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Harris WT, Altieri I, Gieck I, Johnson RJ. A conserved but structurally divergent loop in acyl protein thioesterase 1 regulates its catalytic activity, ligand binding, and folded stability. Proteins 2024; 92:693-704. [PMID: 38179877 DOI: 10.1002/prot.26661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/06/2024]
Abstract
Human acyl protein thioesterases (APTs) catalyze the depalmitoylation of S-acylated proteins attached to the plasma membrane, facilitating reversible cycles of membrane anchoring and detachment. We previously showed that a bacterial APT homologue, FTT258 from the gram-negative pathogen Francisella tularensis, exists in equilibrium between a closed and open state based on the structural dynamics of a flexible loop overlapping its active site. Although the structural dynamics of this loop are not conserved in human APTs, the amino acid sequence of this loop is highly conserved, indicating essential but divergent functions for this loop in human APTs. Herein, we investigated the role of this loop in regulating the catalytic activity, ligand binding, and protein folding of human APT1, a depalmitoylase connected with cancer, immune, and neurological signaling. Using a combination of substitutional analysis with kinetic, structural, and biophysical characterization, we show that even in its divergent structural location in human APT1 that this loop still regulates the catalytic activity of APT1 through contributions to ligand binding and substrate positioning. We confirmed previously known roles for multiple residues (Phe72 and Ile74) in substrate binding and catalysis while adding new roles in substrate selectivity (Pro69), in catalytic stabilization (Asp73 and Ile75), and in transitioning between the membrane binding β-tongue and substrate-binding loops (Trp71). Even conservative substitution of this tryptophan (Trp71) fulcrum led to complete loss of catalytic activity, a 13°C decrease in total protein stability, and drastic drops in ligand affinity, indicating that the combination of the size, shape, and aromaticity of Trp71 are essential to the proper structure of APT1. Mixing buried hydrophobic surface area with contributions to an exposed secondary surface pocket, Trp71 represents a previously unidentified class of essential tryptophans within α/β hydrolase structure and a potential allosteric binding site within human APTs.
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Affiliation(s)
- William Trey Harris
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Isabelle Altieri
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - Isabella Gieck
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, USA
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2
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Selezneva AI, Gutka HJ, Wolf NM, Qurratulain F, Movahedzadeh F, Abad-Zapatero C. Structural and biochemical characterization of the class II fructose-1,6-bisphosphatase from Francisella tularensis. Acta Crystallogr F Struct Biol Commun 2020; 76:524-535. [PMID: 33135671 PMCID: PMC7605111 DOI: 10.1107/s2053230x20013370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/05/2020] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the class II fructose-1,6-bisphosphatase (FBPaseII) from the important pathogen Francisella tularensis is presented at 2.4 Å resolution. Its structural and functional relationships to the closely related phosphatases from Mycobacterium tuberculosis (MtFBPaseII) and Escherichia coli (EcFBPaseII) and to the dual phosphatase from Synechocystis strain 6803 are discussed. FBPaseII from F. tularensis (FtFBPaseII) was crystallized in a monoclinic crystal form (space group P21, unit-cell parameters a = 76.30, b = 100.17, c = 92.02 Å, β = 90.003°) with four chains in the asymmetric unit. Chain A had two coordinated Mg2+ ions in its active center, which is distinct from previous findings, and is presumably deactivated by their presence. The structure revealed an approximate 222 (D2) symmetry homotetramer analogous to that previously described for MtFBPaseII, which is formed by a crystallographic dyad and which differs from the exact tetramer found in EcFBPaseII at a 222 symmetry site in the crystal. Instead, the approximate homotetramer is very similar to that found in the dual phosphatase from Synechocystis, even though no allosteric effector was found in FtFBPase. The amino-acid sequence and folding of the active site of FtFBPaseII result in structural characteristics that are more similar to those of the previously published EcFBPaseII than to those of MtFBPaseII. The kinetic parameters of native FtFBPaseII were found to be in agreement with published studies. Kinetic analyses of the Thr89Ser and Thr89Ala mutations in the active site of the enzyme are consistent with the previously proposed mechanism for other class II bisphosphatases. The Thr89Ala variant enzyme was inactive but the Thr89Ser variant was partially active, with an approximately fourfold lower Km and Vmax than the native enzyme. The structural and functional insights derived from the structure of FtFBPaseII will provide valuable information for the design of specific inhibitors.
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Affiliation(s)
- Anna I. Selezneva
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Hiten J. Gutka
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nina M. Wolf
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fnu Qurratulain
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, Illinois, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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3
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Nau GJ, Horzempa J, O’Dee D, Brown MJ, Russo BC, Hernandez A, Dillon ST, Cheng J, Kane LP, Sanker S, Hukriede NA. A predicted Francisella tularensis DXD-motif glycosyltransferase blocks immune activation. Virulence 2019; 10:643-656. [PMID: 31314675 PMCID: PMC6650193 DOI: 10.1080/21505594.2019.1631662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 02/04/2023] Open
Abstract
Pathogens enhance their survival during infections by manipulating host defenses. Francisella tularensis evades innate immune responses, which we have found to be dependent on an understudied gene ybeX (FTL_0883/FTT_0615c). To understand the function of YbeX, we sought protein interactors in F. tularensis subsp. holarctica live vaccine strain (LVS). An unstudied Francisella protein co-immunoprecipitated with recombinant YbeX, which is a predicted glycosyltransferase with a DXD-motif. There are up to four genomic copies of this gene with identical sequence in strains of F. tularensis pathogenic to humans, despite ongoing genome decay. Disruption mutations were generated by intron insertion into all three copies of this glycosyltransferase domain containing gene in LVS, gdcA1-3. The resulting strains stimulated more cytokines from macrophages in vitro than wild-type LVS and were attenuated in two in vivo infection models. GdcA was released from LVS during culture and was sufficient to block NF-κB activation when expressed in eukaryotic cells. When co-expressed in zebrafish, GdcA and YbeX were synergistically lethal to embryo development. Glycosyltransferases with DXD-motifs are found in a variety of pathogens including NleB, an Escherichia coli type-III secretion system effector that inhibits NF-κB by antagonizing death receptor signaling. To our knowledge, GdcA is the first DXD-motif glycosyltransferase that inhibits NF-κB in immune cells. Together, these findings suggest DXD-motif glycosyltransferases may be a conserved virulence mechanism used by pathogenic bacteria to remodel host defenses.
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Affiliation(s)
- Gerard J. Nau
- Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI, USA
| | - Joseph Horzempa
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, WV, USA
| | - Dawn O’Dee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew J. Brown
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brian C. Russo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ana Hernandez
- Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI, USA
| | - Simon T. Dillon
- Beth Israel Deaconess Medical Center Genomics, Proteomics, and Systems Biology Center, Harvard Medical School, Boston, MA, USA
| | - Jing Cheng
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lawrence P. Kane
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Subramaniam Sanker
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Neil A. Hukriede
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Critical Care Nephrology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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4
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Liu HW, Smith CB, Schmidt MS, Cambronne XA, Cohen MS, Migaud ME, Brenner C, Goodman RH. Pharmacological bypass of NAD + salvage pathway protects neurons from chemotherapy-induced degeneration. Proc Natl Acad Sci U S A 2018; 115:10654-10659. [PMID: 30257945 PMCID: PMC6196523 DOI: 10.1073/pnas.1809392115] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Axon degeneration, a hallmark of chemotherapy-induced peripheral neuropathy (CIPN), is thought to be caused by a loss of the essential metabolite nicotinamide adenine dinucleotide (NAD+) via the prodegenerative protein SARM1. Some studies challenge this notion, however, and suggest that an aberrant increase in a direct precursor of NAD+, nicotinamide mononucleotide (NMN), rather than loss of NAD+, is responsible. In support of this idea, blocking NMN accumulation in neurons by expressing a bacterial NMN deamidase protected axons from degeneration. We hypothesized that protection could similarly be achieved by reducing NMN production pharmacologically. To achieve this, we took advantage of an alternative pathway for NAD+ generation that goes through the intermediate nicotinic acid mononucleotide (NAMN), rather than NMN. We discovered that nicotinic acid riboside (NAR), a precursor of NAMN, administered in combination with FK866, an inhibitor of the enzyme nicotinamide phosphoribosyltransferase that produces NMN, protected dorsal root ganglion (DRG) axons against vincristine-induced degeneration as well as NMN deamidase. Introducing a different bacterial enzyme that converts NAMN to NMN reversed this protection. Collectively, our data indicate that maintaining NAD+ is not sufficient to protect DRG neurons from vincristine-induced axon degeneration, and elevating NMN, by itself, is not sufficient to cause degeneration. Nonetheless, the combination of FK866 and NAR, which bypasses NMN formation, may provide a therapeutic strategy for neuroprotection.
