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Hendrix H, Itterbeek A, Longin H, Delanghe L, Vriens E, Vallino M, Lammens EM, Haque F, Yusuf A, Noben JP, Boon M, Koch MD, van Noort V, Lavigne R. PlzR regulates type IV pili assembly in Pseudomonas aeruginosa via PilZ binding. Nat Commun 2024; 15:8717. [PMID: 39379373 PMCID: PMC11461919 DOI: 10.1038/s41467-024-52732-5] [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: 02/02/2023] [Accepted: 09/16/2024] [Indexed: 10/10/2024] Open
Abstract
Type IV pili (T4P) are thin, flexible filaments exposed on the cell surface of gram-negative bacteria and are involved in pathogenesis-related processes, including cell adsorption, biofilm formation, and twitching motility. Bacteriophages often use these filaments as receptors to infect host cells. Here, we describe the identification of a protein that inhibits T4P assembly in Pseudomonas aeruginosa, discovered during a screen for host factors influencing phage infection. We show that expression of PA2560 (renamed PlzR) in P. aeruginosa inhibits adsorption of T4P-dependent phages. PlzR does this by directly binding the T4P chaperone PilZ, which in turn regulates the ATPase PilB and results in disturbed T4P assembly. As the plzR promoter is induced by cyclic di-GMP, PlzR might play a role in coupling T4P function to levels of this second messenger.
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Affiliation(s)
- Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Annabel Itterbeek
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
- Laboratory for Host Pathogen Interactions in Livestock, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Hannelore Longin
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
- Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, Heverlee, Belgium
| | - Lize Delanghe
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Eveline Vriens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, IPSP-CNR Headquarter, Turin, Italy
| | - Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Farhana Haque
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Ahmed Yusuf
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium
| | - Matthias D Koch
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Vera van Noort
- Computational Systems Biology, Department of Microbial and Molecular Systems, KU Leuven, Heverlee, Belgium
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Heverlee, Belgium.
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2
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Gallegos MT, Garavaglia M, Valverde C. Small Regulatory RNAs of the Rsm Clan in Pseudomonas. Mol Microbiol 2024; 122:563-582. [PMID: 39282792 DOI: 10.1111/mmi.15313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/21/2024] [Accepted: 08/24/2024] [Indexed: 10/17/2024]
Abstract
Bacteria of the genus Pseudomonas are ubiquitous on Earth due to their great metabolic versatility and adaptation to fluctuating environments and different hosts. Some groups are important animal/human and plant pathogens, whereas others are studied for their biotechnological applications, including bioremediation, biological control of phytopathogens and plant growth promotion. Notably, their adaptability is mediated by various signal transduction systems, with the post-transcriptional Gac-Rsm cascade playing a key role. This pervasive Pseudomonas pathway controls major transitions at the population level, such as motile/sessile lifestyle, primary/secondary metabolism or replicative/infective behaviour. A hallmark of the Gac-Rsm cascade is the participation of small, regulatory, non-coding RNAs of the Rsm clan. These RNAs are synthetised in response to cell-density-dependent autoinducer signals channelled through the GacS/GacA two-component system, and they counteract, by molecular mimicry, the translational control that RNA-binding proteins of the RsmA family exert over hundreds of mRNAs. Rsm RNAs have been investigated in a few Pseudomonas model species, evidencing the presence of a variable number and families of genes depending on the taxonomic clade. However, the global picture of the distribution of these riboregulators at the genus level was unknown until now. We have undertaken a comprehensive survey and annotation of the vast array of gene sequences encoding members of the Rsm RNA clan in 245 complete genomes that cover 28 phylogenomic clades across the entire genus. The properties of the different families of rsm genes, their phylogenetic radiation, as well as the features of their promoters and adjacent regions, are discussed. The novel insights presented in our manuscript will significantly boost research on the biology of these prevalent RNAs in understudied species of the genus Pseudomonas and closely related genera.
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Affiliation(s)
- María Trinidad Gallegos
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - Matías Garavaglia
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Bioinsumos, Instituto de Biotecnología, Universidad Nacional de Hurlingham, Hurlingham, Buenos Aires, Argentina
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3
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Khaledi M, Khatami M, Hemmati J, Bakhti S, Hoseini SA, Ghahramanpour H. Role of Small Non-Coding RNA in Gram-Negative Bacteria: New Insights and Comprehensive Review of Mechanisms, Functions, and Potential Applications. Mol Biotechnol 2024:10.1007/s12033-024-01248-w. [PMID: 39153013 DOI: 10.1007/s12033-024-01248-w] [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: 03/18/2024] [Accepted: 08/02/2024] [Indexed: 08/19/2024]
Abstract
Small non-coding RNAs (sRNAs) are a key part of gene expression regulation in bacteria. Many physiologic activities like adaptation to environmental stresses, antibiotic resistance, quorum sensing, and modulation of the host immune response are regulated directly or indirectly by sRNAs in Gram-negative bacteria. Therefore, sRNAs can be considered as potentially useful therapeutic options. They have opened promising perspectives in the field of diagnosis of pathogens and treatment of infections caused by antibiotic-resistant organisms. Identification of sRNAs can be executed by sequence and expression-based methods. Despite the valuable progress in the last two decades, and discovery of new sRNAs, their exact role in biological pathways especially in co-operation with other biomolecules involved in gene expression regulation such as RNA-binding proteins (RBPs), riboswitches, and other sRNAs needs further investigation. Although the numerous RNA databases are available, including 59 databases used by RNAcentral, there remains a significant gap in the absence of a comprehensive and professional database that categorizes experimentally validated sRNAs in Gram-negative pathogens. Here, we review the present knowledge about most recent and important sRNAs and their regulatory mechanism, strengths and weaknesses of current methods of sRNAs identification. Also, we try to demonstrate the potential applications and new insights of sRNAs for future studies.
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Affiliation(s)
- Mansoor Khaledi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
- Department of Microbiology and Immunology, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mehrdad Khatami
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Jaber Hemmati
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahriar Bakhti
- Department of Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
| | | | - Hossein Ghahramanpour
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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4
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Sposato D, Mercolino J, Torrini L, Sperandeo P, Lucidi M, Alegiani R, Varone I, Molesini G, Leoni L, Rampioni G, Visca P, Imperi F. Redundant essentiality of AsmA-like proteins in Pseudomonas aeruginosa. mSphere 2024; 9:e0067723. [PMID: 38305166 PMCID: PMC10900882 DOI: 10.1128/msphere.00677-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
The outer membrane (OM) is an essential structure of Gram-negative bacteria that provides mechanical strength and protection from large and/or hydrophobic toxic molecules, including many antibiotics. The OM is composed of glycerophospholipids (GPLs) and lipopolysaccharide (LPS) in the inner and outer leaflets, respectively, and hosts integral β-barrel proteins and lipoproteins. While the systems responsible for translocation and insertion of LPS and OM proteins have been elucidated, the mechanism(s) mediating transport of GPLs from the inner membrane to the OM has remained elusive for decades. Very recently, studies performed in Escherichia coli proposed a role in this process for AsmA-like proteins that are predicted to share structural features with eukaryotic lipid transporters. In this study, we provide the first systematic investigation of AsmA-like proteins in a bacterium other than E. coli, the opportunistic human pathogen Pseudomonas aeruginosa. Bioinformatic analyses revealed that P. aeruginosa possesses seven AsmA-like proteins. Deletion of asmA-like genes in many different combinations, coupled with conditional mutagenesis, revealed that four AsmA-like proteins are redundantly essential for growth and OM integrity in P. aeruginosa, including a novel AsmA-like protein (PA4735) that is not present in E. coli. Cells depleted of AsmA-like proteins showed severe defects in the OM permeability barrier that were partially rescued by lowering the synthesis or transport of LPS. Since fine balancing of GPL and LPS levels is crucial for OM integrity, this evidence supports the role of AsmA-like proteins in GPL transport toward the OM. IMPORTANCE Given the importance of the outer membrane (OM) for viability and antibiotic resistance in Gram-negative bacteria, in the last decades, several studies have focused on the characterization of the systems involved in OM biogenesis, which have also been explored as targets for antibacterial drug development. However, the mechanism mediating translocation of glycerophospholipids (GPLs) to the OM remained unknown until recent studies provided evidence that AsmA-like proteins could be responsible for this process. Here, we demonstrate for the first time that AsmA-like proteins are essential and redundant for growth and OM integrity in a Gram-negative bacterium other than the model organism Escherichia coli and demonstrate that the human pathogen Pseudomonas aeruginosa has an additional essential AsmA-like protein that is not present in E. coli, thus expanding the range of AsmA-like proteins that play key functions in Gram-negative bacteria.
