1
|
Habich A, Unterweger D. Investigating Secretion Systems and Effectors on Galleria mellonella. Methods Mol Biol 2024; 2715:601-608. [PMID: 37930555 DOI: 10.1007/978-1-0716-3445-5_38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Infection experiments with Galleria mellonella enable the measurement of virulence that is mediated by secretion systems and their effector proteins in vivo. G. mellonella has an innate immune system and shares similarities with the complex host environment of mammals. Unlike other invertebrate model systems, experiments can be performed at mammalian body temperature. Here, we describe the systemic infection of G. mellonella with Pseudomonas aeruginosa with and without functional secretion systems. A Kaplan-Meier curve is constructed showing the percent survival of animals over time.
Collapse
Affiliation(s)
- Antonia Habich
- Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Daniel Unterweger
- Institute for Experimental Medicine, Kiel University, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
| |
Collapse
|
2
|
Booth SC, Smith WPJ, Foster KR. The evolution of short- and long-range weapons for bacterial competition. Nat Ecol Evol 2023; 7:2080-2091. [PMID: 38036633 PMCID: PMC10697841 DOI: 10.1038/s41559-023-02234-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 09/22/2023] [Indexed: 12/02/2023]
Abstract
Bacteria possess a diverse range of mechanisms for inhibiting competitors, including bacteriocins, tailocins, type VI secretion systems and contact-dependent inhibition (CDI). Why bacteria have evolved such a wide array of weapon systems remains a mystery. Here we develop an agent-based model to compare short-range weapons that require cell-cell contact, with long-range weapons that rely on diffusion. Our model predicts that contact weapons are useful when an attacking strain is outnumbered, facilitating invasion and establishment. By contrast, ranged weapons tend to be effective only when attackers are abundant. We test our predictions with the opportunistic pathogen Pseudomonas aeruginosa, which naturally carries multiple weapons, including CDI and diffusing tailocins. As predicted, short-range CDI can function at low and high frequencies, while long-range tailocins require high frequency and cell density to function effectively. Head-to-head competition experiments with the two weapon types further support our predictions: a tailocin attacker defeats CDI only when it is numerically dominant, but then we find it can be devastating. Finally, we show that the two weapons work well together when one strain employs both. We conclude that short- and long-range weapons serve different functions and allow bacteria to fight both as individuals and as a group.
Collapse
Affiliation(s)
- Sean C Booth
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - William P J Smith
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| |
Collapse
|
3
|
Elery ZK, Myers-Morales T, Phillips ED, Garcia EC. Relaxed specificity of BcpB transporters mediates interactions between Burkholderia cepacia complex contact-dependent growth inhibition systems. mSphere 2023; 8:e0030323. [PMID: 37498085 PMCID: PMC10449530 DOI: 10.1128/msphere.00303-23] [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: 06/07/2023] [Accepted: 06/11/2023] [Indexed: 07/28/2023] Open
Abstract
Belonging to the two-partner secretion family of proteins, contact-dependent growth inhibition (CDI) systems mediate interbacterial antagonism among closely related Gram-negative bacteria. The toxic portion of a large surface protein, BcpA/CdiA, is delivered to the cytoplasm of neighboring cells where it inhibits growth. Translocation of the antibacterial polypeptide out of the producing cell requires an associated outer membrane transporter, BcpB/CdiB. Some bacteria, including many Burkholderia species, encode multiple distinct CDI systems, but whether there is interaction between these systems is largely unknown. Using Burkholderia cepacia complex species as a model, here we show that related BcpB transporters exhibit considerable secretion flexibility and can secrete both cognate and non-cognate BcpA substrates. We also identified an additional unique Burkholderia dolosa CDI system capable of mediating interbacterial competition and demonstrated that its BcpB transporter has similar relaxed substrate specificity. Our results showed that two BcpB transporters (BcpB-2 and BcpB-3) were able to secrete all four of the B. dolosa BcpA toxins, while one transporter (BcpB-1) appeared unable to secrete even its cognate BcpA substrate under the tested conditions. This flexibility provided a competitive advantage, as strains lacking the full repertoire of BcpB proteins had decreased CDI activity. Similar results were obtained in Burkholderia multivorans, suggesting that secretion flexibility may be a conserved feature of Burkholderia CDI systems. Together these findings suggest that the interaction between distinct CDI systems enhances the efficiency of bacterial antagonism. IMPORTANCE The Burkholderia cepacia complex (Bcc) is a group of related opportunistic bacterial pathogens that occupy a diverse range of ecological niches and exacerbate disease in patients with underlying conditions. Contact-dependent growth inhibition (CDI) system proteins, produced by Gram-negative bacteria, contain antagonistic properties that allow for intoxication of closely related neighboring bacteria via a secreted protein, BcpA. Multiple unique CDI systems can be found in the same bacterial strain, and here we show that these distinct systems interact in several Bcc species. Our findings suggest that the interaction between CDI system proteins is important for interbacterial toxicity. Understanding the mechanism of interplay between CDI systems provides further insight into the complexity of bacterial antagonism. Moreover, since many bacterial species are predicted to encode multiple CDI systems, this study suggests that interactions between these distinct systems likely contribute to the overall competitive fitness of these species.
