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1.  Saturating Mutagenesis of an Essential Gene: a Majority of the Neisseria gonorrhoeae Major Outer Membrane Porin (PorB) Is Mutable 
Journal of Bacteriology  2014;196(3):540-547.
The major outer membrane porin (PorB) of Neisseria gonorrhoeae is an essential protein that mediates ion exchange between the organism and its environment and also plays multiple roles in human host pathogenesis. To facilitate structure-function studies of porin's multiple roles, we performed saturating mutagenesis at the porB locus and used deep sequencing to identify essential versus mutable residues. Random mutations in porB were generated in a plasmid vector, and mutant gene pools were transformed into N. gonorrhoeae to select for alleles that maintained bacterial viability. Deep sequencing of the input plasmid pools and the output N. gonorrhoeae genomic DNA pools identified mutations present in each, and the mutations in both pools were compared to determine which changes could be tolerated by the organism. We examined the mutability of 328 amino acids in the mature PorB protein and found that 308 of them were likely to be mutable and that 20 amino acids were likely to be nonmutable. A subset of these predictions was validated experimentally. This approach to identifying essential amino acids in a protein of interest introduces an additional application for next-generation sequencing technology and provides a template for future studies of both porin and other essential bacterial genes.
doi:10.1128/JB.01073-13
PMCID: PMC3911144  PMID: 24244002
2.  Structure-Function Studies of the Neisseria gonorrhoeae Major Outer Membrane Porin 
Infection and Immunity  2013;81(12):4383-4391.
The major outer membrane porin (PorB) expressed by Neisseria gonorrhoeae plays multiple roles during infection, in addition to its function as an outer membrane pore. We have generated a panel of mutants of N. gonorrhoeae strain FA1090 expressing a variety of mutant porB genes that all function as porins. We identified multiple regions of porin that are involved in its binding to the complement regulatory factors C4b-binding protein and factor H and confirmed that the ability to bind at least one factor is required for FA1090 to survive the bactericidal effects of human serum. We tested the ability of these mutants to inhibit both apoptosis and the oxidative burst in polymorphonuclear leukocytes but were unable to identify the porin domains required for either function. This study has identified nonessential porin domains and some potentially essential portions of the protein and has further expanded our understanding of the contribution of the porin domains required for complement regulation.
doi:10.1128/IAI.00367-13
PMCID: PMC3837997  PMID: 24042111
3.  Seminal Plasma Initiates a Neisseria gonorrhoeae Transmission State 
mBio  2014;5(2):e01004-13.
ABSTRACT
Niche-restricted pathogens are evolutionarily linked with the specific biological fluids that are encountered during infection. Neisseria gonorrhoeae causes the genital infection gonorrhea and is exposed to seminal fluid during sexual transmission. Treatment of N. gonorrhoeae with seminal plasma or purified semen proteins lactoferrin, serum albumin, and prostate-specific antigen each facilitated type IV pilus-mediated twitching motility of the bacterium. Motility in the presence of seminal plasma was characterized by high velocity and low directional persistence. In addition, infection of epithelial cells with N. gonorrhoeae in the presence of seminal plasma resulted in enhanced microcolony formation. Close association of multiple pili in the form of bundles was also disrupted after seminal plasma treatment leading to an increase in the number of single pilus filaments on the bacterial surface. Thus, exposure of N. gonorrhoeae to seminal plasma is proposed to alter bacterial motility and aggregation characteristics to influence the processes of transmission and colonization.
IMPORTANCE
There are greater than 100 million estimated new cases of gonorrhea annually worldwide. Research characterizing the mechanisms of pathogenesis and transmission of Neisseria gonorrhoeae is important for developing new prevention strategies, since antibiotic resistance of the organism is becoming increasingly prevalent. Our work identifies seminal plasma as a mediator of N. gonorrhoeae twitching motility and microcolony formation through functional modification of the type IV pilus. These findings provide insight into motility dynamics and epithelial cell colonization under conditions that are relevant to sexual transmission. Type IV pili are common virulence factors with diverse functions among bacterial pathogens, and this work identifies interactions between type IV pili and the host environment. Finally, this work illustrates the importance of the host environment and niche-specific fluids on microbial pathogenesis.
doi:10.1128/mBio.01004-13
PMCID: PMC3958800  PMID: 24595372
4.  Neisseria gonorrhoeae RecQ Helicase HRDC Domains Are Essential for Efficient Binding and Unwinding of the pilE Guanine Quartet Structure Required for Pilin Antigenic Variation 
Journal of Bacteriology  2013;195(10):2255-2261.