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Affiliation(s)
| | | | - Luisa Torrini
- Department of Science, University Roma Tre, Rome, Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Milan, Italy
| | - Massimiliano Lucidi
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Ilaria Varone
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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5
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Pastora AB, O’Toole GA. The regulator FleQ both transcriptionally and post-transcriptionally regulates the level of RTX adhesins of Pseudomonas fluorescens. J Bacteriol 2023; 205:e0015223. [PMID: 37655913 PMCID: PMC10521353 DOI: 10.1128/jb.00152-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/07/2023] [Indexed: 09/02/2023] Open
Abstract
Biofilm formation by the Gram-negative, Gammaproteobacteria Pseudomonas fluorescens relies on the repeats-in-toxin adhesins LapA and MapA in the cytoplasm, secretion of these adhesins through their respective type 1 secretion systems, and retention at the cell surface. Published work has shown that retention of the adhesins occurs via a post-translational mechanism involving the cyclic-di-GMP receptor LapD and the protease LapG. However, little is known about the underlying mechanisms that regulate the level of these adhesins. Here, we demonstrate that the master regulator FleQ modulates biofilm formation by both transcriptionally and post-transcriptionally regulating LapA and MapA. We find that a ΔfleQ mutant has a biofilm formation defect compared to the wild-type (WT) strain, which is attributed in part to a decrease in LapA and MapA abundance in the cell, despite the ΔfleQ mutant having increased levels of lapA and mapA transcripts compared to the WT strain. Through transposon mutagenesis and subsequent genetic analysis, we found that overstimulation of the Gac/Rsm pathway partially rescues biofilm formation in the ΔfleQ mutant background. Collectively, these findings provide evidence that FleQ regulates biofilm formation by both transcriptionally regulating the expression of the lapA and mapA genes and post-transcriptionally regulating the abundance of LapA and MapA, and that activation of the Gac/Rsm pathway can post-transcriptionally enhance biofilm formation by P. fluorescens. IMPORTANCE Biofilm formation is a highly coordinated process that bacteria undergo to colonize a variety of surfaces. For Pseudomonas fluorescens, biofilm formation requires the production and localization of repeats-in-toxin adhesins to the cell surface. To date, little is known about the underlying mechanisms that regulate biofilm formation by P. fluorescens. Here, we identify FleQ as a key regulator of biofilm formation that modulates both gene expression and abundance of LapA and MapA through both a transcriptional and post-transcriptional mechanism. We provide further evidence implicating activation of the Gac/Rsm system in FleQ-dependent regulation of biofilm formation. Together, our findings uncover evidence for a dual mechanism of transcriptional and post-transcriptional regulation of the LapA and MapA adhesins.
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Affiliation(s)
- Alexander B. Pastora
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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6
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Pastora AB, O’Toole GA. The Regulator FleQ Post-Transcriptionally Regulates the Production of RTX Adhesins by Pseudomonas fluorescens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540025. [PMID: 37214974 PMCID: PMC10197612 DOI: 10.1101/2023.05.09.540025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biofilm formation by the Gram-negative gammaproteobacterium Pseudomonas fluorescens relies on the production of the repeat-in-toxin (RTX) adhesins LapA and MapA in the cytoplasm, secretion of these adhesins through their respective type 1 secretion systems, and retention at the cell surface. Published work has shown that retention of the adhesins occurs via a post-translational mechanism involving the cyclic-di-GMP receptor LapD and the protease LapG. However, little is known about the underlying mechanisms that regulate the production of these adhesins. Here, we demonstrate that the master regulator FleQ modulates biofilm formation by post-transcriptionally regulating the production of LapA and MapA. We find that a Δ fleQ mutant has a biofilm formation defect compared to the WT strain, which is attributed in part to a decrease in LapA and MapA production, despite the Δ fleQ mutant having increased levels of lapA and mapA transcripts compared to the WT strain. Through transposon mutagenesis and subsequent genetic analysis, we found that over-stimulation of the Gac/Rsm pathway partially rescues biofilm formation in the Δ fleQ mutant background. Collectively, these findings provide evidence that FleQ regulates biofilm formation by post-transcriptionally regulating the production of LapA and MapA, and that activation of the Gac/Rsm pathway can enhance biofilm formation by P. fluorescens . Importance Biofilm formation is a highly coordinated process that bacteria undergo to colonize a variety of surfaces. For Pseudomonas fluorescens , biofilm formation requires the production and localization of RTX adhesins to the cell surface. To date, little is known about the underlying mechanisms that regulate biofilm formation by P. fluorescens . Here, we identify FleQ as a key regulator of biofilm formation that modulates the production of LapA and MapA through a post-transcriptional mechanism. We provide further evidence implicating activation of the Gac/Rsm system in FleQ-dependent regulation of biofilm formation. Together, our findings uncover evidence for a mechanism of post-transcriptional regulation of the LapA/MapA adhesins.
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Affiliation(s)
- Alexander B. Pastora
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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7
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Wang J, Wang Y, Lou H, Wang W. AlgU controls environmental stress adaptation, biofilm formation, motility, pyochelin synthesis and antagonism potential in Pseudomonas protegens SN15-2. Microbiol Res 2023; 272:127396. [PMID: 37141849 DOI: 10.1016/j.micres.2023.127396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
Pseudomonas protegens is a typical plant-growth-promoting rhizobacterium that can serve as an agricultural biocontrol agent. The extracytoplasmic function (ECF) sigma factor AlgU is a global transcription regulator controlling stress adaption and virulence in Pseudomonas aeruginosa and Pseudomonas syringae. Meanwhile, the regulatory role of AlgU in the biocontrol ability of P.protegens has been poorly studied. In this study, deletion mutations of algU and its antagonist coding gene mucA were constructed to investigate the function of AlgU in P.protegens SN15-2 via phenotypic experiment and transcriptome sequencing analysis. On the basis of phenotypic analyses, it was concluded that the AlgU whose transcription was induced by osmotic stress and oxidative stress positively regulated biofilm formation and tolerance towards osmotic, heat, and oxidation stresses, while it negatively regulated motility, pyochelin synthesis, and the ability to inhibit pathogens. On the basis of the RNA-seq analysis, compared to the wild-type strain, 12 genes were significantly upregulated and 77 genes were significantly downregulated in ΔalgU, while 407 genes were significantly upregulated and 279 genes were significantly downregulated in ΔmucA, indicating the involvement of AlgU in several cellular processes, mainly related to resistance, carbohydrate metabolism, membrane formation, alginate production, the type VI secretion system, flagella motility and pyochelin production. Our findings provide insights into the important role of AlgU of P.protegens in biocontrol, which is of value in improving the biocontrol ability of P.protegens.
