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Wuckelt M, Laurent A, Mouville C, Meyer J, Jamet A, Lecuyer H, Nassif X, Bille E, Pelicic V, Coureuil M. Expanding the genetic toolbox for Neisseria meningitidis with efficient tools for unmarked gene editing, complementation, and labeling. Appl Environ Microbiol 2024:e0088024. [PMID: 39140741 DOI: 10.1128/aem.00880-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
The efficient natural transformation of Neisseria meningitidis allows the rapid construction of bacterial mutants in which the genes of interest are interrupted or replaced by antibiotic-resistance cassettes. However, this proved to be a double-edged sword, i.e., although facilitating the genetic characterization of this important human pathogen, it has limited the development of strategies for constructing markerless mutants without antibiotic-resistance markers. In addition, efficient tools for complementation or labeling are also lacking in N. meningitidis. In this study, we significantly expand the meningococcal genetic toolbox by developing new and efficient tools for the construction of markerless mutants (using a dual counterselection strategy), genetic complementation (using integrative vectors), and cell labeling (using a self-labeling protein tag). This expanded toolbox paves the way for more in-depth genetic characterization of N. meningitidis and might also be useful in other Neisseria species.IMPORTANCENeisseria meningitidis and Neisseria gonorrhoeae are two important human pathogens. Research focusing on these bacteria requires genetic engineering, which is facilitated by their natural ability to undergo transformation. However, the ease of mutant engineering has led the Neisseria community to neglect the development of more sophisticated tools for gene editing, particularly for N. meningitidis. In this study, we have significantly expanded the meningococcal genetic toolbox by developing novel and efficient tools for markerless mutant construction, genetic complementation, and cell tagging. This expanded toolbox paves the way for more in-depth genetic characterization of N. meningitidis and might also be useful in other Neisseria species.
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Affiliation(s)
- Morgane Wuckelt
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Audrey Laurent
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Clémence Mouville
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Julie Meyer
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Anne Jamet
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Hervé Lecuyer
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Xavier Nassif
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Emmanuelle Bille
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
| | - Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Mathieu Coureuil
- Université Paris Cité, UFR de Médecine, Paris, France
- Inserm U1151, Institut Necker-Enfants Malades, CNRS UMR 8253, Paris, France
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2
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Geslewitz WE, Cardenas A, Zhou X, Zhang Y, Criss AK, Seifert HS. Development and implementation of a Type I-C CRISPR-based programmable repression system for Neisseria gonorrhoeae. mBio 2024; 15:e0302523. [PMID: 38126782 PMCID: PMC10865793 DOI: 10.1128/mbio.03025-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are prokaryotic adaptive immune systems regularly utilized as DNA-editing tools. While Neisseria gonorrhoeae does not have an endogenous CRISPR, the commensal species Neisseria lactamica encodes a functional Type I-C CRISPR-Cas system. We have established an isopropyl β-d-1-thiogalactopyranoside added (IPTG)-inducible, CRISPR interference (CRISPRi) platform based on the N. lactamica Type I-C CRISPR missing the Cas3 nuclease to allow locus-specific transcriptional repression. As proof of principle, we targeted a non-phase-variable version of the opaD gene. We show that CRISPRi can downregulate opaD gene and protein expression, resulting in bacterial inability to stimulate neutrophil oxidative responses and to bind to an N-terminal fragment of CEACAM1. Importantly, we used CRISPRi to effectively knockdown all the transcripts of all 11 opa genes using a five-spacer CRISPR array, allowing control of the entire phase-variable opa family in strain FA1090. We also report that repression is reversible following IPTG removal. Finally, we showed that the Type I-C CRISPRi system can conditionally reduce the expression of two essential genes. This CRISPRi system will allow the interrogation of every Gc gene, essential and non-essential, to study physiology and pathogenesis and aid in antimicrobial development.IMPORTANCEClustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have proven instrumental in genetically manipulating many eukaryotic and prokaryotic organisms. Despite its usefulness, a CRISPR system had yet to be developed for use in Neisseria gonorrhoeae (Gc), a bacterium that is the main etiological agent of gonorrhea infection. Here, we developed a programmable and IPTG-inducible Type I-C CRISPR interference (CRISPRi) system derived from the commensal species Neisseria lactamica as a gene repression system in Gc. As opposed to generating genetic knockouts, the Type I-C CRISPRi system allows us to block transcription of specific genes without generating deletions in the DNA. We explored the properties of this system and found that a minimal spacer array is sufficient for gene repression while also facilitating efficient spacer reprogramming. Importantly, we also show that we can use CRISPRi to knockdown genes that are essential to Gc that cannot normally be knocked out under laboratory settings. Gc encodes ~800 essential genes, many of which have no predicted function. We predict that this Type I-C CRISPRi system can be used to help categorize gene functions and perhaps contribute to the development of novel therapeutics for gonorrhea.