Collapse
Affiliation(s)
- Zaria K. Elery
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | | | - Erica D. Phillips
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Erin C. Garcia
- University of Kentucky College of Medicine, Lexington, Kentucky, USA
| |
Collapse
|
4
|
Hirsch MJ, Hughes EM, Easter MM, Bollenbecker SE, Howze IV PH, Birket SE, Barnes JW, Kiedrowski MR, Krick S. A novel in vitro model to study prolonged Pseudomonas aeruginosa infection in the cystic fibrosis bronchial epithelium. PLoS One 2023; 18:e0288002. [PMID: 37432929 PMCID: PMC10335692 DOI: 10.1371/journal.pone.0288002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 06/16/2023] [Indexed: 07/13/2023] Open
Abstract
Pseudomonas aeruginosa (PA) is known to chronically infect airways of people with cystic fibrosis (CF) by early adulthood. PA infections can lead to increased airway inflammation and lung tissue damage, ultimately contributing to decreased lung function and quality of life. Existing models of PA infection in vitro commonly utilize 1-6-hour time courses. However, these relatively early time points may not encompass downstream airway cell signaling in response to the chronic PA infections observed in people with cystic fibrosis. To fill this gap in knowledge, the aim of this study was to establish an in vitro model that allows for PA infection of CF bronchial epithelial cells, cultured at the air liquid interface, for 24 hours. Our model shows with an inoculum of 2 x 102 CFUs of PA for 24 hours pro-inflammatory markers such as interleukin 6 and interleukin 8 are upregulated with little decrease in CF bronchial epithelial cell survival or monolayer confluency. Additionally, immunoblotting for phosphorylated phospholipase C gamma, a well-known downstream protein of fibroblast growth factor receptor signaling, showed significantly elevated levels after 24 hours with PA infection that were not seen at earlier timepoints. Finally, inhibition of phospholipase C shows significant downregulation of interleukin 8. Our data suggest that this newly developed in vitro "prolonged PA infection model" recapitulates the elevated inflammatory markers observed in CF, without compromising cell survival. This extended period of PA growth on CF bronchial epithelial cells will have impact on further studies of cell signaling and microbiological studies that were not possible in previous models using shorter PA exposures.
Collapse
Affiliation(s)
- Meghan J. Hirsch
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Emily M. Hughes
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Molly M. Easter
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Seth E. Bollenbecker
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Patrick H. Howze IV
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Susan E. Birket
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jarrod W. Barnes
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Megan R. Kiedrowski
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Stefanie Krick
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States of America
- Gregory Fleming James Cystic Fibrosis Center, The University of Alabama at Birmingham, Birmingham, AL, United States of America
| |
Collapse
|
5
|
Liu Y, McQuillen EA, Rana PSJB, Gloag ES, Wozniak DJ. Cross-Species Protection to Innate Immunity Mediated by A Bacterial Pigment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.15.524085. [PMID: 36711503 PMCID: PMC9882196 DOI: 10.1101/2023.01.15.524085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Bacterial infections are often polymicrobial. Pseudomonas aeruginosa and Staphylococcus aureus cause chronic co-infections, which are more problematic than mono-species infections. We found that the production of S. aureus membrane-bound pigment staphyloxanthin (STX), was induced by the P. aeruginosa exoproduct, 2-heptyl-4-hydroxyquinoline N-oxide (HQNO). The induction phenotype was conserved in P. aeruginosa and S. aureus clinical isolates examined. When subjected to hydrogen peroxide or human neutrophils, P. aeruginosa survival was significantly higher when mixed with wild-type (WT) S. aureus , compared to a mutant deficient in STX production or P. aeruginosa alone. In a murine wound model, co-infection with WT S. aureus , but not the STX-deficient mutant, enhanced P. aeruginosa burden and disease compared to mono-infection. In conclusion, we discovered a novel role for P. aeruginosa HQNO mediating polymicrobial interactions with S. aureus by inducing STX production, which consequently promotes resistance of both pathogens to innate immune effectors. These results further our understanding of how different bacterial species cooperatively cause co-infections.
Collapse
|
6
|
Crisan CV, Goldberg JB. Antibacterial contact-dependent proteins secreted by Gram-negative cystic fibrosis respiratory pathogens. Trends Microbiol 2022; 30:986-996. [PMID: 35487848 PMCID: PMC9474641 DOI: 10.1016/j.tim.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 01/11/2023]
Abstract
Cystic fibrosis (CF) is a genetic disease that affects almost 100 000 people worldwide. CF patients suffer from chronic bacterial airway infections that are often polymicrobial and are the leading cause of mortality. Interactions between pathogens modulate expression of genes responsible for virulence and antibiotic resistance. One of the ways bacteria can interact is through contact-dependent systems, which secrete antibacterial proteins (effectors) that confer advantages to cells that harbor them. Here, we highlight recent work that describes effectors used by Gram-negative CF pathogens to eliminate competitor bacteria. Understanding the mechanisms of secreted effectors may lead to novel insights into the ecology of bacteria that colonize respiratory tracts and could also pave the way for the design of new therapeutics.
Collapse
Affiliation(s)
- Cristian V Crisan
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA; Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, USA
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Emory University School of Medicine, Atlanta, GA, USA; Emory+Children's Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, GA, USA.
| |
Collapse
|
7
|
Bartelli NL, Passanisi VJ, Michalska K, Song K, Nhan DQ, Zhou H, Cuthbert BJ, Stols LM, Eschenfeldt WH, Wilson NG, Basra JS, Cortes R, Noorsher Z, Gabraiel Y, Poonen-Honig I, Seacord EC, Goulding CW, Low DA, Joachimiak A, Dahlquist FW, Hayes CS. Proteolytic processing induces a conformational switch required for antibacterial toxin delivery. Nat Commun 2022; 13:5078. [PMID: 36038560 PMCID: PMC9424206 DOI: 10.1038/s41467-022-32795-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 08/12/2022] [Indexed: 02/08/2023] Open
Abstract
Many Gram-negative bacteria use CdiA effector proteins to inhibit the growth of neighboring competitors. CdiA transfers its toxic CdiA-CT region into the periplasm of target cells, where it is released through proteolytic cleavage. The N-terminal cytoplasm-entry domain of the CdiA-CT then mediates translocation across the inner membrane to deliver the C-terminal toxin domain into the cytosol. Here, we show that proteolysis not only liberates the CdiA-CT for delivery, but is also required to activate the entry domain for membrane translocation. Translocation function depends on precise cleavage after a conserved VENN peptide sequence, and the processed ∆VENN entry domain exhibits distinct biophysical and thermodynamic properties. By contrast, imprecisely processed CdiA-CT fragments do not undergo this transition and fail to translocate to the cytoplasm. These findings suggest that CdiA-CT processing induces a critical structural switch that converts the entry domain into a membrane-translocation competent conformation.