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Affiliation(s)
- Jian Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yaping Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Haibo Lou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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8
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Jia X, Pan Z, Yuan Y, Luo B, Luo Y, Mukherjee S, Jia G, Liu L, Ling X, Yang X, Miao Z, Wei X, Bujnicki JM, Zhao K, Su Z. Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence. Cell Res 2023; 33:328-330. [PMID: 36828938 PMCID: PMC10066318 DOI: 10.1038/s41422-023-00786-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Affiliation(s)
- Xinyu Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhiling Pan
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yang Yuan
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Liu Liu
- Department of Conservative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Zhichao Miao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
| | - Xiawei Wei
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109, Warsaw, Poland
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Wen J, Liao L, Duan Z, Su S, Zhang J, Chen B. Identification and Regulatory Roles of a New Csr Small RNA from Arctic Pseudoalteromonas fuliginea BSW20308 in Temperature Responses. Microbiol Spectr 2023; 11:e0409422. [PMID: 36625662 PMCID: PMC9927453 DOI: 10.1128/spectrum.04094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Small RNAs (sRNAs) play a very important role in gene regulation at the posttranscriptional level. However, sRNAs from nonmodel microorganisms, extremophiles in particular, have been rarely explored. We discovered a putative sRNA, termed Pf1 sRNA, in Pseudoalteromonas fuliginea BSW20308 isolated from the polar regions in our previous work. In this study, we identified the sRNA and investigated its regulatory role in gene expression under different temperatures. Pf1 sRNA was confirmed to be a new member of the CsrB family but has little sequence similarity with Escherichia coli CsrB. However, Pf1 sRNA was able to bind to CsrA from E. coli and P. fuliginea BSW20308 to regulate glycogen synthesis. The Pf1 sRNA knockout strain (ΔPf1) affected motility, fitness, and global gene expression in transcriptomes and proteomes at 4°C and 32°C. Genes related to carbon metabolism, amino acid metabolism, salinity tolerance, antibiotic resistance, oxidative stress, motility, chemotaxis, biofilm, and secretion systems were differentially expressed in the wild-type strain and the ΔPf1 mutant. Our study suggested that Pf1 sRNA might play an important role in response to environmental changes by regulating global gene expression. Specific targets of the Pf1 sRNA-CsrA system were tentatively proposed, such as genes involved in the type VI secretion system, TonB-dependent receptors, and response regulators, but most of them have an unknown function. Since this is the first study of CsrB family sRNA in Pseudoalteromonas and microbes from the polar regions, it provides a novel insight at the posttranscriptional level into the responses and adaptation to temperature changes in bacteria from extreme environments. This study also sheds light on the evolution of sRNA in extreme environments and expands the bacterial sRNA database. IMPORTANCE Previous research on microbial temperature adaptation has focused primarily on functional genes, with little attention paid to posttranscriptional regulation. Small RNAs, the major posttranscriptional modulators of gene expression, are greatly underexplored, especially in nonpathogenic and nonmodel microorganisms. In this study, we verified the first Csr sRNA, named Pf1 sRNA, from Pseudoalteromonas, a model genus for studying cold adaptation. We revealed that Pf1 sRNA played an important role in global regulation and was indispensable in improving fitness. This study provided us a comprehensive view of sRNAs from Pseudoalteromonas and expanded our understanding of bacterial sRNAs from extreme environments.
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Affiliation(s)
- Jiao Wen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Li Liao
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, China
| | - Zedong Duan
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Shiyuan Su
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Jin Zhang
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
| | - Bo Chen
- Key Laboratory for Polar Science, Ministry of Natural Resources, Polar Research Institute of China, Shanghai, China
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10
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Regulatory Landscape of the Pseudomonas aeruginosa Phosphoethanolamine Transferase Gene eptA in the Context of Colistin Resistance. Antibiotics (Basel) 2023; 12:antibiotics12020200. [PMID: 36830112 PMCID: PMC9952513 DOI: 10.3390/antibiotics12020200] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa has the genetic potential to acquire colistin resistance through the modification of lipopolysaccharide by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) or phosphoethanolamine (PEtN), mediated by the arn operon or the eptA gene, respectively. However, in vitro evolution experiments and genetic analysis of clinical isolates indicate that lipopolysaccharide modification with L-Ara4N is invariably preferred over PEtN addition as the colistin resistance mechanism in this bacterium. Since little is known about eptA regulation in P. aeruginosa, we generated luminescent derivatives of the reference strain P. aeruginosa PAO1 to monitor arn and eptA promoter activity. We performed transposon mutagenesis assays to compare the likelihood of acquiring mutations leading to arn or eptA induction and to identify eptA regulators. The analysis revealed that eptA was slightly induced under certain stress conditions, such as arginine or biotin depletion and accumulation of the signal molecule diadenosine tetraphosphate, but the induction did not confer colistin resistance. Moreover, we demonstrated that spontaneous mutations leading to colistin resistance invariably triggered arn rather than eptA expression, and that eptA was not induced in resistant mutants upon colistin exposure. Overall, these results suggest that the contribution of eptA to colistin resistance in P. aeruginosa may be limited by regulatory restraints.
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11
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Lin J, Yang J, Cheng J, Zhang W, Yang X, Ding W, Zhang H, Wang Y, Shen X. Pseudomonas aeruginosa H3-T6SS Combats H 2O 2 Stress by Diminishing the Amount of Intracellular Unincorporated Iron in a Dps-Dependent Manner and Inhibiting the Synthesis of PQS. Int J Mol Sci 2023; 24:1614. [PMID: 36675127 PMCID: PMC9866239 DOI: 10.3390/ijms24021614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
The type VI secretion system (T6SS), a protein translocation nanomachine, is widely distributed in Gram-negative bacteria and delivers effectors directly into target cells or the extracellular environment to help the bacteria gain a competitive fitness advantage and promote bacterial survival in harmful environments. In this study, we demonstrated that the synthesis of the Pseudomonas quinolone signal (PQS) in Pseudomonas aeruginosa PAO1 was inhibited by the H3-T6SS gene cluster under iron-rich conditions, and that this inhibition was relieved under iron starvation conditions. Conversely, PQS differentially regulated the expression of the H3-T6SS structural genes and the effector protein gene tseF. The expression of tseF was inhibited by PQS, while the expressions of the H3-T6SS structural genes were positively regulated by PQS. Further studies showed that the H3-T6SS was involved in the resistance of P. aeruginosa to oxidative stress caused by hydrogen peroxide (H2O2). Interestingly, H3-T6SS expression was neither induced by H2O2 stress nor regulated by OxyR (a global anti-oxidative transcriptional regulator) but was positively regulated by RpoS (a major transcription regulator of the stress response). In addition, we found that the clpV3 (a structural gene of H3-T6SS) mutation resulted in upregulation of two proteins related to PQS synthesis and many proteins related to oxidative stress resistance, while the expression of some iron storage proteins, especially Dps, were significantly downregulated. Furthermore, the clpV3 mutation led to an increase in the intracellular free Fe2+ content of P. aeruginosa. Further studies showed that both the PQS deficient mutation and overexpression of dps effectively restored the H2O2 sensitive phenotype of the H3-T6SS mutant. Finally, we proposed the following model of H3-T6SS-mediated resistance to H2O2 stress in P. aeruginosa. H3-T6SS not only reduces the intracellular free Fe2+ level by upregulating the expression of ferritin Dps, but also inhibits the synthesis of PQS to mediate the resistance of P. aeruginosa to H2O2 stress. This study highlights the important role of H3-T6SS in the ability of P. aeruginosa to combat H2O2 stress and provides a perspective for understanding the stress response mechanism of bacteria.
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Affiliation(s)
- Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan’an University, Yan’an 716000, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jianshe Yang
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Juanli Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Xu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Wei Ding
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Heng Zhang
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, China
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12
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Liu P, Yue C, Liu L, Gao C, Lyu Y, Deng S, Tian H, Jia X. The function of small RNA in Pseudomonas aeruginosa. PeerJ 2022; 10:e13738. [PMID: 35891650 PMCID: PMC9308961 DOI: 10.7717/peerj.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/25/2022] [Indexed: 01/17/2023] Open
Abstract
Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies.
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Affiliation(s)
- Pei Liu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Changwu Yue
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Lihua Liu
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Can Gao
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Yuhong Lyu
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Shanshan Deng
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Hongying Tian
- Yan’an University, Key Laboratory of Microbial Drugs Innovation and Transformation, Yan’an, Shaanxi, China
| | - Xu Jia
- Chengdu Medical College, Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu, Sichuan, China,School of Basic Medical Science, Chengdu Medical College, Chengdu, Sichuan, China
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13
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Yu X, Meng C, Tan X, Su Y, Cao Z, Hwang TS, Li L. RsmA3 modulates RpoS through the RetS-Gac-Rsm signaling pathway in response to H 2 O 2 stress in the phytopathogen Pseudomonas syringae. Environ Microbiol 2022; 24:4755-4770. [PMID: 35837862 DOI: 10.1111/1462-2920.16132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/27/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species are a fatal challenge to the plant pathogenic bacterium Pseudomonas syringae. In this study, we reveal that the global regulatory protein RsmA3 from the RetS-Gac/Rsm signaling pathway modulates RpoS in the early-log growth phase in the P. syringae wild-type strain MB03, thereby regulating oxidative tolerance to H2 O2 and ultimately affecting pathogenicity to the host plant. Following increased H2 O2 by external addition or endogenous induction by menadione, the resistance of the mutant strain ΔretS to H2 O2 is significantly enhanced due to rapid increases in the transcription of Rsm-related non-coding small RNAs (nc sRNAs), a sigma factor RpoS, and H2 O2 -detoxifying enzymes. Moreover, the ΔretS mutant is significantly less pathogenic in cucumber leaves. Seven Rsm-related nc sRNAs (namely, rsmZ, rsmY, and rsmX1-5 ) show functional redundancy in the RetS-Gac-Rsm signaling pathway. External addition of H2 O2 stimulates increases in the transcription of both rsmY and rsmZ. Thus, we propose a regulatory model of the RetS-Gac-Rsm signaling pathway in P. syringae MB03 for the regulation of H2 O2 tolerance and phytopathogenicity in the host plant.
