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      aroA-Deficient Salmonella enterica Serovar Typhimurium Is More Than a Metabolically Attenuated Mutant

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          ABSTRACT

          Recombinant attenuated Salmonella enterica serovar Typhimurium strains are believed to act as powerful live vaccine carriers that are able to elicit protection against various pathogens. Auxotrophic mutations, such as a deletion of aroA, are commonly introduced into such bacteria for attenuation without incapacitating immunostimulation. In this study, we describe the surprising finding that deletion of aroA dramatically increased the virulence of attenuated Salmonella in mouse models. Mutant bacteria lacking aroA elicited increased levels of the proinflammatory cytokine tumor necrosis factor alpha (TNF-α) after systemic application . A detailed genetic and phenotypic characterization in combination with transcriptomic and metabolic profiling demonstrated that Δ aroA mutants display pleiotropic alterations in cellular physiology and lipid and amino acid metabolism, as well as increased sensitivity to penicillin, complement, and phagocytic uptake. In concert with other immunomodulating mutations, deletion of aroA affected flagellin phase variation and gene expression of the virulence-associated genes arnT and ansB. Finally, ΔaroA strains displayed significantly improved tumor therapeutic activity. These results highlight the importance of a functional shikimate pathway to control homeostatic bacterial physiology. They further highlight the great potential of ΔaroA-attenuated Salmonella for the development of vaccines and cancer therapies with important implications for host-pathogen interactions and translational medicine.

          IMPORTANCE

          Recombinant attenuated bacterial vector systems based on genetically engineered Salmonella have been developed as highly potent vaccines. Due to the pathogenic properties of Salmonella, efficient attenuation is required for clinical applications. Since the hallmark study by Hoiseth and Stocker in 1981 (S. K. Hoiseth and B. A. D. Stocker, Nature 291:238–239, 1981, http://dx.doi.org/10.1038/291238a0), the auxotrophic Δ aroA mutation has been generally considered safe and universally used to attenuate bacterial strains. Here, we are presenting the remarkable finding that a deletion of aroA leads to pronounced alterations of gene expression, metabolism, and cellular physiology, which resulted in increased immunogenicity, virulence, and adjuvant potential of Salmonella. These results suggest that the enhanced immunogenicity of aroA-deficient Salmonella strains might be advantageous for optimizing bacterial vaccine carriers and immunotherapy. Accordingly, we demonstrate a superior performance of Δ aroA Salmonella in bacterium-mediated tumor therapy. In addition, the present study highlights the importance of a functional shikimate pathway to sustain bacterial physiology and metabolism.

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          Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

          High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences ("reads") resulting from a sequencing run are first "mapped" (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.
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            Aromatic-dependent Salmonella typhimurium are non-virulent and effective as live vaccines.

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              THE SHIKIMATE PATHWAY.

              The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven metabolic steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, the precursor of the aromatic amino acids and many aromatic secondary metabolites. All pathway intermediates can also be considered branch point compounds that may serve as substrates for other metabolic pathways. The shikimate pathway is found only in microorganisms and plants, never in animals. All enzymes of this pathway have been obtained in pure form from prokaryotic and eukaryotic sources and their respective DNAs have been characterized from several organisms. The cDNAs of higher plants encode proteins with amino terminal signal sequences for plastid import, suggesting that plastids are the exclusive locale for chorismate biosynthesis. In microorganisms, the shikimate pathway is regulated by feedback inhibition and by repression of the first enzyme. In higher plants, no physiological feedback inhibitor has been identified, suggesting that pathway regulation may occur exclusively at the genetic level. This difference between microorganisms and plants is reflected in the unusually large variation in the primary structures of the respective first enzymes. Several of the pathway enzymes occur in isoenzymic forms whose expression varies with changing environmental conditions and, within the plant, from organ to organ. The penultimate enzyme of the pathway is the sole target for the herbicide glyphosate. Glyphosate-tolerant transgenic plants are at the core of novel weed control systems for several crop plants.
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                Author and article information

                Journal
                mBio
                MBio
                mbio
                mbio
                mBio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                6 September 2016
                Sep-Oct 2016
                : 7
                : 5
                : e01220-16
                Affiliations
                [a ]Department of Molecular Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
                [b ]Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
                [c ]Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
                [d ]Department of Molecular Biology, Umeå University, Umeå, Sweden
                [e ]Department of Chemical Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
                [f ]Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida, USA
                [g ]Junior Research Group Infection Biology of Salmonella, , Helmholtz Centre for Infection Research, Braunschweig, Germany
                [h ]Institute of Immunology, Medical School Hannover, Hannover, Germany
                Author notes
                Address correspondence to Sebastian Felgner, sebastian.felgner@ 123456helmholtz-hzi.de .

                M.E. and S.W. contributed equally to this work.

                Editor Stefan H. E. Kaufmann, Max Planck Institute for Infection Biology

                Article
                mBio01220-16
                10.1128/mBio.01220-16
                5013297
                27601574
                91386d64-a215-4bb8-a8c3-d3226e175177
                Copyright © 2016 Felgner et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 15 July 2016
                : 8 August 2016
                Page count
                supplementary-material: 10, Figures: 8, Tables: 0, Equations: 0, References: 48, Pages: 12, Words: 10772
                Funding
                This work was supported in part by the Deutsche Krebshilfe, the Federal Ministry for Education and Research (BMBF), the Helmholtz Association Young Investigator grant no. VH-NG-932 and the People Programme (Marie Curie Actions) of the European Unions's Seventh Framework Programme grant no 334030 (to M.E.). S.F. was funded in the Zoonosis PhD program via a Lichtenberg Fellowship from the Niedersächsische Ministerium für Wissenschaft und Kultur (MWK). D.K. was partially funded by Niedersächsische Krebsgesellschaft. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication
                Categories
                Research Article
                Custom metadata
                September/October 2016

                Life sciences
                Life sciences

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