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Avershina E, Frye SA, Ali J, Taxt AM, Ahmad R. Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Front Microbiol 2022; 13:822402. [PMID: 35369431 PMCID: PMC8970966 DOI: 10.3389/fmicb.2022.822402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Stephan A Frye
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Arne M Taxt
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
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Avershina E, Sharma P, Taxt AM, Singh H, Frye SA, Paul K, Kapil A, Naseer U, Kaur P, Ahmad R. AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae. Comput Struct Biotechnol J 2021; 19:1896-1906. [PMID: 33897984 PMCID: PMC8060595 DOI: 10.1016/j.csbj.2021.03.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours. In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network. Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1–8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Arne M Taxt
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Harpreet Singh
- Informatics, System and Research Management, Indian Council of Medical Research, New Delhi, India
| | - Stephan A Frye
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Kolin Paul
- Department of Computer Science & Engineering, IIT Delhi, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Umaer Naseer
- Department of Zoonotic, Food- and Waterborne Infections, 0213 Oslo, Norwegian Institute of Public Health, Oslo, Norway
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Institute of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Frye SA, Beyene GT, Namouchi A, Gómez-Muñoz M, Homberset H, Kalayou S, Riaz T, Tønjum T, Balasingham SV. The helicase DinG responds to stress due to DNA double strand breaks. PLoS One 2017; 12:e0187900. [PMID: 29121674 PMCID: PMC5679670 DOI: 10.1371/journal.pone.0187900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative nasopharyngeal commensal that can cause septicaemia and meningitis. The neisserial DNA damage-inducible protein DinG is a helicase related to the mammalian helicases XPD and FANCJ. These helicases belong to superfamily 2, are ATP dependent and exert 5′ → 3′ directionality. To better understand the role of DinG in neisserial genome maintenance, the Nm DinG (DinGNm) enzymatic activities were assessed in vitro and phenotypical characterization of a dinG null mutant (NmΔdinG) was performed. Like its homologues, DinGNm possesses 5′ → 3′ directionality and prefers DNA substrates containing a 5′-overhang. ATPase activity of DinGNm is strictly DNA-dependent and DNA unwinding activity requires nucleoside triphosphate and divalent metal cations. DinGNm directly binds SSBNm with a Kd of 313 nM. Genotoxic stress analysis demonstrated that NmΔdinG was more sensitive to double-strand DNA breaks (DSB) induced by mitomycin C (MMC) than the Nm wildtype, defining the role of neisserial DinG in DSB repair. Notably, when NmΔdinG cells grown under MMC stress assessed by quantitative mass spectrometry, 134 proteins were shown to be differentially abundant (DA) compared to unstressed NmΔdinG cells. Among the DNA replication, repair and recombination proteins affected, polymerase III subunits and recombinational repair proteins RuvA, RuvB, RecB and RecD were significantly down regulated while TopA and SSB were upregulated under stress condition. Most of the other DA proteins detected are involved in metabolic functions. The present study shows that the helicase DinG is probably involved in regulating metabolic pathways as well as in genome maintenance.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
| | | | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | - Shewit Kalayou
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V. Balasingham
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- * E-mail: (SVB); (SAF)
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Hovland E, Beyene GT, Frye SA, Homberset H, Balasingham SV, Gómez-Muñoz M, Derrick JP, Tønjum T, Ambur OH. DprA from Neisseria meningitidis: properties and role in natural competence for transformation. Microbiology (Reading) 2017; 163:1016-1029. [PMID: 28696187 PMCID: PMC5817196 DOI: 10.1099/mic.0.000489] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
DNA processing chain A (DprA) is a DNA-binding protein that is ubiquitous in bacteria and expressed in some archaea. DprA is active in many bacterial species that are competent for transformation of DNA, but its role in Neisseriameningitidis (Nm) is not well characterized. An Nm mutant lacking DprA was constructed, and the phenotypes of the wild-type and ΔdprA mutant were compared. The salient feature of the phenotype of dprA null cells is the total lack of competence for genetic transformation shown by all of the donor DNA substrates tested in this study. Here, Nm wild-type and dprA null cells appeared to be equally resistant to genotoxic stress. The gene encoding DprANm was cloned and overexpressed, and the biological activities of DprANm were further investigated. DprANm binds ssDNA more strongly than dsDNA, but lacks DNA uptake sequence-specific DNA binding. DprANm dimerization and interaction with the C-terminal part of the single-stranded binding protein SSBNmwere demonstrated. dprA is co-expressed with smg, a downstream gene of unknown function, and the gene encoding topoisomerase 1, topA.
