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De R, Whiteley M, Azad RK. A gene network-driven approach to infer novel pathogenicity-associated genes: application to Pseudomonas aeruginosa PAO1. mSystems 2023; 8:e0047323. [PMID: 37921470 PMCID: PMC10734507 DOI: 10.1128/msystems.00473-23] [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] [Received: 05/11/2023] [Accepted: 10/04/2023] [Indexed: 11/04/2023] Open
Abstract
IMPORTANCE We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen Pseudomonas aeruginosa PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in P. aeruginosa PAO1. The systems-level investigation of P. aeruginosa PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on P. aeruginosa virulence and resistance. These could potentially act as molecular determinants of P. aeruginosa PAO1 pathogenicity and responses to antibiotics.
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Affiliation(s)
- Ronika De
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
| | - Marvin Whiteley
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children’s Cystic Fibrosis Center, Atlanta, Georgia, USA
| | - Rajeev K. Azad
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
- BioDiscovery Institute, University of North Texas, Denton, Texas, USA
- Department of Mathematics, University of North Texas, Denton, Texas, USA
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2
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Fritsch S, Gasser V, Peukert C, Pinkert L, Kuhn L, Perraud Q, Normant V, Brönstrup M, Schalk IJ. Uptake Mechanisms and Regulatory Responses to MECAM- and DOTAM-Based Artificial Siderophores and Their Antibiotic Conjugates in Pseudomonas aeruginosa. ACS Infect Dis 2022; 8:1134-1146. [PMID: 35500104 DOI: 10.1021/acsinfecdis.2c00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The development of new antibiotics against Gram-negative bacteria has to deal with the low permeability of the outer membrane. This obstacle can be overcome by utilizing siderophore-dependent iron uptake pathways as entrance routes for antibiotic uptake. Iron-chelating siderophores are actively imported by bacteria, and their conjugation to antibiotics allows smuggling the latter into bacterial cells. Synthetic siderophore mimetics based on MECAM (1,3,5-N,N',N″-tris-(2,3-dihydroxybenzoyl)-triaminomethylbenzene) and DOTAM (1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane) cores, both chelating iron via catechol groups, have been recently applied as versatile carriers of functional cargo. In the present study, we show that MECAM and the MECAM-ampicillin conjugate 3 transport iron into Pseudomonas aeruginosa cells via the catechol-type outer membrane transporters PfeA and PirA and DOTAM solely via PirA. Differential proteomics and quantitative real-time polymerase chain reaction (qRT-PCR) showed that MECAM import induced the expression of pfeA, whereas 3 led to an increase in the expression of pfeA and ampc, a gene conferring ampicillin resistance. The presence of DOTAM did not induce the expression of pirA but upregulated the expression of two zinc transporters (cntO and PA0781), pointing out that bacteria become zinc starved in the presence of this compound. Iron uptake experiments with radioactive 55Fe demonstrated that import of this nutrient by MECAM and DOTAM was as efficient as with the natural siderophore enterobactin. The study provides a functional validation for DOTAM- and MECAM-based artificial siderophore mimetics as vehicles for the delivery of cargo into Gram-negative bacteria.
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Affiliation(s)
- Sarah Fritsch
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Véronique Gasser
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Carsten Peukert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Lukas Pinkert
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Lauriane Kuhn
- Plateforme Proteomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, CNRS, FR1589, 15 rue Descartes, Strasbourg Cedex F-67084, France
| | - Quentin Perraud
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Vincent Normant
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
| | - Mark Brönstrup
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Braunschweig 38124, Germany
- Center of Biomolecular Drug Research (BMWZ), Leibniz Universität, Hannover 30159, Germany
| | - Isabelle J. Schalk
- CNRS, University of Strasbourg, UMR7242, ESBS, Bld Sébastien Brant, F-67412 Illkirch, Strasbourg 67070, France
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3
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Fiorillo A, Battistoni A, Ammendola S, Secli V, Rinaldo S, Cutruzzolà F, Demitri N, Ilari A. Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa. Acta Crystallogr D Struct Biol 2021; 77:1401-1410. [PMID: 34726168 PMCID: PMC8561739 DOI: 10.1107/s2059798321009608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023] Open
Abstract
The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063-PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar affinity. Crystallographic characterization, performed both with and without zinc, revealed an α/β-sandwich structure that can be classified as a noncanonical ferredoxin-like fold since it differs in size and topology. The histidine-rich stretches located at the N-terminus and between β3 and β4 are disordered in the apo structure, but a few residues become structured in the presence of zinc, contributing to coordination in one of the two sites. The ability to bind two zinc ions at relatively low affinity, the absence of catalytic cavities and the presence of two histidine-rich loops are properties and structural features which suggest that PA4063 might play a role as a periplasmic zinc chaperone or as a concentration sensor useful for optimizing the response of the pathogen to zinc deficiency.