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Affiliation(s)
- Hui-Wen Liu
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239
| | - Chadwick B Smith
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239
| | - Mark S Schmidt
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 55242
| | - Xiaolu A Cambronne
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239
| | - Michael S Cohen
- Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, OR 97239
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 33604
| | - Charles Brenner
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 55242;
| | - Richard H Goodman
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239;
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5
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Li L, Wei K, Zheng G, Liu X, Chen S, Jiang W, Lu Y. CRISPR-Cpf1-Assisted Multiplex Genome Editing and Transcriptional Repression in Streptomyces. Appl Environ Microbiol 2018. [PMID: 29980561 DOI: 10.1128/aem.00827-818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Streptomyces has a strong capability for producing a large number of bioactive natural products and remains invaluable as a source for the discovery of novel drug leads. Although the Streptococcus pyogenes CRISPR-Cas9-assisted genome editing tool has been developed for rapid genetic engineering in Streptomyces, it has a number of limitations, including the toxicity of SpCas9 expression in some important industrial Streptomyces strains and the need for complex expression constructs when targeting multiple genomic loci. To address these problems, in this study, we developed a high-efficiency CRISPR-Cpf1 system (from Francisella novicida) for multiplex genome editing and transcriptional repression in Streptomyces Using an all-in-one editing plasmid with homology-directed repair (HDR), our CRISPR-Cpf1 system precisely deletes single or double genes at efficiencies of 75 to 95% in Streptomyces coelicolor When no templates for HDR are present, random-sized DNA deletions are achieved by FnCpf1-induced double-strand break (DSB) repair by a reconstituted nonhomologous end joining (NHEJ) pathway. Furthermore, a DNase-deactivated Cpf1 (ddCpf1)-based integrative CRISPRi system is developed for robust, multiplex gene repression using a single customized crRNA array. Finally, we demonstrate that FnCpf1 and SpCas9 exhibit different suitability in tested industrial Streptomyces species and show that FnCpf1 can efficiently promote HDR-mediated gene deletion in the 5-oxomilbemycin-producing strain Streptomyces hygroscopicus SIPI-KF, in which SpCas9 does not work well. Collectively, FnCpf1 is a powerful and indispensable addition to the Streptomyces CRISPR toolbox.IMPORTANCE Rapid, efficient genetic engineering of Streptomyces strains is critical for genome mining of novel natural products (NPs) as well as strain improvement. Here, a novel and high-efficiency Streptomyces genome editing tool is established based on the FnCRISPR-Cpf1 system, which is an attractive and powerful alternative to the S. pyogenes CRISPR-Cas9 system due to its unique features. When combined with HDR or NHEJ, FnCpf1 enables the creation of gene(s) deletion with high efficiency. Furthermore, a ddCpf1-based integrative CRISPRi platform is established for simple, multiplex transcriptional repression. Of importance, FnCpf1-based genome editing proves to be a highly efficient tool for genetic modification of some important industrial Streptomyces strains (e.g., S. hygroscopicus SIPI-KF) that cannot utilize the SpCRISPR-Cas9 system. We expect the CRISPR-Cpf1-assisted genome editing tool to accelerate discovery and development of pharmaceutically active NPs in Streptomyces as well as other actinomycetes.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Keke Wei
- School of Pharmacy, Fudan University, Shanghai, China
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai, China
| | - Guosong Zheng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- School of Life Science, Henan University, Kaifeng, China
| | - Shaoxin Chen
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM, Nanjing, China
| | - Yinhua Lu
- School of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
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6
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Mank NJ, Pote S, Majorek K, Arnette AK, Klapper VG, Hurlburt BK, Chruszcz M. Structure of aspartate β-semialdehyde dehydrogenase from Francisella tularensis. Acta Crystallogr F Struct Biol Commun 2018; 74:14-22. [PMID: 29372903 PMCID: PMC5947688 DOI: 10.1107/s2053230x17017241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/01/2017] [Indexed: 11/10/2022] Open
Abstract
Aspartate β-semialdehyde dehydrogenase (ASADH) is an enzyme involved in the diaminopimelate pathway of lysine biosynthesis. It is essential for the viability of many pathogenic bacteria and therefore has been the subject of considerable research for the generation of novel antibiotic compounds. This manuscript describes the first structure of ASADH from Francisella tularensis, the causative agent of tularemia and a potential bioterrorism agent. The structure was determined at 2.45 Å resolution and has a similar biological assembly to other bacterial homologs. ASADH is known to be dimeric in bacteria and have extensive interchain contacts, which are thought to create a half-sites reactivity enzyme. ASADH from higher organisms shows a tetrameric oligomerization, which also has implications for both reactivity and regulation. This work analyzes the apo form of F. tularensis ASADH, as well as the binding of the enzyme to its cofactor NADP+.
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Affiliation(s)
- N. J. Mank
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - S. Pote
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - K.A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, PO Box 800736, Charlottesville, VA 22908, USA
| | - A. K. Arnette
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - V. G. Klapper
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
| | - B. K. Hurlburt
- Agricultural Research Service, Southern Regional Research Center, US Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - M. Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, SC 29208, USA
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7
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Gutka HJ, Wolf NM, Bondoc JMG, Movahedzadeh F. Enzymatic Characterization of Fructose 1,6-Bisphosphatase II from Francisella tularensis, an Essential Enzyme for Pathogenesis. Appl Biochem Biotechnol 2017; 183:1439-1454. [PMID: 28547120 PMCID: PMC5698383 DOI: 10.1007/s12010-017-2512-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/11/2017] [Indexed: 11/27/2022]
Abstract
The glpX gene from Francisella tularensis encodes for the class II fructose 1,6-bisphosphatase (FBPaseII) enzyme. The glpX gene has been verified to be essential in F. tularensis, and the inactivation of this gene leads to impaired bacterial growth on gluconeogenic substrates. In the present work, we have complemented a ∆glpX mutant of Escherichia coli with the glpX gene of F. tularensis (FTF1631c). Our complementation work independently verifies that the glpX gene (FTF1631c) in F. tularensis is indeed an FBPase and supports the growth of the ΔglpX E. coli mutant on glycerol-containing media. We have performed heterologous expression and purification of the glpX encoded FBPaseII in F. tularensis. We have confirmed the function of glpX as an FBPase and optimized the conditions for enzymatic activity. Mn2+ was found to be an absolute requirement for activity, with no other metal substitutions rendering the enzyme active. The kinetic parameters for this enzyme were found as follows: Km 11 μM, Vmax 2.0 units/mg, kcat 1.2 s-1, kcat/Km 120 mM-1 s-1, and a specific activity of 2.0 units/mg. Size exclusion data suggested an abundance of a tetrameric species in solution. Our findings on the enzyme's properties will facilitate the initial stages of a structure-based drug design program targeting this essential gene of F. tularensis.
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Affiliation(s)
- Hiten J Gutka
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Oncobiologics Inc., Cranbury, NJ, USA
| | - Nina M Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Jasper Marc G Bondoc
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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8
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Su PC, Johnson ME. Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors. J Comput Chem 2016; 37:836-47. [PMID: 26666582 PMCID: PMC4769659 DOI: 10.1002/jcc.24274] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/23/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme.
