51
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Liang SH, Anderson MZ, Hirakawa MP, Wang JM, Frazer C, Alaalm LM, Thomson GJ, Ene IV, Bennett RJ. Hemizygosity Enables a Mutational Transition Governing Fungal Virulence and Commensalism. Cell Host Microbe 2019; 25:418-431.e6. [PMID: 30824263 DOI: 10.1016/j.chom.2019.01.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/03/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Candida albicans is a commensal fungus of human gastrointestinal and reproductive tracts, but also causes life-threatening systemic infections. The balance between colonization and pathogenesis is associated with phenotypic plasticity, with alternative cell states producing different outcomes in a mammalian host. Here, we reveal that gene dosage of a master transcription factor regulates cell differentiation in diploid C. albicans cells, as EFG1 hemizygous cells undergo a phenotypic transition inaccessible to "wild-type" cells with two functional EFG1 alleles. Notably, clinical isolates are often EFG1 hemizygous and thus licensed to undergo this transition. Phenotypic change corresponds to high-frequency loss of the functional EFG1 allele via de novo mutation or gene conversion events. This phenomenon also occurs during passaging in the gastrointestinal tract with the resulting cell type being hypercompetitive for commensal and systemic infections. A "two-hit" genetic model therefore underlies a key phenotypic transition in C. albicans that enables adaptation to host niches.
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Affiliation(s)
- Shen-Huan Liang
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew P Hirakawa
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Joshua M Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Corey Frazer
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Leenah M Alaalm
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Gregory J Thomson
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Iuliana V Ene
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA
| | - Richard J Bennett
- Molecular Microbiology and Immunology Department, Brown University, Providence, RI 02912, USA.
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52
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Abstract
Neisseria gonorrhoeae is quickly becoming untreatable due to its acquisition of resistance to multiple antimicrobials. It is vital that we begin to understand the mechanisms by which this is occurring. Neisseria gonorrhoeae is quickly becoming untreatable due to its acquisition of resistance to multiple antimicrobials. It is vital that we begin to understand the mechanisms by which this is occurring. The paper by C. E. Rouquette-Loughlin, J. L. Reimche, J. T. Balthazar, V. Dhulipala, et al. (mBio 9:e02281-18, https://doi.org/10.1128/mBio.02281-18) has shown that horizontal transfer of DNA from a nasopharyngeal commensal, Neisseria polysaccharea, has resulted in multiple sequence changes in the mtr locus that affect both regulatory and structural regions of the MtrCDE pump, resulting in low-level azithromycin resistance. Studies such as this are increasingly important in our understanding of the movement of resistance between species and for devising strategies to overcome such events.
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53
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Lagunas-Rangel FA, Bermúdez-Cruz RM. Epigenetics in the early divergent eukaryotic Giardia duodenalis: An update. Biochimie 2019; 156:123-128. [DOI: 10.1016/j.biochi.2018.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/12/2018] [Indexed: 11/29/2022]
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54
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Abstract
Laboratory techniques for transformation of the pathogenic Neisseria are well developed, and take advantage of the natural transformability of these species. More recently, these techniques have been successfully applied to some nonpathogenic species of Neisseria as well. This chapter provides foundational information on the mechanism of Neisseria transformation, considerations for DNA transformation substrate design, two methods for transforming Neisseria in the laboratory, and guidelines for identifying successful transformants.
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Affiliation(s)
- Melanie M Callaghan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
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55
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Abstract
Neisseria meningitidis (the meningococcus) is a member of the normal nasopharyngeal microbiome in healthy individuals, but can cause septicemia and meningitis in susceptible individuals. In this chapter we provide an overview of the disease caused by N. meningitidis and the schemes used to type the meningococcus. We also review the adhesions, virulence factors, and phase variable genes that enable it to successfully colonize the human host. Finally, we outline the history and current status of meningococcal vaccines and highlight the importance of continued molecular investigation of the epidemiology and the structural analysis of the antigens of this pathogen to aid future vaccine development.
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56
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Handing JW, Ragland SA, Bharathan UV, Criss AK. The MtrCDE Efflux Pump Contributes to Survival of Neisseria gonorrhoeae From Human Neutrophils and Their Antimicrobial Components. Front Microbiol 2018; 9:2688. [PMID: 30515136 PMCID: PMC6256084 DOI: 10.3389/fmicb.2018.02688] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/22/2018] [Indexed: 12/24/2022] Open
Abstract
The mucosal inflammatory response to Neisseria gonorrhoeae (Gc) is characterized by recruitment of neutrophils to the site of infection. Gc survives exposure to neutrophils by limiting the ability of neutrophils to make antimicrobial products and by expressing factors that defend against these products. The multiple transferable resistance (Mtr) system is a tripartite efflux pump, comprised of the inner membrane MtrD, the periplasmic attachment protein MtrC, and the outer membrane channel MtrE. Gc MtrCDE exports a diverse array of substrates, including certain detergents, dyes, antibiotics, and host-derived antimicrobial peptides. Here we report that MtrCDE contributes to the survival of Gc after exposure to adherent, chemokine-treated primary human neutrophils, specifically in the extracellular milieu. MtrCDE enhanced survival of Gc in neutrophil extracellular traps and in the supernatant from neutrophils that had undergone degranulation (granule exocytosis), a process that releases antimicrobial proteins into the extracellular milieu. The extent of degranulation was unaltered in neutrophils exposed to parental or mtr mutant Gc. MtrCDE expression contributed to Gc defense against some neutrophil-derived antimicrobial peptides but not others. These findings demonstrate that the Mtr system contributes to Gc survival after neutrophil challenge, a key feature of the host immune response to acute gonorrhea.
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Affiliation(s)
- Jonathan W Handing
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Stephanie A Ragland
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Urmila V Bharathan
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Alison K Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, United States
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57
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Analysis of Pilin Antigenic Variation in Neisseria meningitidis by Next-Generation Sequencing. J Bacteriol 2018; 200:JB.00465-18. [PMID: 30181126 DOI: 10.1128/jb.00465-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 01/07/2023] Open
Abstract
Many pathogenic microbes evade host immune surveillance by varying the surface antigens, a process termed antigenic variation. While the process of pilin antigenic variation has been extensively studied in the human pathogen Neisseria gonorrhoeae (gonococcus [Gc]), relatively few studies of pilin antigenic variation have been conducted with Neisseria meningitidis (meningococcus [Mc]). Mc is usually a commensal organism that colonizes the human nasopharynx, but when it translocates to the bloodstream or meninges, it results in the severe and often deadly meningococcal disease. The type IV pili of Mc isolates play a critical role in host surface adherence, and its major pilin component (PilE) can undergo antigenic variation. In this study, Roche 454 pyrosequencing was used to examine the pilin antigenic variation of Mc strain 8013, as well as 8013 recA, recX, recQ, rep, and recJ mutants, Gc orthologues which have been shown to play a role in pilin antigenic variation. This study confirms that the Mc recA, rep, and recJ genes are essential for pilin antigenic variation. While the Mc recQ and recX gene products contribute to normal frequencies of antigenic variation, the loss of these factors does not alter the types of pilin variants produced. Overall, this study shows that the mechanisms of pilin antigenic variation are conserved between Gc and Mc.IMPORTANCE Antigenic variation is a strategy used by many pathogens to escape host immune surveillance and establish persistent infections. This study successfully applies next-generation sequencing to study pilin antigenic variation in the human pathogen Neisseria meningitidis This assay provides an affordable and efficient solution for quantifying antigenic variation frequency in mutant strains and for defining the recombination products of the process. We determined that there is a nonuniformity of silent donor copies used during meningococcus antigenic variation, and by the analysis of selected mutants deficient for specific recombination pathways, we show for the first time that the processes are conserved between N. meningitidis and Neisseria gonorrhoeae.