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Affiliation(s)
- Xun Yu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Cui Meng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Xiaocheng Tan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Yuwei Su
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Zhiping Cao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
| | - Tzann-Shun Hwang
- Graduate Institute of Biotechnology, Chinese Culture University, Taipei, Taiwan
| | - Lin Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agriculture University, Wuhan, PR China
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14
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RetS Regulates Phage Infection in Pseudomonas aeruginosa via Modulating the GacS/GacA Two-Component System. J Virol 2022; 96:e0019722. [PMID: 35348363 DOI: 10.1128/jvi.00197-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In Pseudomonas aeruginosa, the complex multisensing regulatory networks RetS-GacS/GacA have been demonstrated to play key roles in controlling the switch between planktonic and sessile lifestyles. However, whether this multisensing system is involved in the regulation of phage infection has not been investigated. Here, we provide a link between the sensors RetS/GacS and infection of phages vB_Pae_QDWS and vB_Pae_W3. Our data suggest that the sensors kinases RetS and GacS in Pseudomonas aeruginosa play opposite regulatory functions on phage infection. Mutation in retS increased phage resistance. Cellular levels of RsmY and RsmZ increased in PaΔretS and were positively correlated with phage resistance. Further analysis demonstrated that RetS regulated phage infection by affecting the type IV pilus (T4P)-mediated adsorption. The regulation of RetS on phage infection depends on the GacS/GacA two-component system and is likely a dynamic process in response to environmental signals. The findings offer additional support for the rapid emergence of phage resistance. IMPORTANCE Our knowledge on the molecular mechanisms behind bacterium-phage interactions remains limited. Our study reported that the complex multisensing regulatory networks RetS-GacS/GacA of Pseudomonas aeruginosa PAO1 play key roles in controlling phage infection. The main observation was that the mutation in RetS could result in increased phage resistance by reducing the type IV pilus-mediated phage adsorption. The bacterial defense strategy is generally applicable to various phages since many P. aeruginosa phages can use type IV pilus as their receptors. The results also suggest that the phage infection is likely to be regulated dynamically, which depends on the environmental stimuli. Reduction of the signals that RetS favors would increase phage resistance. Our study is particularly remarkable for uncovering a signal transduction system that was involved in phage infection, which may help in filling some knowledge gaps in this field.
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15
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Hendrix H, Zimmermann-Kogadeeva M, Zimmermann M, Sauer U, De Smet J, Muchez L, Lissens M, Staes I, Voet M, Wagemans J, Ceyssens PJ, Noben JP, Aertsen A, Lavigne R. Metabolic reprogramming of Pseudomonas aeruginosa by phage-based quorum sensing modulation. Cell Rep 2022; 38:110372. [PMID: 35172131 DOI: 10.1016/j.celrep.2022.110372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/29/2021] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
The Pseudomonas quinolone signal (PQS) is a multifunctional quorum sensing molecule of key importance to P. aeruginosa. Here, we report that the lytic Pseudomonas bacterial virus LUZ19 targets this population density-dependent signaling system by expressing quorum sensing targeting protein (Qst) early during infection. We demonstrate that Qst interacts with PqsD, a key host quinolone signal biosynthesis pathway enzyme, resulting in decreased levels of PQS and its precursor 2-heptyl-4(1H)-quinolone. The lack of a functional PqsD enzyme impairs LUZ19 infection but is restored by external supplementation of 2-heptyl-4(1H)-quinolone, suggesting that LUZ19 exploits the PQS system for successful infection. We establish a broad functional interaction network of Qst, which includes enzymes of cofactor biosynthesis pathways (CoaC/ThiD) and a non-ribosomal peptide synthetase pathway (PA1217). Qst therefore represents an exquisite example of intricate reprogramming of the bacterium by a phage, which may be further exploited as tool to combat antibiotic resistant bacterial pathogens.
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Affiliation(s)
- Hanne Hendrix
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | | | - Michael Zimmermann
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Jeroen De Smet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Laurens Muchez
- Centre for Surface Chemistry and Catalysis, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Maries Lissens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Ines Staes
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, KU Leuven, 3001 Heverlee, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, 3001 Heverlee, Belgium.
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16
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Spinnato MC, Lo Sciuto A, Mercolino J, Lucidi M, Leoni L, Rampioni G, Visca P, Imperi F. Effect of a Defective Clamp Loader Complex of DNA Polymerase III on Growth and SOS Response in Pseudomonas aeruginosa. Microorganisms 2022; 10:423. [PMID: 35208877 PMCID: PMC8879598 DOI: 10.3390/microorganisms10020423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
DNA polymerase III (Pol III) is the replicative enzyme in bacteria. It consists of three subcomplexes, the catalytic core, the β clamp, and the clamp loader. While this complex has been thoroughly characterized in the model organism Escherichia coli, much less is known about its functioning and/or its specific properties in other bacteria. Biochemical studies highlighted specific features in the clamp loader subunit ψ of Pseudomonas aeruginosa as compared to its E. coli counterpart, and transposon mutagenesis projects identified the ψ-encoding gene holD among the strictly essential core genes of P. aeruginosa. By generating a P. aeruginosa holD conditional mutant, here we demonstrate that, as previously observed for E. coli holD mutants, HolD-depleted P. aeruginosa cells show strongly decreased growth, induction of the SOS response, and emergence of suppressor mutants at high frequency. However, differently from what was observed in E. coli, the growth of P. aeruginosa cells lacking HolD cannot be rescued by the deletion of genes for specialized DNA polymerases. We also observed that the residual growth of HolD-depleted cells is strictly dependent on homologous recombination functions, suggesting that recombination-mediated rescue of stalled replication forks is crucial to support replication by a ψ-deficient Pol III enzyme in P. aeruginosa.
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Affiliation(s)
- Maria Concetta Spinnato
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
| | - Alessandra Lo Sciuto
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
| | - Jessica Mercolino
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
| | - Massimiliano Lucidi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
| | - Livia Leoni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
| | - Giordano Rampioni
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Rome, Italy; (M.C.S.); (A.L.S.); (J.M.); (M.L.); (L.L.); (G.R.); (P.V.)
- IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
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17
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Katsuya-Gaviria K, Paris G, Dendooven T, Bandyra KJ. Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism. RNA Biol 2021; 19:419-436. [PMID: 35438047 PMCID: PMC9037510 DOI: 10.1080/15476286.2022.2048565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/26/2022] [Indexed: 11/02/2022] Open
Abstract
In all domains of life, RNA chaperones safeguard and guide the fate of the cellular RNA pool. RNA chaperones comprise structurally diverse proteins that ensure proper folding, stability, and ribonuclease resistance of RNA, and they support regulatory activities mediated by RNA. RNA chaperones constitute a topologically diverse group of proteins that often present an unstructured region and bind RNA with limited nucleotide sequence preferences. In bacteria, three main proteins - Hfq, ProQ, and CsrA - have been shown to regulate numerous complex processes, including bacterial growth, stress response and virulence. Hfq and ProQ have well-studied activities as global chaperones with pleiotropic impact, while CsrA has a chaperone-like role with more defined riboregulatory function. Here, we describe relevant novel insights into their common features, including RNA binding properties, unstructured domains, and interplay with other proteins important to RNA metabolism.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CambridgeCB2 1GA, UK
| | - Giulia Paris
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CambridgeCB2 1GA, UK
| | - Tom Dendooven
- Department of Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Katarzyna J. Bandyra
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089Warsaw, Poland
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18
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Alvarez AF, Rodríguez C, González-Chávez R, Georgellis D. The Escherichia coli two-component signal sensor BarA binds protonated acetate via a conserved hydrophobic-binding pocket. J Biol Chem 2021; 297:101383. [PMID: 34743001 PMCID: PMC8639471 DOI: 10.1016/j.jbc.2021.101383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/11/2022] Open
Abstract
The BarA/UvrY two-component signal transduction system is widely conserved in γ-proteobacteria and provides a link between the metabolic state of the cells and the Csr posttranscriptional regulatory system. In Escherichia coli, the BarA/UvrY system responds to the presence of acetate and other short-chain carboxylic acids by activating transcription of the noncoding RNAs, CsrB and CsrC, which sequester the RNA-binding protein CsrA, a global regulator of gene expression. However, the state of the carboxyl group in the acetate molecule, which serves as the BarA stimulus, and the signal reception site of BarA remain unknown. In this study, we show that the deletion or replacement of the periplasmic domain of BarA and also the substitution of certain hydroxylated and hydrophobic amino acid residues in this region, result in a sensor kinase that remains unresponsive to its physiological stimulus, demonstrating that the periplasmic region of BarA constitutes a functional detector domain. Moreover, we provide evidence that the protonated state of acetate or formate serves as the physiological stimulus of BarA. In addition, modeling of the BarA sensor domain and prediction of the signal-binding site, by blind molecular docking, revealed a calcium channels and chemotaxis receptors domain with a conserved binding pocket, which comprised uncharged polar and hydrophobic amino acid residues. Based on the comparative sequence and phylogenetic analyses, we propose that, at least, two types of BarA orthologues diverged and evolved separately to acquire distinct signal-binding properties, illustrating the wide adaptability of the bacterial sensor kinase proteins.
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Affiliation(s)
- Adrián F Alvarez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Claudia Rodríguez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Ricardo González-Chávez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Dimitris Georgellis
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México.
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19
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Ferreiro MD, Behrmann LV, Corral A, Nogales J, Gallegos MT. Exploring the expression and functionality of the rsm sRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biol 2021; 18:1818-1833. [PMID: 33406981 PMCID: PMC8583166 DOI: 10.1080/15476286.2020.1871217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/08/2020] [Accepted: 12/29/2020] [Indexed: 12/18/2022] Open
Abstract
The Gac-rsm pathway is a global regulatory network that governs mayor lifestyle and metabolic changes in gamma-proteobacteria. In a previous study, we uncovered the role of CsrA proteins promoting growth and repressing motility, alginate production and virulence in the model phytopathogen Pseudomonas syringae pv. tomato (Pto) DC3000. Here, we focus on the expression and regulation of the rsm regulatory sRNAs, since Pto DC3000 exceptionally has seven variants (rsmX1-5, rsmY and rsmZ). The presented results offer further insights into the functioning of the complex Gac-rsm pathway and the interplay among its components. Overall, rsm expressions reach maximum levels at high cell densities, are unaffected by surface detection, and require GacA for full expression. The rsm levels of expression and GacA-dependence are determined by the sequences found in their -35/-10 promoter regions and GacA binding boxes, respectively. rsmX5 stands out for being the only rsm in Pto DC3000 whose high expression does not require GacA, constituting the main component of the total rsm pool in a gacA mutant. The deletion of rsmY and rsmZ had minor effects on Pto DC3000 motility and virulence phenotypes, indicating that rsmX1-5 can functionally replace them. On the other hand, rsmY or rsmZ overexpression in a gacA mutant did not revert its phenotype. Additionally, a negative feedback regulatory loop in which the CsrA3 protein promotes its own titration by increasing the levels of several rsm RNAs in a GacA-dependent manner has been disclosed as part of this work.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Lara Vanessa Behrmann
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Ana Corral
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - Joaquina Nogales
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental Del Zaidín (EEZ-CSIC), Granada, Spain
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20
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Hall JPJ, Wright RCT, Harrison E, Muddiman KJ, Wood AJ, Paterson S, Brockhurst MA. Plasmid fitness costs are caused by specific genetic conflicts enabling resolution by compensatory mutation. PLoS Biol 2021; 19:e3001225. [PMID: 34644303 PMCID: PMC8544851 DOI: 10.1371/journal.pbio.3001225] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 10/25/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmids play an important role in bacterial genome evolution by transferring genes between lineages. Fitness costs associated with plasmid carriage are expected to be a barrier to gene exchange, but the causes of plasmid fitness costs are poorly understood. Single compensatory mutations are often sufficient to completely ameliorate plasmid fitness costs, suggesting that such costs are caused by specific genetic conflicts rather than generic properties of plasmids, such as their size, metabolic burden, or gene expression level. By combining the results of experimental evolution with genetics and transcriptomics, we show here that fitness costs of 2 divergent large plasmids in Pseudomonas fluorescens are caused by inducing maladaptive expression of a chromosomal tailocin toxin operon. Mutations in single genes unrelated to the toxin operon, and located on either the chromosome or the plasmid, ameliorated the disruption associated with plasmid carriage. We identify one of these compensatory loci, the chromosomal gene PFLU4242, as the key mediator of the fitness costs of both plasmids, with the other compensatory loci either reducing expression of this gene or mitigating its deleterious effects by up-regulating a putative plasmid-borne ParAB operon. The chromosomal mobile genetic element Tn6291, which uses plasmids for transmission, remained up-regulated even in compensated strains, suggesting that mobile genetic elements communicate through pathways independent of general physiological disruption. Plasmid fitness costs caused by specific genetic conflicts are unlikely to act as a long-term barrier to horizontal gene transfer (HGT) due to their propensity for amelioration by single compensatory mutations, helping to explain why plasmids are so common in bacterial genomes.
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Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C. T. Wright
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Katie J. Muddiman
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - A. Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Steve Paterson
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Michael A. Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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21
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Liu K, Li L, Yao W, Wang W, Huang Y, Wang R, Li P. Genetic engineering of Pseudomonas chlororaphis Lzh-T5 to enhance production of trans-2,3-dihydro-3-hydroxyanthranilic acid. Sci Rep 2021; 11:16451. [PMID: 34385485 PMCID: PMC8361184 DOI: 10.1038/s41598-021-94674-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) is a cyclic β-amino acid used for the synthesis of non-natural peptides and chiral materials. And it is an intermediate product of phenazine production in Pseudomonas spp. Lzh-T5 is a P. chlororaphis strain isolated from tomato rhizosphere found in China. It can synthesize three antifungal phenazine compounds. Disruption the phzF gene of P. chlororaphis Lzh-T5 results in DHHA accumulation. Several strategies were used to improve production of DHHA: enhancing the shikimate pathway by overexpression, knocking out negative regulatory genes, and adding metal ions to the medium. In this study, three regulatory genes (psrA, pykF, and rpeA) were disrupted in the genome of P. chlororaphis Lzh-T5, yielding 5.52 g/L of DHHA. When six key genes selected from the shikimate, pentose phosphate, and gluconeogenesis pathways were overexpressed, the yield of DHHA increased to 7.89 g/L. Lastly, a different concentration of Fe3+ was added to the medium for DHHA fermentation. This genetically engineered strain increased the DHHA production to 10.45 g/L. According to our result, P. chlororaphis Lzh-T5 could be modified as a microbial factory to produce DHHA. This study laid a good foundation for the future industrial production and application of DHHA.
