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Zhang Y, Bharathi V, Dokoshi T, de Anda J, Ursery LT, Kulkarni NN, Nakamura Y, Chen J, Luo EWC, Wang L, Xu H, Coady A, Zurich R, Lee MW, Matsui T, Lee H, Chan LC, Schepmoes AA, Lipton MS, Zhao R, Adkins JN, Clair GC, Thurlow LR, Schisler JC, Wolfgang MC, Hagan RS, Yeaman MR, Weiss TM, Chen X, Li MMH, Nizet V, Antoniak S, Mackman N, Gallo RL, Wong GCL. Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes. Proc Natl Acad Sci U S A 2024; 121:e2300644120. [PMID: 38306481 PMCID: PMC10861912 DOI: 10.1073/pnas.2300644120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 10/28/2023] [Indexed: 02/04/2024] Open
Abstract
It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin's role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.
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Affiliation(s)
- Yue Zhang
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
- Biomedical Engineering, School of Engineering, Westlake University, Hangzhou, Zhejiang310012, China
| | - Vanthana Bharathi
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Tatsuya Dokoshi
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Lauryn Tumey Ursery
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nikhil N. Kulkarni
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Yoshiyuki Nakamura
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Jonathan Chen
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Elizabeth W. C. Luo
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Lamei Wang
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Hua Xu
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Alison Coady
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Raymond Zurich
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Michelle W. Lee
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - HongKyu Lee
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
| | - Liana C. Chan
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Institute for Infection & Immunity, Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, CA90502
| | - Athena A. Schepmoes
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Mary S. Lipton
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Rui Zhao
- Environmental Molecular Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Joshua N. Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Geremy C. Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA99354
| | - Lance R. Thurlow
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jonathan C. Schisler
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Matthew C. Wolfgang
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Robert S. Hagan
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Michael R. Yeaman
- Division of Molecular Medicine, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Division of Infectious Diseases, Harbor-University of California Los Angeles Medical Center, Los Angeles County, Torrance, CA90502
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Institute for Infection & Immunity, Lundquist Institute for Biomedical Innovation, Harbor-University of California Los Angeles Medical Center, Torrance, CA90502
| | - Thomas M. Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA94025
| | - Xinhua Chen
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02215
| | - Melody M. H. Li
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA92093
| | - Silvio Antoniak
- Department of Pathology and Laboratory Medicine, University of North Carolina Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Nigel Mackman
- University of North Carolina Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Richard L. Gallo
- Department of Dermatology, University of California San Diego, La Jolla, CA92093
| | - Gerard C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA9009
- California NanoSystems Institute, University of California, Los Angeles, CA90095
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA90095
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Schauer J, Gatermann SG, Hoffmann D, Hupfeld L, Pfennigwerth N. GPC-1, a novel class A carbapenemase detected in a clinical Pseudomonas aeruginosa isolate. J Antimicrob Chemother 2021; 75:911-916. [PMID: 31960033 DOI: 10.1093/jac/dkz536] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/05/2019] [Accepted: 12/02/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To investigate the carbapenem resistance mechanism of a carbapenem-resistant clinical Pseudomonas aeruginosa isolate. METHODS A carbapenem-resistant P. aeruginosa isolate was recovered from a tracheal swab from a patient of a general ward in central Germany. Various phenotypic tests confirmed production of a carbapenemase that could not be identified further by PCR. A novel bla gene was identified by WGS and its carbapenemase activity was verified by heterologous expression in an Escherichia coli cloning strain. Kinetic parameters of the novel β-lactamase were determined by spectrophotometric measurements using purified enzyme. RESULTS WGS confirmed the presence of a novel class A carbapenemase. The novel bla gene was named GPC-1 (GPC standing for German Pseudomonas Carbapenemase) and exhibited 77% amino acid identity to BKC-1. WGS also showed that blaGPC-1 was located on the chromosome surrounded by multiple ISs as part of a 26 kb genetic island. Heterologous expression of GPC-1 in E. coli TOP10 led to increased MICs of penicillins, oxyimino-cephalosporins, aztreonam and imipenem, but not of meropenem or ertapenem. Spectrophotometric measurements supported the MIC studies, but detected a slight hydrolysis of ertapenem and meropenem when using high concentrations of purified enzyme. CONCLUSIONS The biochemical characterization of GPC-1 emphasizes the ongoing emergence of novel carbapenemases. Strains expressing a weak carbapenemase like GPC-1 might go unrecognized by routine diagnostics due to low MICs for the bacterial strains producing such enzymes.
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Affiliation(s)
- Jennifer Schauer
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Sören G Gatermann
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Daniel Hoffmann
- SYNLAB MVZ Kassel GmbH, Kurt-Wolters-Straße 2-4, 34125 Kassel, Germany
| | - Lars Hupfeld
- SYNLAB MVZ Kassel GmbH, Kurt-Wolters-Straße 2-4, 34125 Kassel, Germany
| | - Niels Pfennigwerth
- German National Reference Centre for Multidrug-resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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Mahto KU, Das S. Whole genome characterization and phenanthrene catabolic pathway of a biofilm forming marine bacterium Pseudomonas aeruginosa PFL-P1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 206:111087. [PMID: 32871516 DOI: 10.1016/j.ecoenv.2020.111087] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 05/02/2023]
Abstract
Pseudomonas aeruginosa is a small rod shaped Gram-negative bacterium of Gammaproteobacteria class known for its metabolic versatility. P. aeruginosa PFL-P1 was isolated from Polycyclic Aromatic Hydrocarbons (PAHs) contaminated site of Paradip Port, Odisha Coast, India. The strain showed excellent biofilm formation and could retain its ability to form biofilm grown with different PAHs in monoculture as well as co-cultures. To explore mechanistic insights of PAHs metabolism, the whole genome of the strain was sequenced. Next generation sequencing unfolded a genome size of 6,333,060 bp encoding 5857 CDSs. Gene ontology distribution assigned to a total of 2862 genes, wherein 2235 genes were allocated to biological process, 1549 genes to cellular component and 2339 genes to molecular function. A total of 318 horizontally transferred genes were identified when the genome was compared with the reference genomes of P. aeruginosa PAO1 and P. aeruginosa DSM 50071. Further comparison of P. aeruginosa PFL-P1 genome with P. putida containing TOL plasmids revealed similarities in the meta cleavage pathway employed for degradation of aromatic compounds like xylene and toluene. Gene annotation and pathway analysis unveiled 145 genes involved in xenobiotic biodegradation and metabolism. The biofilm cultures of P. aeruginosa PFL-P1 could degrade ~74% phenanthrene within 120 h while degradation increased up to ~76% in co-culture condition. GC-MS analysis indicated presence of diverse metabolites indicating the involvement of multiple pathways for one of the PAHs (phenanthrene) degradation. The strain also possesses the genetic machinery to utilize diverse toxic aromatic compounds such as naphthalene, benzoate, aminobenzoate, fluorobenzoate, toluene, xylene, styrene, atrazine, caprolactam etc. Common catabolic gene clusters such as benABCD, xylXYZ and catAB were observed within the genome of P. aeruginosa PFL-P1 which play key roles in the degradation of various toxic aromatic compounds.
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Affiliation(s)
- Kumari Uma Mahto
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. Pathogens 2020; 9:pathogens9120980. [PMID: 33255203 PMCID: PMC7760384 DOI: 10.3390/pathogens9120980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Iron homeostasis offers a significant bacterial vulnerability because pathogens obtain essential iron from their mammalian hosts, but host-defenses maintain vanishingly low levels of free iron. Although pathogens have evolved mechanisms to procure host-iron, these depend on well-regulated iron homeostasis. To disrupt iron homeostasis, our work has targeted iron mobilization from the iron storage protein bacterioferritin (BfrB) by blocking a required interaction with its cognate ferredoxin partner (Bfd). The blockade of the BfrB–Bfd complex by deletion of the bfd gene (Δbfd) causes iron to irreversibly accumulate in BfrB. In this study we used mass spectrometry and NMR spectroscopy to compare the proteomic response and the levels of key intracellular metabolites between wild type (wt) and isogenic ΔbfdP. aeruginosa strains. We find that the irreversible accumulation of unusable iron in BfrB leads to acute intracellular iron limitation, even if the culture media is iron-sufficient. Importantly, the iron limitation and concomitant iron metabolism dysregulation trigger a cascade of events that lead to broader metabolic homeostasis disruption, which includes sulfur limitation, phenazine-mediated oxidative stress, suboptimal amino acid synthesis and altered carbon metabolism.