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58
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Identification of Neisseria meningitidis by MALDI-TOF MS may not be reliable. Clin Microbiol Infect 2018; 25:717-722. [PMID: 30287414 DOI: 10.1016/j.cmi.2018.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVES The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique is increasingly used in hospital laboratories for routine identification of microorganisms. However, its performance is variable, particularly for highly variable species such as Neisseria meningitidis. Reliable identification of N. meningitidis is crucial for the management of invasive meningococcal disease by rapid implementation of treatment and preventive measures among close contacts. We assessed and improved N. meningitidis identification by MALDI-TOF MS by enriching the databases with reference strains identified using whole genome sequencing (WGS) as a reference standard. METHODS We first built a collection of 24 strains from several species of the Neisseria genus that we characterized by WGS. This collection was added to the available database to test by MALDI-TOF MS another collection of 32 clinical isolates received between 2015 and 2017 at the French National Reference Laboratory for Meningococci. RESULTS Using the commercially available library of mass spectrometry profiles, only 67% (95% confidence interval (CI), 47-82) concordance was observed at the species level between MALDI-TOF MS and WGS characterization. However, when the new enriched reference collection was used on the second subset of isolates, the identification of N. meningitidis was significantly improved (p 0.0016), showing 92% (95% CI, 75-98) specificity while that of the manufacturer's database alone was 52% (95% CI, 34-70). CONCLUSIONS Our data highlight the need to update the available MALDI-TOF MS database with high-quality references to enhance the identification of N. meningitidis and avoid unwarranted preventive measures or missing identification.
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59
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Lamelas A, Hamid AWM, Dangy JP, Hauser J, Jud M, Röltgen K, Hodgson A, Junghanss T, Harris SR, Parkhill J, Bentley SD, Pluschke G. Loss of Genomic Diversity in a Neisseria meningitidis Clone Through a Colonization Bottleneck. Genome Biol Evol 2018; 10:2102-2109. [PMID: 30060167 PMCID: PMC6110524 DOI: 10.1093/gbe/evy152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 01/11/2023] Open
Abstract
Neisseria meningitidis is the leading cause of epidemic meningitis in the "meningitis belt" of Africa, where clonal waves of colonization and disease are observed. Point mutations and horizontal gene exchange lead to constant diversification of meningococcal populations during clonal spread. Maintaining a high genomic diversity may be an evolutionary strategy of meningococci that increases chances of fixing occasionally new highly successful "fit genotypes". We have performed a longitudinal study of meningococcal carriage and disease in northern Ghana by analyzing cerebrospinal fluid samples from all suspected meningitis cases and monitoring carriage of meningococci by twice yearly colonization surveys. In the framework of this study, we observed complete replacement of an A: sequence types (ST)-2859 clone by a W: ST-2881 clone. However, after a gap of 1 year, A: ST-2859 meningococci re-emerged both as colonizer and meningitis causing agent. Our whole genome sequencing analyses compared the A population isolated prior to the W colonization and disease wave with the re-emerging A meningococci. This analysis revealed expansion of one clone differing in only one nonsynonymous SNP from several isolates already present in the original A: ST-2859 population. The colonization bottleneck caused by the competing W meningococci thus resulted in a profound reduction in genomic diversity of the A meningococcal population.
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Affiliation(s)
- Araceli Lamelas
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C., Xalapa, Veracruz, México
| | - Abdul-Wahab M Hamid
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
- Navrongo Health Research Centre, Ministry of Health, Navrongo, Ghana
| | - Jean-Pierre Dangy
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Julia Hauser
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Maja Jud
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Katharina Röltgen
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Abraham Hodgson
- Navrongo Health Research Centre, Ministry of Health, Navrongo, Ghana
- Research and Development Division, Ghana Health Service, Accra, Ghana
| | - Thomas Junghanss
- Section of Clinical Tropical Medicine, University Hospital Heidelberg, Germany
| | - Simon R Harris
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen D Bentley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gerd Pluschke
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
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60
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Abstract
Advances in understanding mechanisms of nucleic acids have revolutionized molecular biology and medicine, but understanding of nontraditional nucleic acid conformations is less developed. The guanine quadruplex (G4) alternative DNA structure was first described in the 1960s, but the existence of G4 structures (G4-S) and their participation in myriads of biological functions are still underappreciated. Despite many tools to study G4s and many examples of roles for G4s in eukaryotic molecular processes and issues with uncontrolled G4-S formation, there is relatively little knowledge about the roles of G4-S in viral or prokaryotic systems. This review summarizes the state of the art with regard to G4-S in eukaryotes and their potential roles in human disease before discussing the evidence that G4-S have equivalent importance in affecting viral and bacterial life.
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Affiliation(s)
- H Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA;
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61
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Bonazzi D, Lo Schiavo V, Machata S, Djafer-Cherif I, Nivoit P, Manriquez V, Tanimoto H, Husson J, Henry N, Chaté H, Voituriez R, Duménil G. Intermittent Pili-Mediated Forces Fluidize Neisseria meningitidis Aggregates Promoting Vascular Colonization. Cell 2018; 174:143-155.e16. [PMID: 29779947 DOI: 10.1016/j.cell.2018.04.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/11/2018] [Accepted: 04/10/2018] [Indexed: 12/13/2022]
Abstract
Neisseria meningitidis, a bacterium responsible for meningitis and septicemia, proliferates and eventually fills the lumen of blood capillaries with multicellular aggregates. The impact of this aggregation process and its specific properties are unknown. We first show that aggregative properties are necessary for efficient infection and study their underlying physical mechanisms. Micropipette aspiration and single-cell tracking unravel unique features of an atypical fluidized phase, with single-cell diffusion exceeding that of isolated cells. A quantitative description of the bacterial pair interactions combined with active matter physics-based modeling show that this behavior relies on type IV pili active dynamics that mediate alternating phases of bacteria fast mutual approach, contact, and release. These peculiar fluid properties proved necessary to adjust to the geometry of capillaries upon bacterial proliferation. Intermittent attractive forces thus generate a fluidized phase that allows for efficient colonization of the blood capillary network during infection.