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Affiliation(s)
- Wendy E. Geslewitz
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois, USA
| | - Amaris Cardenas
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Xufei Zhou
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Yan Zhang
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Alison K. Criss
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | - H Steven Seifert
- Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois, USA
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3
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Frost KM, Charron-Smith SL, Cotsonas TC, Dimartino DC, Eisenhart RC, Everingham ET, Holland EC, Imtiaz K, Kornowicz CJ, Lenhard LE, Lynch LH, Moore NP, Phadke K, Reed ML, Smith SR, Ward LL, Wadsworth CB. Rolling the evolutionary dice: Neisseria commensals as proxies for elucidating the underpinnings of antibiotic resistance mechanisms and evolution in human pathogens. Microbiol Spectr 2024; 12:e0350723. [PMID: 38179941 PMCID: PMC10871548 DOI: 10.1128/spectrum.03507-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Species within the genus Neisseria are adept at sharing adaptive allelic variation, with commensal species repeatedly transferring resistance to their pathogenic relative Neisseria gonorrhoeae. However, resistance in commensals is infrequently characterized, limiting our ability to predict novel and potentially transferable resistance mechanisms that ultimately may become important clinically. Unique evolutionary starting places of each Neisseria species will have distinct genomic backgrounds, which may ultimately control the fate of evolving populations in response to selection as epistatic and additive interactions coerce lineages along divergent evolutionary trajectories. Alternatively, similar genetic content present across species due to shared ancestry may constrain existing adaptive solutions. Thus, identifying the paths to resistance across commensals may aid in characterizing the Neisseria resistome-or the reservoir of alleles within the genus as well as its depth. Here, we use in vitro evolution of four commensal species to investigate the potential and repeatability of resistance evolution to two antimicrobials, the macrolide azithromycin and the β-lactam penicillin. After 20 days of selection, commensals evolved resistance to penicillin and azithromycin in 11/16 and 12/16 cases, respectively. Almost all cases of resistance emergence converged on mutations within ribosomal components or the mtrRCDE efflux pump for azithromycin-based selection and mtrRCDE, penA, and rpoB for penicillin selection, thus supporting constrained adaptive solutions despite divergent evolutionary starting points across the genus for these particular drugs. Though drug-selected loci were limited, we do identify novel resistance-imparting mutations. Continuing to explore paths to resistance across different experimental conditions and genomic backgrounds, which could shunt evolution down alternative evolutionary trajectories, will ultimately flesh out the full Neisseria resistome.IMPORTANCENeisseria gonorrhoeae is a global threat to public health due to its rapid acquisition of antibiotic resistance to all first-line treatments. Recent work has documented that alleles acquired from close commensal relatives have played a large role in the emergence of resistance to macrolides and beta-lactams within gonococcal populations. However, commensals have been relatively underexplored for the resistance genotypes they may harbor. This leaves a gap in our understanding of resistance that could be rapidly acquired by the gonococcus through a known highway of horizontal gene exchange. Here, we characterize resistance mechanisms that can emerge in commensal Neisseria populations via in vitro selection to multiple antimicrobials and begin to define the number of paths to resistance. This study, and other similar works, may ultimately aid both surveillance efforts and clinical diagnostic development by nominating novel and conserved resistance mechanisms that may be at risk of rapid dissemination to pathogen populations.
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Affiliation(s)
- Kelly M. Frost
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Sierra L. Charron-Smith
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Terence C. Cotsonas
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Daniel C. Dimartino
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Rachel C. Eisenhart
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Eric T. Everingham
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Elle C. Holland
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Kainat Imtiaz
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Cory J. Kornowicz
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Lydia E. Lenhard
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Liz H. Lynch
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Nadia P. Moore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Kavya Phadke
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Makayla L. Reed
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Samantha R. Smith
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Liza L. Ward
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Crista B. Wadsworth
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
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4
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Seow VY, Tsygelnytska O, Biais N. Multisite transformation in Neisseria gonorrhoeae: insights on transformations mechanisms and new genetic modification protocols. Front Microbiol 2023; 14:1178128. [PMID: 37408636 PMCID: PMC10319059 DOI: 10.3389/fmicb.2023.1178128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/31/2023] [Indexed: 07/07/2023] Open
Abstract
Natural transformation, or the uptake of naked DNA from the external milieu by bacteria, holds a unique place in the history of biology. This is both the beginning of the realization of the correct chemical nature of genes and the first technical step to the molecular biology revolution that sees us today able to modify genomes almost at will. Yet the mechanistic understanding of bacterial transformation still presents many blind spots and many bacterial systems lag behind power horse model systems like Escherichia coli in terms of ease of genetic modification. Using Neisseria gonorrhoeae as a model system and using transformation with multiple DNA molecules, we tackle in this paper both some aspects of the mechanistic nature of bacterial transformation and the presentation of new molecular biology techniques for this organism. We show that similarly to what has been demonstrated in other naturally competent bacteria, Neisseria gonorrhoeae can incorporate, at the same time, different DNA molecules modifying DNA at different loci within its genome. In particular, co-transformation of a DNA molecule bearing an antibiotic selection cassette and another non-selected DNA piece can lead to the integration of both molecules in the genome while selecting only through the selective cassette at percentages above 70%. We also show that successive selections with two selection markers at the same genetic locus can drastically reduce the number of genetic markers needed to do multisite genetic modifications in Neisseria gonorrhoeae. Despite public health interest heightened with the recent rise in antibiotic resistance, the causative agent of gonorrhea still does not possess a plethora of molecular techniques. This paper will extend the techniques available to the Neisseria community while providing some insights into the mechanisms behind bacterial transformation in Neisseria gonorrhoeae. We are providing a suite of new techniques to quickly obtain modifications of genes and genomes in the Neisserial naturally competent bacteria.