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Walker JN, Poppler LH, Pinkner CL, Hultgren SJ, Myckatyn TM. Establishment and Characterization of Bacterial Infection of Breast Implants in a Murine Model. Aesthet Surg J 2020; 40:516-528. [PMID: 31259380 DOI: 10.1093/asj/sjz190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Staphylococcus epidermidis and Pseudomonas aeruginosa are the most common causes of Gram-positive and Gram-negative breast implant-associated infection. Little is known about how these bacteria infect breast implants as a function of implant surface characteristics and timing of infection. OBJECTIVES The aim of this work was to establish a mouse model for studying the impact of various conditions on breast implant infection. METHODS Ninety-one mice were implanted with 273 breast implant shells and infected with S. epidermidis or P. aeruginosa. Smooth, microtextured, and macrotextured breast implant shells were implanted in each mouse. Bacterial inoculation occurred during implantation or 1 day later. Implants were retrieved 1 or 7 days later. Explanted breast implant shells were sonicated, cultured, and colony-forming units determined or analyzed with scanning electron microscopy. RESULTS P. aeruginosa could be detected on all device surfaces at 1- and 7- days post infection (dpi), when mice were implanted and infected concurrently or when they were infected 1- day after implantation. However, P. aeruginosa infection was more robust on implant shells retrieved at 7 dpi and particularly on the macrotextured devices that were infected 1 day post implantation. S. epidermidis was mostly cleared from implants when mice were infected and implanted concurrently. Other the other hand, S. epidermidis could be detected on all device surfaces at 1 dpi and 2 days post implantation. However, S. epidermdis infection was suppressed by 7 dpi and 8 days post implantation. CONCLUSIONS S. epidermidis required higher inoculating doses to cause infection and was cleared within 7 days. P. aeruginosa infected at lower inoculating doses, with robust biofilms noted 7 days later.
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Shaw E, Wuest WM. Virulence attenuating combination therapy: a potential multi-target synergy approach to treat Pseudomonas aeruginosa infections in cystic fibrosis patients. RSC Med Chem 2020; 11:358-369. [PMID: 33479641 PMCID: PMC7580779 DOI: 10.1039/c9md00566h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
The World Health Organization considers the discovery of new treatments for P. aeruginosa a top priority. Virulence attenuating combination therapy (VACT) is a pragmatic strategy to improve bacterial clearance, repurpose outmoded antibiotics, improve drug efficacy at lower doses, and reduce the evolution of resistance. In vitro and in vivo studies have shown that adding a quorum sensing inhibitor or an extracellular polymeric substance repressor to classical antibiotics synergistically improves antipseudomonal activity. This review highlights why VACT could specifically benefit cystic fibrosis patients harboring chronic P. aeruginosa infections, outlines the current landscape of synergistic combinations between virulence-targeting small-molecules and anti-pseudomonal drugs, and suggests future directions for VACT research.
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Affiliation(s)
- Elana Shaw
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
| | - William M Wuest
- Department of Chemistry , Emory University , 1515 Dickey Drive , Atlanta , Georgia 30322 , USA .
- Emory Antibiotic Resistance Center , Emory University School of Medicine , 201 Dowman Drive , Atlanta , Georgia 30322 , USA
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Abstract
Cystic fibrosis (CF) is an autosomal recessive, inherited congenital disease caused by the mutation of the family autosomal CF gene, with cumulative exocrine secretion characterized by inflammation, tracheal remodeling, and mucus accumulation. With the development of modern medical technology, CF patients are living longer lives and receiving more and more treatments, including traditional drugs, physical therapy, and gene therapy. Exercise is widely used to prevent and treat metabolic diseases such as cardiovascular diseases, obesity, diabetes, and metabolic syndrome. Regular exercise is beneficial to aerobic capacity and lung health. Exercise therapy has been of great interest since people realized that CF can be affected by exercise. Exercise alone can be used as an ACT (airway clearance technique), which promotes the removal of mucosal cilia. Exercise therapy is more easily accepted by any society, which helps to normalize the lives of CF patients, rather than placing a psychological burden on them. In this chapter, we will review the latest research progress about exercise in CF.
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Affiliation(s)
- Shengguang Ding
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Chongjun Zhong
- Department of Thoracic and Cardiovascular Surgery, The Second Affiliated Hospital of Nantong University, Nantong, China
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The Pseudomonas aeruginosa PilSR Two-Component System Regulates Both Twitching and Swimming Motilities. mBio 2018; 9:mBio.01310-18. [PMID: 30042200 PMCID: PMC6058289 DOI: 10.1128/mbio.01310-18] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Motility is an important virulence trait for many bacterial pathogens, allowing them to position themselves in appropriate locations at appropriate times. The motility structures type IV pili and flagella are also involved in sensing surface contact, which modulates pathogenicity. In Pseudomonas aeruginosa, the PilS-PilR two-component system (TCS) regulates expression of the type IV pilus (T4P) major subunit PilA, while biosynthesis of the single polar flagellum is regulated by a hierarchical system that includes the FleSR TCS. Previous studies of Geobacter sulfurreducens and Dichelobacter nodosus implicated PilR in regulation of non-T4P-related genes, including some involved in flagellar biosynthesis. Here we used transcriptome sequencing (RNA-seq) analysis to identify genes in addition to pilA with changes in expression in the absence of pilR. Among the genes identified were 10 genes whose transcription increased in the pilA mutant but decreased in the pilR mutant, despite both mutants lacking T4P and pilus-related phenotypes. The products of these inversely dysregulated genes, many of which were hypothetical, may be important for virulence and surface-associated behaviors, as mutants had altered swarming motility, biofilm formation, type VI secretion system expression, and pathogenicity in a nematode model. Further, the PilSR TCS positively regulated transcription of fleSR, and thus many genes in the FleSR regulon. As a result, pilSR deletion mutants had defects in swimming motility that were independent of the loss of PilA. Together, these data suggest that in addition to controlling T4P expression, PilSR could have a broader role in the regulation of P. aeruginosa motility and surface sensing behaviors. Surface appendages such as type IV pili and flagella are important for establishing surface attachment and infection in a host in response to appropriate cues. The PilSR regulatory system that controls type IV pilus expression in Pseudomonas aeruginosa has an established role in expression of the major pilin PilA. Here we provide evidence supporting a new role for PilSR in regulating flagellum-dependent swimming motility in addition to pilus-dependent twitching motility. Further, even though both pilA and pilR mutants lack PilA and pili, we identified sets of genes downregulated in the pilR mutant and upregulated in a pilA mutant as well as genes downregulated only in a pilR mutant, independent of pilus expression. This finding suggests that change in the inner membrane levels of PilA is only one of the cues to which PilR responds to modulate gene expression. Identification of PilR as a regulator of multiple motility pathways may make it an interesting therapeutic target for antivirulence compounds.
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Ha AD, Denver DR. Comparative Genomic Analysis of 130 Bacteriophages Infecting Bacteria in the Genus Pseudomonas. Front Microbiol 2018; 9:1456. [PMID: 30022972 PMCID: PMC6039544 DOI: 10.3389/fmicb.2018.01456] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022] Open
Abstract
Bacteria of the genus Pseudomonas are genetically diverse and ubiquitous in the environment. Like other bacteria, those of the genus Pseudomonas are susceptible to bacteriophages which can significantly affect their host in many ways, ranging from cell lysis to major changes in morphology and virulence. Insights into phage genomes, evolution, and functional relationships with their hosts have the potential to contribute to a broader understanding of Pseudomonas biology, and the development of novel phage therapy strategies. Here we provide a broad-based comparative and evolutionary analysis of 130 complete Pseudomonas phage genome sequences available in online databases. We discovered extensive variation in genome size (ranging from 3 to 316 kb), G + C percentage (ranging from 37 to 66%), and overall gene content (ranging from 81–96% of genome space). Based on overall nucleotide similarity and the numbers of shared gene products, 100 out of 130 genome sequences were grouped into 12 different clusters; 30 were characterized as singletons, which do not have close relationships with other phage genomes. For 5/12 clusters, constituent phage members originated from two or more different Pseudomonas host species, suggesting that phage in these clusters can traverse bacterial species boundaries. An analysis of CRISPR spacers in Pseudomonas bacterial genome sequences supported this finding. Substantial diversity was revealed in analyses of phage gene families; out of 4,462 total families, the largest had only 39 members and there were 2,992 families with only one member. An evolutionary analysis of 72 phage gene families, based on patterns of nucleotide diversity at non-synonymous and synonymous sites, revealed strong and consistent signals for purifying selection. Our study revealed highly diverse and dynamic Pseudomonas phage genomes, and evidence for a dominant role of purifying selection in shaping the evolution of genes encoded in them.