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Affiliation(s)
- Kaiquan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Ling Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, People's Republic of China.
| | - Wentao Yao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Yujie Huang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
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22
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A Complex of LaoA and LaoB Acts as a Tat-Dependent Dehydrogenase for Long-Chain Alcohols in Pseudomonas aeruginosa. Appl Environ Microbiol 2021; 87:e0076221. [PMID: 34085859 DOI: 10.1128/aem.00762-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa can utilize unusual carbon sources, like sodium dodecyl sulfate (SDS) and alkanes. Whereas the initiating enzymatic steps of the corresponding degradation pathways have been characterized in detail, the oxidation of the emerging long-chain alcohols has received little attention. Recently, the genes for the Lao (long-chain-alcohol/aldehyde oxidation) system were discovered to be involved in the oxidation of long-chain alcohols derived from SDS and alkane degradation. In the Lao system, LaoA is predicted to be an alcohol dehydrogenase/oxidase; however, according to genetic studies, efficient long-chain-alcohol oxidation additionally required the Tat-dependent protein LaoB. In the present study, the Lao system was further characterized. In vivo analysis revealed that the Lao system complements the substrate spectrum of the well-described Exa system, which is required for growth with ethanol and other short-chain alcohols. Mutational analysis revealed that the Tat site of LaoB was required for long-chain-alcohol oxidation activity, strongly suggesting a periplasmic localization of the complex. Purified LaoA was fully active only when copurified with LaoB. Interestingly, in vitro activity of the purified LaoAB complex also depended on the presence of the Tat site. The copurified LaoAB complex contained a flavin cofactor and preferentially oxidized a range of saturated, unbranched primary alcohols. Furthermore, the LaoAB complex could reduce cytochrome c550-type redox carriers like ExaB, a subunit of the Exa alcohol dehydrogenase system. LaoAB complex activity was stimulated by rhamnolipids in vitro. In summary, LaoAB constitutes an unprecedented protein complex with specific properties apparently required for oxidizing long-chain alcohols. IMPORTANCE Pseudomonas aeruginosa is a major threat to public health. Its ability to thrive in clinical settings, water distribution systems, or even jet fuel tanks is linked to detoxification and degradation of diverse hydrophobic substrates that are metabolized via alcohol intermediates. Our study illustrates a novel flavoprotein long-chain-alcohol dehydrogenase consisting of a facultative two-subunit complex, which is unique among related enzymes, while the homologs of the corresponding genes are found in numerous bacterial genomes. Understanding the catalytic and compartmentalization processes involved is of great interest for biotechnological and hygiene research, as it may be a potential starting point for rationally designing novel antibacterial substances with high specificity against this opportunistic pathogen.
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Li E, Zhang H, Jiang H, Pieterse CMJ, Jousset A, Bakker PAHM, de Jonge R. Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens. mBio 2021; 12:e0092721. [PMID: 34101491 PMCID: PMC8262913 DOI: 10.1128/mbio.00927-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics have led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges, such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant/one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining the finding that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. All together, these results underscore the strength of experimental evolution in identifying key genes, pathways, and processes for bacterial rhizosphere colonization and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. IMPORTANCE Beneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We found that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility, accumulate in parallel, emphasizing these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. All together, our results demonstrate the power of experimental evolution in identifying key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.
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Affiliation(s)
- Erqin Li
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Henan Jiang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Ecology and Biodiversity, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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Wang Z, Huang X, Jan M, Kong D, Wang W, Zhang X. Lon protease downregulates phenazine-1-carboxamide biosynthesis by degrading the quorum sensing signal synthase PhzI and exhibits negative feedback regulation of Lon itself in Pseudomonas chlororaphis HT66. Mol Microbiol 2021; 116:690-706. [PMID: 34097792 DOI: 10.1111/mmi.14764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
Pseudomonas chlororaphis HT66 exhibits strong antagonistic activity against various phytopathogenic fungi due to its main antibiotic phenazine-1-carboxamide (PCN). PCN gene cluster consists of phzABCDEFG, phzH, phzI, and phzR operons. phzABCDEFG transcription is activated by the PhzI/R quorum sensing system. Deletion of the lon gene encoding an ATP-dependent protease resulted in significant enhancement of PCN production in strain HT66. However, the regulatory pathway and mechanism of Lon on PCN biosynthesis remain unknown. Here, lon mutation was shown to significantly improve antimicrobial activity of strain HT66. The N-acyl-homoserine lactone synthase PhzI mediates the negative regulation of PCN biosynthesis and phzABCDEFG transcription by Lon. Western blot showed that PhzI protein abundance and stability were significantly enhanced by lon deletion. The in vitro degradation assay suggested that Lon could directly degrade PhzI protein. However, Lon with an amino acid replacement (S674 -A) could not degrade PhzI protein. Lon-recognized region was located within the first 50 amino acids of PhzI. In addition, Lon formed a new autoregulatory feedback circuit to modulate its own degradation by other potential proteases. In summary, we elucidated the Lon-regulated pathway mediated by PhzI during PCN biosynthesis and the molecular mechanism underlying the degradation of PhzI by Lon in P. chlororaphis HT66.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xianqing Huang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Malik Jan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Deyu Kong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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25
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O’Malley MR, Anderson JC. Regulation of the Pseudomonas syringae Type III Secretion System by Host Environment Signals. Microorganisms 2021; 9:microorganisms9061227. [PMID: 34198761 PMCID: PMC8228185 DOI: 10.3390/microorganisms9061227] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Pseudomonas syringae are Gram-negative, plant pathogenic bacteria that use a type III secretion system (T3SS) to disarm host immune responses and promote bacterial growth within plant tissues. Despite the critical role for type III secretion in promoting virulence, T3SS-encoding genes are not constitutively expressed by P. syringae and must instead be induced during infection. While it has been known for many years that culturing P. syringae in synthetic minimal media can induce the T3SS, relatively little is known about host signals that regulate the deployment of the T3SS during infection. The recent identification of specific plant-derived amino acids and organic acids that induce T3SS-inducing genes in P. syringae has provided new insights into host sensing mechanisms. This review summarizes current knowledge of the regulatory machinery governing T3SS deployment in P. syringae, including master regulators HrpRS and HrpL encoded within the T3SS pathogenicity island, and the environmental factors that modulate the abundance and/or activity of these key regulators. We highlight putative receptors and regulatory networks involved in linking the perception of host signals to the regulation of the core HrpRS–HrpL pathway. Positive and negative regulation of T3SS deployment is also discussed within the context of P. syringae infection, where contributions from distinct host signals and regulatory networks likely enable the fine-tuning of T3SS deployment within host tissues. Last, we propose future research directions necessary to construct a comprehensive model that (a) links the perception of host metabolite signals to T3SS deployment and (b) places these host–pathogen signaling events in the overall context of P. syringae infection.
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26
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Ortet P, Fochesato S, Bitbol AF, Whitworth DE, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M. Evolutionary history expands the range of signaling interactions in hybrid multikinase networks. Sci Rep 2021; 11:11763. [PMID: 34083699 PMCID: PMC8175716 DOI: 10.1038/s41598-021-91260-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions (‘phylogenetic promiscuity’). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS–GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.
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Affiliation(s)
- Philippe Ortet
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Sylvain Fochesato
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Anne-Florence Bitbol
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin (UMR8237), Sorbonne Université, 75005, Paris, France.,Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - David E Whitworth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, SY23 3DD, UK
| | - David Lalaouna
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.,CNRS, ARN UPR 9002, Université de Strasbourg, 67000, Strasbourg, France
| | - Catherine Santaella
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Thierry Heulin
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Wafa Achouak
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France
| | - Mohamed Barakat
- Aix Marseille Univ, CEA, CNRS, BIAM, LEMIRE, 13108, Saint Paul-Lez-Durance, France.
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27
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Ferreiro MD, Gallegos MT. Distinctive features of the Gac-Rsm pathway in plant-associated Pseudomonas. Environ Microbiol 2021; 23:5670-5689. [PMID: 33939255 DOI: 10.1111/1462-2920.15558] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 02/04/2023]
Abstract
Productive plant-bacteria interactions, either beneficial or pathogenic, require that bacteria successfully sense, integrate and respond to continuously changing environmental and plant stimuli. They use complex signal transduction systems that control a vast array of genes and functions. The Gac-Rsm global regulatory pathway plays a key role in controlling fundamental aspects of the apparently different lifestyles of plant beneficial and phytopathogenic Pseudomonas as it coordinates adaptation and survival while either promoting plant health (biocontrol strains) or causing disease (pathogenic strains). Plant-interacting Pseudomonas stand out for possessing multiple Rsm proteins and Rsm RNAs, but the physiological significance of this redundancy is not yet clear. Strikingly, the components of the Gac-Rsm pathway and the controlled genes/pathways are similar, but the outcome of its regulation may be opposite. Therefore, identifying the target mRNAs bound by the Rsm proteins and their mode of action (repression or activation) is essential to explain the resulting phenotype. Some technical considerations to approach the study of this system are also given. Overall, several important features of the Gac-Rsm cascade are now understood in molecular detail, particularly in Pseudomonas protegens CHA0, but further questions remain to be solved in other plant-interacting Pseudomonas.
