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Dennehy R, Duggan N, Dignam S, McCormack S, Dillon E, Molony J, Romano M, Hou Y, Ardill L, Whelan MVX, Drulis‐Kawa Z, Ó'Cróinín T, Valvano MA, Berisio R, McClean S. Protein with negative surface charge distribution, Bnr1, shows characteristics of a DNA-mimic protein and may be involved in the adaptation of Burkholderia cenocepacia. Microbiologyopen 2022; 11:e1264. [PMID: 35212475 PMCID: PMC9060813 DOI: 10.1002/mbo3.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
Adaptation of opportunistic pathogens to their host environment requires reprogramming of a vast array of genes to facilitate survival in the host. Burkholderia cenocepacia, a Gram-negative bacterium with a large genome of ∼8 Mb that colonizes environmental niches, is exquisitely adaptable to the hypoxic environment of the cystic fibrosis lung and survives in macrophages. We previously identified an immunoreactive acidic protein encoded on replicon 3, BCAS0292. Deletion of the BCAS0292 gene significantly altered the abundance of 979 proteins by 1.5-fold or more; 19 proteins became undetectable while 545 proteins showed ≥1.5-fold reduced abundance, suggesting the BCAS0292 protein is a global regulator. Moreover, the ∆BCAS0292 mutant showed a range of pleiotropic effects: virulence and host-cell attachment were reduced, antibiotic susceptibility was altered, and biofilm formation enhanced. Its growth and survival were impaired in 6% oxygen. In silico prediction of its three-dimensional structure revealed BCAS0292 presents a dimeric β-structure with a negative surface charge. The ΔBCAS0292 mutant displayed altered DNA supercoiling, implicated in global regulation of gene expression. Three proteins were identified in pull-downs with FLAG-tagged BCAS0292, including the Histone H1-like protein, HctB, which is recognized as a global transcriptional regulator. We propose that BCAS0292 protein, which we have named Burkholderia negatively surface-charged regulatory protein 1 (Bnr1), acts as a DNA-mimic and binds to DNA-binding proteins, altering DNA topology and regulating the expression of multiple genes, thereby enabling the adaptation of B. cenocepacia to highly diverse environments.
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Affiliation(s)
- Ruth Dennehy
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Niamh Duggan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Simon Dignam
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
| | - Sarah McCormack
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Eugene Dillon
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Jessica Molony
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Maria Romano
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Yueran Hou
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
| | - Laura Ardill
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Matthew V. X. Whelan
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Zuzanna Drulis‐Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and MicrobiologyUniversity of WroclawWroclawPoland
| | - Tadhg Ó'Cróinín
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
| | - Miguel A. Valvano
- School of Medicine, Dentistry and Biomedical Sciences, Wellcome‐Wolfson Institute for Experimental MedicineQueen's University BelfastBelfastUK
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- Centre of Microbial Host InteractionsInstitute of Technology TallaghtDublinIreland
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinIreland
- UCD Conway Institute of Biomolecular and Biomedical ResearchUniversity College DublinBelfield, DublinIreland
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Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D. Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae. BMC Biol 2020; 18:43. [PMID: 32349767 PMCID: PMC7191768 DOI: 10.1186/s12915-020-00777-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/31/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined. RESULTS We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains. CONCLUSIONS The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.
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Affiliation(s)
- Alfonso Soler-Bistué
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | | | - Marc Garcia-Garcerá
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
- Department of Fundamental Microbiology, University of Lausanne, Quartier SORGE, 1003, Lausanne, Switzerland
| | - Marie-Eve Val
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Hugo Varet
- Institut Pasteur, Plate-forme Transcriptome et Épigenome, Biomics, Centre d'Innovation et Recherche Technologique (Citech), Paris, France
| | - Rodrigo Sieira
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Evelyne Krin
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Diego J Comerci
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo A. Ugalde," CONICET - Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Département Génomes et Génétique, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique UMR3525, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, UMR3525, CNRS, Paris, France.
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Pakkulnan R, Anutrakunchai C, Kanthawong S, Taweechaisupapong S, Chareonsudjai P, Chareonsudjai S. Extracellular DNA facilitates bacterial adhesion during Burkholderia pseudomallei biofilm formation. PLoS One 2019; 14:e0213288. [PMID: 30856240 PMCID: PMC6411153 DOI: 10.1371/journal.pone.0213288] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 10/12/2018] [Accepted: 02/18/2019] [Indexed: 12/21/2022] Open
Abstract
The biofilm-forming ability of Burkholderia pseudomallei is crucial for its survival in unsuitable environments and is correlated with antibiotic resistance and relapsing cases of melioidosis. Extracellular DNA (eDNA) is an essential component for biofilm development and maturation in many bacteria. The aim of this study was to investigate the eDNA released by B. pseudomallei during biofilm formation using DNase treatment. The extent of biofilm formation and quantity of eDNA were assessed by crystal-violet staining and fluorescent dye-based quantification, respectively, and visualized by confocal laser scanning microscopy (CLSM). Variation in B. pseudomallei biofilm formation and eDNA quantity was demonstrated among isolates. CLSM images of biofilms stained with FITC-ConA (biofilm) and TOTO-3 (eDNA) revealed the localization of eDNA in the biofilm matrix. A positive correlation of biofilm biomass with quantity of eDNA during the 2-day biofilm-formation observation period was found. The increasing eDNA quantity over time, despite constant living/dead ratios of bacterial cells during the experiment suggests that eDNA is delivered from living bacterial cells. CLSM images demonstrated that depletion of eDNA by DNase I significantly lessened bacterial attachment (if DNase added at 0 h) and biofilm developing stages (if added at 24 h) but had no effect on mature biofilm (if added at 45 h). Collectively, our results reveal that eDNA is released from living B. pseudomallei and is correlated with biofilm formation. It was also apparent that eDNA is essential during bacterial cell attachment and biofilm-forming steps. The depletion of eDNA by DNase may provide an option for the prevention or dispersal of B. pseudomallei biofilm.
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Affiliation(s)
- Rattiyaphorn Pakkulnan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
| | | | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Suwimol Taweechaisupapong
- Biofilm Research Group, Khon Kaen University, Khon Kaen, Thailand
- Department of Oral Diagnosis, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Pisit Chareonsudjai
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Khon Kaen University, Khon Kaen, Thailand
- Department of Environmental Science, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Biofilm Research Group, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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Aun E, Brauer A, Kisand V, Tenson T, Remm M. A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria. PLoS Comput Biol 2018; 14:e1006434. [PMID: 30346947 PMCID: PMC6211763 DOI: 10.1371/journal.pcbi.1006434] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 04/09/2018] [Revised: 11/01/2018] [Accepted: 08/15/2018] [Indexed: 11/18/2022] Open
Abstract
We have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) identifies phenotype-specific k-mers, (b) generates a k-mer-based statistical model for predicting a given phenotype and (c) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167 Klebsiella pneumoniae isolates (virulence), 200 Pseudomonas aeruginosa isolates (ciprofloxacin resistance) and 459 Clostridium difficile isolates (azithromycin resistance). The phenotype prediction models trained from these datasets obtained the F1-measure of 0.88 on the K. pneumoniae test set, 0.88 on the P. aeruginosa test set and 0.97 on the C. difficile test set. The F1-measures were the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets. PhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (https://github.com/bioinfo-ut/PhenotypeSeeker/).
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Affiliation(s)
- Erki Aun
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Age Brauer
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Heberling T, Davis L, Gedeon J, Morgan C, Gedeon T. A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases. PLoS Comput Biol 2016; 12:e1005069. [PMID: 27517607 PMCID: PMC4982667 DOI: 10.1371/journal.pcbi.1005069] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 02/09/2016] [Accepted: 07/20/2016] [Indexed: 11/19/2022] Open
Abstract
In fast-transcribing prokaryotic genes, such as an rrn gene in Escherichia coli, many RNA polymerases (RNAPs) transcribe the DNA simultaneously. Active elongation of RNAPs is often interrupted by pauses, which has been observed to cause RNAP traffic jams; yet some studies indicate that elongation seems to be faster in the presence of multiple RNAPs than elongation by a single RNAP. We propose that an interaction between RNAPs via the torque produced by RNAP motion on helically twisted DNA can explain this apparent paradox. We have incorporated the torque mechanism into a stochastic model and simulated transcription both with and without torque. Simulation results illustrate that the torque causes shorter pause durations and fewer collisions between polymerases. Our results suggest that the torsional interaction of RNAPs is an important mechanism in maintaining fast transcription times, and that transcription should be viewed as a cooperative group effort by multiple polymerases.
