1
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Hajjar H, Berry L, Wu Y, Touqui L, Vergunst AC, Blanc-Potard AB. Contribution of intramacrophage stages to Pseudomonas aeruginosa infection outcome in zebrafish embryos: insights from mgtC and oprF mutants. Sci Rep 2024; 14:6297. [PMID: 38491095 PMCID: PMC10943088 DOI: 10.1038/s41598-024-56725-8] [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: 10/02/2023] [Accepted: 03/10/2024] [Indexed: 03/18/2024] Open
Abstract
Pseudomonas aeruginosa often colonizes immunocompromised patients, causing acute and chronic infections. This bacterium can reside transiently inside cultured macrophages, but the contribution of the intramacrophic stage during infection remains unclear. MgtC and OprF have been identified as important bacterial factors when P. aeruginosa resides inside cultured macrophages. In this study, we showed that P. aeruginosa mgtC and oprF mutants, particular the latter one, had attenuated virulence in both mouse and zebrafish animal models of acute infection. To further investigate P. aeruginosa pathogenesis in zebrafish at a stage different from acute infection, we monitored bacterial load and visualized fluorescent bacteria in live larvae up to 4 days after infection. Whereas the attenuated phenotype of the oprF mutant was associated with a rapid elimination of bacteria, the mgtC mutant was able to persist at low level, a feature also observed with the wild-type strain in surviving larvae. Interestingly, these persistent bacteria can be visualized in macrophages of zebrafish. In a short-time infection model using a macrophage cell line, electron microscopy revealed that internalized P. aeruginosa wild-type bacteria were either released after macrophage lysis or remained intracellularly, where they were localized in vacuoles or in the cytoplasm. The mgtC mutant could also be detected inside macrophages, but without causing cell damage, whereas the oprF mutant was almost completely eliminated after phagocytosis, or localized in phagolysosomes. Taken together, our results show that the main role of OprF for intramacrophage survival impacts both acute and persistent infection by this bacterium. On the other hand, MgtC plays a clear role in acute infection but is not essential for bacterial persistence, in relation with the finding that the mgtC mutant is not completely eliminated by macrophages.
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Affiliation(s)
- Hélène Hajjar
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS-UMR5294, INSERM, Montpellier, France
| | - Laurence Berry
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS-UMR5294, INSERM, Montpellier, France
| | - Yongzheng Wu
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Cellular Biology and Microbial Infection Unit, Paris, France
| | - Lhousseine Touqui
- Sorbonne Université, Inserm U938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Institut Pasteur, Université de Paris Cité, Mucoviscidose et Bronchopathies Chroniques, Paris, France
| | - Annette C Vergunst
- Bacterial Virulence and Chronic Infections (VBIC), Université de Montpellier, INSERM, U1047, Nîmes, France.
| | - Anne-Béatrice Blanc-Potard
- Laboratory of Pathogens and Host Immunity (LPHI), Université de Montpellier, CNRS-UMR5294, INSERM, Montpellier, France.
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2
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Kaszab E, Jiang D, Szabó I, Kriszt B, Urbányi B, Szoboszlay S, Sebők R, Bock I, Csenki-Bakos Z. Evaluating the In Vivo Virulence of Environmental Pseudomonas aeruginosa Using Microinjection Model of Zebrafish ( Danio rerio). Antibiotics (Basel) 2023; 12:1740. [PMID: 38136774 PMCID: PMC10740789 DOI: 10.3390/antibiotics12121740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/10/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: Microinjection of zebrafish (Danio rerio) embryos offers a promising model for studying the virulence and potential environmental risks associated with Pseudomonas aeruginosa. (2) Methods: This work aimed to develop a P. aeruginosa infection model using two parallel exposition pathways on zebrafish larvae with microinjection into the yolk and the perivitelline space to simultaneously detect the invasive and cytotoxic features of the examined strains. The microinjection infection model was validated with 15 environmental and clinical strains of P. aeruginosa of various origins, antibiotic resistance profiles, genotypes and phenotypes: both exposition pathways were optimized with a series of bacterial dilutions, different drop sizes (injection volumes) and incubation periods. Besides mortality, sublethal symptoms of the treated embryos were detected and analyzed. (3) Results: According to the statistical evaluation of our results, the optimal parameters (dilution, drop size and incubation period) were determined. (4) Conclusions: The tested zebrafish embryo microinjection infection model is now ready for use to determine the in vivo virulence and ecological risk of environmental P. aeruginosa.
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Affiliation(s)
- Edit Kaszab
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Dongze Jiang
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - István Szabó
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary;
| | - Sándor Szoboszlay
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Rózsa Sebők
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (E.K.); (D.J.); (S.S.); (R.S.)
| | - Illés Bock
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
| | - Zsolt Csenki-Bakos
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Hungary; (I.S.); (I.B.); (Z.C.-B.)
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3
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Trouillon J, Attrée I, Elsen S. The regulation of bacterial two-partner secretion systems. Mol Microbiol 2023; 120:159-177. [PMID: 37340956 DOI: 10.1111/mmi.15112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Two-partner secretion (TPS) systems, also known as Type Vb secretion systems, allow the translocation of effector proteins across the outer membrane of Gram-negative bacteria. By secreting different classes of effectors, including cytolysins and adhesins, TPS systems play important roles in bacterial pathogenesis and host interactions. Here, we review the current knowledge on TPS systems regulation and highlight specific and common regulatory mechanisms across TPS functional classes. We discuss in detail the specific regulatory networks identified in various bacterial species and emphasize the importance of understanding the context-dependent regulation of TPS systems. Several regulatory cues reflecting host environment during infection, such as temperature and iron availability, are common determinants of expression for TPS systems, even across relatively distant species. These common regulatory pathways often affect TPS systems across subfamilies with different effector functions, representing conserved global infection-related regulatory mechanisms.
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Affiliation(s)
- Julian Trouillon
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Ina Attrée
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
| | - Sylvie Elsen
- Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, Team Bacterial Pathogenesis and Cellular Responses, Grenoble, France
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4
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Sánchez-Jiménez A, Llamas MA, Marcos-Torres FJ. Transcriptional Regulators Controlling Virulence in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11895. [PMID: 37569271 PMCID: PMC10418997 DOI: 10.3390/ijms241511895] [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: 07/04/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/13/2023] Open
Abstract
Pseudomonas aeruginosa is a pathogen capable of colonizing virtually every human tissue. The host colonization competence and versatility of this pathogen are powered by a wide array of virulence factors necessary in different steps of the infection process. This includes factors involved in bacterial motility and attachment, biofilm formation, the production and secretion of extracellular invasive enzymes and exotoxins, the production of toxic secondary metabolites, and the acquisition of iron. Expression of these virulence factors during infection is tightly regulated, which allows their production only when they are needed. This process optimizes host colonization and virulence. In this work, we review the intricate network of transcriptional regulators that control the expression of virulence factors in P. aeruginosa, including one- and two-component systems and σ factors. Because inhibition of virulence holds promise as a target for new antimicrobials, blocking the regulators that trigger the production of virulence determinants in P. aeruginosa is a promising strategy to fight this clinically relevant pathogen.
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Affiliation(s)
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Francisco Javier Marcos-Torres
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
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5
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Otero-Asman JR, Sánchez-Jiménez A, Bastiaansen KC, Wettstadt S, Civantos C, García-Puente A, Bitter W, Llamas MA. The Prc and CtpA proteases modulate cell-surface signaling activity and virulence in Pseudomonas aeruginosa. iScience 2023; 26:107216. [PMID: 37534181 PMCID: PMC10392083 DOI: 10.1016/j.isci.2023.107216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/17/2023] [Accepted: 06/22/2023] [Indexed: 08/04/2023] Open
Abstract
Cell-surface signaling (CSS) is a signal transfer system of Gram-negative bacteria that produces the activation of an extracytoplasmic function σ factor (σECF) in the cytosol in response to an extracellular signal. Activation requires the regulated and sequential proteolysis of the σECF-associated anti-σ factor, and the function of the Prc and RseP proteases. In this work, we have identified another protease that modulates CSS activity, namely the periplasmic carboxyl-terminal processing protease CtpA. CtpA functions upstream of Prc in the proteolytic cascade and seems to prevent the Prc-mediated proteolysis of the CSS anti-σ factor. Importantly, using zebrafish embryos and the A549 lung epithelial cell line as hosts, we show that mutants in the rseP and ctpA proteases of the human pathogen Pseudomonas aeruginosa are considerably attenuated in virulence while the prc mutation increases virulence likely by enhancing the production of membrane vesicles.
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Affiliation(s)
- Joaquín R. Otero-Asman
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Ana Sánchez-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Karlijn C. Bastiaansen
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centres, location VU University, 1081 HV Amsterdam, The Netherlands
| | - Sarah Wettstadt
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Cristina Civantos
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Alicia García-Puente
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centres, location VU University, 1081 HV Amsterdam, The Netherlands
| | - María A. Llamas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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6
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Patel P, Nandi A, Verma SK, Kaushik N, Suar M, Choi EH, Kaushik NK. Zebrafish-based platform for emerging bio-contaminants and virus inactivation research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162197. [PMID: 36781138 PMCID: PMC9922160 DOI: 10.1016/j.scitotenv.2023.162197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 05/27/2023]
Abstract
Emerging bio-contaminants such as viruses have affected health and environment settings of every country. Viruses are the minuscule entities resulting in severe contagious diseases like SARS, MERS, Ebola, and avian influenza. Recent epidemic like the SARS-CoV-2, the virus has undergone mutations strengthen them and allowing to escape from the remedies. Comprehensive knowledge of viruses is essential for the development of targeted therapeutic and vaccination treatments. Animal models mimicking human biology like non-human primates, rats, mice, and rabbits offer competitive advantage to assess risk of viral infections, chemical toxins, nanoparticles, and microbes. However, their economic maintenance has always been an issue. Furthermore, the redundancy of experimental results due to aforementioned aspects is also in examine. Hence, exploration for the alternative animal models is crucial for risk assessments. The current review examines zebrafish traits and explores the possibilities to monitor emerging bio-contaminants. Additionally, a comprehensive picture of the bio contaminant and virus particle invasion and abatement mechanisms in zebrafish and human cells is presented. Moreover, a zebrafish model to investigate the emerging viruses such as coronaviridae and poxviridae has been suggested.