Collapse
Affiliation(s)
- Nicholas L Bartelli
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Victor J Passanisi
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Kiho Song
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Dinh Q Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Bonnie J Cuthbert
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
| | - Nicholas G Wilson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Jesse S Basra
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Ricardo Cortes
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Zainab Noorsher
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Youssef Gabraiel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Isaac Poonen-Honig
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Elizabeth C Seacord
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
- Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - David A Low
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, IL, USA
- Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Christopher S Hayes
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.
| |
Collapse
|
8
|
Antimicrobial Weapons of Pseudomonas aeruginosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:223-256. [DOI: 10.1007/978-3-031-08491-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
9
|
Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt W(S, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia‐Delgado M, Schwede T. Target highlights in CASP14: Analysis of models by structure providers. Proteins 2021; 89:1647-1672. [PMID: 34561912 PMCID: PMC8616854 DOI: 10.1002/prot.26247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/11/2022]
Abstract
The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.
Collapse
Affiliation(s)
- Leila T. Alexander
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | | | - Athanassios Adamopoulos
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Ann M. Arvin
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Yannick J. Bomble
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | - Valerio Chiarini
- Program in Structural Biology and BiophysicsInstitute of Biotechnology, University of HelsinkiHelsinkiFinland
| | - Naga babu Chinnam
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
| | - Wah Chiu
- Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
- BioengineeringStanford University School of MedicineStanfordCaliforniaUSA
- Division of Cryo‐EM and Bioimaging SSRLSLAC National Accelerator LaboratoryMenlo ParkCaliforniaUSA
| | | | - Rhys Grinter
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Gagan D. Gupta
- Radiation Biology & Health Sciences DivisionBhabha Atomic Research CentreMumbaiIndia
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental BiologyUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
- Biomolecular Science and Engineering ProgramUniversity of California, Santa BarbaraSanta BarbaraCaliforniaUSA
| | - Tatjana Heidebrecht
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology of the National Research Council of Italy (CNR)RomeItaly
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Youngchang Kim
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Romain Linares
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural BiologyGrenobleFrance
| | | | - Vladimir V. Lunin
- Bioscience Center, National Renewable Energy LaboratoryGoldenColoradoUSA
| | - Andrei N. Lupas
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingenGermany
| | - Cihan Makbul
- Biocenter and Rudolf Virchow Center, Julius‐Maximilians Universität WürzburgWürzburgGermany
| | - Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John Moult
- Department of Cell Biology and Molecular GeneticsInstitute for Bioscience and Biotechnology Research, University of MarylandRockvilleMarylandUSA
| | - Prasun K. Mukherjee
- Nuclear Agriculture & Biotechnology DivisionBhabha Atomic Research CentreMumbaiIndia
| | - William (Sam) Nutt
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - Stefan L. Oliver
- Department of PediatricsStanford University School of MedicineStanfordCaliforniaUSA
| | - Anastassis Perrakis
- Oncode Institute and Division of BiochemistryNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lucy Stols
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of ChicagoChicagoIllinoisUSA
- X‐ray Science DivisionArgonne National Laboratory, Structural Biology CenterArgonneIllinoisUSA
| | - John A. Tainer
- Department of Molecular and Cellular OncologyThe University of Texas M.D. Anderson Cancer CenterHoustonTexasUSA
- Department of Cancer BiologyUniversity of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College LondonLondonUK
- Centre for Structural Systems Biology, Leibniz‐Institut für Experimentelle VirologieHamburgGermany
| | - Susan E. Tsutakawa
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | | | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| |
Collapse
|
10
|
Figueiredo ART, Özkaya Ö, Kümmerli R, Kramer J. Siderophores drive invasion dynamics in bacterial communities through their dual role as public good versus public bad. Ecol Lett 2021; 25:138-150. [PMID: 34753204 PMCID: PMC9299690 DOI: 10.1111/ele.13912] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/21/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022]
Abstract
Microbial invasions can compromise ecosystem services and spur dysbiosis and disease in hosts. Nevertheless, the mechanisms determining invasion outcomes often remain unclear. Here, we examine the role of iron‐scavenging siderophores in driving invasions of Pseudomonas aeruginosa into resident communities of environmental pseudomonads. Siderophores can be ‘public goods’ by delivering iron to individuals possessing matching receptors; but they can also be ‘public bads’ by withholding iron from competitors lacking these receptors. Accordingly, siderophores should either promote or impede invasion, depending on their effects on invader and resident growth. Using supernatant feeding and invasion assays, we show that invasion success indeed increased when the invader could use its siderophores to inhibit (public bad) rather than stimulate (public good) resident growth. Conversely, invasion success decreased the more the invader was inhibited by the residents’ siderophores. Our findings identify siderophores as a major driver of invasion dynamics in bacterial communities under iron‐limited conditions.
