which is 97% identical to the meningococcal aspA gene, contains multiple termination codons, suggesting that it may be a pseudogene in N. gonorrhoeae. The presence of the polycytidine tract in aspA, 287 bp from the putative ATG initiation codon, suggests that aspA may be phase variable due to the "slipped-strand mispairing" mechanism (16,28). The length of the polycytidine tract in the aspA gene was identical (10 bp) in strains Z2491, MC58, and Z4181, but was 15 bp in strain SD, thus placing a premature termination codon in-frame.…”

“…Unlike the serine proteases (and Ssp-H1/H2) of S. marcescens, however, an RGD motif was absent (15). In comparison with PrtS and Ssp-H1/H2 of S. marcescens, an N-terminal domain (from 28 Cys-661 Asp; ϳ67 kDa), a junctional domain ( 662 Ser-747 Thr), and a C-terminal domain ( 748 Phe-1068 Phe; ϳ33 kDa) were identified.…”

Bacteria are small but not stupid: cognition, natural genetic engineering and socio-bacteriology

“…-flagellar phase variation in Salmonella (Zieg at el., 1977) -fimbrial phase variation in E. coli (Blomfield, 2001) -Borrelia VSG expression (Barbour et al, 2000) -R64 plasmid sex pilus structure changes (Gyohda et al, 2004) -Neisseria pilus and opacity protein changes (Saunders et al, 2000) -Bordetella reverse transcriptase (Doulatov et al, 2004) 2000). Thus, the DNA segments that move through the genome, the places they move, and the sequences they rearrange can have both flexibility and predictability.…”

Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage

“…Illegitimate recombination occurs between short closely spaced repetitive DNA sequences with few or no identical nucleotides (Bichara et al, 2006). These repeats are located either within ORFs, such that alteration in the length of the repeat promotes antigenic or phase variation, or within regulatory regions, where sequence change influences transcription (Saunders et al, 2000;Rocha & Blanchard, 2002). This allows the generation of a vast repertoire of abilities by which pathogenic strains can adapt to the different microenvironments of the host and evade host immune responses.…”