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Affiliation(s)
- Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea
| | - Aditya Nandi
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Suresh K Verma
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, 18323 Hwaseong, Republic of Korea
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
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7
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The Alginate and Motility Regulator AmrZ is Essential for the Regulation of the Dispersion Response by Pseudomonas aeruginosa Biofilms. mSphere 2022; 7:e0050522. [PMID: 36374041 PMCID: PMC9769550 DOI: 10.1128/msphere.00505-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dispersion is an active process exhibited by Pseudomonas aeruginosa during the late stages of biofilm development or in response to various cues, including nitric oxide and glutamate. Upon cue sensing, biofilm cells employ enzymes that actively degrade the extracellular matrix, thereby allowing individual cells to become liberated. While the mechanism by which P. aeruginosa senses and relays dispersion cues has been characterized, little is known about how dispersion cue sensing mechanisms result in matrix degradation. Considering that the alginate and motility regulator AmrZ has been reported to regulate genes that play a role in dispersion, including those affecting virulence, c-di-GMP levels, Pel and Psl abundance, and motility, we asked whether AmrZ contributes to the regulation of dispersion. amrZ was found to be significantly increased in transcript abundance under dispersion-inducing conditions, with the inactivation of amrZ impairing dispersion by P. aeruginosa biofilms in response to glutamate and nitric oxide. While the overexpression of genes encoding matrix-degrading enzymes pelA, pslG, and/or endA resulted in the dispersion of wild-type biofilms, similar conditions failed to disperse biofilms formed by dtamrZ. Likewise, the inactivation of amrZ abrogated the hyperdispersive phenotype of PAO1/pJN-bdlA_G31A biofilms, with dtamrZ-impaired dispersion being independent of the expression, production, and activation of BdlA. Instead, dispersion was found to require the AmrZ-target genes napB and PA1891. Our findings indicate that AmrZ is essential for the regulation of dispersion by P. aeruginosa biofilms, functions downstream of BdlA postdispersion cue sensing, and regulates the expression of genes contributing to biofilm matrix degradation as well as napB and PA1891. IMPORTANCE In P. aeruginosa, biofilm dispersion has been well-characterized with respect to dispersion cue perception, matrix degradation, and the consequences of dispersion. While the intracellular signaling molecule c-di-GMP has been linked to many of the phenotypic changes ascribed to dispersion, including the modulation of motility and matrix production, little is known about the regulatory mechanisms leading to matrix degradation and cells actively leaving the biofilm. In this study, we report for the first time an essential role of the transcriptional regulator AmrZ and two AmrZ-dependent genes, napB, and PA1891, in the dispersion response, thereby linking dispersion cue sensing via BdlA to the regulation of matrix degradation and to the ultimate liberation of bacterial cells from the biofilm.
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8
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Plant-Derived Catechols Are Substrates of TonB-Dependent Transporters and Sensitize Pseudomonas aeruginosa to Siderophore-Drug Conjugates. mBio 2022; 13:e0149822. [PMID: 35770947 PMCID: PMC9426570 DOI: 10.1128/mbio.01498-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen responsible for acute and chronic infections in immunocompromised hosts. This organism is known to compete efficiently against coinfecting microorganisms, due in part to the secretion of antimicrobial molecules and the synthesis of siderophore molecules with high affinity for iron. P. aeruginosa possess a large repertoire of TonB-dependent transporters for the uptake of its own, as well as xenosiderophores released from other bacteria or fungi. Here, we show that P. aeruginosa is also capable of utilizing plant-derived polyphenols as an iron source. We found that exclusively plant-derived phenols containing a catechol group (i.e., chlorogenic acid, caffeic acid, quercetin, luteolin) induce the expression of the TonB-dependent transporters PiuA or PirA. This induction requires the two-component system PirR-PirS. Chlorogenic acid in its Fe(III)-loaded form was actively transported by PiuA and PirA and supported growth under iron-limiting conditions. Coincidentally, PiuA and PirA are also the main TonB transporters for the recently approved siderophore-drug conjugate cefiderocol. Surprisingly, quercetin supplementation increased the susceptibility of P. aeruginosa to siderophore-drug conjugates, due to induction of piuA and pirA expression mediated by the PirR-PirS two-component system. These findings suggest a potential novel therapeutic application for these biologically active dietary polyphenols.
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9
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Zhao H, Clevenger AL, Coburn PS, Callegan MC, Rybenkov V. Condensins are essential for Pseudomonas aeruginosa corneal virulence through their control of lifestyle and virulence programs. Mol Microbiol 2022; 117:937-957. [PMID: 35072315 PMCID: PMC9512581 DOI: 10.1111/mmi.14883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/01/2022]
Abstract
Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. aeruginosa virulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures of smc and mksB mutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and numerous virulence factors, including type 3 and type 6 secretion systems. The in vitro phenotypes of condensin mutants mirrored their transcriptional profiles and included impaired production and secretion of multiple virulence factors, growth deficiencies under nutrient limiting conditions, and altered c-di-GMP signaling. Notably, c-di-GMP mediated some but not all transcriptional responses of the mutants. Thus, condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior of P. aeruginosa.
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Affiliation(s)
- Hang Zhao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
| | - April L Clevenger
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
| | - Phillip S Coburn
- Department of Ophthalmology, the University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, USA
| | - Michelle C Callegan
- Department of Ophthalmology, the University of Oklahoma Health Sciences Center, 608 Stanton L. Young Blvd, Oklahoma City, USA
| | - Valentin Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, USA
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10
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Iron Homeostasis in Pseudomonas aeruginosa: Targeting Iron Acquisition and Storage as an Antimicrobial Strategy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:29-68. [DOI: 10.1007/978-3-031-08491-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Pont S, Blanc-Potard AB. Zebrafish Embryo Infection Model to Investigate Pseudomonas aeruginosa Interaction With Innate Immunity and Validate New Therapeutics. Front Cell Infect Microbiol 2021; 11:745851. [PMID: 34660345 PMCID: PMC8515127 DOI: 10.3389/fcimb.2021.745851] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa is responsible for a variety of acute infections and is a major cause of mortality in chronically infected patients with cystic fibrosis (CF). Considering the intrinsic and acquired resistance of P. aeruginosa to currently used antibiotics, new therapeutic strategies against this pathogen are urgently needed. Whereas virulence factors of P. aeruginosa are well characterized, the interplay between P. aeruginosa and the innate immune response during infection remains unclear. Zebrafish embryo is now firmly established as a potent vertebrate model for the study of infectious human diseases, due to strong similarities of its innate immune system with that of humans and the unprecedented possibilities of non-invasive real-time imaging. This model has been successfully developed to investigate the contribution of bacterial and host factors involved in P. aeruginosa pathogenesis, as well as rapidly assess the efficacy of anti-Pseudomonas molecules. Importantly, zebrafish embryo appears as the state-of-the-art model to address in vivo the contribution of innate immunity in the outcome of P. aeruginosa infection. Of interest, is the finding that the zebrafish encodes a CFTR channel closely related to human CFTR, which allowed to develop a model to address P. aeruginosa pathogenesis, innate immune response, and treatment evaluation in a CF context.
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Affiliation(s)
- Stéphane Pont
- Laboratory of Pathogen-Host Interactions (LPHI), Université Montpellier, Montpellier, France.,CNRS, UMR5235, Montpellier, France
| | - Anne-Béatrice Blanc-Potard
- Laboratory of Pathogen-Host Interactions (LPHI), Université Montpellier, Montpellier, France.,CNRS, UMR5235, Montpellier, France
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12
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Specific and Global RNA Regulators in Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22168632. [PMID: 34445336 PMCID: PMC8395346 DOI: 10.3390/ijms22168632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 01/20/2023] Open
Abstract
Pseudomonas aeruginosa (Pae) is an opportunistic pathogen showing a high intrinsic resistance to a wide variety of antibiotics. It causes nosocomial infections that are particularly detrimental to immunocompromised individuals and to patients suffering from cystic fibrosis. We provide a snapshot on regulatory RNAs of Pae that impact on metabolism, pathogenicity and antibiotic susceptibility. Different experimental approaches such as in silico predictions, co-purification with the RNA chaperone Hfq as well as high-throughput RNA sequencing identified several hundreds of regulatory RNA candidates in Pae. Notwithstanding, using in vitro and in vivo assays, the function of only a few has been revealed. Here, we focus on well-characterized small base-pairing RNAs, regulating specific target genes as well as on larger protein-binding RNAs that sequester and thereby modulate the activity of translational repressors. As the latter impact large gene networks governing metabolism, acute or chronic infections, these protein-binding RNAs in conjunction with their cognate proteins are regarded as global post-transcriptional regulators.
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13
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Ottoni C, Borić D, Cheronet O, Sparacello V, Dori I, Coppa A, Antonović D, Vujević D, Price TD, Pinhasi R, Cristiani E. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc Natl Acad Sci U S A 2021; 118:e2102116118. [PMID: 34312252 PMCID: PMC8364157 DOI: 10.1073/pnas.2102116118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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Affiliation(s)
- Claudio Ottoni
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Vitale Sparacello
- Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Irene Dori
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138
| | | | - Dario Vujević
- Department of Archaeology, University of Zadar, 23000 Zadar, Croatia
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Emanuela Cristiani
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
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14
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Gaultney RA, Vincent AT, Lorioux C, Coppée JY, Sismeiro O, Varet H, Legendre R, Cockram CA, Veyrier FJ, Picardeau M. 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans. Nucleic Acids Res 2020; 48:12102-12115. [PMID: 33301041 PMCID: PMC7708080 DOI: 10.1093/nar/gkaa966] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022] Open
Abstract
In bacteria, DNA methylation can be facilitated by ‘orphan’ DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
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Affiliation(s)
| | - Antony T Vincent
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
| | - Céline Lorioux
- Unité Biologie des Spirochètes, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Odile Sismeiro
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Hugo Varet
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France.,Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | - Rachel Legendre
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France.,Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | | | - Frédéric J Veyrier
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
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15
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Galán-Vásquez E, Luna-Olivera BC, Ramírez-Ibáñez M, Martínez-Antonio A. RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1. Database (Oxford) 2020; 2020:baaa106. [PMID: 33258965 PMCID: PMC7706183 DOI: 10.1093/database/baaa106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 11/21/2022]
Abstract
We present RegulomePA, a database that contains biological information on regulatory interactions between transcription factors (TFs), sigma factor (SFs) and target genes in Pseudomonas aeruginosa PAO1. RegulomePA consists of 4827 regulatory interactions between 2831 nodes, which represent the interactions of TFs and SFs with their target genes, from the total of predicted RegulomePA including 27.27% of the TFs, 54.16% of SFs and 50.8% of the total genes. Each entry in the database corresponds to one node in the network and provides comprehensive details about the gene and its regulatory interactions such as gene description, nucleotide sequence, genome-strand position and links to other databases as well as the type of regulation it exerts or to which it is being subject (repression or activation), the associated experimental evidence and references, and topological information. Additionally, RegulomePA provides a way to recover information on the regulatory circuits of the network to which a gene pertains and also makes available the source codes to analyze the topology of any other regulatory network. The database will be updated yearly, by our team, with the contributions from ourselves and users, since the users are provided with an interactive platform where they can add interactions to the regulatory network feeding it with their respective references. Database URL: www.regulome.pcyt.unam.mx.