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Affiliation(s)
- Pin-Chih Su
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
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9
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Shakerley NL, Chandrasekaran A, Trebak M, Miller BA, Melendez JA. Francisella tularensis Catalase Restricts Immune Function by Impairing TRPM2 Channel Activity. J Biol Chem 2016; 291:3871-81. [PMID: 26679996 PMCID: PMC4759167 DOI: 10.1074/jbc.m115.706879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 12/16/2015] [Indexed: 12/12/2022] Open
Abstract
As an innate defense mechanism, macrophages produce reactive oxygen species that weaken pathogens and serve as secondary messengers involved in immune function. The Gram-negative bacterium Francisella tularensis utilizes its antioxidant armature to limit the host immune response, but the mechanism behind this suppression is not defined. Here we establish that F. tularensis limits Ca(2+) entry in macrophages, thereby limiting actin reorganization and IL-6 production in a redox-dependent fashion. Wild type (live vaccine strain) or catalase-deficient F. tularensis (ΔkatG) show distinct profiles in their H2O2 scavenging rates, 1 and 0.015 pm/s, respectively. Murine alveolar macrophages infected with ΔkatG display abnormally high basal intracellular Ca(2+) concentration that did not increase further in response to H2O2. Additionally, ΔkatG-infected macrophages displayed limited Ca(2+) influx in response to ionomycin, as a result of ionophore H2O2 sensitivity. Exogenously added H2O2 or H2O2 generated by ΔkatG likely oxidizes ionomycin and alters its ability to transport Ca(2+). Basal increases in cytosolic Ca(2+) and insensitivity to H2O2-mediated Ca(2+) entry in ΔkatG-infected cells are reversed by the Ca(2+) channel inhibitors 2-aminoethyl diphenylborinate and SKF-96365. 2-Aminoethyl diphenylborinate but not SKF-96365 abrogated ΔkatG-dependent increases in macrophage actin remodeling and IL-6 secretion, suggesting a role for H2O2-mediated Ca(2+) entry through the transient receptor potential melastatin 2 (TRPM2) channel in macrophages. Indeed, increases in basal Ca(2+), actin polymerization, and IL-6 production are reversed in TRPM2-null macrophages infected with ΔkatG. Together, our findings provide compelling evidence that F. tularensis catalase restricts reactive oxygen species to temper macrophage TRPM2-mediated Ca(2+) signaling and limit host immune function.
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Affiliation(s)
- Nicole L Shakerley
- From the Colleges of Nanoscale Science, State University of New York, Polytechnic Institute, Albany, New York 12203 and
| | - Akshaya Chandrasekaran
- From the Colleges of Nanoscale Science, State University of New York, Polytechnic Institute, Albany, New York 12203 and
| | - Mohamed Trebak
- From the Colleges of Nanoscale Science, State University of New York, Polytechnic Institute, Albany, New York 12203 and the Departments of Cellular & Molecular Physiology and
| | - Barbara A Miller
- Pediatrics and Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - J Andrés Melendez
- From the Colleges of Nanoscale Science, State University of New York, Polytechnic Institute, Albany, New York 12203 and
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10
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Su PC, Tsai CC, Mehboob S, Hevener KE, Johnson ME. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI). J Comput Chem 2015; 36:1859-73. [PMID: 26216222 PMCID: PMC4688044 DOI: 10.1002/jcc.24011] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/20/2015] [Accepted: 06/22/2015] [Indexed: 01/10/2023]
Abstract
To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM-PBSA, MM-GBSA, and QM/MM-GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM-GBSA using 6 ns MD simulation trajectories together with GB(neck2) , PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r(2) = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called "multiple independent sampling"), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB(HCT) and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r(2) = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive "multiple independent sampling method" may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM-P(G)BSA were limited to inhibitors' relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program.
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Affiliation(s)
- Pin-Chih Su
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Cheng-Chieh Tsai
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Kirk E. Hevener
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, U.S.A., 60607
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11
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Zhang YY, Liu Y, Mehboob S, Song JH, Boci T, Johnson ME, Ghosh AK, Jeong H. Metabolism-directed structure optimization of benzimidazole-based Francisella tularensis enoyl-reductase (FabI) inhibitors. Xenobiotica 2014; 44:404-16. [PMID: 24171690 PMCID: PMC4355941 DOI: 10.3109/00498254.2013.850553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
1. FabI is a potential antibiotic target against Francisella tularensis, which has been classified as a Category A biowarfare agent of high risk to public health. Our previous work demonstrated that N-benzyl benzimidazole compounds possess promising FabI inhibitory activity, but their druggability properties, including metabolic stability, are unknown. 2. The objective of this study was to characterize structure-metabolism relationships of a series of N-benzyl benzimidazole compounds to guide chemical optimization for better metabolic stability. To this end, metabolic stability data were obtained for 22 initial lead compounds using mouse hepatic microsomes. 3. Metabolic hotspots on the benzimidazole core structure as well as the benzyl ring were identified and verified by metabolite identification studies of four model compounds. Interestingly, the proposed structure-metabolism relationships did not apply to nine newly synthesized cyclopentane or oxacyclopentane derivatives of N-benzyl benzimidazole. 4. Subsequently, in silico quantitative structure-property relationship models were developed. Four molecular descriptors representing molecular polarity/polarisability, symmetry and size were identified to best explain variability in metabolic stability of different compounds. Multi-linear and non-linear regression models based on the selected molecular descriptors were developed and validated. 5. The structure-metabolism relationships for N-benzyl benzimidazole compounds should help optimization of N-benzyl benzimidazole compounds for better pharmacokinetic behavior.
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Affiliation(s)
- Yan-Yan Zhang
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, USA
| | - Yong Liu
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, USA
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Jin-Hua Song
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Teuta Boci
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Hyunyoung Jeong
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, USA
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, USA
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12
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Light SH, Minasov G, Duban ME, Anderson WF. Adherence to Bürgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes. Acta Crystallogr D Biol Crystallogr 2014; 70:544-52. [PMID: 24531488 PMCID: PMC3940192 DOI: 10.1107/s1399004713030666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 11/10/2022]
Abstract
The Bürgi-Dunitz angle (αBD) describes the trajectory of approach of a nucleophile to an electrophile. The adoption of a stereoelectronically favorable αBD can necessitate significant reactive-group repositioning over the course of bond formation. In the context of enzyme catalysis, interactions with the protein constrain substrate rotation, which could necessitate structural transformations during bond formation. To probe this theoretical framework vis-à-vis biocatalysis, Schiff-base formation was analysed in Francisella tularensis transaldolase (TAL). Crystal structures of wild-type and Lys→Met mutant TAL in covalent and noncovalent complexes with fructose 6-phosphate and sedoheptulose 7-phosphate clarify the mechanism of catalysis and reveal that substrate keto moieties undergo significant conformational changes during Schiff-base formation. Structural changes compelled by the trajectory considerations discussed here bear relevance to bond formation in a variety of constrained enzymic/engineered systems and can inform the design of covalent therapeutics.
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Affiliation(s)
- Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mark-Eugene Duban
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Chemistry and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60201, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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13
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Tsimbalistova MV, Pavlovich NV. [Features of resistance formation to beta-lactam antibiotics in Francisella tularensis subsp. mediasiatica]. Zh Mikrobiol Epidemiol Immunobiol 2014:3-8. [PMID: 24738287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
AIM Determination of penicillin resistance features in tularemia causative agents of the mediasiatica subspecies, stability evaluation of differences in strains of various taxa and development of a rapid method of F. tularensis intraspecies differentiation. MATERIALS AND METHODS Beta-lactamase activity was determined in 30 strains of Francisella genus bacteria by quantitative iodometric method. RESULTS All the strains regardless of subspecies membership were characterized by high resistance to beta-lactam antibiotics, and bacteria of the mediasiatica subspecies in contrast to other francisella did not synthesize beta-lactamase. Our attempts to induce beta-lactamase activity in vitro and in vivo in strains of this subspecies did not succeed. A method of intraspecies differentiation of F. tularensis by nitorcefin disks is proposed based on the distinctive feature. CONCLUSION A high level of F. tularensis subsp. mediasiatica resistance to beta-lactams in vitro and their inefficiency during therapy of experimental tularemia due to a beta-lactamase negative strain suggests that F. tularensis beta-lactamase is not the leading factor in formation of native penicillin resistance of tularemia causative agent.