The strict human pathogen Neisseria gonorrhoeae utilizes homologous recombination to antigenically vary the pilus, thus evading the host immune response. High-frequency gene conversion reactions between many silent pilin loci and the expressed pilin locus (pilE) allow for numerous pilus variants per strain to be produced from a single strain. For pilin antigenic variation (Av) to occur, a guanine quartet (G4) structure must form upstream of pilE. The RecQ helicase is one of several recombination or repair enzymes required for efficient levels of pilin Av, and RecQ family members have been shown to bind to and unwind G4 structures. Additionally, the vast majority of RecQ helicase family members encode one “helicase and RNase D C-terminal” (HRDC) domain, whereas the N. gonorrhoeae RecQ helicase gene encodes three HRDC domains, which are critical for pilin Av. Here, we confirm that deletion of RecQ HRDC domains 2 and 3 causes a decrease in the frequency of pilin Av comparable to that obtained with a functional knockout. We demonstrate that the N. gonorrhoeae RecQ helicase can bind and unwind the pilE G4 structure. Deletion of the RecQ HRDC domains 2 and 3 resulted in a decrease in G4 structure binding and unwinding. These data suggest that the decrease in pilin Av observed in the RecQ HRDC domain 2 and 3 deletion mutant is a result of the enzyme's inability to efficiently bind and unwind the pilE G4 structure.
doi:10.1128/JB.02217-12
PMCID: PMC3650551  PMID: 23475972
5.  Neisseria gonorrhoeae Metalloprotease NGO1686 Is Required for Full Piliation, and Piliation Is Required for Resistance to H2O2- and Neutrophil-Mediated Killing 
mBio  2013;4(4):e00399-13.
ABSTRACT
The sexually transmitted infection gonorrhea is caused exclusively by the human-specific pathogen Neisseria gonorrhoeae. Type IV pili are an essential virulence factor uniformly expressed on clinical gonococcal isolates and are required for several aspects of gonococcal pathogenesis, including adherence to host tissues, autoagglutination, twitching motility, and the uptake of DNA during transformation. Symptomatic gonococcal infection is characterized by the influx of neutrophils or polymorphonuclear leukocytes (PMNs) to the site of infection. PMNs are a key component of gonococcal pathogenesis, mediating the innate immune response through the use of oxidative and nonoxidative killing mechanisms. The M23B family zinc metallopeptidase NGO1686 is required for gonococci to survive oxidative killing by H2O2- and PMN-mediated killing through unknown mechanisms, but the only known target of NGO1686 is peptidoglycan. We report that the effect of NGO1686 on survival after exposure to H2O2 and PMNs is mediated through its role in elaborating pili and that nonpiliated mutants of N. gonorrhoeae are less resistant to killing by H2O2, LL-37, and PMNs than the corresponding piliated strains. These findings add to the various virulence-associated functions attributable to gonococcal pili and may explain the selection basis for piliation in clinical isolates of N. gonorrhoeae.
IMPORTANCE
Successful infectious agents need to overcome host defense systems to establish infection. We show that the Neisseria pilus, a major virulence factor of this organism, which causes gonorrhea, helps protect the bacterium from two major killing mechanisms used by the host to combat infections. We also show that to express the pilus, an enzyme needs to partially degrade the cell wall of the bacterium.
doi:10.1128/mBio.00399-13
PMCID: PMC3735123  PMID: 23839218
6.  Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis 
Molecular cell  2013;50(4):488-503.
CRISPR interference confers adaptive, sequence-based immunity against viruses and plasmids and is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from spacer-repeat units. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here, our studies of crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp. reveal a unique crRNA maturation pathway in which crRNAs are transcribed from promoters that are embedded within each repeat, yielding crRNA 5’ ends formed by transcription and not by processing. Although crRNA 3’ end formation involves RNase III and trans-encoded tracrRNA, as in other Type II CRISPR systems, this processing is dispensable for interference. The meningococcal pathway is the most streamlined CRISPR/cas system characterized to date. Endogenous CRISPR spacers limit natural transformation, which is the primary source of genetic variation that contributes to immune evasion, antibiotic resistance, and virulence in the human pathogen N. meningitidis.
doi:10.1016/j.molcel.2013.05.001
PMCID: PMC3694421  PMID: 23706818
Neisseria; CRISPR/Cas; dRNA-seq; RNA surveillance system; pathogen; RNA processing; crRNA; Cas9; Type II-C
7.  Neisseria gonorrhoeae and humans perform an evolutionary LINE dance 
Mobile Genetic Elements  2011;1(1):85-87.