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Affiliation(s)
- María-Dolores Ferreiro
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
| | - María-Trinidad Gallegos
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ-CSIC), Granada, Spain
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28
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De Smet J, Wagemans J, Hendrix H, Staes I, Visnapuu A, Horemans B, Aertsen A, Lavigne R. Bacteriophage-mediated interference of the c-di-GMP signalling pathway in Pseudomonas aeruginosa. Microb Biotechnol 2021; 14:967-978. [PMID: 33314648 PMCID: PMC8085984 DOI: 10.1111/1751-7915.13728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/19/2020] [Accepted: 11/22/2020] [Indexed: 01/10/2023] Open
Abstract
C-di-GMP is a key signalling molecule which impacts bacterial motility and biofilm formation and is formed by the condensation of two GTP molecules by a diguanylate cyclase. We here describe the identification and characterization of a family of bacteriophage-encoded peptides that directly impact c-di-GMP signalling in Pseudomonas aeruginosa. These phage proteins target Pseudomonas diguanylate cyclase YfiN by direct protein interaction (termed YIPs, YfiN Interacting Peptides). YIPs induce an increase of c-di-GMP production in the host cell, resulting in a decrease in motility and an increase in biofilm mass in P. aeruginosa. A dynamic analysis of the biofilm morphology indicates a denser biofilm structure after induction of the phage protein. This intracellular signalling interference strategy by a lytic phage constitutes an unexplored phage-based mechanism of metabolic regulation and could potentially serve as inspiration for the development of molecules that interfere with biofilm formation in P. aeruginosa and other pathogens.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
- Present address:
Lab4FoodDepartment of Microbial and Molecular Systems (M2S)KU Leuven Campus GeelGeel2440Belgium
| | - Jeroen Wagemans
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Hanne Hendrix
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Ines Staes
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Annegrete Visnapuu
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Benjamin Horemans
- Department of Earth and Environmental SciencesKU LeuvenHeverlee3001Belgium
| | - Abram Aertsen
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Rob Lavigne
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
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Biessy A, Filion M. Phloroglucinol Derivatives in Plant-Beneficial Pseudomonas spp.: Biosynthesis, Regulation, and Functions. Metabolites 2021; 11:metabo11030182. [PMID: 33804595 PMCID: PMC8003664 DOI: 10.3390/metabo11030182] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Plant-beneficial Pseudomonas spp. aggressively colonize the rhizosphere and produce numerous secondary metabolites, such as 2,4-diacetylphloroglucinol (DAPG). DAPG is a phloroglucinol derivative that contributes to disease suppression, thanks to its broad-spectrum antimicrobial activity. A famous example of this biocontrol activity has been previously described in the context of wheat monoculture where a decline in take-all disease (caused by the ascomycete Gaeumannomyces tritici) has been shown to be associated with rhizosphere colonization by DAPG-producing Pseudomonas spp. In this review, we discuss the biosynthesis and regulation of phloroglucinol derivatives in the genus Pseudomonas, as well as investigate the role played by DAPG-producing Pseudomonas spp. in natural soil suppressiveness. We also tackle the mode of action of phloroglucinol derivatives, which can act as antibiotics, signalling molecules and, in some cases, even as pathogenicity factors. Finally, we discuss the genetic and genomic diversity of DAPG-producing Pseudomonas spp. as well as its importance for improving the biocontrol of plant pathogens.
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30
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Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments. Microorganisms 2021; 9:microorganisms9020250. [PMID: 33530561 PMCID: PMC7911923 DOI: 10.3390/microorganisms9020250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.
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31
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Takeuchi K, Tsuchiya W, Fujimoto Z, Yamada K, Someya N, Yamazaki T. Discovery of an Antibiotic-Related Small Protein of Biocontrol Strain Pseudomonas sp. Os17 by a Genome-Mining Strategy. Front Microbiol 2020; 11:605705. [PMID: 33324389 PMCID: PMC7726476 DOI: 10.3389/fmicb.2020.605705] [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: 09/13/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Many root-colonizing Pseudomonas spp. exhibiting biocontrol activities produce a wide range of secondary metabolites that exert antibiotic effects against other microbes, nematodes, and insects in the rhizosphere. The expression of these secondary metabolites depends on the Gac/Rsm signal transduction pathway. Based on the findings of a previous genomic study on newly isolated biocontrol pseudomonad strains, we herein investigated the novel gene cluster OS3, which consists of four genes (Os1348–Os1351) that are located upstream of putative efflux transporter genes (Os1352–Os1355). Os1348 was predicted to encode an 85-aa small precursor protein, the expression of which was under the control of GacA, and an X-ray structural analysis suggested that the Os1348 protein formed a dimer. The mutational loss of the Os1348 gene decreased the antibiotic activity of Pseudomonas sp. Os17 without changing its growth rate. The Os1349–1351 genes were predicted to be involved in post-translational modifications. Intracellular levels of the Os1348 protein in the deficient mutant of each gene differed from that in wild-type cells. These results suggest that Os1348 is involved in antibiotic activity and that the structure or expression of this protein is under the control of downstream gene products.
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Affiliation(s)
- Kasumi Takeuchi
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Wataru Tsuchiya
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Zui Fujimoto
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kosumi Yamada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobutaka Someya
- Division of Vegetable Production System, Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Toshimasa Yamazaki
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
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32
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Latour X. The Evanescent GacS Signal. Microorganisms 2020; 8:microorganisms8111746. [PMID: 33172195 PMCID: PMC7695008 DOI: 10.3390/microorganisms8111746] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 12/18/2022] Open
Abstract
The GacS histidine kinase is the membrane sensor of the major upstream two-component system of the regulatory Gac/Rsm signal transduction pathway. This pathway governs the expression of a wide range of genes in pseudomonads and controls bacterial fitness and motility, tolerance to stress, biofilm formation, and virulence or plant protection. Despite the importance of these roles, the ligands binding to the sensor domain of GacS remain unknown, and their identification is an exciting challenge in this domain. At high population densities, the GacS signal triggers a switch from primary to secondary metabolism and a change in bacterial lifestyle. It has been suggested, based on these observations, that the GacS signal is a marker of the emergence of nutritional stress and competition. Biochemical investigations have yet to characterize the GacS signal fully. However, they portray this cue as a low-molecular weight, relatively simple and moderately apolar metabolite possibly resembling, but nevertheless different, from the aliphatic organic acids acting as quorum-sensing signaling molecules in other Proteobacteria. Significant progress in the development of metabolomic tools and new databases dedicated to Pseudomonas metabolism should help to unlock some of the last remaining secrets of GacS induction, making it possible to control the Gac/Rsm pathway.
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Affiliation(s)
- Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), Normandy University (University of Rouen Normandy), 55 rue Saint-Germain, 27000 Evreux, France;
- Research Federation NORVEGE Fed4277, Normandy University, F-76821 Mont-Saint-Aignan, France
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Pourciau C, Lai YJ, Gorelik M, Babitzke P, Romeo T. Diverse Mechanisms and Circuitry for Global Regulation by the RNA-Binding Protein CsrA. Front Microbiol 2020; 11:601352. [PMID: 33193284 PMCID: PMC7652899 DOI: 10.3389/fmicb.2020.601352] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
The carbon storage regulator (Csr) or repressor of stationary phase metabolites (Rsm) system of Gammaproteobacteria is among the most complex and best-studied posttranscriptional regulatory systems. Based on a small RNA-binding protein, CsrA and homologs, it controls metabolism, physiology, and bacterial lifestyle decisions by regulating gene expression on a vast scale. Binding of CsrA to sequences containing conserved GGA motifs in mRNAs can regulate translation, RNA stability, riboswitch function, and transcript elongation. CsrA governs the expression of dozens of transcription factors and other regulators, further expanding its influence on cellular physiology, and these factors can participate in feedback to the Csr system. Expression of csrA itself is subject to autoregulation via translational inhibition and indirect transcriptional activation. CsrA activity is controlled by small noncoding RNAs (sRNAs), CsrB and CsrC in Escherichia coli, which contain multiple high affinity CsrA binding sites that compete with those of mRNA targets. Transcription of CsrB/C is induced by certain nutrient limitations, cellular stresses, and metabolites, while these RNAs are targeted for degradation by the presence of a preferred carbon source. Consistent with these findings, CsrA tends to activate pathways and processes that are associated with robust growth and repress stationary phase metabolism and stress responses. Regulatory loops between Csr components affect the signaling dynamics of the Csr system. Recently, systems-based approaches have greatly expanded our understanding of the roles played by CsrA, while reinforcing the notion that much remains to be learned about the Csr system.