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Affiliation(s)
- Annarita Fiorillo
- Department of Biochemical Sciences, Sapienza University of Rome, Pizzale Aldo Moro 5, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), Pizzale Aldo Moro 5, Rome, Italy
| | - Andrea Battistoni
- Department of Biology, University of Tor Vegata, Via delle Ricerca Scientifica 1, Rome, Italy
| | - Serena Ammendola
- Department of Biology, University of Tor Vegata, Via delle Ricerca Scientifica 1, Rome, Italy
| | - Valerio Secli
- Department of Biology, University of Tor Vegata, Via delle Ricerca Scientifica 1, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Pizzale Aldo Moro 5, 00185 Rome, Italy
- Laboratory Affiliated To Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Pizzale Aldo Moro 5, 00185 Rome, Italy
- Laboratory Affiliated To Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Rome, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste S.C.p.A., S.S. 14 km 163.5 in Area Science Park, Basovizza, 34149 Trieste, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), Pizzale Aldo Moro 5, Rome, Italy
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4
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Ducret V, Abdou M, Goncalves Milho C, Leoni S, Martin-Pelaud O, Sandoz A, Segovia Campos I, Tercier-Waeber ML, Valentini M, Perron K. Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics. Front Microbiol 2021; 12:739988. [PMID: 34690984 PMCID: PMC8531726 DOI: 10.3389/fmicb.2021.739988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022] Open
Abstract
Zinc is one of the most important trace elements for life and its deficiency, like its excess, can be fatal. In the bacterial opportunistic pathogen Pseudomonas aeruginosa, Zn homeostasis is not only required for survival, but also for virulence and antibiotic resistance. Thus, the bacterium possesses multiple Zn import/export/storage systems. In this work, we determine the expression dynamics of the entire P. aeruginosa Zn homeostasis network at both transcript and protein levels. Precisely, we followed the switch from a Zn-deficient environment, mimicking the initial immune strategy to counteract bacterial infections, to a Zn-rich environment, representing the phagocyte metal boost used to eliminate an engulfed pathogen. Thanks to the use of the NanoString technology, we timed the global silencing of Zn import systems and the orchestrated induction of Zn export systems. We show that the induction of Zn export systems is hierarchically organized as a function of their impact on Zn homeostasis. Moreover, we identify PA2807 as a novel Zn resistance component in P. aeruginosa and highlight new regulatory links among Zn-homeostasis systems. Altogether, this work unveils a sophisticated and adaptive homeostasis network, which complexity is key in determining a pathogen spread in the environment and during host-colonization.