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Affiliation(s)
- Vui Yin Seow
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
| | - Olga Tsygelnytska
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
| | - Nicolas Biais
- Brooklyn College of the City University of New York, Brooklyn, NY, United States
- The Graduate Center of the City University of New York, New York, NY, United States
- Laboratoire Jean Perrin, UMR8237, Sorbonne Université, Paris, France
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5
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Santer M, Kupczok A, Dagan T, Uecker H. Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids. Genetics 2022; 222:6663764. [PMID: 35959975 PMCID: PMC9526072 DOI: 10.1093/genetics/iyac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022] Open
Abstract
Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution of bacteria and archaea is often studied by models for the allele dynamics in monoploid populations. However, many prokaryotic organisms harbor multicopy replicons—chromosomes and plasmids—and theory for the allele dynamics in populations of polyploid prokaryotes remains lacking. Here, we present a population genetics model for replicons with multiple copies in the cell. Using this model, we characterize the fixation process of a dominant beneficial mutation at 2 levels: the phenotype and the genotype. Our results show that depending on the mode of replication and segregation, the fixation of the mutant phenotype may precede genotypic fixation by many generations; we term this time interval the heterozygosity window. We furthermore derive concise analytical expressions for the occurrence and length of the heterozygosity window, showing that it emerges if the copy number is high and selection strong. Within the heterozygosity window, the population is phenotypically adapted, while both alleles persist in the population. Replicon ploidy thus allows for the maintenance of genetic variation following phenotypic adaptation and consequently for reversibility in adaptation to fluctuating environmental conditions.
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Affiliation(s)
- Mario Santer
- Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Anne Kupczok
- Institute of General Microbiology, Kiel University, 24118 Kiel, Germany.,Bioinformatics group, Department of Plant Sciences, Wageningen University & Research, 6708PB Wageningen, Netherlands
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, 24118 Kiel, Germany
| | - Hildegard Uecker
- Research group Stochastic Evolutionary Dynamics, Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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6
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Wassing GM, Lidberg K, Sigurlásdóttir S, Frey J, Schroeder K, Ilehag N, Lindås AC, Jonas K, Jonsson AB. DNA Blocks the Lethal Effect of Human Beta-Defensin 2 Against Neisseria meningitidis. Front Microbiol 2021; 12:697232. [PMID: 34276631 PMCID: PMC8278289 DOI: 10.3389/fmicb.2021.697232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
Neisseria meningitidis is a gram-negative bacterium that often asymptomatically colonizes the human nasopharyngeal tract. These bacteria cross the epithelial barrier can cause life-threatening sepsis and/or meningitis. Antimicrobial peptides are one of the first lines of defense against invading bacterial pathogens. Human beta-defensin 2 (hBD2) is an antimicrobial peptide with broad antibacterial activity, although its mechanism of action is poorly understood. Here, we investigated the effect of hBD2 on N. meningitidis. We showed that hBD2 binds to and kills actively growing meningococcal cells. The lethal effect was evident after 2 h incubation with the peptide, which suggests a slow killing mechanism. Further, the membrane integrity was not changed during hBD2 treatment. Incubation with lethal doses of hBD2 decreased the presence of diplococci; the number and size of bacterial microcolonies/aggregates remained constant, indicating that planktonic bacteria may be more susceptible to the peptide. Meningococcal DNA bound hBD2 in mobility shift assays and inhibited the lethal effect of hBD2 in a dose-dependent manner both in suspension and biofilms, supporting the interaction between hBD2 and DNA. Taken together, the ability of meningococcal DNA to bind hBD2 opens the possibility that extracellular DNA due to bacterial lysis may be a means of N. meningitidis to evade immune defenses.
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Affiliation(s)
- Gabriela M Wassing
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kenny Lidberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sara Sigurlásdóttir
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jonas Frey
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kristen Schroeder
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nathalie Ilehag
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kristina Jonas
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Beth Jonsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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7
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Kulkarni A, Mochnáčová E, Majerova P, Čurlík J, Bhide K, Mertinková P, Bhide M. Single Domain Antibodies Targeting Receptor Binding Pockets of NadA Restrain Adhesion of Neisseria meningitidis to Human Brain Microvascular Endothelial Cells. Front Mol Biosci 2020; 7:573281. [PMID: 33425985 PMCID: PMC7785856 DOI: 10.3389/fmolb.2020.573281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/03/2020] [Indexed: 01/02/2023] Open
Abstract
Neisseria adhesin A (NadA), one of the surface adhesins of Neisseria meningitides (NM), interacts with several cell types including human brain microvascular endothelial cells (hBMECs) and play important role in the pathogenesis. Receptor binding pockets of NadA are localized on the globular head domain (A33 to K69) and the first coiled-coil domain (L121 to K158). Here, the phage display was used to develop a variable heavy chain domain (VHH) that can block receptor binding sites of recombinant NadA (rec-NadA). A phage library displaying VHH was panned against synthetic peptides (NadA-gdA33−K69 or NadA-ccL121−K158), gene encoding VHH was amplified from bound phages and re-cloned in the expression vector, and the soluble VHHs containing disulfide bonds were overexpressed in the SHuffle E. coli. From the repertoire of 96 clones, two VHHs (VHHF3–binding NadA-gdA33−K69 and VHHG9–binding NadA-ccL121−K158) were finally selected as they abrogated the interaction between rec-NadA and the cell receptor. Preincubation of NM with VHHF3 and VHHG9 significantly reduced the adhesion of NM on hBMECs in situ and hindered the traversal of NM across the in-vitro BBB model. The work presents a phage display pipeline with a single-round of panning to select receptor blocking VHHs. It also demonstrates the production of soluble and functional VHHs, which blocked the interaction between NadA and its receptor, decreased adhesion of NM on hBMECs, and reduced translocation of NM across BBB in-vitro. The selected NadA blocking VHHs could be promising molecules for therapeutic translation.