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Affiliation(s)
- Tamra Heberling
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lisa Davis
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jakub Gedeon
- Computer Science Department, Montana State University, Bozeman, Montana, United States of America
| | - Charles Morgan
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Tomáš Gedeon
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
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6
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Kinet R, Dzaomuho P, Baert J, Taminiau B, Daube G, Nezer C, Brostaux Y, Nguyen F, Dumont G, Thonart P, Delvigne F. Flow cytometry community fingerprinting and amplicon sequencing for the assessment of landfill leachate cellulolytic bioaugmentation. Bioresour Technol 2016; 214:450-459. [PMID: 27160955 DOI: 10.1016/j.biortech.2016.04.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 06/05/2023]
Abstract
Flow cytometry (FCM) is a high throughput single cell technology that is actually becoming widely used for studying phenotypic and genotypic diversity among microbial communities. This technology is considered in this work for the assessment of a bioaugmentation treatment in order to enhance cellulolytic potential of landfill leachate. The experimental results reveal the relevant increase of leachate cellulolytic potential due to bioaugmentation. Cytometric monitoring of microbial dynamics along these assays is then realized. The flow FP package is used to establish microbial samples fingerprint from initial 2D cytometry histograms. This procedure allows highlighting microbial communities' variation along the assays. Cytometric and 16S rRNA gene sequencing fingerprinting methods are then compared. The two approaches give same evidence about microbial dynamics throughout digestion assay. There are however a lack of significant correlation between cytometric and amplicon sequencing fingerprint at genus or species level. Same phenotypical profiles of microbiota during assays matched to several 16S rRNA gene sequencing ones. Flow cytometry fingerprinting can thus be considered as a promising routine on-site method suitable for the detection of stability/variation/disturbance of complex microbial communities involved in bioprocesses.
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Affiliation(s)
- R Kinet
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - P Dzaomuho
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - J Baert
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium
| | - B Taminiau
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - G Daube
- Fundamental and Applied Research for Animal & Health (FARAH), Food Science Department, Faculty of Veterinary Medicine, University of Liège, Sart-Tilman, B43b, Liège B-4000, Belgium
| | - C Nezer
- Quality Partner S.A., Rue Hayeneux, 62, Herstal, B-4040, Belgium
| | - Y Brostaux
- Computer Science and Modeling, Applied Statistics, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, Gembloux, B-5030, Belgium
| | - F Nguyen
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - G Dumont
- University of Liege, Applied Geophysics, Department ArGEnCo, Engineering Faculty, B52, B-4000 Liege, Belgium
| | - P Thonart
- Artechno S.A., Rue Herman Méganck, 21, Isnes, B-5032, Belgium
| | - F Delvigne
- University of Liège, Gembloux Agro-Bio Tech, Microbial Processes and Interactions (MiPI), Passage des déportés 2, Gembloux, B-5030, Belgium.
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7
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Regina VR, Lokanathan AR, Modrzyński JJ, Sutherland DS, Meyer RL. Surface physicochemistry and ionic strength affects eDNA's role in bacterial adhesion to abiotic surfaces. PLoS One 2014; 9:e105033. [PMID: 25122477 PMCID: PMC4133339 DOI: 10.1371/journal.pone.0105033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 12/02/2013] [Accepted: 07/20/2014] [Indexed: 11/22/2022] Open
Abstract
Extracellular DNA (eDNA) is an important structural component of biofilms formed by many bacteria, but few reports have focused on its role in initial cell adhesion. The aim of this study was to investigate the role of eDNA in bacterial adhesion to abiotic surfaces, and determine to which extent eDNA-mediated adhesion depends on the physicochemical properties of the surface and surrounding liquid. We investigated eDNA alteration of cell surface hydrophobicity and zeta potential, and subsequently quantified the effect of eDNA on the adhesion of Staphylococcus xylosus to glass surfaces functionalised with different chemistries resulting in variable hydrophobicity and charge. Cell adhesion experiments were carried out at three different ionic strengths. Removal of eDNA from S. xylosus cells by DNase treatment did not alter the zeta potential, but rendered the cells more hydrophilic. DNase treatment impaired adhesion of cells to glass surfaces, but the adhesive properties of S. xylosus were regained within 30 minutes if DNase was not continuously present, implying a continuous release of eDNA in the culture. Removal of eDNA lowered the adhesion of S. xylosus to all surfaces chemistries tested, but not at all ionic strengths. No effect was seen on glass surfaces and carboxyl-functionalised surfaces at high ionic strength, and a reverse effect occurred on amine-functionalised surfaces at low ionic strength. However, eDNA promoted adhesion of cells to hydrophobic surfaces irrespective of the ionic strength. The adhesive properties of eDNA in mediating initial adhesion of S. xylosus is thus highly versatile, but also dependent on the physicochemical properties of the surface and ionic strength of the surrounding medium.
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Affiliation(s)
| | | | | | | | - Rikke L. Meyer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus C, Denmark
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
- * E-mail:
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8
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Cameron TA, Roper M, Zambryski PC. Quantitative image analysis and modeling indicate the Agrobacterium tumefaciens type IV secretion system is organized in a periodic pattern of foci. PLoS One 2012; 7:e42219. [PMID: 22860087 PMCID: PMC3408489 DOI: 10.1371/journal.pone.0042219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [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: 03/31/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022] Open
Abstract
The Gram negative plant pathogen Agrobacterium tumefaciens is uniquely capable of genetically transforming eukaryotic host cells during the infection process. DNA and protein substrates are transferred into plant cells via a type IV secretion system (T4SS), which forms large cell-envelope spanning complexes at multiple sites around the bacterial circumference. To gain a detailed understanding of T4SS positioning, the spatial distribution of fluorescently labeled T4SS components was quantitatively assessed to distinguish between random and structured localization processes. Through deconvolution microscopy followed by Fourier analysis and modeling, T4SS foci were found to localize in a non-random periodic pattern. These results indicate that T4SS complexes are dependent on an underlying scaffold or assembly process to obtain an organized distribution suitable for effective delivery of substrates into host cells.
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Affiliation(s)
- Todd A. Cameron
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Marcus Roper
- Department of Mathematics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Patricia C. Zambryski
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
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9
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Maianskiĭ AN, Chebotar' IV, Rudneva EI, Chistiakova VP. [Pseudomonas aeruginosa: characteristics of biofilm process]. Mol Gen Mikrobiol Virusol 2012:3-8. [PMID: 22702137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Definition of the biofilm process as one of the types of intercellular bacterial communications is presented. The modern data concerning the structure of the Pseudomonas aeruginosa biofilm matrix and genetic mechanisms necessary for its production are described. Active and passive rejections of biofilm bacteria, which are the basis of bacterial spreading to new surfaces, are discussed. The complexity and chain type of the reactions associated with biofilm formation are emphasized.
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Wang Y, Guo Y, Wang F, Sun S. Pathogen DNA also contributes to interferon regulatory factor 3 activation in hepatic cells: Implications for alcoholic liver diseases. Hepatology 2011; 53:1783-4. [PMID: 21520189 DOI: 10.1002/hep.24089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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11
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Lu J, Chen J, Kang L. [Genotypic analysis and plant growth-promoting ability of four plant growth-promoting bacteria from mangrove]. Wei Sheng Wu Xue Bao 2010; 50:1358-1365. [PMID: 21141471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE We identified four strains of plant growth-promoting bacteria (PGPB) and their plant growth-promoting ability. METHODS Four PGPB strains were genetically analyzed by PCR detection of nifH and 16S rRNA gene. Phosphate-solubilizing and nitrogen-fixation capacity were examined by spectrophotometric quantification and acetylene reduction assay, respectively. Effect of strain inoculation on plant growth was also evaluated. RESULTS Phylogenetic analysis based on nifH and 16S rRNA gene sequences indicated that strain HN011 was mostly related to Vibrio natriegens, and SZ7-1 and SZ7-2 resembled Klebsiella oxytoca. Although similarity of 16S rRNA sequence showed that SZ002 belongs to Paenibacillus sp., nifH gene of SZ002 had high sequence similarity with Klebsiella genus. Phosphate solubilization showed that insoluble phosphate was well solubilized in the liquid medium by all four strains of PGPB, which also had high nitrogen-fixation capacity. Plant dry weight, total N and total P were higher in some inoculated than in the non-inoculated plants (P < 0.05). CONCLUSION Our results showed that all four strains of PGPB isolated from mangrove had both phosphate solubilization and nitrogen fixation ability, resulting in beneficial effects on growth.
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MESH Headings
- Bacteria/chemistry
- Bacteria/classification
- Bacteria/genetics
- Cadaver
- DNA, Bacterial/analysis
- DNA, Bacterial/physiology
- DNA, Ribosomal/analysis
- DNA, Ribosomal/physiology
- Genes, rRNA/genetics
- Genotype
- Humans
- Nitrogen Fixation/genetics
- Nitrogen Fixation/physiology
- Plant Roots/growth & development
- Plant Roots/microbiology
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/analysis
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/physiology
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Affiliation(s)
- Junkun Lu
- Research Institute of Tropical Forestry, CAF, Guangzhou 510520, China.
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12
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He J, Deem MW. Heterogeneous diversity of spacers within CRISPR (clustered regularly interspaced short palindromic repeats). Phys Rev Lett 2010; 105:128102. [PMID: 20867676 DOI: 10.1103/physrevlett.105.128102] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Indexed: 05/29/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.