Collapse
Affiliation(s)
- Alexandre R T Figueiredo
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Özhan Özkaya
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
Peterson SB, Bertolli SK, Mougous JD. The Central Role of Interbacterial Antagonism in Bacterial Life. Curr Biol 2021; 30:R1203-R1214. [PMID: 33022265 DOI: 10.1016/j.cub.2020.06.103] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of bacteria interacting with their environment has historically centered on strategies for obtaining nutrients and resisting abiotic stresses. We argue this focus has deemphasized a third facet of bacterial life that is equally central to their existence: namely, the threat to survival posed by antagonizing bacteria. The diversity and ubiquity of interbacterial antagonism pathways is becoming increasingly apparent, and the insidious manner by which interbacterial toxins disarm their targets emphasizes the highly evolved nature of these processes. Studies examining the role of antagonism in natural communities reveal it can serve many functions, from facilitating colonization of naïve habitats to maintaining bacterial community stability. The pervasiveness of antagonistic pathways is necessarily matched by an equally extensive array of defense strategies. These overlap with well characterized, central stress response pathways, highlighting the contribution of bacterial interactions to shaping cell physiology. In this review, we build the case for the ubiquity and importance of interbacterial antagonism.
Collapse
Affiliation(s)
- S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA.
| |
Collapse
|
12
|
Guérin J, Buchanan SK. Protein import and export across the bacterial outer membrane. Curr Opin Struct Biol 2021; 69:55-62. [PMID: 33901701 DOI: 10.1016/j.sbi.2021.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/09/2021] [Accepted: 03/21/2021] [Indexed: 01/06/2023]
Abstract
The bacterial outer membrane forms an impermeable barrier to the environment, but a wide variety of substances must cross it without compromising the membrane. Perhaps, the most fascinating transport phenomenon is the import and export of very large protein toxins using relatively small β-barrel proteins residing in the outer membrane. Progress has been made on three systems in recent years that shed light on this process. In this review, we summarize bacteriocin (toxin) import using TonB-dependent transporters and protein secretion by autotransporters and two partner secretion systems.
Collapse
Affiliation(s)
- Jérémy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
13
|
Vesga P, Flury P, Vacheron J, Keel C, Croll D, Maurhofer M. Transcriptome plasticity underlying plant root colonization and insect invasion by Pseudomonas protegens. THE ISME JOURNAL 2020; 14:2766-2782. [PMID: 32879461 PMCID: PMC7784888 DOI: 10.1038/s41396-020-0729-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/08/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022]
Abstract
Pseudomonas protegens shows a high degree of lifestyle plasticity since it can establish both plant-beneficial and insect-pathogenic interactions. While P. protegens protects plants against soilborne pathogens, it can also invade insects when orally ingested leading to the death of susceptible pest insects. The mechanism whereby pseudomonads effectively switch between lifestyles, plant-beneficial or insecticidal, and the specific factors enabling plant or insect colonization are poorly understood. We generated a large-scale transcriptomics dataset of the model P. protegens strain CHA0 which includes data from the colonization of wheat roots, the gut of Plutella xylostella after oral uptake and the Galleria mellonella hemolymph after injection. We identified extensive plasticity in transcriptomic profiles depending on the environment and specific factors associated to different hosts or different stages of insect infection. Specifically, motor-activity and Reb toxin-related genes were highly expressed on wheat roots but showed low expression within insects, while certain antimicrobial compounds (pyoluteorin), exoenzymes (a chitinase and a polyphosphate kinase), and a transposase exhibited insect-specific expression. We further identified two-partner secretion systems as novel factors contributing to pest insect invasion. Finally, we use genus-wide comparative genomics to retrace the evolutionary origins of cross-kingdom colonization.
Collapse
Affiliation(s)
- Pilar Vesga
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Pascale Flury
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Crop Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
14
|
Contact-Dependent Growth Inhibition in Bacteria: Do Not Get Too Close! Int J Mol Sci 2020; 21:ijms21217990. [PMID: 33121148 PMCID: PMC7662968 DOI: 10.3390/ijms21217990] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
Over millions of years of evolution, bacteria have developed complex strategies for intra-and interspecies interactions and competition for ecological niches and resources. Contact-dependent growth inhibition systems (CDI) are designed to realize a direct physical contact of one bacterial cell with other cells in proximity via receptor-mediated toxin delivery. These systems are found in many microorganisms including clinically important human pathogens. The main purpose of these systems is to provide competitive advantages for the growth of the population. In addition, non-competitive roles for CDI toxin delivery systems including interbacterial signal transduction and mediators of bacterial collaboration have been suggested. In this review, our goal was to systematize the recent findings on the structure, mechanisms, and purpose of CDI systems in bacterial populations and discuss the potential biological and evolutionary impact of CDI-mediated interbacterial competition and/or cooperation.
Collapse
|
15
|
Guerin J, Botos I, Zhang Z, Lundquist K, Gumbart JC, Buchanan SK. Structural insight into toxin secretion by contact-dependent growth inhibition transporters. eLife 2020; 9:58100. [PMID: 33089781 PMCID: PMC7644211 DOI: 10.7554/elife.58100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Bacterial contact-dependent growth inhibition (CDI) systems use a type Vb secretion mechanism to export large CdiA toxins across the outer membrane by dedicated outer membrane transporters called CdiB. Here, we report the first crystal structures of two CdiB transporters from Acinetobacter baumannii and Escherichia coli. CdiB transporters adopt a TpsB fold, containing a 16-stranded transmembrane β-barrel connected to two periplasmic domains. The lumen of the CdiB pore is occluded by an N-terminal α-helix and the conserved extracellular loop 6; these two elements adopt different conformations in the structures. We identified a conserved DxxG motif located on strand β1 that connects loop 6 through different networks of interactions. Structural modifications of DxxG induce rearrangement of extracellular loops and alter interactions with the N-terminal α-helix, preparing the system for α-helix ejection. Using structural biology, functional assays, and molecular dynamics simulations, we show how the barrel pore is primed for CdiA toxin secretion.