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Affiliation(s)
- Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y en Sistemas. Universidad Nacional Autónoma de México, Circuito Escolar 3000, Ciudad Universitaria, CP 04510 Ciudad de México, México
| | - Beatriz Carely Luna-Olivera
- Academia de matemáticas, UPN unidad 201, camino a la Zanjita, Nochebuena, CP 71230, Oaxaca de Juárez, Oaxaca, México-visiting researcher at Centro de Altos Estudios de la Mixteca, CALMIX, Oaxaca, México
| | - Marcelino Ramírez-Ibáñez
- Academia de matemáticas, UPN unidad 201, camino a la Zanjita, Nochebuena, CP 71230, Oaxaca de Juárez, Oaxaca, México-visiting researcher at Centro de Altos Estudios de la Mixteca, CALMIX, Oaxaca, México
- CONACyT-UPN unidad 201, camino a la Zanjita, Nochebuena, CP 71230, Oaxaca de Juárez CP 71230, Oaxaca de Juárez, Oaxaca, México
| | - Agustino Martínez-Antonio
- Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute-Irapuato Unit. Km. 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824, Irapuato Guanajuato, México
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16
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Veyrier FJ, Nieves C, Lefrancois LH, Trigui H, Vincent AT, Behr MA. RskA Is a Dual Function Activator-Inhibitor That Controls SigK Activity Across Distinct Bacterial Genera. Front Microbiol 2020; 11:558166. [PMID: 33013790 PMCID: PMC7509140 DOI: 10.3389/fmicb.2020.558166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/14/2020] [Indexed: 01/25/2023] Open
Abstract
It has been previously shown that RskA, the anti-Sigma factor K of Mycobacterium tuberculosis, inhibits SigK and that mutations in RskA promote high expression of the SigK regulon. The latter observation led us to hypothesize that RskA mutations lead to loss of the anti-Sigma factor function. In this report, we used natural and artificial mutations in RskA to determine the basis of the SigK-RskA partnership. Consistent with predictions, the N-terminal cytoplasmic portion of RskA was sufficient on its own to inhibit SigK. Unexpectedly, RskA also served as an activator of SigK. This activation depended on the same N-terminal region and was enhanced by the membrane-extracellular portion of RskA. Based on this, we engineered similar truncations in a Gram-negative bacterium, namely Yersinia enterocolitica. Again, we observed that, with specific alterations of RskA, we were able to enhance SigK activity. Together these results support an alternative mechanism of anti-Sigma factor function, that we could term modulator (activator-inhibitor) in both Actinobacteria and Gram-negative bacteria, suggesting that Sigma factor activation by anti-Sigma factors could be under-recognized.
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Affiliation(s)
- Frédéric J Veyrier
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Cecilia Nieves
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Louise H Lefrancois
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Hana Trigui
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Antony T Vincent
- Bacterial Symbionts Evolution, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada
- McGill International TB Centre, Montreal, QC, Canada
| | - Marcel A Behr
- McGill International TB Centre, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
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17
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Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics. PLoS Genet 2020; 16:e1008783. [PMID: 32813693 PMCID: PMC7480860 DOI: 10.1371/journal.pgen.1008783] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/09/2020] [Accepted: 06/20/2020] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas aeruginosa and Candida albicans are opportunistic pathogens whose interactions involve the secreted products ethanol and phenazines. Here, we describe the role of ethanol in mixed-species co-cultures by dual-seq analyses. P. aeruginosa and C. albicans transcriptomes were assessed after growth in mono-culture or co-culture with either ethanol-producing C. albicans or a C. albicans mutant lacking the primary ethanol dehydrogenase, Adh1. Analysis of the RNA-Seq data using KEGG pathway enrichment and eADAGE methods revealed several P. aeruginosa responses to C. albicans-produced ethanol including the induction of a non-canonical low-phosphate response regulated by PhoB. C. albicans wild type, but not C. albicans adh1Δ/Δ, induces P. aeruginosa production of 5-methyl-phenazine-1-carboxylic acid (5-MPCA), which forms a red derivative within fungal cells and exhibits antifungal activity. Here, we show that C. albicans adh1Δ/Δ no longer activates P. aeruginosa PhoB and PhoB-regulated phosphatase activity, that exogenous ethanol complements this defect, and that ethanol is sufficient to activate PhoB in single-species P. aeruginosa cultures at permissive phosphate levels. The intersection of ethanol and phosphate in co-culture is inversely reflected in C. albicans; C. albicans adh1Δ/Δ had increased expression of genes regulated by Pho4, the C. albicans transcription factor that responds to low phosphate, and Pho4-dependent phosphatase activity. Together, these results show that C. albicans-produced ethanol stimulates P. aeruginosa PhoB activity and 5-MPCA-mediated antagonism, and that both responses are dependent on local phosphate concentrations. Further, our data suggest that phosphate scavenging by one species improves phosphate access for the other, thus highlighting the complex dynamics at play in microbial communities. Pseudomonas aeruginosa and Candida albicans are opportunistic pathogens that are frequently isolated from co-infections. Using a combination of dual-seq transcriptomics and genetics approaches, we found that ethanol produced by C. albicans stimulates the PhoB regulon in P. aeruginosa asynchronously with activation of the Pho4 regulon in C. albicans. We validated our result by showing that PhoB plays multiple roles in co-culture including orchestrating the competition for phosphate and the production of 5-methyl-phenazine-1-carboxylic acid; the P. aeruginosa phenazine response to C. albicans-produced ethanol depends on phosphate availability. The conditional stimulation of antifungal production in response to sub-inhibitory concentrations of ethanol only under phosphate limitation highlights the importance of considering nutrient concentrations in the analysis of co-culture interactions and suggests that the low-phosphate response in one species influences phosphate availability for the other.
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18
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Otero-Asman JR, Quesada JM, Jim KK, Ocampo-Sosa A, Civantos C, Bitter W, Llamas MA. The extracytoplasmic function sigma factor σ VreI is active during infection and contributes to phosphate starvation-induced virulence of Pseudomonas aeruginosa. Sci Rep 2020; 10:3139. [PMID: 32081993 PMCID: PMC7035377 DOI: 10.1038/s41598-020-60197-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The extracytoplasmic function sigma factor σVreI of the human pathogen Pseudomonas aeruginosa promotes transcription of potential virulence determinants, including secretion systems and secreted proteins. Its activity is modulated by the VreR anti-σ factor that inhibits the binding of σVreI to the RNA polymerase in the absence of a (still unknown) inducing signal. The vreI-vreR genes are expressed under inorganic phosphate (Pi) starvation, a physiological condition often encountered in the host that increases P. aeruginosa pathogenicity. However, whether or not σVreI is active in vivo during infection and contributes to the Pi starvation-induced virulence of this pathogen has not been analyzed yet. Using zebrafish embryos and a human alveolar basal epithelial cell line as P. aeruginosa hosts, we demonstrate in this work that σVreI is active during infection and that lack of σVreI considerably reduces the Pi starvation-induced virulence of this pathogen. Surprisingly, lack of the σVreI inhibitor, the VreR anti-σ factor, also diminishes the virulence of P. aeruginosa. By transcriptomic analyses we show that VreR modulates gene expression not only in a σVreI-dependent but also in a σVreI-independent manner. This includes potential virulence determinants and transcriptional regulators that could be responsible for the reduced virulence of the ΔvreR mutant.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Kin K Jim
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centers, location VU University, Amsterdam, The Netherlands
| | - Alain Ocampo-Sosa
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Sanitaria Valdecilla, Santander, Spain
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam University medical centers, location VU University, Amsterdam, The Netherlands
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain.
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19
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Otero-Asman JR, Wettstadt S, Bernal P, Llamas MA. Diversity of extracytoplasmic function sigma (σ ECF ) factor-dependent signaling in Pseudomonas. Mol Microbiol 2019; 112:356-373. [PMID: 31206859 DOI: 10.1111/mmi.14331] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/23/2022]
Abstract
Pseudomonas bacteria are widespread and are found in soil and water, as well as pathogens of both plants and animals. The ability of Pseudomonas to colonize many different environments is facilitated by the multiple signaling systems these bacteria contain that allow Pseudomonas to adapt to changing circumstances by generating specific responses. Among others, signaling through extracytoplasmic function σ (σECF ) factors is extensively present in Pseudomonas. σECF factors trigger expression of functions required under particular conditions in response to specific signals. This manuscript reviews the phylogeny and biological roles of σECF factors in Pseudomonas, and highlights the diversity of σECF -signaling pathways of this genus in terms of function and activation. We show that Pseudomonas σECF factors belong to 16 different phylogenetic groups. Most of them are included within the iron starvation group and are mainly involved in iron acquisition. The second most abundant group is formed by RpoE-like σECF factors, which regulate the responses to cell envelope stress. Other groups controlling solvent tolerance, biofilm formation and the response to oxidative stress, among other functions, are present in lower frequency. The role of σECF factors in the virulence of Pseudomonas pathogenic species is described.
