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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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Rai LS, van Wijlick L, Chauvel M, d'Enfert C, Legrand M, Bachellier-Bassi S. Overexpression approaches to advance understanding of Candida albicans. Mol Microbiol 2021; 117:589-599. [PMID: 34569668 PMCID: PMC9298300 DOI: 10.1111/mmi.14818] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022]
Abstract
Candida albicans is an opportunistic fungal pathogen that is responsible for infections linked to high mortality. Loss‐of‐function approaches, taking advantage of gene knockouts or inducible down‐regulation, have been successfully used in this species in order to understand gene function. However, overexpression of a gene provides an alternative, powerful tool to elucidate gene function and identify novel phenotypes. Notably, overexpression can identify pathway components that might remain undetected using loss‐of‐function approaches. Several repressible or inducible promoters have been developed which allow to shut off or turn on the expression of a gene in C. albicans upon growth in the presence of a repressor or inducer. In this review, we summarize recent overexpression approaches used to study different aspects of C. albicans biology, including morphogenesis, biofilm formation, drug tolerance, and commensalism.
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Affiliation(s)
- Laxmi Shanker Rai
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Lasse van Wijlick
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Murielle Chauvel
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
| | - Sophie Bachellier-Bassi
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université de Paris, INRAE, USC2019, Paris, France
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3
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Legrand M, Bachellier-Bassi S, Lee KK, Chaudhari Y, Tournu H, Arbogast L, Boyer H, Chauvel M, Cabral V, Maufrais C, Nesseir A, Maslanka I, Permal E, Rossignol T, Walker LA, Zeidler U, Znaidi S, Schoeters F, Majgier C, Julien RA, Ma L, Tichit M, Bouchier C, Van Dijck P, Munro CA, d’Enfert C. Generating genomic platforms to study Candida albicans pathogenesis. Nucleic Acids Res 2018; 46:6935-6949. [PMID: 29982705 PMCID: PMC6101633 DOI: 10.1093/nar/gky594] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
The advent of the genomic era has made elucidating gene function on a large scale a pressing challenge. ORFeome collections, whereby almost all ORFs of a given species are cloned and can be subsequently leveraged in multiple functional genomic approaches, represent valuable resources toward this endeavor. Here we provide novel, genome-scale tools for the study of Candida albicans, a commensal yeast that is also responsible for frequent superficial and disseminated infections in humans. We have generated an ORFeome collection composed of 5099 ORFs cloned in a Gateway™ donor vector, representing 83% of the currently annotated coding sequences of C. albicans. Sequencing data of the cloned ORFs are available in the CandidaOrfDB database at http://candidaorfeome.eu. We also engineered 49 expression vectors with a choice of promoters, tags and selection markers and demonstrated their applicability to the study of target ORFs transferred from the C. albicans ORFeome. In addition, the use of the ORFeome in the detection of protein-protein interaction was demonstrated. Mating-compatible strains as well as Gateway™-compatible two-hybrid vectors were engineered, validated and used in a proof of concept experiment. These unique and valuable resources should greatly facilitate future functional studies in C. albicans and the elucidation of mechanisms that underlie its pathogenicity.
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Affiliation(s)
- Mélanie Legrand
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Sophie Bachellier-Bassi
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Keunsook K Lee
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Yogesh Chaudhari
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Hélène Tournu
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Laurence Arbogast
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Hélène Boyer
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Murielle Chauvel
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Vitor Cabral
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France
| | - Corinne Maufrais
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP CNRS-Paris 75015, France
| | - Audrey Nesseir
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris 75015, France
| | - Irena Maslanka
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Emmanuelle Permal
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Tristan Rossignol
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Louise A Walker
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Ute Zeidler
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Sadri Znaidi
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
| | - Floris Schoeters
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Charlotte Majgier
- Modul-Bio, Parc Scientifique Luminy Biotech II, Marseille 13009, France
| | - Renaud A Julien
- Modul-Bio, Parc Scientifique Luminy Biotech II, Marseille 13009, France
| | - Laurence Ma
- Institut Pasteur-Biomics Pole-CITECH-Paris 75015, France
| | - Magali Tichit
- Institut Pasteur-Biomics Pole-CITECH-Paris 75015, France
| | | | - Patrick Van Dijck
- VIB-KU Leuven Center for Microbiology, Leuven 3001, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Leuven 3001, Belgium
| | - Carol A Munro
- Medical Research Council Centre for Medical Mycology at the University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Christophe d’Enfert
- Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, INRA, Paris 75015, France
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Brucella abortus Senses the Intracellular Environment through the BvrR/BvrS Two-Component System, Which Allows B. abortus To Adapt to Its Replicative Niche. Infect Immun 2018; 86:IAI.00713-17. [PMID: 29378792 DOI: 10.1128/iai.00713-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
Brucella abortus is a facultative extracellular-intracellular pathogen belonging to a group of Alphaproteobacteria that establishes close interactions with animal cells. This bacterium enters host cells in a membrane-bound compartment, avoiding the lysosomal route and reaching the endoplasmic reticulum through the action of the type IV secretion system, VirB. In this work, we demonstrate that the BvrR/BvrS two-component system senses the intracellular environment to mount the transcriptional response required for intracellular life adaptation. By combining a method to purify intracellularly extracted bacteria with a strategy that allows direct determination of BvrR phosphorylation, we showed that upon entrance to host cells, the regulatory protein BvrR was activated (BvrR-P) by phosphorylation at aspartate 58. This activation takes place in response to intracellular cues found in early compartments, such as low pH and nutrient deprivation. Furthermore, BvrR activation was followed by an increase in the expression of VjbR and VirB. The in vitro activation of this BvrR-P/VjbR/VirB virulence circuit rescued B. abortus from the inhibition of intracellular replication induced by bafilomycin treatment of cells, demonstrating the relevance of this mechanism for intracellular bacterial survival and replication. All together, our results indicate that B. abortus senses the transition from the extracellular to the intracellular milieu through BvrR/BvrS, allowing the bacterium to transit safely to its replicative niche. These results serve as a working model for understanding the role of this family of two-component systems in the adaptation to intracellular life of Alphaproteobacteria.
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Conde-Álvarez R, Palacios-Chaves L, Gil-Ramírez Y, Salvador-Bescós M, Bárcena-Varela M, Aragón-Aranda B, Martínez-Gómez E, Zúñiga-Ripa A, de Miguel MJ, Bartholomew TL, Hanniffy S, Grilló MJ, Vences-Guzmán MÁ, Bengoechea JA, Arce-Gorvel V, Gorvel JP, Moriyón I, Iriarte M. Identification of lptA, lpxE, and lpxO, Three Genes Involved in the Remodeling of Brucella Cell Envelope. Front Microbiol 2018; 8:2657. [PMID: 29375522 PMCID: PMC5767591 DOI: 10.3389/fmicb.2017.02657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022] Open
Abstract
The brucellae are facultative intracellular bacteria that cause a worldwide extended zoonosis. One of the pathogenicity mechanisms of these bacteria is their ability to avoid rapid recognition by innate immunity because of a reduction of the pathogen-associated molecular pattern (PAMP) of the lipopolysaccharide (LPS), free-lipids, and other envelope molecules. We investigated the Brucella homologs of lptA, lpxE, and lpxO, three genes that in some pathogens encode enzymes that mask the LPS PAMP by upsetting the core-lipid A charge/hydrophobic balance. Brucella lptA, which encodes a putative ethanolamine transferase, carries a frame-shift in B. abortus but not in other Brucella spp. and phylogenetic neighbors like the opportunistic pathogen Ochrobactrum anthropi. Consistent with the genomic evidence, a B. melitensis lptA mutant lacked lipid A-linked ethanolamine and displayed increased sensitivity to polymyxin B (a surrogate of innate immunity bactericidal peptides), while B. abortus carrying B. melitensis lptA displayed increased resistance. Brucella lpxE encodes a putative phosphatase acting on lipid A or on a free-lipid that is highly conserved in all brucellae and O. anthropi. Although we found no evidence of lipid A dephosphorylation, a B. abortus lpxE mutant showed increased polymyxin B sensitivity, suggesting the existence of a hitherto unidentified free-lipid involved in bactericidal peptide resistance. Gene lpxO putatively encoding an acyl hydroxylase carries a frame-shift in all brucellae except B. microti and is intact in O. anthropi. Free-lipid analysis revealed that lpxO corresponded to olsC, the gene coding for the ornithine lipid (OL) acyl hydroxylase active in O. anthropi and B. microti, while B. abortus carrying the olsC of O. anthropi and B. microti synthesized hydroxylated OLs. Interestingly, mutants in lptA, lpxE, or olsC were not attenuated in dendritic cells or mice. This lack of an obvious effect on virulence together with the presence of the intact homolog genes in O. anthropi and B. microti but not in other brucellae suggests that LptA, LpxE, or OL β-hydroxylase do not significantly alter the PAMP properties of Brucella LPS and free-lipids and are therefore not positively selected during the adaptation to intracellular life.