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Affiliation(s)
- Daria Bonazzi
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France
| | - Valentina Lo Schiavo
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France
| | - Silke Machata
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France
| | - Ilyas Djafer-Cherif
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Pierre Nivoit
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France
| | - Valeria Manriquez
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France
| | | | - Julien Husson
- Laboratoire d'Hydrodynamique (LadHyX), Department of Mechanics, Ecole Polytechnique-CNRS UMR7646, 91128 Palaiseau, France
| | - Nelly Henry
- Laboratoire Jean Perrin, CNRS UMR 3231, Université Pierre et Marie Curie, 75005 Paris, France
| | - Hugues Chaté
- Service de Physique de l'Etat Condensé, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; Computational Science Research Center, Beijing 100193, China; Laboratoire de Physique Théorique de la Matière Condensée, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Raphael Voituriez
- Laboratoire Jean Perrin, CNRS UMR 3231, Université Pierre et Marie Curie, 75005 Paris, France; Laboratoire de Physique Théorique de la Matière Condensée, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Duménil
- Pathogenesis of Vascular Infections Unit, INSERM, Institut Pasteur, 75015 Paris, France.
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62
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Abstract
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoeae, possesses several mobile genetic elements (MGEs). The MGEs such as transposable elements mediate intrachromosomal rearrangements, while plasmids and the gonococcal genetic island are involved in interchromosomal gene transfer. Additionally, gonococcal MGEs serve as hotspots for recombination and integration of other genetic elements such as bacteriophages, contribute to gene regulation or spread genes through gonococcal populations by horizontal gene transfer. In this review, we summarise the literature on the structure and biology of MGEs and discuss how these genetic elements may play a role in the pathogenesis and spread of antimicrobial resistance in N. gonorrhoeae. Although an abundance of information about gonococcal MGEs exists (mainly from whole genome sequencing and bioinformatic analysis), there are still many open questions on how MGEs influence the biology of N. gonorrhoeae.
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Affiliation(s)
- Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Steven B Lewis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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63
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Rice PA, Shafer WM, Ram S, Jerse AE. Neisseria gonorrhoeae: Drug Resistance, Mouse Models, and Vaccine Development. Annu Rev Microbiol 2018; 71:665-686. [PMID: 28886683 DOI: 10.1146/annurev-micro-090816-093530] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gonorrhea, an obligate human infection, is on the rise worldwide and gonococcal strains resistant to many antibiotics are emerging. Appropriate antimicrobial treatment and prevention, including effective vaccines, are urgently needed. To guide investigation, an experimental model of genital tract infection has been developed in female mice to study mechanisms by which Neisseria gonorrhoeae evades host-derived antimicrobial factors and to identify protective and immunosuppressive pathways. Refinements of the animal model have also improved its use as a surrogate host of human infection and accelerated the testing of novel therapeutic and prophylactic compounds against gonococcal infection. Reviewed herein are the (a) history of antibiotic usage and resistance against gonorrhea and the consequences of resistance mechanisms that may increase gonococcal fitness and therefore the potential for spread, (b) use of gonococcal infection in the animal model system to study mechanisms of pathogenesis and host defenses, and
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Affiliation(s)
- Peter A Rice
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605-4321; ,
| | - William M Shafer
- Department of Microbiology and Immunology and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia 30322.,Laboratories of Bacterial Pathogenesis, Veterans Affairs Medical Center, Decatur, Georgia 30033;
| | - Sanjay Ram
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605-4321; ,
| | - Ann E Jerse
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University, Bethesda, Maryland 20814-4799;
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64
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Retchless AC, Kretz CB, Chang HY, Bazan JA, Abrams AJ, Norris Turner A, Jenkins LT, Trees DL, Tzeng YL, Stephens DS, MacNeil JR, Wang X. Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles. BMC Genomics 2018; 19:176. [PMID: 29499642 PMCID: PMC5834837 DOI: 10.1186/s12864-018-4560-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/20/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Increased reports of Neisseria meningitidis urethritis in multiple U.S. cities during 2015 have been attributed to the emergence of a novel clade of nongroupable N. meningitidis within the ST-11 clonal complex, the "U.S. NmNG urethritis clade". Genetic recombination with N. gonorrhoeae has been proposed to enable efficient sexual transmission by this clade. To understand the evolutionary origin and diversification of the U.S. NmNG urethritis clade, whole-genome phylogenetic analysis was performed to identify its members among the N. meningitidis strain collection from the Centers for Disease Control and Prevention, including 209 urogenital and rectal N. meningitidis isolates submitted by U.S. public health departments in eleven states starting in 2015. RESULTS The earliest representatives of the U.S. NmNG urethritis clade were identified from cases of invasive disease that occurred in 2013. Among 209 urogenital and rectal isolates submitted from January 2015 to September 2016, the clade accounted for 189/198 male urogenital isolates, 3/4 female urogenital isolates, and 1/7 rectal isolates. In total, members of the clade were isolated in thirteen states between 2013 and 2016, which evolved from a common ancestor that likely existed during 2011. The ancestor contained N. gonorrhoeae-like alleles in three regions of its genome, two of which may facilitate nitrite-dependent anaerobic growth during colonization of urogenital sites. Additional gonococcal-like alleles were acquired as the clade diversified. Notably, one isolate contained a sequence associated with azithromycin resistance in N. gonorrhoeae, but no other gonococcal antimicrobial resistance determinants were detected. CONCLUSIONS Interspecies genetic recombination contributed to the early evolution and subsequent diversification of the U.S. NmNG urethritis clade. Ongoing acquisition of N. gonorrhoeae alleles by the U.S. NmNG urethritis clade may facilitate the expansion of its ecological niche while also increasing the frequency with which it causes urethritis.
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Affiliation(s)
- Adam C. Retchless
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Cécilia B. Kretz
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
- Present address: Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - How-Yi Chang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Jose A. Bazan
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH USA
- Sexual Health Clinic, Columbus Public Health, Columbus, OH USA
| | - A. Jeanine Abrams
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Abigail Norris Turner
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH USA
| | - Laurel T. Jenkins
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - David L. Trees
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Yih-Ling Tzeng
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA USA
| | - Jessica R. MacNeil
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Xin Wang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
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65
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Abstract
Bacteria and archaea possess numerous defense systems to combat viral infections and other mobile genetic elements. Uniquely among these, CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR associated) provides adaptive genetic interference against foreign nucleic acids. Here we review recent advances on the CRISPR-Cas9 system in Neisseria spp, with a focus on its biological functions in genetic transfer, its mechanistic features that establish new paradigms and its technological applications in eukaryotic genome engineering.