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Affiliation(s)
- Anh D Ha
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
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Flores E, Gadda G. Kinetic Characterization of PA1225 from Pseudomonas aeruginosa PAO1 Reveals a New NADPH:Quinone Reductase. Biochemistry 2018; 57:3050-3058. [PMID: 29715013 DOI: 10.1021/acs.biochem.8b00090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The pa1225 gene of Pseudomonas aeruginosa strain PAO1 was cloned, and the resulting enzyme (PA1225) was purified and revealed to be an NADPH:quinone reductase. By using kinetics, fluorescence, and mass spectrometric analyses, PA1225 was shown to utilize FAD to transfer a hydride ion from NADPH to quinones. The enzyme could also use NADH, but with an efficiency that was 40-fold lower than that of NADPH as suggested by the kcat/ Km values at pH 6.0. Similar initial rates of reaction were determined with 1,4-benzoquinone and 2,6-dimethoxy-1,4-benzoquinone in the range between 25 and 200 μM, suggesting a low Km value for the quinone-oxidizing substrate. The lack of inhibition by NADP+ versus NADPH at saturating concentrations of 1,4-benzoquinone was consistent with a ping-pong bi-bi mechanism. The reductive half-reaction at pH 6.0 had Kd values of 0.07 mM with NADPH and 1.8 mM with NADH; the kred for flavin reduction was independent of pH with values of ∼10 s-1 with NADPH and ∼5 s-1 with NADH. Thus, the enzyme specificity for the reducing substrate arises primarily from a tighter binding of NADPH than of NADH. At pH 6.0, the kcat value with NADPH and 1,4-benzoquinone was 10.1 s-1, consistent with the hydride transfer from NADPH to FAD being fully rate limiting for the overall turnover of the enzyme. The enzyme showed negligible NADPH oxidase and azoreductase activities. This study enables annotation of the pa1225 gene as NADPH:quinone reductase, elucidates the enzymatic function of PA1225 in P. aeruginosa PAO1, and establishes that PA1225 is not an azoreductase as previously proposed.
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TfoI produced by Tepidimonas fonticaldi PL17, a moderate thermophilic bacterium, is an isoschizomer of MseI. Extremophiles 2017; 21:523-535. [DOI: 10.1007/s00792-017-0922-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
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Seiler CY, Eschbacher J, Bowser R, LaBaer J. Sustainability in a Hospital-Based Biobank and University-Based DNA Biorepository: Strategic Roadmaps. Biopreserv Biobank 2016; 13:401-9. [PMID: 26697909 DOI: 10.1089/bio.2015.0076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sustainability in the biobanking community has recently become an important and oft-discussed issue as biorepositories struggle to balance limited external funding and complex cost recovery models with high operating costs and the desire to provide the highest quality materials and services to the research community. A multi-faceted view of biobanking sustainability requires consideration of operational and social sustainability in addition to the historical focus exclusively on financial sustainability. Planning and implementing this three pillar model creates a well-rounded biorepository that meets the needs of all the major stakeholders: the funders, the patients/depositors, and the researcher recipients. Often the creation of a detailed business plan is the first step to develop goals and objectives that lead down a path towards sustainability. The definition of sustainability and the complexity of a sustainable business plan may differ for each biorepository. The DNASU Plasmid Repository at Arizona State University stores and distributes DNA plasmids to researchers worldwide, and the Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute consents patients and collects, stores, and distributes human tissue and blood samples. We will discuss these two biorepositories, their similar and different approaches to sustainability and business planning, their challenges in creating and implementing their sustainability plan, and their responses to some of these challenges. From these experiences, the biobanks share lessons learned about planning for sustainability that are applicable to all biorepositories.
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Affiliation(s)
- Catherine Y Seiler
- 1 The Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute , Phoenix, Arizona
| | - Jennifer Eschbacher
- 1 The Biobank Core Facility at St. Joseph's Hospital and Barrow Neurological Institute , Phoenix, Arizona
| | - Robert Bowser
- 2 Divisions of Neurology and Neurobiology, Barrow Neurological Institute , Phoenix, Arizona
| | - Joshua LaBaer
- 3 DNASU Plasmid Repository, Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona
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13
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Farha MA, Brown ED. Strategies for target identification of antimicrobial natural products. Nat Prod Rep 2016; 33:668-80. [DOI: 10.1039/c5np00127g] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite a pervasive decline in natural product research at many pharmaceutical companies over the last two decades, natural products have undeniably been a prolific and unsurpassed source for new lead antibacterial compounds.
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Affiliation(s)
- Maya A. Farha
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
| | - Eric D. Brown
- M.G. DeGroote Institute for Infectious Disease Research and Department of Biochemistry and Biomedical Sciences
- McMaster University
- Hamilton
- Canada
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Abstract
Allelic exchange is an efficient method of bacterial genome engineering. This protocol describes the use of this technique to make gene knockouts and knock-ins, as well as single-nucleotide insertions, deletions and substitutions, in Pseudomonas aeruginosa. Unlike other approaches to allelic exchange, this protocol does not require heterologous recombinases to insert or excise selective markers from the target chromosome. Rather, positive and negative selections are enabled solely by suicide vector-encoded functions and host cell proteins. Here, mutant alleles, which are flanked by regions of homology to the recipient chromosome, are synthesized in vitro and then cloned into allelic exchange vectors using standard procedures. These suicide vectors are then introduced into recipient cells by conjugation. Homologous recombination then results in antibiotic-resistant single-crossover mutants in which the plasmid has integrated site-specifically into the chromosome. Subsequently, unmarked double-crossover mutants are isolated directly using sucrose-mediated counter-selection. This two-step process yields seamless mutations that are precise to a single base pair of DNA. The entire procedure requires ∼2 weeks.
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Nair AV, Joseph N, Krishna K, Sneha KG, Tom N, Jangid K, Nair S. A comparative study of coastal and clinical isolates of Pseudomonas aeruginosa. Braz J Microbiol 2015; 46:725-34. [PMID: 26413053 PMCID: PMC4568853 DOI: 10.1590/s1517-838246320140502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium having a versatile metabolic potential and great ecological and clinical significance. The geographical distribution of P. aeruginosahas revealed the existence of an unbiased genetic arrangement in terrestrial isolates. In contrast, there are very few reports about P. aeruginosa strains from marine environments. The present work was aimed at studying the distribution of P. aeruginosa in coastal waters along the Indian Peninsula and understanding the environmental influence on genotypic, metabolic and phenotypic characteristics by comparing marine and clinical isolates. Of the 785 marine isolates obtained on selective media, only 32 (~4.1%) were identified as P. aeruginosa, based on their fatty acid methyl ester profiles. A low Euclidian distance value (< 2.5) obtained from chemotaxonomic analysis suggested that all the environmental (coastal and marine) isolates originated from a single species. While UPGMA analyses of AP-PCR and phenotypic profiles separated the environmental and clinical isolates, fatty acid biotyping showed overlapping between most clinical and environmental isolates. Our study revealed the genetic diversity among different environmental isolates of P. aeruginosa. While biogeographical separation was not evident based solely on phenotypic and metabolic typing, genomic and metatranscriptomic studies are more likely to show differences between these isolates. Thus, newer and more insightful methods are required to understand the ecological distribution of this complex group of bacteria.
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Affiliation(s)
- Anusree V. Nair
- Central Marine Fisheries Research Institute, Indian Council of
Agricultural Research, Kochi, India
| | - Neetha Joseph
- Microbial Culture Collection, National Centre for Cell Science, Pune,
India
| | - Kiran Krishna
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - K. G. Sneha
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - Neenu Tom
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Kochi, India
| | - Kamlesh Jangid
- Microbial Culture Collection, National Centre for Cell Science, Pune,
India
| | - Shanta Nair
- Council of Scientific and Industrial Research, National Institute of
Oceanography, Panjim, India
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Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet J, Paeshuyse J, Cenens W, Aertsen A, Uetz P, Delattre AS, Ceyssens PJ, Lavigne R. Functional elucidation of antibacterial phage ORFans targetingPseudomonas aeruginosa. Cell Microbiol 2014; 16:1822-35. [DOI: 10.1111/cmi.12330] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/27/2014] [Accepted: 07/03/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Jeroen Wagemans
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Bob G. Blasdel
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - An Van den Bossche
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Birgit Uytterhoeven
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jeroen De Smet
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Jan Paeshuyse
- Department of Microbiology and Immunology; Katholieke Universiteit Leuven; Minderbroedersstraat 10 - box 1030 3000 Leuven Belgium
| | - William Cenens
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems; Katholieke Universiteit Leuven; Kasteelpark Arenberg 22 - box 2457 3001 Leuven Belgium
| | - Peter Uetz
- Centre for the Study of Biological Complexity; Virginia Commonwealth University; 1000 West Cary Street - room 333 Richmond VA 23284 USA
| | - Anne-Sophie Delattre
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
| | - Pieter-Jan Ceyssens
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
- Bacterial Diseases Division; Scientific Institute of Public Health (WIV-ISP); J. Wytsmanstraat 14 1050 Brussels Belgium
| | - Rob Lavigne
- Division of Gene Technology; Katholieke Universiteit Leuven; Kasteelpark Arenberg 21 - box 2462 3001 Leuven Belgium
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17
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Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Am J Cancer Res 2014; 4:808-22. [PMID: 24955142 PMCID: PMC4063979 DOI: 10.7150/thno.8255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/27/2014] [Indexed: 12/24/2022] Open
Abstract
Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.