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Affiliation(s)
- Jiankui He
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, USA
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13
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Dai X, You C, Wang L, Chen G, Zhang Q, Wu C. Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice. Plant Mol Biol 2009; 71:469-81. [PMID: 19688299 DOI: 10.1007/s11103-009-9537-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 07/30/2009] [Indexed: 05/23/2023]
Abstract
COBRA-like proteins play important roles in cell expansion and cell wall biosynthesis in Arabidopsis. In rice, a COBRA-like gene, BRITTLE CULM1 (BC1), has been identified as a regulator controlling the culm mechanical strength. Analysis of the rice genome indicated that BC1 belongs to an 11-member multigene family, termed the OsBC1L family in this study. Based on sequence comparisons and phylogenetic analysis, the OsBC1L family comprises two main subgroups. Expression patterns examined by microarray and reverse transcription polymerase chain reaction revealed that OsBC1L genes exhibit universal or specific expression patterns. Through T-DNA or Tos17 insertion mutant lines, the functions of six OsBC1L family members have been examined by investigating the phenotype variations of knockout mutants under normal growth conditions. Results suggest that the OsBC1L genes perform a range of functions and participate in various developmental processes in rice.
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Affiliation(s)
- Xiaoxia Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
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14
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Kuroha T, Tokunaga H, Kojima M, Ueda N, Ishida T, Nagawa S, Fukuda H, Sugimoto K, Sakakibara H. Functional analyses of LONELY GUY cytokinin-activating enzymes reveal the importance of the direct activation pathway in Arabidopsis. Plant Cell 2009; 21:3152-69. [PMID: 19837870 PMCID: PMC2782294 DOI: 10.1105/tpc.109.068676] [Citation(s) in RCA: 273] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cytokinins play crucial roles in diverse aspects of plant growth and development. Spatiotemporal distribution of bioactive cytokinins is finely regulated by metabolic enzymes. LONELY GUY (LOG) was previously identified as a cytokinin-activating enzyme that works in the direct activation pathway in rice (Oryza sativa) shoot meristems. In this work, nine Arabidopsis thaliana LOG genes (At LOG1 to LOG9) were predicted as homologs of rice LOG. Seven At LOGs, which are localized in the cytosol and nuclei, had enzymatic activities equivalent to that of rice LOG. Conditional overexpression of At LOGs in transgenic Arabidopsis reduced the content of N(6)-(Delta(2)-isopentenyl)adenine (iP) riboside 5'-phosphates and increased the levels of iP and the glucosides. Multiple mutants of At LOGs showed a lower sensitivity to iP riboside in terms of lateral root formation and altered root and shoot morphology. Analyses of At LOG promoter:beta-glucuronidase fusion genes revealed differential expression of LOGs in various tissues during plant development. Ectopic overexpression showed pleiotropic phenotypes, such as promotion of cell division in embryos and leaf vascular tissues, reduced apical dominance, and a delay of leaf senescence. Our results strongly suggest that the direct activation pathway via LOGs plays a pivotal role in regulating cytokinin activity during normal growth and development in Arabidopsis.
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Affiliation(s)
- Takeshi Kuroha
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroki Tokunaga
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Mikiko Kojima
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
| | - Nanae Ueda
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Ishida
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
| | - Shingo Nagawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033 Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo, Tokyo 113-0033 Japan
| | - Keiko Sugimoto
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan
- Address correspondence to
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15
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Abstract
Temperature is among the most important of the parameters that free-living microbes monitor. Microbial physiology needs to be readjusted in response to sudden temperature changes. When the ambient temperature rises or drops to potentially harmful levels, cells mount protective stress responses--so-called heat or cold shock responses, respectively. Pathogenic microorganisms often respond to a temperature of around 37 degrees C by inducing virulence gene expression. There are two main ways in which temperature can be measured. Often, the consequences of a sudden temperature shift are detected. Such indirect signals are known to be the accumulation of denatured proteins (heat shock) or stalled ribosomes (cold shock). However, this article focuses solely on direct thermosensors. Since the conformation of virtually every biomolecule is susceptible to temperature changes, primary sensors include DNA, RNA, proteins and lipids.
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Affiliation(s)
- Birgit Klinkert
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF 06/783, 44780 Bochum, Germany
| | - Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, NDEF 06/783, 44780 Bochum, Germany
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16
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Chang PW, Zhang QM, Takatori K, Tachibana A, Yonei S. Increased sensitivity to sparsely ionizing radiation due to excessive base excision in clustered DNA damage sites inEscherichia coli. Int J Radiat Biol 2009; 81:115-23. [PMID: 16019921 DOI: 10.1080/09553000500103009] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
PURPOSE In order to clarify the cellular processing and repair mechanisms for radiation-induced clustered DNA damage, we examined the correlation between the levels of DNA glycosylases and the sensitivity to ionizing radiation in Escherichia coli. MATERIALS AND METHODS The lethal effects of gamma-rays, X-rays, alpha-particles and H2O2 were determined in E. coli with different levels of DNA glycosylases. The formation of double-strand breaks by post-irradiation treatment with DNA glycosylase was assayed with gamma-irradiated plasmid DNA in vitro. RESULTS An E. coli mutM nth nei triple mutant was less sensitive to the lethal effect of sparsely ionizing radiation (gamma-rays and X-rays) than the wild-type strain. Overproduction of MutM (8-oxoguanine-DNA glycosylase), Nth (endonuclease III) and Nei (endonulease VIII) increased the sensitivity to gamma-rays, whereas it did not affect the sensitivity to alpha-particles. Increased sensitivity to gamma-rays also occurred in E. coli overproducing human 8-oxoguanine-DNA glycosylase (hOgg1). Treatment of gamma-irradiated plasmid DNA with purified MutM converted the covalently closed circular to the linear form of the DNA. On the other hand, overproduction of MutM conferred resistance to H2O2 on the E. coli mutM nth nei mutant. CONCLUSIONS The levels of DNA glycosylases affect the sensitivity of E. coli to gamma-rays and X-rays. Excessive excision by DNA glycosylases converts nearly opposite base damage in clustered DNA damage to double-strand breaks, which are potentially lethal.
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Affiliation(s)
- P W Chang
- Laboratory of Radiation Biology, Graduate School of Science, Kyoto University, Japan
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17
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Abstract
Held et al. (1984a,b) demonstrated previously that glutathione (GSH), a negatively charged thiol, is significantly less efficient in the hydrogen atom donation repair reaction with radicals induced by radiation in transforming DNA (t-DNA) than are other thiol compounds. Fahey et al. (1991a,b) postulated that the charge on thiols can influence their ability to radioprotect DNA. GSH, which is excluded from the vicinity of DNA due to its negative charge, is less protective than neutral or positively charged thiols. We have investigated this phenomenon further with trypanothione, the conjugate of glutathione and spermidine, N1,N8-bis (L-gamma-glutamyl-L-hemicystinyl-glycyl)-spermidine. Trypanothione exists in aerobic solution largely as the disulphide (T(S)2) but is maintained in the cell in the reduced form (T(SH)2) by means of an NADPH-dependent flavo-enzyme, trypanothione reductase (TR). Experimental data show that T(S)2 in the presence of TR radioprotects t-DNA in the absence of oxygen much better than GSH or spermidine alone or in combination. Little radioprotection by T(S)2 is seen when TR is not present. The results obtained with reduced trypanothione at low concentrations suggest that radioprotection of t-DNA in hypoxia occurs predominantly by H atom donation and slightly by .OH radical scavenging, and the protection is greater than that by GSH or spermidine because the polyamine moiety in trypanothione allows a greater concentration of GSH near the DNA molecule.
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Affiliation(s)
- S Awad
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston 02114
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18
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Qi D, Meng Q. [Mobility of bacterial group II introns--a review]. Wei Sheng Wu Xue Bao 2009; 49:703-709. [PMID: 19673404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Group II introns are both catalytic RNAs (ribozymes) and mobile retroelements that were discovered about 14 years ago. Mobile Group II introns were also found in bacteria recently, and they can either retrohome into cognate alleles that lack the intron or retrotranspose to ectopic sites. We reviewed the main mobility (homing) pathways of bacterial group II introns by describing the relationship between Intron-encoded protein activities and intron mobility. We discussed whether mobility of Cyanobacteria group II introns could occur and possible mechanisms of their mobility. Furthermore, the biological implications of group II introns transferring within a species or among different species are also discussed.
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Affiliation(s)
- Dan Qi
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai 201620, China.