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66
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Zhang A, Zhao P, Zhu B, Shi F, Xu L, Gao Y, Xie N, Shao Z. Characterization and Distribution of the autB Gene in Neisseria meningitidis. Front Cell Infect Microbiol 2017; 7:436. [PMID: 29057217 PMCID: PMC5635059 DOI: 10.3389/fcimb.2017.00436] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/21/2017] [Indexed: 11/16/2022] Open
Abstract
We aimed to investigate and understand the characterization and distribution of the autB gene in Neisseria meningitidis in China. autB is flanked by two conservative genes, smpB and glcD, and it can be present in the majority of meningococcal isolates, but not in 053442 of clonal complex 4821 (CC4821) which contains a 968 bp sequence. In this study, we sequenced the intervenient region between smpB and glcD in 178 Chinese N. meningitidis strains isolated from both patients and carriers. There were 110 serogroupable strains, other 68 were non-groupable (NG). Ninety nine of the 178 strains were clustered into 13 CCs, the remaining 79 were unassigned (UA). CC4821 is one of the dominant CCs in China. Forty of the 42 CC4821 strains and 26 of the 79 UA strains were autB-null, while the remaining 12 CCs were autB-positive. According to the N-terminal sequence, most (97/112) of the autB-positive strains were clustered into AutB1 and the remaining 15 were AutB2. The autB gene and its flanking intergenic sequences was superseded by a perfectly conservative sequence of an identical 968 bp in all of the autB-null N. meningitidis strains which had no identity with the relatively conservative intergenic sequences that flanked the autB gene in autB-positive strains. There was a 10 bp DNA uptake sequence (DUS) at the beginning of the interval 968 bp sequence in the autB-null strains while there was a 9 bp Haemophilus-specific uptake sequence (hUS) at the beginning of the partial holB gene and at the end of the partial tmk gene in autB-positive strains, holB and tmk gene were flanking the autB gene in Haemophilus. In conclusion, not all pathogenic N. meningitidis strains especially CC4821 possess the autB gene in China and the corresponding spacer region of the autB-null strains was not homologous to that found in autB-positive strains. There's a hypothesis that the DUS and hUS are likely to play a key part in the mechanism of uptake or loss of the autB gene.
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Affiliation(s)
- Aiyu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Pan Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bingqing Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fenglin Shi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Gao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Xie
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhujun Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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67
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Phase and antigenic variation govern competition dynamics through positioning in bacterial colonies. Sci Rep 2017; 7:12151. [PMID: 28939833 PMCID: PMC5610331 DOI: 10.1038/s41598-017-12472-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023] Open
Abstract
Cellular positioning towards the surface of bacterial colonies and biofilms can enhance dispersal, provide a selective advantage due to increased nutrient and space availability, or shield interior cells from external stresses. Little is known about the molecular mechanisms that govern bacterial positioning. Using the type IV pilus (T4P) of Neisseria gonorrhoeae, we tested the hypothesis that the processes of phase and antigenic variation govern positioning and thus enhance bacterial fitness in expanding gonococcal colonies. By independently tuning growth rate and T4P-mediated interaction forces, we show that the loss of T4P and the subsequent segregation to the front confers a strong selective advantage. Sequencing of the major pilin gene of the spatially segregated sub-populations and an investigation of the spatio-temporal population dynamics was carried out. Our findings indicate that pilin phase and antigenic variation generate a standing variation of pilin sequences within the inoculation zone, while variants associated with a non-piliated phenotype segregate to the front of the growing colony. We conclude that tuning of attractive forces by phase and antigenic variation is a powerful mechanism for governing the dynamics of bacterial colonies.
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68
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Pandey AK, Cleary DW, Laver JR, Maiden MCJ, Didelot X, Gorringe A, Read RC. Neisseria lactamica Y92-1009 complete genome sequence. Stand Genomic Sci 2017; 12:41. [PMID: 28770026 PMCID: PMC5525351 DOI: 10.1186/s40793-017-0250-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
We present the high quality, complete genome assembly of Neisseria lactamica Y92–1009 used to manufacture an outer membrane vesicle (OMV)-based vaccine, and a member of the Neisseria genus. The strain is available on request from the Public Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid bacterium is an organism of worldwide clinical interest because human nasopharyngeal carriage is related inversely to the incidence of meningococcal disease, caused by Neisseria meningitidis. The organism sequenced was isolated during a school carriage survey in Northern Ireland in 1992 and has been the subject of a variety of laboratory and clinical studies. Four SMRT cells on a RSII machine by Pacific Biosystems were used to produce a complete, closed genome assembly. Sequence data were obtained for a total of 30,180,391 bases from 2621 reads and assembled using the HGAP algorithm. The assembly was corrected using short reads obtained from an Illumina HiSeq 2000instrument. This resulted in a 2,146,723 bp assembly with approximately 460 fold mean coverage depth and a GC ratio of 52.3%.
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Affiliation(s)
- Anish K Pandey
- Faculty of Medicine, Southampton NIHR Biomedical Research Centre and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - David W Cleary
- Faculty of Medicine, Southampton NIHR Biomedical Research Centre and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Jay R Laver
- Faculty of Medicine, Southampton NIHR Biomedical Research Centre and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford, UK
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | | | - Robert C Read
- Faculty of Medicine, Southampton NIHR Biomedical Research Centre and Institute for Life Sciences, University of Southampton, Southampton, UK
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69
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Abstract
Whether prokaryotes (Bacteria and Archaea) are naturally organized into phenotypically and genetically cohesive units comparable to animal or plant species remains contested, frustrating attempts to estimate how many such units there might be, or to identify the ecological roles they play. Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive recombination are understood to be drivers of cluster formation ("speciation"). However, observed patterns are rarely compared with those obtainable with simple null models of diversification under stochastic lineage birth and death and random genetic drift. Via a combination of simulations and analyses of core and phylogenetic marker genes, we show that patterns of diversity for the genera Escherichia, Neisseria, and Borrelia are generally indistinguishable from patterns arising under a null model. We suggest that caution should thus be taken in interpreting observed clustering as a result of selective evolutionary forces. Unknown forces do, however, appear to play a role in Helicobacter pylori, and some individual genes in all groups fail to conform to the null model. Taken together, we recommend the presented birth-death model as a null hypothesis in prokaryotic speciation studies. It is only when the real data are statistically different from the expectations under the null model that some speciation process should be invoked.
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Affiliation(s)
- Timothy J Straub
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755;
- Department of Computer Science, Dartmouth College, Hanover, NH 03755
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70
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Bårnes GK, Brynildsrud OB, Børud B, Workalemahu B, Kristiansen PA, Beyene D, Aseffa A, Caugant DA. Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia. BMC Genomics 2017; 18:407. [PMID: 28545446 PMCID: PMC5445459 DOI: 10.1186/s12864-017-3806-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/17/2017] [Indexed: 11/17/2022] Open
Abstract
Background Meningococcal colonization is a prerequisite for transmission and disease, but the bacterium only very infrequently causes disease while asymptomatic carriage is common. Carriage is highly dynamic, showing a great variety across time and space within and across populations, but also within individuals. The understanding of genetic changes in the meningococcus during carriage, when the bacteria resides in its natural niche, is important for understanding not only the carriage state, but the dynamics of the entire meningococcal population. Results Paired meningococcal isolates, obtained from 50 asymptomatic carriers about 2 months apart were analyzed with whole genome sequencing (WGS). Phylogenetic analysis revealed that most paired isolates from the same individual were closely related, and the average and median number of allelic differences between paired isolates defined as the same strain was 35. About twice as many differences were seen between isolates from different individuals within the same sequence type (ST). In 8%, different strains were detected at different time points. A difference in ST was observed in 6%, including an individual who was found to carry three different STs over the course of 9 weeks. One individual carried different strains from the same ST. In total, 566 of 1605 cgMLST genes had undergone within-host genetic changes in one or more pairs. The most frequently changed cgMLST gene was relA that was changed in 47% of pairs. Across the whole genome, pilE, differed mostly, in 85% of the pairs. The most frequent mechanisms of genetic difference between paired isolates were phase variation and recombination, including gene conversion. Different STs showed variation with regard to which genes that were most frequently changed, mostly due to absence/presence of phase variation. Conclusions This study revealed within-host genetic differences in meningococcal isolates during short-term asymptomatic carriage. The most frequently changed genes were genes belonging to the pilin family, the restriction/modification system, opacity proteins and genes involved in glycosylation. Higher resolution genome-wide sequence typing is necessary to resolve the diversity of isolates and reveals genetic differences not discovered by traditional typing schemes, and would be the preferred choice of technology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3806-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guro K Bårnes
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ola Brønstad Brynildsrud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Bente Børud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Paul A Kristiansen
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo, Norway
| | - Demissew Beyene
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.,Hamlin Fistula Ethiopia, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. .,WHO Collaborating Center for Reference and Research on Meningococci, Norwegian Institute of Public Health, Oslo, Norway. .,Faculty of Medicine, University of Oslo, Oslo, Norway.
