Structural analysis of the pilE region of Neisseria gonorrhoeae P9

Analyzing Neisseria gonorrhoeae Pilin Antigenic Variation Using 454 Sequencing Technology

Many pathogens use homologous recombination to vary surface antigens in order to avoid immune surveillance. Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted infection gonorrhea, achieves this in part by changing the sequence of the major subunit of the type IV pilus in a process termed pilin antigenic variation (Av). The N. gonorrhoeae chromosome contains one expression locus (pilE) and many promoterless, partial-coding silent copies (pilS) that act as reservoirs for variant pilin information. Pilin Av occurs by high-frequency gene conversion reactions, which transfer pilS sequences into the pilE locus. We have developed a 454 sequencing-based assay to analyze the frequency and characteristics of pilin Av that allows a more robust analysis of pilin Av than previous assays. We used this assay to analyze mutations and conditions previously shown to affect pilin Av, confirming many but not all of the previously reported phenotypes. We show that mutations or conditions that cause growth defects can result in Av phenotypes when analyzed by phase variation-based assays. Adapting the 454 sequencing to analyze pilin Av demonstrates the utility of this technology to analyze any diversity generation system that uses recombination to develop biological diversity.

IMPORTANCE

Measuring and analyzing complex recombination-based systems constitute a major barrier to understanding the mechanisms used to generate diversity. We have analyzed the contributions of many gonococcal mutations or conditions to the process of pilin antigenic variation.

Algorithmic assessment of vaccine-induced selective pressure and its implications on future vaccine candidates

Posttrial assessment of a vaccine's selective pressure on infecting strains may be realized through a bioinformatic tool such as parsimony phylogenetic analysis. Following a failed gonococcal pilus vaccine trial of Neisseria gonorrhoeae, we conducted a phylogenetic analysis of pilin DNA and predicted peptide sequences from clinical isolates to assess the extent of the vaccine's effect on the type of field strains that the volunteers contracted. Amplified pilin DNA sequences from infected vaccinees, placebo recipients, and vaccine specimens were phylogenetically analyzed. Cladograms show that the vaccine peptides have diverged substantially from their paternal isolate by clustering distantly from each other. Pilin genes of the field clinical isolates were heterogeneous, and their peptides produced clades comprised of vaccinated and placebo recipients' strains indicating that the pilus vaccine did not exert any significant selective pressure on gonorrhea field strains. Furthermore, sequences of the semivariable and hypervariable regions pointed out heterotachous rates of mutation and substitution.

Pilin gene variation in Neisseria gonorrhoeae: reassessing the old paradigms

Neisseria gonorrhoeae displays considerable potential for antigenic variation as shown in human experimental studies. Various surface antigens can change either by antigenic variation using RecA-dependent recombination schemes (e.g. PilE antigenic variation) or, alternatively, through phase variation (on/off switching) in a RecA-independent fashion (e.g. Opa and lipooligosaccharide phase variation). PilE antigenic variation has been well documented over the years. However, with the availability of the N. gonorrhoeae FA1090 genome sequence, considerable genetic advances have recently been made regarding the mechanistic considerations of the gene conversion event, leading to an altered PilE protein. This review will compare the various models that have been presented and will highlight potential mechanistic problems that may constrain any genetic model for pilE gene variation.

Recombination, repair and replication in the pathogenic Neisseriae: the 3 R's of molecular genetics of two human-specific bacterial pathogens

Most of the detailed mechanisms that have been established for the molecular biological processes that mediate recombination, repair and replication of DNA have come from studies of the Escherichia coli paradigm. The human specific pathogens, Neisseria gonorrhoeae and N. meningitidis, are Gram-negative bacteria that have some molecular processes that are similar to E. coli and others that appear to be divergent. We propose that the pathogenic Neisseriae have evolved a specialized collection of molecular mechanisms to adapt to life limited to human hosts. In this MicroReview, we explore what is known about the basic processes of DNA repair, DNA recombination (genetic exchange and pilin variation) and DNA replication in these human specific pathogens.