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Toll-like receptor 9 deficiency protects mice against Pseudomonas aeruginosa lung infection. PLoS One 2014; 9:e90466. [PMID: 24595157 PMCID: PMC3942450 DOI: 10.1371/journal.pone.0090466] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 02/03/2014] [Indexed: 01/15/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen involved in nosocomial infections. While a number of studies have demonstrated the roles of TLR2, TLR4 and TLR5 in host defense againt P. aeruginosa infection, the implication of TLR9 in this process has been overlooked. Here, we show that P. aeruginosa DNA stimulates the inflammatory response through TLR9 pathway in both a cell line and primary alveolar macrophages (AMs). This activation requires asparagine endopeptidase- and endosomal acidification. Interestingly, TLR9-/- mice resisted to lethal lung infection by P. aeruginosa, compared to WT C57BL/6 mice. The resistance of TLR9-/- mice to P. aeruginosa infection was associated with: (i) a higher ability of TLR9-/- AMs to kill P. aeruginosa; (ii) a rapid increase in the pro-inflammatory cytokines such as TNFα, IL-1β and IL-6 production; and (iii) an increase in nitric oxide (NO) production and inductible NO synthase expression in AMs. In addition, inhibition of both IL-1β and NO production resulted in a significant decrease of P. aeruginosa clearance by AMs. Altogether these results indicate that TLR9 plays a detrimental role in pulmonary host defense toward P. aeruginosa by reducing the AMs clearance activity and production of IL-1β and NO necessary for bacteria killing.
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Brochado AR, Typas A. High-throughput approaches to understanding gene function and mapping network architecture in bacteria. Curr Opin Microbiol 2013; 16:199-206. [DOI: 10.1016/j.mib.2013.01.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/09/2013] [Accepted: 01/11/2013] [Indexed: 11/24/2022]
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20
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Nagels Durand A, Moses T, De Clercq R, Goossens A, Pauwels L. A MultiSite Gateway™ vector set for the functional analysis of genes in the model Saccharomyces cerevisiae. BMC Mol Biol 2012; 13:30. [PMID: 22994806 PMCID: PMC3519679 DOI: 10.1186/1471-2199-13-30] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 09/17/2012] [Indexed: 12/02/2022] Open
Abstract
Background Recombinatorial cloning using the GatewayTM technology has been the method of choice for high-throughput omics projects, resulting in the availability of entire ORFeomes in GatewayTM compatible vectors. The MultiSite GatewayTM system allows combining multiple genetic fragments such as promoter, ORF and epitope tag in one single reaction. To date, this technology has not been accessible in the yeast Saccharomyces cerevisiae, one of the most widely used experimental systems in molecular biology, due to the lack of appropriate destination vectors. Results Here, we present a set of three-fragment MultiSite GatewayTM destination vectors that have been developed for gene expression in S. cerevisiae and that allow the assembly of any promoter, open reading frame, epitope tag arrangement in combination with any of four auxotrophic markers and three distinct replication mechanisms. As an example of its applicability, we used yeast three-hybrid to provide evidence for the assembly of a ternary complex of plant proteins involved in jasmonate signalling and consisting of the JAZ, NINJA and TOPLESS proteins. Conclusion Our vectors make MultiSite GatewayTM cloning accessible in S. cerevisiae and implement a fast and versatile cloning method for the high-throughput functional analysis of (heterologous) proteins in one of the most widely used model organisms for molecular biology research.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
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21
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A novel virulence strategy for Pseudomonas aeruginosa mediated by an autotransporter with arginine-specific aminopeptidase activity. PLoS Pathog 2012; 8:e1002854. [PMID: 22927813 PMCID: PMC3426542 DOI: 10.1371/journal.ppat.1002854] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/26/2012] [Indexed: 12/22/2022] Open
Abstract
The opportunistic human pathogen, Pseudomonas aeruginosa, is a major cause of infections in chronic wounds, burns and the lungs of cystic fibrosis patients. The P. aeruginosa genome encodes at least three proteins exhibiting the characteristic three domain structure of autotransporters, but much remains to be understood about the functions of these three proteins and their role in pathogenicity. Autotransporters are the largest family of secreted proteins in Gram-negative bacteria, and those characterised are virulence factors. Here, we demonstrate that the PA0328 autotransporter is a cell-surface tethered, arginine-specific aminopeptidase, and have defined its active site by site directed mutagenesis. Hence, we have assigned PA0328 with the name AaaA, for arginine-specific autotransporter of P. aeruginosa. We show that AaaA provides a fitness advantage in environments where the sole source of nitrogen is peptides with an aminoterminal arginine, and that this could be important for establishing an infection, as the lack of AaaA led to attenuation in a mouse chronic wound infection which correlated with lower levels of the cytokines TNFα, IL-1α, KC and COX-2. Consequently AaaA is an important virulence factor playing a significant role in the successful establishment of P. aeruginosa infections. We present a new Pseudomonas aeruginosa virulence factor that promotes chronic skin wound infections. We propose the name AaaA for this cell-surface tethered autotransporter. This arginine-specific aminopeptidase confers a growth advantage upon P. aeruginosa, providing a fitness advantage by creating a supply of arginine in chronic wounds where oxygen availability is limited and biofilm formation is involved. To our knowledge, this is the first mechanistic evidence linking the upregulation of genes involved in arginine metabolism with pathogenicity of P. aeruginosa, and we propose potential underlying mechanisms. The superbug P. aeruginosa is the leading cause of morbidity in cystic fibrosis patients. The ineffective host immune response to bacterial colonization is likely to play a critical role in the demise of these patients, making the possibility that AaaA could interface with the innate immune system, influencing the activity of iNOS and consequently the host's defence against invading pathogens. The surface localisation of AaaA makes it accessible to inhibitors that could reduce growth of P. aeruginosa during colonisation and alter biofilm formation, potentially improving the efficacy of current antimicrobials. Indeed, structurally related aminopeptidases play a central role in several disease states (stroke, diabetes, cancer, HIV and neuropsychiatric disorders), and inhibitors alleviate symptoms.
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22
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Type II-dependent secretion of a Pseudomonas aeruginosa DING protein. Res Microbiol 2012; 163:457-69. [PMID: 22835944 DOI: 10.1016/j.resmic.2012.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/16/2012] [Indexed: 11/24/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen that uses a wide range of protein secretion systems to interact with its host. Genes encoding the PAO1 Hxc type II secretion system are linked to genes encoding phosphatases (LapA/LapB). Microarray genotyping suggested that Pseudomonas aeruginosa clinical isolates, including urinary tract (JJ692) and blood (X13273) isolates, lacked the lapA/lapB genes. Instead, we show that they carry a gene encoding a protein of the PstS family. This protein, which we call LapC, also has significant similarities with LapA/LapB. LapC belongs to the family of DING proteins and displays the canonical DINGGG motif within its N terminus. DING proteins are members of a prokaryotic phosphate binding protein superfamily. We show that LapC is secreted in an Hxc-dependent manner and is under the control of the PhoB response regulator. The genetic organization hxc-lapC found in JJ692 and X13273 is similar to PA14, which is the most frequent P. aeruginosa genotype. While the role of LapA, LapB and LapC proteins remains unclear in P. aeruginosa pathogenesis, they are likely to be part of a phosphate scavenging or sensing system needed to survive and thrive when low phosphate environments are encountered within the host.
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Santoro DO, Romão CMCA, Clementino MM. Decreased aztreonam susceptibility among Pseudomonas aeruginosa isolates from hospital effluent treatment system and clinical samples. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2012; 22:560-570. [PMID: 22540159 DOI: 10.1080/09603123.2012.678000] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The aim of this study was to evaluate the antimicrobial resistance patterns of Pseudomonas aeruginosa isolates from hospital wastewater treatment system (HWTS) and clinical specimens in a hospital of Rio de Janeiro city, Brazil. Forty-three isolates obtained from four of the five steps of the HWTS (n = 27) and clinical samples (n = 16) from patients were analyzed regarding their susceptibility profiles to 12 antibiotics. Clinical isolates exhibited higher resistance profiles to antibiotics than wastewater isolates. However, out of 27 isolates from sewage, 62.9% showed decreased susceptibility to aztreonam while 50% of clinical isolates were resistant to this antibiotic. Isolates were not detected at the chlorination stage but they were obtained from the following stage of the treatment revealing the capacity of regrowth after chlorinated sewage effluent. To our knowledge, this is the first study reporting decreased aztreonam susceptibility among P. aeruginosa isolates from a hospital wastewater treatment system. Further investigations are being conducted by our laboratory including a larger sampling program in order to obtain more data.