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14
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Mohapatra NP, Soni S, Rajaram MVS, Strandberg KL, Gunn JS. Type A Francisella tularensis acid phosphatases contribute to pathogenesis. PLoS One 2013; 8:e56834. [PMID: 23457625 PMCID: PMC3574111 DOI: 10.1371/journal.pone.0056834] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 01/15/2013] [Indexed: 12/02/2022] Open
Abstract
Different Francisella spp. produce five or six predicted acid phosphatases (AcpA, AcpB, AcpC, AcpD, HapA and HapB). The genes encoding the histidine acid phosphatases (hapA, hapB) and acpD of F. tularensis subsp. Schu S4 strain are truncated or disrupted. However, deletion of HapA (FTT1064) in F. tularensis Schu S4 resulted in a 33% reduction in acid phosphatase activity and loss of the four functional acid phosphatases in F. tularensis Schu S4 (ΔABCH) resulted in a>99% reduction in acid phosphatase activity compared to the wild type strain. All single, double and triple mutants tested, demonstrated a moderate decrease in mouse virulence and survival and growth within human and murine phagocytes, whereas the ΔABCH mutant showed >3.5-fold decrease in intramacrophage survival and 100% attenuation of virulence in mouse. While the Schu S4 ΔABCH strain was attenuated in the mouse model, it showed only limited protection against wild type challenge. F. tularensis Schu S4 failed to stimulate reactive oxygen species production in phagocytes, whereas infection by the ΔABCH strain stimulated 5- and 56-fold increase in reactive oxygen species production in neutrophils and human monocyte-derived macrophages, respectively. The ΔABCH mutant but not the wild type strain strongly co-localized with p47phox and replicated in macrophages isolated from p47phox knockout mice. Thus, F. tularensis Schu S4 acid phosphatases, including the truncated HapA, play a major role in intramacrophage survival and virulence of this human pathogen.
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Affiliation(s)
- Nrusingh P. Mohapatra
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Shilpa Soni
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Murugesan V. S. Rajaram
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Kristi L. Strandberg
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - John S. Gunn
- Department of Microbial Infection and Immunity, Center for Microbial Interface Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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15
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Egge-Jacobsen W, Salomonsson EN, Aas FE, Forslund AL, Winther-Larsen HC, Maier J, Macellaro A, Kuoppa K, Oyston PCF, Titball RW, Thomas RM, Forsberg Å, Prior JL, Koomey M. O-linked glycosylation of the PilA pilin protein of Francisella tularensis: identification of the endogenous protein-targeting oligosaccharyltransferase and characterization of the native oligosaccharide. J Bacteriol 2011; 193:5487-97. [PMID: 21804002 PMCID: PMC3187425 DOI: 10.1128/jb.00383-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/20/2011] [Indexed: 12/22/2022] Open
Abstract
Findings from a number of studies suggest that the PilA pilin proteins may play an important role in the pathogenesis of disease caused by species within the genus Francisella. As such, a thorough understanding of PilA structure and chemistry is warranted. Here, we definitively identified the PglA protein-targeting oligosaccharyltransferase by virtue of its necessity for PilA glycosylation in Francisella tularensis and its sufficiency for PilA glycosylation in Escherichia coli. In addition, we used mass spectrometry to examine PilA affinity purified from Francisella tularensis subsp. tularensis and F. tularensis subsp. holarctica and demonstrated that the protein undergoes multisite, O-linked glycosylation with a pentasaccharide of the structure HexNac-Hex-Hex-HexNac-HexNac. Further analyses revealed microheterogeneity related to forms of the pentasaccharide carrying unusual moieties linked to the distal sugar via a phosphate bridge. Type A and type B strains of Francisella subspecies thus express an O-linked protein glycosylation system utilizing core biosynthetic and assembly pathways conserved in other members of the proteobacteria. As PglA appears to be highly conserved in Francisella species, O-linked protein glycosylation may be a feature common to members of this genus.
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Affiliation(s)
- Wolfgang Egge-Jacobsen
- Department of Molecular Biosciences
- Glyconor Mass Spectrometry & Proteomics Unit, University of Oslo, 0316 Oslo, Norway
| | | | - Finn Erik Aas
- Department of Molecular Biosciences
- Centre for Molecular Biology and Neuroscience, University of Oslo, 0316 Oslo, Norway
| | - Anna-Lena Forslund
- CBRN Defence and Security, FOI Swedish Defence Research Agency, 901 82 Umeå, Sweden
| | - Hanne C. Winther-Larsen
- Department of Molecular Biosciences
- Centre for Molecular Biology and Neuroscience, University of Oslo, 0316 Oslo, Norway
| | - Josef Maier
- IStLS Information Services to Life Science, 78727 Oberndorf, Germany
| | - Anna Macellaro
- CBRN Defence and Security, FOI Swedish Defence Research Agency, 901 82 Umeå, Sweden
| | - Kerstin Kuoppa
- CBRN Defence and Security, FOI Swedish Defence Research Agency, 901 82 Umeå, Sweden
| | - Petra C. F. Oyston
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Richard W. Titball
- School of Biosciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Rebecca M. Thomas
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Åke Forsberg
- Umeå Centre for Microbial Research (UCMR) and Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Joann L. Prior
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Michael Koomey
- Department of Molecular Biosciences
- Centre for Molecular Biology and Neuroscience, University of Oslo, 0316 Oslo, Norway
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16
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Tsang A, Seidle H, Jawaid S, Zhou W, Smith C, Couch RD. Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase: kinetic characterization and phosphoregulation. PLoS One 2011; 6:e20884. [PMID: 21694781 PMCID: PMC3111433 DOI: 10.1371/journal.pone.0020884] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 05/11/2011] [Indexed: 11/29/2022] Open
Abstract
Deliberate and natural outbreaks of infectious disease, the prevalence of antibiotic resistant strains, and the ease by which antibiotic resistant bacteria can be intentionally engineered all underscore the necessity of effective vaccines and continued development of novel antimicrobial/antiviral therapeutics. Isoprenes, a group of molecules fundamentally involved in a variety of crucial biological functions, are derived from either the mevalonic acid (MVA) or methylerythritol phosphate (MEP) pathway. While mammals utilize the MVA pathway, many bacteria utilize the MEP pathway, highlighting the latter as an attractive target for antibiotic development. In this report we describe the cloning and characterization of Francisella tularensis MEP cytidylyltransferase, a MEP pathway enzyme and potential target for antibiotic development. Size exclusion chromatography indicates the protein exists as a dimer in solution. Enzyme assays produced an apparentK(MEP)(M) = 178 μM, K(CTP)(M) = 73 μM , k(MEP)(cat) = 1(s-1), k(CTP)(cat) = 0.8( s-1), and a k(MEP)(cat)/ K(MEP)(M) = 3.4 x 10(5) M(-1) min(-1). The enzyme exhibits a strict preference for Mg(+2) as a divalent cation and CTP as the nucleotide. Titanium dioxide chromatography-tandem mass spectrometry identified Thr141 as a site of phosphorylation. T141D and T141E site-directed mutants are catalytically inactive, suggesting a mechanism for post-translational control of metabolic flux through the F. tularensis MEP pathway. Overall, our study suggests that MEP cytidylyltransferase is an excellent target for the development of novel antibiotics against F. tularensis.