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Affiliation(s)
- Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Patricia Bernal
- Department of Biology, Faculty of Sciences, Universidad Autónoma de Madrid, Madrid, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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20
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Milivojevic D, Šumonja N, Medic S, Pavic A, Moric I, Vasiljevic B, Senerovic L, Nikodinovic-Runic J. Biofilm-forming ability and infection potential of Pseudomonas aeruginosa strains isolated from animals and humans. Pathog Dis 2018; 76:4978417. [PMID: 29684116 DOI: 10.1093/femspd/fty041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa has been amongst the top 10 'superbugs' worldwide and is causing infections with poor outcomes in both humans and animals. From 202 P. aeruginosa isolates (n = 121 animal and n = 81 human), 40 were selected on the basis of biofilm-forming ability and were comparatively characterized in terms of virulence determinants to the type strain P. aeruginosa PAO1. Biofilm formation, pyocyanin and hemolysin production, and bacterial motility patterns were compared with the ability to kill human cell line A549 in vitro. On average, there was no significant difference between levels of animal and human cytotoxicity, while human isolates produced higher amounts of pyocyanin, hemolysins and showed increased swimming ability. Non-parametric statistical analysis identified the highest positive correlation between hemolysis and the swarming ability. For the first time an ensemble machine learning approach used on the in vitro virulence data determined the highest relative predictive importance of the submerged biofilm formation for the cytotoxicity, as an indicator of the infection ability. The findings from the in vitro study were validated in vivo using zebrafish (Danio rerio) embryos. This study highlighted no major differences between P. aeruginosa species isolated from animal and human infections and the importance of pyocyanin production in cytotoxicity and infection ability.
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Affiliation(s)
- Dusan Milivojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia.,Faculty of Veterinary Medicine, University of Belgrade, Bulevar Oslobodjenja 18, 11000 Belgrade, Serbia
| | - Neven Šumonja
- Centre for Multidisciplinary Research, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica Alasa 12-14, 11001, Belgrade, Serbia
| | - Strahinja Medic
- VetLab Ltd., Veterinary Laboratory for Clinical Diagnostics, Savska 31, 11000 Belgrade, Serbia
| | - Aleksandar Pavic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Ivana Moric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Branka Vasiljevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Lidija Senerovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia
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21
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Romero M, Silistre H, Lovelock L, Wright VJ, Chan KG, Hong KW, Williams P, Cámara M, Heeb S. Genome-wide mapping of the RNA targets of the Pseudomonas aeruginosa riboregulatory protein RsmN. Nucleic Acids Res 2018; 46:6823-6840. [PMID: 29718466 PMCID: PMC6061880 DOI: 10.1093/nar/gky324] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/10/2018] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In Pseudomonas aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities of RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. aeruginosa. About 200 of the mRNAs identified encode proteins of demonstrated function including some determining acute and chronic virulence traits. For example, RsmN reduces biofilm development both directly and indirectly via multiple pathways, involving control of Pel exopolysaccharide biosynthesis and c-di-GMP levels. The RsmN targets identified are also shared with RsmA, although deletion of rsmN generally results in less pronounced phenotypes than those observed for ΔrsmA or ΔrsmArsmNind mutants, probably as a consequence of different binding affinities. Targets newly identified for the Rsm system include the small non-coding RNA CrcZ involved in carbon catabolite repression, for which differential binding of RsmN and RsmA to specific CrcZ regions is demonstrated. The results presented here provide new insights into the intricacy of riboregulatory networks involving multiple but distinct RsmA homologues.
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Affiliation(s)
- Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Hazel Silistre
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Laura Lovelock
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Victoria J Wright
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kok-Gan Chan
- International Genome Centre, Jiangsu University,Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kar-Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Paul Williams
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Cámara
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stephan Heeb
- School of Life Sciences, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
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22
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Luscher A, Moynié L, Auguste PS, Bumann D, Mazza L, Pletzer D, Naismith JH, Köhler T. TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates. Antimicrob Agents Chemother 2018; 62:e00097-18. [PMID: 29555629 PMCID: PMC5971595 DOI: 10.1128/aac.00097-18] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/12/2018] [Indexed: 12/22/2022] Open
Abstract
The conjugation of siderophores to antimicrobial molecules is an attractive strategy to overcome the low outer membrane permeability of Gram-negative bacteria. In this Trojan horse approach, the transport of drug conjugates is redirected via TonB-dependent receptors (TBDR), which are involved in the uptake of essential nutrients, including iron. Previous reports have demonstrated the involvement of the TBDRs PiuA and PirA from Pseudomonas aeruginosa and their orthologues in Acinetobacter baumannii in the uptake of siderophore-beta-lactam drug conjugates. By in silico screening, we further identified a PiuA orthologue, termed PiuD, present in clinical isolates, including strain LESB58. The piuD gene in LESB58 is located at the same genetic locus as piuA in strain PAO1. PiuD has a similar crystal structure as PiuA and is involved in the transport of the siderophore-drug conjugates BAL30072, MC-1, and cefiderocol in strain LESB58. To screen for additional siderophore-drug uptake systems, we overexpressed 28 of the 34 TBDRs of strain PAO1 and identified PfuA, OptE, OptJ, and the pyochelin receptor FptA as novel TBDRs conferring increased susceptibility to siderophore-drug conjugates. The existence of a TBDR repertoire in P. aeruginosa able to transport siderophore-drug molecules potentially decreases the likelihood of resistance emergence during therapy.
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Affiliation(s)
- Alexandre Luscher
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Lucile Moynié
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | | | - Dirk Bumann
- Biozentrum, University of Basel, Basel, Switzerland
| | - Lena Mazza
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | | | - James H Naismith
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | - Thilo Köhler
- Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
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23
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Chevalier S, Bouffartigues E, Bazire A, Tahrioui A, Duchesne R, Tortuel D, Maillot O, Clamens T, Orange N, Feuilloley MGJ, Lesouhaitier O, Dufour A, Cornelis P. Extracytoplasmic function sigma factors in Pseudomonas aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:706-721. [PMID: 29729420 DOI: 10.1016/j.bbagrm.2018.04.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/06/2018] [Accepted: 04/30/2018] [Indexed: 01/26/2023]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, like all members of the genus Pseudomonas, has the capacity to thrive in very different environments, ranging from water, plant roots, to animals, including humans to whom it can cause severe infections. This remarkable adaptability is reflected in the number of transcriptional regulators, including sigma factors in this bacterium. Among those, the 19 to 21 extracytoplasmic sigma factors (ECFσ) are endowed with different regulons and functions, including the iron starvation σ (PvdS, FpvI, HasI, FecI, FecI2 and others), the cell wall stress ECFσ AlgU, SigX and SbrI, and the unorthodox σVreI involved in the expression of virulence. Recently published data show that these ECFσ have separate regulons although presenting some cross-talk. We will present evidence that these different ECFσ are involved in the expression of different phenotypes, ranging from cell-wall stress response, production of extracellular polysaccharides, formation of biofilms, to iron acquisition.
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Affiliation(s)
- Sylvie Chevalier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France.
| | - Emeline Bouffartigues
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alexis Bazire
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Ali Tahrioui
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Rachel Duchesne
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Damien Tortuel
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Maillot
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Thomas Clamens
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Nicole Orange
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Marc G J Feuilloley
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Olivier Lesouhaitier
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
| | - Alain Dufour
- IUEM, Université de Bretagne-Sud (UBL), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Pierre Cornelis
- Laboratory of Microbiology Signals and Microenvironment LMSM EA 4312, Normandy University, University of Rouen, 27000 Evreux, France
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24
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Rampioni G, Pillai CR, Longo F, Bondì R, Baldelli V, Messina M, Imperi F, Visca P, Leoni L. Effect of efflux pump inhibition on Pseudomonas aeruginosa transcriptome and virulence. Sci Rep 2017; 7:11392. [PMID: 28900249 PMCID: PMC5596013 DOI: 10.1038/s41598-017-11892-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Efflux pumps of the resistance-nodulation-cell-division (RND) family increase antibiotic resistance in many bacterial pathogens, representing candidate targets for the development of antibiotic adjuvants. RND pumps have also been proposed to contribute to bacterial infection, implying that efflux pump inhibitors (EPIs) could also act as anti-virulence drugs. Nevertheless, EPIs are usually investigated only for their properties as antibiotic adjuvants, while their potential anti-virulence activity is seldom taken into account. In this study it is shown that RND efflux pumps contribute to Pseudomonas aeruginosa PAO1 pathogenicity in an insect model of infection, and that the well-characterized EPI Phe-Arg-β-naphthylamide (PAβN) is able to reduce in vivo virulence of the P. aeruginosa PAO1 laboratory strain, as well as of clinical isolates. The production of quorum sensing (QS) molecules and of QS-dependent virulence phenotypes is differentially affected by PAβN, depending on the strain. Transcriptomic and phenotypic analyses showed that the protection exerted by PAβN from P. aeruginosa PAO1 infection in vivo correlates with the down-regulation of key virulence genes (e.g. genes involved in iron and phosphate starvation). Since PAβN impacts P. aeruginosa virulence, anti-virulence properties of EPIs are worthy to be explored, taking into account possible strain-specificity of their activity.
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Affiliation(s)
| | - Cejoice Ramachandran Pillai
- Department of Science, University Roma Tre, Rome, Italy
- Inter University Centre for Bioscience, Kannur University, Palayad, Kerala, India
| | | | - Roslen Bondì
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Marco Messina
- Department of Science, University Roma Tre, Rome, Italy
| | - Francesco Imperi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy.