Collapse
Affiliation(s)
- Jeremy Guerin
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
| | - Istvan Botos
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
| | - Zijian Zhang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, United States
| |
Collapse
|
16
|
Locke LW, Shankaran K, Gong L, Stoodley P, Vozar SL, Cole SL, Tweedle MF, Wozniak DJ. Evaluation of Peptide-Based Probes toward In Vivo Diagnostic Imaging of Bacterial Biofilm-Associated Infections. ACS Infect Dis 2020; 6:2086-2098. [PMID: 32603591 PMCID: PMC7429274 DOI: 10.1021/acsinfecdis.0c00125] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The clinical management of bacterial biofilm infections represents an enormous challenge in today's healthcare setting. The NIH estimates that 65% of bacterial infections are biofilm-related, and therapeutic outcomes are positively correlated with early intervention. Currently, there is no reliable imaging technique to detect biofilm infections in vivo, and current clinical protocols for accurate and direct biofilm identification are nonexistent. In orthopedic implant-associated biofilm infections, for example, current detection methods are based on nonspecific X-ray or radiolabeled white blood cell imaging, coupled with peri-prosthetic tissue or fluid samples taken invasively, and must be cultured. This approach is time-consuming and often fails to detect biofilm bacteria due to sampling errors and a lack of sensitivity. The ability to quantify bacterial biofilms by real-time noninvasive imaging is an urgent unmet clinical need that would revolutionize the management and treatment of these devastating types of infections. In the present study, we assembled a collection of fluorescently labeled peptide candidates to specifically explore their biofilm targeting properties. We evaluated these fluorescently labeled peptides using various in vitro assays for their ability to specifically and nondestructively target biofilms produced by model bacterial pathogen Pseudomonas aeruginosa. The lead candidate that emerged, 4Iphf-HN17, demonstrated rapid biofilm labeling kinetics, a lack of bactericidal activity, and biofilm targeting specificity in human cell infection models. In vivo fluorescently labeled 4Iphf-HN17 showed enhanced accumulation in biofilm-infected wounds, thus warranting further study.
Collapse
Affiliation(s)
- Landon W. Locke
- Dept. of Microbial Infection and Immunity, The Ohio State University
| | - Kothandaraman Shankaran
- Dept. of Radiology, The Wright Center for Innovation in Biomedical Eng, The Ohio State University
| | - Li Gong
- Dept. of Radiology, The Wright Center for Innovation in Biomedical Eng, The Ohio State University
| | - Paul Stoodley
- Dept. of Microbial Infection and Immunity, The Ohio State University
| | | | - Sara L. Cole
- Campus Microscopy and Imaging Facility, The Ohio State University
| | - Michael F. Tweedle
- Dept. of Radiology, The Wright Center for Innovation in Biomedical Eng, The Ohio State University
| | - Daniel J. Wozniak
- Dept. of Microbial Infection and Immunity, The Ohio State University,Dept. of Microbiology, The Ohio State University
| |
Collapse
|
17
|
Welp AL, Bomberger JM. Bacterial Community Interactions During Chronic Respiratory Disease. Front Cell Infect Microbiol 2020; 10:213. [PMID: 32477966 PMCID: PMC7240048 DOI: 10.3389/fcimb.2020.00213] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.
Collapse
Affiliation(s)
- Allison L. Welp
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Graduate Program in Microbiology and Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
18
|
A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant. Proc Natl Acad Sci U S A 2020; 117:6811-6821. [PMID: 32156726 DOI: 10.1073/pnas.1919198117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence suggests the Pseudomonas aeruginosa accessory genome is enriched with uncharacterized virulence genes. Identification and characterization of such genes may reveal novel pathogenic mechanisms used by particularly virulent isolates. Here, we utilized a mouse bacteremia model to quantify the virulence of 100 individual P. aeruginosa bloodstream isolates and performed whole-genome sequencing to identify accessory genomic elements correlated with increased bacterial virulence. From this work, we identified a specific contact-dependent growth inhibition (CDI) system enriched among highly virulent P. aeruginosa isolates. CDI systems contain a large exoprotein (CdiA) with a C-terminal toxin (CT) domain that can vary between different isolates within a species. Prior work has revealed that delivery of a CdiA-CT domain upon direct cell-to-cell contact can inhibit replication of a susceptible target bacterium. Aside from mediating interbacterial competition, we observed our virulence-associated CdiA-CT domain to promote toxicity against mammalian cells in culture and lethality during mouse bacteremia. Structural and functional studies revealed this CdiA-CT domain to have in vitro tRNase activity, and mutations that abrogated this tRNAse activity in vitro also attenuated virulence. Furthermore, CdiA contributed to virulence in mice even in the absence of contact-dependent signaling. Overall, our findings indicate that this P. aeruginosa CDI system functions as both an interbacterial inhibition system and a bacterial virulence factor against a mammalian host. These findings provide an impetus for continued studies into the complex role of CDI systems in P. aeruginosa pathogenesis.
Collapse
|
19
|
Cornforth DM, Diggle FL, Melvin JA, Bomberger JM, Whiteley M. Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case. mBio 2020; 11:e03042-19. [PMID: 31937646 PMCID: PMC6960289 DOI: 10.1128/mbio.03042-19] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 01/14/2023] Open
Abstract
Laboratory models are a cornerstone of modern microbiology, but the accuracy of these models has not been systematically evaluated. As a result, researchers often choose models based on intuition or incomplete data. We propose a general quantitative framework to assess model accuracy from RNA sequencing data and use this framework to evaluate models of Pseudomonas aeruginosa cystic fibrosis (CF) lung infection. We found that an in vitro synthetic CF sputum medium model and a CF airway epithelial cell model had the highest genome-wide accuracy but underperformed on distinct functional categories, including porins and polyamine biosynthesis for the synthetic sputum medium and protein synthesis for the epithelial cell model. We identified 211 "elusive" genes that were not mimicked in a reference strain grown in any laboratory model but found that many were captured by using a clinical isolate. These methods provide researchers with an evidence-based foundation to select and improve laboratory models.IMPORTANCE Laboratory models have become a cornerstone of modern microbiology. However, the accuracy of even the most commonly used models has never been evaluated. Here, we propose a quantitative framework based on gene expression data to evaluate model performance and apply it to models of Pseudomonas aeruginosa cystic fibrosis lung infection. We discovered that these models captured different aspects of P. aeruginosa infection physiology, and we identify which functional categories are and are not captured by each model. These methods will provide researchers with a solid basis to choose among laboratory models depending on the scientific question of interest and will help improve existing experimental models.