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Affiliation(s)
- Amod Kulkarni
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Evelína Mochnáčová
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
| | - Ján Čurlík
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Katarína Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Patrícia Mertinková
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia
| | - Mangesh Bhide
- Laboratory of Biomedical Microbiology and Immunology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovakia.,Institute of Neuroimmunology of Slovak Academy of Sciences, Bratislava, Slovakia
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8
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Alfsnes K, Frye SA, Eriksson J, Eldholm V, Brynildsrud OB, Bohlin J, Harrison OB, Hood DW, Maiden MCJ, Tønjum T, Ambur OH. A genomic view of experimental intraspecies and interspecies transformation of a rifampicin-resistance allele into Neisseria meningitidis. Microb Genom 2018; 4. [PMID: 30251949 PMCID: PMC6321871 DOI: 10.1099/mgen.0.000222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The spread of antibiotic resistance within and between different bacterial populations is a major health problem on a global scale. The identification of genetic transformation in genomic data from Neisseria meningitidis, the meningococcus (Mc), and other bacteria is problematic, since similar or even identical alleles may be involved. A particular challenge in naturally transformable bacteria generally is to distinguish between common ancestry and true recombined sites in sampled genome sequences. Furthermore, the identification of recombination following experimental transformation of homologous alleles requires identifiable differences between donor and recipient, which in itself influences the propensity for homologous recombination (HR). This study identifies the distribution of HR events following intraspecies and interspecies Mc transformations of rpoB alleles encoding rifampicin resistance by whole-genome DNA sequencing and single nucleotide variant analysis. The HR events analysed were confined to the genomic region surrounding the single nucleotide genetic marker used for selection. An exponential length distribution of these recombined events was found, ranging from a few nucleotides to about 72 kb stretches. The lengths of imported sequences were on average found to be longer following experimental transformation of the recipient with genomic DNA from an intraspecies versus an interspecies donor (P<0.001). The recombination events were generally observed to be mosaic, with donor sequences interspersed with recipient sequence. Here, we present four models to explain these observations, by fragmentation of the transformed DNA, by interruptions of the recombination mechanism, by secondary recombination of endogenous self-DNA, or by repair/replication mechanisms.
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Affiliation(s)
| | - Stephan A Frye
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Jens Eriksson
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Vegard Eldholm
- 3Department of Molecular Biology, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola Brønstad Brynildsrud
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jon Bohlin
- 4Department of Methodology Research and Analysis, Domain of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Odile B Harrison
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Derek W Hood
- 6Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, UK
| | - Martin C J Maiden
- 5The Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Tone Tønjum
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,7Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole Herman Ambur
- 2Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,8OsloMet - Oslo Metropolitan University, Oslo, Norway
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9
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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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10
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Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J. The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res 2017; 45:6147-6167. [PMID: 28334889 PMCID: PMC5449619 DOI: 10.1093/nar/gkx168] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of −35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
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Affiliation(s)
- Nadja Heidrich
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Saskia Bauriedl
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christoph Schoen
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), D-97080 Würzburg, Germany
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11
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Abstract
Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within the mammalian host. Whereas viruses make use of a minimal proofreading capacity combined with large amounts of progeny to use random mutation for variant generation, antigenically variant bacteria have evolved mechanisms which use a stable genome, which aids in protecting the fitness of the progeny. Here, three well-characterized and highly antigenically variant bacterial pathogens are discussed: Anaplasma, Borrelia, and Neisseria. These three pathogens display a variety of mechanisms used to create the structural and antigenic variation needed for immune escape and long-term persistence. Intrahost antigenic variation is the focus; however, the role of these immune escape mechanisms at the population level is also presented.
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12
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Hanage WP. Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a018069. [PMID: 27091940 DOI: 10.1101/cshperspect.a018069] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The pervasive nature of bacterial recombination has become clear. Despite this, the population genetics of bacteria persist in being viewed as simple. Here, I argue against that characterization. After summarizing the history of the topic, I survey the evidence for remarkable and unexplained variation in recombination rate among and within bacterial species. I finally argue that despite recent assertions that recombination means bacterial genes are "public goods," in bacteria the level of selection is the gene, and genes can be understood to have niches with dimensions including the other contents of the genome in which they find themselves.
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Affiliation(s)
- William P Hanage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
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13
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Lever MA, Rogers KL, Lloyd KG, Overmann J, Schink B, Thauer RK, Hoehler TM, Jørgensen BB. Life under extreme energy limitation: a synthesis of laboratory- and field-based investigations. FEMS Microbiol Rev 2015; 39:688-728. [PMID: 25994609 DOI: 10.1093/femsre/fuv020] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
The ability of microorganisms to withstand long periods with extremely low energy input has gained increasing scientific attention in recent years. Starvation experiments in the laboratory have shown that a phylogenetically wide range of microorganisms evolve fitness-enhancing genetic traits within weeks of incubation under low-energy stress. Studies on natural environments that are cut off from new energy supplies over geologic time scales, such as deeply buried sediments, suggest that similar adaptations might mediate survival under energy limitation in the environment. Yet, the extent to which laboratory-based evidence of starvation survival in pure or mixed cultures can be extrapolated to sustained microbial ecosystems in nature remains unclear. In this review, we discuss past investigations on microbial energy requirements and adaptations to energy limitation, identify gaps in our current knowledge, and outline possible future foci of research on life under extreme energy limitation.