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Affiliation(s)
- Deborah O Santoro
- Department of Microbiology, National Institute of Quality Control in Health, Fiocruz, Rio de Janeiro, Brazil
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24
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Nguyen KC, Seligy VL, Tayabali AF. Cadmium telluride quantum dot nanoparticle cytotoxicity and effects on model immune responses to Pseudomonas aeruginosa. Nanotoxicology 2012; 7:202-11. [PMID: 22264036 PMCID: PMC3581059 DOI: 10.3109/17435390.2011.648667] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
This study examines dose effects of cadmium telluride quantum dots (CdTe-QDs) from two commercial sources on model macrophages (J774A.1) and colonic epithelial cells (HT29). Effects on cellular immune signalling responses were measured following sequential exposure to QDs and Pseudomonasaeruginosa strain PA01. At CdTe-QD concentrations between 10-2 and 10 µg/ml, cells exhibited changes in metabolism and morphology. Confocal imaging revealed QD internalisation and changes in cell–cell contacts, shapes and internal organisations. QD doses below 10-2 µg/ml caused no observed effects. When QD exposures at 10-7 to 10-3 µg/ml preceded PA01 (107 bacteria/ml) challenges, there were elevated cytotoxicity (5–22%, p < 0.05) and reduced levels (two- to fivefold, p < 0.001) of nitric oxide (NO), TNF-α, KC/CXC−1 and IL-8, compared with PA01 exposures alone. These results demonstrate that exposures to sub-toxic levels of CdTe-QDs can depress cell immune-defence functions, which if occurred in vivo would likely interfere with normal neutrophil recruitment for defence against bacteria.
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Affiliation(s)
- Kathy C Nguyen
- Biotechnology Laboratory, Mechanistic Studies Division, Environmental Health Science and Research Bureau , Health Canada, Ottawa, Ontario , Canada
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25
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Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, LaBaer J. PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2011; 12:55-62. [PMID: 21360289 PMCID: PMC3184641 DOI: 10.1007/s10969-011-9100-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/02/2011] [Indexed: 01/08/2023]
Abstract
The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; http://psimr.asu.edu ) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU ( http://dnasu.asu.edu ), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase ( http://sbkb.org ), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. As of March 2011, over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR's repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI.
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Affiliation(s)
- Catherine Y. Cormier
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jin G. Park
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Michael Fiacco
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jason Steel
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Preston Hunter
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jason Kramer
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Rajeev Singla
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
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de Barsy M, Jamet A, Filopon D, Nicolas C, Laloux G, Rual JF, Muller A, Twizere JC, Nkengfac B, Vandenhaute J, Hill DE, Salcedo SP, Gorvel JP, Letesson JJ, De Bolle X. Identification of a Brucella spp. secreted effector specifically interacting with human small GTPase Rab2. Cell Microbiol 2011; 13:1044-58. [PMID: 21501366 DOI: 10.1111/j.1462-5822.2011.01601.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacteria of the Brucella genus are facultative intracellular class III pathogens. These bacteria are able to control the intracellular trafficking of their vacuole, presumably by the use of yet unknown translocated effectors. To identify such effectors, we used a high-throughput yeast two-hybrid screen to identify interactions between putative human phagosomal proteins and predicted Brucella spp. proteins. We identified a specific interaction between the human small GTPase Rab2 and a Brucella spp. protein named RicA. This interaction was confirmed by GST-pull-down with the GDP-bound form of Rab2. A TEM-β-lactamase-RicA fusion was translocated from Brucella abortus to RAW264.7 macrophages during infection. This translocation was not detectable in a strain deleted for the virB operon, coding for the type IV secretion system. However, RicA secretion in a bacteriological culture was still observed in a ΔvirB mutant. In HeLa cells, a ΔricA mutant recruits less GTP-locked myc-Rab2 on its Brucella-containing vacuoles, compared with the wild-type strain. We observed altered kinetics of intracellular trafficking and faster proliferation of the B. abortusΔricA mutant in HeLa cells, compared with the wild-type control. Altogether, the data reported here suggest RicA as the first reported effector with a proposed function for B. abortus.
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Smallwood SE, Rahman MM, Werden SJ, Martino MF, McFadden G. Production of Myxoma virus gateway entry and expression libraries and validation of viral protein expression. CURRENT PROTOCOLS IN MICROBIOLOGY 2011; Chapter 14:Unit 14A.2. [PMID: 21538302 PMCID: PMC3104670 DOI: 10.1002/9780471729259.mc14a02s21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Invitrogen's Gateway technology is a recombination-based cloning method that allows for rapid transfer of numerous open reading frames (ORFs) into multiple plasmid vectors, making it useful for diverse high-throughput applications. Gateway technology has been utilized to create an ORF library for Myxoma virus (MYXV), a member of the Poxviridae family of DNA viruses. MYXV is the prototype virus for the genus Leporipoxvirus, and is pathogenic only in European rabbits. MYXV replicates exclusively in the host cell cytoplasm, and its genome encodes 171 ORFs. A number of these ORFs encode proteins that interfere with or modulate host defense mechanisms, particularly the inflammatory responses. Furthermore, MYXV is able to productively infect a variety of human cancer cell lines and is being developed as an oncolytic virus for treating human cancers. MYXV is therefore an excellent model for studying poxvirus biology, pathogenesis, and host tropism, and a good candidate for ORFeome development.
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Affiliation(s)
- Sherin E Smallwood
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, USA
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Hachani A, Lossi NS, Hamilton A, Jones C, Bleves S, Albesa-Jové D, Filloux A. Type VI secretion system in Pseudomonas aeruginosa: secretion and multimerization of VgrG proteins. J Biol Chem 2011; 286:12317-27. [PMID: 21325275 PMCID: PMC3069435 DOI: 10.1074/jbc.m110.193045] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium causing chronic infections in cystic fibrosis patients. Such infections are associated with an active type VI secretion system (T6SS), which consists of about 15 conserved components, including the AAA+ ATPase, ClpV. The T6SS secretes two categories of proteins, VgrG and Hcp. Hcp is structurally similar to a phage tail tube component, whereas VgrG proteins show similarity to the puncturing device at the tip of the phage tube. In P. aeruginosa, three T6SSs are known. The expression of H1-T6SS genes is controlled by the RetS sensor. Here, 10 vgrG genes were identified in the PAO1 genome, among which three are co-regulated with H1-T6SS, namely vgrG1a/b/c. Whereas VgrG1a and VgrG1c were secreted in a ClpV1-dependent manner, secretion of VgrG1b was ClpV1-independent. We show that VgrG1a and VgrG1c form multimers, which confirmed the VgrG model predicting trimers similar to the tail spike. We demonstrate that Hcp1 secretion requires either VgrG1a or VgrG1c, which may act independently to puncture the bacterial envelope and give Hcp1 access to the surface. VgrG1b is not required for Hcp1 secretion. Thus, VgrG1b does not require H1-T6SS for secretion nor does H1-T6SS require VgrG1b for its function. Finally, we show that VgrG proteins are required for secretion of a genuine H1-T6SS substrate, Tse3. Our results demonstrate that VgrG proteins are not only secreted components but are essential for secretion of other T6SS substrates. Overall, we emphasize variability in behavior of three P. aeruginosa VgrGs, suggesting that, although very similar, distinct VgrGs achieve specific functions.
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Affiliation(s)
- Abderrahman Hachani
- Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, United Kingdom
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Sivaneson M, Mikkelsen H, Ventre I, Bordi C, Filloux A. Two-component regulatory systems in Pseudomonas aeruginosa: an intricate network mediating fimbrial and efflux pump gene expression. Mol Microbiol 2011; 79:1353-66. [PMID: 21205015 PMCID: PMC3083521 DOI: 10.1111/j.1365-2958.2010.07527.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Pseudomonas aeruginosa is responsible for chronic and acute infections in humans. Chronic infections are associated with production of fimbriae and the formation of a biofilm. The two-component system Roc1 is named after its role in the regulation of cup genes, which encode components of a machinery allowing assembly of fimbriae. A non-characterized gene cluster, roc2, encodes components homologous to the Roc1 system. We show that cross-regulation occurs between the Roc1 and Roc2 signalling pathways. We demonstrate that the sensors RocS2 and RocS1 converge on the response regulator RocA1 to control cupC gene expression. This control is independent of the response regulator RocA2. Instead, we show that these sensors act via the RocA2 response regulator to repress the mexAB-oprM genes. These genes encode a multidrug efflux pump and are upregulated in the rocA2 mutant, which is less susceptible to antibiotics. It has been reported that in cystic fibrosis lungs, in which P. aeruginosa adopts the biofilm lifestyle, most isolates have an inactive MexAB-OprM pump. The concomitant RocS2-dependent upregulation of cupC genes (biofilm formation) and downregulation of mexAB-oprM genes (antibiotic resistance) is in agreement with this observation. It suggests that the Roc systems may sense the environment in the cystic fibrosis lung.