Horizontal gene transfer is an important mechanism for generating genetic diversity. As the number of sequenced genomes continues to increase, so do the examples of horizontal genetic exchange between both related and divergent organisms. Here we discuss the recent finding that certain strains of the human pathogen Neisseria gonorrhoeae have incorporated a small fragment of human DNA sequence into their genomes. The horizontally acquired sequence exhibits 98–100% nucleotide identity to a 685 bp portion of the highly repetitive retrotransposable element L1 and its presence in the gonococcal genome has been confirmed by multiple molecular techniques. The possibility of similar L1 horizontal gene transfer events having occurred in other bacteria based on genomic sequence evidence is explored. Potential mechanisms of how N. gonorrhoeae was able to acquire and maintain this human sequence are also discussed in addition to the evolutionary implications of such an event.
doi:10.4161/mge.1.1.15868
PMCID: PMC3190277  PMID: 22016852
Neisseria gonorrhoeae; horizontal gene transfer; LINE; L1
8.  The RecF protein antagonizes RecX function via direct interaction 
Molecular cell  2006;21(1):41-50.
Summary
The RecX protein inhibits RecA filament extension leading to net filament disassembly. The RecF protein physically interacts with the RecX protein and protects RecA from the inhibitory effects of RecX. In vitro, efficient RecA filament formation onto SSB-coated circular single-stranded DNA in the presence of RecX occurs only when all of the RecFOR proteins are present. The RecOR proteins contribute only to RecA filament nucleation onto SSB-coated single-stranded DNA and are unable to counter the inhibitory effects of RecX on RecA filaments. RecF protein uniquely supports substantial RecA filament extension in the presence of RecX. In vivo, RecF protein counters a RecX-mediated inhibition of plasmid recombination. Thus, a significant positive contribution of RecF to RecA filament assembly is to antagonize the effects of the negative modulator, RecX, specifically during the extension phase.
doi:10.1016/j.molcel.2005.11.011
PMCID: PMC3894658  PMID: 16387652
9.  Opportunity and Means: Horizontal Gene Transfer from the Human Host to a Bacterial Pathogen 
mBio  2011;2(1):e00005-11.
The acquisition and incorporation of genetic material between nonmating species, or horizontal gene transfer (HGT), has been frequently described for phylogenetically related organisms, but far less evidence exists for HGT between highly divergent organisms. Here we report the identification and characterization of a horizontally transferred fragment of the human long interspersed nuclear element L1 to the genome of the strictly human pathogen Neisseria gonorrhoeae. A 685-bp sequence exhibiting 98 to 100% identity to copies of the human L1 element was identified adjacent to the irg4 gene in some N. gonorrhoeae genomes. The L1 fragment was observed in ~11% of the N. gonorrhoeae population sampled but was not detected in Neisseria meningitidis or commensal Neisseria isolates. In addition, N. gonorrhoeae transcripts containing the L1 sequence were detected by reverse transcription-PCR, indicating that an L1-derived gene product may be produced. The high degree of identity between human and gonococcal L1 sequences, together with the absence of L1 sequences from related Neisseria species, indicates that this HGT event occurred relatively recently in evolutionary history. The identification of L1 sequences in N. gonorrhoeae demonstrates that HGT can occur between a mammalian host and a resident bacterium, which has important implications for the coevolution of both humans and their associated microorganisms.
IMPORTANCE
The interactions between microbes and their hosts are relevant to several aspects of biology, including evolution, development, immunity, and disease. Neisseria gonorrhoeae serves as a particularly informative model for this interaction because it has exclusively coevolved with humans and is not known to be found in any other environment. In addition, investigation of the evolutionary relationship between N. gonorrhoeae and humans has practical implications, since gonorrhea is a prevalent sexually transmitted infection worldwide. This study was undertaken to characterize the horizontal transfer of genetic information from humans to N. gonorrhoeae, an event that has been scarcely recognized between any mammalian host and bacterial pathogen. Here we provide evidence that this genetic exchange was the result of a recent evolutionary event that has been propagated within the gonococcal population.
doi:10.1128/mBio.00005-11
PMCID: PMC3042738  PMID: 21325040
10.  The RecA-binding pilE G4 Sequence Essential for Pilin Antigenic Variation forms Parallel-stranded Monomeric and 5´-End Stacked Dimeric G-quadruplexes 
Structure (London, England : 1993)  2012;20(12):10.1016/j.str.2012.09.013.