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Affiliation(s)
- Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Melina Abdou
- Department of Inorganic and Analytical Chemistry, University of Geneva, Geneva, Switzerland
| | - Catarina Goncalves Milho
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Oriane Martin-Pelaud
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Antoine Sandoz
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Inés Segovia Campos
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Department of Earth Sciences, University of Geneva, Geneva, Switzerland
| | | | - Martina Valentini
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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5
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Khademi SMH, Gabrielaite M, Paulsson M, Knulst M, Touriki E, Marvig RL, Påhlman LI. Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. mSystems 2021; 6:e0052321. [PMID: 34184916 PMCID: PMC8269239 DOI: 10.1128/msystems.00523-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Bacterial pathogens evolve during chronic colonization of the human host by selection for pathoadaptive mutations. One of the emerging and understudied bacterial species causing chronic airway infections in patients with cystic fibrosis (CF) is Achromobacter xylosoxidans. It can establish chronic infections in patients with CF, but the genetic and phenotypic changes associated with adaptation during these infections are not completely understood. In this study, we analyzed the whole-genome sequences of 55 clinical A. xylosoxidans isolates longitudinally collected from the sputum of 6 patients with CF. Four genes encoding regulatory proteins and two intergenic regions showed convergent evolution, likely driven by positive selection for pathoadaptive mutations, across the different clones of A. xylosoxidans. Most of the evolved isolates had lower swimming motility and were resistant to multiple classes of antibiotics, while fewer of the evolved isolates had slower growth or higher biofilm production than the first isolates. Using a genome-wide association study method, we identified several putative genetic determinants of biofilm formation, motility and β-lactam resistance in this pathogen. With respect to antibiotic resistance, we discovered that a combination of mutations in pathoadaptive genes (phoQ and bigR) and two other genes encoding regulatory proteins (spoT and cpxA) were associated with increased resistance to meropenem and ceftazidime. Altogether, our results suggest that genetic changes within regulatory loci facilitate within-host adaptation of A. xylosoxidans and the emergence of adaptive phenotypes, such as antibiotic resistance or biofilm formation. IMPORTANCE A thorough understanding of bacterial pathogen adaptation is essential for the treatment of chronic bacterial infections. One unique challenge in the analysis and interpretation of genomics data is identifying the functional impact of mutations accumulated in the bacterial genome during colonization in the human host. Here, we investigated the genomic and phenotypic evolution of A. xylosoxidans in chronic airway infections of patients with CF and identified several mutations associated with the phenotypic evolution of this pathogen using genome-wide associations. Identification of phenotypes under positive selection and the associated mutations can enlighten the adaptive processes of this emerging pathogen in human infections and pave the way for novel therapeutic interventions.
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Affiliation(s)
- S. M. Hossein Khademi
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | | | - Magnus Paulsson
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
- Division of Infectious Diseases, Skåne University Hospital Lund, Lund, Sweden
| | - Mattis Knulst
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
| | - Eleni Touriki
- Clinical Microbiology, Labmedicin Skåne, Lund, Sweden
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Lisa I. Påhlman
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, Lund, Sweden
- Division of Infectious Diseases, Skåne University Hospital Lund, Lund, Sweden
- Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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6
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Gomez NO, Tetard A, Ouerdane L, Laffont C, Brutesco C, Ball G, Lobinski R, Denis Y, Plésiat P, Llanes C, Arnoux P, Voulhoux R. Involvement of the Pseudomonas aeruginosa MexAB-OprM efflux pump in the secretion of the metallophore pseudopaline. Mol Microbiol 2020; 115:84-98. [PMID: 32896017 DOI: 10.1111/mmi.14600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/07/2020] [Accepted: 08/28/2020] [Indexed: 12/16/2022]
Abstract
To overcome the metal restriction imposed by the host's nutritional immunity, pathogenic bacteria use high metal affinity molecules called metallophores. Metallophore-mediated metal uptake pathways necessitate complex cycles of synthesis, secretion, and recovery of the metallophore across the bacterial envelope. We recently discovered staphylopine and pseudopaline, two members of a new family of broad-spectrum metallophores important for bacterial survival during infections. Here, we are expending the molecular understanding of the pseudopaline transport cycle across the diderm envelope of the Gram-negative bacterium Pseudomonas aeruginosa. We first explored pseudopaline secretion by performing in vivo quantifications in various genetic backgrounds and revealed the specific involvement of the MexAB-OprM efflux pump in pseudopaline transport across the outer membrane. We then addressed the recovery part of the cycle by investigating the fate of the recaptured metal-loaded pseudopaline. To do so, we combined in vitro reconstitution experiments and in vivo phenotyping in absence of pseudopaline transporters to reveal the existence of a pseudopaline modification mechanism, possibly involved in the metal release following pseudopaline recovery. Overall, our data allowed us to provide an improved molecular model of secretion, recovery, and fate of this important metallophore by P. aeruginosa.