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Affiliation(s)
- Eirik Hovland
- Department of Microbiology, University of Oslo, Oslo, Norway.,Present address: Lovisenberg Diaconal Hospital, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Jeremy P Derrick
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, UK
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ole H Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Present address: Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, Norway
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Beyene GT, Balasingham SV, Frye SA, Namouchi A, Homberset H, Kalayou S, Riaz T, Tønjum T. Characterization of the Neisseria meningitidis Helicase RecG. PLoS One 2016; 11:e0164588. [PMID: 27736945 PMCID: PMC5063381 DOI: 10.1371/journal.pone.0164588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.
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Affiliation(s)
| | | | - Stephan A. Frye
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | | | - Shewit Kalayou
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- * E-mail:
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7
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Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, Balasingham SV. The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics 2016; 17:791. [PMID: 27724857 PMCID: PMC5057432 DOI: 10.1186/s12864-016-3132-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. Results The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. Conclusions Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3132-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | - Line Victoria Moen
- Department of Informatics, University of Oslo, Oslo, Norway.,Current address: Department of Nutrition, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.
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Frye SA, Lång E, Beyene GT, Balasingham SV, Homberset H, Rowe AD, Ambur OH, Tønjum T. The Inner Membrane Protein PilG Interacts with DNA and the Secretin PilQ in Transformation. PLoS One 2015; 10:e0134954. [PMID: 26248334 PMCID: PMC4527729 DOI: 10.1371/journal.pone.0134954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/15/2015] [Indexed: 11/19/2022] Open
Abstract
Expression of type IV pili (Tfp), filamentous appendages emanating from the bacterial surface, is indispensable for efficient neisserial transformation. Tfp pass through the secretin pore consisting of the membrane protein PilQ. PilG is a polytopic membrane protein, conserved in Gram-positive and Gram-negative bacteria, that is required for the biogenesis of neisserial Tfp. PilG null mutants are devoid of pili and non-competent for transformation. Here, recombinant full-length, truncated and mutated variants of meningococcal PilG were overexpressed, purified and characterized. We report that meningococcal PilG directly binds DNA in vitro, detected by both an electromobility shift analysis and a solid phase overlay assay. PilG DNA binding activity was independent of the presence of the consensus DNA uptake sequence. PilG-mediated DNA binding affinity was mapped to the N-terminus and was inactivated by mutation of residues 43 to 45. Notably, reduced meningococcal transformation of DNA in vivo was observed when PilG residues 43 to 45 were substituted by alanine in situ, defining a biologically significant DNA binding domain. N-terminal PilG also interacted with the N-terminal region of PilQ, which previously was shown to bind DNA. Collectively, these data suggest that PilG and PilQ in concert bind DNA during Tfp-mediated transformation.
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Affiliation(s)
- Stephan A. Frye
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | | | - Ole Herman Ambur
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Department of Microbiology, University of Oslo, Oslo, Norway
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Ricanek P, Lunde LK, Frye SA, Støen M, Nygård S, Morth JP, Rydning A, Vatn MH, Amiry-Moghaddam M, Tønjum T. Reduced expression of aquaporins in human intestinal mucosa in early stage inflammatory bowel disease. Clin Exp Gastroenterol 2015; 8:49-67. [PMID: 25624769 PMCID: PMC4296881 DOI: 10.2147/ceg.s70119] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Objectives The aim of this study was to investigate the relationship between aquaporin (AQP) water channel expression and the pathological features of early untreated inflammatory bowel disease (IBD) in humans. Methods Patients suspected to have IBD on the basis of predefined symptoms, including abdominal pain, diarrhea, and/or blood in stool for more than 10 days, were examined at the local hospital. Colonoscopy with biopsies was performed and blood samples were taken. Patients who did not meet the diagnostic criteria for IBD and who