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71
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Marin MA, Fonseca E, Encinas F, Freitas F, Camargo DA, Coimbra RS, de Filippis I, Vicente AC. The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire. Sci Rep 2017; 7:1617. [PMID: 28487566 PMCID: PMC5431661 DOI: 10.1038/s41598-017-01671-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.
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Affiliation(s)
- Michel Abanto Marin
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil.
| | - Erica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernando Encinas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | | | - Roney Santos Coimbra
- Neurogenômica, Centro de Pesquisas René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, MG, Brazil
| | - Ivano de Filippis
- Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
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72
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Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C. Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease. PLoS One 2017; 12:e0169892. [PMID: 28081260 PMCID: PMC5231331 DOI: 10.1371/journal.pone.0169892] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022] Open
Abstract
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation. In line with the hypothesis that phase variation evolved as an adaptation to colonize diverse hosts, computational comparisons of all 27 to date completely sequenced and annotated meningococcal genomes retrieved from public databases showed that contingency genes are indeed enriched for genes involved in host interactions. To assess within-host genetic changes in meningococci, we further used ultra-deep whole-genome sequencing of throat-blood strain pairs isolated from four patients suffering from invasive meningococcal disease. We detected up to three mutations per strain pair, affecting predominantly contingency genes involved in type IV pilus biogenesis. However, there was not a single (set) of mutation(s) that could invariably be found in all four pairs of strains. Phenotypic assays further showed that these genetic changes were generally not associated with increased serum resistance, higher fitness in human blood ex vivo or differences in the interaction with human epithelial and endothelial cells in vitro. In conclusion, we hypothesize that virulence of meningococci results from accidental emergence of invasive variants during carriage and without within host evolution of invasive phenotypes during disease progression in vivo.
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Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Institute of Human Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Vera Mitesser
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Ulrich Vogel
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- German Reference Laboratory for Meningococci and Haemophilus influenzae, Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Matthias Frosch
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- German Reference Laboratory for Meningococci and Haemophilus influenzae, Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- * E-mail:
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73
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Edwards JL, Jennings MP, Apicella MA, Seib KL. Is gonococcal disease preventable? The importance of understanding immunity and pathogenesis in vaccine development. Crit Rev Microbiol 2016; 42:928-41. [PMID: 26805040 PMCID: PMC4958600 DOI: 10.3109/1040841x.2015.1105782] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/01/2015] [Accepted: 10/06/2015] [Indexed: 12/31/2022]
Abstract
Gonorrhea is a major, global public health problem for which there is no vaccine. The continuing emergence of antibiotic-resistant strains raises concerns that untreatable Neisseria gonorrhoeae may become widespread in the near future. Consequently, there is an urgent need for increased efforts towards the development of new anti-gonococcal therapeutics and vaccines, as well as suitable models for potential pre-clinical vaccine trials. Several current issues regarding gonorrhea are discussed herein, including the global burden of disease, the emergence of antibiotic-resistance, the status of vaccine development and, in particular, a focus on the model systems available to evaluate drug and vaccine candidates. Finally, alternative approaches to evaluate vaccine candidates are presented. Such approaches may provide valuable insights into the protective mechanisms, and correlates of protection, required to prevent gonococcal transmission, local infection and disease sequelae.
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Affiliation(s)
- Jennifer L. Edwards
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital and The Ohio State UniversityColumbus,
OH,
USA
| | | | | | - Kate L. Seib
- Institute for Glycomics, Griffith University,
Gold Coast,
Australia
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74
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Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism. Proc Natl Acad Sci U S A 2016; 113:12467-12472. [PMID: 27791096 DOI: 10.1073/pnas.1608110113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Horizontal gene transfer can speed up adaptive evolution and support chromosomal DNA repair. A particularly widespread mechanism of gene transfer is transformation. The initial step to transformation, namely the uptake of DNA from the environment, is supported by the type IV pilus system in most species. However, the molecular mechanism of DNA uptake remains elusive. Here, we used single-molecule techniques for characterizing the force-dependent velocity of DNA uptake by Neisseria gonorrhoeae We found that the DNA uptake velocity depends on the concentration of the periplasmic DNA-binding protein ComE, indicating that ComE is directly involved in the uptake process. The velocity-force relation of DNA uptake is in very good agreement with a translocation ratchet model where binding of chaperones in the periplasm biases DNA diffusion through a membrane pore in the direction of uptake. The model yields a speed of DNA uptake of 900 bp⋅s-1 and a reversal force of 17 pN. Moreover, by comparing the velocity-force relation of DNA uptake and type IV pilus retraction, we can exclude pilus retraction as a mechanism for DNA uptake. In conclusion, our data strongly support the model of a translocation ratchet with ComE acting as a ratcheting chaperone.
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75
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Duffin PM, Barber DA. DprA is required for natural transformation and affects pilin variation in Neisseria gonorrhoeae. Microbiology (Reading) 2016; 162:1620-1628. [DOI: 10.1099/mic.0.000343] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Paul M. Duffin
- Division of Natural Sciences and Mathematics, Transylvania University, Lexington, KY, USA
| | - Daniel A. Barber
- Division of Natural Sciences and Mathematics, Transylvania University, Lexington, KY, USA
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76
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Single-Stranded DNA Uptake during Gonococcal Transformation. J Bacteriol 2016; 198:2515-23. [PMID: 27381919 DOI: 10.1128/jb.00464-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Neisseria gonorrhoeae is naturally competent for transformation. The first step of the transformation process is the uptake of DNA from the environment into the cell. This transport step is driven by a powerful molecular machine. Here, we addressed the question whether this machine imports single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) at similar rates. The fluorescence signal associated with the uptake of short DNA fragments labeled with a single fluorescent marker molecule was quantified. We found that ssDNA with a double-stranded DNA uptake sequence (DUS) was taken up with a similar efficiency as dsDNA. Imported ssDNA was degraded rapidly, and the thermonuclease Nuc was required for degradation. In a nuc deletion background, dsDNA and ssDNA with a double-stranded DUS were imported and used as the substrates for transformation, whereas the import and transformation efficiencies of ssDNA with single-stranded DUS were below the detection limits. We conclude that the DNA uptake machine requires a double-stranded DUS for efficient DNA recognition and transports ssDNA and dsDNA with comparable efficiencies. IMPORTANCE Bacterial transformation enables bacteria to exchange genetic information. It can speed up adaptive evolution and enhances the potential of DNA repair. The transport of DNA through the outer membrane is the first step of transformation in Gram-negative species. It is driven by a powerful molecular machine whose mechanism remains elusive. Here, we show for Neisseria gonorrhoeae that the machine transports single- and double-stranded DNA at comparable rates, provided that the species-specific DNA uptake sequence is double stranded. Moreover, we found that single-stranded DNA taken up into the periplasm is rapidly degraded by the thermonuclease Nuc. We conclude that the secondary structure of transforming DNA is important for the recognition of self DNA but not for the process of transport through the outer membrane.