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25
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Díaz-Pascual F, Ortíz-Severín J, Varas MA, Allende ML, Chávez FP. In vivo Host-Pathogen Interaction as Revealed by Global Proteomic Profiling of Zebrafish Larvae. Front Cell Infect Microbiol 2017; 7:334. [PMID: 28791256 PMCID: PMC5524664 DOI: 10.3389/fcimb.2017.00334] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/10/2017] [Indexed: 11/17/2022] Open
Abstract
The outcome of a host-pathogen interaction is determined by the conditions of the host, the pathogen, and the environment. Although numerous proteomic studies of in vitro-grown microbial pathogens have been performed, in vivo proteomic approaches are still rare. In addition, increasing evidence supports that in vitro studies inadequately reflect in vivo conditions. Choosing the proper host is essential to detect the expression of proteins from the pathogen in vivo. Numerous studies have demonstrated the suitability of zebrafish (Danio rerio) embryos as a model to in vivo studies of Pseudomonas aeruginosa infection. In most zebrafish-pathogen studies, infection is achieved by microinjection of bacteria into the larvae. However, few reports using static immersion of bacterial pathogens have been published. In this study we infected 3 days post-fertilization (DPF) zebrafish larvae with P. aeruginosa PAO1 by immersion and injection and tracked the in vivo immune response by the zebrafish. Additionally, by using non-isotopic (Q-exactive) metaproteomics we simultaneously evaluated the proteomic response of the pathogen (P. aeruginosa PAO1) and the host (zebrafish). We found some zebrafish metabolic pathways, such as hypoxia response via HIF activation pathway, were exclusively enriched in the larvae exposed by static immersion. In contrast, we found that inflammation mediated by chemokine and cytokine signaling pathways was exclusively enriched in the larvae exposed by injection, while the integrin signaling pathway and angiogenesis were solely enriched in the larvae exposed by immersion. We also found important virulence factors from P. aeruginosa that were enriched only after exposure by injection, such as the Type-III secretion system and flagella-associated proteins. On the other hand, P. aeruginosa proteins involved in processes like biofilm formation, and cellular responses to antibiotic and starvation were enriched exclusively after exposure by immersion. We demonstrated the suitability of zebrafish embryos as a model for in vivo host-pathogen based proteomic studies in P. aeruginosa. Our global proteomic profiling identifies novel molecular signatures that give systematic insight into zebrafish-Pseudomonas interaction.
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Affiliation(s)
- Francisco Díaz-Pascual
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Javiera Ortíz-Severín
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Miguel L Allende
- Centro FONDAP de Regulación del Genoma, Universidad de ChileSantiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
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26
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Guérin J, Bigot S, Schneider R, Buchanan SK, Jacob-Dubuisson F. Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions. Front Cell Infect Microbiol 2017; 7:148. [PMID: 28536673 PMCID: PMC5422565 DOI: 10.3389/fcimb.2017.00148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022] Open
Abstract
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
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Affiliation(s)
- Jeremy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, Centre National de La Recherche Scientifique UMR 5086-Université Lyon 1, Institute of Biology and Chemistry of ProteinsLyon, France
| | - Robert Schneider
- NMR and Molecular Interactions, Université de Lille, Centre National de La Recherche Scientifique, UMR 8576-Unité de Glycobiologie Structurale et FonctionnelleLille, France
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Françoise Jacob-Dubuisson
- Université de Lille, Centre National de La Recherche Scientifique, Institut National de La Santé et de La Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-Centre d'Infection et d'Immunité de LilleLille, France
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27
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Bastiaansen KC, Civantos C, Bitter W, Llamas MA. New Insights into the Regulation of Cell-Surface Signaling Activity Acquired from a Mutagenesis Screen of the Pseudomonas putida IutY Sigma/Anti-Sigma Factor. Front Microbiol 2017; 8:747. [PMID: 28512454 PMCID: PMC5411451 DOI: 10.3389/fmicb.2017.00747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 01/18/2023] Open
Abstract
Cell-surface signaling (CSS) is a signal transfer system that allows Gram-negative bacteria to detect environmental signals and generate a cytosolic response. These systems are composed of an outer membrane receptor that senses the inducing signal, an extracytoplasmic function sigma factor (σECF) that targets the cytosolic response by modifying gene expression and a cytoplasmic membrane anti-sigma factor that keeps the σECF in an inactive state in the absence of the signal and transduces its presence from the outer membrane to the cytosol. Although CSS systems regulate bacterial processes as crucial as stress response, iron scavenging and virulence, the exact mechanisms that drive CSS are still not completely understood. Binding of the signal to the CSS receptor is known to trigger a signaling cascade that results in the regulated proteolysis of the anti-sigma factor and the activation of the σECF in the cytosol. This study was carried out to generate new insights in the proteolytic activation of CSS σECF. We performed a random mutagenesis screen of the unique IutY protein of Pseudomonas putida, a protein that combines a cytosolic σECF domain and a periplasmic anti-sigma factor domain in a single polypeptide. In response to the presence of an iron carrier, the siderophore aerobactin, in the extracellular medium, IutY is processed by two different proteases, Prc and RseP, which results in the release and activation of the σIutY domain. Our experiments show that all IutY mutant proteins that contain periplasmic residues depend on RseP for activation. In contrast, Prc is only required for mutant variants with a periplasmic domain longer than 50 amino acids, which indicates that the periplasmic region of IutY is trimmed down to ~50 amino acids creating the RseP substrate. Moreover, we have identified several conserved residues in the CSS anti-sigma factor family of which mutation leads to constitutive activation of their cognate σECF. These findings advance our knowledge on how CSS activity is regulated by the consecutive action of two proteases. Elucidation of the exact mechanism behind CSS activation will enable the development of strategies to block CSS in pathogenic bacteria.
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Affiliation(s)
- Karlijn C Bastiaansen
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC)Granada, Spain.,Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University AmsterdamAmsterdam, Netherlands
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC)Granada, Spain
| | - Wilbert Bitter
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University AmsterdamAmsterdam, Netherlands
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC)Granada, Spain
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28
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The Pseudomonas aeruginosa PrrF Small RNAs Regulate Iron Homeostasis during Acute Murine Lung Infection. Infect Immun 2017; 85:IAI.00764-16. [PMID: 28289146 DOI: 10.1128/iai.00764-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/06/2017] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that requires iron for virulence. Iron homeostasis is maintained in part by the PrrF1 and PrrF2 small RNAs (sRNAs), which block the expression of iron-containing proteins under iron-depleted conditions. The PrrF sRNAs also promote the production of the Pseudomonas quinolone signal (PQS), a quorum sensing molecule that activates the expression of several virulence genes. The tandem arrangement of the prrF genes allows for expression of a third sRNA, PrrH, which is predicted to regulate gene expression through its unique sequence derived from the prrF1-prrF2 intergenic (IG) sequence (the PrrHIG sequence). Previous studies showed that the prrF locus is required for acute lung infection. However, the individual functions of the PrrF and PrrH sRNAs were not determined. Here, we describe a system for differentiating PrrF and PrrH functions by deleting the PrrHIG sequence [prrF(ΔHIG)]. Our analyses of this construct indicate that the PrrF sRNAs, but not PrrH, are required for acute lung infection by P. aeruginosa Moreover, we show that the virulence defect of the ΔprrF1-prrF2 mutant is due to decreased bacterial burden during acute lung infection. In vivo analysis of gene expression in lung homogenates shows that PrrF-mediated regulation of genes for iron-containing proteins is disrupted in the ΔprrF1-prrF2 mutant during infection, while the expression of genes that mediate PrrF-regulated PQS production are not affected by prrF deletion in vivo Combined, these studies demonstrate that regulation of iron utilization plays a critical role in P. aeruginosa's ability to survive during infection.
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29
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Reinhart AA, Oglesby-Sherrouse AG. Regulation of Pseudomonas aeruginosa Virulence by Distinct Iron Sources. Genes (Basel) 2016; 7:genes7120126. [PMID: 27983658 PMCID: PMC5192502 DOI: 10.3390/genes7120126] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/02/2016] [Accepted: 12/05/2016] [Indexed: 02/06/2023] Open
Abstract
Pseudomonas aeruginosa is a ubiquitous environmental bacterium and versatile opportunistic pathogen. Like most other organisms, P. aeruginosa requires iron for survival, yet iron rapidly reacts with oxygen and water to form stable ferric (FeIII) oxides and hydroxides, limiting its availability to living organisms. During infection, iron is also sequestered by the host innate immune system, further limiting its availability. P. aeruginosa’s capacity to cause disease in diverse host environments is due to its ability to scavenge iron from a variety of host iron sources. Work over the past two decades has further shown that different iron sources can affect the expression of distinct virulence traits. This review discusses how the individual components of P. aeruginosa’s iron regulatory network allow this opportunist to adapt to a multitude of host environments during infection.
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Affiliation(s)
- Alexandria A Reinhart
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
| | - Amanda G Oglesby-Sherrouse
- Department of Pharmaceutical Sciences, School of Pharmacy, and Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
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30
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Liu X, Long D, You H, Yang D, Zhou S, Zhang S, Li M, He M, Xiong M, Wang X. Phosphatidylcholine affects the secretion of the alkaline phosphatase PhoA in Pseudomonas strains. Microbiol Res 2016; 192:21-29. [DOI: 10.1016/j.micres.2016.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/05/2016] [Accepted: 02/01/2016] [Indexed: 01/13/2023]
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31
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Zhao X, Chen C, Jiang X, Shen W, Huang G, Le S, Lu S, Zou L, Ni Q, Li M, Zhao Y, Wang J, Rao X, Hu F, Tan Y. Transcriptomic and Metabolomic Analysis Revealed Multifaceted Effects of Phage Protein Gp70.1 on Pseudomonas aeruginosa. Front Microbiol 2016; 7:1519. [PMID: 27725812 PMCID: PMC5035744 DOI: 10.3389/fmicb.2016.01519] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
The impact of phage infection on the host cell is severe. In order to take over the cellular machinery, some phage proteins were produced to shut off the host biosynthesis early in the phage infection. The discovery and identification of these phage-derived inhibitors have a significant prospect of application in antibacterial treatment. This work presented a phage protein, gp70.1, with non-specific inhibitory effects on Pseudomonas aeruginosa and Escherichia coli. Gp70.1 was encoded by early gene – orf 70.1 from P. aeruginosa phage PaP3. The P. aeruginosa with a plasmid encoding gp70.1 showed with delayed growth and had the appearance of a small colony. The combination of multifaceted analysis including microarray-based transcriptomic analysis, RT-qPCR, nuclear magnetic resonance (NMR) spectroscopy-based metabolomics and phenotype experiments were performed to investigate the effects of gp70.1 on P. aeruginosa. A total of 178 genes of P. aeruginosa mainly involved in extracellular function and metabolism were differentially expressed in the presence of gp70.1 at three examined time points. Furthermore, our results indicated that gp70.1 had an extensive impact on the extracellular phenotype of P. aeruginosa, such as motility, pyocyanin, extracellular protease, polysaccharide, and cellulase. For the metabolism of P. aeruginosa, the main effect of gp70.1 was the reduction of amino acid consumption. Finally, the RNA polymerase sigma factor RpoS was identified as a potential cellular target of gp70.1. Gp70.1 was the first bacterial inhibitor identified from Pseudomonas aeruginosa phage PaP3. It was also the first phage protein that interacted with the global regulator RpoS of bacteria. Our results indicated the potential value of gp70.1 in antibacterial applications. This study preliminarily revealed the biological function of gp70.1 and provided a reference for the study of other phage genes sharing similarities with orf70.1.