displayed no evidence of infection or other pathology in the gut were included as symptomatic non-IBD controls. AQP1, 3, 4, 5, 7, 8, and 9 messenger RNA (mRNA) levels were quantified in biopsies from the distal ileum and colon by quantitative real-time polymerase chain reaction. Protein expression of selected AQPs was assessed by confocal microscopy. Through multiple alignments of the deduced amino acid sequences, the putative three-dimensional structures of AQP1, 3, 7, and 8 were modeled. Results AQP1, 3, 7, and 8 mRNAs were detected in all parts of the intestinal mucosa. Notably, AQP1 and AQP3 mRNA levels were reduced in the ileum of patients with Crohn’s disease, and AQP7 and AQP8 mRNA levels were reduced in the ileum and the colon of patients with ulcerative colitis. Immunofluorescence confocal microscopy showed localization of AQP3, 7, and 8 at the mucosal epithelium, whereas the expression of AQP1 was mainly confined to the endothelial cells and erythrocytes. The reduction in the level of AQP3, 7, and 8 mRNA was confirmed by immunofluorescence, which also indicated a reduction of apical immunolabeling for AQP8 in the colonic surface epithelium and crypts of the IBD samples. This could indicate loss of epithelial polarity in IBD, leading to disrupted barrier function. Conclusion AQPs 1 and 8 and the aquaglyceroporins AQPs 3 and 7 are the AQPs predominantly expressed in the lower intestinal tract of humans. Their expression is significantly reduced in patients with IBD, and they are differentially expressed in specific bowel segments in patients with Crohn’s disease and ulcerative colitis. The data present a link between gut inflammation and water/solute homeostasis, suggesting that AQPs may play a significant role in IBD pathophysiology.
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Affiliation(s)
- Petr Ricanek
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway ; Department of Gastroenterology, Akershus University Hospital, Lørenskog and Campus Ahus, Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway
| | - Lisa K Lunde
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Mari Støen
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ståle Nygård
- Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital and University of Oslo, Norway
| | - Jens P Morth
- Centre for Molecular Medicine, Nordic EMBL Partnership, University of Oslo, Norway ; Institute for Experimental Research, Oslo University Hospital (Ullevaal), Oslo, Norway
| | - Andreas Rydning
- Department of Gastroenterology, Akershus University Hospital, Lørenskog and Campus Ahus, Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway
| | - Morten H Vatn
- EpiGen Institute, Campus Ahus, Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway ; Section of Gastroenterology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | | | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway ; Department of Microbiology, University of Oslo, Oslo, Norway
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Ricanek P, Lothe SM, Frye SA, Rydning A, Vatn MH, Tønjum T. Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease. Clin Exp Gastroenterol 2012; 5:173-86. [PMID: 23049264 PMCID: PMC3459595 DOI: 10.2147/ceg.s33858] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Indexed: 12/22/2022] Open
Abstract
Objectives: The aim of this study was to define the composition of the gut bacterial flora in Norwegian patients with early stage Crohn’s disease (CD). Methods: By using a nonselective metagenomics approach, the general bacterial composition in mucosal biopsies from the ileum and the colon of five subjects, four patients with different phenotypes of CD, and one noninflammatory bowel disease control, was characterized. After partial 16S ribosomal RNA (rRNA) gene sequencing, BLAST homology searches for species identification and phylogenetic analysis were performed. Results: An overall biodiversity of 106 different bacterial operational taxonomic units (OTUs) was detected in the cloned libraries. Nearly all OTUs belonged to the phylae Bacteroidetes (42% in CD, 71% in the control) or Firmicutes (42% in CD, 28% in the control), except for some OTUs that belonged to the phylum Proteobacteria (15% in CD, 0% in the control) and a few OTUs that could not be assigned to a phylum (2% in CD, 1% in the control). Conclusion: Based on the high incidence of inflammatory bowel disease (IBD) in Norway, this pilot study represents a relevant determination of the gut microbiota in Norwegian patients compared to previous findings in other countries. The bacterial profile of Norwegian CD patients was found to be similar to that of CD patients in other countries. The findings do not support a particular bacterial composition as a predominant causative factor for the high incidence of IBD that exists in some countries.