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19
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Abstract
During the last years, our understanding of the mechanisms that control plant response to salt stress has been steadily progressing. Pharmacological studies have allowed the suggestion that the cytoskeleton may be involved in regulating such a response. Nevertheless, genetic evidence establishing that the cytoskeleton has a role in plant tolerance to salt stress has not been reported yet. Here, we have characterized Arabidopsis T-DNA mutants for genes encoding proteins orthologous to prefoldin (PFD) subunits 3 and 5 from yeast and mammals. In these organisms, PFD subunits, also known as Genes Involved in Microtubule biogenesis (GIM), form a heterohexameric PFD complex implicated in tubulin and actin folding. We show that, indeed, PFD3 and PFD5 can substitute for the loss of their yeast orthologs, as they are able to complement yeast gim2Delta and gim5Delta mutants, respectively. Our results indicate that pfd3 and pfd5 mutants have reduced levels of alpha- and beta-tubulin compared to the wild-type plants when growing under both control and salt-stress conditions. In addition, pfd3 and pfd5 mutants display alterations in their developmental patterns and microtubule organization, and, more importantly, are hypersensitive to high concentrations of NaCl but not of LiCl or mannitol. These results demonstrate that the cytoskeleton plays an essential role in plant tolerance to salt stress.
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Affiliation(s)
- Miguel A Rodríguez-Milla
- Departamento de Biología de Plantas, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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20
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Yamamoto S, Uraji M, Tanaka K, Moriguchi K, Suzuki K. Identification of pTi-SAKURA DNA region conferring enhancement of plasmid incompatibility and stability. Genes Genet Syst 2007; 82:197-206. [PMID: 17660690 DOI: 10.1266/ggs.82.197] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In Agrobacterium tumefaciens, the stability of Ti plasmids differs depending on the strain. So far, little is known about genes that cause the difference in stability. The repABC operon is responsible for replication and incompatibility of Ti plasmids. We constructed recombinant plasmids carrying the repABC operon and different portions of pTi-SAKURA. Cells having the recombinant plasmids that harbored a 2.6-kbp NheI fragment of pTi-SAKURA were found to be transformed via conjugation 100-fold less frequently with a small incompatible repABC plasmid than cells having the recombinant plasmids lacking the 2.6-kbp NheI fragment. Since the phenomenon occurred only when the resident and incoming plasmids belonged to the same incompatibility group, it was suggested that the 2.6-kbp NheI fragment bears the potential enhancing incompatibility. The fragment contained an operon consisting of two open reading frames, tiorf24 and tiorf25. tiorf24 is an orphan gene, whereas tiorf25 is a homologue of a group of plasmid stability genes. Removal of the 2.6-kbp fragment from the resident pTi-SAKURA increased the resident plasmid ejection ratio by the incoming repABC plasmid, whereas addition of the fragment to pTiC58 decreased the ejection ratio, and the loss ratio during growth at 37 degrees C. These data suggest that tiorf24 and tiorf25 are responsible for the stability of pTi-SAKURA, and reduce, in the host bacterium, the frequency of ejection of the resident plasmid, presumably through an incompatibility mechanism.
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Affiliation(s)
- Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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21
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Abstract
Recent studies have revealed that the regulated death of bacterial cells is important for biofilm development. Following cell death, a sub-population of the dead bacteria lyse and release genomic DNA, which then has an essential role in intercellular adhesion and biofilm stability. This Opinion focuses on the role of regulated cell death and lysis in biofilm development and provides a functional comparison between bacterial programmed cell death and apoptosis. The hypothesis that the differential regulation of these processes during biofilm development contributes to the antibiotic tolerance of biofilm cells is also explored.
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Affiliation(s)
- Kenneth W Bayles
- Department of Pathology & Microbiology, University of Nebraska Medical Center, 986,495 Nebraska Medical Center, Omaha, Nebraska, USA.
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22
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Kim SI, Gelvin SB. Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J 2007; 51:779-91. [PMID: 17605756 DOI: 10.1111/j.1365-313x.2007.03183.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Previous work from numerous laboratories has suggested that integration of Agrobacterium tumefaciens T-DNA into the plant genome occurs preferentially in promoter or transcriptionally active regions. However, all of these studies were conducted on plants recovered from selective conditions requiring the expression of transgenes. The conclusions of these studies may therefore have been biased because of the selection of transformants. In this study, we investigated T-DNA integration sites in the Arabidopsis genome by analyzing T-DNA/plant DNA junctions generated under non-selective conditions. We found a relatively high frequency of T-DNA insertions in heterochromatic regions, including centromeres, telomeres and rDNA repeats. These T-DNA insertion regions are disfavored under selective conditions. The frequency with which T-DNA insertions mapped to exon, intron, 5' upstream and 3' downstream regions closely resembled their respective proportions in the Arabidopsis genome. Transcriptional profiling indicated that expression levels of T-DNA pre-integration target sites recovered using selective conditions were significantly higher than those of random Arabidopsis sequences, whereas expression levels of genomic sequences targeted by T-DNA under non-selective conditions were similar to those of random Arabidopsis sequences. T-DNA target sites identified using non-selective conditions did not correlate with DNA methylation status, suggesting that T-DNA integration occurs without regard to DNA methylation. Our results indicate that T-DNA integration may occur more randomly than previously indicated, and that selection pressure may shift the recovery of T-DNA insertions into gene-rich or transcriptionally active regions of chromatin.
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Affiliation(s)
- Sang-Ic Kim
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
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23
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Abstract
Magnetotactic bacteria (MTB) contain membrane-bound magnetic iron minerals and are globally abundant in the suboxic/anoxic portions of chemically stratified marine and freshwater environments. However, their population dynamics and potential quantitative contribution to the biogeochemical cycles that they influence (iron, sulfur, carbon) have not been previously considered. Here we report the first quantitative description of the distribution of individual species of magnetite- and greigite-producing MTB in a natural system. We developed a quantitative polymerase chain reaction assay targeting 16s rRNA genes to enumerate four major groups of marine MTB, and applied the assay to samples collected with respect to geochemical parameters during summer 2003 in seasonally stratified Salt Pond, MA. Using catalysed reporter deposition-fluorescent in situ hybridization, we also show that a large greigite-producing bacterium is distantly related to Thiomicrospira pelophila in the Gammaproteobacteria. Ribosomal RNA copy numbers obtained with quantitative polymerase chain reaction indicate that MTB comprise up to 10% of total Bacteria and that each organism has a characteristic distributional profile with respect to the chemocline.
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Affiliation(s)
- Sheri L Simmons
- MIT-WHOI Joint Program in Oceanography, MS 52, WHOI, Woods Hole, MA 02543, USA
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24
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Magnusson M, Tobes R, Sancho J, Pareja E. Cutting edge: natural DNA repetitive extragenic sequences from gram-negative pathogens strongly stimulate TLR9. J Immunol 2007; 179:31-5. [PMID: 17579017 DOI: 10.4049/jimmunol.179.1.31] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacterial DNA exerts immunostimulatory effects on mammalian cells via the intracellular TLR9. Although broad analysis of TLR9-mediated immunostimulatory potential of synthetic oligonucleotides has been developed, which kinds of natural bacterial DNA sequences are responsible for immunostimulation are not known. This work provides evidence that the natural DNA sequences named repetitive extragenic palindromic (REPs) sequences present in Gram-negative bacteria are able to produce innate immune system stimulation via TLR9. A strong induction of IFN-alpha production by REPs from Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, and Neisseria meningitidis was detected in splenocytes from 129 mice. In addition, the involvement of TLR9 in immune stimulation by REPs was confirmed using B6.129P2-Tlr9(tm1Aki) knockout mice. Considering the involvement of TLRs in Gram-negative septic shock, it is conceivable that REPs play a role in its pathogenesis. This study highlights REPs as a potential novel target in septic shock treatment.
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MESH Headings
- Adjuvants, Immunologic/genetics
- Adjuvants, Immunologic/physiology
- Animals
- Cells, Cultured
- DNA, Bacterial/metabolism
- DNA, Bacterial/physiology
- Escherichia coli K12/genetics
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/immunology
- Humans
- Immunity, Innate/genetics
- Ligands
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neisseria meningitidis, Serogroup B/genetics
- Pseudomonas aeruginosa/genetics
- Repetitive Sequences, Nucleic Acid
- Salmonella typhi/genetics
- Toll-Like Receptor 9/deficiency
- Toll-Like Receptor 9/genetics
- Toll-Like Receptor 9/metabolism
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Affiliation(s)
- Mattias Magnusson
- Department of Rheumatology and Inflammation Research, Göteborg University, Göteborg, Sweden
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25
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Prozorov AA. [Regularities of the location of genes having different functions and of some other nucleotide sequences in the bacterial chromosome]. Mikrobiologiia 2007; 76:437-447. [PMID: 17974199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The review considers the results of genomic research performed over the last decade that shed light on the location in the bacterial chromosomes of genes having different functions. A tendency towards polarity of the chromosome composition is observed: vitally important genes tend to be concentrated in the region of replication origin (oriC), and their concentration decreases toward the region of replication termination (terC). An oppositely directed polarity (an increase near the terC region) is observed for the distribution of certain oligonucleotides involved in the process of chromosome recombination and segregation.