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77
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Why should 1 gram of ceftriaxone monotherapy be considered as a therapeutic option in gonococcal sexually transmitted diseases? Clin Microbiol Infect 2016; 22:903-904. [PMID: 27404364 DOI: 10.1016/j.cmi.2016.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/28/2016] [Accepted: 07/02/2016] [Indexed: 11/21/2022]
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78
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Davis KM, Isberg RR. Defining heterogeneity within bacterial populations via single cell approaches. Bioessays 2016; 38:782-90. [PMID: 27273675 DOI: 10.1002/bies.201500121] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations.
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Affiliation(s)
- Kimberly M Davis
- Howard Hughes Medical Institute, Tufts University School of Medicine, Boston, MA, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Ralph R Isberg
- Howard Hughes Medical Institute, Tufts University School of Medicine, Boston, MA, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
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79
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Zheng W, Mutha NVR, Heydari H, Dutta A, Siow CC, Jakubovics NS, Wee WY, Tan SY, Ang MY, Wong GJ, Choo SW. NeisseriaBase: a specialised Neisseria genomic resource and analysis platform. PeerJ 2016; 4:e1698. [PMID: 27017950 PMCID: PMC4806638 DOI: 10.7717/peerj.1698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/26/2016] [Indexed: 01/27/2023] Open
Abstract
Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.
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Affiliation(s)
- Wenning Zheng
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia
| | - Naresh V R Mutha
- Genome Informatics Research Laboratory, HIR Building, University of Malaya , Kuala Lumpur , Malaysia
| | - Hamed Heydari
- Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia; Computer Science and Engineering Department, University of NE-Lincoln, Lincoln NE, United States of America
| | - Avirup Dutta
- Genome Informatics Research Laboratory, HIR Building, University of Malaya , Kuala Lumpur , Malaysia
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, HIR Building, University of Malaya , Kuala Lumpur , Malaysia
| | - Nicholas S Jakubovics
- Centre for Oral Health Research, School of Dental Sciences, Newcastle University , Newcastle upon Tyne , United Kingdom
| | - Wei Yee Wee
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia
| | - Shi Yang Tan
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia
| | - Mia Yang Ang
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia
| | - Guat Jah Wong
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia; Genome Informatics Research Laboratory, HIR Building, University of Malaya, Kuala Lumpur, Malaysia; Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, Kuala Lumpur, Malaysia
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Connor DO, Zantow J, Hust M, Bier FF, von Nickisch-Rosenegk M. Identification of Novel Immunogenic Proteins of Neisseria gonorrhoeae by Phage Display. PLoS One 2016; 11:e0148986. [PMID: 26859666 PMCID: PMC4747489 DOI: 10.1371/journal.pone.0148986] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Neisseria gonorrhoeae is one of the most prevalent sexually transmitted diseases worldwide with more than 100 million new infections per year. A lack of intense research over the last decades and increasing resistances to the recommended antibiotics call for a better understanding of gonococcal infection, fast diagnostics and therapeutic measures against N. gonorrhoeae. Therefore, the aim of this work was to identify novel immunogenic proteins as a first step to advance those unresolved problems. For the identification of immunogenic proteins, pHORF oligopeptide phage display libraries of the entire N. gonorrhoeae genome were constructed. Several immunogenic oligopeptides were identified using polyclonal rabbit antibodies against N. gonorrhoeae. Corresponding full-length proteins of the identified oligopeptides were expressed and their immunogenic character was verified by ELISA. The immunogenic character of six proteins was identified for the first time. Additional 13 proteins were verified as immunogenic proteins in N. gonorrhoeae.
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Affiliation(s)
- Daniel O. Connor
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Jonas Zantow
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Michael Hust
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Frank F. Bier
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Biosystem Integration and Automation, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Markus von Nickisch-Rosenegk
- Department of Bioanalytics and Biosensorics, Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
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81
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Ershova A, Rusinov I, Vasiliev M, Spirin S, Karyagina A. Restriction-Modification systems interplay causes avoidance of GATC site in prokaryotic genomes. J Bioinform Comput Biol 2016; 14:1641003. [PMID: 26972562 DOI: 10.1142/s0219720016410031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5[Formula: see text]-GATC-3[Formula: see text] site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes. In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.
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Affiliation(s)
- Anna Ershova
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,† Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia.,‡ Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia
| | - Ivan Rusinov
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,§ Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia
| | - Mikhail Vasiliev
- ¶ Moscow Institute of Physics and Technology, the Ministry of Education and Science of the Russian Federation, Dolgoprudny, Moscow Region, 141700, Russia
| | - Sergey Spirin
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,§ Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow 119992, Russia.,∥ Scientific Research Institute for System Studies, the Russian Academy of Science (NIISI RAS), Moscow 117218, Russia
| | - Anna Karyagina
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,† Gamaleya Center for Epidemiology and Microbiology, the Ministry of Health of the Russian Federation, Moscow 123098, Russia.,‡ Institute of Agricultural Biotechnology, the Russian Academy of Sciences, Moscow 127550, Russia
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82
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Zhang Y, Rajan R, Seifert HS, Mondragón A, Sontheimer EJ. DNase H Activity of Neisseria meningitidis Cas9. Mol Cell 2015; 60:242-55. [PMID: 26474066 PMCID: PMC4609032 DOI: 10.1016/j.molcel.2015.09.020] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 08/17/2015] [Accepted: 09/21/2015] [Indexed: 12/22/2022]
Abstract
Type II CRISPR systems defend against invasive DNA by using Cas9 as an RNA-guided nuclease that creates double-stranded DNA breaks. Dual RNAs (CRISPR RNA [crRNA] and tracrRNA) are required for Cas9's targeting activities observed to date. Targeting requires a protospacer adjacent motif (PAM) and crRNA-DNA complementarity. Cas9 orthologs (including Neisseria meningitidis Cas9 [NmeCas9]) have also been adopted for genome engineering. Here we examine the DNA cleavage activities and substrate requirements of NmeCas9, including a set of unusually complex PAM recognition patterns. Unexpectedly, NmeCas9 cleaves single-stranded DNAs in a manner that is RNA guided but PAM and tracrRNA independent. Beyond the need for guide-target pairing, this "DNase H" activity has no apparent sequence requirements, and the cleavage sites are measured from the 5' end of the DNA substrate's RNA-paired region. These results indicate that tracrRNA is not strictly required for NmeCas9 enzymatic activation, and expand the list of targeting activities of Cas9 endonucleases.