Collapse
Affiliation(s)
- Daniel M Cornforth
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Frances L Diggle
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Jeffrey A Melvin
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
| |
Collapse
|
20
|
Roussin M, Rabarioelina S, Cluzeau L, Cayron J, Lesterlin C, Salcedo SP, Bigot S. Identification of a Contact-Dependent Growth Inhibition (CDI) System That Reduces Biofilm Formation and Host Cell Adhesion of Acinetobacter baumannii DSM30011 Strain. Front Microbiol 2019; 10:2450. [PMID: 31736897 PMCID: PMC6831553 DOI: 10.3389/fmicb.2019.02450] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Acinetobacter baumannii is a multidrug-resistant nosocomial opportunistic pathogen that is becoming a major health threat worldwide. In this study, we have focused on the A. baumannii DSM30011 strain, an environmental isolate that retains many virulence-associated traits. We found that its genome contains two loci encoding for contact-dependent growth inhibition (CDI) systems. These systems serve to kill or inhibit the growth of non-sibling bacteria by delivering toxins into the cytoplasm of target cells, thereby conferring the host strain a significant competitive advantage. We show that one of the two toxins functions as a DNA-damaging enzyme, capable of inducing DNA double-stranded breaks to the chromosome of Escherichia coli strain. The second toxin has unknown catalytic activity but stops the growth of E. coli without bactericidal effect. In our conditions, only one of the CDI systems was highly expressed in the A. baumannii DSM30011 strain and was found to mediate interbacterial competition. Surprisingly, the absence of this CDI system promotes adhesion of A. baumannii DSM30011 to both abiotic and biotic surfaces, a phenotype that differs from previously described CDI systems. Our results suggest that a specific regulation mediated by this A. baumannii DSM30011 CDI system may result in changes in bacterial physiology that repress host cell adhesion and biofilm formation.
Collapse
Affiliation(s)
- Morgane Roussin
- Cell Biology of Bacterial Pathogenicity Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Sedera Rabarioelina
- Cell Biology of Bacterial Pathogenicity Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Laurence Cluzeau
- Cell Biology of Bacterial Pathogenicity Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Julien Cayron
- Cell to Cell DNA Transfer Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Christian Lesterlin
- Cell to Cell DNA Transfer Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Suzana P Salcedo
- Cell Biology of Bacterial Pathogenicity Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| | - Sarah Bigot
- Cell Biology of Bacterial Pathogenicity Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France.,Cell to Cell DNA Transfer Team, Laboratory of Molecular Microbiology and Structural Biochemistry, CNRS UMR 5086, University of Lyon, Lyon, France
| |
Collapse
|
21
|
Bottery MJ, Passaris I, Dytham C, Wood AJ, van der Woude MW. Spatial Organization of Expanding Bacterial Colonies Is Affected by Contact-Dependent Growth Inhibition. Curr Biol 2019; 29:3622-3634.e5. [PMID: 31630946 PMCID: PMC6839403 DOI: 10.1016/j.cub.2019.08.074] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 12/22/2022]
Abstract
Identifying how microbes are able to manipulate, survive, and thrive in complex multispecies communities has expanded our understanding of how microbial ecosystems impact human health and the environment. The ability of bacteria to negatively affect neighbors, through explicit toxin delivery systems, provides them with an opportunity to manipulate the composition of growing microbial communities. Contact-dependent inhibition (CDI) systems (a Type Vb secretion system) are a distinct subset of competition systems whose contribution to shaping the development of spatially structured bacterial communities are yet to be fully understood. Here, we compare the impact of different CDI systems, at both the single-cell and population level, to determine the key drivers of CDI-mediated competition within spatially structured bacterial populations. Through an iterative approach using both an Escherichia coli experimental system and computational modeling, we show that CDI systems have subtle and system-specific effects at the single-cell level, generating single-cell-wide boundaries between CDI-expressing inhibitor cells and their neighboring targets. Despite the subtle effects of CDI at a single-cell level, CDI systems greatly diminished the ability of susceptible targets to expand their range during colony growth. The inoculum density of the population, together with the CDI system-specific variables of the speed of inhibition after contact and biological cost of CDI, strongly affects CDI-mediated competition. In contrast, the magnitude of the toxin-induced growth retardation of target cells only weakly impacts the composition of the population. Our work reveals how distinct CDI systems can differentially affect the composition and spatial arrangement of bacterial populations. CDI causes subtle growth inhibition in a subset of contacted target cells Model describes and predicts observed effects on spatial distribution of strains CDI facilitates success of inhibitor strain increasing population patch size A CDI system’s inhibition rate dominates toxicity in driving competition outcome
Collapse
Affiliation(s)
- Michael J Bottery
- Centre for Immunology and Infection and Hull York Medical School, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5DD, UK
| | - Ioannis Passaris
- Centre for Immunology and Infection and Hull York Medical School, University of York, York YO10 5DD, UK; Department of Biology, University of York, York YO10 5DD, UK
| | - Calvin Dytham
- Department of Biology, University of York, York YO10 5DD, UK
| | - A Jamie Wood
- Department of Biology, University of York, York YO10 5DD, UK; Department of Mathematics, University of York, York YO10 5DD, UK.
| | - Marjan W van der Woude
- Centre for Immunology and Infection and Hull York Medical School, University of York, York YO10 5DD, UK; York Biomedical Research Institute, University of York YO10 5DD, UK.
| |
Collapse
|
22
|
Lepore R, Kryshtafovych A, Alahuhta M, Veraszto HA, Bomble YJ, Bufton JC, Bullock AN, Caba C, Cao H, Davies OR, Desfosses A, Dunne M, Fidelis K, Goulding CW, Gurusaran M, Gutsche I, Harding CJ, Hartmann MD, Hayes CS, Joachimiak A, Leiman PG, Loppnau P, Lovering AL, Lunin VV, Michalska K, Mir-Sanchis I, Mitra AK, Moult J, Phillips GN, Pinkas DM, Rice PA, Tong Y, Topf M, Walton JD, Schwede T. Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins 2019; 87:1037-1057. [PMID: 31442339 PMCID: PMC6851490 DOI: 10.1002/prot.25805] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
Abstract
The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.