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Affiliation(s)
- Petr Ricanek
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo ; Department of Gastroenterology, Akershus University Hospital, Lørenskog and Faculty Division Akershus University Hospital, University of Oslo, Lørenskog
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Ambur OH, Frye SA, Nilsen M, Hovland E, Tønjum T. Restriction and sequence alterations affect DNA uptake sequence-dependent transformation in Neisseria meningitidis. PLoS One 2012; 7:e39742. [PMID: 22768309 PMCID: PMC3388099 DOI: 10.1371/journal.pone.0039742] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/26/2012] [Indexed: 12/17/2022] Open
Abstract
Transformation is a complex process that involves several interactions from the binding and uptake of naked DNA to homologous recombination. Some actions affect transformation favourably whereas others act to limit it. Here, meticulous manipulation of a single type of transforming DNA allowed for quantifying the impact of three different mediators of meningococcal transformation: NlaIV restriction, homologous recombination and the DNA Uptake Sequence (DUS). In the wildtype, an inverse relationship between the transformation frequency and the number of NlaIV restriction sites in DNA was observed when the transforming DNA harboured a heterologous region for selection (ermC) but not when the transforming DNA was homologous with only a single nucleotide heterology. The influence of homologous sequence in transforming DNA was further studied using plasmids with a small interruption or larger deletions in the recombinogenic region and these alterations were found to impair transformation frequency. In contrast, a particularly potent positive driver of DNA uptake in Neisseria sp. are short DUS in the transforming DNA. However, the molecular mechanism(s) responsible for DUS specificity remains unknown. Increasing the number of DUS in the transforming DNA was here shown to exert a positive effect on transformation. Furthermore, an influence of variable placement of DUS relative to the homologous region in the donor DNA was documented for the first time. No effect of altering the orientation of DUS was observed. These observations suggest that DUS is important at an early stage in the recognition of DNA, but does not exclude the existence of more than one level of DUS specificity in the sequence of events that constitute transformation. New knowledge on the positive and negative drivers of transformation may in a larger perspective illuminate both the mechanisms and the evolutionary role(s) of one of the most conserved mechanisms in nature: homologous recombination.
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Lillenes MS, Espeseth T, Støen M, Lundervold AJ, Frye SA, Rootwelt H, Reinvang I, Tønjum T. DNA base excision repair gene polymorphisms modulate human cognitive performance and decline during normal life span. Mech Ageing Dev 2011; 132:449-58. [DOI: 10.1016/j.mad.2011.08.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 06/25/2011] [Accepted: 08/14/2011] [Indexed: 10/17/2022]
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Benam AV, Lång E, Alfsnes K, Fleckenstein B, Rowe AD, Hovland E, Ambur OH, Frye SA, Tønjum T. Structure-function relationships of the competence lipoprotein ComL and SSB in meningococcal transformation. Microbiology (Reading) 2011; 157:1329-1342. [PMID: 21330432 PMCID: PMC3140584 DOI: 10.1099/mic.0.046896-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neisseria meningitidis, the meningococcus, is naturally competent for transformation throughout its growth cycle. The uptake of exogenous DNA into the meningococcus cell during transformation is a multi-step process. Beyond the requirement for type IV pilus expression for efficient transformation, little is known about the neisserial proteins involved in DNA binding, uptake and genome integration. This study aimed to identify and characterize neisserial DNA binding proteins in order to further elucidate the multi-factorial transformation machinery. The meningococcus inner membrane and soluble cell fractions were searched for DNA binding components by employing 1D and 2D gel electrophoresis approaches in combination with a solid-phase overlay assay with DNA substrates. Proteins that bound DNA were identified by MS analysis. In the membrane fraction, multiple components bound DNA, including the neisserial competence lipoprotein ComL. In the soluble fraction, the meningococcus orthologue of the single-stranded DNA binding protein SSB was predominant. The DNA binding activity of the recombinant ComL and SSB proteins purified to homogeneity was verified by electromobility shift assay, and the ComL-DNA interaction was shown to be Mg²+-dependent. In 3D models of the meningococcus ComL and SSB predicted structures, potential DNA binding sites were suggested. ComL was found to co-purify with the outer membrane, directly interacting with the secretin PilQ. The combined use of 1D/2D solid-phase overlay assays with MS analysis was a useful strategy for identifying DNA binding components. The ComL DNA binding properties and outer membrane localization suggest that this lipoprotein plays a direct role in neisserial transformation, while neisserial SSB is a DNA binding protein that contributes to the terminal part of the transformation process.