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Affiliation(s)
- Arthur Tsang
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Heather Seidle
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Safdar Jawaid
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Weidong Zhou
- Department of Molecular and Microbiology, George Mason University, Manassas, Virginia, United States of America
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, United States of America
| | - Clint Smith
- Geospatial Research and Engineering Division, U.S. Army Engineer Research and Development Center, Alexandria, Virginia, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
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17
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Champion MD. Host-pathogen o-methyltransferase similarity and its specific presence in highly virulent strains of Francisella tularensis suggests molecular mimicry. PLoS One 2011; 6:e20295. [PMID: 21637805 PMCID: PMC3102702 DOI: 10.1371/journal.pone.0020295] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 04/28/2011] [Indexed: 12/28/2022] Open
Abstract
Whole genome comparative studies of many bacterial pathogens have shown an overall high similarity of gene content (>95%) between phylogenetically distinct subspecies. In highly clonal species that share the bulk of their genomes subtle changes in gene content and small-scale polymorphisms, especially those that may alter gene expression and protein-protein interactions, are more likely to have a significant effect on the pathogen's biology. In order to better understand molecular attributes that may mediate the adaptation of virulence in infectious bacteria, a comparative study was done to further analyze the evolution of a gene encoding an o-methyltransferase that was previously identified as a candidate virulence factor due to its conservation specifically in highly pathogenic Francisella tularensis subsp. tularensis strains. The o-methyltransferase gene is located in the genomic neighborhood of a known pathogenicity island and predicted site of rearrangement. Distinct o-methyltransferase subtypes are present in different Francisella tularensis subspecies. Related protein families were identified in several host species as well as species of pathogenic bacteria that are otherwise very distant phylogenetically from Francisella, including species of Mycobacterium. A conserved sequence motif profile is present in the mammalian host and pathogen protein sequences, and sites of non-synonymous variation conserved in Francisella subspecies specific o-methyltransferases map proximally to the predicted active site of the orthologous human protein structure. Altogether, evidence suggests a role of the F. t. subsp. tularensis protein in a mechanism of molecular mimicry, similar perhaps to Legionella and Coxiella. These findings therefore provide insights into the evolution of niche-restriction and virulence in Francisella, and have broader implications regarding the molecular mechanisms that mediate host-pathogen relationships.
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Affiliation(s)
- Mia D Champion
- Division of Pathogen Genomics, Translational Genomics Research Institute, Arizona, United States of America.
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18
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Pemble CW, Mehta PK, Mehra S, Li Z, Nourse A, Lee RE, White SW. Crystal structure of the 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase•dihydropteroate synthase bifunctional enzyme from Francisella tularensis. PLoS One 2010; 5:e14165. [PMID: 21152407 PMCID: PMC2994781 DOI: 10.1371/journal.pone.0014165] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 11/09/2010] [Indexed: 11/30/2022] Open
Abstract
The 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) and dihydropteroate synthase (DHPS) enzymes catalyze sequential metabolic reactions in the folate biosynthetic pathway of bacteria and lower eukaryotes. Both enzymes represent validated targets for the development of novel anti-microbial therapies. We report herein that the genes which encode FtHPPK and FtDHPS from the biowarfare agent Francisella tularensis are fused into a single polypeptide. The potential of simultaneously targeting both modules with pterin binding inhibitors prompted us to characterize the molecular details of the multifunctional complex. Our high resolution crystallographic analyses reveal the structural organization between FtHPPK and FtDHPS which are tethered together by a short linker. Additional structural analyses of substrate complexes reveal that the active sites of each module are virtually indistinguishable from those of the monofunctional enzymes. The fused bifunctional enzyme therefore represents an excellent vehicle for finding inhibitors that engage the pterin binding pockets of both modules that have entirely different architectures. To demonstrate that this approach has the potential of producing novel two-hit inhibitors of the folate pathway, we identify and structurally characterize a fragment-like molecule that simultaneously engages both active sites. Our study provides a molecular framework to study the enzyme mechanisms of HPPK and DHPS, and to design novel and much needed therapeutic compounds to treat infectious diseases.
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Affiliation(s)
- Charles W. Pemble
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Perdeep K. Mehta
- Department of Information Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Smriti Mehra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Amanda Nourse
- The Hartwell Center, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Richard E. Lee
- Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- Department of Molecular Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail: (SWW); (REL)
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19
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Chalabaev S, Kim TH, Ross R, Derian A, Kasper DL. 3-Deoxy-D-manno-octulosonic acid (Kdo) hydrolase identified in Francisella tularensis, Helicobacter pylori, and Legionella pneumophila. J Biol Chem 2010; 285:34330-6. [PMID: 20801884 PMCID: PMC2966046 DOI: 10.1074/jbc.m110.166314] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 08/19/2010] [Indexed: 11/06/2022] Open
Abstract
3-Deoxy-D-manno-octulosonic acid (Kdo) is an eight-carbon sugar ubiquitous in Gram-negative bacterial lipopolysaccharides (LPS). Although its biosynthesis is well described, no protein has yet been identified as a Kdo hydrolase. However, Kdo hydrolase enzymatic activity has been detected in membranes of Helicobacter pylori and Francisella tularensis and may be responsible for the removal of side-chain Kdo from the LPS core saccharides. We now report the identification of genes encoding a Kdo hydrolase in F. tularensis Schu S4 and live vaccine strain strains, in H. pylori 26695 strain and in Legionella pneumophila Philadelphia 1 strain. We have renamed the genes kdhA for keto-deoxyoctulosonate hydrolase A. Deletion of kdhA abolished Kdo hydrolase activity in membranes of F. tularensis live vaccine strain. The F. tularensis kdhA mutant synthesized a core oligosaccharide containing a Kdo disaccharide with one of the Kdo residues being a terminal side chain. This side-chain Kdo monosaccharide was absent in the wild-type core oligosaccharide. Expression in Escherichia coli of recombinant KdhA from F. tularensis, H. pylori, and L. pneumophila resulted in a reduction of membrane-associated side-chain Kdo. The identification of this previously faceless enzyme will accelerate study of the biosynthetic basis and biologic impact for postbiosynthetic LPS structural modification.
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Affiliation(s)
- Sabina Chalabaev
- From the Department of Microbiology and Molecular Genetics and
- the Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Tae-Hyun Kim
- From the Department of Microbiology and Molecular Genetics and
- the Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Robin Ross
- From the Department of Microbiology and Molecular Genetics and
- the Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Alec Derian
- From the Department of Microbiology and Molecular Genetics and
| | - Dennis L. Kasper
- From the Department of Microbiology and Molecular Genetics and
- the Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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20
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Singh H, Felts RL, Ma L, Malinski TJ, Calcutt MJ, Reilly TJ, Tanner JJ. Expression, purification and crystallization of class C acid phosphatases from Francisella tularensis and Pasteurella multocida. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:226-31. [PMID: 19255471 PMCID: PMC2650447 DOI: 10.1107/s1744309109001511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 01/12/2009] [Indexed: 11/10/2022]
Abstract
Class C nonspecific acid phosphatases are bacterial enzymes that are secreted across the cytoplasmic membrane and hydrolyze a variety of phosphomonoesters at acidic pH. These enzymes are of interest for the development of improved vaccines and clinical diagnostic methods. In one case, the category A pathogen Francisella tularensis, the class C phosphatase plays a role in bacterial fitness. Here, the cloning, expression, purification and crystallization methods for the class C acid phosphatases from F. tularensis and Pasteurella multocida are reported. Crystals of the F. tularensis enzyme diffracted to 2.0 A resolution and belonged to space group C222(1), with one enzyme molecule in the asymmetric unit. Crystals of the P. multocida enzyme diffracted to 1.85 A resolution and belonged to space group C2, with three molecules in the asymmetric unit. Diffraction patterns from crystals of the P. multocida enzyme exhibited multiple interpenetrating reciprocal-space lattices, indicating epitaxial twinning. Despite this aberrance, autoindexing was robust and the data could be satisfactorily processed to 1.85 A resolution using MOSFLM and SCALA.
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Affiliation(s)
- Harkewal Singh
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Richard L. Felts
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Li Ma
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Thomas J. Malinski
- Department of Veterinary Pathobiology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Michael J. Calcutt
- Department of Veterinary Pathobiology, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Thomas J. Reilly
- Department of Veterinary Pathobiology, University of Missouri-Columbia, Columbia, MO 65211, USA
- Veterinary Medicine Diagnostic Laboratory, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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21
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Charity JC, Costante-Hamm MM, Balon EL, Boyd DH, Rubin EJ, Dove SL. Twin RNA polymerase-associated proteins control virulence gene expression in Francisella tularensis. PLoS Pathog 2007; 3:e84. [PMID: 17571921 PMCID: PMC1891329 DOI: 10.1371/journal.ppat.0030084] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Accepted: 04/24/2007] [Indexed: 01/24/2023] Open
Abstract
The MglA protein is the only known regulator of virulence gene expression in Francisella tularensis, yet it is unclear how it functions. F. tularensis also contains an MglA-like protein called SspA. Here, we show that MglA and SspA cooperate with one another to control virulence gene expression in F. tularensis. Using a directed proteomic approach, we show that both MglA and SspA associate with RNA polymerase (RNAP) in F. tularensis, and that SspA is required for MglA to associate with RNAP. Furthermore, bacterial two-hybrid and biochemical assays indicate that MglA and SspA interact with one another directly. Finally, through genome-wide expression analyses, we demonstrate that MglA and SspA regulate the same set of genes. Our results suggest that a complex involving both MglA and SspA associates with RNAP to positively control virulence gene expression in F. tularensis. The F. tularensis genome is unusual in that it contains two genes encoding different alpha subunits of RNAP, and we show here that these two alpha subunits are incorporated into RNAP. Thus, as well as identifying SspA as a second critical regulator of virulence gene expression in F. tularensis, our findings provide a framework for understanding the mechanistic basis for virulence gene control in a bacterium whose transcription apparatus is unique.