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Affiliation(s)
- Mark A Lever
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Karyn L Rogers
- Rensselaer Polytechnic Institute, Earth and Environmental Sciences, Jonsson-Rowland Science Center, 1W19, 110 8th Street, Troy, NY 12180, USA
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee at Knoxville, M409 Walters Life Sciences, Knoxville, TN 37996-0845, USA
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Bernhard Schink
- Microbial Ecology, Department of Biology, University of Konstanz, P.O. Box 55 60, D-78457 Konstanz, Germany
| | - Rudolf K Thauer
- Max Planck Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043 Marburg, Germany
| | - Tori M Hoehler
- NASA Ames Research Center, Mail Stop 239-4, Moffett Field, CA 94035-1000, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Institute of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
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14
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Abstract
Neisseria gonorrhoeae and Neisseria meningitidis are closely related organisms that cause the sexually transmitted infection gonorrhea and serious bacterial meningitis and septicemia, respectively. Both species possess multiple mechanisms to alter the expression of surface-exposed proteins through the processes of phase and antigenic variation. This potential for wide variability in surface-exposed structures allows the organisms to always have subpopulations of divergent antigenic types to avoid immune surveillance and to contribute to functional variation. Additionally, the Neisseria are naturally competent for DNA transformation, which is their main means of genetic exchange. Although bacteriophages and plasmids are present in this genus, they are not as effective as DNA transformation for horizontal genetic exchange. There are barriers to genetic transfer, such as restriction-modification systems and CRISPR loci, that limit particular types of exchange. These host-restricted pathogens illustrate the rich complexity of genetics that can help define the similarities and differences of closely related organisms.
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Affiliation(s)
- Ella Rotman
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611; ,
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15
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Zerulla K, Soppa J. Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 2014; 5:274. [PMID: 24982654 PMCID: PMC4056108 DOI: 10.3389/fmicb.2014.00274] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023] Open
Abstract
The investigated haloarchaeal species, Halobacterium salinarum, Haloferax mediterranei, and H. volcanii, have all been shown to be polyploid. They contain several replicons that have independent copy number regulation, and most have a higher copy number during exponential growth phase than in stationary phase. The possible evolutionary advantages of polyploidy for haloarchaea, most of which have experimental support for at least one species, are discussed. These advantages include a low mutation rate and high resistance toward X-ray irradiation and desiccation, which depend on homologous recombination. For H. volcanii, it has been shown that gene conversion operates in the absence of selection, which leads to the equalization of genome copies. On the other hand, selective forces might lead to heterozygous cells, which have been verified in the laboratory. Additional advantages of polyploidy are survival over geological times in halite deposits as well as at extreme conditions on earth and at simulated Mars conditions. Recently, it was found that H. volcanii uses genomic DNA as genetic material and as a storage polymer for phosphate. In the absence of phosphate, H. volcanii dramatically decreases its genome copy number, thereby enabling cell multiplication, but diminishing the genetic advantages of polyploidy. Stable storage of phosphate is proposed as an alternative driving force for the emergence of DNA in early evolution. Several additional potential advantages of polyploidy are discussed that have not been addressed experimentally for haloarchaea. An outlook summarizes selected current trends and possible future developments.
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Affiliation(s)
- Karolin Zerulla
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
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16
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Zielke RA, Wierzbicki IH, Weber JV, Gafken PR, Sikora AE. Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. Mol Cell Proteomics 2014; 13:1299-317. [PMID: 24607996 PMCID: PMC4014286 DOI: 10.1074/mcp.m113.029538] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 02/28/2014] [Indexed: 01/29/2023] Open
Abstract
Neisseria gonorrhoeae (GC) is a human-specific pathogen, and the agent of a sexually transmitted disease, gonorrhea. There is a critical need for new approaches to study and treat GC infections because of the growing threat of multidrug-resistant isolates and the lack of a vaccine. Despite the implied role of the GC cell envelope and membrane vesicles in colonization and infection of human tissues and cell lines, comprehensive studies have not been undertaken to elucidate their constituents. Accordingly, in pursuit of novel molecular therapeutic targets, we have applied isobaric tagging for absolute quantification coupled with liquid chromatography and mass spectrometry for proteome quantitative analyses. Mining the proteome of cell envelopes and native membrane vesicles revealed 533 and 168 common proteins, respectively, in analyzed GC strains FA1090, F62, MS11, and 1291. A total of 22 differentially abundant proteins were discovered including previously unknown proteins. Among those proteins that displayed similar abundance in four GC strains, 34 were found in both cell envelopes and membrane vesicles fractions. Focusing on one of them, a homolog of an outer membrane protein LptD, we demonstrated that its depletion caused loss of GC viability. In addition, we selected for initial characterization six predicted outer membrane proteins with unknown function, which were identified as ubiquitous in the cell envelopes derived from examined GC isolates. These studies entitled a construction of deletion mutants and analyses of their resistance to different chemical probes. Loss of NGO1985, in particular, resulted in dramatically decreased GC viability upon treatment with detergents, polymyxin B, and chloramphenicol, suggesting that this protein functions in the maintenance of the cell envelope permeability barrier. Together, these findings underscore the concept that the cell envelope and membrane vesicles contain crucial, yet under-explored determinants of GC physiology, which may represent promising targets for designing new therapeutic interventions.