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Affiliation(s)
- Raquel Conde-Álvarez
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Leyre Palacios-Chaves
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas - Universidad Pública de Navarra - Gobierno de Navarra, Pamplona, Spain
| | - Yolanda Gil-Ramírez
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Miriam Salvador-Bescós
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Marina Bárcena-Varela
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Beatriz Aragón-Aranda
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Estrella Martínez-Gómez
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - María J de Miguel
- Unidad de Producción y Sanidad Animal, Instituto Agroalimentario de Aragón, Centro de Investigación y Tecnología Agroalimentaria de Aragón - Universidad de Zaragoza, Zaragoza, Spain
| | - Toby Leigh Bartholomew
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Sean Hanniffy
- Institut National de la Santé et de la Recherche Médicale, U1104, Centre National de la Recherche Scientifique UMR7280, Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Marseille, France
| | - María-Jesús Grilló
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas - Universidad Pública de Navarra - Gobierno de Navarra, Pamplona, Spain
| | | | - José A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
| | - Vilma Arce-Gorvel
- Institut National de la Santé et de la Recherche Médicale, U1104, Centre National de la Recherche Scientifique UMR7280, Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Marseille, France
| | - Jean-Pierre Gorvel
- Institut National de la Santé et de la Recherche Médicale, U1104, Centre National de la Recherche Scientifique UMR7280, Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University UM2, Marseille, France
| | - Ignacio Moriyón
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
| | - Maite Iriarte
- Universidad de Navarra, Facultad de Medicina, Departamento de Microbiología y Parasitología, Instituto de Salud Tropical (ISTUN) e Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
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Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P. A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications. PLoS One 2016; 11:e0159277. [PMID: 27500400 PMCID: PMC4976983 DOI: 10.1371/journal.pone.0159277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022] Open
Abstract
Recombination-based cloning is a quick and efficient way to generate expression vectors. Recent advancements have provided powerful recombinant DNA methods for molecular manipulations. Here, we describe a novel collection of three-fragment MultiSite Gateway cloning system-compatible vectors providing expanded molecular tools for vertebrate research. The components of this toolkit encompass a broad range of uses such as fluorescent imaging, dual gene expression, RNA interference, tandem affinity purification, chemically-inducible dimerization and lentiviral production. We demonstrate examples highlighting the utility of this toolkit for producing multi-component vertebrate expression vectors with diverse primary research applications. The vectors presented here are compatible with other Gateway toolkits and collections, facilitating the rapid generation of a broad range of innovative DNA constructs for biological research.
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Affiliation(s)
- Daniel K. Fowler
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott Stewart
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Steve Seredick
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Philip Washbourne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 2015; 408:345-57. [PMID: 26391338 PMCID: PMC4684507 DOI: 10.1016/j.ydbio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 08/18/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
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Affiliation(s)
- Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prasad Trivedi
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Karpinka
- Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Limin Liu
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - P Todd Stukenberg
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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8
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Deghelt M, Mullier C, Sternon JF, Francis N, Laloux G, Dotreppe D, Van der Henst C, Jacobs-Wagner C, Letesson JJ, De Bolle X. G1-arrested newborn cells are the predominant infectious form of the pathogen Brucella abortus. Nat Commun 2014; 5:4366. [PMID: 25006695 PMCID: PMC4104442 DOI: 10.1038/ncomms5366] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 12/15/2022] Open
Abstract
Several intracellular pathogens, such as Brucella abortus, display a biphasic infection process starting with a non-proliferative stage of unclear nature. Here, we study the cell cycle of B. abortus at the single-cell level, in culture and during infection of HeLa cells and macrophages. The localization of segregation and replication loci of the two bacterial chromosomes indicates that, immediately after being engulfed by host-cell endocytic vacuoles, most bacterial cells are newborn. These bacterial cells do not initiate DNA replication for the next 4 to 6 h, indicating a G1 arrest. Moreover, growth is completely stopped during that time, reflecting a global cell cycle block. Growth and DNA replication resume later, although bacteria still reside within endosomal-like compartments. We hypothesize that the predominance of G1-arrested bacteria in the infectious population, and the bacterial cell cycle arrest following internalization, may constitute a widespread strategy among intracellular pathogens to colonize new proliferation niches. Certain pathogenic bacteria such as Brucella abortus undergo a temporary non-proliferative stage after infecting host cells. Here, the authors study chromosomal replication and segregation in B. abortus during infection, showing that the non-proliferative stage consists of G1-arrested newborn cells.
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Affiliation(s)
- Michaël Deghelt
- 1] Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium [2]
| | - Caroline Mullier
- 1] Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium [2]
| | - Jean-François Sternon
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Nayla Francis
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Géraldine Laloux
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA [3] Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Delphine Dotreppe
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Charles Van der Henst
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Christine Jacobs-Wagner
- 1] Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA [2] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520, USA [3] Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean-Jacques Letesson
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
| | - Xavier De Bolle
- Microorganisms biology research unit (URBM), University of Namur (UNamur), Namur, Belgium
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9
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Gil-Ramírez Y, Conde-Álvarez R, Palacios-Chaves L, Zúñiga-Ripa A, Grilló MJ, Arce-Gorvel V, Hanniffy S, Moriyón I, Iriarte M. The identification of wadB, a new glycosyltransferase gene, confirms the branched structure and the role in virulence of the lipopolysaccharide core of Brucella abortus. Microb Pathog 2014; 73:53-9. [PMID: 24927935 DOI: 10.1016/j.micpath.2014.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 12/20/2022]
Abstract
Brucellosis is a worldwide extended zoonosis caused by Brucella spp. These gram-negative bacteria are not readily detected by innate immunity, a virulence-related property largely linked to their surface lipopolysaccharide (LPS). The role of the LPS lipid A and O-polysaccharide in virulence is well known. Moreover, mutation of the glycosyltransferase gene wadC of Brucella abortus, although not affecting O-polysaccharide assembly onto the lipid-A core section causes a core oligosaccharide defect that increases recognition by innate immunity. Here, we report on a second gene (wadB) encoding a LPS core glycosyltransferase not involved in the assembly of the O-polysaccharide-linked core section. As compared to wild-type B. abortus, a wadB mutant was sensitive to bactericidal peptides and non-immune serum, and was attenuated in mice and dendritic cells. These observations show that as WadC, WadB is also involved in the assembly of a branch of Brucella LPS core and support the concept that this LPS section is a virulence-related structure.
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Affiliation(s)
- Yolanda Gil-Ramírez
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
| | - Raquel Conde-Álvarez
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
| | - Leyre Palacios-Chaves
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
| | - Amaia Zúñiga-Ripa
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
| | - María-Jesús Grilló
- Instituto de Agrobiotecnología (CSIC-Universidad Pública de Navarra-Gobierno de Navarra), 31006 Pamplona, Spain.
| | - Vilma Arce-Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France; INSERM U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France.
| | - Sean Hanniffy
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France; INSERM U1104, 13288 Marseille, France; CNRS UMR7280, 13288 Marseille, France.
| | - Ignacio Moriyón
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
| | - Maite Iriarte
- Departamento de Microbiología y Parasitología e Instituto de Salud Tropical, Universidad de Navarra, 31008 Pamplona, Spain.
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10
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Van der Henst C, de Barsy M, Zorreguieta A, Letesson JJ, De Bolle X. The Brucella pathogens are polarized bacteria. Microbes Infect 2013; 15:998-1004. [PMID: 24141086 DOI: 10.1016/j.micinf.2013.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 10/01/2013] [Accepted: 10/03/2013] [Indexed: 11/30/2022]
Abstract
Brucella pathogens are responsible for brucellosis, a worldwide zoonosis. They are facultative intracellular pathogens characterized by their asymmetric division and their unipolar growth. This growth modality generates poles with specialized functions (through polar recruitment of polar adhesins or of cell cycle regulators) and progeny cells with potentially different fates.
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Affiliation(s)
- Charles Van der Henst
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Station 19, 1015 Lausanne, Switzerland
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11
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Salcedo SP, Marchesini MI, Degos C, Terwagne M, Von Bargen K, Lepidi H, Herrmann CK, Santos Lacerda TL, Imbert PRC, Pierre P, Alexopoulou L, Letesson JJ, Comerci DJ, Gorvel JP. BtpB, a novel Brucella TIR-containing effector protein with immune modulatory functions. Front Cell Infect Microbiol 2013; 3:28. [PMID: 23847770 PMCID: PMC3703528 DOI: 10.3389/fcimb.2013.00028] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/18/2013] [Indexed: 12/29/2022] Open
Abstract
Several bacterial pathogens have TIR domain-containing proteins that contribute to their pathogenesis. We identified a second TIR-containing protein in Brucella spp. that we have designated BtpB. We show it is a potent inhibitor of TLR signaling, probably via MyD88. BtpB is a novel Brucella effector that is translocated into host cells and interferes with activation of dendritic cells. In vivo mouse studies revealed that BtpB is contributing to virulence and control of local inflammatory responses with relevance in the establishment of chronic brucellosis. Together, our results show that BtpB is a novel Brucella effector that plays a major role in the modulation of host innate immune response during infection.
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Affiliation(s)
- Suzana P Salcedo
- Aix-Marseille Univ UM 2, Centre d'Immunologie de Marseille-Luminy Marseille, France
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12
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Waaijers S, Koorman T, Kerver J, Boxem M. Identification of human protein interaction domains using an ORFeome-based yeast two-hybrid fragment library. J Proteome Res 2013; 12:3181-92. [PMID: 23718855 DOI: 10.1021/pr400047p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Physical interactions between proteins are essential for biological processes. Hence, there have been major efforts to elucidate the complete networks of protein-protein interactions, or "interactomes", of various organisms. Detailed descriptions of protein interaction networks should include information on the discrete domains that mediate these interactions, yet most large-scale efforts model interactions between whole proteins only. We previously developed a yeast two-hybrid-based strategy to systematically map interaction domains and generated a domain-based interactome network for 750 proteins involved in C. elegans early embryonic development. Here, we expand the concept of Y2H-based interaction domain mapping to the genome-wide level. We generated a human fragment library by randomly fragmenting the full-length open reading frames (ORFs) present in the human ORFeome collection. Screens using several proteins required for cell division or polarity establishment as baits demonstrate the ability to accurately identify interaction domains for human proteins using this approach, while the experimental quality of the Y2H data was independently verified in coaffinity purification assays. The library generation strategy can easily be adapted to generate libraries from full-length ORF collections of other organisms.