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Affiliation(s)
- Yan Zhang
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-2324, USA
| | - Rakhi Rajan
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
| | - H Steven Seifert
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, IL 60611, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, Program in Molecular Medicine, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-2324, USA.
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83
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Barber MF, Elde NC. Buried Treasure: Evolutionary Perspectives on Microbial Iron Piracy. Trends Genet 2015; 31:627-636. [PMID: 26431675 PMCID: PMC4639441 DOI: 10.1016/j.tig.2015.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 08/18/2015] [Accepted: 09/04/2015] [Indexed: 12/14/2022]
Abstract
Host–pathogen interactions provide valuable systems for the study of evolutionary genetics and natural selection. The sequestration of essential iron has emerged as a crucial innate defense system termed nutritional immunity, leading pathogens to evolve mechanisms of ‘iron piracy’ to scavenge this metal from host proteins. This battle for iron carries numerous consequences not only for host–pathogen evolution but also microbial community interactions. Here we highlight recent and potential future areas of investigation on the evolutionary implications of microbial iron piracy in relation to molecular arms races, host range, competition, and virulence. Applying evolutionary genetic approaches to the study of microbial iron acquisition could also provide new inroads for understanding and combating infectious disease. The battle between microbes and their hosts for nutrient iron is emerging as a new front of evolutionary genetic conflict. Molecular arms races can emerge between host iron-binding proteins and microbial ‘iron piracy’ factors that steal this nutrient for growth. Such rapid evolution may also contribute to the host range of pathogenic microbes. Iron acquisition plays an important role in evolutionary interactions between microbes, both in the environment and within the host. Competition for iron can prevent infection by pathogens, while genetic changes in iron acquisition systems can enhance microbial virulence. Evolutionary conflicts for nutrient iron are revealing potential new genetic mechanisms of disease resistance as well as avenues for therapeutic development.
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Affiliation(s)
- Matthew F Barber
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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84
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Oldewurtel ER, Kouzel N, Dewenter L, Henseler K, Maier B. Differential interaction forces govern bacterial sorting in early biofilms. eLife 2015; 4. [PMID: 26402455 PMCID: PMC4625442 DOI: 10.7554/elife.10811] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/23/2015] [Indexed: 12/30/2022] Open
Abstract
Bacterial biofilms can generate micro-heterogeneity in terms of surface structures. However, little is known about the associated changes in the physics of cell–cell interaction and its impact on the architecture of biofilms. In this study, we used the type IV pilus of Neisseria gonorrhoeae to test whether variation of surface structures induces cell-sorting. We show that the rupture forces between pili are fine-tuned by post-translational modification. Bacterial sorting was dependent on pilus post-translational modification and pilus density. Active force generation was necessary for defined morphologies of mixed microcolonies. The observed morphotypes were in remarkable agreement with the differential strength of adhesion hypothesis proposing that a tug-of-war among surface structures of different cells governs cell sorting. We conclude that in early biofilms the density and rupture force of bacterial surface structures can trigger cell sorting based on similar physical principles as in developing embryos. DOI:http://dx.doi.org/10.7554/eLife.10811.001 Communities of bacterial cells can live together embedded within a slime-like molecular matrix as a biofilm. This allows the bacteria to hide from external stresses. A single bacterium can replicate itself and develop into a biofilm, and over time the bacterial cells in specific regions of the biofilm will start to interact with their neighbors in different ways. These interactions occur via structures on the surface of the bacterial cells, and the differences in these interactions resemble those that occur as cells specialize during the development of animal embryos. Previous research into embryonic development has shown how differences in the physical interactions between embryonic cells are essential for sorting the cells into their correct locations and shaping the embryo. However, little is known about which processes govern the development of biofilms. Now, Oldewurtel et al. have asked whether differences in the physical interactions between bacteria trigger cell sorting during the early stages of biofilm development. The experiments involved measuring the force required to break the cell–cell connections (called the ‘rupture force’) in biofilms of a bacterium called Neisseria gonorrhoeae. Oldewurtel et al. found that, in agreement with previous predictions, physical interactions were important for sorting bacterial cells into clusters based on the structures on their surfaces. Bacterial cells actively pull on the surface structures of their neighbors, which allows the cells to sort themselves in a tug-of-war fashion. This means that a cell will move in the direction where it can pull the strongest (i.e., in the direction where the rupture force is highest). While bacteria and embryos use different molecules to generate these pulling forces, these findings indicate that the basic physical principles are similar in both systems. One of the next challenges will be to evaluate how biofilms might benefit from the structures that develop due to cell sorting. DOI:http://dx.doi.org/10.7554/eLife.10811.002
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Affiliation(s)
| | - Nadzeya Kouzel
- Department of Physics, University of Cologne, Cologne, Germany
| | - Lena Dewenter
- Department of Physics, University of Cologne, Cologne, Germany
| | - Katja Henseler
- Department of Physics, University of Cologne, Cologne, Germany
| | - Berenike Maier
- Department of Physics, University of Cologne, Cologne, Germany
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85
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Gault J, Ferber M, Machata S, Imhaus AF, Malosse C, Charles-Orszag A, Millien C, Bouvier G, Bardiaux B, Péhau-Arnaudet G, Klinge K, Podglajen I, Ploy MC, Seifert HS, Nilges M, Chamot-Rooke J, Duménil G. Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation. PLoS Pathog 2015; 11:e1005162. [PMID: 26367394 PMCID: PMC4569582 DOI: 10.1371/journal.ppat.1005162] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
The ability of pathogens to cause disease depends on their aptitude to escape the immune system. Type IV pili are extracellular filamentous virulence factors composed of pilin monomers and frequently expressed by bacterial pathogens. As such they are major targets for the host immune system. In the human pathogen Neisseria meningitidis, strains expressing class I pilins contain a genetic recombination system that promotes variation of the pilin sequence and is thought to aid immune escape. However, numerous hypervirulent clinical isolates express class II pilins that lack this property. This raises the question of how they evade immunity targeting type IV pili. As glycosylation is a possible source of antigenic variation it was investigated using top-down mass spectrometry to provide the highest molecular precision on the modified proteins. Unlike class I pilins that carry a single glycan, we found that class II pilins display up to 5 glycosylation sites per monomer on the pilus surface. Swapping of pilin class and genetic background shows that the pilin primary structure determines multisite glycosylation while the genetic background determines the nature of the glycans. Absence of glycosylation in class II pilins affects pilus biogenesis or enhances pilus-dependent aggregation in a strain specific fashion highlighting the extensive functional impact of multisite glycosylation. Finally, molecular modeling shows that glycans cover the surface of class II pilins and strongly decrease antibody access to the polypeptide chain. This strongly supports a model where strains expressing class II pilins evade the immune system by changing their sugar structure rather than pilin primary structure. Overall these results show that sequence invariable class II pilins are cloaked in glycans with extensive functional and immunological consequences. During infection pathogens and their host engage in a series of measures and counter-measures to promote their own survival: pathogens express virulence factors, the immune system targets these surface structures and pathogens modify them to evade detection. Like numerous bacterial pathogens, Neisseria meningitidis express type IV pili, long filamentous adhesive structures composed of pilins. Intriguingly the amino acid sequences of pilins from most hypervirulent strains do not vary, raising the question of how they evade the immune system. This study shows that the pilus structure is completely coated with sugars thus limiting access of antibodies to the pilin polypeptide chain. We propose that multisite glycosylation and thus variation in the type of sugar mediates immune evasion in these strains.