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Affiliation(s)
- Melissa Sivaneson
- Imperial College London, Division of Cell and Molecular Biology, Centre for Molecular Microbiology and Infection, South Kensington Campus, Flowers Building, SW7 2AZ London, UK
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Qiu J, LaBaer J. Nucleic acid programmable protein array a just-in-time multiplexed protein expression and purification platform. Methods Enzymol 2011; 500:151-63. [PMID: 21943897 DOI: 10.1016/b978-0-12-385118-5.00009-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Systematic study of proteins requires the availability of thousands of proteins in functional format. However, traditional recombinant protein expression and purification methods have many drawbacks for such study at the proteome level. We have developed an innovative in situ protein expression and capture system, namely NAPPA (nucleic acid programmable protein array), where C-terminal tagged proteins are expressed using an in vitro expression system and efficiently captured/purified by antitag antibodies coprinted at each spot. The NAPPA technology presented in this chapter enable researchers to produce and display fresh proteins just in time in a multiplexed high-throughput fashion and utilize them for various downstream biochemical researches of interest. This platform could revolutionize the field of functional proteomics with it ability to produce thousands of spatially separated proteins in high density with narrow dynamic rand of protein concentrations, reproducibly and functionally.
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Affiliation(s)
- Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Giraud C, Bernard CS, Calderon V, Yang L, Filloux A, Molin S, Fichant G, Bordi C, de Bentzmann S. The PprA-PprB two-component system activates CupE, the first non-archetypal Pseudomonas aeruginosa chaperone-usher pathway system assembling fimbriae. Environ Microbiol 2010; 13:666-83. [DOI: 10.1111/j.1462-2920.2010.02372.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Barker CA, Farha MA, Brown ED. Chemical Genomic Approaches to Study Model Microbes. ACTA ACUST UNITED AC 2010; 17:624-32. [DOI: 10.1016/j.chembiol.2010.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 12/15/2022]
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Bordi C, Lamy MC, Ventre I, Termine E, Hachani A, Fillet S, Roche B, Bleves S, Méjean V, Lazdunski A, Filloux A. Regulatory RNAs and the HptB/RetS signalling pathways fine-tune Pseudomonas aeruginosa pathogenesis. Mol Microbiol 2010; 76:1427-43. [PMID: 20398205 PMCID: PMC2904497 DOI: 10.1111/j.1365-2958.2010.07146.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacterial pathogenesis often depends on regulatory networks, two-component systems and small RNAs (sRNAs). In Pseudomonas aeruginosa, the RetS sensor pathway downregulates expression of two sRNAs, rsmY and rsmZ. Consequently, biofilm and the Type Six Secretion System (T6SS) are repressed, whereas the Type III Secretion System (T3SS) is activated. We show that the HptB signalling pathway controls biofilm and T3SS, and fine-tunes P. aeruginosa pathogenesis. We demonstrate that RetS and HptB intersect at the GacA response regulator, which directly controls sRNAs production. Importantly, RetS controls both sRNAs, whereas HptB exclusively regulates rsmY expression. We reveal that HptB signalling is a complex regulatory cascade. This cascade involves a response regulator, with an output domain belonging to the phosphatase 2C family, and likely an anti-anti-σ factor. This reveals that the initial input in the Gac system comes from several signalling pathways, and the final output is adjusted by a differential control on rsmY and rsmZ. This is exemplified by the RetS-dependent but HptB-independent control on T6SS. We also demonstrate a redundant action of the two sRNAs on T3SS gene expression, while the impact on pel gene expression is additive. These features underpin a novel mechanism in the fine-tuned regulation of gene expression.
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Affiliation(s)
- Christophe Bordi
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UPR9027, CNRS-IMM, Université de la Méditerranée, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
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Bannantine JP, Stabel JR, Bayles DO, Geisbrecht BV. Characteristics of an extensive Mycobacterium avium subspecies paratuberculosis recombinant protein set. Protein Expr Purif 2010; 72:223-33. [PMID: 20359537 DOI: 10.1016/j.pep.2010.03.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 03/17/2010] [Accepted: 03/25/2010] [Indexed: 12/16/2022]
Abstract
In the first step of a comprehensive large-scale antigen discovery project, 651 genes of Mycobacterium avium subspecies paratuberculosis were expressed in Escherichia coli. All of these were purified by affinity chromatography, dialyzed in phosphate buffered saline, and analyzed on SDS-PAGE gels. Collectively, these purified recombinant proteins represent 14.9% of the total M. avium subsp. paratuberculosis proteome. This volume of protein expression and purification has yielded unique observations that may be missed in smaller scale expression and purification projects. For example, the 252 putative membrane proteins predicted by PSORTb analysis, resulted in lower average expression yields (3.51mg/l culture) than the 176 predicted cytoplasmic proteins (7.27mg/l culture). A few proteins (MAP0107c, MAP3169c and MAP3640) appear to promote lysis of E. coli since there was a drop in optical density of the growth culture minutes after the inducing agent was added. Certain M. avium subsp. paratuberculosis proteins, when expressed in E. coli changed the color of the column resin or appearance of harvested cell pellets. Finally, 19 proteins showed an absorbance maximum at 260nm rather than 280nm that was attributed to binding of nucleic acid during purification. This extensive recombinant protein repository provides a powerful tool for proteome- and genome-scale research of this organism.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-ARS, Ames, IA 50010, United States.
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Salacha R, Kovacić F, Brochier-Armanet C, Wilhelm S, Tommassen J, Filloux A, Voulhoux R, Bleves S. The Pseudomonas aeruginosa patatin-like protein PlpD is the archetype of a novel Type V secretion system. Environ Microbiol 2010; 12:1498-512. [PMID: 20192961 DOI: 10.1111/j.1462-2920.2010.02174.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We discovered a novel secreted protein by Pseudomonas aeruginosa, PlpD, as a member of the bacterial lipolytic enzyme family of patatin-like proteins (PLPs). PlpD is synthesized as a single molecule consisting of a secreted domain fused to a transporter domain. The N-terminus of PlpD includes a classical signal peptide followed by the four PLP conserved blocks that account for its lipase activity. The C-terminus consists of a POTRA (polypeptide transport-associated) motif preceding a putative 16-stranded beta-barrel similar to those of TpsB transporters of Type Vb secretion system. We showed that the C-terminus remains inserted into the outer membrane while the patatin moiety is secreted. The association between a TpsB component and a passenger protein is a unique hybrid organization that we propose to classify as Type Vd. More than 200 PlpD orthologues exist among pathogenic and environmental bacteria, which suggests that bacteria secrete numerous PLPs using this newly defined mechanism.
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Affiliation(s)
- Richard Salacha
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Cormier CY, Mohr SE, Zuo D, Hu Y, Rolfs A, Kramer J, Taycher E, Kelley F, Fiacco M, Turnbull G, LaBaer J. Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res 2009; 38:D743-9. [PMID: 19906724 PMCID: PMC2808882 DOI: 10.1093/nar/gkp999] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery.
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Affiliation(s)
- Catherine Y Cormier
- Arizona State University, Biodesign Institute, Virginia G Piper Center for Personalized Diagnostics, 1001 S McAllister Dr Tempe, AZ 85287-6401, USA
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Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays. Infect Immun 2009; 77:4877-86. [PMID: 19737893 DOI: 10.1128/iai.00698-09] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is responsible for potentially life-threatening infections in individuals with compromised defense mechanisms and those with cystic fibrosis. P. aeruginosa infection is notable for the appearance of a humoral response to some known antigens, such as flagellin C, elastase, alkaline protease, and others. Although a number of immunogenic proteins are known, no effective vaccine has been approved yet. Here, we report a comprehensive study of all 262 outer membrane and exported P. aeruginosa PAO1 proteins by a modified protein microarray methodology called the nucleic acid-programmable protein array. From this study, it was possible to identify 12 proteins that trigger an adaptive immune response in cystic fibrosis and acutely infected patients, providing valuable information about which bacterial proteins are actually recognized by the immune system in vivo during the natural course of infection. The differential detections of these proteins in patients and controls proved to be statistically significant (P<0.01). The study provides a list of potential candidates for the improvement of serological diagnostics and the development of vaccines.