SUMMARY
Neisseria gonorrhoeae is an obligate human pathogen that can escape immune surveillance through antigenic variation of surface structures such as pili. A G-quadruplex-forming (G4) sequence (5´-G3TG3TTG3TG3) located upstream of the N. gonorrhoeae pilin expression locus (pilE) is necessary for initiation of pilin antigenic variation, a recombination-based, high-frequency, diversity-generation system. We have determined NMR-based structures of the all-parallel-stranded monomeric and novel 5´-end-stacked dimeric pilE G-quadruplexes in monovalent cation-containing solutions. We demonstrate that the three-layered all-parallel-stranded monomeric pilE G-quadruplex containing single residue double-chain-reversal loops, that can be modeled without steric clashes into the three-nucleotide DNA-binding site of RecA, binds and promotes E. coli RecA mediated strand exchange in vitro. We discuss how interactions between RecA and monomeric pilE G-quadruplex could facilitate the specialized recombination reactions leading to pilin diversification.
doi:10.1016/j.str.2012.09.013
PMCID: PMC3845372  PMID: 23085077
11.  Genetic transformation of Neisseria gonorrhoeae shows a strand preference 
FEMS microbiology letters  2012;334(1):44-48.
Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing a non-palindromic 10 or 12 nucleotide DNA uptake sequence (DUS10 or DUS12). We investigated the ability of the DUS12 to enhance single-stranded DNA (ssDNA) transformation. Given the non-palindromic nature of the DUS12, we tested whether both strands of the DUS equally enhance transformation. Recombinant single-stranded M13 phage harboring transforming DNA with the Watson DUS12, the Crick DUS12, or no DUS (DUS0) were constructed and circular ssDNA was purified. Southern blots of the purified DNA probed with strand-specific oligonucleotide probes showed greater than 10,000:1 ratio of ssDNA to contaminating dsDNA. The Crick strand of the DUS12 enhanced ssDNA transformation 180–470 fold over DUS0 ssDNA whereas the Watson strand of the DUS only modestly enhanced ssDNA transformation in two strains of N. gonorrhoeae. These data confirm that ssDNA efficiently transforms N. gonorrhoeae but that there is a strand preference, and that part of this strand preference is a greater efficiency of the Crick strand of the DUS12 in enhancing transformation.
doi:10.1111/j.1574-6968.2012.02612.x
PMCID: PMC3466376  PMID: 22676068
genetic exchange; pathogen; recombination
12.  Phase Variation Leads to the Misidentification of a Neisseria Gonorrhoeae Virulence Gene 
PLoS ONE  2013;8(8):e72183.
Neisseria gonorrhoeae is the causative agent of gonorrhea and an obligate pathogen of humans. The Opa proteins of these bacteria are known to mediate attachment and internalization by host cells, including neutrophils. The Opa protein repertoire of a typical N. gonorrhoeae isolate is encoded on ∼11 genes distributed throughout the chromosome and is subject to stochastic changes in expression through phase variation. Together, these characteristics make Opa proteins a critical yet unpredictable aspect of any experimental investigation into the interaction of N. gonorrhoeae with host cells. The goal of this study was to identify novel virulence factors of N. gonorrhoeae by assessing the contribution of a set of uncharacterized hydrogen peroxide-induced genes to bacterial survival against neutrophil-mediated killing. To this end, a strain harboring an engineered mutation in the NGO0322 gene was identified that exhibited increased sensitivity to neutrophil-mediated killing, enhanced internalization by neutrophils, and the ability to induce high levels of neutrophil-generated reactive oxygen species. Each of these phenotypes reverted to near wild-type levels following genetic complementation of the NGO0322 mutation. However, after immunoblot analysis of Opa proteins expressed by the isogenic parent, mutant, and genetically complemented strains, it was determined that phase variation had resulted in a disparity between the Opa profiles of these strains. To determine whether Opa phase variation, rather than NGO0322 mutation, was the cause of the observed neutrophil-related phenotypes, NGO0322 function was investigated in N. gonorrhoeae strains lacking all Opa proteins or constitutively expressing the OpaD variant. In both cases, mutation of NGO0322 did not alter survival of gonococci in the presence of neutrophils. These results demonstrate the importance of controlling for the frequent and random variation in Opa protein production by N. gonorrhoeae when investigating host cell interactions.
doi:10.1371/journal.pone.0072183
PMCID: PMC3745409  PMID: 23977246
13.  Microbial antigenic variation mediated by homologous DNA recombination 
FEMS microbiology reviews  2011;10.1111/j.1574-6976.2011.00321.x.