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MESH Headings
- Amino Acid Sequence
- Bacterial Adhesion
- Cell Line
- Cells, Cultured
- Conserved Sequence
- Endothelium, Vascular/cytology
- Endothelium, Vascular/immunology
- Endothelium, Vascular/microbiology
- Endothelium, Vascular/pathology
- Fimbriae Proteins/chemistry
- Fimbriae Proteins/genetics
- Fimbriae Proteins/metabolism
- Fimbriae, Bacterial/immunology
- Fimbriae, Bacterial/metabolism
- Fimbriae, Bacterial/ultrastructure
- Gene Deletion
- Glycosylation
- Host-Pathogen Interactions
- Human Umbilical Vein Endothelial Cells/cytology
- Human Umbilical Vein Endothelial Cells/immunology
- Human Umbilical Vein Endothelial Cells/microbiology
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Immune Evasion
- Meningococcal Infections/immunology
- Meningococcal Infections/metabolism
- Meningococcal Infections/microbiology
- Meningococcal Infections/pathology
- Microscopy, Electron, Transmission
- Models, Molecular
- Neisseria meningitidis/immunology
- Neisseria meningitidis/metabolism
- Neisseria meningitidis/ultrastructure
- Protein Processing, Post-Translational
- Sequence Homology, Amino Acid
- Species Specificity
- Surface Properties
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Affiliation(s)
- Joseph Gault
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Mathias Ferber
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Silke Machata
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Anne-Flore Imhaus
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Christian Malosse
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Arthur Charles-Orszag
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Corinne Millien
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Guillaume Bouvier
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | | | - Kelly Klinge
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Isabelle Podglajen
- Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges-Pompidou, Paris, France
| | - Marie Cécile Ploy
- INSERM UMR1092, Faculté de Médecine, Université de Limoges, Limoges, France
| | - H. Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Julia Chamot-Rooke
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Guillaume Duménil
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
- * E-mail:
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86
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Gasparini R, Panatto D, Bragazzi NL, Lai PL, Bechini A, Levi M, Durando P, Amicizia D. How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines. J Immunol Res 2015; 2015:189153. [PMID: 26351643 PMCID: PMC4553322 DOI: 10.1155/2015/189153] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/09/2015] [Indexed: 01/17/2023] Open
Abstract
In the last decades, tremendous advancement in dissecting the mechanisms of pathogenicity of Neisseria meningitidis at a molecular level has been achieved, exploiting converging approaches of different disciplines, ranging from pathology to microbiology, immunology, and omics sciences (such as genomics and proteomics). Here, we review the molecular biology of the infectious agent and, in particular, its interactions with the immune system, focusing on both the innate and the adaptive responses. Meningococci exploit different mechanisms and complex machineries in order to subvert the immune system and to avoid being killed. Capsular polysaccharide and lipooligosaccharide glycan composition, in particular, play a major role in circumventing immune response. The understanding of these mechanisms has opened new horizons in the field of vaccinology. Nowadays different licensed meningococcal vaccines are available and used: conjugate meningococcal C vaccines, tetravalent conjugate vaccines, an affordable conjugate vaccine against the N. menigitidis serogroup A, and universal vaccines based on multiple antigens each one with a different and peculiar function against meningococcal group B strains.
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Affiliation(s)
- R. Gasparini
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Panatto
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - N. L. Bragazzi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - P. L. Lai
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - A. Bechini
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - M. Levi
- Department of Health Sciences, University of Florence, Viale G.B. Morgagni 48, 50134 Florence, Italy
| | - P. Durando
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
| | - D. Amicizia
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16132 Genoa, Italy
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87
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Moir JWB. Meningitis in adolescents: the role of commensal microbiota. Trends Microbiol 2015; 23:181-2. [PMID: 25818619 DOI: 10.1016/j.tim.2015.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/02/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
The pathogen Neisseria meningitidis causes disease amongst infants and adolescents/young adults. Here we argue that disease amongst adolescents is due largely to interaction between N. meningitidis and other members of the upper respiratory tract microbiota, through a metabolic interaction involving exchange of propionic acid.
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Affiliation(s)
- James W B Moir
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK.
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88
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Neisseria gonorrhoeae MutS affects pilin antigenic variation through mismatch correction and not by pilE guanine quartet binding. J Bacteriol 2015; 197:1828-38. [PMID: 25777677 DOI: 10.1128/jb.02594-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/08/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many pathogens use homologous recombination to vary surface antigens to avoid immune surveillance. Neisseria gonorrhoeae achieves this in part by changing the properties of its surface pili in a process called pilin antigenic variation (AV). Pilin AV occurs by high-frequency gene conversion reactions that transfer silent pilS sequences into the expressed pilE locus and requires the formation of an upstream guanine quartet (G4) DNA structure to initiate this process. The MutS and MutL proteins of the mismatch correction (MMC) system act to correct mismatches after replication and prevent homeologous (i.e., partially homologous) recombination, but MutS orthologs can also bind to G4 structures. A previous study showed that mutation of MutS resulted in a 3-fold increase in pilin AV, which could be due to the loss of MutS antirecombination properties or loss of G4 binding. We tested two site-directed separation-of-function MutS mutants that are both predicted to bind to G4s but are not able to perform MMC. Pilus phase variation assays and DNA sequence analysis of pilE variants produced in these mutants showed that all three mutS mutants and a mutL mutant had similar increased frequencies of pilin AV. Moreover, the mutS mutants all showed similar increased levels of pilin AV-dependent synthetic lethality. These results show that antirecombination by MMC is the reason for the effect that MutS has on pilin AV and is not due to pilE G4 binding by MutS. IMPORTANCE Neisseria gonorrhoeae continually changes its outer surface proteins to avoid recognition by the immune system. N. gonorrhoeae alters the antigenicity of the pilus by directed recombination between partially homologous pilin copies in a process that requires a guanine quartet (G4) structure. The MutS protein of the mismatch correction (MMC) system prevents recombination between partially homologous sequences and can also bind to G4s. We confirmed that loss of MMC increases the frequency of pilin antigenic variation and that two MutS mutants that are predicted to separate the two different functions of MutS inhibit pilin variation similarly to a complete-loss-of-function mutant, suggesting that interaction of MutS with the G4 structure is not a major factor in this process.
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