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Affiliation(s)
- Selma Waaijers
- Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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13
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de Barsy M, Greub G. Functional genomics of intracellular bacteria. Brief Funct Genomics 2013; 12:341-53. [DOI: 10.1093/bfgp/elt012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Smirnova EA, Vasin AV, Sandybaev NT, Klotchenko SA, Plotnikova MA, Chervyakova OV, Sansyzbay AR, Kiselev OI. Current Methods of Human and Animal Brucellosis Diagnostics. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aid.2013.33026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Evaluation of the effects of erythritol on gene expression in Brucella abortus. PLoS One 2012; 7:e50876. [PMID: 23272076 PMCID: PMC3522698 DOI: 10.1371/journal.pone.0050876] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/25/2012] [Indexed: 11/19/2022] Open
Abstract
Bacteria of the genus Brucella have the unusual capability to catabolize erythritol and this property has been associated with their virulence mainly because of the presence of erythritol in bovine foetal tissues and because the attenuated S19 vaccine strain is the only Brucella strain unable to oxydize erythritol. In this work we have analyzed the transcriptional changes produced in Brucella by erythritol by means of two high throughput approaches: RNA hybridization against a microarray containing most of Brucella ORF's constructed from the Brucella ORFeome and next generation sequencing of Brucella mRNA in an Illumina GAIIx platform. The results obtained showed the overexpression of a group of genes, many of them in a single cluster around the ery operon, able to co-ordinately mediate the transport and degradation of erythritol into three carbon atoms intermediates that will be then converted into fructose-6P (F6P) by gluconeogenesis. Other induced genes participating in the nonoxidative branch of the pentose phosphate shunt and the TCA may collaborate with the ery genes to conform an efficient degradation of sugars by this route. On the other hand, several routes of amino acid and nucleotide biosynthesis are up-regulated whilst amino acid transport and catabolism genes are down-regulated. These results corroborate previous descriptions indicating that in the presence of erythritol, this sugar was used preferentially over other compounds and provides a neat explanation of the the reported stimulation of growth induced by erythritol.
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16
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Gallegos ME, Balakrishnan S, Chandramouli P, Arora S, Azameera A, Babushekar A, Bargoma E, Bokhari A, Chava SK, Das P, Desai M, Decena D, Saramma SDD, Dey B, Doss AL, Gor N, Gudiputi L, Guo C, Hande S, Jensen M, Jones S, Jones N, Jorgens D, Karamchedu P, Kamrani K, Kolora LD, Kristensen L, Kwan K, Lau H, Maharaj P, Mander N, Mangipudi K, Menakuru H, Mody V, Mohanty S, Mukkamala S, Mundra SA, Nagaraju S, Narayanaswamy R, Ndungu-Case C, Noorbakhsh M, Patel J, Patel P, Pendem SV, Ponakala A, Rath M, Robles MC, Rokkam D, Roth C, Sasidharan P, Shah S, Tandon S, Suprai J, Truong TQN, Uthayaruban R, Varma A, Ved U, Wang Z, Yu Z. The C. elegans rab family: identification, classification and toolkit construction. PLoS One 2012; 7:e49387. [PMID: 23185324 PMCID: PMC3504004 DOI: 10.1371/journal.pone.0049387] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 10/09/2012] [Indexed: 11/29/2022] Open
Abstract
Rab monomeric GTPases regulate specific aspects of vesicle transport in eukaryotes including coat recruitment, uncoating, fission, motility, target selection and fusion. Moreover, individual Rab proteins function at specific sites within the cell, for example the ER, golgi and early endosome. Importantly, the localization and function of individual Rab subfamily members are often conserved underscoring the significant contributions that model organisms such as Caenorhabditis elegans can make towards a better understanding of human disease caused by Rab and vesicle trafficking malfunction. With this in mind, a bioinformatics approach was first taken to identify and classify the complete C. elegans Rab family placing individual Rabs into specific subfamilies based on molecular phylogenetics. For genes that were difficult to classify by sequence similarity alone, we did a comparative analysis of intron position among specific subfamilies from yeast to humans. This two-pronged approach allowed the classification of 30 out of 31 C. elegans Rab proteins identified here including Rab31/Rab50, a likely member of the last eukaryotic common ancestor (LECA). Second, a molecular toolset was created to facilitate research on biological processes that involve Rab proteins. Specifically, we used Gateway-compatible C. elegans ORFeome clones as starting material to create 44 full-length, sequence-verified, dominant-negative (DN) and constitutive active (CA) rab open reading frames (ORFs). Development of this toolset provided independent research projects for students enrolled in a research-based molecular techniques course at California State University, East Bay (CSUEB).
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Affiliation(s)
- Maria E Gallegos
- Department of Biological Sciences, California State University East Bay, Hayward, CA, USA.
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17
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Maier CJ, Maier RH, Virok DP, Maass M, Hintner H, Bauer JW, Onder K. Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae. BMC Genomics 2012; 13:632. [PMID: 23157390 PMCID: PMC3534531 DOI: 10.1186/1471-2164-13-632] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background The Gram-negative bacterium Chlamydia pneumoniae (Cpn) is the leading intracellular human pathogen responsible for respiratory infections such as pneumonia and bronchitis. Basic and applied research in pathogen biology, especially the elaboration of new mechanism-based anti-pathogen strategies, target discovery and drug development, rely heavily on the availability of the entire set of pathogen open reading frames, the ORFeome. The ORFeome of Cpn will enable genome- and proteome-wide systematic analysis of Cpn, which will improve our understanding of the molecular networks and mechanisms underlying and governing its pathogenesis. Results Here we report the construction of a comprehensive gene collection covering 98.5% of the 1052 predicted and verified ORFs of Cpn (Chlamydia pneumoniae strain CWL029) in Gateway® ‘entry’ vectors. Based on genomic DNA isolated from the vascular chlamydial strain CV-6, we constructed an ORFeome library that contains 869 unique Gateway® entry clones (83% coverage) and an additional 168 PCR-verified ‘pooled’ entry clones, reaching an overall coverage of ~98.5% of the predicted CWL029 ORFs. The high quality of the ORFeome library was verified by PCR-gel electrophoresis and DNA sequencing, and its functionality was demonstrated by expressing panels of recombinant proteins in Escherichia coli and by genome-wide protein interaction analysis for a test set of three Cpn virulence factors in a yeast 2-hybrid system. The ORFeome is available in different configurations of resource stocks, PCR-products, purified plasmid DNA, and living cultures of E. coli harboring the desired entry clone or pooled entry clones. All resources are available in 96-well microtiterplates. Conclusion This first ORFeome library for Cpn provides an essential new tool for this important pathogen. The high coverage of entry clones will enable a systems biology approach for Cpn or host–pathogen analysis. The high yield of recombinant proteins and the promising interactors for Cpn virulence factors described here demonstrate the possibilities for proteome-wide studies.
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Affiliation(s)
- Christina J Maier
- Department of Dermatology, Paracelsus Medical University, Salzburg, Austria
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18
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Nagels Durand A, Moses T, De Clercq R, Goossens A, Pauwels L. A MultiSite Gateway™ vector set for the functional analysis of genes in the model Saccharomyces cerevisiae. BMC Mol Biol 2012; 13:30. [PMID: 22994806 PMCID: PMC3519679 DOI: 10.1186/1471-2199-13-30] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 09/17/2012] [Indexed: 12/02/2022] Open
Abstract
Background Recombinatorial cloning using the GatewayTM technology has been the method of choice for high-throughput omics projects, resulting in the availability of entire ORFeomes in GatewayTM compatible vectors. The MultiSite GatewayTM system allows combining multiple genetic fragments such as promoter, ORF and epitope tag in one single reaction. To date, this technology has not been accessible in the yeast Saccharomyces cerevisiae, one of the most widely used experimental systems in molecular biology, due to the lack of appropriate destination vectors. Results Here, we present a set of three-fragment MultiSite GatewayTM destination vectors that have been developed for gene expression in S. cerevisiae and that allow the assembly of any promoter, open reading frame, epitope tag arrangement in combination with any of four auxotrophic markers and three distinct replication mechanisms. As an example of its applicability, we used yeast three-hybrid to provide evidence for the assembly of a ternary complex of plant proteins involved in jasmonate signalling and consisting of the JAZ, NINJA and TOPLESS proteins. Conclusion Our vectors make MultiSite GatewayTM cloning accessible in S. cerevisiae and implement a fast and versatile cloning method for the high-throughput functional analysis of (heterologous) proteins in one of the most widely used model organisms for molecular biology research.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
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19
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Liu W, Dong H, Liu W, Gao X, Zhang C, Wu Q. OtpR regulated the growth, cell morphology of B. melitensis and tolerance to β-lactam agents. Vet Microbiol 2012; 159:90-8. [DOI: 10.1016/j.vetmic.2012.03.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Revised: 02/10/2012] [Accepted: 03/20/2012] [Indexed: 11/17/2022]
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20
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Mirabella A, Yañez Villanueva RM, Delrue RM, Uzureau S, Zygmunt MS, Cloeckaert A, De Bolle X, Letesson JJ. The two-component system PrlS/PrlR of Brucella melitensis is required for persistence in mice and appears to respond to ionic strength. MICROBIOLOGY-SGM 2012; 158:2642-2651. [PMID: 22859617 DOI: 10.1099/mic.0.060863-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacterial adaptation to environmental conditions is essential to ensure maximal fitness in the face of several stresses. In this context, two-component systems (TCSs) represent a predominant signal transduction mechanism, allowing an appropriate response to be mounted when a stimulus is sensed. As facultative intracellular pathogens, Brucella spp. face various environmental conditions, and an adequate response is required for a successful infection process. Recently, bioinformatic analysis of Brucella genomes predicted a set of 15 bona fide TCS pairs, among which some have been previously investigated. In this report, we characterized a new TCS locus called prlS/R, for probable proline sensor-regulator. It encodes a hybrid histidine kinase (PrlS) with an unusual Na(+)/solute symporter N-terminal domain and a transcriptional regulator (belonging to the LuxR family) (PrlR). In vitro, Brucella spp. with a functional PrlR/S system form bacterial aggregates, which seems to be an adaptive response to a hypersaline environment, while a prlS/R mutant does not. We identified ionic strength as a possible signal sensed by this TCS. Finally, this work correlates the absence of a functional PrlR/S system with the lack of hypersaline-induced aggregation in particular marine Brucella spp.