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Affiliation(s)
- Nicolas Oswaldo Gomez
- Laboratoire de Chimie Bactérienne (LCB) UMR7283, Institut de Microbiologie de la Méditerranée (IMM), CNRS, Aix-Marseille Université, Marseille, France
| | - Alexandre Tetard
- Laboratoire de Bactériologie, UMR CNRS 6249 Chrono-Environnement, Faculté de Médecine-Pharmacie, Université de Bourgogne Franche-Comté, Besançon, France
| | - Laurent Ouerdane
- Université de Pau et des Pays de l'Adour, e2s UPPA, CNRS, IPREM-UMR5254, Hélioparc, Pau, France
| | - Clémentine Laffont
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR, CEA Cadarache, Saint-Paul-lez Durance, France
| | - Catherine Brutesco
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR, CEA Cadarache, Saint-Paul-lez Durance, France
| | - Geneviève Ball
- Laboratoire de Chimie Bactérienne (LCB) UMR7283, Institut de Microbiologie de la Méditerranée (IMM), CNRS, Aix-Marseille Université, Marseille, France
| | - Ryszard Lobinski
- Université de Pau et des Pays de l'Adour, e2s UPPA, CNRS, IPREM-UMR5254, Hélioparc, Pau, France
| | - Yann Denis
- CNRS, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Patrick Plésiat
- Laboratoire de Bactériologie, UMR CNRS 6249 Chrono-Environnement, Faculté de Médecine-Pharmacie, Université de Bourgogne Franche-Comté, Besançon, France
| | - Catherine Llanes
- Laboratoire de Bactériologie, UMR CNRS 6249 Chrono-Environnement, Faculté de Médecine-Pharmacie, Université de Bourgogne Franche-Comté, Besançon, France
| | - Pascal Arnoux
- CEA, CNRS, Aix-Marseille Université, Institut de Biosciences et Biotechnologies d'Aix-Marseille, UMR, CEA Cadarache, Saint-Paul-lez Durance, France
| | - Romé Voulhoux
- Laboratoire de Chimie Bactérienne (LCB) UMR7283, Institut de Microbiologie de la Méditerranée (IMM), CNRS, Aix-Marseille Université, Marseille, France
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7
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Khademi SMH, Sazinas P, Jelsbak L. Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa. Genome Biol Evol 2019; 11:1385-1397. [PMID: 30980662 PMCID: PMC6505451 DOI: 10.1093/gbe/evz083] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial pathogens evolve during the course of infection as they adapt to the selective pressures that confront them inside the host. Identification of adaptive mutations and their contributions to pathogen fitness remains a central challenge. Although mutations can either target intergenic or coding regions in the pathogen genome, studies of host adaptation have focused predominantly on molecular evolution within coding regions, whereas the role of intergenic mutations remains unclear. Here, we address this issue and investigate the extent to which intergenic mutations contribute to the evolutionary response of a clinically important bacterial pathogen, Pseudomonas aeruginosa, to the host environment, and whether intergenic mutations have distinct roles in host adaptation. We characterize intergenic evolution in 44 clonal lineages of P. aeruginosa and identify 77 intergenic regions in which parallel evolution occurs. At the genetic level, we find that mutations in regions under selection are located primarily within regulatory elements upstream of transcriptional start sites. At the functional level, we show that some of these mutations both increase or decrease transcription of genes and are directly responsible for evolution of important pathogenic phenotypes including antibiotic sensitivity. Importantly, we find that intergenic mutations facilitate essential genes to become targets of evolution. In summary, our results highlight the evolutionary significance of intergenic mutations in creating host-adapted strains, and that intergenic and coding regions have different qualitative contributions to this process.
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Affiliation(s)
- S M Hossein Khademi
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.,Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Pavelas Sazinas
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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