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Laborda P, Lolle S, Hernando-Amado S, Alcalde-Rico M, Aanæs K, Martínez JL, Molin S, Johansen HK. Mutations in the efflux pump regulator MexZ shift tissue colonization by Pseudomonas aeruginosa to a state of antibiotic tolerance. Nat Commun 2024; 15:2584. [PMID: 38519499 PMCID: PMC10959964 DOI: 10.1038/s41467-024-46938-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Mutations in mexZ, encoding a negative regulator of the expression of the mexXY efflux pump genes, are frequently acquired by Pseudomonas aeruginosa at early stages of lung infection. Although traditionally related to resistance to the first-line drug tobramycin, mexZ mutations are associated with low-level aminoglycoside resistance when determined in the laboratory, suggesting that their selection during infection may not be necessarily, or only, related to tobramycin therapy. Here, we show that mexZ-mutated bacteria tend to accumulate inside the epithelial barrier of a human airway infection model, thus colonising the epithelium while being protected against diverse antibiotics. This phenotype is mediated by overexpression of lecA, a quorum sensing-controlled gene, encoding a lectin involved in P. aeruginosa tissue invasiveness. We find that lecA overexpression is caused by a disrupted equilibrium between the overproduced MexXY and another efflux pump, MexAB, which extrudes quorum sensing signals. Our results indicate that mexZ mutations affect the expression of quorum sensing-regulated pathways, thus promoting tissue invasiveness and protecting bacteria from the action of antibiotics within patients, something unnoticeable using standard laboratory tests.
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Affiliation(s)
- Pablo Laborda
- Department of Clinical Microbiology 9301, Rigshospitalet, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Signe Lolle
- Department of Clinical Microbiology 9301, Rigshospitalet, Copenhagen, Denmark
| | | | - Manuel Alcalde-Rico
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen Macarena, CSIC, Universidad de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Kasper Aanæs
- Department of Otorhinolaryngology, Head and Neck Surgery & Audiology, Rigshospitalet, Copenhagen, Denmark
| | | | - Søren Molin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Helle Krogh Johansen
- Department of Clinical Microbiology 9301, Rigshospitalet, Copenhagen, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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Zhu J, Lolle S, Tang A, Guel B, Kvitko B, Cole B, Coaker G. Single-cell profiling of Arabidopsis leaves to Pseudomonas syringae infection. Cell Rep 2023; 42:112676. [PMID: 37342910 PMCID: PMC10528479 DOI: 10.1016/j.celrep.2023.112676] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/07/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Plant response to pathogen infection varies within a leaf, yet this heterogeneity is not well resolved. We expose Arabidopsis to Pseudomonas syringae or mock treatment and profile >11,000 individual cells using single-cell RNA sequencing. Integrative analysis of cell populations from both treatments identifies distinct pathogen-responsive cell clusters exhibiting transcriptional responses ranging from immunity to susceptibility. Pseudotime analyses through pathogen infection reveals a continuum of disease progression from an immune to a susceptible state. Confocal imaging of promoter-reporter lines for transcripts enriched in immune cell clusters shows expression surrounding substomatal cavities colonized or in close proximity to bacterial colonies, suggesting that cells within immune clusters represent sites of early pathogen invasion. Susceptibility clusters exhibit more general localization and are highly induced at later stages of infection. Overall, our work shows cellular heterogeneity within an infected leaf and provides insight into plant differential response to infection at a single-cell level.
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Affiliation(s)
- Jie Zhu
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Signe Lolle
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Andrea Tang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Bella Guel
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA
| | - Brian Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Benjamin Cole
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA.
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Lolle S, Simões FB, Lausen M, Molin S, Johansen HK. ePS3.03 Using patient-derived airway models to study Pseudomonas aeruginosa colonisation and infection. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lolle S, del Mar M, Amieva M, Molin S, Krogh Johansen H. EPS3.03 Using airway organoids and Air Liquid Interface cultures to profile the spatial and temporal dynamics of Pseudomonas aeruginosa infections. J Cyst Fibros 2021. [DOI: 10.1016/s1569-1993(21)01020-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rodriguez E, Chevalier J, Olsen J, Ansbøl J, Kapousidou V, Zuo Z, Svenning S, Loefke C, Koemeda S, Drozdowskyj PS, Jez J, Durnberger G, Kuenzl F, Schutzbier M, Mechtler K, Ebstrup EN, Lolle S, Dagdas Y, Petersen M. Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells. EMBO J 2020; 39:e103315. [PMID: 31930531 PMCID: PMC7024839 DOI: 10.15252/embj.2019103315] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/05/2019] [Accepted: 12/12/2019] [Indexed: 10/18/2023] Open
Abstract
Somatic cells acclimate to changes in the environment by temporary reprogramming. Much has been learned about transcription factors that induce these cell-state switches in both plants and animals, but how cells rapidly modulate their proteome remains elusive. Here, we show rapid induction of autophagy during temporary reprogramming in plants triggered by phytohormones, immune, and danger signals. Quantitative proteomics following sequential reprogramming revealed that autophagy is required for timely decay of previous cellular states and for tweaking the proteome to acclimate to the new conditions. Signatures of previous cellular programs thus persist in autophagy-deficient cells, affecting cellular decision-making. Concordantly, autophagy-deficient cells fail to acclimatize to dynamic climate changes. Similarly, they have defects in dedifferentiating into pluripotent stem cells, and redifferentiation during organogenesis. These observations indicate that autophagy mediates cell-state switches that underlie somatic cell reprogramming in plants and possibly other organisms, and thereby promotes phenotypic plasticity.