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Affiliation(s)
- Aurélie Mirabella
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Rosse-Mary Yañez Villanueva
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Rose-May Delrue
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Sophie Uzureau
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Michel S Zygmunt
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France
| | - Axel Cloeckaert
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, F-37000 Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, F-37380 Nouzilly, France
| | - Xavier De Bolle
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie des Microorganismes (URBM), NARILIS, University of Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
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de Barsy M, Mirabella A, Letesson JJ, De Bolle X. A Brucella abortus cstA mutant is defective for association with endoplasmic reticulum exit sites and displays altered trafficking in HeLa cells. MICROBIOLOGY-SGM 2012; 158:2610-2618. [PMID: 22820839 DOI: 10.1099/mic.0.060509-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Members of the genus Brucella are facultative intracellular pathogenic bacteria able to control maturation of their vacuoles. In several cell types, Brucella is able to reach a proliferation compartment derived from the endoplasmic reticulum (ER). Since ER exit site (ERES) functions are required for Brucella proliferation, we performed a yeast two-hybrid screen between human ERES-associated proteins and the predicted brucella proteome. This screening led to the identification of CstA, a conserved protein that specifically interacts with Sec24A, a component of the ERES. We found that a tagged CstA is secreted in Brucella abortus culture medium. This secretion is independent of the type IV secretion system VirB and the flagellum, suggesting that CstA is secreted through another system. We also discovered that a B. abortus cstA mutant is impaired for its association with the Sec23 ERES marker. The B. abortus cstA mutant displayed peculiar trafficking, with reduced association with LAMP1 and Calnexin 12 h post-infection in HeLa cells. However, its intracellular proliferation kinetics was not affected. The data reported here suggest that CstA could be directly or indirectly involved in the control of B. abortus intracellular trafficking in HeLa cells.
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Affiliation(s)
- Marie de Barsy
- Research Unit in Microorganisms Biology (URBM), University of Namur (FUNDP), Namur, Belgium
| | - Aurélie Mirabella
- Research Unit in Microorganisms Biology (URBM), University of Namur (FUNDP), Namur, Belgium
| | - Jean-Jacques Letesson
- Research Unit in Microorganisms Biology (URBM), University of Namur (FUNDP), Namur, Belgium
| | - Xavier De Bolle
- Research Unit in Microorganisms Biology (URBM), University of Namur (FUNDP), Namur, Belgium
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The lipopolysaccharide core of Brucella abortus acts as a shield against innate immunity recognition. PLoS Pathog 2012; 8:e1002675. [PMID: 22589715 PMCID: PMC3349745 DOI: 10.1371/journal.ppat.1002675] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 03/15/2012] [Indexed: 12/16/2022] Open
Abstract
Innate immunity recognizes bacterial molecules bearing pathogen-associated molecular patterns to launch inflammatory responses leading to the activation of adaptive immunity. However, the lipopolysaccharide (LPS) of the gram-negative bacterium Brucella lacks a marked pathogen-associated molecular pattern, and it has been postulated that this delays the development of immunity, creating a gap that is critical for the bacterium to reach the intracellular replicative niche. We found that a B. abortus mutant in the wadC gene displayed a disrupted LPS core while keeping both the LPS O-polysaccharide and lipid A. In mice, the wadC mutant induced proinflammatory responses and was attenuated. In addition, it was sensitive to killing by non-immune serum and bactericidal peptides and did not multiply in dendritic cells being targeted to lysosomal compartments. In contrast to wild type B. abortus, the wadC mutant induced dendritic cell maturation and secretion of pro-inflammatory cytokines. All these properties were reproduced by the wadC mutant purified LPS in a TLR4-dependent manner. Moreover, the core-mutated LPS displayed an increased binding to MD-2, the TLR4 co-receptor leading to subsequent increase in intracellular signaling. Here we show that Brucella escapes recognition in early stages of infection by expressing a shield against recognition by innate immunity in its LPS core and identify a novel virulence mechanism in intracellular pathogenic gram-negative bacteria. These results also encourage for an improvement in the generation of novel bacterial vaccines.
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Gupta VK, Radhakrishnan G, Harms J, Splitter G. Invasive Escherichia coli vaccines expressing Brucella melitensis outer membrane proteins 31 or 16 or periplasmic protein BP26 confer protection in mice challenged with B. melitensis. Vaccine 2012; 30:4017-22. [PMID: 22546330 DOI: 10.1016/j.vaccine.2012.04.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 11/30/2022]
Abstract
Because of the serious economic and medical consequences of brucellosis, efforts are to prevent infection of domestic animals through vaccines. Many disadvantages are associated with the current Brucella melitensis Rev.1 vaccine prompting development of alternative vaccines and delivery. Escherichia coli (DH5α) was engineered to express a plasmid containing the inv gene from Yersinia pseudotuberculosis and the hly gene from Listeria monocytogenes. These recombinant invasive E. coli expressing B. melitensis outer membrane proteins (Omp31 or 16) or the periplasmic protein BP26 were evaluated for protection of mice against virulent B. melitensis. Importantly, these invasive E. coli vaccines induced significant protection against B. melitensis challenged mice. Invasive E. coli may be an ideal vaccine platform with natural adjuvant properties for application against B. melitensis since the E. coli delivery system is non-pathogenic and can deliver antigens to antigen-presenting cells promoting cellular immune responses.
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Affiliation(s)
- V K Gupta
- Central Institute for Research On Goats, Makhdoom, PO Farah, Mathura 281 122, India.
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24
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Palacios-Chaves L, Zúñiga-Ripa A, Gutiérrez A, Gil-Ramírez Y, Conde-Álvarez R, Moriyón I, Iriarte M. Identification and functional analysis of the cyclopropane fatty acid synthase of Brucella abortus. Microbiology (Reading) 2012; 158:1037-1044. [DOI: 10.1099/mic.0.055897-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Leyre Palacios-Chaves
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Yolanda Gil-Ramírez
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Raquel Conde-Álvarez
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Maite Iriarte
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
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Dotreppe D, Mullier C, Letesson JJ, De Bolle X. The alkylation response protein AidB is localized at the new poles and constriction sites in Brucella abortus. BMC Microbiol 2011; 11:257. [PMID: 22111948 PMCID: PMC3236019 DOI: 10.1186/1471-2180-11-257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 11/23/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brucella abortus is the etiological agent of a worldwide zoonosis called brucellosis. This alpha-proteobacterium is dividing asymmetrically, and PdhS, an essential histidine kinase, was reported to be an old pole marker. RESULTS We were interested to identify functions that could be recruited to bacterial poles. The Brucella ORFeome, a collection of cloned predicted coding sequences, was placed in fusion with yellow fluorescent protein (YFP) coding sequence and screened for polar localizations in B. abortus. We report that AidB-YFP was systematically localized to the new poles and at constrictions sites in B. abortus, either in culture or inside infected HeLa cells or RAW264.7 macrophages. AidB is an acyl-CoA dehydrogenase (ACAD) homolog, similar to E. coli AidB, an enzyme putatively involved in destroying alkylating agents. Accordingly, a B. abortus aidB mutant is more sensitive than the wild-type strain to the lethality induced by methanesulphonic acid ethyl ester (EMS). The exposure to EMS led to a very low frequency of constriction events, suggesting that cell cycle is blocked during alkylation damage. The localization of AidB-YFP at the new poles and at constriction sites seems to be specific for this ACAD homolog since two other ACAD homologs fused to YFP did not show specific localization. The overexpression of aidB, but not the two other ACAD coding sequences, leads to multiple morphological defects. CONCLUSIONS Data reported here suggest that AidB is a marker of new poles and constriction sites, that could be considered as sites of preparation of new poles in the sibling cells originating from cell division. The possible role of AidB in the generation or the function of new poles needs further investigation.
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Affiliation(s)
- Delphine Dotreppe
- URBM, University of Namur (FUNDP), 61 rue de Bruxelles, Namur, 5000, Belgium
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Brucella melitensis cyclic di-GMP phosphodiesterase BpdA controls expression of flagellar genes. J Bacteriol 2011; 193:5683-91. [PMID: 21856843 DOI: 10.1128/jb.00428-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Brucella melitensis encounters a variety of conditions and stimuli during its life cycle--including environmental growth, intracellular infection, and extracellular dissemination--which necessitates flexibility of bacterial signaling to promote virulence. Cyclic-di-GMP is a bacterial secondary signaling molecule that plays an important role in adaptation to changing environments and altering virulence in a number of bacteria. To investigate the role of cyclic-di-GMP in B. melitensis, all 11 predicted cyclic-di-GMP-metabolizing proteins were separately deleted and the effect on virulence was determined. Three of these cyclic-di-GMP-metabolizing proteins were found to alter virulence. Deletion of the bpdA and bpdB genes resulted in attenuation of virulence of the bacterium, while deletion of the cgsB gene produced a hypervirulent strain. In a Vibrio reporter system to monitor apparent alteration in levels of cyclic-di-GMP, both BpdA and BpdB displayed a phenotype consistent with cyclic-di-GMP-specific phosphodiesterases, while CgsB displayed a cyclic-di-GMP synthase phenotype. Further analysis found that deletion of bpdA resulted in a dramatic decrease in flagellar promoter activities, and a flagellar mutant showed similar phenotypes to the bpdA and bpdB mutant strains in mouse models of infection. These data indicate a potential role for regulation of flagella in Brucella melitensis via cyclic-di-GMP.