Pathogenic microorganisms employ numerous molecular strategies in order to delay or circumvent recognition by the immune system of their host. One of the most widely used strategies of immune evasion is antigenic variation, in which immunogenic molecules expressed on the surface of a microorganism are continuously modified. As a consequence, the host is forced to constantly adapt its humoral immune response against this pathogen. An antigenic change thus provides the microorganism with an opportunity to persist and/or replicate within the host (population) for an extended period of time or to effectively infect a previously infected host. In most cases, antigenic variation is caused by genetic processes that lead to modification of the amino acid sequence of a particular antigen or to alterations in the expression of biosynthesis genes that induce changes in expression of a variant antigen. Here, we will review antigenic variation systems that rely on homologous DNA recombination and which are found in a wide range of cellular, human pathogens, including bacteria (such as Neisseria spp., Borrelia spp., Treponema pallidum and Mycoplasma spp.), fungi (like Pneumocystis carinii) and parasites (such as the African trypanosome Trypanosoma brucei). Specifically, the various DNA recombination-based antigenic variation systems will be discussed with a focus on the employed mechanisms of recombination, the DNA substrates, and the enzymatic machinery involved.
doi:10.1111/j.1574-6976.2011.00321.x
PMCID: PMC3334452  PMID: 22212019
gene conversion; Mycoplasma; Neisseria; Pneumocystis; Treponema; Trypanosoma
14.  A bacterial siren song: intimate interactions between neutrophils and pathogenic Neisseria 
Nature reviews. Microbiology  2012;10(3):178-190.
Preface
Neisseria gonorrhoeae and Neisseria meningitidis are Gram-negative bacterial pathogens that are exquisitely adapted for growth at human mucosal surfaces and for efficient transmission between hosts. One factor that is essential to neisserial pathogenesis is the interaction between the bacteria and neutrophils, which are recruited in high numbers during infection. Although this vigorous host response could simply reflect effective immune recognition of the bacteria, there is mounting evidence that in fact these obligate human pathogens manipulate the innate immune response to promote infectious processes. This Review summarizes the mechanisms used by pathogenic neisseriae to resist and modulate the antimicrobial activities of neutrophils. It also details some of the major outstanding questions about the Neisseria–neutrophil relationship and proposes potential benefits of this relationship for the pathogen.
doi:10.1038/nrmicro2713
PMCID: PMC3569855  PMID: 22290508
15.  Transcription of a cis-acting, Noncoding, Small RNA Is Required for Pilin Antigenic Variation in Neisseria gonorrhoeae 
PLoS Pathogens  2013;9(1):e1003074.
The strict human pathogen Neisseria gonorrhoeae can utilize homologous recombination to generate antigenic variability in targets of immune surveillance. To evade the host immune response, N. gonorrhoeae promotes high frequency gene conversion events between many silent pilin copies and the expressed pilin locus (pilE), resulting in the production of variant pilin proteins. Previously, we identified a guanine quartet (G4) structure localized near pilE that is required for the homologous recombination reactions leading to pilin antigenic variation (Av). In this work, we demonstrate that inactivating the promoter of a small non-coding RNA (sRNA) that initiates within the G4 forming sequence blocks pilin Av. The sRNA promoter is conserved in all sequenced gonococcal strains, and mutations in the predicted transcript downstream of the G4 forming sequence do not alter pilin Av. A mutation that produces a stronger promoter or substitution of the pilE G4-associated sRNA promoter with a phage promoter (when the phage polymerase was expressed) produced wild-type levels of pilin Av. Altering the direction and orientation of the pilE G4-associated sRNA disrupted pilin Av. In addition, expression of the sRNA at a distal site on the gonococcal chromosome in the context of a promoter mutant did not support pilin Av. We conclude that the DNA containing the G-rich sequence can only form the G4 structure during transcription of this sRNA, thus providing a unique molecular step for the initiation of programmed recombination events.