Insertion mutations in pilE differentially alter gonococcal pilin antigenic variation

Pilus antigenic variation in Neisseria gonorrhoeae occurs by the high-frequency, unidirectional transfer of DNA sequences from one of several silent pilin loci (pilS) into the expressed pilin gene (pilE), resulting in a change in the primary pilin protein sequence. Previously, we investigated the effects of large or small heterologous insertions in conserved and variable portions of a pilS copy on antigenic variation. We observed differential effects on pilin recombination by the various insertions, and the severity of the defect correlated with the disruption or displacement of a conserved pilin DNA sequence called cys2. In this study, we show that disruption or displacement of the pilE cys2 sequence by the same insertions or a deletion also affects pilin recombination. However, in contrast to the insertions in pilS, the analogous insertions in pilE impaired, but did not block, recombination of the flanking pilin sequences. These results, the change in the spectrum of donor silent copies used during variation, and our previous results with pilS mutations show that the donor pilS and recipient pilE play different roles in antigenic variation. We conclude that when high-frequency recombination mechanisms are blocked, alternative mechanisms are operative.

Formation of single-stranded DNA during DNA transformation of Neisseria gonorrhoeae

Neisseria gonorrhoeae is naturally competent for DNA transformation. In contrast to other natural prokaryotic DNA transformation systems, single-stranded donor DNA (ssDNA) has not previously been detected during transformation of N. gonorrhoeae. We have reassessed the physical nature of gonococcal transforming DNA by using a sensitive nondenaturing native blotting technique that detects ssDNA. Consistent with previous analyses, we found that the majority of donor DNA remained in the double-stranded form, and only plasmid DNAs that carried the genus-specific DNA uptake sequence were sequestered in a DNase I-resistant state. However, when the DNA was examined under native conditions, S1 nuclease-sensitive ssDNA was identified in all strains tested except for those bacteria that carried the dud-1 mutation. Surprisingly, ssDNA was also found during transformation of N. gonorrhoeae comA mutants, which suggested that ssDNA was initially formed within the periplasm.

Analysis of protein binding to the Sma/Cla DNA repeat in pathogenic Neisseriae

Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recombination, the factors which maintain the silent reservoir of pilin sequences and/or allow unidirectional recombination from silent to expression loci remain undefined. We have previously shown that a conserved sequence at the 3'end of all pilin loci (the Sma/Cla repeat) is required to be present at the expression locus for efficient recombination from the silent loci. In this study, the binding of gonococcal proteins to this DNA sequence was investigated. Gel mobility shift assays and competition experiments using deletion derivatives of the repeat, show that multiple activities bind to different regions of the Sma/Cla repeat and define the boundaries of the binding sequences. Moreover, only the pathogenic Neisseria harbor proteins which specifically bind to this repeat, suggesting a correlation between the expression of these DNA binding proteins and the potential to cause disease.

Questions about gonococcal pilus phase- and antigenic variation

Pathogenic organisms inhabit one of several defined locations within a host where temperature, pH, and nutrients are relatively constant. While the microorganism must adapt to different environments within the host, the host immune system is the most formidable predator that can limit the growth of a pathogen. Neisseria gonorrhoeae (the gonococcus, Gc) is the causative agent of gonorrhoea, and has evolved several systems for varying the antigenicity of different surface antigens, presumably to help evade the effects of the human immune system. The On/Off/On phase variation of surface structure expression also alters the antigenic characteristics of the bacterial cell surface. Antigenic variation of the major subunit of the pilus, pilin, occurs by unidirectional, homologous recombination between a silent locus and the expression locus. The silent loci lie from 1 to 900 kb from the expression locus in the chromosome yet all can donate their sequences to the expression locus. The genetic composition of the pilin loci of two Gc strains has been elucidated, and the types of changes that lead to altered forms of the pilus have been extensively characterized. However, little is known about the precise molecular mechanisms used to allow high-frequency, non-reciprocal, chromosomal recombination between pilin loci or about what regulates the process of maintaining chromosome fidelity.

Identification and characterization of specific sequences encoding pathogenicity associated proteins in the genome of commensal Neisseria species

The distribution of distinct sequences in pathogenic and commensal Neisseria species was investigated systematically by dot blot analysis. Probes representing the genes of Rmp, pilin and IgA1 protease were found to hybridize exclusively to the chromosomal DNA of the pathogenic species, Neisseria gonorrhoeae and/or Neisseria meningitidis. In contrast, specific sequences for the genes of the porin protein Por and the opacity protein (Opa) were also detected in a panel of commensal Neisseria species such as N. lactamica, N. subflava, N. flava, N. mucosa and N. sicca. Using opa-specific oligonucleotides as probes in chromosomal blots, the genomes of the commensal Neisseria species show a totally reduced repertoire of cross-hybridizing loci compared to the complex opa gene family of N. gonorrhoeae. DNA sequence analysis of one opa-related gene derived from N. flava and N. sicca, respectively, revealed a large degree of homology with previously described gonococcal and meningococcal genes, e.g., a typical repetitive sequence in the leader peptide and the distribution of the hypervariable and conserved regions. This observation, together with the finding, that the gene is constitutively transcribed, leads to the assumption that some of the commensal Neisseria species may have the potential for the expression of a protein harboring similar functions as the Opa proteins in pathogenic Neisseriae.