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Affiliation(s)
- James C Charity
- Division of Infectious Diseases, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michelle M Costante-Hamm
- Division of Infectious Diseases, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emmy L Balon
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Dana H Boyd
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Simon L Dove
- Division of Infectious Diseases, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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22
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Abstract
Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria, and the lipid A region of LPS mediates stimulation of the immune system in a structure-dependent manner. Unlike the LPS of many other gram-negative bacteria, the LPS of Francisella tularensis isolated from in vitro cultures is not proinflammatory. This observed lack of proinflammatory prowess may reflect structural features of the lipid A, such as the number and length of the acyl chains and the single-phosphate group. To better understand this phenotype, we have begun to elucidate LPS biosynthesis in F. tularensis. We present complementation, mutational, and chemical data demonstrating that F. tularensis FTT0232c encodes a functional late acyltransferase enzyme with specificity similar to that of the Escherichia coli LpxL ortholog. Expression of this late acyltransferase complemented the temperature-sensitive and hypoacylated lipid A phenotypes of an E. coli lpxL mutant, expression of FTT0232c is increased during intracellular growth relative to that during in vitro growth, and finally, LPS obtained from a mutant of F. tularensis lacking FTT0232c showed an abundant triacyl lipid A species after mass spectrometric analysis, consistent with the loss of an LpxL late acyltransferase.
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Affiliation(s)
- Molly K McLendon
- Department of Microbiology and Inflammation Program, University of Iowa, Iowa City, Iowa, USA
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23
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Abstract
Francisella tularensis causes tularemia, a highly contagious disease of animals and humans, but the virulence features of F. tularensis are poorly defined. F. tularensis and the related mouse pathogen Francisella novicida synthesize unusual lipid A molecules lacking the 4'-monophosphate group typically found in the lipid A of Gram-negative bacteria. LpxF, a selective phosphatase located on the periplasmic surface of the inner membrane, removes the 4'-phosphate moiety in the late stages of F. novicida lipid A assembly. To evaluate the relevance of the 4'-phosphatase to pathogenesis, we constructed a deletion mutant of lpxF and compared its virulence with wild-type F. novicida. Intradermal injection of 10(6) wild-type but not 10(8) mutant F. novicida cells is lethal to mice. The rapid clearance of the lpxF mutant is associated with a stronger local cytokine response and a greater influx of neutrophils compared with wild-type. The F. novicida mutant was highly susceptible to the cationic antimicrobial peptide polymyxin. LpxF therefore represents a kind of virulence factor that confers a distinct lipid A phenotype, preventing Francisella from activating the host innate immune response and preventing the bactericidal actions of cationic peptides. Francisella lpxF mutants may be useful for immunization against tularemia.
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Affiliation(s)
| | | | | | | | - Christian R. H. Raetz
- Departments of *Biochemistry and
- To whom correspondence should be addressed at:
Box 3711, Duke University Medical Center, Durham, NC 27710. E-mail:
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Lindgren H, Shen H, Zingmark C, Golovliov I, Conlan W, Sjöstedt A. Resistance of Francisella tularensis strains against reactive nitrogen and oxygen species with special reference to the role of KatG. Infect Immun 2007; 75:1303-9. [PMID: 17210667 PMCID: PMC1828546 DOI: 10.1128/iai.01717-06] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a facultative intracellular bacterial pathogen capable of proliferating within host macrophages. The mechanisms that explain the differences in virulence between various strains of the species are not well characterized. In the present study, we show that both attenuated (strain LVS) and virulent (strains FSC200 and SCHU S4) strains of the pathogen replicate at similar rates in resting murine peritoneal exudate cells (PEC). However, when PEC were activated by exposure to gamma interferon (IFN-gamma), they killed LVS more rapidly than virulent strains of the pathogen. Addition of N(G)-monomethyl-l-arginine, an inhibitor of inducible nitric oxide synthase, to IFN-gamma-treated PEC, completely inhibited killing of the virulent strains, whereas it only partially blocked the killing of LVS. Similarly, in a cell-free system, SCHU S4 and FSC200 were more resistant to killing by H(2)O(2) and ONOO(-) than F. tularensis LVS. Catalase encoded by katG is a bacterial factor that can detoxify bactericidal compounds such as H(2)O(2) and ONOO(-). To investigate its contribution to the virulence of F. tularensis, katG deletion-containing mutants of SCHU S4 and LVS were generated. Both mutants demonstrated enhanced susceptibility to H(2)O(2) in vitro but replicated as effectively as the parental strains in unstimulated PEC. In mice, LVS-DeltakatG was significantly attenuated compared to LVS whereas SCHU S4-DeltakatG, despite slower replication, killed mice as quickly as SCHU S4. This implies that clinical strains of the pathogen have katG-independent mechanisms to combat the antimicrobial effects exerted by H(2)O(2) and ONOO(-), the loss of which could have contributed to the attenuation of LVS.
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Affiliation(s)
- Helena Lindgren
- Department of Clinical Microbiology, Clinical Bacteriology, Umeå University, SE-901 85 Umeå, Sweden.
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25
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Abstract
AcpA is a respiratory burst-inhibiting acid phosphatase from the Centers for Disease Control and Prevention Category A bioterrorism agent Francisella tularensis and prototype of a superfamily of acid phosphatases and phospholipases C. We report the 1.75-A resolution crystal structure of AcpA complexed with the inhibitor orthovanadate, which is the first structure of any F. tularensis protein and the first for any member of this superfamily. The core domain is a twisted 8-stranded beta-sheet flanked by three alpha-helices on either side, with the active site located above the carboxyl-terminal edge of the beta-sheet. This architecture is unique among acid phosphatases and resembles that of alkaline phosphatase. Unexpectedly, the active site features a serine nucleophile and metal ion with octahedral coordination. Structure-based sequence analysis of the AcpA superfamily predicts that the hydroxyl nucleophile and metal center are also present in AcpA-like phospholipases C. These results imply a phospholipase C catalytic mechanism that is radically different from that of zinc metallophospholipases.
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Affiliation(s)
- Richard L Felts
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, USA
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26
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Bakshi CS, Malik M, Regan K, Melendez JA, Metzger DW, Pavlov VM, Sellati TJ. Superoxide dismutase B gene (sodB)-deficient mutants of Francisella tularensis demonstrate hypersensitivity to oxidative stress and attenuated virulence. J Bacteriol 2006; 188:6443-8. [PMID: 16923916 PMCID: PMC1595384 DOI: 10.1128/jb.00266-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Accepted: 06/26/2006] [Indexed: 01/10/2023] Open
Abstract
A Francisella tularensis live vaccine strain mutant (sodB(Ft)) with reduced Fe-superoxide dismutase gene expression was generated and found to exhibit decreased sodB activity and increased sensitivity to redox cycling compounds compared to wild-type bacteria. The sodB(Ft) mutant also was significantly attenuated for virulence in mice. Thus, this study has identified sodB as an important F. tularensis virulence factor.