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26
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Thomas CM, Jones JDG. Molecular analysis of Agrobacterium T-DNA integration in tomato reveals a role for left border sequence homology in most integration events. Mol Genet Genomics 2007; 278:411-20. [PMID: 17574477 DOI: 10.1007/s00438-007-0259-4] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Revised: 05/09/2007] [Accepted: 05/25/2007] [Indexed: 11/29/2022]
Abstract
Studies in several plants have shown that Agrobacterium tumefaciens T-DNA can integrate into plant chromosomal DNA by different mechanisms involving single-stranded (ss) or double-stranded (ds) forms. One mechanism requires sequence homology between plant target and ssT-DNA border sequences and another double-strand-break repair in which preexisting chromosomal DSBs "capture" dsT-DNAs. To learn more about T-DNA integration in Solanum lycopersicum we characterised 98 T-DNA/plant DNA junction sequences and show that T-DNA left border (LB) and right border transfer is much more variable than previously reported in Arabidopsis thaliana and Populus tremula. The analysis of seven plant target sequences showed that regions of homology between the T-DNA LB and plant chromosomal DNA plays an important role in T-DNA integration. One T-DNA insertion generated a target sequence duplication that resulted from nucleolytic processing of a LB/plant DNA heteroduplex that generated a DSB in plant chromosomal DNA. One broken end contained a captured T-DNA that served as a template for DNA repair synthesis. We propose that most T-DNA integrations in tomato require sequence homology between the ssT-DNA LB and plant target DNA which results in the generation of DSBs in plant chromosomal DNA.
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Affiliation(s)
- Colwyn M Thomas
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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27
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Sasaki K, Ose T, Okamoto N, Maenaka K, Tanaka T, Masai H, Saito M, Shirai T, Kohda D. Structural basis of the 3'-end recognition of a leading strand in stalled replication forks by PriA. EMBO J 2007; 26:2584-93. [PMID: 17464287 PMCID: PMC1868909 DOI: 10.1038/sj.emboj.7601697] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 03/29/2007] [Indexed: 11/08/2022] Open
Abstract
In eubacteria, PriA helicase detects the stalled DNA replication forks. This critical role of PriA is ascribed to its ability to bind to the 3' end of a nascent leading DNA strand in the stalled replication forks. The crystal structures in complexes with oligonucleotides and the combination of fluorescence correlation spectroscopy and mutagenesis reveal that the N-terminal domain of PriA possesses a binding pocket for the 3'-terminal nucleotide residue of DNA. The interaction with the deoxyribose 3'-OH is essential for the 3'-terminal recognition. In contrast, the direct interaction with 3'-end nucleobase is unexpected, considering the same affinity for oligonucleotides carrying the four bases at the 3' end. Thus, the N-terminal domain of PriA recognizes the 3'-end base in a base-non-selective manner, in addition to the deoxyribose and 5'-side phosphodiester group, of the 3'-terminal nucleotide to acquire both sufficient affinity and non-selectivity to find all of the stalled replication forks generated during DNA duplication. This unique feature is prerequisite for the proper positioning of the helicase domain of PriA on the unreplicated double-stranded DNA.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Binding Sites
- Buffers
- Crystallography, X-Ray
- DNA Helicases/chemistry
- DNA Helicases/genetics
- DNA Helicases/isolation & purification
- DNA Helicases/metabolism
- DNA Helicases/physiology
- DNA Replication/physiology
- DNA, Bacterial/physiology
- Databases, Protein
- Escherichia coli/physiology
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/isolation & purification
- Escherichia coli Proteins/metabolism
- Escherichia coli Proteins/physiology
- Histidine/chemistry
- Hydrogen Bonding
- Hydrogen-Ion Concentration
- Hydrophobic and Hydrophilic Interactions
- Ligands
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Oligonucleotides/analysis
- Oligonucleotides/chemistry
- Phosphates/chemistry
- Point Mutation
- Protein Binding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Rhodamines/metabolism
- Sequence Homology, Amino Acid
- Spectrometry, Fluorescence
- Spectrum Analysis, Raman
- Thrombin/pharmacology
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Affiliation(s)
- Kaori Sasaki
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Toyoyuki Ose
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Katsumi Maenaka
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Taku Tanaka
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mihoko Saito
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, and JST-BIRD, Siga, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, and JST-BIRD, Siga, Japan
| | - Daisuke Kohda
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan. Tel.:+81 92 642 6968; Fax: +81 92 642 6764; E-mail:
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28
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Abstract
Living organisms make great efforts to maintain their genetic information integrity. However, DNA is vulnerable to many chemical or physical agents. To rescue the cell timely and effectively, the DNA damage response system must be well controlled. Recently, single cell experiments showing that after DNA damage, expression of the key DNA damage response regulatory protein oscillates with time. This phenomenon is observed both in eukaryotic and bacterial cells. We establish a model to simulate the DNA damage response (SOS response) in bacterial cell Escherichia coli. The simulation results are compared to the experimental data. Our simulation results suggest that the modulation observed in the experiment is due to the fluctuation of inducing signal, which is coupled with DNA replication. The inducing signal increases when replication is blocked by DNA damage and decreases when replication resumes.
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Affiliation(s)
- Ming Ni
- Center for Theoretical Biology and Department of Physics, Peking University, Beijing, China
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29
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Abstract
Mobile DNAs use many mechanisms to minimize damage to their hosts. Here we show that a subclass of group II introns avoids host damage by inserting directly after transcriptional terminator motifs in bacterial genomes (stem-loops followed by Ts). This property contrasts with the site-specific behavior of most group II introns, which insert into homing site sequences. Reconstituted ribonucleo protein particles of the Bacillus halodurans intron B.h.I1 are shown to reverse-splice into DNA targets in vitro but require the DNA to be single-stranded and fold into a stem-loop analogous to the RNA structure that forms during transcription termination. Recognition of this DNA stem-loop motif accounts for in vivo target specificity. Insertion after terminators is a previously unrecognized strategy for a selfish DNA because it prevents interruption of coding sequences and restricts expression of the mobile DNA after integration.
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Affiliation(s)
- Aaron R. Robart
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4
| | - Wooseok Seo
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4
| | - Steven Zimmerly
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 1N4
- To whom correspondence should be addressed. E-mail:
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30
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Göttler T, Klostermeier D. Dissection of the Nucleotide Cycle of B. subtilis DNA Gyrase and its Modulation by DNA. J Mol Biol 2007; 367:1392-404. [PMID: 17320901 DOI: 10.1016/j.jmb.2007.01.055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 01/03/2007] [Accepted: 01/20/2007] [Indexed: 11/30/2022]
Abstract
DNA topoisomerases catalyze the inter-conversion of different topological forms of DNA. While all type II DNA topoisomerases relax supercoiled DNA, DNA gyrase is the only enyzme that introduces negative supercoils into DNA at the expense of ATP hydrolysis. We present here a biophysical characterization of the nucleotide cycle of DNA gyrase from Bacillus subtilis, both in the absence and presence of DNA. B. subtilis DNA gyrase is highly homologous to its well-studied Escherichia coli counterpart, but exhibits unique mechanistic features. The active heterotetramer of B. subtilis DNA gyrase is formed by mixing the GyrA and GyrB subunits. GyrB undergoes nucleotide-induced dimerization and is an ATP-operated clamp. The intrinsic ATPase activity of gyrase is stimulated tenfold in the presence of plasmid DNA. However, in contrast to the E. coli homolog, the rate-limiting step in the nucleotide cycle of B. subtilis GyrB is ATP hydrolysis, not product dissociation or an associated conformational change. Furthermore, there is no cooperativity between the two DNA and ATP binding sites in B. subtilis DNA gyrase. Nevertheless, the enzyme is as efficient in negative supercoiling as the E. coli DNA gyrase. Our results provide evidence that the evolutionary goal of efficient DNA supercoiling can be realized by similar architecture, but differences in the underlying mechanism. The basic mechanistic features are conserved among DNA gyrases, but the kinetics of individual steps can vary significantly even between closely related enzymes. This suggests that each topoisomerase represents a different solution to the complex reaction sequence in DNA supercoiling.
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Affiliation(s)
- Thomas Göttler
- Division of Biophysical Chemistry, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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31
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Bowers LM, Krüger R, Filutowicz M. Mechanism of origin activation by monomers of R6K-encoded pi protein. J Mol Biol 2007; 368:928-38. [PMID: 17383678 PMCID: PMC2001305 DOI: 10.1016/j.jmb.2007.02.074] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [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] [Received: 11/16/2006] [Revised: 02/15/2007] [Accepted: 02/16/2007] [Indexed: 10/23/2022]
Abstract
One recurring theme in plasmid duplication is the recognition of the origin of replication (ori) by specific Rep proteins that bind to DNA sequences called iterons. For plasmid R6K, this process involves a complex interplay between monomers and dimers of the Rep protein, pi, with seven tandem iterons of gamma ori. Remarkably, both pi monomers and pi dimers can bind to iterons, a new paradigm in replication control. Dimers, the predominant form in the cell, inhibit replication, while monomers facilitate open complex formation and activate the ori. Here, we investigate a mechanism by which pi monomers out-compete pi dimers for iteron binding, and in so doing activate the ori. With an in vivo plasmid incompatibility assay, we find that pi monomers bind cooperatively to two adjacent iterons. Cooperative binding is eliminated by insertion of a half-helical turn between two iterons but is diminished only slightly by insertion of a full helical turn between two iterons. These studies show also that pi bound to a consensus site promotes occupancy of an adjacent mutated site, another hallmark of cooperative interactions. pi monomer/iteron interactions were quantified using a monomer-biased pi variant in vitro with the same collection of two-iteron constructs. The cooperativity coefficients mirror the plasmid incompatibility results for each construct tested. pi dimer/iteron interactions were quantified with a dimer-biased mutant in vitro and it was found that pi dimers bind with negligible cooperativity to two tandem iterons.