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de Barsy M, Jamet A, Filopon D, Nicolas C, Laloux G, Rual JF, Muller A, Twizere JC, Nkengfac B, Vandenhaute J, Hill DE, Salcedo SP, Gorvel JP, Letesson JJ, De Bolle X. Identification of a Brucella spp. secreted effector specifically interacting with human small GTPase Rab2. Cell Microbiol 2011; 13:1044-58. [PMID: 21501366 DOI: 10.1111/j.1462-5822.2011.01601.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacteria of the Brucella genus are facultative intracellular class III pathogens. These bacteria are able to control the intracellular trafficking of their vacuole, presumably by the use of yet unknown translocated effectors. To identify such effectors, we used a high-throughput yeast two-hybrid screen to identify interactions between putative human phagosomal proteins and predicted Brucella spp. proteins. We identified a specific interaction between the human small GTPase Rab2 and a Brucella spp. protein named RicA. This interaction was confirmed by GST-pull-down with the GDP-bound form of Rab2. A TEM-β-lactamase-RicA fusion was translocated from Brucella abortus to RAW264.7 macrophages during infection. This translocation was not detectable in a strain deleted for the virB operon, coding for the type IV secretion system. However, RicA secretion in a bacteriological culture was still observed in a ΔvirB mutant. In HeLa cells, a ΔricA mutant recruits less GTP-locked myc-Rab2 on its Brucella-containing vacuoles, compared with the wild-type strain. We observed altered kinetics of intracellular trafficking and faster proliferation of the B. abortusΔricA mutant in HeLa cells, compared with the wild-type control. Altogether, the data reported here suggest RicA as the first reported effector with a proposed function for B. abortus.
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Ferooz J, Lemaire J, Letesson JJ. Role of FlbT in flagellin production in Brucella melitensis. MICROBIOLOGY-SGM 2011; 157:1253-1262. [PMID: 21273249 DOI: 10.1099/mic.0.044867-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It was recently demonstrated that the pathogen Brucella melitensis produces a polar sheathed flagellum under the control of the master regulator FtcR. However, the regulatory mechanism controlling the flagellar assembly remains unknown. In this work, we investigate the flagellar hierarchy of B. melitensis as well as the flagellin FliC regulation. We show that a mutation in fliF or flgE (coding for the basal body structure and the hook, respectively) does not affect FliC synthesis, suggesting that production of FliC does not depend on the flagellar assembly. We demonstrate that FlbT is a FliC activator since inactivation of flbT causes a decrease in fliC expression by using a fliC-lacZ translational reporter construct. Moreover, the quantitative real-time PCR and Western blot analysis show a marked decrease in fliC mRNA and FliC protein level, respectively. Conversely, the B. melitensis wild-type strain overexpressing flaF fails to produce FliC, suggesting an opposite function. Interestingly, the expression of the flbT gene in an ftcR or an flbT mutant restores FliC production, demonstrating that FlbT plays a regulatory checkpoint role in FliC synthesis. This mechanism could be conserved in the Rhizobiales since complementation of an flbT or an ftcR mutant with flbT from Sinorhizobium meliloti restores FliC synthesis.
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Affiliation(s)
- Jonathan Ferooz
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Julien Lemaire
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires Notre-Dame de la Paix Namur (FUNDP), 61 rue de Bruxelles, B-5000 Namur, Belgium
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Palacios-Chaves L, Conde-Álvarez R, Gil-Ramírez Y, Zúñiga-Ripa A, Barquero-Calvo E, Chacón-Díaz C, Chaves-Olarte E, Arce-Gorvel V, Gorvel JP, Moreno E, de Miguel MJ, Grilló MJ, Moriyón I, Iriarte M. Brucella abortus ornithine lipids are dispensable outer membrane components devoid of a marked pathogen-associated molecular pattern. PLoS One 2011; 6:e16030. [PMID: 21249206 PMCID: PMC3017556 DOI: 10.1371/journal.pone.0016030] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022] Open
Abstract
The brucellae are α-Proteobacteria facultative intracellular parasites that cause an important zoonosis. These bacteria escape early detection by innate immunity, an ability associated to the absence of marked pathogen-associated molecular patterns in the cell envelope lipopolysaccharide, lipoproteins and flagellin. We show here that, in contrast to the outer membrane ornithine lipids (OL) of other Gram negative bacteria, Brucella abortus OL lack a marked pathogen-associated molecular pattern activity. We identified two OL genes (olsB and olsA) and by generating the corresponding mutants found that olsB deficient B. abortus did not synthesize OL or their lyso-OL precursors. Liposomes constructed with B. abortus OL did not trigger IL-6 or TNF-α release by macrophages whereas those constructed with Bordetella pertussis OL and the olsB mutant lipids as carriers were highly active. The OL deficiency in the olsB mutant did not promote proinflammatory responses or generated attenuation in mice. In addition, OL deficiency did not increase sensitivity to polymyxins, normal serum or complement consumption, or alter the permeability to antibiotics and dyes. Taken together, these observations indicate that OL have become dispensable in the extant brucellae and are consistent within the trend observed in α-Proteobacteria animal pathogens to reduce and eventually eliminate the envelope components susceptible of recognition by innate immunity.
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Affiliation(s)
- Leyre Palacios-Chaves
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Raquel Conde-Álvarez
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
- Focal Area Infection Biology, Biozentrum of the University of Basel, Basel, Switzerland
| | - Yolanda Gil-Ramírez
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Amaia Zúñiga-Ripa
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Vilma Arce-Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Faculté de Sciences de Luminy, Marseille, INSERM U631, CNRS UMR6102, Marseille, France
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Faculté de Sciences de Luminy, Marseille, INSERM U631, CNRS UMR6102, Marseille, France
| | - Edgardo Moreno
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San Pedro, Costa Rica
| | - María-Jesús de Miguel
- Centro de Investigación y Tecnología Agroalimentaria (CITA), Unidad de Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - María-Jesús Grilló
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Maite Iriarte
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
- * E-mail:
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Uzureau S, Lemaire J, Delaive E, Dieu M, Gaigneaux A, Raes M, De Bolle X, Letesson JJ. Global analysis of quorum sensing targets in the intracellular pathogen Brucella melitensis 16 M. J Proteome Res 2010; 9:3200-17. [PMID: 20387905 PMCID: PMC2880877 DOI: 10.1021/pr100068p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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Many pathogenic bacteria use a regulatory process termed quorum sensing (QS) to produce and detect small diffusible molecules to synchronize gene expression within a population. In Gram-negative bacteria, the detection of, and response to, these molecules depends on transcriptional regulators belonging to the LuxR family. Such a system has been discovered in the intracellular pathogen Brucella melitensis, a Gram-negative bacterium responsible for brucellosis, a worldwide zoonosis that remains a serious public health concern in countries were the disease is endemic. Genes encoding two LuxR-type regulators, VjbR and BabR, have been identified in the genome of B. melitensis 16 M. A ΔvjbR mutant is highly attenuated in all experimental models of infection tested, suggesting a crucial role for QS in the virulence of Brucella. At present, no function has been attributed to BabR. The experiments described in this report indicate that 5% of the genes in the B. melitensis 16 M genome are regulated by VjbR and/or BabR, suggesting that QS is a global regulatory system in this bacterium. The overlap between BabR and VjbR targets suggest a cross-talk between these two regulators. Our results also demonstrate that VjbR and BabR regulate many genes and/or proteins involved in stress response, metabolism, and virulence, including those potentially involved in the adaptation of Brucella to the oxidative, pH, and nutritional stresses encountered within the host. These findings highlight the involvement of QS as a major regulatory system in Brucella and lead us to suggest that this regulatory system could participate in the spatial and sequential adaptation of Brucella strains to the host environment. Some pathogens use the regulatory process termed Quorum Sensing (QS) to synchronize gene expression within bacterial population. We report here the first genome scale study of the Quorum Sensing system of the intracellular pathogen Brucella melitensis. Our combined proteomic and transcriptomic data suggest that Quorum Sensing is involved in the spatial and sequential adaptation of B. melitensis to the host environment.
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Affiliation(s)
- Sophie Uzureau
- Unité de Recherche en Biologie Moléculaire, Laboratoire d'Immunologie-Microbiologie, FUNDP - University of Namur, Namur, Belgium
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Laloux G, Deghelt M, de Barsy M, Letesson JJ, De Bolle X. Identification of the essential Brucella melitensis porin Omp2b as a suppressor of Bax-induced cell death in yeast in a genome-wide screening. PLoS One 2010; 5:e13274. [PMID: 20949000 PMCID: PMC2952587 DOI: 10.1371/journal.pone.0013274] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 09/09/2010] [Indexed: 01/08/2023] Open
Abstract
Background Inhibition of apoptosis is one of the mechanisms selected by numerous intracellular pathogenic bacteria to control their host cell. Brucellae, which are the causative agent of a worldwide zoonosis, prevent apoptosis of infected cells, probably to support survival of their replication niche. Methodology/Principal Findings In order to identify Brucella melitensis anti-apoptotic effector candidates, we performed a genome-wide functional screening in yeast. The B. melitensis ORFeome was screened to identify inhibitors of Bax-induced cell death in S. cerevisiae. B. melitensis porin Omp2b, here shown to be essential, prevents Bax lethal effect in yeast, unlike its close paralog Omp2a. Our results based on Omp2b size variants characterization suggest that signal peptide processing is required for Omp2b effect in yeast. Conclusion/Significance We report here the first application to a bacterial genome-wide library of coding sequences of this “yeast-rescue” screening strategy, previously used to highlight several new apoptosis regulators. Our work provides B. melitensis proteins that are candidates for an anti-apoptotic function, and can be tested in mammalian cells in the future. Hypotheses on possible molecular mechanisms of Bax inhibition by the B. melitensis porin Omp2b are discussed.