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Affiliation(s)
- Eleazar Rodriguez
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jonathan Chevalier
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Olsen
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jeppe Ansbøl
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Vaitsa Kapousidou
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Zhangli Zuo
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Steingrim Svenning
- Molecular Cancer Research GroupDepartment of Medical BiologyUniversity of TromsøTromsøNorway
| | - Christian Loefke
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | | | - Jakub Jez
- Vienna Biocenter Core Facilities (VBCF)ViennaAustria
| | - Gerhard Durnberger
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Fabian Kuenzl
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Michael Schutzbier
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Karl Mechtler
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Elise Nagel Ebstrup
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Signe Lolle
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
- Present address:
Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI)Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Morten Petersen
- Functional Genomic SectionDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
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Lolle S, Greeff C, Petersen K, Roux M, Jensen MK, Bressendorff S, Rodriguez E, Sømark K, Mundy J, Petersen M. Matching NLR Immune Receptors to Autoimmunity in camta3 Mutants Using Antimorphic NLR Alleles. Cell Host Microbe 2017; 21:518-529.e4. [DOI: 10.1016/j.chom.2017.03.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/16/2016] [Accepted: 03/09/2017] [Indexed: 11/29/2022]
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Roux ME, Rasmussen MW, Palma K, Lolle S, Regué ÀM, Bethke G, Glazebrook J, Zhang W, Sieburth L, Larsen MR, Mundy J, Petersen M. The mRNA decay factor PAT1 functions in a pathway including MAP kinase 4 and immune receptor SUMM2. EMBO J 2015; 34:593-608. [PMID: 25603932 DOI: 10.15252/embj.201488645] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multi-layered defense responses are activated in plants upon recognition of invading pathogens. Transmembrane receptors recognize conserved pathogen-associated molecular patterns (PAMPs) and activate MAP kinase cascades, which regulate changes in gene expression to produce appropriate immune responses. For example, Arabidopsis MAP kinase 4 (MPK4) regulates the expression of a subset of defense genes via at least one WRKY transcription factor. We report here that MPK4 is found in complexes in vivo with PAT1, a component of the mRNA decapping machinery. PAT1 is also phosphorylated by MPK4 and, upon flagellin PAMP treatment, PAT1 accumulates and localizes to cytoplasmic processing (P) bodies which are sites for mRNA decay. Pat1 mutants exhibit dwarfism and de-repressed immunity dependent on the immune receptor SUMM2. Since mRNA decapping is a critical step in mRNA turnover, linking MPK4 to mRNA decay via PAT1 provides another mechanism by which MPK4 may rapidly instigate immune responses.
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Affiliation(s)
- Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Signe Lolle
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Àngels Mateu Regué
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Gerit Bethke
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Jane Glazebrook
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Weiping Zhang
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Leslie Sieburth
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Martin R Larsen
- University of Southern Denmark Institute for Biochemistry and Molecular Biology, Odense, Denmark
| | - John Mundy
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Lolle S, Skipper N, Bussey H, Thomas DY. The expression of cDNA clones of yeast M1 double-stranded RNA in yeast confers both killer and immunity phenotypes. EMBO J 1984; 3:1383-7. [PMID: 6086322 PMCID: PMC557527 DOI: 10.1002/j.1460-2075.1984.tb01981.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Two cDNA clones of the segment of Saccharomyces cerevisiae M1 double-stranded RNA, which codes for the yeast killer toxin, have been expressed in yeast using the expression vector pYT760. Toxin expression and secretion depended upon the presence of a yeast promoter. Transformants not only contain an authentic preprotoxin precursor, as determined by precipitation of intracellular proteins with antitoxin antisera, but also display an immunity phenotype. The evidence is that the immunity protein is part of the preprotoxin and may act by masking toxin binding sites. Neither cDNA clone had a complete 5' terminus and the preprotoxin translational start was missing. The promoter and the initiator ATG were supplied by the expression vector. One clone with a full-length preprotoxin but altered N-terminal amino acids gave a normal glycosylated intracellular precursor. A clone with an N-terminal nine amino acid deletion gave a precursor which was not glycosylated but toxin was still secreted.
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