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Affiliation(s)
- Lisa M. Bowers
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA
| | | | - Marcin Filutowicz
- Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, Madison, WI 53706, USA
- *Corresponding author (M. Filutowicz): Tel. 608-262-6947; Fax. 608-262-9865; E-mail:
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32
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Abstract
In both prokaryotes and eukaryotes, proteins involved in DNA repair often organize into multicomponent complexes that can be visualized as foci in living cells. We used a RecA-GFP fusion to examine the subcellular cues that direct RecA-GFP to assemble as foci in response to DNA damage. We used two different methods to inhibit initiation of DNA replication and determined that DNA replication is required for the cell to establish RecA-GFP foci after exposure to DNA-damaging agents. Furthermore, use of endonuclease cleavage to generate a site-specific double-strand break demonstrated that the replication machinery (replisome) and DNA synthesis are required for assembly of RecA-GFP foci during repair of a double-strand break. We monitored the cellular levels of RecA and found that focus formation does not require further induction of protein levels, suggesting that foci result from a redistribution of existing protein to sites of damage encountered by the replisome. Taken together, our results support the model that existing RecA protein is recruited to ssDNA generated by the replisome at sites of DNA damage. These results provide insight into the mechanisms that the cell uses to recruit repair proteins to damaged DNA in living cells.
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Affiliation(s)
- Lyle A. Simmons
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- *To whom correspondence should be addressed at:
Department of Biology, Building 68-633, Massachusetts Institute of Technology, Cambridge, MA 02139. E-mail:
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33
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Frenkiel-Krispin D, Minsky A. Nucleoid organization and the maintenance of DNA integrity in E. coli, B. subtilis and D. radiodurans. J Struct Biol 2006; 156:311-9. [PMID: 16935006 DOI: 10.1016/j.jsb.2006.05.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 05/27/2006] [Accepted: 05/31/2006] [Indexed: 11/21/2022]
Abstract
For enzymatic activities to be effectively carried out, basic prerequisites must be met. Many enzymatic tasks require continuous consumption and dissipation of energy, sometimes in massive amounts. Some activities, such as DNA replication, transcription, and repair through homologous recombination rely upon templates that provide the information required for these transactions. Yet, circumstances where intracellular energy pools are severely depleted, or where intact templates are not available, frequently occur. Moreover, the fact that in order to reach their targets, enzymes must cope with an extremely crowded and viscous cellular milieu that drastically slows down their diffusion is often neglected. These impediments are particularly evident under stress conditions such as prolonged starvation or continuous exposure to DNA-damaging agents. Here we survey recent studies, which imply that when enzymatically-mediated DNA repair pathways are hindered, alternative strategies are deployed, whose common denominator is the reorganization of bacterial nucleoids into morphologies that promote DNA repair and protection.
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34
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Noirot-Gros MF. Dissection fonctionnelle d’un nouveau régulateur de l’initiation de la réplication du chromosome bactérien. Med Sci (Paris) 2006; 22:801-2. [PMID: 17026923 DOI: 10.1051/medsci/20062210801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Matsumoto S. [Molecular mechanisms of persistent infection and adherence/entry to host cells with Mycobacterium tuberculosis for the development of a novel therapeutic and prophylactic intervention]. Nihon Saikingaku Zasshi 2006; 61:345-52. [PMID: 17002206 DOI: 10.3412/jsb.61.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sohkichi Matsumoto
- Department of Host Defense, Osaka City University Graduate School of Medicine, Japan
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36
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Alvarez ME, Fuxman Bass JI, Geffner JR, Fernández Calotti PX, Costas M, Coso OA, Gamberale R, Vermeulen ME, Salamone G, Martinez D, Tanos T, Trevani AS. Neutrophil Signaling Pathways Activated by Bacterial DNA Stimulation. J Immunol 2006; 177:4037-46. [PMID: 16951367 DOI: 10.4049/jimmunol.177.6.4037] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have previously shown that bacterial DNA activates human neutrophils in a CpG-independent manner. In this study, we have characterized the signaling pathways involved in the activation mechanism. We found that p38 MAPK, ERK1/2, and JNK pathways, as well as the PI3K/Akt pathway, are activated by bacterial DNA. We also determined that bacterial DNA induces NF-kappaB and AP-1 activation. When analyzing the role of these pathways on neutrophil functions, we observed that up-regulation of CD11b triggered by bacterial DNA was decreased by pharmacological inhibitors of the p38 MAPK, ERK1/2, and JNK, whereas stimulation of IL-8 release was dependent on p38, ERK1/2, and NF-kappaB. Moreover, we found that IL-8 production was markedly enhanced by inhibition of JNK, suggesting that this pathway negatively modulates NF-kappaB-dependent transcription. We also observed that bacterial DNA stimulated IL-1R-associated kinase-1 kinase activity and its partial degradation. Finally, we determined that bacterial DNA stimulated CD11b up-regulation in TLR9(-/-) but not in MyD88(-/-) mouse neutrophils, supporting that bacterial DNA induces neutrophil activation through a TLR9-independent and MyD88-dependent pathway.
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Affiliation(s)
- María E Alvarez
- Departamento de Inmunología, Instituto de Investigaciones Hematológicas e Instituto de Estudios Oncológicos Fundación Maissa, Academia Nacional de Medicina, Buenos Aires, Argentina
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37
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Friis LM, Pin C, Taylor DE, Pearson BM, Wells JM. A role for the tet(O) plasmid in maintaining Campylobacter plasticity. Plasmid 2006; 57:18-28. [PMID: 16934869 DOI: 10.1016/j.plasmid.2006.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 05/05/2006] [Accepted: 06/09/2006] [Indexed: 11/23/2022]
Abstract
Genomic sequencing projects are beginning to reveal regions of extensive DNA homology between bacterial genera. Public fears of the spread of genetically modified organisms into the food chain and the increasing prevalence of multi-drug resistant disease in humans highlight the implications of horizontal gene transfer. The striking DNA sequence similarity between the two uniquely identified tetracycline resistant (Tc(R)) Campylobacter plasmids, pCC31 and pTet, suggests their conserved acquisition and maintenance within Campylobacter [Batchelor, R.A., Pearson, B.M., Friis, L.M., Guerry, P., Wells, J.M. 2004. Nucleotide sequences and comparison of two large conjugative plasmids from different Campylobacter species. Microbiology 150, 3507-3517]. It is thus likely that these and other conjugative plasmids are highly prevalent and broadly distributed across several continents. Microarray technology is now enabling fast and extensive genomic comparisons to be made and allows us to investigate intra- and inter-genetic conservation and variability. This study details the development of a microarray specific for genes from Campylobacter plasmids pCC31, pTet and pVir and its application to the analysis of Campylobacter plasmid gene presence and preservation throughout environmental and clinical isolates. Application of the iterative algorithm GENCOM (freely available at ) is used as a rapid and effective way of comparing the content and conservation of plasmids in bacteria and provides details of the Campylobacter flexible gene pool and its contribution to genomic plasticity.
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Affiliation(s)
- L M Friis
- Institute of Food Research, Colney Lane, Norwich, Norfolk NR4 7UA, UK.
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38
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Moscoso M, García E, López R. Biofilm formation by Streptococcus pneumoniae: role of choline, extracellular DNA, and capsular polysaccharide in microbial accretion. J Bacteriol 2006; 188:7785-95. [PMID: 16936041 PMCID: PMC1636320 DOI: 10.1128/jb.00673-06] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [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
Streptococcus pneumoniae colonizes the human upper respiratory tract, and this asymptomatic colonization is known to precede pneumococcal disease. In this report, chemically defined and semisynthetic media were used to identify the initial steps of biofilm formation by pneumococcus during growth on abiotic surfaces such as polystyrene or glass. Unencapsulated pneumococci adhered to abiotic surfaces and formed a three-dimensional structure about 25 microm deep, as observed by confocal laser scanning microscopy and low-temperature scanning electron microscopy. Choline residues of cell wall teichoic acids were found to play a fundamental role in pneumococcal biofilm development. The role in biofilm formation of choline-binding proteins, which anchor to the teichoic acids of the cell envelope, was determined using unambiguously characterized mutants. The results showed that LytA amidase, LytC lysozyme, LytB glucosaminidase, CbpA adhesin, PcpA putative adhesin, and PspA (pneumococcal surface protein A) mutants had a decreased capacity to form biofilms, whereas no such reduction was observed in Pce phosphocholinesterase or CbpD putative amidase mutants. Moreover, encapsulated, clinical pneumococcal isolates were impaired in their capacity to form biofilms. In addition, a role for extracellular DNA and proteins in the establishment of S. pneumoniae biofilms was demonstrated. Taken together, these observations provide information on conditions that favor the sessile mode of growth by S. pneumoniae. The experimental approach described here should facilitate the study of bacterial genes that are required for biofilm formation. Those results, in turn, may provide insight into strategies to prevent pneumococcal colonization of its human host.