Author Summary
To evade the host immune response, pathogens have evolved mechanisms to provide genetic diversity in targets of immune surveillance. Organisms that express these diversification systems are under strong evolutionary pressure to provide subpopulations of preexisting variants and often rely on cellular recombination machinery to catalyze dedicated high-frequency reactions without disturbing genome integrity. Previously, we defined a guanine quartet (G4) structure in the strict human pathogen Neisseria gonorrhoeae that is required for initiating the homologous recombination reactions leading to pilin antigenic variation (Av). G4 structures have been implicated in many biological processes, however the mechanisms allowing their formation within a chromosome have not been elucidated. In this work, we show a direct link between transcription of a small RNA (sRNA) that initiates within the G4 structure forming sequence and pilin Av and conclude that the process of transcription is necessary for G4 structure formation. sRNAs have emerged as important regulatory molecules in both eukaryotes and prokaryotes, and this is a novel activity of a sRNA in a bacterium. We anticipate that the reliance of G4 structure formation on transcription is a mechanism used by other biological systems that rely on this alternative DNA structure.
doi:10.1371/journal.ppat.1003074
PMCID: PMC3547852  PMID: 23349628
16.  Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria 
Molecular microbiology  2011;81(5):1136-1143.
Summary
Some pathogenic microbes utilize homologous recombination to generate antigenic variability in targets of immune surveillance. These specialized systems rely on the cellular recombination machinery to catalyze dedicated, high-frequency reactions that provide extensive diversity in the genes encoding surface antigens. A description of the specific mechanisms that allow unusually high rates of recombination without deleterious effects on the genome in the well characterized pilin antigenic variation systems of Neisseria gonorrhoeae and Neisseria meningitidis is presented. We will also draw parallels to selected bacterial and eukaryotic antigenic variation systems, and suggest the most pressing unanswered questions related to understanding these important processes.
doi:10.1111/j.1365-2958.2011.07773.x
PMCID: PMC3181079  PMID: 21812841
Neisseria; pili; antigenic variation; recombination; gene conversion
17.  Neisseria gonorrhoeae-Mediated Inhibition of Apoptotic Signalling in Polymorphonuclear Leukocytes▿ 
Infection and Immunity  2011;79(11):4447-4458.
The human pathogen Neisseria gonorrhoeae recruits and interacts extensively with polymorphonuclear leukocytes (PMNs) during infection. N. gonorrhoeae is able to survive the bactericidal activity of these innate immune cells and can actively modulate PMN functions in vitro. PMNs are short-lived cells which readily undergo apoptosis, and thus the effect of N. gonorrhoeae infection on PMN survival has implications for whether PMNs might serve as an important site of bacterial replication during infection. We developed and validated an HL-60 myeloid leukemia cell culture model for PMN infection and used both these cells and primary PMNs to show that N. gonorrhoeae infection alone does not induce apoptosis and furthermore that N. gonorrhoeae can inhibit both spontaneous apoptosis and apoptosis induced by the intrinsic and extrinsic apoptosis inducers staurosporine (STS) and tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), respectively. N. gonorrhoeae infection also results in the activation of NF-κB signaling in neutrophils and induces secretion of an identical profile of proinflammatory cytokines and chemokines in both HL-60 cells and primary PMNs. Our data show that the HL-60 cell line can be used to effectively model N. gonorrhoeae-PMN interactions and that N. gonorrhoeae actively inhibits apoptosis induced by multiple stimuli to prolong PMN survival and potentially facilitate bacterial survival, replication, and transmission.
doi:10.1128/IAI.01267-10
PMCID: PMC3257915  PMID: 21844239
18.  The Neisseria gonorrhoeae photolyase orthologue phrB is required for proper DNA supercoiling but does not function in photo-reactivation 
Molecular microbiology  2010;79(3):729-742.
Summary
Neisseria gonorrhoeae (Gc) is an obligate human pathogen and the causative agent of the sexually transmitted infection, gonorrhea. Despite the fact that the gonococcus is not normally exposed to UV irradiation or visible light, the bacterium expresses a phrB orthologue which in other organisms encodes a DNA photolyase that repairs UV-induced pyrimidine dimers with energy provided by visible light. We show that a Gc phrB mutant is not more sensitive to UV irradiation, independent of visible light exposure, and that the Gc phrB cannot complement an Escherichia coli phrB mutant strain. The Gc phrB mutant had a reduced colony size that was not a result of a growth defect and the mutant cells exhibited an altered morphology. Although the phrB mutant exhibited increased sensitivity to oxidative killing; it showed increased survival on media containing nalidixic acid or rifampicin, but did not have an increased mutation rate to these antibiotics or spectinomycin and kasugamycin. The Gc phrB mutant showed increased negative DNA supercoiling, but while the protein bound double-stranded DNA, it did not express topoisomerase activity. We conclude that the Gc PhrB has a previously unrecognized role in maintaining DNA supercoiling that is important for normal cell physiology.
doi:10.1111/j.1365-2958.2010.07481.x
PMCID: PMC3079310  PMID: 21255115
Gonorrhea; Neisseria; photolyase; supercoiling; DNA repair; oxidative damage
19.  The DNA binding activity of the Neisseria gonorrhoeae LexA ortholog NG1427 is modulated by oxidation 
Molecular microbiology  2010;79(4):846-860.