Collapse
Affiliation(s)
- Rosalba Lepore
- BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Markus Alahuhta
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Harshul A Veraszto
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Joshua C Bufton
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Alex N Bullock
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Cody Caba
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
| | - Hongnan Cao
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Owen R Davies
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ambroise Desfosses
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, Zurich, Switzerland
| | | | - Celia W Goulding
- Department of Molecular Biology and Biochemistry; Pharmaceutical Sciences, University of California Irvine, Irvine, California
| | - Manickam Gurusaran
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California
| | - Andrzej Joachimiak
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Petr G Leiman
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Vladimir V Lunin
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado
| | - Karolina Michalska
- Structural Biology Center, Biosciences Division, Midwest Center for Structural Genomics, Argonne
| | - Ignacio Mir-Sanchis
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - A K Mitra
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of Maryland, Rockville, Maryland, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas.,Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Daniel M Pinkas
- Nuffield Department of Medicine; Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, UK
| | - Jonathan D Walton
- Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - Torsten Schwede
- Biozentrum University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
| |
Collapse
|
23
|
Ramos-Hegazy L, Chakravarty S, Anderson GG. Phosphoglycerate mutase affects Stenotrophomonas maltophilia attachment to biotic and abiotic surfaces. Microbes Infect 2019; 22:60-64. [PMID: 31430538 DOI: 10.1016/j.micinf.2019.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 10/26/2022]
Abstract
Stenotrophomonas maltophilia biofilm formation is of increasing medical concern, particularly for lung infections. However, the molecular mechanisms facilitating the biofilm lifestyle in S. maltophilia are poorly understood. We generated and screened a transposon mutant library for mutations that lead to altered biofilm formation compared to wild type. One of these mutations, in the gene for glycolytic enzyme phosphoglycerate mutase (gpmA), resulted in impaired attachment on abiotic and biotic surfaces. As adherence to a surface is the initial step in biofilm developmental processes, our results reveal a unique factor that could affect S. maltophilia biofilm initiation and, possibly, subsequent development.
Collapse
Affiliation(s)
- Layla Ramos-Hegazy
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | | | - Gregory G Anderson
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA.
| |
Collapse
|
24
|
Diversity of Contact-Dependent Growth Inhibition Systems of Pseudomonas aeruginosa. J Bacteriol 2019; 201:JB.00776-18. [PMID: 31036723 DOI: 10.1128/jb.00776-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are used in bacterial competition to hinder the growth of neighboring microbes. These systems utilize a two-partner secretion mechanism to display the CdiA exoprotein at the bacterial cell surface. CdiA forms a long filamentous stalk that facilitates binding to a target cell and delivery of a C-terminal toxin (CT) domain. This CT domain is processed and delivered into the cytoplasm of a target cell upon contact. CDI systems also encode a cognate immunity protein (CdiI) that protects siblings and resistant targeted cells from intoxication by high-affinity binding to the CT. CdiA CT domains vary among strains within a species, and many alleles encode enzymatic functions that target nucleic acids. This variation is thought to help drive diversity and adaptation within a species. CdiA diversity is well studied in Escherichia coli and several other bacteria, but little is known about the extent of this diversity in Pseudomonas aeruginosa. The purpose of this review is to highlight the variability that exists in CDI systems of P. aeruginosa. We show that this diversity is apparent even among strains isolated from a single geographical region, suggesting that CDI systems play an important role in the ecology of P. aeruginosa.
Collapse
|
25
|
Burkholderia cepacia Complex Contact-Dependent Growth Inhibition Systems Mediate Interbacterial Competition. J Bacteriol 2019; 201:JB.00012-19. [PMID: 30962350 DOI: 10.1128/jb.00012-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022] Open
Abstract
Burkholderia species, including opportunistic pathogens in the Burkholderia cepacia complex (Bcc), have genes to produce contact-dependent growth inhibition (CDI) system proteins. CDI is a phenomenon in which Gram-negative bacteria use the toxic C terminus of a polymorphic surface-exposed exoprotein, BcpA, to inhibit the growth of susceptible bacteria upon direct cell-cell contact. Production of a small immunity protein, BcpI, prevents autoinhibition. Although CDI systems appear widespread in Gram-negative bacteria, their function has been primarily examined in several model species. Here we demonstrate that genes encoding predicted CDI systems in Bcc species exhibit considerable diversity. We also show that Burkholderia multivorans, which causes pulmonary infections in patients with cystic fibrosis, expresses genes that encode two CDI systems, both of which appear distinct from the typical Burkholderia-type CDI system. Each system can mediate intrastrain interbacterial competition and contributes to bacterial adherence. Surprisingly, the immunity-protein-encoding bcpI gene of CDI system 1 could be mutated without obvious deleterious effects. We also show that nonpathogenic Burkholderia thailandensis uses CDI to control B. multivorans growth during coculture, providing one of the first examples of interspecies CDI and suggesting that CDI systems could be manipulated to develop therapeutic strategies targeting Bcc pathogens.IMPORTANCE Competition among bacteria affects microbial colonization of environmental niches and host organisms, particularly during polymicrobial infections. The Bcc is a group of environmental bacteria that can cause life-threatening opportunistic infections in patients who have cystic fibrosis or are immunocompromised. Understanding the mechanisms used by these bacterial pathogens to compete with one another may lead to the development of more effective therapies. Findings presented here demonstrate that a Bcc species, Burkholderia multivorans, produces functional CDI system proteins and that growth of this pathogen can be controlled by CDI system proteins produced by neighboring Burkholderia cells.