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Vincent F, Round A, Reynaud A, Bordi C, Filloux A, Bourne Y. Distinct oligomeric forms of the Pseudomonas aeruginosa RetS sensor domain modulate accessibility to the ligand binding site. Environ Microbiol 2009; 12:1775-86. [DOI: 10.1111/j.1462-2920.2010.02264.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Screening colonies of pooled ORFeomes (SCOOP): a rapid and efficient strategy for expression screening ORFeomes in Escherichia coli. Protein Expr Purif 2009; 68:121-7. [PMID: 19635569 DOI: 10.1016/j.pep.2009.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 07/18/2009] [Accepted: 07/20/2009] [Indexed: 11/22/2022]
Abstract
We have designed and evaluated a novel strategy for screening large gene collections available as GATEWAY-adapted ORFeomes for soluble recombinant overexpression in Escherichia coli, called "Screening Colonies of ORFeome Pools" (SCOOP). From a large gene collection we could, without expensive multi-well based cloning and expression screening, determine which targets were suitable for large-scale expression and purification. Normalized bacterial overnight cultures of an ORF collection of entry clones derived from the Kaposi's sarcoma associated herpesvirus (KSHV) were pooled and used for the isolation of plasmid DNA. The resulting ORF library was subcloned into a prokaryotic expression vector in a single recombination reaction and was subsequently screened with the colony filtration (CoFi) blot for soluble recombinant overexpression in E. coli. ORFs determined to express soluble recombinant proteins were identified by sequencing and analysed by small-scale IMAC and SDS-PAGE. As a reference, we subcloned all ORFs individually using a traditional multi-well based procedure and screened them for soluble expression. Our results show that the two processes have a similar efficiency as 23 and 25 out of 74 assessable clones were identified as soluble expressers using SCOOP and the traditional multi-well procedure, respectively. Because SCOOP minimises costs for cloning and expression screening, it constitutes an interesting alternative for establishing expression of large gene collections. SCOOP also allows affordable screening in alternative vectors, expression strains and physical conditions, which is challenging in large-scale protein production programs. With this strategy in hand success rates for future proteome-wide protein production efforts can be significantly increased.
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El-Solh AA, Amsterdam D, Alhajhusain A, Akinnusi ME, Saliba RG, Lynch SV, Wiener-Kronish JP. Matrix metalloproteases in bronchoalveolar lavage fluid of patients with type III Pseudomonas aeruginosa pneumonia. J Infect 2009; 59:49-55. [PMID: 19535150 DOI: 10.1016/j.jinf.2009.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Revised: 05/12/2009] [Accepted: 05/17/2009] [Indexed: 11/19/2022]
Abstract
OBJECTIVES In patients with ventilator-associated pneumonia (VAP), Pseudomonas aeruginosa type III (TTSS) secreting isolates have been linked to poor clinical outcomes. Differential expression of matrix metalloproteinases (MMPs) induced by type III effector proteins may herald an irreversible lung injury. METHODS Serial bronchoalveolar lavage fluids collected from 41 patients with P. aeruginosa at onset of VAP, day 4, and day 8 after antibiotic therapy were assayed for MMP-8, MMP-9, tissue inhibitor of metalloproteinase-1 (TIMP-1), and alpha-2 macroglobulin levels. RESULTS At the onset of VAP, isolates secreting ExoU had the highest MMP-9 levels. The response to antimicrobial therapy showed a differential drop in MMPs with significant decrease in MMP-8 and MMP-9 levels on days 4 and 8 in patients with TTSS(-) compared to TTSS(+) phenotype. The ratio of MMP-9/TIMP-1 was significantly associated with alpha-2 macroglobulin at end of therapy (r=0.4, p=0.02). Patients who survived had a lower MMP-9/TIMP-1 ratio than those who died (p=0.003). CONCLUSIONS VAP linked to P. aeruginosa Type III phenotype portrays a divergent antibiotic treatment response in regards to the concentrations of metalloproteinases in the alveolar space. The imbalance between MMP-9 and TIMP-1 may determine the intensity of alveolocapillary damage and ultimate outcome of P. aeruginosa VAP.
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Affiliation(s)
- Ali A El-Solh
- The Veterans Affairs Western New York Healthcare System, Medical Research Building 20, 3495 Bailey Avenue, Buffalo, NY 14215-1199, USA.
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Gooderham WJ, Hancock REW. Regulation of virulence and antibiotic resistance by two-component regulatory systems inPseudomonas aeruginosa. FEMS Microbiol Rev 2009; 33:279-94. [DOI: 10.1111/j.1574-6976.2008.00135.x] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Role of LecA and LecB lectins in Pseudomonas aeruginosa-induced lung injury and effect of carbohydrate ligands. Infect Immun 2009; 77:2065-75. [PMID: 19237519 DOI: 10.1128/iai.01204-08] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa is a frequently encountered pathogen that is involved in acute and chronic lung infections. Lectin-mediated bacterium-cell recognition and adhesion are critical steps in initiating P. aeruginosa pathogenesis. This study was designed to evaluate the contributions of LecA and LecB to the pathogenesis of P. aeruginosa-mediated acute lung injury. Using an in vitro model with A549 cells and an experimental in vivo murine model of acute lung injury, we compared the parental strain to lecA and lecB mutants. The effects of both LecA- and Lec B-specific lectin-inhibiting carbohydrates (alpha-methyl-galactoside and alpha-methyl-fucoside, respectively) were evaluated. In vitro, the parental strain was associated with increased cytotoxicity and adhesion on A549 cells compared to the lecA and lecB mutants. In vivo, the P. aeruginosa-induced increase in alveolar barrier permeability was reduced with both mutants. The bacterial burden and dissemination were decreased for both mutants compared with the parental strain. Coadministration of specific lectin inhibitors markedly reduced lung injury and mortality. Our results demonstrate that there is a relationship between lectins and the pathogenicity of P. aeruginosa. Inhibition of the lectins by specific carbohydrates may provide new therapeutic perspectives.
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Abstract
During the last 10 years, there has been a large increase in the number of genome sequences available for study, altering the way that the biology of organisms is studied. In particular, scientific attention has increasingly focused on the proteome, and specifically on the role of all the proteins encoded by the genome. We focus here on several aspects of this problem. We describe several technologies in widespread use to clone genes on a genome-wide scale, and to express and purify the proteins encoded by these genes. We also describe a number of methods that have been developed to analyze various biochemical properties of the proteins, with attention to the methodology and the limitations of the approaches, followed by a look at possible developments in the next decade.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine, Rochester, NY 14642, USA.
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Drake EJ, Gulick AM. Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin. J Mol Biol 2008; 384:193-205. [PMID: 18824174 DOI: 10.1016/j.jmb.2008.09.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 09/01/2008] [Accepted: 09/09/2008] [Indexed: 10/21/2022]
Abstract
The pvcABCD operon of Pseudomonas aeruginosa encodes four proteins (PA2254, PA2255, PA2256, and PA2257) that form a cluster that is responsible for the synthesis of a cyclized isocyano derivative of tyrosine. These proteins, which were identified originally as being responsible for a step in the maturation of the chromophore of the peptide siderophore pyoverdine, have been identified recently as belonging to a family of proteins that produce small organic isonitriles. We report that strains harboring a disruption in the pvcA or pvcB genes are able to grow in iron-depleted conditions and to produce pyoverdine. Additionally, we have determined the three-dimensional crystal structures of PvcA and PvcB. The structure of PvcA demonstrates a novel enzyme architecture that is built upon a Rossmann fold. We have analyzed the sequence conservation of enzymes within this family and identified six conserved motifs. These regions of the protein cluster around a putative active site cavity. The structure of the PvcB protein confirms it is a member of the Fe2+/alpha-ketoglutarate-dependent oxygenase family of enzymes. The active site of PvcB is compared to the structures of other family members and suggests that a conformational change to order several loops will accompany the binding of ligands.
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Affiliation(s)
- Eric J Drake
- Hauptman-Woodward Medical Research Institute, Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203-1102, USA
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Ramachandran N, Srivastava S, Labaer J. Applications of protein microarrays for biomarker discovery. Proteomics Clin Appl 2008; 2:1444-59. [PMID: 21136793 DOI: 10.1002/prca.200800032] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Indexed: 01/18/2023]
Abstract
The search for new biomarkers for diagnosis, prognosis, and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large-scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers.
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Affiliation(s)
- Niroshan Ramachandran
- Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
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Gao H, Pattison D, Yan T, Klingeman DM, Wang X, Petrosino J, Hemphill L, Wan X, Leaphart AB, Weinstock GM, Palzkill T, Zhou J. Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display. PLoS One 2008; 3:e2983. [PMID: 18714347 PMCID: PMC2500165 DOI: 10.1371/journal.pone.0002983] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 07/28/2008] [Indexed: 12/02/2022] Open
Abstract
A comprehensive gene collection for S. oneidensis was constructed using the lambda recombinase (Gateway) cloning system. A total of 3584 individual ORFs (85%) have been successfully cloned into the entry plasmids. To validate the use of the clone set, three sets of ORFs were examined within three different destination vectors constructed in this study. Success rates for heterologous protein expression of S. oneidensis His- or His/GST- tagged proteins in E. coli were approximately 70%. The ArcA and NarP transcription factor proteins were tested in an in vitro binding assay to demonstrate that functional proteins can be successfully produced using the clone set. Further functional validation of the clone set was obtained from phage display experiments in which a phage encoding thioredoxin was successfully isolated from a pool of 80 different clones after three rounds of biopanning using immobilized anti-thioredoxin antibody as a target. This clone set complements existing genomic (e.g., whole-genome microarray) and other proteomic tools (e.g., mass spectrometry-based proteomic analysis), and facilitates a wide variety of integrated studies, including protein expression, purification, and functional analyses of proteins both in vivo and in vitro.