A conserved DNA sequence is required for efficient gonococcal pilin antigenic variation

Antigenic variation of the Neisseria gonorrhoeae pilus occurs when a variant pilin sequence from a silent locus recombines into the expression locus by predominantly unidirectional, homologous recombination. At the 3' end of all pilin loci lies a conserved DNA sequence, called the Sma/Cla repeat, which has sequence similarity to several recombinase-binding sites, and therefore may be involved in pilin recombination. We have developed a novel reverse transcriptase/polymerase chain reaction (RT-PCR) assay for direct monitoring of pilin recombination, and both RT-PCR and phase variation were used to examine pilin recombination in a gonococcal strain that had had the pilE Sma/Cla repeat removed. Results from these experiments showed a decrease in pilin recombination when the Sma/Cla sequence was deleted from the expression locus, showing that a specialized site (Sma/Cla) is involved in efficient pilin recombination.

Control of gonococcal pilin-encoding gene expression in Escherichia coli

The pilE gene from Neisseria gonorrhoeae, unlike other type-4 pilin-encoding genes, is well expressed in Escherichia coli. Two putative promoters have been implicated in the transcription of this gene. Besides the -24/-12 promoter used to transcribe type-4 pilin-encoding genes in most species, the consensus sequence for a conventional promoter is also present. The two promoters overlap and would have almost identical transcription start points (tsp). Transcription from a -24/-12 promoter should be abolished in an E. coli rpoN mutant. A recombinant plasmid carrying pilE could not be transformed into such a mutant, apparently because the synthesis of the N-terminal hydrophobic domain of pilin is lethal to the rpoN mutant. This suggests that pilE is expressed at a higher level in an rpoN mutant than it is in a wild-type (wt) strain of E. coli. This suggestion was confirmed by constructing fusions between the pilE promoter region and a promoter-less cat gene. We suggest that the conventional promoter is primarily responsible for the transcription of pilE, but that the binding of the RpoN sigma factor partially represses transcription of this gene in wt strains. In an rpoN mutant, the repression is removed and transcription occurs at a level that is lethal to the mutant host.

Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae

Rapid identification of Neisseria gonorrhoeae in clinical specimens is essential for effective control. Traditional culture requires a minimum of 24 h, and for some specimens harboring gonococci, the gonococci fail to grow or are misidentified. The recently described ligase chain reaction (LCR) is a highly specific and sensitive DNA amplification technique which was evaluated as an alternative to routine culture. Three LCR probe sets were used. Two of the probe sets were directed against the multi-copy Opa genes (Omp-II), while the third set was targeted against the multicopy Pilin genes. Each LCR probe set was evaluated with 260 microorganisms including 136 global isolates of N. gonorrhoeae, 41 isolates of N. meningitidis, and 10 isolates of N. lactamica; 26 nonpathogenic Neisseria strains; and 47 isolates of non-Neisseria species that may reside in clinical specimens. Amplification products were detected by using the IMx LCR format (Abbott Laboratories, Abbott Park, Ill.). Strains of N. gonorrhoeae were assayed at 270 cells per LCR (approximately 6.7 x 10(4) CFU/ml) with the Opa and Pilin probes, producing signals at least 21 and 15 times above background, respectively. In contrast, only background values were observed when testing the probe sets with 124 nongonococcal strains at 1.3 x 10(6) cells per LCR (approximately 3.2 x 10(8) CFU/ml). One hundred urogenital specimens were assayed by LCR, and compared with culture, the three probes were 100% sensitive (8 of 8) and 97.8% specific (90 of 92), resulting in an agreement of 98% (98 of 100). On the basis of the results of these preliminary studies, LCR has the potential to be an accurate and rapid DNA probe assay for the detection of N. gonorrhoeae in clinical specimens.