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Affiliation(s)
- Afsaneh V Benam
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Emma Lång
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Kristian Alfsnes
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Burkhard Fleckenstein
- Centre for Immune Regulation, Institute of Immunology, University of Oslo, NO-0027 Oslo, Norway
| | - Alexander D Rowe
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
| | - Eirik Hovland
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Stephan A Frye
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Oslo University Hospital (Rikshospitalet), NO-0027 Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, NO-0027 Oslo, Norway
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15
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Abstract
Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content encoding proteins provides clues toward understanding the microbial lifestyle related to habitat and niche. Campylobacter jejuni, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, the pathogenic Neisseria, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus are major human pathogens causing detrimental morbidity and mortality at a global scale. An algorithm for the clustering of orthologs was established in order to identify whether orthologs of selected genes were present or absent in the genomes of the pathogenic bacteria under study. Based on the known genes for the various functions and their orthologs in selected pathogenic bacteria, an overview of the presence of the different types of genes was created. In this context, we focus on selected processes enabling genome dynamics in these particular pathogens, namely DNA repair, recombination and horizontal gene transfer. An understanding of the precise molecular functions of the enzymes participating in DNA metabolism and their importance in the maintenance of bacterial genome integrity has also, in recent years, indicated a future role for these enzymes as targets for therapeutic intervention.
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Affiliation(s)
- Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, Oslo University Hospital, Norway
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16
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Lång E, Haugen K, Fleckenstein B, Homberset H, Frye SA, Ambur OH, Tønjum T. Identification of neisserial DNA binding components. Microbiology (Reading) 2009; 155:852-862. [PMID: 19246756 PMCID: PMC2885667 DOI: 10.1099/mic.0.022640-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type IV pili, a feature correlating with the uptake of exogenous DNA from the environment by natural transformation. The outer membrane complex PilQ, through which pili are extruded and retracted, has previously been shown to bind DNA in its pore region. In order to further elucidate how DNA is transported across the membranes, we searched for DNA binding proteins within the meningococcal inner membrane. Inner membrane fractions from a panel of neisserial strains were subjected to a solid-phase overlay assay with DNA substrates, and MS was subsequently employed to identify proteins that bind DNA. A number of DNA binding components were detected, including the pilus biogenesis component PilG, the competence protein ComL, and the cell division ATP-binding protein FtsE, as well as two hypothetical proteins. The DNA binding activity of these components was not dependent on the presence of the neisserial DNA uptake sequence. Null mutants, corresponding to each of the proteins identified, were constructed to assess their phenotypes. Only mutants defective in pilus biogenesis were non-competent and non-piliated. The DNA binding activity of the pilus biogenesis components PilQ and PilG and the phenotypes of their respective null mutants suggest that these proteins are directly involved as players in natural transformation, and not only indirectly, through pilus biogenesis.
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Affiliation(s)
- Emma Lång
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Kristine Haugen
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway
| | | | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Stephan A Frye
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
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17
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Tibballs KL, Ambur OH, Alfsnes K, Homberset H, Frye SA, Davidsen T, Tønjum T. Characterization of the meningococcal DNA glycosylase Fpg involved in base excision repair. BMC Microbiol 2009; 9:7. [PMID: 19134198 PMCID: PMC2628661 DOI: 10.1186/1471-2180-9-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 01/09/2009] [Indexed: 11/10/2022] Open
Abstract
Background Neisseria meningitidis, the causative agent of meningococcal disease, is exposed to high levels of reactive oxygen species inside its exclusive human host. The DNA glycosylase Fpg of the base excision repair pathway (BER) is a central player in the correction of oxidative DNA damage. This study aimed at characterizing the meningococcal Fpg and its role in DNA repair. Results The deduced N. meningitidis Fpg amino acid sequence was highly homologous to other Fpg orthologues, with particularly high conservation of functional domains. As for most N. meningitidis DNA repair genes, the fpg gene contained a DNA uptake sequence mediating efficient transformation of DNA. The recombinant N. meningitidis Fpg protein was over-expressed, purified to homogeneity and assessed for enzymatic activity. N. meningitidis Fpg was found to remove 2,6-diamino-4-hydroxy-5-formamidopyrimidine (faPy) lesions and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8oxoG) opposite of C, T and G and to a lesser extent opposite of A. Moreover, the N. meningitidis fpg single mutant was only slightly affected in terms of an increase in the frequency of phase variation as compared to a mismatch repair mutant. Conclusion Collectively, these findings show that meningococcal Fpg functions are similar to those of prototype Fpg orthologues in other bacterial species.
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Affiliation(s)
- Katrina L Tibballs
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Rikshospitalet, NO-0027 Oslo, Norway.