Summary
Neisseria gonorrhoeae is a human-specific organism that is not usually exposed to UV light or chemicals but is likely to encounter reactive oxygen species during infection. Exposure of N. gonorrhoeae to sublethal hydrogen peroxide revealed that the ng1427 gene was up regulated 6-fold (Stohl et al., 2005). N. gonorrhoeae was thought to lack an SOS system, although NG1427 shows amino acid sequence similarity to the SOS response regulator LexA from E. coli. Similar to LexA and other S24 peptidases, NG1427 undergoes autoproteolysis in vitro, which is facilitated by either the gonococcal or E. coli RecA proteins or high pH, and autoproteolysis requires the active and cleavage site residues conserved between LexA and NG1427. NG1427 controls a three gene regulon: itself; ng1428, a Neisseria-specific, putative integral membrane protein; and recN, a DNA repair gene known to be required for oxidative damage survival. Full NG1427 regulon de-repression requires RecA following methyl methanesulfonate or mitomycin C treatment, but is largely RecA-independent following hydrogen peroxide treatment. NG1427 binds specifically to the operator regions of the genes it controls, and DNA-binding is abolished by oxidation of the single cysteine residue encoded in NG1427. We propose that NG1427 is inactivated independently of RecA by oxidation.
doi:10.1111/j.1365-2958.2010.07491.x
PMCID: PMC3080098  PMID: 21299643
21.  DNA Uptake Sequence-Mediated Enhancement of Transformation in Neisseria gonorrhoeae Is Strain Dependent ▿  
Journal of Bacteriology  2010;192(17):4436-4444.
Natural transformation is the main means of horizontal genetic exchange in the obligate human pathogen Neisseria gonorrhoeae. Neisseria spp. have been shown to preferentially take up and transform their own DNA by recognizing the nonpalindromic 10- or 12-nucleotide sequence 5′-ATGCCGTCTGAA-3′ (additional semiconserved nucleotides are underlined), termed the DNA uptake sequence (DUS10 or DUS12). Here we investigated the effects of the DUS on transformation and DNA uptake for several laboratory strains of N. gonorrhoeae. We found that all strains showed efficient transformation of DUS containing DNA (DUS10 and DUS12) but that the level of transformation with DNA lacking a DUS (DUS0) was variable in different strains. The DUS-enhanced transformation was 20-fold in two strains, FA1090 and FA19, but was approximately 150-fold in strains MS11 and 1291. All strains tested provide some level of DUS0 transformation, and DUS0 transformation was type IV pilus dependent. Competition with plasmid DNA revealed that transformation of MS11 was enhanced by the addition of excess plasmid DNA containing a DUS while FA1090 transformation was competitively inhibited. Although FA1090 was able to mediate much more efficient transformation of DNA lacking a DUS than was MS11, DNA uptake experiments showed similar levels of uptake of DNA containing and lacking a DUS in FA1090 and MS11. Finally, DNA uptake was competitively inhibited in both FA1090 and MS11. Taken together, our data indicate that the role of the DUS during DNA transformation is variable between strains of N. gonorrhoeae and may influence multiple steps during transformation.
doi:10.1128/JB.00442-10
PMCID: PMC2937394  PMID: 20601472
22.  Purification and Characterization of the RecA Protein from Neisseria gonorrhoeae 
PLoS ONE  2011;6(2):e17101.