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Affiliation(s)
- Ryszard A. Zielke
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Igor H. Wierzbicki
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Jacob V. Weber
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Philip R. Gafken
- §Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - Aleksandra E. Sikora
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
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17
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Um HY, Kong HG, Lee HJ, Choi HK, Park EJ, Kim ST, Murugiyan S, Chung E, Kang KY, Lee SW. Altered Gene Expression and Intracellular Changes of the Viable But Nonculturable State in Ralstonia solanacearum by Copper Treatment. THE PLANT PATHOLOGY JOURNAL 2013; 29:374-85. [PMID: 25288966 PMCID: PMC4174814 DOI: 10.5423/ppj.oa.07.2013.0067] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/08/2013] [Accepted: 08/21/2013] [Indexed: 05/30/2023]
Abstract
Environmental stresses induce several plant pathogenic bacteria into a viable but nonculturable (VBNC) state, but the basis for VBNC is largely uncharacterized. We investigated the physiology and morphology ofthe copper-induced VBNC state in the plant pathogen Ralstonia solanacearum in liquid microcosm. Supplementation of 200 μM copper sulfate to the liquid microcosm completely suppressed bacterial colony formation on culture media; however, LIVE/DEAD BacLight bacterial viability staining showed that the bacterial cells maintained viability, and that the viable cells contain higher level of DNA. Based on electron microscopic observations, the bacterial cells in the VBNC state were unchanged in size, but heavily aggregated and surrounded by an unknown extracellular material. Cellular ribosome contents, however, were less, resulting in a reduction of the total RNA in VBNC cells. Proteome comparison and reverse transcription PCR analysis showed that the Dps protein production was up-regulated at the transcriptional level and that 2 catalases/peroxidases were present at lower level in VBNC cells. Cell aggregation and elevated levels of Dps protein are typical oxidative stress responses. H2O2 levels also increased in VBNC cells, which could result if catalase/peroxidase levels are reduced. Some of phenotypic changes in VBNC cells of R. solanacearum could be an oxidative stress response due to H2O2 accumulation. This report is the first of the distinct phenotypic changes in cells of R. solanacearum in the VBNC state.
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Affiliation(s)
- Hae Young Um
- Department of Medical Bioscience, Dong-A University, Busan 604-714, Korea
| | - Hyun Gi Kong
- Department of Applied Biology, Dong-A University, Busan 604-714, Korea
| | - Hyoung Ju Lee
- Department of Applied Biology, Dong-A University, Busan 604-714, Korea
| | - Hye Kyung Choi
- Department of Medical Bioscience, Dong-A University, Busan 604-714, Korea
| | - Eun Jin Park
- Department of Applied Biology, Dong-A University, Busan 604-714, Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 627-706, Korea
| | | | - Eunsook Chung
- Department of Medical Bioscience, Dong-A University, Busan 604-714, Korea
| | - Kyu Young Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Korea
| | - Seon-Woo Lee
- Department of Medical Bioscience, Dong-A University, Busan 604-714, Korea
- Department of Applied Biology, Dong-A University, Busan 604-714, Korea
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18
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Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 2013; 50:488-503. [PMID: 23706818 DOI: 10.1016/j.molcel.2013.05.001] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/11/2013] [Accepted: 04/29/2013] [Indexed: 12/26/2022]
Abstract
CRISPR interference confers adaptive, sequence-based immunity against viruses and plasmids and is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from spacer-repeat units. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here, our studies of crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp. reveal a unique crRNA maturation pathway in which crRNAs are transcribed from promoters that are embedded within each repeat, yielding crRNA 5' ends formed by transcription and not by processing. Although crRNA 3' end formation involves RNase III and trans-encoded tracrRNA, as in other type II CRISPR systems, this processing is dispensable for interference. The meningococcal pathway is the most streamlined CRISPR/Cas system characterized to date. Endogenous CRISPR spacers limit natural transformation, which is the primary source of genetic variation that contributes to immune evasion, antibiotic resistance, and virulence in the human pathogen N. meningitidis.
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19
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Abstract
Several species of haloarchaea have been shown to be polyploid and thus this trait might be typical for and widespread in haloarchaea. In the present paper, nine different possible evolutionary advantages of polyploidy for haloarchaea are discussed, including low mutation rate, radiation/desiccation resistance, gene redundancy and survival over geological times and at extraterrestrial sites. Experimental indications exist for all but one of these evolutionary advantages. Several of the advantages require gene conversion, which has been shown to be present and active in haloarchaea.
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20
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Abstract
Large cell size is not restricted to a particular bacterial lifestyle, dispersal method, or cell envelope type. What is conserved among the very large bacteria are the quantity and arrangement of their genomic resources. All large bacteria described to date appear to be highly polyploid. This review focuses on Epulopiscium sp. type B, which maintains tens of thousands of genome copies throughout its life cycle. Only a tiny proportion of mother cell DNA is inherited by intracellular offspring, but surprisingly DNA replication takes place in the terminally differentiated mother cell as offspring grow. Massive polyploidy supports the acquisition of unstable genetic elements normally not seen in essential genes. Further studies of how large bacteria manage their genomic resources will provide insight into how simple cellular modifications can support unusual lifestyles and exceptional cell forms.
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Affiliation(s)
- Esther R Angert
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA.