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Affiliation(s)
- Chandra Shekhar Bakshi
- Center for Immunology and Microbial Disease, Albany Medical College, 47 New Scotland Avenue, Albany, NY 12208-3479, USA
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27
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Reilly TJ, Felts RL, Henzl MT, Calcutt MJ, Tanner JJ. Characterization of recombinant Francisella tularensis acid phosphatase A. Protein Expr Purif 2006; 45:132-41. [PMID: 15964202 DOI: 10.1016/j.pep.2005.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Revised: 05/05/2005] [Accepted: 05/06/2005] [Indexed: 11/30/2022]
Abstract
Francisella tularensis is the etiologic agent of the potentially fatal human disease tularemia and is capable of survival and multiplication within professional phagocytes of the host. While the mechanisms that allow intracellular survival of the bacterium are only now beginning to be elucidated at the molecular level, previous work demonstrated that F. tularensis produces copious levels of an acid phosphatase which in crude and purified form affected the dose-dependent abrogation of the respiratory burst of stimulated neutrophils. The work presented here was undertaken to provide a source of recombinant F. tularensis acid phosphatase for detailed biochemical, biological, and structural studies. Results from this work are consistent with the ability to generate milligram amounts of recombinant enzyme whose attributes are demonstrably equivalent to those of the native enzyme. Such properties include molecular mass, broad substrate specificity, sensitivity and resistance to various inhibitors, pH optimum, and reactivity with rabbit polyclonal antibody to the native enzyme.
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Affiliation(s)
- Thomas J Reilly
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
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28
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Felts RL, Reilly TJ, Calcutt MJ, Tanner JJ. Crystallization of a newly discovered histidine acid phosphatase from Francisella tularensis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 62:32-5. [PMID: 16511256 PMCID: PMC2150932 DOI: 10.1107/s1744309105039813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2005] [Accepted: 11/29/2005] [Indexed: 11/10/2022]
Abstract
Francisella tularensis is a highly infectious bacterial pathogen that is considered by the Centers for Disease Control and Prevention to be a potential bioterrorism weapon. Here, the crystallization of a 37.2 kDa phosphatase encoded by the genome of F. tularensis subsp. holarctica live vaccine strain is reported. This enzyme shares 41% amino-acid sequence identity with Legionella pneumophila major acid phosphatase and contains the RHGXRXP motif that is characteristic of the histidine acid phosphatase family. Large diffraction-quality crystals were grown in the presence of Tacsimate, HEPES and PEG 3350. The crystals belong to space group P4(1)2(1)2, with unit-cell parameters a = 61.96, c = 210.78 A. The asymmetric unit is predicted to contain one protein molecule, with a solvent content of 53%. A 1.75 A resolution native data set was recorded at beamline 4.2.2 of the Lawrence Berkeley National Laboratory Advanced Light Source. Molecular-replacement trials using the human prostatic acid phosphatase structure as the search model (28% amino-acid sequence identity) did not produce a satisfactory solution. Therefore, the structure of F. tularensis histidine acid phosphatase will be determined by multiwavelength anomalous dispersion phasing using a selenomethionyl derivative.
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Affiliation(s)
- Richard L. Felts
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
| | - Thomas J. Reilly
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212, USA
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212, USA
| | - Michael J. Calcutt
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, Missouri 65212, USA
| | - John J. Tanner
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Department of Biochemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
- Correspondence e-mail:
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29
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Felts RL, Reilly TJ, Tanner JJ. Crystallization of AcpA, a respiratory burst-inhibiting acid phosphatase from Francisella tularensis. Biochim Biophys Acta 2005; 1752:107-10. [PMID: 15935744 DOI: 10.1016/j.bbapap.2005.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 05/06/2005] [Accepted: 05/09/2005] [Indexed: 12/19/2022]
Abstract
Francisella tularensis is a highly infectious bacterial pathogen that is classified as a Category A Pathogen by the Centers for Disease Control and Prevention. Here, we report crystallization of a recombinant form of F. tularensis AcpA, a unique and highly expressed acid phosphatase that is thought to play a role in intracellular survival by inhibiting the host respiratory burst. Three crystal forms have been obtained, with form III being the most suitable for high-resolution structure determination. Form III crystals were grown in the presence of PEG 1500 and the competitive inhibitor sodium orthovanadate (5 mM). The space group is C222(1) with unit cell parameters a=112.1 A, b=144.4 A, c=123.9 A. The asymmetric unit is predicted to contain two protein molecules and 43% solvent. A 1.75-A native data set was recorded at beamline 8.3.1 of the Advanced Light Source. To our knowledge, this is the first report of high-resolution crystals of any F. tularensis protein.
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Affiliation(s)
- Richard L Felts
- Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
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30
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Prior JL, Prior RG, Hitchen PG, Diaper H, Griffin KF, Morris HR, Dell A, Titball RW. Characterization of the O antigen gene cluster and structural analysis of the O antigen of Francisella tularensis subsp. tularensis. J Med Microbiol 2003; 52:845-851. [PMID: 12972577 DOI: 10.1099/jmm.0.05184-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gene cluster encoding enzymes involved in LPS O antigen biosynthesis was identified from the partial genome sequence of Francisella tularensis subsp. tularensis Schu S4. All of the genes within the cluster were assigned putative functions based on sequence similarity with genes from O antigen biosynthetic clusters from other bacteria. Ten pairs of overlapping primers were designed to amplify the O antigen biosynthetic cluster by PCR from nine strains of F. tularensis. Although the gene cluster was present in all strains, there was a size difference in one of the PCR products between subsp. tularensis strains and subsp. holarctica strains. LPS was purified from F. tularensis subsp. tularensis Schu S4 and the O antigen was shown by mass spectrometry to have a structure similar to that of F. tularensis subsp. holarctica strain 15. When LPS from F. tularensis subsp. tularensis Schu S4 was used to immunize mice that were then challenged with F. tularensis subsp. tularensis Schu S4, an extended time to death was observed.
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Affiliation(s)
- Joann L Prior
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Richard G Prior
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Paul G Hitchen
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Helen Diaper
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Kate F Griffin
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Howard R Morris
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Anne Dell
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Richard W Titball
- Dstl Porton Down, Salisbury, Wiltshire SP4 0JQ, UK 2Department of Biological Sciences, Imperial College, London SW7 2AZ, UK 3M-SCAN Mass Spectrometry Research and Training Centre, Silwood Park, Ascot SL5 7PZ, UK 4Department of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
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Abstract
Francisella tularensis subsp. tularensis is the common causal agent of tularemia in the USA and Canada, while F. tularensis subsp. palaearctica (holarctica) occurs in Europe, Asia, and to a minor extent in North America. F. tularensis subsp. mediaasiatica was found only in central Asia in a part of the former Soviet Union. Of the total of 155 F. tularensis strains isolated over the years 1978-1996 during the surveillance of tularemia in Slovakia, 65 were from small mammals, 68 from ticks and 22 from mites and fleas. They were characterized and classified by basic markers of infraspecific taxonomy in tests in vitro and compared with type strains of three subspecies and biovars of F. tularensis. Comparative studies have revealed biological properties characteristic of F. tularensis subsp. tularensis in 17 strains isolated from fleas and mites parasiting on small terrestrial mammals, collected in the Danube region, near Bratislava. These strains fermented glycerol, glucose, were positive for citrulline ureidase and sensitive to erythromycin, in contrast to the other 138 isolates classified as F. tularensis subsp. palaearctica (holarctica), biovar II, which fermented only glucose, were negative for citrulline ureidase and resistant to erythromycin. Two selected pairs of isolates with properties characteristic of F. tularensis subsp. palaearctica (holarctica), biovar II (SE-210, SE-234) and of F. tularensis subsp. tularensis (SE-219, SE-221), as shown in tests in vitro, were further examined for their pathogenicity on white mice, guinea pigs and domestic rabbits. In tests of virulence on domestic rabbits, the isolates SE-210 and SE-234 had low pathogenicity, while the isolates SE-219 and SE-221 exhibited high pathogenicity, which along with their biochemical properties confirmed their identification as strains of F. tularensis subsp. tularensis. The first findings of the highly virulent strains of F. tularensis subsp. tularensis in Europe indicate a serious event from epidemiologic and epiozootologic aspects, requiring systematic surveillance.