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18
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Assalkhou R, Balasingham S, Collins RF, Frye SA, Davidsen T, Benam AV, Bjørås M, Derrick JP, Tønjum T. The outer membrane secretin PilQ from Neisseria meningitidis binds DNA. Microbiology (Reading) 2007; 153:1593-1603. [PMID: 17464074 PMCID: PMC2884949 DOI: 10.1099/mic.0.2006/004200-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria meningitidis is naturally competent for transformation throughout its growth cycle. Transformation in neisserial species is coupled to the expression of type IV pili, which are present on the cell surface as bundled filamentous appendages, and are assembled, extruded and retracted by the pilus biogenesis components. During the initial phase of the transformation process, binding and uptake of DNA takes place with entry through a presumed outer-membrane channel into the periplasm. This study showed that DNA associates only weakly with purified pili, but binds significantly to the PilQ complex isolated directly from meningococcal membranes. By assessing the DNA-binding activity of the native complex PilQ, as well as recombinant truncated PilQ monomers, it was shown that the N-terminal region of PilQ is involved in the interaction with DNA. It was evident that the binding of ssDNA to PilQ had a higher affinity than the binding of dsDNA. The binding of DNA to PilQ did not, however, depend on the presence of the neisserial DNA-uptake sequence. It is suggested that transforming DNA is introduced into the cell through the outer-membrane channel formed by the PilQ complex, and that DNA uptake occurs by non-specific introduction of DNA coupled to pilus retraction, followed by presentation to DNA-binding component(s), including PilQ.
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Affiliation(s)
- Reza Assalkhou
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
| | - Seetha Balasingham
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
| | - Richard F. Collins
- Faculty of Life Sciences, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
| | - Stephan A. Frye
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
| | - Tonje Davidsen
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
| | - Afsaneh V. Benam
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
| | - Jeremy P. Derrick
- Faculty of Life Sciences, The University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
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19
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Balasingham SV, Collins RF, Assalkhou R, Homberset H, Frye SA, Derrick JP, Tønjum T. Interactions between the lipoprotein PilP and the secretin PilQ in Neisseria meningitidis. J Bacteriol 2007; 189:5716-27. [PMID: 17526700 PMCID: PMC1951802 DOI: 10.1128/jb.00060-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Neisseria meningitidis can be the causative agent of meningitis or septicemia. This bacterium expresses type IV pili, which mediate a variety of functions, including autoagglutination, twitching motility, biofilm formation, adherence, and DNA uptake during transformation. The secretin PilQ supports type IV pilus extrusion and retraction, but it also requires auxiliary proteins for its assembly and localization in the outer membrane. Here we have studied the physical properties of the lipoprotein PilP and examined its interaction with PilQ. We found that PilP was an inner membrane protein required for pilus expression and transformation, since pilP mutants were nonpiliated and noncompetent. These mutant phenotypes were restored by the expression of PilP in trans. The pilP gene is located upstream of pilQ, and analysis of their transcripts indicated that pilP and pilQ were cotranscribed. Furthermore, analysis of the level of PilQ expression in pilP mutants revealed greatly reduced amounts of PilQ only in the deletion mutant, exhibiting a polar effect on pilQ transcription. In vitro experiments using recombinant fragments of PilP and PilQ showed that the N-terminal region of PilP interacted with the middle part of the PilQ polypeptide. A three-dimensional reconstruction of the PilQ-PilP interacting complex was obtained at low resolution by transmission electron microscopy, and PilP was shown to localize around the cap region of the PilQ oligomer. These findings suggest a role for PilP in pilus biogenesis. Although PilQ does not need PilP for its stabilization or membrane localization, the specific interaction between these two proteins suggests that they might have another coordinated activity in pilus extrusion/retraction or related functions.