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21
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John CM, Liu M, Phillips NJ, Yang Z, Funk CR, Zimmerman LI, Griffiss JM, Stein DC, Jarvis GA. Lack of lipid A pyrophosphorylation and functional lptA reduces inflammation by Neisseria commensals. Infect Immun 2012; 80:4014-26. [PMID: 22949553 PMCID: PMC3486066 DOI: 10.1128/iai.00506-12] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/29/2012] [Indexed: 11/20/2022] Open
Abstract
The interaction of the immune system with Neisseria commensals remains poorly understood. We have previously shown that phosphoethanolamine on the lipid A portion of lipooligosaccharide (LOS) plays an important role in Toll-like receptor 4 (TLR4) signaling. For pathogenic Neisseria, phosphoethanolamine is added to lipid A by the phosphoethanolamine transferase specific for lipid A, which is encoded by lptA. Here, we report that Southern hybridizations and bioinformatics analyses of genomic sequences from all eight commensal Neisseria species confirmed that lptA was absent in 15 of 17 strains examined but was present in N. lactamica. Mass spectrometry of lipid A and intact LOS revealed the lack of both pyrophosphorylation and phosphoethanolaminylation in lipid A of commensal species lacking lptA. Inflammatory signaling in human THP-1 monocytic cells was much greater with pathogenic than with commensal Neisseria strains that lacked lptA, and greater sensitivity to polymyxin B was consistent with the absence of phosphoethanolamine. Unlike the other commensals, whole bacteria of two N. lactamica commensal strains had low inflammatory potential, whereas their lipid A had high-level pyrophosphorylation and phosphoethanolaminylation and induced high-level inflammatory signaling, supporting previous studies indicating that this species uses mechanisms other than altering lipid A to support commensalism. A meningococcal lptA deletion mutant had reduced inflammatory potential, further illustrating the importance of lipid A pyrophosphorylation and phosphoethanolaminylation in the bioactivity of LOS. Overall, our results indicate that lack of pyrophosphorylation and phosphoethanolaminylation of lipid A contributes to the immune privilege of most commensal Neisseria strains by reducing the inflammatory potential of LOS.
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Affiliation(s)
- Constance M. John
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
| | - Mingfeng Liu
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Laboratory Medicine
| | - Nancy J. Phillips
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, USA
| | - Zhijie Yang
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
| | - Courtney R. Funk
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
| | - Lindsey I. Zimmerman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - J. McLeod Griffiss
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Laboratory Medicine
| | - Daniel C. Stein
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Gary A. Jarvis
- Center for Immunochemistry, Veterans Affairs Medical Center, San Francisco, California, USA
- Department of Laboratory Medicine
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22
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Vink C, Rudenko G, Seifert HS. Microbial antigenic variation mediated by homologous DNA recombination. FEMS Microbiol Rev 2012; 36:917-948. [PMID: 22212019 PMCID: PMC3334452 DOI: 10.1111/j.1574-6976.2011.00321.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/12/2011] [Accepted: 12/13/2011] [Indexed: 11/27/2022] Open
Abstract
Pathogenic microorganisms employ numerous molecular strategies in order to delay or circumvent recognition by the immune system of their host. One of the most widely used strategies of immune evasion is antigenic variation, in which immunogenic molecules expressed on the surface of a microorganism are continuously modified. As a consequence, the host is forced to constantly adapt its humoral immune response against this pathogen. An antigenic change thus provides the microorganism with an opportunity to persist and/or replicate within the host (population) for an extended period of time or to effectively infect a previously infected host. In most cases, antigenic variation is caused by genetic processes that lead to the modification of the amino acid sequence of a particular antigen or to alterations in the expression of biosynthesis genes that induce changes in the expression of a variant antigen. Here, we will review antigenic variation systems that rely on homologous DNA recombination and that are found in a wide range of cellular, human pathogens, including bacteria (such as Neisseria spp., Borrelia spp., Treponema pallidum, and Mycoplasma spp.), fungi (such as Pneumocystis carinii) and parasites (such as the African trypanosome Trypanosoma brucei). Specifically, the various DNA recombination-based antigenic variation systems will be discussed with a focus on the employed mechanisms of recombination, the DNA substrates, and the enzymatic machinery involved.
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Affiliation(s)
- Cornelis Vink
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Gloria Rudenko
- Division of Cell and Molecular Biology, Imperial College-South Kensington, London, UK
| | - H. Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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23
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Analysis of IS1236-mediated gene amplification events in Acinetobacter baylyi ADP1. J Bacteriol 2012; 194:4395-405. [PMID: 22707704 DOI: 10.1128/jb.00783-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recombination between insertion sequence copies can cause genetic deletion, inversion, or duplication. However, it is difficult to assess the fraction of all genomic rearrangements that involve insertion sequences. In previous gene duplication and amplification studies of Acinetobacter baylyi ADP1, an insertion sequence was evident in approximately 2% of the characterized duplication sites. Gene amplification occurs frequently in all organisms and has a significant impact on evolution, adaptation, drug resistance, cancer, and various disorders. To understand the molecular details of this important process, a previously developed system was used to analyze gene amplification in selected mutants. The current study focused on amplification events in two chromosomal regions that are near one of six copies of the only transposable element in ADP1, IS1236 (an IS3 family member). Twenty-one independent mutants were analyzed, and in contrast to previous studies of a different chromosomal region, IS1236 was involved in 86% of these events. IS1236-mediated amplification could occur through homologous recombination between insertion sequences on both sides of a duplicated region. However, this mechanism presupposes that transposition generates an appropriately positioned additional copy of IS1236. To evaluate this possibility, PCR and Southern hybridization were used to determine the chromosomal configurations of amplification mutants involving IS1236. Surprisingly, the genomic patterns were inconsistent with the hypothesis that intramolecular homologous recombination occurred between insertion sequences following an initial transposition event. These results raise a novel possibility that the gene amplification events near the IS1236 elements arise from illegitimate recombination involving transposase-mediated DNA cleavage.