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Affiliation(s)
- D Gurycová
- Department of Epidemiology, Medical Faculty, Comenius University, Bratislava, Slovak Republic
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32
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Abstract
We have cloned and sequenced genes for triosephosphate isomerase (TPI) from the gamma-proteobacterium Francisella tularensis, the green non-sulfur bacterium Chloroflexus aurantiacus, and the alpha-proteobacterium Rhizobium etli and used these in phylogenetic analysis with TPI sequences from other members of the Bacteria, Archaea, and Eukarya. These analyses show that eukaryotic TPI genes are most closely related to the homologue from the alpha-proteobacterium and most distantly related to archaebacterial homologues. This relationship suggests that the TPI genes present in modern eukaryotic genomes were derived from an alpha-proteobacterial genome (possibly that of the protomitochondrial endosymbiont) after the divergence of Archaea and Eukarya. Among these eukaryotic genes are some from deeply branching, amitochondrial eukaryotes (namely Giardia), which further suggests that this event took place quite early in eukaryotic evolution.
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Affiliation(s)
- P J Keeling
- Department of Biochemistry, Dalhousie University, Halifax, NS Canada
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33
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Reilly TJ, Baron GS, Nano FE, Kuhlenschmidt MS. Characterization and sequencing of a respiratory burst-inhibiting acid phosphatase from Francisella tularensis. J Biol Chem 1996; 271:10973-83. [PMID: 8631917 DOI: 10.1074/jbc.271.18.10973] [Citation(s) in RCA: 128] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acid phosphatases (Acp) of intracellular pathogens have recently been implicated as virulence factors that enhance intracellular survival through suppression of the respiratory burst. We describe here the identification, purification, characterization, and sequencing of a novel burst-inhibiting acid phosphatase from the facultative intracellular bacterium, Francisella tularensis. Similar to other the burst-inhibiting Acps, F. tularensis Acp (AcpA) is tartrate-resistant and has broad substrate specificity. The AcpA enzyme is unique, however, in that it is easily released from the bacterial cell in soluble form, is a basic enzyme, suppresses the respiratory burst of not only fMet-Leu-Phe but also phorbol 12-myristate 13-acetate-stimulated neutrophils and does not fit into any of the three currently recognized classes of acid phosphatase. We also report the complete nucleotide sequence of the gene acpA, encoding AcpA, and the deduced primary structure of its encoded polypeptide. Comparative sequence analyses of AcpA is discussed. To our knowledge, this is the first report describing the cloning and sequencing of a burst-inhibiting acid phosphatase.
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Affiliation(s)
- T J Reilly
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois, Urbana 61801, USA
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34
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Pomerantsev AP, Domaradskiĭ IV, Doronin IP, Ershov IV. [Features of the interaction of Escherichia coli and Francisella tularensis RNA polymerases with hybrid plasmids bearing fragments of Francisella tularensis chromosomal DNA]. Mol Gen Mikrobiol Virusol 1991:12-5. [PMID: 1745260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hybrid plasmids containing the fragments of Francisella tularensis chromosomal DNA and capable of tet-gene expression both in Escherichia coli and Francisella tularensis cells were constructed. The regions of francisella chromosomal DNA binding the RNA-polymerases of Escherichia coli and Francisella tularensis were found by the electron microscopy technique. Interconnection of those regions with the expression of tet-gene of the hybrid plasmids was demonstrated.
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Pomerantsev AP, Doronin IP, Domaradskiĭ IV, Zhilenkov EL. [Comparison of the structural-functional properties of DNA-dependent RNA polymerase of the tularemia microbe and intestinal bacterial]. Mol Gen Mikrobiol Virusol 1991:9-13. [PMID: 1944326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The subunit compositions of RNA-polymerases from Escherichia coli and Francisella tularensis were compared. The activities of the enzymes on the corresponding chromosomal DNAs and their mixtures were defined.
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Pavlovich NV, Shimaniuk NI, Mishan'kin BN. [Isolation and purification of penicillinase from Francisella tularensis]. Antibiotiki 1983; 28:743-7. [PMID: 6606391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
beta-Lactamase was isolated from the cells of a penicillinase-producing strain of the tularemia causative agent. It was purified 100 times. By its properties (the substrate profile, Km, temperature optimum and thermostability) beta-lactamase differed from penicillinases isolated from other sources.
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Pavlovich NV, Shimaniuk NI, Mishan'kin BN. [Mechanism of natural penicillin resistance in the causative agent of tularemia]. Antibiotiki 1983; 28:517-21. [PMID: 6605111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
beta-Lactamase and penicillinacylase were detected in the tularemia causative agent. These enzymes participated in the mechanism of natural resistance of the microorganisms to penicillins. It was shown that the growth temperature had a significant effect on the beta-lactamase activity. The penicillin resistance marker was not eliminated with the use of acridine orange, ethidium bromide or sodium dodecylsulfate.
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Rodionova IV. [Detection of alpha-naphthyl acetate esterase in Francisella tularensis]. Zh Mikrobiol Epidemiol Immunobiol 1982:69-73. [PMID: 7113529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The activity of alpha-naphthyl-acetate esterase (alpha-NAE) has been studied in Francisella tularensis strains belonging to 3 subspecies. Alpha-NAE has been detected spectrophotometrically in native cells and cell extracts of the virulent nonarctic strains Schu and Cole, holarctic virulent strain No. 503/841 and holarctic vaccine strain No. 15/10, Central Asian virulent strain No. 543, as well as their attenuated variants. In all the strains studied the presence of 7 alpha-NAE isoenzymes has been established by means of electrophoresis in acrylamide gel, and the relative electrophoretic activity and the enzymatic activity of these isoenzymes have been determined. The nonarctic and holarctic strains have been found to differ from the Central Asian strain in the activity of 2 alpha-NAE isoenzymes, named characteristic isoenzymes. After the attenuation of the strains belonging to all subspecies the enzymatic composition of these strains remained unchanged, but at the same time the total activity of the holarctic and Central Asian strains increased, while that of the nonarctic strains decreased. These differences in the activity of alpha-NAE isoenzymes, if confirmed in further studies on a greater number of strains belonging to 3 Francisella tularensis subspecies, can be used as an additional sign for differentiation.
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Rodionova IV. [Peroxidase activity of tularemia bacteria]. Zh Mikrobiol Epidemiol Immunobiol 1981:101-2. [PMID: 7234236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Rodionova IV. [Catalase activity in the agent of tularemia]. Zh Mikrobiol Epidemiol Immunobiol 1976:60-3. [PMID: 941605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The catalase activity was studied in the extracts of 27 strains of Francisella tularensis belonging to three geographical races. The most active enzyme was possessed by nonarctic strains, and the least--by holarctic. Japanese variant of the holarctic race was separated in an individual group since it possessed a higher catalase activity in comparison with the typical strains. The Central Asian race occupied an intermediate position by this sign and was placed between the Japanese variant and the nonarctic race. Attenuation of the strains of all the three races of F. tularensis led to a marked reduction of the catalase activity.
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Rodionova IV. [Some characteristics of the metabolism of Francisella tularensis media asiatica Aikimb]. Zh Mikrobiol Epidemiol Immunobiol 1972; 49:7-11. [PMID: 5018219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Kunitsa GM, Aikimbaev MA, Tleugabylov MK, Rodionova IV, Meshcheriakova IS. [Biochemical characteristics of tularemia strains from Central Asia]. Zh Mikrobiol Epidemiol Immunobiol 1972; 49:124-7. [PMID: 5027035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Domaradskiĭ IV, Shimaniuk NI. [Presence of amino acid decarboxylases in Francisella tularensis]. Zh Mikrobiol Epidemiol Immunobiol 1971; 48:32-5. [PMID: 5099097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Beck RW, Schawel KW. Properties of aldolase from Francisella tularensis. J Bacteriol 1971; 105:1232-3. [PMID: 5547987 PMCID: PMC248576 DOI: 10.1128/jb.105.3.1232-1233.1971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The aldolase of Francisella tularensis resembles Class II aldolases in its requirement for divalent ions and its inactivation by metal chelating agents. Cysteine and other reducing agents stimulated the activity of the enzyme.
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Rodionova IV. [Citrulline ureidase activity in geographical races of Francisella tularensis]. Dokl Akad Nauk SSSR 1968; 179:457-60. [PMID: 5745533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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