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Affiliation(s)
- Xia Zhao
- Department of Microbiology, Third Military Medical University Chongqing, China
| | | | - Xingyu Jiang
- Department of Clinical Laboratory, Xinqiao Hospital, Third Military Medical University Chongqing, China
| | - Wei Shen
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Guangtao Huang
- Institute of Burn Research, Southwest Hospital, Third Military Medical University Chongqing, China
| | - Shuai Le
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Shuguang Lu
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Lingyun Zou
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Qingshan Ni
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Ming Li
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Yan Zhao
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Jing Wang
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Xiancai Rao
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Fuquan Hu
- Department of Microbiology, Third Military Medical University Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Third Military Medical University Chongqing, China
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32
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Quesada JM, Otero-Asman JR, Bastiaansen KC, Civantos C, Llamas MA. The Activity of the Pseudomonas aeruginosa Virulence Regulator σ(VreI) Is Modulated by the Anti-σ Factor VreR and the Transcription Factor PhoB. Front Microbiol 2016; 7:1159. [PMID: 27536271 PMCID: PMC4971064 DOI: 10.3389/fmicb.2016.01159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/12/2016] [Indexed: 11/13/2022] Open
Abstract
Gene regulation in bacteria is primarily controlled at the level of transcription initiation by modifying the affinity of the RNA polymerase (RNAP) for the promoter. This control often occurs through the substitution of the RNAP sigma (σ) subunit. Next to the primary σ factor, most bacteria contain a variable number of alternative σ factors of which the extracytoplasmic function group (σECF) is predominant. Pseudomonas aeruginosa contains nineteen σECF, including the virulence regulator σVreI. σVreI is encoded by the vreAIR operon, which also encodes a receptor-like protein (VreA) and an anti-σ factor (VreR). These three proteins form a signal transduction pathway known as PUMA3, which controls expression of P. aeruginosa virulence functions. Expression of the vreAIR operon occurs under inorganic phosphate (Pi) limitation and requires the PhoB transcription factor. Intriguingly, the genes of the σVreI regulon are also expressed in low Pi despite the fact that the σVreI repressor, the anti-σ factor VreR, is also produced in this condition. Here we show that although σVreI is partially active under Pi starvation, maximal transcription of the σVreI regulon genes requires the removal of VreR. This strongly suggests that an extra signal, probably host-derived, is required in vivo for full σVreI activation. Furthermore, we demonstrate that the activity of σVreI is modulated not only by VreR but also by the transcription factor PhoB. Presence of this regulator is an absolute requirement for σVreI to complex the DNA and initiate transcription of the PUMA3 regulon. The potential DNA binding sites of these two proteins, which include a pho box and −10 and −35 elements, are proposed.
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Affiliation(s)
- Jose M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Karlijn C Bastiaansen
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones CientíficasGranada, Spain; Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University AmsterdamAmsterdam, Netherlands
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas Granada, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas Granada, Spain
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33
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Pletzer D, Braun Y, Weingart H. Swarming motility is modulated by expression of the putative xenosiderophore transporter SppR-SppABCD in Pseudomonas aeruginosa PA14. Antonie van Leeuwenhoek 2016; 109:737-53. [PMID: 26995781 DOI: 10.1007/s10482-016-0675-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/03/2016] [Indexed: 12/14/2022]
Abstract
In the present study, we characterised the putative peptide ABC transporter SppABCD, which is co-transcribed with the TonB-dependent receptor SppR in Pseudomonas aeruginosa PA14. However, our data show that this transporter complex is not involved in the uptake of peptides. The fact that the TonB-dependent receptor SppR is regulated by an iron starvation ECF sigma factor suggested that this transporter is probably involved in the uptake of xenosiderophores. Therefore, we screened culture supernatants of 23 siderophore-producing bacteria for their ability to induce the expression of the SppR-regulating ECF sigma factor. However, none of them had an effect on the expression of this ECF sigma factor. Since the spp operon is not expressed under standard laboratory conditions, we overexpressed it from plasmids in PA14, which led to an impairment of its swarming motility on semisolid agar. Since we excluded the possibility that the uptake of a culture medium component was responsible for the observed phenotype, we hypothesize that the Spp transport system is involved in the uptake of a compound from the periplasmic space or a compound secreted by P. aeruginosa. Furthermore, we found that rhamnolipid synthesis was decreased while biofilm and exopolysaccharide synthesis was slightly increased upon overexpression of the spp operon. Moreover, we observed an impact of spp overexpression on regulation of genes involved in siderophore and phenazine biosynthesis.
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Affiliation(s)
- Daniel Pletzer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany.
- R.E.W. Hancock Laboratory, Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.
| | - Yvonne Braun
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
| | - Helge Weingart
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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34
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Harvie EA, Huttenlocher A. Neutrophils in host defense: new insights from zebrafish. J Leukoc Biol 2015; 98:523-37. [PMID: 25717145 PMCID: PMC4569048 DOI: 10.1189/jlb.4mr1114-524r] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 12/11/2022] Open
Abstract
Neutrophils are highly motile phagocytic cells that play a critical role in the immune response to infection. Zebrafish (Danio rerio) are increasingly used to study neutrophil function and host-pathogen interactions. The generation of transgenic zebrafish lines with fluorescently labeled leukocytes has made it possible to visualize the neutrophil response to infection in real time by use of optically transparent zebrafish larvae. In addition, the genetic tractability of zebrafish has allowed for the generation of models of inherited neutrophil disorders. In this review, we discuss several zebrafish models of infectious disease, both in the context of immunocompetent, as well as neutrophil-deficient hosts and how these models have shed light on neutrophil behavior during infection.
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Affiliation(s)
- Elizabeth A Harvie
- *Microbiology Doctoral Training Program, Departments of Medical Microbiology and Immunology and Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Anna Huttenlocher
- *Microbiology Doctoral Training Program, Departments of Medical Microbiology and Immunology and Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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35
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Dou Y, Aruni W, Muthiah A, Roy F, Wang C, Fletcher HM. Studies of the extracytoplasmic function sigma factor PG0162 in Porphyromonas gingivalis. Mol Oral Microbiol 2015. [PMID: 26216199 DOI: 10.1111/omi.12122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PG0162, annotated as an extracytoplasmic function (ECF) sigma factor in Porphyromonas gingivalis, is composed of 193 amino acids. As previously reported, the PG0162-deficient mutant, P. gingivalis FLL350 showed significant reduction in gingipain activity compared with the parental strain. Because this ECF sigma factor could be involved in the virulence regulation in P. gingivalis, its genetic properties were further characterized. A 5'-RACE analysis showed that the start of transcription of the PG0162 gene occurred from a guanine (G) residue 69 nucleotides upstream of the ATG translation initiation codon. The function of PG0162 as a sigma factor was confirmed in a run-off in vitro transcription assay using the purified rPG0162 and RNAP core enzyme from Escherichia coli with the PG0162 promoter as template. As an appropriate PG0162 inducing environmental signal is unknown, a strain overexpressing the PG0162 gene designated P. gingivalis FLL391 was created. Compared with the wild-type strain, transcriptome analysis of P. gingivalis FLL391 showed that approximately 24% of the genome displayed altered gene expression (260 upregulated genes; 286 downregulated genes). Two other ECF sigma factors (PG0985 and PG1660) were upregulated more than two-fold. The autoregulation of PG0162 was confirmed with the binding of the rPG0162 protein to the PG0162 promoter in electrophoretic mobility shift assay. In addition, the rPG0162 protein also showed the ability to bind to the promoter region of two genes (PG0521 and PG1167) that were most upregulated in P. gingivalis FLL391. Taken together, our data suggest that PG0162 is a sigma factor that may play an important role in the virulence regulatory network in P. gingivalis.
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Affiliation(s)
- Y Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - W Aruni
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - A Muthiah
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - F Roy
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - C Wang
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - H M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Institute of Oral Biology, Kyung Hee University, Seoul, Republic of Korea
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Dourado MN, Santos DS, Nunes LR, Costa de Oliveira RLBD, de Oliveira MV, Araújo WL. Differential gene expression in Xylella fastidiosa 9a5c during co-cultivation with the endophytic bacterium Methylobacterium mesophilicum SR1.6/6. J Basic Microbiol 2015. [PMID: 26218710 DOI: 10.1002/jobm.201400916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Xylella fastidiosa, the causal agent of citrus variegated chlorosis (CVC), colonizes plant xylem, reducing sap flow, and inducing internerval chlorosis, leaf size reduction, necrosis, and harder and smaller fruits. This bacterium may be transmitted from plant to plant by sharpshooter insects, including Bucephalogonia xanthopis. The citrus endophytic bacterium Methylobacterium mesophilicum SR1.6/6 colonizes citrus xylem and previous studies showed that this strain is also transferred from plant to plant by B. xanthopis (Insecta), suggesting that this endophytic bacterium may interact with X. fastidiosa in planta and inside the insect vector during co-transmission by the same insect vector. To better understand the X. fastidiosa behavior in the presence of M. mesophilicum, we evaluated the X. fastidiosa transcriptional profile during in vitro interaction with M. mesophilicum SR1.6/6. The results showed that during co-cultivation, X. fastidiosa down-regulated genes related to growth and up-regulated genes related to energy production, stress, transport, and motility, suggesting the existence of a specific adaptive response to the presence of M. mesophilicum in the culture medium.