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24
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Abstract
The human-restricted pathogens Neisseria meningitidis and Neisseria gonorrhoeae are naturally competent for DNA uptake. This trait has been exploited extensively for genetic manipulation of these bacteria in the laboratory. Most transformation protocols were developed for N. gonorrhoeae, but appear to work also for N. meningitidis. In this chapter, we describe a number of protocols for genetic manipulation of N. meningitidis. Specifically, we describe how to (1) obtain knock-out mutants containing antibiotic-resistance markers, (2) generate markerless knock-out mutants, and (3) construct complementation strains. The generation of such mutants provides a valuable resource for studies of bacterial pathogenesis and vaccine development.
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25
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Cahoon LA, Seifert HS. Focusing homologous recombination: pilin antigenic variation in the pathogenic Neisseria. Mol Microbiol 2011; 81:1136-43. [PMID: 21812841 DOI: 10.1111/j.1365-2958.2011.07773.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Some pathogenic microbes utilize homologous recombination to generate antigenic variability in targets of immune surveillance. These specialized systems rely on the cellular recombination machinery to catalyse dedicated, high-frequency reactions that provide extensive diversity in the genes encoding surface antigens. A description of the specific mechanisms that allow unusually high rates of recombination without deleterious effects on the genome in the well-characterized pilin antigenic variation systems of Neisseria gonorrhoeae and Neisseria meningitidis is presented. We will also draw parallels to selected bacterial and eukaryotic antigenic variation systems, and suggest the most pressing unanswered questions related to understanding these important processes.
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Affiliation(s)
- Laty A Cahoon
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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26
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Ayora S, Carrasco B, Cárdenas PP, César CE, Cañas C, Yadav T, Marchisone C, Alonso JC. Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev 2011; 35:1055-81. [PMID: 21517913 DOI: 10.1111/j.1574-6976.2011.00272.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In all living organisms, the response to double-strand breaks (DSBs) is critical for the maintenance of chromosome integrity. Homologous recombination (HR), which utilizes a homologous template to prime DNA synthesis and to restore genetic information lost at the DNA break site, is a complex multistep response. In Bacillus subtilis, this response can be subdivided into five general acts: (1) recognition of the break site(s) and formation of a repair center (RC), which enables cells to commit to HR; (2) end-processing of the broken end(s) by different avenues to generate a 3'-tailed duplex and RecN-mediated DSB 'coordination'; (3) loading of RecA onto single-strand DNA at the RecN-induced RC and concomitant DNA strand exchange; (4) branch migration and resolution, or dissolution, of the recombination intermediates, and replication restart, followed by (5) disassembly of the recombination apparatus formed at the dynamic RC and segregation of sister chromosomes. When HR is impaired or an intact homologous template is not available, error-prone nonhomologous end-joining directly rejoins the two broken ends by ligation. In this review, we examine the functions that are known to contribute to DNA DSB repair in B. subtilis, and compare their properties with those of other bacterial phyla.
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Affiliation(s)
- Silvia Ayora
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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Pecoraro V, Zerulla K, Lange C, Soppa J. Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-)oligoploid and polyploid species. PLoS One 2011; 6:e16392. [PMID: 21305010 PMCID: PMC3031548 DOI: 10.1371/journal.pone.0016392] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 12/14/2010] [Indexed: 11/20/2022] Open
Abstract
Bacteria are generally assumed to be monoploid (haploid). This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, Escherichia coli (a gamma-proteobacterium), which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes) and fast-growing (doubling time 25 minutes) E. coli cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of Caulobacter crescentus (an alpha-proteobacterium) and Wolinella succinogenes (an epsilon-proteobacterium), both of which are monoploid. In contrast, Pseudomonas putida (a gamma-proteobacterium) contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life.
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Affiliation(s)
- Vito Pecoraro
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
| | - Karolin Zerulla
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
| | - Christian Lange
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe-University, Frankfurt, Germany
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Kumar P, Sannigrahi S, Scoullar J, Kahler CM, Tzeng YL. Characterization of DsbD in Neisseria meningitidis. Mol Microbiol 2011; 79:1557-73. [PMID: 21219471 DOI: 10.1111/j.1365-2958.2011.07546.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proper periplasmic disulfide bond formation is important for folding and stability of many secreted and membrane proteins, and is catalysed by three DsbA oxidoreductases in Neisseria meningitidis. DsbD provides reducing power to DsbC that shuffles incorrect disulfide bond in misfolded proteins as well as to the periplasmic enzymes that reduce apo-cytochrome c (CcsX) or repair oxidative protein damages (MrsAB). The expression of dsbD, but not other dsb genes, is positively regulated by the MisR/S two-component system. Quantitative real-time PCR analyses showed significantly reduced dsbD expression in all misR/S mutants, which was rescued by genetic complementation. The direct and specific interaction of MisR with the upstream region of the dsbD promoter was demonstrated by electrophoretic mobility shift assay, and the MisR binding sequences were mapped. Further, the expression of dsbD was found to be induced by dithiothrietol (DTT), through the MisR/S regulatory system. Surprisingly, we revealed that inactivation of dsbD can only be achieved in a strain carrying an ectopically located dsbD, in the dsbA1A2 double mutant or in the dsbA1A2A3 triple mutant, thus DsbD is indispensable for DsbA-catalysed oxidative protein folding in N. meningitidis. The defects of the meningococcal dsbA1A2 mutant in transformation and resistance to oxidative stress were more severe in the absence of dsbD.
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Affiliation(s)
- Pradeep Kumar
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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