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Affiliation(s)
- Géraldine Laloux
- Research Unit in Molecular Biology, Department of Biology, University of Namur (FUNDP), Namur, Belgium
| | - Michaël Deghelt
- Research Unit in Molecular Biology, Department of Biology, University of Namur (FUNDP), Namur, Belgium
| | - Marie de Barsy
- Research Unit in Molecular Biology, Department of Biology, University of Namur (FUNDP), Namur, Belgium
| | - Jean-Jacques Letesson
- Research Unit in Molecular Biology, Department of Biology, University of Namur (FUNDP), Namur, Belgium
| | - Xavier De Bolle
- Research Unit in Molecular Biology, Department of Biology, University of Namur (FUNDP), Namur, Belgium
- * E-mail:
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Functional characterization of the incomplete phosphotransferase system (PTS) of the intracellular pathogen Brucella melitensis. PLoS One 2010; 5. [PMID: 20844759 PMCID: PMC2937029 DOI: 10.1371/journal.pone.0012679] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 08/15/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In many bacteria, the phosphotransferase system (PTS) is a key player in the regulation of the assimilation of alternative carbon sources notably through catabolic repression. The intracellular pathogens Brucella spp. possess four PTS proteins (EINtr, NPr, EIIANtr and an EIIA of the mannose family) but no PTS permease suggesting that this PTS might serve only regulatory functions. METHODOLOGY/PRINCIPAL FINDINGS In vitro biochemical analyses and in vivo detection of two forms of EIIANtr (phosphorylated or not) established that the four PTS proteins of Brucella melitensis form a functional phosphorelay. Moreover, in vitro the protein kinase HprK/P phosphorylates NPr on a conserved serine residue, providing an additional level of regulation to the B. melitensis PTS. This kinase activity was inhibited by inorganic phosphate and stimulated by fructose-1,6 bisphosphate. The genes encoding HprK/P, an EIIAMan-like protein and NPr are clustered in a locus conserved among α-proteobacteria and also contain the genes for the crucial two-component system BvrR-BvrS. RT-PCR revealed a transcriptional link between these genes suggesting an interaction between PTS and BvrR-BvrS. Mutations leading to the inactivation of EINtr or NPr significantly lowered the synthesis of VirB proteins, which form a type IV secretion system. These two mutants also exhibit a small colony phenotype on solid media. Finally, interaction partners of PTS proteins were identified using a yeast two hybrid screen against the whole B. melitensis ORFeome. Both NPr and HprK/P were shown to interact with an inorganic pyrophosphatase and the EIIAMan-like protein with the E1 component (SucA) of 2-oxoglutarate dehydrogenase. CONCLUSIONS/SIGNIFICANCE The B. melitensis can transfer the phosphoryl group from PEP to the EIIAs and a link between the PTS and the virulence of this organism could be established. Based on the protein interaction data a preliminary model is proposed in which this regulatory PTS coordinates also C and N metabolism.
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Christopher S, Umapathy BL, Ravikumar KL. Brucellosis: review on the recent trends in pathogenicity and laboratory diagnosis. J Lab Physicians 2010; 2:55-60. [PMID: 21346896 PMCID: PMC3040083 DOI: 10.4103/0974-2727.72149] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Brucellosis is a zoonotic infection transmitted from animals to humans by the ingestion of infected food products, direct contact with an infected animal or inhalation of aerosols. The last method is remarkably efficient given the relatively low concentration of organisms (10 - 100 bacteria) needed to establish infection in humans, and has brought renewed attention to this old disease. Brucella is a facultative intracellular pathogen that has the ability to survive and multiply in the phagocytes and cause abortion in cattle and undulant fever in humans. Brucella spp particularly B. melitensis, B. abortus, and B. suis represent a significant public health concern. At present, B. melitensis is the principle cause of human brucellosis in India. Molecular studies have demonstrated the phylogenetic affiliation of Brucella to Agrobacterium, Ochrobactrum, and Rhizobium. Human brucellosis still presents scientists and clinicians with several challenges, with regard to the understanding of its pathogenic mechanism, severity, progression, and development of improved treatment regimens. Molecular studies have now highlighted the pathogenesis of Brucella, for the development of newer diagnostic tools that will be useful in developing countries where brucellosis is a common, but often a neglected disease. This review compiles all these issues in general and the pathogenicity and newer diagnostic tools in particular.
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Affiliation(s)
- Supriya Christopher
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
| | - B L Umapathy
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
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Lamontagne J, Béland M, Forest A, Côté-Martin A, Nassif N, Tomaki F, Moriyón I, Moreno E, Paramithiotis E. Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome. BMC Genomics 2010; 11:300. [PMID: 20462421 PMCID: PMC2877026 DOI: 10.1186/1471-2164-11-300] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 05/12/2010] [Indexed: 12/23/2022] Open
Abstract
Background Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data. Results The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes. Conclusions An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.
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Affiliation(s)
- Julie Lamontagne
- Caprion Proteomics Inc, 7150 Alexander-Fleming, Montreal, Quebec, Canada
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Viadas C, Rodríguez MC, Sangari FJ, Gorvel JP, García-Lobo JM, López-Goñi I. Transcriptome analysis of the Brucella abortus BvrR/BvrS two-component regulatory system. PLoS One 2010; 5:e10216. [PMID: 20422049 PMCID: PMC2858072 DOI: 10.1371/journal.pone.0010216] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 03/20/2010] [Indexed: 12/11/2022] Open
Abstract
Background The two-component BvrR/BvrS system is essential for Brucella abortus virulence. It was shown previously that its dysfunction alters the expression of some major outer membrane proteins and the pattern of lipid A acylation. To determine the genes regulated by BvrR/BvrS, we performed a whole-genome microarray analysis using B. abortus RNA obtained from wild type and bvrR mutant cells grown in the same conditions. Methodology/Principal Findings A total of 127 differentially expressed genes were found: 83 were over expressed and 44 were less expressed in the bvrR mutant. Two operons, the phosphotransferase system and the maltose transport system, were down-regulated. Several genes involved in cell envelope or outer membrane biogenesis were differentially expressed: genes for outer membrane proteins (omp25a, omp25d), lipoproteins, LPS and fatty acid biosynthesis, stress response proteins, chaperones, flagellar genes, and twelve genes encoding ABC transport systems. Ten genes related with carbon metabolism (pckA and fumB among others) were up-regulated in the bvrR mutant, and denitrification genes (nirK, norC and nosZ) were also regulated. Notably, seven transcriptional regulators were affected, including VjbR, ExoR and OmpR that were less expressed in the bvrR mutant. Finally, the expression of eleven genes which have been previously related with Brucella virulence was also altered. Conclusions/Significance All these data corroborate the impact of BvrR/BvrS on cell envelope modulation, confirm that this system controls the carbon and nitrogen metabolism, and suggest a cross-talk among some regulators to adjust the Brucella physiology to the shift expected to occur during the transit from the extracellular to the intracellular niche.
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Affiliation(s)
- Cristina Viadas
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - María C. Rodríguez
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC/CSIC/IDICAN, Santander, Spain
| | - Felix J. Sangari
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC/CSIC/IDICAN, Santander, Spain
| | - Jean-Pierre Gorvel
- Faculté des Sciences de Luminy, Centre d'Immunologie de Marseille-Luminy (CIML), UMR6546, Aix Marseille Université, Marseille, France
- Inserm, U631, Marseille, France
- CNRS, UMR6102, Marseille, France
| | - Juan M. García-Lobo
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC/CSIC/IDICAN, Santander, Spain
| | - Ignacio López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
- * E-mail:
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Godefroid M, Svensson MV, Cambier P, Uzureau S, Mirabella A, De Bolle X, Van Cutsem P, Widmalm G, Letesson JJ. Brucella melitensis 16M produces a mannan and other extracellular matrix components typical of a biofilm. ACTA ACUST UNITED AC 2010; 59:364-77. [PMID: 20497223 DOI: 10.1111/j.1574-695x.2010.00689.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mutations in the Brucella melitensis quorum-sensing (QS) system are involved in the formation of clumps containing an exopolysaccharide. Here, we show that the overexpression of a gene called aiiD in B. melitensis gives rise to a similar clumping phenotype. The AiiD enzyme degrades AHL molecules and leads therefore to a QS-deficient strain. We demonstrated the presence of exopolysaccharide and DNA, two classical components of extracellular matrices, in clumps produced by this strain. We also observed that the production of outer membrane vesicles is strongly increased in the aiiD-overexpressing strain. Moreover, this strain allowed us to purify the exopolysaccharide and to obtain its composition and the first structural information on the complex exopolysaccharide produced by B. melitensis 16M, which was found to have a molecular weight of about 16 kDa and to be composed of glucosamine, glucose and mostly mannose. In addition, we found the presence of 2- and/or 6-substituted mannosyl residues, which provide the first insights into the linkages involved in this polymer. We used a classical biofilm attachment assay and an HeLa cell infection model to demonstrate that the clumping strain is more adherent to polystyrene plates and to HeLa cell surfaces than the wild-type one. Taken together, these data reinforce the evidence that B. melitensis could form biofilms in its lifecycle.