The strict human pathogen Neisseria gonorrhoeae is the only causative agent of the sexually transmitted infection gonorrhea. The recA gene from N. gonorrhoeae is essential for DNA repair, natural DNA transformation, and pilin antigenic variation, all processes that are important for the pathogenesis and persistence of N. gonorrhoeae in the human population. To understand the biochemical features of N. gonorrhoeae RecA (RecANg), we overexpressed and purified the RecANg and SSBNg proteins and compared their activities to those of the well-characterized E. coli RecA and SSB proteins in vitro. We observed that RecANg promoted more strand exchange at early time points than RecAEc through DNA homologous substrates, and exhibited the highest ATPase activity of any RecA protein characterized to date. Further analysis of this robust ATPase activity revealed that RecANg is more efficient at displacing SSB from ssDNA and that RecANg shows higher ATPase activity during strand exchange than RecAEc. Using substrates created to mimic the cellular processes of DNA transformation and pilin antigenic variation we observed that RecAEc catalyzed more strand exchange through a 100 bp heterologous insert, but that RecANg catalyzed more strand exchange through regions of microheterology. Together, these data suggest that the processes of ATP hydrolysis and DNA strand exchange may be coupled differently in RecANg than in RecAEc. This difference may explain the unusually high ATPase activity observed for RecANg with the strand exchange activity between RecANg and RecAEc being more similar.
doi:10.1371/journal.pone.0017101
PMCID: PMC3040777  PMID: 21359151
23.  Frequency and Rate of Pilin Antigenic Variation of Neisseria meningitidis▿  
Journal of Bacteriology  2010;192(14):3822-3823.
The rates of pilin antigenic variation (Av) of two strains of Neisseria meningitidis were determined using an unbiased DNA sequencing assay. Strain MC58 underwent pilin Av at a rate similar to that of N. gonorrhoeae strain MS11 but lower than that of N. gonorrhoeae strain FA1090. Pilin Av was undetectable in strain FAM18.
doi:10.1128/JB.00280-10
PMCID: PMC2897326  PMID: 20472803
24.  Genomic Content of Neisseria Species ▿  
Journal of Bacteriology  2010;192(8):2160-2168.
The physical properties of most bacterial genomes are largely unexplored. We have previously demonstrated that the strict human pathogen Neisseria gonorrhoeae is polyploid, carrying an average of three chromosome copies per cell and only maintaining one pair of replication forks per chromosome (D. M. Tobiason and H. S. Seifert, PLos Biol. 4:1069-1078, 2006). We are following up this initial report to test several predictions of the polyploidy model of gonococcal chromosome organization. We demonstrate that the N. gonorrhoeae chromosomes exist solely as monomers and not covalently linked dimers, and in agreement with the monomer status, we show that distinct nucleoid regions can be detected by electron microscopy. Two different approaches to isolate heterozygous N. gonorrhoeae resulted in the formation of merodiploids, showing that even with more than one chromosome copy, these bacteria are genetically haploid. We show that the closely related bacterium Neisseria meningitidis is also polyploid, while the commensal organism Neisseria lactamica maintains chromosomes in single copy. We conclude that the pathogenic Neisseria strains are homozygous diploids.
doi:10.1128/JB.01593-09
PMCID: PMC2849444  PMID: 20172999
25.  Genetic Characterization of the Nucleotide Excision Repair System of Neisseria gonorrhoeae▿  
Journal of Bacteriology  2009;192(3):665-673.
Nucleotide excision repair (NER) is universally used to recognize and remove many types of DNA damage. In eubacteria, the NER system typically consists of UvrA, UvrB, UvrC, the UvrD helicase, DNA polymerase I, and ligase. In addition, when DNA damage blocks transcription, transcription-repair coupling factor (TRCF), the product of the mfd gene, recruits the Uvr complex to repair the damage. Previous work using selected mutants and assays have indicated that pathogenic Neisseria spp. carry a functional NER system. In order to comprehensively examine the role of NER in Neisseria gonorrhoeae DNA recombination and repair processes, the predicted NER genes (uvrA, uvrB, uvrC, uvrD, and mfd) were each disrupted by a transposon insertion, and the uvrB and uvrD mutants were complemented with a copy of each gene in an ectopic locus. Each uvr mutant strain was highly sensitive to UV irradiation and also showed sensitivity to hydrogen peroxide killing, confirming that all of the NER genes in N. gonorrhoeae are functional. The effect of RecA expression on UV survival was minor in uvr mutants but much larger in the mfd mutant. All of the NER mutants demonstrated wild-type levels of pilin antigenic variation and DNA transformation. However, the uvrD mutant exhibited higher frequencies of PilC-mediated pilus phase variation and spontaneous mutation, a finding consistent with a role for UvrD in mismatch repair. We conclude that NER functions are conserved in N. gonorrhoeae and are important for the DNA repair capabilities of this strict human pathogen.
doi:10.1128/JB.01018-09
PMCID: PMC2812444  PMID: 19933360

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