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Affiliation(s)
- Miriam Moscoso
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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39
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Castilla-Llorente V, Muñoz-Espín D, Villar L, Salas M, Meijer WJJ. Spo0A, the key transcriptional regulator for entrance into sporulation, is an inhibitor of DNA replication. EMBO J 2006; 25:3890-9. [PMID: 16888621 PMCID: PMC1553192 DOI: 10.1038/sj.emboj.7601266] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 07/10/2006] [Indexed: 11/09/2022] Open
Abstract
The transcription factor Spo0A is a master regulator for entry into sporulation in Bacillus subtilis and also regulates expression of the virulent B. subtilis phage phi29. Here, we describe a novel function for Spo0A, being an inhibitor of DNA replication of both, the phi29 genome and the B. subtilis chromosome. Binding of Spo0A near the phi29 DNA ends, constituting the two origins of replication of the linear phi29 genome, prevents formation of phi29 protein p6-nucleoprotein initiation complex resulting in inhibition of phi29 DNA replication. At the B. subtilis oriC, binding of Spo0A to specific sequences, which mostly coincide with DnaA-binding sites, prevents open complex formation. Thus, by binding to the origins of replication, Spo0A prevents the initiation step of DNA replication of either genome. The implications of this novel role of Spo0A for phage phi29 development and the bacterial chromosome replication during the onset of sporulation are discussed.
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Affiliation(s)
- Virginia Castilla-Llorente
- Instituto de Biología Molecular ‘Eladio Viñuela' (CSIC), Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Daniel Muñoz-Espín
- Instituto de Biología Molecular ‘Eladio Viñuela' (CSIC), Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Laurentino Villar
- Instituto de Biología Molecular ‘Eladio Viñuela' (CSIC), Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Margarita Salas
- Instituto de Biología Molecular ‘Eladio Viñuela' (CSIC), Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Wilfried J J Meijer
- Instituto de Biología Molecular ‘Eladio Viñuela' (CSIC), Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
- Facultad de Ciencias, Centro de Biología Molecular ‘Severo Ochoa' (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain. Tel.: (+34) 91 497 8434; Fax: (+34) 91 497 8490; E-mail:
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40
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Duggin IG. DNA Replication Fork Arrest by the Bacillus subtilis RTP–DNA Complex Involves a Mechanism that Is Independent of the Affinity of RTP–DNA Binding. J Mol Biol 2006; 361:1-6. [PMID: 16822523 DOI: 10.1016/j.jmb.2006.06.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 06/02/2006] [Accepted: 06/05/2006] [Indexed: 10/24/2022]
Abstract
In order to elucidate the mechanism of DNA replication fork arrest by the replication terminator protein (RTP)-DNA complex, a set of RTP fusion proteins were constructed in which peptides of various sizes were fused to the C terminus; this placed the peptides at a surface location that was predicted to come into contact with the DNA replication machinery during fork arrest. The fusion proteins were capable of replication fork arrest in vivo, but they had a significantly reduced efficiency compared to wild-type RTP, which was not directly proportional to peptide size or sequence. Importantly, the fusion proteins retained completely normal RTP-DNA binding affinity. These findings rule out the molecular clamp model as the sole explanation for fork arrest by RTP, and suggest that RTP interacts with the replication machinery in a manner that directly contributes to the fork arrest mechanism.
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Affiliation(s)
- Iain G Duggin
- School of Molecular and Microbial Biosciences, The University of Sydney, Australia.
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41
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Cortez-Gonzalez X, Pellicciotta I, Gerloni M, Wheeler MC, Castiglioni P, Lenert P, Zanetti M. TLR9-independent activation of B lymphocytes by bacterial DNA. DNA Cell Biol 2006; 25:253-61. [PMID: 16716115 DOI: 10.1089/dna.2006.25.253] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 01/22/2023] Open
Abstract
The intracellular Toll-like receptor 9 (TLR9) is unique in its ability to recognize single-stranded DNA unmethylated at CpG motifs. Work from this laboratory showed that plasmid DNA is spontaneously internalized in B lymphocytes. This event is followed by the upregulation of costimulatory molecules and the acquisition of antigen presenting function by these cells. However, it is not known whether this phenomenon depends on TLR9. Because of the relevant role played by DNA-based drugs in immunotherapy and vaccination, and the central role of TLR9 signaling by CpG motifs, we decided to investigate whether signaling through TLR9 is a prerequisite for spontaneous transgenesis of lymphocytes. Here we found that transgene expression and upregulation of CD40 and CD86 costimulatory molecules was not inhibited by chloroquine treatment. Spontaneous transgenesis also occurred in B lymphocytes from TLR9-/- mice, and the injection of TLR9-/- transgenic B lymphocytes in C57Bl/6 mice induced both CD4 and CD8 T cell responses comparable to those induced by wild-type B lymphocytes. Collectively, these results suggest that plasmid DNA activates mammalian B lymphocytes through a TLR9 independent pathway.
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Affiliation(s)
- Xochitl Cortez-Gonzalez
- The Laboratory of Immunology, Department of Medicine and Cancer Center, University of California, San Diego, La Jolla, California 92093-0837, USA
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42
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Hohn B, Hohn T. Single-stranded DNA plant pathogens in Eilat. Plant Mol Biol 2006; 61:357-64. [PMID: 16786312 DOI: 10.1007/s11103-006-0017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2006] [Accepted: 01/26/2006] [Indexed: 05/10/2023]
Abstract
An international conference on "Inter- and Intracellular Dynamics of ssDNA Plant Pathogens: Implications for Improving Resistance'' was sponsored by the United States-Israel Binational Agricultural Research and Development Fund (BARD) and organized in Eilat, Israel in November 2005. The topic of this meeting was single-stranded plant pathogens, their inter- as well as intra-cellular dynamics and their implications for improving resistance. Most of the talks concentrated on new and very new findings on principles of virus and bacterium-host interactions, studies that no doubt will lead eventually to the establishment of plants resistant to viral and bacterial infections.
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Affiliation(s)
- Barbara Hohn
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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43
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Abstract
The genomic DNA in cells of Escherichia coli is localized in one or two compact, phase-like regions with characteristic shapes. Nucleoids undergo progressive changes in shape and compaction in the presence of drugs such as chloramphenicol or puromycin. Forces which influence nucleoid shape and compaction are reviewed, with particular emphasis on crowding effects of the cytoplasm and confinement effects of the cell envelope. Based in part on the theory of Kornyshev and Leikin for interaction between DNA duplexes, the folding of DNA caused by binding of DNA-associated proteins is suggested to antagonize DNA condensation and, thereby, increase access to DNA sequences. These views are incorporated into a working model for nucleoid organization.
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Affiliation(s)
- Steven B Zimmerman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA
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44
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Tsunoda I, Kuang L, Theil DJ, Fujinami RS. Antibody association with a novel model for primary progressive multiple sclerosis: induction of relapsing-remitting and progressive forms of EAE in H2s mouse strains. Brain Pathol 2006; 10:402-18. [PMID: 10885659 PMCID: PMC8098387 DOI: 10.1111/j.1750-3639.2000.tb00272.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [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: 02/05/2023] Open
Abstract
Multiple sclerosis (MS) can be divided into 4 clinical forms: relapsing-remitting (RR), primary progressive (PP), secondary progressive (SP), and progressive relapsing (PR). Since PP-MS is notably different from the other forms of MS, both clinically and pathologically, the question arises whether PP-MS is immunologically similar to the other forms. The pathogenesis of the PP-MS remains unclear, partly due to a lack of highly relevant animal models. Using an encephalitogenic peptide from myelin oligodendrocyte glycoprotein (MOG)92-106, we have established animal models that mimic different forms of MS in 2 strains of H-2s mice, SJL/J and A.SW. We induced experimental allergic encephalomyelitis (EAE) using MOG92-106 in the presence or absence of supplemental Bordetella pertussis (BP). Although, SJL/J mice developed RR-EAE whether BP was given or not, A.SW mice developed PP-EAE without BP and SP-EAE with BP. Histologically, SJL/J mice developed mild demyelinating disease with T cell infiltration, while A.SW mice developed large areas of plaque-like demyelination with immunoglobulin deposition and neutrophil infiltration, but with minimal T cell infiltration. In A.SW mice without BP, high titer serum anti-MOG antibody was detected and the anti-MOG IgG2a/IgG1 ratio correlated with survival times of mice. We hypothesized that, in A.SW mice, a Th2 response favors production of myelinotoxic antibodies, leading to progressive forms with early death. Our new models indicate that a single encephalitogen could induce either RR-, PP-, or SP- forms of demyelinating disease in hosts with immunologically different humoral immune responses.