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Affiliation(s)
- Seetha V Balasingham
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, Oslo, Norway
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20
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Frye SA, Assalkhou R, Collins RF, Ford RC, Petersson C, Derrick JP, Tønjum T. Topology of the outer-membrane secretin PilQ from Neisseria meningitidis. Microbiology (Reading) 2007; 152:3751-3764. [PMID: 17159226 DOI: 10.1099/mic.0.2006/000315-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria meningitidis is the causative agent of epidemic meningococcal meningitis and septicaemia. Type IV pili are surface organelles that mediate a variety of functions, including adhesion, twitching motility, and competence for DNA binding and uptake in transformation. The secretin PilQ is required for type IV pilus expression at the cell surface, and forms a dodecameric cage-like macromolecular complex in the meningococcal outer membrane. PilQ-null mutants are devoid of surface pili, and prevailing evidence suggests that the PilQ complex facilitates extrusion and retraction of type IV pili across the outer membrane. Defining the orientation of the meningococcal PilQ complex in the membrane is a prerequisite for understanding the structure-function relationships of this important protein in pilus biology. In order to begin to define the topology of the PilQ complex in the outer membrane, polyhistidine insertions in N- and C-terminal regions of PilQ were constructed, and their subcellular locations examined. Notably, the insertion epitopes at residues 205 and 678 were located within the periplasm, whereas residue 656 was exposed at the outer surface of the outer membrane. Using electron microscopy with Ni-NTA gold labelling, it was demonstrated that the insertion at residue 205 within the N-terminus mapped to a site on the arm-like features of the 3D structure of the PilQ multimer. Interestingly, mutation of the same region gave rise to an increase in vancomycin permeability through the PilQ complex. The results yield novel information on the PilQ N-terminal location and function in the periplasm, and reveal a complex organization of the membrane-spanning secretin in vivo.
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Affiliation(s)
- Stephan A Frye
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Norway
| | - Reza Assalkhou
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Norway
| | - Richard F Collins
- Faculty of Life Sciences, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK
| | - Robert C Ford
- Faculty of Life Sciences, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK
| | - Christoffer Petersson
- Division of Medical Microbiology, Department of Molecular and Clinical Medicine, Faculty of Health Sciences, Linköping University, Sweden
| | - Jeremy P Derrick
- Faculty of Life Sciences, The University of Manchester, Sackville Street, PO Box 88, Manchester M60 1QD, UK
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, Norway
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Norway
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21
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Ambur OH, Frye SA, Tønjum T. New functional identity for the DNA uptake sequence in transformation and its presence in transcriptional terminators. J Bacteriol 2006; 189:2077-85. [PMID: 17194793 PMCID: PMC1855724 DOI: 10.1128/jb.01408-06] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The frequently occurring DNA uptake sequence (DUS), recognized as a 10-bp repeat, is required for efficient genetic transformation in the human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Genome scanning for DUS occurrences in three different species of Neisseria demonstrated that 76% of the nearly 2,000 neisserial DUS were found to have two semiconserved base pairs extending from the 5' end of DUS to constitute a 12-mer repeat. Plasmids containing sequential variants of the neisserial DUS were tested for their ability to transform N. meningitidis and N. gonorrhoeae, and the 12-mer was found to outperform the 10-mer DUS in transformation efficiency. Assessment of meningococcal uptake of DNA confirmed the enhanced performance of the 12-mer compared to the 10-mer DUS. An inverted repeat DUS was not more efficient in transformation than DNA species containing a single or direct repeat DUS. Genome-wide analysis revealed that half of the nearly 1,500 12-mer DUS are arranged as inverted repeats predicted to be involved in rho-independent transcriptional termination or attenuation. The distribution of the uptake signal sequence required for transformation in the Pasteurellaceae was also biased towards transcriptional terminators, although to a lesser extent. In addition to assessing the intergenic location of DUS, we propose that the 10-mer identity of DUS should be extended and recognized as a 12-mer DUS. The dual role of DUS in transformation and as a structural component on RNA affecting transcription makes this a relevant model system for assessing significant roles of repeat sequences in biology.
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Affiliation(s)
- O Herman Ambur
- Institute of Microbiology and Centre for Molecular Biology and Neuroscience, University of Oslo, Rikshospitalet-Radiumhospitalet Medical Center, NO-0027 Oslo, Norway
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22
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Collins RF, Frye SA, Balasingham S, Ford RC, Tønjum T, Derrick JP. Interaction with type IV pili induces structural changes in the bacterial outer membrane secretin PilQ. J Biol Chem 2005; 280:18923-30. [PMID: 15753075 DOI: 10.1074/jbc.m411603200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type IV pili are cell surface organelles found on many Gram-negative bacteria. They mediate a variety of functions, including adhesion, twitching motility, and competence for DNA uptake. The type IV pilus is a helical polymer of pilin protein subunits and is capable of rapid polymerization or depolymerization, generating large motor forces in the process. Here we show that a specific interaction between the outer membrane secretin PilQ and the type IV pilus fiber can be detected by far-Western analysis and sucrose density gradient centrifugation. Transmission electron microscopy of preparations of purified pili, to which the purified PilQ oligomer had been added, showed that PilQ was uniquely located at one end of the pilus fiber, effectively forming a "mallet-type" structure. Determination of the three-dimensional structure of the PilQ-type IV pilus complex at 26-angstroms resolution showed that the cavity within the protein complex was filled. Comparison with a previously determined structure of PilQ at 12-angstroms resolution indicated that binding of the pilus fiber induced a dissociation of the "cap" feature and lateral movement of the "arms" of the PilQ oligomer. The results demonstrate that the PilQ structure exhibits a dynamic response to the binding of its transported substrate and suggest that the secretin could play an active role in type IV pilus assembly as well as secretion.