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Affiliation(s)
| | - Daiene Souza Santos
- Núcleo Integrado de Biotecnologia, NIB, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil
| | - Luiz Roberto Nunes
- Núcleo Integrado de Biotecnologia, NIB, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | | | | | - Welington Luiz Araújo
- Núcleo Integrado de Biotecnologia, NIB, University of Mogi das Cruzes, Mogi das Cruzes, SP, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, São Paulo, 05508-900, SP, Brazil
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37
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Schulz S, Eckweiler D, Bielecka A, Nicolai T, Franke R, Dötsch A, Hornischer K, Bruchmann S, Düvel J, Häussler S. Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk. PLoS Pathog 2015; 11:e1004744. [PMID: 25780925 PMCID: PMC4362757 DOI: 10.1371/journal.ppat.1004744] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/11/2015] [Indexed: 12/31/2022] Open
Abstract
Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN. Pseudomonas aeruginosa is well known for its high adaptability to a large range of environmental conditions, including those encountered within the human host. Transcription initiation represents a major regulatory target which drives versatility, and enables bacterial adaptation to challenging conditions and expression of virulence and pathogenicity. In bacteria, this process is largely orchestrated by sigma factors. Here, we performed an integrative approach, and by the combined use of three global profiling technologies uncovered the networks of 10 alternative sigma factors in the opportunistic pathogen P. aeruginosa. We demonstrate that these networks largely represent self-contained functional modules which exhibit a limited but highly specific crosstalk to build up higher-level functions. Our results do not only give extensive information on sigma factor binding sites throughout the P. aeruginosa genome, but also advance the understanding of sigma factor network architecture which provides bacteria with a framework to function adequately in their environment.
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Affiliation(s)
- Sebastian Schulz
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Denitsa Eckweiler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata Bielecka
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Tanja Nicolai
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Raimo Franke
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Dötsch
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Hornischer
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sebastian Bruchmann
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Juliane Düvel
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center for Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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Bastiaansen KC, Otero-Asman JR, Luirink J, Bitter W, Llamas MA. Processing of cell-surface signalling anti-sigma factors prior to signal recognition is a conserved autoproteolytic mechanism that produces two functional domains. Environ Microbiol 2015; 17:3263-77. [PMID: 25581349 DOI: 10.1111/1462-2920.12776] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 02/02/2023]
Abstract
Cell-surface signalling (CSS) enables Gram-negative bacteria to transduce an environmental signal into a cytosolic response. This regulatory cascade involves an outer membrane receptor that transmits the signal to an anti-sigma factor in the cytoplasmic membrane, allowing the activation of an extracytoplasmic function (ECF) sigma factor. Recent studies have demonstrated that RseP-mediated proteolysis of the anti-sigma factors is key to σ(ECF) activation. Using the Pseudomonas aeruginosa FoxR anti-sigma factor, we show here that RseP is responsible for the generation of an N-terminal tail that likely contains pro-sigma activity. Furthermore, it has been reported previously that this anti-sigma factor is processed in two separate domains prior to signal recognition. Here, we demonstrate that this process is common in these types of proteins and that the processing event is probably due to autoproteolytic activity. The resulting domains interact and function together to transduce the CSS signal. However, our results also indicate that this processing event is not essential for activity. In fact, we have identified functional CSS anti-sigma factors that are not cleaved prior to signal perception. Together, our results indicate that CSS regulation can occur through both complete and initially processed anti-sigma factors.
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Affiliation(s)
- Karlijn C Bastiaansen
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain.,Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, Amsterdam, The Netherlands
| | - Joaquín R Otero-Asman
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Joen Luirink
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, Amsterdam, The Netherlands
| | - Wilbert Bitter
- Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University, Amsterdam, The Netherlands
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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Abstract
In recent years, chemical biology and chemical genomics have been increasingly applied to the field of microbiology to uncover new potential therapeutics as well as to probe virulence mechanisms in pathogens. The approach offers some clear advantages, as identified compounds (i) can serve as a proof of principle for the applicability of drugs to specific targets; (ii) can serve as conditional effectors to explore the function of their targets in vitro and in vivo; (iii) can be used to modulate gene expression in otherwise genetically intractable organisms; and (iv) can be tailored to a narrow or broad range of bacteria. This review highlights recent examples from the literature to illustrate how the use of small molecules has advanced discovery of novel potential treatments and has been applied to explore biological mechanisms underlying pathogenicity. We also use these examples to discuss practical considerations that are key to establishing a screening or discovery program. Finally, we discuss the advantages and challenges of different approaches and the methods that are emerging to address these challenges.
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Affiliation(s)
- Rebecca Anthouard
- Laboratory of Genetics & Molecular Biology of Intestinal Pathogens, Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Victor J DiRita
- Laboratory of Genetics & Molecular Biology of Intestinal Pathogens, Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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40
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The prrF-encoded small regulatory RNAs are required for iron homeostasis and virulence of Pseudomonas aeruginosa. Infect Immun 2014; 83:863-75. [PMID: 25510881 DOI: 10.1128/iai.02707-14] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part of P. aeruginosa's iron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem in P. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ΔprrF1,2 mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identified phuS, encoding a heme binding protein involved in heme acquisition, and vreR, encoding a previously identified regulator of P. aeruginosa virulence genes, as novel targets of prrF-mediated heme regulation. Finally, we showed that the prrF locus encoding the PrrF and PrrH sRNAs is required for P. aeruginosa virulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ΔprrF1,2 deletion mutant protects against future challenge with wild-type P. aeruginosa. Combined, these data demonstrate that the prrF-encoded sRNAs are critical regulators of P. aeruginosa virulence.
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41
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Ouidir T, Jarnier F, Cosette P, Jouenne T, Hardouin J. Potential of liquid-isoelectric-focusing protein fractionation to improve phosphoprotein characterization of Pseudomonas aeruginosa PA14. Anal Bioanal Chem 2014; 406:6297-309. [DOI: 10.1007/s00216-014-8045-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/09/2014] [Accepted: 07/16/2014] [Indexed: 11/29/2022]
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42
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Faure LM, Garvis S, de Bentzmann S, Bigot S. Characterization of a novel two-partner secretion system implicated in the virulence of Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2014; 160:1940-1952. [PMID: 25009238 DOI: 10.1099/mic.0.079616-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen implicated in nosocomial infection and infecting people with compromised immune systems such as cystic fibrosis patients. Although multiple genes involved in P. aeruginosa pathogenesis have been characterized, the overall mechanism of virulence is not fully understood. In this study, we identified a functional two-partner secretion (TPS) system, composed of the PdtA exoprotein and its cognate pore-forming β-barrel PdtB transporter, which is implicated in the virulence of P. aeruginosa. We found that the predicted PdtA exoprotein is related to the HMW-like adhesins subfamily TPS systems. We demonstrate here that limitation of inorganic phosphate (Pi) allows the production of PdtA protein. We show that PdtA is processed during its outer-membrane translocation, with an N-terminal domain released into the extracellular environment and a C-terminal domain associated with the outer membrane of the cell. We also obtained evidence that the transport of PdtA is strictly dependent on the production of PdtB, a result confirming that these proteins constitute a functional TPS system. Furthermore, using the Caenorhabditis elegans model of infection, we show that a pdtA mutant is less virulent than the wild-type strain.
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Affiliation(s)
- Laura M Faure
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Steve Garvis
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Sophie de Bentzmann
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Sarah Bigot
- UMR7255, CNRS - Aix Marseille Université, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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43
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Llamas MA, Imperi F, Visca P, Lamont IL. Cell-surface signaling inPseudomonas: stress responses, iron transport, and pathogenicity. FEMS Microbiol Rev 2014; 38:569-97. [DOI: 10.1111/1574-6976.12078] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 05/20/2014] [Accepted: 05/27/2014] [Indexed: 01/06/2023] Open
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Malki I, Simenel C, Wojtowicz H, Cardoso de Amorim G, Prochnicka-Chalufour A, Hoos S, Raynal B, England P, Chaffotte A, Delepierre M, Delepelaire P, Izadi-Pruneyre N. Interaction of a partially disordered antisigma factor with its partner, the signaling domain of the TonB-dependent transporter HasR. PLoS One 2014; 9:e89502. [PMID: 24727671 PMCID: PMC3984077 DOI: 10.1371/journal.pone.0089502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/21/2022] Open
Abstract
Bacteria use diverse signaling pathways to control gene expression in response to external stimuli. In Gram-negative bacteria, the binding of a nutrient is sensed by an outer membrane transporter. This signal is then transmitted to an antisigma factor and subsequently to the cytoplasm where an ECF sigma factor induces expression of genes related to the acquisition of this nutrient. The molecular interactions involved in this transmembrane signaling are poorly understood and structural data on this family of antisigma factor are rare. Here, we present the first structural study of the periplasmic domain of an antisigma factor and its interaction with the transporter. The study concerns the signaling in the heme acquisition system (Has) of Serratia marcescens. Our data support unprecedented partially disordered periplasmic domain of an anti-sigma factor HasS in contact with a membrane-mimicking environment. We solved the 3D structure of the signaling domain of HasR transporter and identified the residues at the HasS-HasR interface. Their conservation in several bacteria suggests wider significance of the proposed model for the understanding of bacterial transmembrane signaling.
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Affiliation(s)
- Idir Malki
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
| | - Catherine Simenel
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Halina Wojtowicz
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Gisele Cardoso de Amorim
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Ada Prochnicka-Chalufour
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Sylviane Hoos
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Bertrand Raynal
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Patrick England
- Institut Pasteur, Plate-forme de Biophysique des Macromolécules et de leurs Interactions, Département de Biologie Structurale et Chimie, Paris, France
| | - Alain Chaffotte
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Muriel Delepierre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Philippe Delepelaire
- Institut de Biologie Physico-Chimique, CNRS Université Paris-Diderot UMR 7099, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Unité de RMN des Biomolécules, Département de Biologie Structurale et Chimie, Paris, France
- CNRS, UMR 3528, Paris, France
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Bastiaansen KC, Ibañez A, Ramos JL, Bitter W, Llamas MA. The Prc and RseP proteases control bacterial cell-surface signalling activity. Environ Microbiol 2014; 16:2433-43. [PMID: 24373018 DOI: 10.1111/1462-2920.12371] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/09/2013] [Accepted: 12/15/2013] [Indexed: 11/29/2022]
Abstract
Extracytoplasmic function (ECF) sigma factors play a key role in the regulation of vital functions in the bacterial response to the environment. In Gram-negative bacteria, activity of these sigma factors is often controlled by cell-surface signalling (CSS), a regulatory system that also involves an outer membrane receptor and a transmembrane anti-sigma factor. To get more insight into the molecular mechanism behind CSS regulation, we have focused on the unique Iut system of Pseudomonas putida. This system contains a hybrid protein containing both a cytoplasmic ECF sigma domain and a periplasmic anti-sigma domain, apparently leading to a permanent interaction between the sigma and anti-sigma factor. We show that the Iut ECF sigma factor regulates the response to aerobactin under iron deficiency conditions and is activated by a proteolytic pathway that involves the sequential action of two proteases: Prc, which removes the periplasmic anti-sigma domain, and RseP, which subsequently removes the transmembrane domain and thereby generates the ECF active transcriptional form. We furthermore demonstrate the role of these proteases in the regulation of classical CSS systems in which the sigma and anti-sigma factors are two different proteins.