Collapse
|
26
|
Russell AL, Rebolleda‐Gómez M, Shaible TM, Ashman T. Movers and shakers: Bumble bee foraging behavior shapes the dispersal of microbes among and within flowers. Ecosphere 2019. [DOI: 10.1002/ecs2.2714] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Avery L. Russell
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - María Rebolleda‐Gómez
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Tierney Marie Shaible
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
- Entomology and Insect Science Graduate Interdisciplinary Program University of Arizona Tucson Arizona 85721 USA
| | - Tia‐Lynn Ashman
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| |
Collapse
|
27
|
Sentausa E, Basso P, Berry A, Adrait A, Bellement G, Couté Y, Lory S, Elsen S, Attrée I. Insertion sequences drive the emergence of a highly adapted human pathogen. Microb Genom 2019; 6. [PMID: 30946644 PMCID: PMC7643977 DOI: 10.1099/mgen.0.000265] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of β-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.
Collapse
Affiliation(s)
- Erwin Sentausa
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Evotec ID (Lyon) SAS, Marcy l'Étoile, France
| | - Pauline Basso
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Present address: Department of Microbiology and Immunology, University of California San Francisco (UCSF) School of Medicine, San Francisco, CA, USA
| | - Alice Berry
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Annie Adrait
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Gwendoline Bellement
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France.,Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France.,Present address: Biozentrum, University of Basel, Basel, Switzerland
| | - Yohann Couté
- Université Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000 Grenoble, France
| | - Stephen Lory
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS ERL5261, INSERM U1036, CEA, Laboratory Biology of Cancer and Infection, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, 38000 Grenoble, France
| |
Collapse
|
28
|
Torres A, Kasturiarachi N, DuPont M, Cooper VS, Bomberger J, Zemke A. NADH Dehydrogenases in Pseudomonas aeruginosa Growth and Virulence. Front Microbiol 2019; 10:75. [PMID: 30804898 PMCID: PMC6370648 DOI: 10.3389/fmicb.2019.00075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/15/2019] [Indexed: 01/23/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen with a complex respiratory chain. The bacterium is predicted to express three NADH:ubiquinone oxidoreductases (NDH-1, NDH-2 and Nqr). We created deletions strains of the predicted NADH:ubiquinone oxidoreductases alone, and in combination to determine the respective roles of the NADH dehydrogenases in growth and virulence. NDH-1 and NDH-2 were largely redundant under aerobic conditions. Aerobic NADH dehydrogenase enzymatic activity assay was lost with deletion of both NDH-1 and NDH-2. Under anaerobic conditions, NDH-1 was required for robust growth, and overexpression of NDH-2 rescued the NDH-1 anaerobic growth defect in rich media. There was not compensatory upregulation of NDH-2 under anaerobic conditions in NDH-1 deletion strains. To test which genes were required for in vivo virulence, we used both an insect and plant disease model. In the Galleria mellonella model, neither deletion of NDH-1 nor NDH-2 led to a change in median lethal dose, although death occurred more slowly in the NDH-1 deletion infections. In a lettuce model of virulence, loss of NDH-1 caused a decrease in recovered viable bacteria and a decrease in visual tissue damage. The compound deletion of NDH-1/NDH-2 causes a severe growth defect, both under aerobic and anaerobic conditions, and was avirulent in a lettuce model. Together, these results demonstrate the redundancy of the P. aeruginosa respiratory chain at the NADH dehydrogenase level in aerobic growth and virulence.
Collapse
Affiliation(s)
- Angela Torres
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Naomi Kasturiarachi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew DuPont
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jennifer Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Anna Zemke
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| |
Collapse
|
29
|
Perault AI, Cotter PA. Three Distinct Contact-Dependent Growth Inhibition Systems Mediate Interbacterial Competition by the Cystic Fibrosis Pathogen Burkholderia dolosa. J Bacteriol 2018; 200:e00428-18. [PMID: 30150233 PMCID: PMC6199481 DOI: 10.1128/jb.00428-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 02/08/2023] Open
Abstract
The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of Bdolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode contact-dependent growth inhibition (CDI) systems. CDI systems function by translocating the toxic C terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci were expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but contact-dependent signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to the death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant, as it has identified three functional contact-dependent growth inhibition systems in Bdolosa that may provide this pathogen a competitive advantage during polymicrobial infections.
Collapse
Affiliation(s)
- Andrew I Perault
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
30
|
Duckworth PF, Rowlands RS, Barbour ME, Maddocks SE. A novel flow-system to establish experimental biofilms for modelling chronic wound infection and testing the efficacy of wound dressings. Microbiol Res 2018; 215:141-147. [DOI: 10.1016/j.micres.2018.07.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/09/2018] [Accepted: 07/18/2018] [Indexed: 01/09/2023]
|
31
|
Ghosh A, Baltekin Ö, Wäneskog M, Elkhalifa D, Hammarlöf DL, Elf J, Koskiniemi S. Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations. EMBO J 2018; 37:embj.201798026. [PMID: 29572241 DOI: 10.15252/embj.201798026] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/08/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts.
Collapse
Affiliation(s)
- Anirban Ghosh
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Özden Baltekin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Dina Elkhalifa
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Disa L Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|