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Affiliation(s)
- Marie Godefroid
- Unité de Recherche en Biologie Moléculaire, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgium
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Sangari FJ, Cayón AM, Seoane A, García-Lobo JM. Brucella abortus ure2 region contains an acid-activated urea transporter and a nickel transport system. BMC Microbiol 2010; 10:107. [PMID: 20380737 PMCID: PMC2868824 DOI: 10.1186/1471-2180-10-107] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 04/10/2010] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Urease is a virulence factor that plays a role in the resistance of Brucella to low pH conditions, both in vivo and in vitro. Brucella contains two separate urease gene clusters, ure1 and ure2. Although only ure1 codes for an active urease, ure2 is also transcribed, but its contribution to Brucella biology is unknown. RESULTS Re-examination of the ure2 locus showed that the operon includes five genes downstream of ureABCEFGDT that are orthologs to a nikKMLQO cluster encoding an ECF-type transport system for nickel. ureT and nikO mutants were constructed and analyzed for urease activity and acid resistance. A non-polar ureT mutant was unaffected in urease activity at neutral pH but showed a significantly decreased activity at acidic pH. It also showed a decreased survival rate to pH 2 at low concentration of urea when compared to the wild type. The nikO mutant had decreased urease activity and acid resistance at all urea concentrations tested, and this phenotype could be reverted by the addition of nickel to the growth medium. CONCLUSIONS Based on these results, we concluded that the operon ure2 codes for an acid-activated urea transporter and a nickel transporter necessary for the maximal activity of the urease whose structural subunits are encoded exclusively by the genes in the ure1 operon.
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Affiliation(s)
- Félix J Sangari
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Ana M Cayón
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Asunción Seoane
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
| | - Juan M García-Lobo
- Departamento de Biología Molecular, Universidad de Cantabria, and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), UC-CSIC-IDICAN, Santander, Spain
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PdhS, an old-pole-localized histidine kinase, recruits the fumarase FumC in Brucella abortus. J Bacteriol 2010; 192:3235-9. [PMID: 20382762 DOI: 10.1128/jb.00066-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial pathogen Brucella abortus was recently demonstrated to recruit the essential cytoplasmic histidine kinase PdhS to its old pole. Here, we report identification of the fumarase FumC as a specific partner for the N-terminal "sensing" domain of PdhS, using an ORFeome-based yeast two-hybrid screen. We observed that FumC and PdhS colocalize at the old pole of B. abortus, while the other fumarase FumA is not polarly localized. FumC is not required for PdhS localization, and polar FumC localization is not FumA dependent. FumC homologs are not polarly localized in Sinorhizobium meliloti and Caulobacter crescentus, suggesting that polar recruitment of FumC by PdhS is evolutionarily recent.
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Abstract
Herein, we describe a protocol for the global identification of in vitro substrates targeted by protein kinases using protein microarray technology. Large numbers of fusion proteins tagged at their carboxy-termini are purified in 96-well format and spotted in duplicate onto amino-silane-coated slides in a spatially addressable manner. These arrays are incubated in the presence of purified kinase and radiolabeled ATP, and then washed, dried and analyzed by autoradiography. The extent of phosphorylation of each spot is quantified and normalized, and proteins that are reproducibly phosphorylated in the presence of the active kinase relative to control slides are scored as positive substrates. This approach enables the rapid determination of kinase-substrate relationship on a proteome-wide scale, and although developed using yeast, has since been adapted to higher eukaryotic systems. Expression, purification and printing of the yeast proteome require about 3 weeks. Afterwards, each kinase assay takes approximately 3 h to perform.
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Zhang L, Villa NY, Rahman MM, Smallwood S, Shattuck D, Neff C, Dufford M, Lanchbury JS, Labaer J, McFadden G. Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings. J Proteome Res 2009; 8:4311-8. [PMID: 19637933 PMCID: PMC2738428 DOI: 10.1021/pr900491n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccinia virus, a large double-stranded DNA virus, is the prototype of the Orthopoxvirus genus, which includes several pathogenic poxviruses of humans, such as monkeypox virus and variola virus. Here, we report a comprehensive yeast two-hybrid (Y2H) screening for the protein-protein interactions between vaccinia and human proteins. A total of 109 novel vaccinia-human protein interactions were detected among 33 viral proteins. To validate subsets of those interactions, we constructed an ORFeome library of vaccinia virus strain WR using the Gateway plasmid cloning system. By co-expressing selected vaccinia and host proteins in a variety of expression systems, we found that at least 17 of the Y2H hits identified between vaccinia and human proteins can be verified by independent methods using GST pull-down assays, representing a 63% validation rate for the Y2H hits examined (17/27). Because the cloned ORFs are conveniently transferable from the entry vectors to various destination expression vectors, the vaccinia ORFeome library will be a useful resource for future high-throughput functional proteomic experiments.
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Affiliation(s)
- Leiliang Zhang
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
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Pellet J, Tafforeau L, Lucas-Hourani M, Navratil V, Meyniel L, Achaz G, Guironnet-Paquet A, Aublin-Gex A, Caignard G, Cassonnet P, Chaboud A, Chantier T, Deloire A, Demeret C, Le Breton M, Neveu G, Jacotot L, Vaglio P, Delmotte S, Gautier C, Combet C, Deleage G, Favre M, Tangy F, Jacob Y, Andre P, Lotteau V, Rabourdin-Combe C, Vidalain PO. ViralORFeome: an integrated database to generate a versatile collection of viral ORFs. Nucleic Acids Res 2009; 38:D371-8. [PMID: 20007148 PMCID: PMC2808970 DOI: 10.1093/nar/gkp1000] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions in high-throughput assays. Such ‘ORFeome’ resources have been developed for several organisms but in virology, plasmid collections covering a significant fraction of the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway® system. ViralORFeome provides a convenient interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to validate the sequence of generated constructs and to browse established collections of virus ORFs. Most importantly, ViralORFeome has been designed to manage all possible variants or mutants of a given ORF so that the cloning procedure can be applied to any emerging virus strain. A subset of plasmid constructs generated with ViralORFeome platform has been tested with success for heterologous protein expression in different expression systems at proteome scale. ViralORFeome should provide our community with a framework to establish a large collection of virus ORF clones, an instrumental resource to determine functions, activities and binding partners of viral proteins.
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Affiliation(s)
- J Pellet
- INSERM U851, Lyon, IFR128-BioSciences, Université Lyon 1, Université de Lyon, Lyon, France
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Construction and evaluation of an ORFeome-based Brucella whole-genome DNA microarray. Microb Pathog 2009; 47:189-95. [DOI: 10.1016/j.micpath.2009.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 05/28/2009] [Accepted: 06/04/2009] [Indexed: 11/21/2022]
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Abstract
Biochemical assay of proteomic libraries derived from the Saccharomyces cerevisiae genome provides a powerful new tool for the assignment of activities to proteins. Particular advantages of this approach include the speed with which a protein can be identified and the generality for any biological activity for which an assay can be developed. We discuss the utility of this approach for the identification of RNA-modifying enzymes using a yeast proteomic library derived from a genomic set of strains expressing GST-ORF fusion proteins. This technique is also broadly applicable to other classes of RNA-protein interactions, including RNA binding and RNA degradation, and can be used with any of the proteomic libraries that are available.
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Harms JS, Durward MA, Magnani DM, Splitter GA. Evaluation of recombinant invasive, non-pathogenic Eschericia coli as a vaccine vector against the intracellular pathogen, Brucella. JOURNAL OF IMMUNE BASED THERAPIES AND VACCINES 2009; 7:1. [PMID: 19126207 PMCID: PMC2633335 DOI: 10.1186/1476-8518-7-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/06/2009] [Indexed: 01/18/2023]
Abstract
Background There is no safe, effective human vaccine against brucellosis. Live attenuated Brucella strains are widely used to vaccinate animals. However these live Brucella vaccines can cause disease and are unsafe for humans. Killed Brucella or subunit vaccines are not effective in eliciting long term protection. In this study, we evaluate an approach using a live, non-pathogenic bacteria (E. coli) genetically engineered to mimic the brucellae pathway of infection and present antigens for an appropriate cytolitic T cell response. Methods E. coli was modified to express invasin of Yersinia and listerialysin O (LLO) of Listeria to impart the necessary infectivity and antigen releasing traits of the intracellular pathogen, Brucella. This modified E. coli was considered our vaccine delivery system and was engineered to express Green Fluorescent Protein (GFP) or Brucella antigens for in vitro and in vivo immunological studies including cytokine profiling and cytotoxicity assays. Results The E. coli vaccine vector was able to infect all cells tested and efficiently deliver therapeutics to the host cell. Using GFP as antigen, we demonstrate that the E. coli vaccine vector elicits a Th1 cytokine profile in both primary and secondary immune responses. Additionally, using this vector to deliver a Brucella antigen, we demonstrate the ability of the E. coli vaccine vector to induce specific Cytotoxic T Lymphocytes (CTLs). Conclusion Protection against most intracellular bacterial pathogens can be obtained mostly through cell mediated immunity. Data presented here suggest modified E. coli can be used as a vaccine vector for delivery of antigens and therapeutics mimicking the infection of the pathogen and inducing cell mediated immunity to that pathogen.
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Affiliation(s)
- Jerome S Harms
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 1656 Linden Drive, Madison, WI 53706, USA.
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Abstract
Predicting the behavior of living organisms is an enormous challenge given their vast complexity. Efforts to model biological systems require large datasets generated by physical binding experiments and perturbation studies. Genetic perturbations have proven important and are greatly facilitated by the advent of comprehensive mutant libraries in model organisms. Small-molecule chemical perturbagens provide a complementary approach, especially for systems that lack mutant libraries, and can easily probe the function of essential genes. Though single chemical or genetic perturbations provide crucial information associating individual components (for example, genes, proteins or small molecules) with pathways or phenotypes, functional relationships between pathways and modules of components are most effectively obtained from combined perturbation experiments. Here we review the current state of and discuss some future directions for 'combination chemical genetics', the systematic application of multiple chemical or mixed chemical and genetic perturbations, both to gain insight into biological systems and to facilitate medical discoveries.
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Affiliation(s)
- Joseph Lehár
- CombinatoRx Incorporated, 245 First Street, Cambridge, Massachusetts 02142, USA.