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Affiliation(s)
- Karlijn C Bastiaansen
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain; Section of Molecular Microbiology, Department of Molecular Cell Biology, VU University Amsterdam, Amsterdam, The Netherlands
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46
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Llamas MA, van der Sar AM. Assessing Pseudomonas virulence with nonmammalian host: zebrafish. Methods Mol Biol 2014; 1149:709-21. [PMID: 24818945 DOI: 10.1007/978-1-4939-0473-0_55] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the last years, the zebrafish (Danio rerio) has become an important vertebrate animal model to study host-pathogen interactions, especially in its embryonic stage. The presence of a fully developed innate immune system in the first days of embryogenesis, the facility of obtaining and manipulating large numbers of embryos, the optical transparency of the embryos that allow the direct visualization of bacterial infections, a wide range of genetic tools, and extensive mutant resources and collections of transgenic reporter lines are important advantages of the zebrafish-embryo model. Pseudomonas aeruginosa is able to lethally infect zebrafish embryos when the amount of cells injected exceeds the phagocytic capacity of the embryo. Different studies have proved the suitability of zebrafish embryos as a model to analyze P. aeruginosa infection. Here we describe the detailed protocols to establish a P. aeruginosa infection in zebrafish embryos and to image the interaction of the bacterium with this host with fluorescent microscopy.
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Affiliation(s)
- María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-CSIC, 18008, Granada, Spain,
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47
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Boechat AL, Kaihami GH, Politi MJ, Lépine F, Baldini RL. A novel role for an ECF sigma factor in fatty acid biosynthesis and membrane fluidity in Pseudomonas aeruginosa. PLoS One 2013; 8:e84775. [PMID: 24386415 PMCID: PMC3875570 DOI: 10.1371/journal.pone.0084775] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 11/18/2013] [Indexed: 01/27/2023] Open
Abstract
Extracytoplasmic function (ECF) sigma factors are members of cell-surface signaling systems, abundant in the opportunistic pathogen Pseudomonas aeruginosa. Twenty genes coding for ECF sigma factors are present in P. aeruginosa sequenced genomes, most of them being part of TonB systems related to iron uptake. In this work, poorly characterized sigma factors were overexpressed in strain PA14, in an attempt to understand their role in the bacterium's physiology. Cultures overexpressing SigX displayed a biphasic growth curve, reaching stationary phase earlier than the control strain, followed by subsequent growth resumption. During the first stationary phase, most cells swell and die, but the remaining cells return to the wild type morphology and proceed to a second exponential growth. This is not due to compensatory mutations, since cells recovered from late time points and diluted into fresh medium repeated this behavior. Swollen cells have a more fluid membrane and contain higher amounts of shorter chain fatty acids. A proteomic analysis was performed to identify differentially expressed proteins due to overexpression of sigX, revealing the induction of several fatty acid synthesis (FAS) enzymes. Using qRT-PCR, we showed that at least one isoform from each of the FAS pathway enzymes were upregulated at the mRNA level in the SigX overexpressing strain thus pointing to a role for this ECF sigma factor in the FAS regulation in P. aeruginosa.
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Affiliation(s)
- Ana Laura Boechat
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Gilberto Hideo Kaihami
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Mario José Politi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - François Lépine
- INRS-Institut Armand-Frappier, Université du Québec, Laval, Québec, Canada
| | - Regina L. Baldini
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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Kumari H, Murugapiran SK, Balasubramanian D, Schneper L, Merighi M, Sarracino D, Lory S, Mathee K. LTQ-XL mass spectrometry proteome analysis expands the Pseudomonas aeruginosa AmpR regulon to include cyclic di-GMP phosphodiesterases and phosphoproteins, and identifies novel open reading frames. J Proteomics 2013; 96:328-342. [PMID: 24291602 DOI: 10.1016/j.jprot.2013.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 12/23/2022]
Abstract
UNLABELLED Pseudomonas aeruginosa is well known for its antibiotic resistance and intricate regulatory network, contributing to its success as an opportunistic pathogen. This study is an extension of our transcriptomic analyses (microarray and RNA-Seq) to understand the global changes in PAO1 upon deleting a gene encoding a transcriptional regulator AmpR, in the presence and absence of β-lactam antibiotic. This study was performed under identical conditions to explore the proteome profile of the ampR deletion mutant (PAOΔampR) using LTQ-XL mass spectrometry. The proteomic data identified ~53% of total PAO1 proteins and expanded the master regulatory role of AmpR in determining antibiotic resistance and multiple virulence phenotypes in P. aeruginosa. AmpR proteome analysis identified 853 AmpR-dependent proteins, which include 102 transcriptional regulators and 21 two-component system proteins. AmpR also regulates cyclic di-GMP phosphodiesterases (PA4367, PA4969, PA4781) possibly affecting major virulence systems. Phosphoproteome analysis also suggests a significant role for AmpR in Ser, Thr and Tyr phosphorylation. These novel mechanisms of gene regulation were previously not associated with AmpR. The proteome analysis also identified many unannotated and misannotated ORFs in the P. aeruginosa genome. Thus, our data sheds light on important virulence regulatory pathways that can potentially be exploited to deal with P. aeruginosa infections. BIOLOGICAL SIGNIFICANCE The AmpR proteome data not only confirmed the role of AmpR in virulence and resistance to multiple antibiotics, but also expanded the perimeter of AmpR regulon. The data presented here points to the role of AmpR in regulating cyclic di-GMP levels and phosphorylation of Ser, Thr and Tyr, adding another dimension to the regulatory functions of AmpR. We also identify some previously unannotated/misannotated ORFs in the P. aeruginosa genome, indicating the limitations of existing ORF analyses software. This study will contribute towards understanding complex genetic organization of P. aeruginosa. Whole genome proteomic picture of regulators at higher nodal positions in the regulatory network will not only help us link various virulence phenotypes but also design novel therapeutic strategies.
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Affiliation(s)
- Hansi Kumari
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL
| | - Senthil K Murugapiran
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL
| | - Deepak Balasubramanian
- Department of Biological Sciences, College of Arts and Sciences, Florida International University, Miami, FL United States
| | - Lisa Schneper
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL
| | - Massimo Merighi
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA
| | - David Sarracino
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA
| | - Stephen Lory
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA
| | - Kalai Mathee
- Department of Molecular Microbiology and Infectious Diseases, Herbert Wertheim College of Medicine, Florida International University, Miami, FL
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Gicquel G, Bouffartigues E, Bains M, Oxaran V, Rosay T, Lesouhaitier O, Connil N, Bazire A, Maillot O, Bénard M, Cornelis P, Hancock REW, Dufour A, Feuilloley MGJ, Orange N, Déziel E, Chevalier S. The extra-cytoplasmic function sigma factor sigX modulates biofilm and virulence-related properties in Pseudomonas aeruginosa. PLoS One 2013; 8:e80407. [PMID: 24260387 PMCID: PMC3832394 DOI: 10.1371/journal.pone.0080407] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 10/02/2013] [Indexed: 11/23/2022] Open
Abstract
SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF. We conducted a comparative transcriptomic study between the wildtype H103 strain and its sigX mutant PAOSX, which revealed a total of 307 differentially expressed genes that differed by more than 2 fold. Most dysregulated genes belonged to six functional classes, including the “chaperones and heat shock proteins”, “antibiotic resistance and susceptibility”, “energy metabolism”, “protein secretion/export apparatus”, and “secreted factors”, and “motility and attachment” classes. In this latter class, the large majority of the affected genes were down-regulated in the sigX mutant. In agreement with the array data, the sigX mutant was shown to demonstrate substantially reduced motility, attachment to biotic and abiotic surfaces, and biofilm formation. In addition, virulence towards the nematode Caenorhabditis elegans was reduced in the sigX mutant, suggesting that SigX is involved in virulence-related phenotypes.
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Affiliation(s)
- Gwendoline Gicquel
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Emeline Bouffartigues
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Manjeet Bains
- Centre for Microbal Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - Virginie Oxaran
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Thibaut Rosay
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Olivier Lesouhaitier
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Nathalie Connil
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Alexis Bazire
- IUEM, Université de Bretagne-Sud (UEB), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Olivier Maillot
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Magalie Bénard
- Cell Imaging Platform of Normandy (PRIMACEN), IRIB, Faculty of Sciences, University of Rouen, Mont-Saint-Aignan, France
| | - Pierre Cornelis
- Department of Bioengineering Sciences, Research group Microbiology, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Robert E. W. Hancock
- Centre for Microbal Diseases and Immunity Research, University of British Columbia, Vancouver, Canada
| | - Alain Dufour
- IUEM, Université de Bretagne-Sud (UEB), Laboratoire de Biotechnologie et Chimie Marines EA 3884, Lorient, France
| | - Marc G. J. Feuilloley
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Nicole Orange
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
| | - Eric Déziel
- INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | - Sylvie Chevalier
- Normandie Université, Université de Rouen, Laboratoire de Microbiologie Signaux et Micro-environnement EA 4312, Evreux, France
- * E-mail:
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50
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Draft Genome Sequence of Pseudomonas fluorescens LMG 5329, a White Line-Inducing Principle-Producing Bioindicator for the Mushroom Pathogen Pseudomonas tolaasii. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00383-13. [PMID: 23887909 PMCID: PMC3735071 DOI: 10.1128/genomea.00383-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas tolaasii, the causative agent of Agaricus bisporus brown blotch disease, can be identified by the white line reaction, occurring upon confrontation of the tolaasin-producing mushroom pathogen with “Pseudomonas reactans,” producing the lipopeptide white line-inducing principle (WLIP). The draft genome sequence of the WLIP-producing indicator Pseudomonas fluorescens strain LMG 5329 is reported here.
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