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Affiliation(s)
- Haichun Gao
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Donna Pattison
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Tingfen Yan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Dawn M. Klingeman
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Xiaohu Wang
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Petrosino
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Lisa Hemphill
- Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiufeng Wan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Adam B. Leaphart
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | - Timothy Palzkill
- Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail: (TP); (JZ)
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, United States of America
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail: (TP); (JZ)
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Slagowski NL, Kramer RW, Morrison MF, LaBaer J, Lesser CF. A functional genomic yeast screen to identify pathogenic bacterial proteins. PLoS Pathog 2008; 4:e9. [PMID: 18208325 PMCID: PMC2211553 DOI: 10.1371/journal.ppat.0040009] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 12/10/2007] [Indexed: 11/19/2022] Open
Abstract
Many bacterial pathogens promote infection and cause disease by directly injecting into host cells proteins that manipulate eukaryotic cellular processes. Identification of these translocated proteins is essential to understanding pathogenesis. Yet, their identification remains limited. This, in part, is due to their general sequence uniqueness, which confounds homology-based identification by comparative genomic methods. In addition, their absence often does not result in phenotypes in virulence assays limiting functional genetic screens. Translocated proteins have been observed to confer toxic phenotypes when expressed in the yeast Saccharomyces cerevisiae. This observation suggests that yeast growth inhibition can be used as an indicator of protein translocation in functional genomic screens. However, limited information is available regarding the behavior of non-translocated proteins in yeast. We developed a semi-automated quantitative assay to monitor the growth of hundreds of yeast strains in parallel. We observed that expression of half of the 19 Shigella translocated proteins tested but almost none of the 20 non-translocated Shigella proteins nor ∼1,000 Francisella tularensis proteins significantly inhibited yeast growth. Not only does this study establish that yeast growth inhibition is a sensitive and specific indicator of translocated proteins, but we also identified a new substrate of the Shigella type III secretion system (TTSS), IpaJ, previously missed by other experimental approaches. In those cases where the mechanisms of action of the translocated proteins are known, significant yeast growth inhibition correlated with the targeting of conserved cellular processes. By providing positive rather than negative indication of activity our assay complements existing approaches for identification of translocated proteins. In addition, because this assay only requires genomic DNA it is particularly valuable for studying pathogens that are difficult to genetically manipulate or dangerous to culture. Many bacterial pathogens promote infection and ultimately cause disease, in part, through the actions of proteins that the bacteria directly inject into host cells. These proteins subvert host cell processes to favor survival of the pathogen. The identification of such proteins can be limited since many of the injected proteins lack homology with other virulence proteins and pathogens that no longer express the proteins are often unimpaired in conventional assays of pathogenesis. Many of these proteins target cellular processes conserved from mammals to yeast, and overexpression of these proteins in yeast results in growth inhibition. We have established a high throughput growth assay amenable to systematically screening open reading frames from bacterial pathogens for those that inhibit yeast growth. We observe that yeast growth inhibition is a sensitive and specific indicator of proteins that are injected into host cells. Expression of about half of the injected bacterial proteins but almost none of the bacteria-confined proteins results in yeast growth inhibition. Since this assay only requires genomic DNA it is particularly valuable for studying pathogens that are difficult to genetically manipulate or dangerous to grow in the laboratory.
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Affiliation(s)
- Naomi L Slagowski
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Roger W Kramer
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Monica F Morrison
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Joshua LaBaer
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Cammie F Lesser
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proc Natl Acad Sci U S A 2008; 105:4364-9. [PMID: 18337508 DOI: 10.1073/pnas.0712049105] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cholera, an infectious disease with global impact, is caused by pathogenic strains of the bacterium Vibrio cholerae. High-throughput functional proteomics technologies now offer the opportunity to investigate all aspects of the proteome, which has led to an increased demand for comprehensive protein expression clone resources. Genome-scale reagents for cholera would encourage comprehensive analyses of immune responses and systems-wide functional studies that could lead to improved vaccine and therapeutic strategies. Here, we report the production of the FLEXGene clone set for V. cholerae O1 biovar eltor str. N16961: a complete-genome collection of ORF clones. This collection includes 3,761 sequence-verified clones from 3,887 targeted ORFs (97%). The ORFs were captured in a recombinational cloning vector to facilitate high-throughput transfer of ORF inserts into suitable expression vectors. To demonstrate its application, approximately 15% of the collection was transferred into the relevant expression vector and used to produce a protein microarray by transcribing, translating, and capturing the proteins in situ on the array surface with 92% success. In a second application, a method to screen for protein triggers of Toll-like receptors (TLRs) was developed. We tested in vitro-synthesized proteins for their ability to stimulate TLR5 in A549 cells. This approach appropriately identified FlaC, and previously uncharacterized TLR5 agonist activities. These data suggest that the genome-scale, fully sequenced ORF collection reported here will be useful for high-throughput functional proteomic assays, immune response studies, structure biology, and other applications.
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Yashiroda Y, Matsuyama A, Yoshida M. New insights into chemical biology from ORFeome libraries. Curr Opin Chem Biol 2008; 12:55-9. [PMID: 18282487 DOI: 10.1016/j.cbpa.2008.01.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 01/15/2008] [Indexed: 01/30/2023]
Abstract
As the genomes of many organisms have been sequenced, a variety of global analyses, called 'omics,' have been initiated. Cloning of the set of all open reading frames encoded by the genome (ORFeome) of an organism is a major challenge, which serves as an indispensable provision before one launches into the ocean of the postgenomic world. A suitable strategy for high-throughput cloning and expression of thousands of genes is crucial to success. Recently developed systems employing site-specific or homologous recombination have made it feasible to manipulate thousands of ORFs en masse. Using these technologies, several recent studies have successfully fished biologically active small molecules and target proteins out of this bountiful ocean.
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Affiliation(s)
- Yoko Yashiroda
- Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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50
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Arnoldo A, Curak J, Kittanakom S, Chevelev I, Lee VT, Sahebol-Amri M, Koscik B, Ljuma L, Roy PJ, Bedalov A, Giaever G, Nislow C, Merrill RA, Lory S, Stagljar I. Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen. PLoS Genet 2008; 4:e1000005. [PMID: 18454192 PMCID: PMC2265467 DOI: 10.1371/journal.pgen.1000005] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 01/17/2008] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is a key factor in the mortality of cystic fibrosis patients, and infection represents an increased threat for human health worldwide. Because resistance of Pseudomonas aeruginosa to antibiotics is increasing, new inhibitors of pharmacologically validated targets of this bacterium are needed. Here we demonstrate that a cell-based yeast phenotypic assay, combined with a large-scale inhibitor screen, identified small molecule inhibitors that can suppress the toxicity caused by heterologous expression of selected Pseudomonas aeruginosa ORFs. We identified the first small molecule inhibitor of Exoenzyme S (ExoS), a toxin involved in Type III secretion. We show that this inhibitor, exosin, modulates ExoS ADP-ribosyltransferase activity in vitro, suggesting the inhibition is direct. Moreover, exosin and two of its analogues display a significant protective effect against Pseudomonas infection in vivo. Furthermore, because the assay was performed in yeast, we were able to demonstrate that several yeast homologues of the known human ExoS targets are likely ADP-ribosylated by the toxin. For example, using an in vitro enzymatic assay, we demonstrate that yeast Ras2p is directly modified by ExoS. Lastly, by surveying a collection of yeast deletion mutants, we identified Bmh1p, a yeast homologue of the human FAS, as an ExoS cofactor, revealing that portions of the bacterial toxin mode of action are conserved from yeast to human. Taken together, our integrated cell-based, chemical-genetic approach demonstrates that such screens can augment traditional drug screening approaches and facilitate the discovery of new compounds against a broad range of human pathogens.
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Affiliation(s)
- Anthony Arnoldo
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Jasna Curak
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Saranya Kittanakom
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Igor Chevelev
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Vincent T. Lee
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehdi Sahebol-Amri
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Becky Koscik
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Lana Ljuma
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Peter J. Roy
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Antonio Bedalov
- Clinical Research and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Guri Giaever
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Corey Nislow
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Ontario, Canada
| | - Rod A. Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada
| | - Stephen Lory
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Igor Stagljar
- Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Biochemistry, University of Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, Canada
- * E-mail:
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