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Abstract
During the last 10 years, there has been a large increase in the number of genome sequences available for study, altering the way that the biology of organisms is studied. In particular, scientific attention has increasingly focused on the proteome, and specifically on the role of all the proteins encoded by the genome. We focus here on several aspects of this problem. We describe several technologies in widespread use to clone genes on a genome-wide scale, and to express and purify the proteins encoded by these genes. We also describe a number of methods that have been developed to analyze various biochemical properties of the proteins, with attention to the methodology and the limitations of the approaches, followed by a look at possible developments in the next decade.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA.
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Gao H, Pattison D, Yan T, Klingeman DM, Wang X, Petrosino J, Hemphill L, Wan X, Leaphart AB, Weinstock GM, Palzkill T, Zhou J. Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display. PLoS One 2008; 3:e2983. [PMID: 18714347 PMCID: PMC2500165 DOI: 10.1371/journal.pone.0002983] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/28/2008] [Indexed: 12/02/2022] Open
Abstract
A comprehensive gene collection for S. oneidensis was constructed using the lambda recombinase (Gateway) cloning system. A total of 3584 individual ORFs (85%) have been successfully cloned into the entry plasmids. To validate the use of the clone set, three sets of ORFs were examined within three different destination vectors constructed in this study. Success rates for heterologous protein expression of S. oneidensis His- or His/GST- tagged proteins in E. coli were approximately 70%. The ArcA and NarP transcription factor proteins were tested in an in vitro binding assay to demonstrate that functional proteins can be successfully produced using the clone set. Further functional validation of the clone set was obtained from phage display experiments in which a phage encoding thioredoxin was successfully isolated from a pool of 80 different clones after three rounds of biopanning using immobilized anti-thioredoxin antibody as a target. This clone set complements existing genomic (e.g., whole-genome microarray) and other proteomic tools (e.g., mass spectrometry-based proteomic analysis), and facilitates a wide variety of integrated studies, including protein expression, purification, and functional analyses of proteins both in vivo and in vitro.
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Affiliation(s)
- Haichun Gao
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Donna Pattison
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Tingfen Yan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dawn M. Klingeman
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaohu Wang
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Petrosino
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Lisa Hemphill
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiufeng Wan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Adam B. Leaphart
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Timothy Palzkill
- Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (TP); (JZ)
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail: (TP); (JZ)
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González D, Grilló MJ, De Miguel MJ, Ali T, Arce-Gorvel V, Delrue RM, Conde-Álvarez R, Muñoz P, López-Goñi I, Iriarte M, Marín CM, Weintraub A, Widmalm G, Zygmunt M, Letesson JJ, Gorvel JP, Blasco JM, Moriyón I. Brucellosis vaccines: assessment of Brucella melitensis lipopolysaccharide rough mutants defective in core and O-polysaccharide synthesis and export. PLoS One 2008; 3:e2760. [PMID: 18648644 PMCID: PMC2453230 DOI: 10.1371/journal.pone.0002760] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 06/24/2008] [Indexed: 11/19/2022] Open
Abstract
Background The brucellae are facultative intracellular bacteria that cause brucellosis, one of the major neglected zoonoses. In endemic areas, vaccination is the only effective way to control this disease. Brucella melitensis Rev 1 is a vaccine effective against the brucellosis of sheep and goat caused by B. melitensis, the commonest source of human infection. However, Rev 1 carries a smooth lipopolysaccharide with an O-polysaccharide that elicits antibodies interfering in serodiagnosis, a major problem in eradication campaigns. Because of this, rough Brucella mutants lacking the O-polysaccharide have been proposed as vaccines. Methodology/Principal Findings To examine the possibilities of rough vaccines, we screened B. melitensis for lipopolysaccharide genes and obtained mutants representing all main rough phenotypes with regard to core oligosaccharide and O-polysaccharide synthesis and export. Using the mouse model, mutants were classified into four attenuation patterns according to their multiplication and persistence in spleens at different doses. In macrophages, mutants belonging to three of these attenuation patterns reached the Brucella characteristic intracellular niche and multiplied intracellularly, suggesting that they could be suitable vaccine candidates. Virulence patterns, intracellular behavior and lipopolysaccharide defects roughly correlated with the degree of protection afforded by the mutants upon intraperitoneal vaccination of mice. However, when vaccination was applied by the subcutaneous route, only two mutants matched the protection obtained with Rev 1 albeit at doses one thousand fold higher than this reference vaccine. These mutants, which were blocked in O-polysaccharide export and accumulated internal O-polysaccharides, stimulated weak anti-smooth lipopolysaccharide antibodies. Conclusions/Significance The results demonstrate that no rough mutant is equal to Rev 1 in laboratory models and question the notion that rough vaccines are suitable for the control of brucellosis in endemic areas.
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Affiliation(s)
- David González
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
| | - María-Jesús Grilló
- Instituto de Agrobiotecnología, CSIC-UPNA-Gobierno de Navarra, Pamplona, Spain
| | - María-Jesús De Miguel
- Centro de Investigación y Tecnología Agroalimentaria (CITA), Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - Tara Ali
- Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Vilma Arce-Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Faculté de Sciences de Luminy, Marseille, France
- INSERM, U631, Marseille, France
- CNRS, UMR6102, Marseille, France
| | - Rose-May Delrue
- Laboratoire d'Immunologie et Microbiologie - Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires - Notre-Dame de la Paix (FUNDP), Namur, Belgium
| | - Raquel Conde-Álvarez
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
| | - Pilar Muñoz
- Centro de Investigación y Tecnología Agroalimentaria (CITA), Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - Ignacio López-Goñi
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
| | - Maite Iriarte
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
| | - Clara-M. Marín
- Centro de Investigación y Tecnología Agroalimentaria (CITA), Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - Andrej Weintraub
- Karolinska Institute, Department Laboratory Medicine, Division of Clinical Bacteriology, Karolinska University Hospital, Stockholm, Sweden
| | - Göran Widmalm
- Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Michel Zygmunt
- INRA, UR1282, Infectiologie Animale et Santé Publique, IASP, Nouzilly, France
| | - Jean-Jacques Letesson
- Laboratoire d'Immunologie et Microbiologie - Unité de Recherche en Biologie Moléculaire (URBM), Facultés Universitaires - Notre-Dame de la Paix (FUNDP), Namur, Belgium
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Faculté de Sciences de Luminy, Marseille, France
- INSERM, U631, Marseille, France
- CNRS, UMR6102, Marseille, France
| | - José-María Blasco
- Centro de Investigación y Tecnología Agroalimentaria (CITA), Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - Ignacio Moriyón
- Department of Microbiology and Parasitology, University of Navarra, Pamplona, Spain
- * E-mail:
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Brandner CJ, Maier RH, Henderson DS, Hintner H, Bauer JW, Onder K. The ORFeome of Staphylococcus aureus v 1.1. BMC Genomics 2008; 9:321. [PMID: 18605992 PMCID: PMC2474624 DOI: 10.1186/1471-2164-9-321] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 07/07/2008] [Indexed: 12/16/2022] Open
Abstract
Background The bacterium Staphylococcus aureus causes significant morbidity and mortality in humans, primarily due to the emergence of strains that are resistant to antibiotics – notably methicillin-resistant S. aureus (MRSA) isolates. Development of effective strategies for the control and treatment of MRSA infections may best be achieved through 'omics' approaches, which first requires cloning the entire set of S. aureus' protein-encoding open reading frames (ORFs), or ORFeome. Results The complete genome sequence of S. aureus strain Mu50 has 2697 predicted protein-coding ORFs. Based on the sequence of this strain we designed PCR primers to construct from an S. aureus (non-MRSA) clinical isolate an ORFeome library that contains 2562 unique Gateway® entry clones (95% coverage), each corresponding to a defined ORF. The high quality of the ORFeome library was verified by DNA sequencing and PCR amplification, and its functionality was demonstrated by expressing recombinant proteins and observing protein interactions in a yeast 2-hybrid homodimerization screen. Conclusion This first ORFeome library for S. aureus provides an essential new tool for investigating the systems biology of this important pathogen.
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Affiliation(s)
- Christina J Brandner
- Department of Cell Biology, University of Salzburg, Hellbrunner Strasse 34, A-5020 Salzburg, Austria.
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50
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Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proc Natl Acad Sci U S A 2008; 105:4364-9. [PMID: 18337508 DOI: 10.1073/pnas.0712049105] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cholera, an infectious disease with global impact, is caused by pathogenic strains of the bacterium Vibrio cholerae. High-throughput functional proteomics technologies now offer the opportunity to investigate all aspects of the proteome, which has led to an increased demand for comprehensive protein expression clone resources. Genome-scale reagents for cholera would encourage comprehensive analyses of immune responses and systems-wide functional studies that could lead to improved vaccine and therapeutic strategies. Here, we report the production of the FLEXGene clone set for V. cholerae O1 biovar eltor str. N16961: a complete-genome collection of ORF clones. This collection includes 3,761 sequence-verified clones from 3,887 targeted ORFs (97%). The ORFs were captured in a recombinational cloning vector to facilitate high-throughput transfer of ORF inserts into suitable expression vectors. To demonstrate its application, approximately 15% of the collection was transferred into the relevant expression vector and used to produce a protein microarray by transcribing, translating, and capturing the proteins in situ on the array surface with 92% success. In a second application, a method to screen for protein triggers of Toll-like receptors (TLRs) was developed. We tested in vitro-synthesized proteins for their ability to stimulate TLR5 in A549 cells. This approach appropriately identified FlaC, and previously uncharacterized TLR5 agonist activities. These data suggest that the genome-scale, fully sequenced ORF collection reported here will be useful for high-throughput functional proteomic assays, immune response studies, structure biology, and other applications.
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