Pathogenic neisseriae--a model of bacterial virulence and genetic flexibility

The outcome of the early stages of a neisserial infection is determined by receptor-mediated events that culminate in the attachment and invasion of human mucosal tissues. The factors participating in this process, including pili, opacity proteins (Opa), and perhaps lipopolysaccharide (LPS), are subject to complex genetic controls that allow these factors to be produced in multiple forms. Antigenic variation allows the pathogenic Neisseriae to evade the human immune response, and facilitates their interaction with a variety of different cells and tissues of the human host. One of the major genetic mechanisms causing antigenic variation is transformation, which allows virulence genes to be exchanged and recombined between independent Neisseria strains within multiply infected individuals. A number of other factors, such as IgA protease, alpha-factor, and the meningococcal capsule are also implicated in pathogenesis and render the pathogenic Neisseriae an excellent model for the investigation of bacterial virulence.

Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae

The NgoPII restriction endonuclease, which recognizes the sequence 5'-GG decreases CC-3', differs from its isoschizomer HaeIII in being sensitive to methylation at the external cytosine residue. The entire nucleotide sequence of a cloned 3.3 kb segment of Neisseria gonorrhoeae strain P9 chromosomal DNA which harbours the NgoPII restriction-modification system has been determined. This data, coupled with sub-cloning experiments, indicates that the restriction endonuclease (R.NgoII) and modification (M.NgoII) genes are transcribed from separate promoters but are arranged in tandem, with the R.NgoPII gene being located on the 5' side of the M.NgoPII gene. Unlike all previously reported restriction systems the 3' end of the endonuclease open reading frame overlaps the 5' end of the methylase open reading frame by 8 codons. This overlap may have implications for the regulation of the NgoPII restriction-modification system.

Nucleotide sequence of the structural gene for class I pilin from Neisseria meningitidis: homologies with the pilE locus of Neisseria gonorrhoeae

The nucleotide sequence has been determined for the expressed pilin (pilE) locus of Neisseria meningitidis strain C311 which produces class I pili that are antigenically and structurally similar to those of gonococci. The deduced amino acid sequence of the N. meningitidis pilE translation product contains a 7 amino acid N-terminal pre-pilin leader sequence which is identical to that found in gonococcal pilin and which is characteristic of N-methylphenylalanine pili in general. The succeeding N-terminal 53 amino acids are identical to those found in the equivalent position in antigenically variant gonococcal pilins and confirm direct peptide sequencing of the amino-terminus of at least one type of meningococcal pilin. Other regions that are conserved in variant pilin polypeptides from Neisseria gonorrhoeae are conserved at the amino acid level in the class I meningococcal pilin but the coding DNA contains numerous base substitutions when compared with the equivalent gonococcal pil sequence. Sequences extending downstream for about 140 bp on the 3' side of the coding region for both pilin genes are only about 85% homologous.

Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9: homologies with other enzymes recognizing the sequence 5'-GGCC-3'

Recombinant plasmids harbouring the functional M.NgoPII methyltransferase (specificity 5'-GGCC-3') were isolated from amplified gene libraries of gonococcal chromosomal DNA cloned in pBR322 and in Escherichia coli RR1. The M.NgoPII gene was localized by sub-cloning and the nucleotide sequence of a cloned 1.6 kb segment of Neisseria gonorrhoeae DNA harbouring the methylase gene was determined. This data, coupled with sub-cloning experiments and in vitro transcription-translation studies, indicates a theoretical size of 38.5 kd for the methylase protein. The predicted amino acid sequence of the methylase contains significant regions of homology with the projected sequences of other cytosine-modifying methylases, upon which the activity of these enzymes is likely to depend.

Neisseria meningitidis C114 contains silent, truncated pilin genes that are homologous to Neisseria gonorrhoeae pil sequences

Neisseria meningitidis pili can be classified into two groups: those (referred to here as class I pili) which are similar to gonococcal pili in that they react with monoclonal antibody SM1 and those that are dissimilar to gonococcal pili in that they lack the SM1-reactive epitope (class II pili). Pilus expression in N. meningitidis C114, a class II pilus-producing isolate, was investigated. The sole genomic segment of this strain that bore extensive homology with the pilE locus of Neisseria gonorrhoeae P9 was cloned in Escherichia coli. The production of the pilus structural subunit (pilin) from this meningococcal segment could not be detected by immunological and coupled in vitro transcription-translation analyses. Nucleotide sequence analysis revealed the presence in the C114 genome of two variant, tandemly arranged pilin genes (copies 1 and 2). Copies 1 and 2 are partial pilin genes that constitute part of a silent meningococcal pilin gene (pil gene) region, designated pilS. Both copies are truncated, corresponding to variable domains of the gonococcal pilE gene but lacking homologous N-terminal coding sequences. Located within sequences surrounding copies 1 and 2 were several classes of repeated elements that are associated with pil loci in N. gonorrhoeae.