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Affiliation(s)
- Richard F Collins
- Faculty of Life Sciences, The University of Manchester, Faculty of Life Sciences, Sackville Street, P. O. Box 88, Manchester M60 1QD, United Kingdom
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Collins RF, Frye SA, Kitmitto A, Ford RC, Tønjum T, Derrick JP. Structure of the Neisseria meningitidis Outer Membrane PilQ Secretin Complex at 12 Å Resolution. J Biol Chem 2004; 279:39750-6. [PMID: 15254043 DOI: 10.1074/jbc.m405971200] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial pathogen Neisseria meningitidis expresses long, thin, retractile fibers (called type IV pili) from its cell surface and uses these adhesive structures to mediate primary attachment to epithelial cells during host colonization and invasion. PilQ is an outer membrane protein complex that is essential for the translocation of these pili across the outer membrane. Here, we present the structure of the PilQ complex determined by cryoelectron microscopy to 12 A resolution. The dominant feature of the structure is a large central cavity, formed by four arm features that spiral upwards from a squared ring base and meet to form a prominent cap region. The cavity, running through the center of the complex, is continuous and is effectively sealed at both the top and bottom. Analysis of the complex using self-orientation and by examination of two-dimensional crystals indicates a strong C4 rotational symmetry, with a much weaker C12 rotational symmetry, consistent with PilQ possessing true C4 symmetry with C12 quasi-symmetry. We therefore suggest that the complex is a homododecamer, formed by association of 12 PilQ polypeptide chains into a tetramer of trimers. The structure of the PilQ complex, with its large and well defined central chamber, suggests that it may not function solely as a passive portal in the outer membrane, but could be actively involved in mediating pilus assembly or modification.
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Affiliation(s)
- Richard F Collins
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, United Kingdom
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24
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Lenz P, Day PM, Pang YY, Frye SA, Jensen PN, Lowy DR, Schiller JT. Papillomavirus-like particles induce acute activation of dendritic cells. J Immunol 2001; 166:5346-55. [PMID: 11313370 DOI: 10.4049/jimmunol.166.9.5346] [Citation(s) in RCA: 202] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The role of viral structural proteins in the initiation of adaptive immune responses is poorly understood. To address this issue, we focused on the effect of noninfectious papillomavirus-like particles (VLPs) on dendritic cell (DC) activation. We found that murine bone marrow-derived dendritic cells (BMDCs) effectively bound and rapidly internalized bovine papillomavirus VLPS: Exposure to fully assembled VLPs of bovine papillomavirus, human papillomavirus (HPV)16 or HPV18, but not to predominately disordered HPV16 capsomers, induced acute phenotypic maturation of BMDCS: Structurally similar polyomavirus VLPs bound to the DC surface and were internalized, but failed to induce maturation. DCs that had incorporated HPV16 VLPs produced proinflammatory cytokines IL-6 and TNF-alpha; however, the release of these cytokines was delayed relative to LPS activation. Production of IL-12p70 by VLP-exposed DCs required the addition of syngeneic T cells or rIFN-gamma. Finally, BMDCs pulsed with HPV16 VLPs induced Th1-dominated primary T cell responses in vitro. Our data provide evidence that DCs respond to intact papillomavirus capsids and that they play a central role in VLP-induced immunity. These results offer a mechanistic explanation for the striking ability of papillomavirus VLP-based vaccines to induce potent T and B cell responses even in the absence of adjuvant.
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Affiliation(s)
- P Lenz
- Laboratory of Cellular Oncology, National Cancer Institute, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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