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MESH Headings
- Animals
- Antibodies/analysis
- Central Nervous System/pathology
- DNA, Bacterial/physiology
- Disease Models, Animal
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Encephalomyelitis, Autoimmune, Experimental/physiopathology
- Female
- Immunoglobulins/metabolism
- In Situ Nick-End Labeling
- Lymphocytes/pathology
- Mice
- Mice, Mutant Strains
- Multiple Sclerosis, Chronic Progressive/immunology
- Multiple Sclerosis, Relapsing-Remitting/immunology
- Myelin Proteins
- Myelin-Associated Glycoprotein/immunology
- Myelin-Oligodendrocyte Glycoprotein
- Nervous System/pathology
- Peptide Fragments/immunology
- Plasmids/genetics
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Affiliation(s)
- Ikuo Tsunoda
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Li‐Qing Kuang
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Diethilde J. Theil
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Robert S. Fujinami
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah 84132
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45
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Abstract
DNA vaccines that were being investigated in mice for prophylactic use against tuberculosis were soon found also to be surprisingly effective as treatment against established infection. The immune system was stimulated to kill the bacteria, even including the persistent latent bacteria that are otherwise refractory to the immune system and antibacterial chemotherapeutic drugs alike. Subsequent results from a range of laboratories using diverse DNA vaccines in diverse murine models of infection have been very varied, ranging from enhanced pathology, through negligible effects, to major additive benefit from combined vaccine and chemotherapy. This review summarises the data and assesses future prospects.
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Affiliation(s)
- Douglas B Lowrie
- National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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46
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Abstract
Bacterial plasmids encode partitioning (par) loci that ensure ordered plasmid segregation prior to cell division. par loci come in two types: those that encode actin-like ATPases and those that encode deviant Walker-type ATPases. ParM, the actin-like ATPase of plasmid R1, forms dynamic filaments that segregate plasmids paired at mid-cell to daughter cells. Like microtubules, ParM filaments exhibit dynamic instability (i.e., catastrophic decay) whose regulation is an important component of the DNA segregation process. The Walker box ParA ATPases are related to MinD and form highly dynamic, oscillating filaments that are required for the subcellular movement and positioning of plasmids. The role of the observed ATPase oscillation is not yet understood. However, we propose a simple model that couples plasmid segregation to ParA oscillation. The model is consistent with the observed movement and localization patterns of plasmid foci and does not require the involvement of plasmid-specific host-encoded factors.
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Affiliation(s)
- Gitte Ebersbach
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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47
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Abstract
The fim genetic switch in the chromosome of Escherichia coli K-12 is an invertible DNA element that harbors the promoter for transcription of the downstream fim structural genes and a transcription terminator that acts on the upstream fimE regulatory gene. Switches oriented appropriately for structural gene transcription also allow fimE mRNA to read through, whereas those in the opposite orientation terminate the fimE message. We show here that termination is Rho dependent and is suppressed in a rho mutant or by bicyclomycin treatment when fimE mRNA is expressed by the fimE gene, either from a multicopy recombinant plasmid or in its native chromosomal location. Two cis-acting elements within the central portion of the 314-bp invertible DNA switch were identified as contributors to Rho-dependent termination and dissected. These fim sequence elements show similarities to well-characterized Rho utilization (rut) sites and consist of a boxA motif and a C-rich and G-poor region of approximately 40 bp. Deletion of the boxA motif alone had only a subtle negative effect on Rho function. However, when this element was deleted in combination with the C-rich, G-poor region, Rho function was considerably decreased. Altering the C-to-G ratio in favor of G in this portion of the switch also strongly attenuated transcription termination. The implications of the existence of a fimE-specific Rho-dependent terminator within the invertible switch are discussed in the context of the fim regulatory circuit.
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MESH Headings
- Base Composition/genetics
- Base Composition/physiology
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- DNA, Bacterial/genetics
- DNA, Bacterial/physiology
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Enzyme Inhibitors/pharmacology
- Escherichia coli K12/genetics
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/physiology
- Fimbriae, Bacterial/genetics
- Gene Expression Regulation, Bacterial
- Integrases/genetics
- Integrases/physiology
- Models, Biological
- Promoter Regions, Genetic
- RNA, Bacterial/analysis
- RNA, Messenger/analysis
- Reverse Transcriptase Polymerase Chain Reaction
- Rho Factor/genetics
- Rho Factor/physiology
- Terminator Regions, Genetic
- Transcription, Genetic
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Affiliation(s)
- Paul Hinde
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin 2, Ireland
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48
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Xu Q, Seemanapalli SV, Lomax L, McShan K, Li X, Fikrig E, Liang FT. Association of linear plasmid 28-1 with an arthritic phenotype of Borrelia burgdorferi. Infect Immun 2005; 73:7208-15. [PMID: 16239515 PMCID: PMC1273894 DOI: 10.1128/iai.73.11.7208-7215.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 11/20/2022] Open
Abstract
Borrelia burgdorferi, the Lyme disease spirochete, has a genome comprised of a linear chromosome and up to 21 plasmids. Loss of plasmids is associated with decreased infectivity and pathogenicity. Sixteen transformants were generated by transforming the noninfectious clone 5A13 with the recombinant plasmid pBBE22. The transformants were classified into nine groups based on plasmid content analysis. An infectivity study revealed that all nine transformants examined, each of which represented one of the plasmid patterns, were infectious in mice with severe combined immunodeficiency (SCID) regardless of their genomic compositions. Tissue bacterial quantification revealed that the loss of plasmids significantly reduced the spirochete burden in the heart and joint tissues, not in the skin, suggesting virulence factors may be tissue specific. Four transformants containing lp28-1 induced severe arthritis in SCID mice, in contrast to the five transformants lacking lp28-1. These pathogenicity studies associated lp28-1 with an arthritic phenotype and further studies may identify factors that contribute to arthritic pathology.
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Affiliation(s)
- Qilong Xu
- Department of Pathobiological Sciences, Louisiana State University, Skip Bertman Drive at River Road, Baton Rouge, LA 70803, USA
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49
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Miksch G, Bettenworth F, Friehs K, Flaschel E. The sequence upstream of the -10 consensus sequence modulates the strength and induction time of stationary-phase promoters in Escherichia coli. Appl Microbiol Biotechnol 2005; 69:312-20. [PMID: 16088348 DOI: 10.1007/s00253-005-0016-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 04/21/2005] [Accepted: 04/25/2005] [Indexed: 10/25/2022]
Abstract
We constructed a library of synthetic stationary-phase promoters for Escherichia coli. For designing the promoters, the known -10 consensus sequence, as well as the extended -10 region, and an A/T-rich region downstream of the -10 region were kept constant, whereas sequences from -37 to -14 were partially or completely randomised. For detection and selection of stationary-phase promoters, green fluorescent protein (GFP) with enhanced fluorescence was used. To establish the library, 33 promoters were selected, which differ in strength from 670 to more than 13,000 specific fluorescence units, indicating that the strength of promoters can be modulated by the sequence upstream of the -10 region. DNA sequencing revealed a preferential insertion of nucleotides depending on the position. By expressing the promoters in an rpoS-deficient strain, a special group of stationary-phase promoters was identified, which were expressed exclusively or preferentially by RNA polymerase holoenzyme Esigma(s). The DNA sequence of these promoters differed significantly in the region from -25 to -16. Furthermore, it was shown that the DNA curvature of the promoter region had no effect on promoter strength. The broad range of promoter activities make these promoters very suitable for fine-tuning of gene expression and for cost-effective large-scale applications in industrial bioprocesses.
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Affiliation(s)
- Gerhard Miksch
- Lehrstuhl für Fermentationstechnik, Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany.
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50
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Abstract
We show that RecN protein is recruited to a defined DNA double strand break (DSB) in Bacillus subtilis cells at an early time point during repair. Because RecO and RecF are successively recruited to DSBs, it is now clear that dynamic DSB repair centers (RCs) exist in prokaryotes. RecA protein was also recruited to RCs and formed highly dynamic filamentous structures, which we term threads, across the nucleoids. Formation of RecA threads commenced ∼30 min after the induction of DSBs, after RecN recruitment to RCs, and disassembled after 2 h. Time-lapse microscopy showed that the threads rapidly changed in length, shape, and orientation within minutes and can extend at 1.02 μm/min. The formation of RecA threads was abolished in recJ addAB mutant cells but not in each of the single mutants, suggesting that RecA filaments can be initiated via two pathways. Contrary to proteins forming RCs, DNA polymerase I did not form foci but was present throughout the nucleoids (even after induction of DSBs or after UV irradiation), suggesting that it continuously scans the chromosome for DNA lesions.
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Affiliation(s)
- Dawit Kidane
- Biochemie, Fachbereich Chemie, Hans-Meerwein-Strasse, Philipps-Universität Marburg, 35032 Marburg, Germany
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