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Affiliation(s)
- Christine Pourciau
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Ying-Jung Lai
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Mark Gorelik
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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Habjanič J, Mathew A, Eberl L, Freisinger E. Deciphering the Enigmatic Function of Pseudomonas Metallothioneins. Front Microbiol 2020; 11:1709. [PMID: 32793167 PMCID: PMC7387436 DOI: 10.3389/fmicb.2020.01709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/29/2020] [Indexed: 11/20/2022] Open
Abstract
Metallothioneins (MTs) are low molecular weight, Cys-rich proteins that sequester both essential and non-essential metal ions. Despite being highly conserved in the Pseudomonas genus of Gram-negative bacteria, knowledge of their physiological function in this species is scarce. Using the strain P. fluorescens Q2-87 as a model organism, we investigated the role of a conserved MT in zinc homeostasis, cadmium detoxification as well as its implications in stress response. We show that MT expression is only induced in the stationary phase and provides a fitness benefit for long-term starvation survival, while it is not required for metal resistance and acquisition, oxidative or nitrosative stress response, biofilm formation or motility.
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Affiliation(s)
- Jelena Habjanič
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Anugraha Mathew
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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Sobrero PM, Valverde C. Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. Front Mol Biosci 2020; 7:127. [PMID: 32754614 PMCID: PMC7366521 DOI: 10.3389/fmolb.2020.00127] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
Gene expression is adjusted according to cellular needs through a combination of mechanisms acting at different layers of the flow of genetic information. At the posttranscriptional level, RNA-binding proteins are key factors controlling the fate of nascent and mature mRNAs. Among them, the members of the CsrA family are small dimeric proteins with heterogeneous distribution across the bacterial tree of life, that act as global regulators of gene expression because they recognize characteristic sequence/structural motifs (short hairpins with GGA triplets in the loop) present in hundreds of mRNAs. The regulatory output of CsrA binding to mRNAs is counteracted in most cases by molecular mimic, non-protein coding RNAs that titrate the CsrA dimers away from the target mRNAs. In γ-proteobacteria, the regulatory modules composed by CsrA homologs and the corresponding antagonistic sRNAs, are mastered by two-component systems of the GacS-GacA type, which control the transcription and the abundance of the sRNAs, thus constituting the rather linear cascade Gac-Rsm that responds to environmental or cellular signals to adjust and coordinate the expression of a set of target genes posttranscriptionally. Within the γ-proteobacteria, the genus Pseudomonas has been shown to contain species with different number of active CsrA (RsmA) homologs and of molecular mimic sRNAs. Here, with the help of the increasing availability of genomic data we provide a comprehensive state-of-the-art picture of the remarkable multiplicity of CsrA lineages, including novel yet uncharacterized paralogues, and discuss evolutionary aspects of the CsrA subfamilies of the genus Pseudomonas, and implications of the striking presence of csrA alleles in natural mobile genetic elements (phages and plasmids).
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Affiliation(s)
- Patricio Martín Sobrero
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
| | - Claudio Valverde
- Laboratorio de Fisiología y Genética de Bacterias Beneficiosas para Plantas, Centro de Bioquímica y Microbiología del Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - CONICET, Buenos Aires, Argentina
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Scala R, Di Matteo A, Coluccia A, Lo Sciuto A, Federici L, Travaglini-Allocatelli C, Visca P, Silvestri R, Imperi F. Mutational analysis of the essential lipopolysaccharide-transport protein LptH of Pseudomonas aeruginosa to uncover critical oligomerization sites. Sci Rep 2020; 10:11276. [PMID: 32647254 PMCID: PMC7347655 DOI: 10.1038/s41598-020-68054-7] [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: 02/10/2020] [Accepted: 06/16/2020] [Indexed: 01/24/2023] Open
Abstract
Lipopolysaccharide (LPS) is a critical component of the outer membrane (OM) of many Gram-negative bacteria. LPS is translocated to the OM by the LPS transport (Lpt) system. In the human pathogen Pseudomonas aeruginosa, the periplasmic Lpt component, LptH, is essential for LPS transport, planktonic and biofilm growth, OM stability and infectivity. LptH has been proposed to oligomerize and form a protein bridge that accommodates LPS during transport. Based on the known LptH crystal structure, here we predicted by in silico modeling five different sites likely involved in LptH oligomerization. The relevance of these sites for LptH activity was verified through plasmid-mediated expression of site-specific mutant proteins in a P. aeruginosa lptH conditional mutant. Complementation and protein expression analyses provided evidence that all mutated sites are important for LptH activity in vivo. It was observed that the lptH conditional mutant overcomes the lethality of nonfunctional lptH variants through RecA-mediated homologous recombination between the wild-type lptH gene in the genome and mutated copies in the plasmid. Finally, biochemical assays on purified recombinant proteins showed that some LptH variants are indeed specifically impaired in oligomerization, while others appear to have defects in protein folding and/or stability.
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Affiliation(s)
- Romina Scala
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandra Lo Sciuto
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy.,Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Science and C.A.S.T. Center for Advanced Studies and Technology, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy.
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Maier C, Huptas C, von Neubeck M, Scherer S, Wenning M, Lücking G. Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk. Front Microbiol 2020; 11:1190. [PMID: 32587583 PMCID: PMC7298200 DOI: 10.3389/fmicb.2020.01190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/11/2020] [Indexed: 11/30/2022] Open
Abstract
Psychrotolerant Pseudomonas species are a main cause of proteolytic spoilage of ultra-high temperature (UHT) milk products due to the secretion of the heat-resistant metallopeptidase AprX, which is encoded by the first gene of the aprX-lipA2 operon. While the proteolytic property has been characterized for many different Pseudomonas isolates, the underlying aprX-lipA2 gene organization was only described for a few strains so far. In this study, the phylogenomic analysis of 185 Pseudomonas type strains revealed that the presence of aprX is strongly associated to a monophylum composed of 81 species, of which 83% carried the aprX locus. Furthermore, almost all type strains of known milk-relevant species were shown to be members of the three monophyletic groups P. fluorescens, P. gessardii, and P. fragi. In total, 22 different types of aprX-lipA2 genetic organizations were identified in the genus, whereby 31% of the species tested carried the type 1 operon structure consisting of eight genes (aprXIDEF prtAB lipA2). Other genetic structures differed from type 1 mainly in the presence and location of genes coding for two lipases (lipA1 and lipA2) and putative autotransporters (prtA and prtB). The peptidase activity of 129 strains, as determined on skim milk agar and in UHT-milk, correlated largely with different aprX-lipA2 gene compositions. Particularly, isolates harboring the type 1 operon were highly proteolytic, while strains with other operon types, especially ones lacking prtA and prtB, exhibited significantly lower peptidase activities. In conclusion, the phylogenomic position and the aprX-lipA2 gene organization specify the proteolytic potential of Pseudomonas isolates. In addition, however, an interplay of several environmental factors and intrinsic traits influences production and activity of AprX, leading to strain-specific proteolytic phenotypes.
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Affiliation(s)
- Christopher Maier
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Christopher Huptas
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Mario von Neubeck
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Siegfried Scherer
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
- Lehrstuhl für Mikrobielle Ökologie, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Mareike Wenning
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Genia Lücking
- ZIEL Institute for Food and Health, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
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Auxin-dependent alleviation of oxidative stress and growth promotion of Scenedesmus obliquus C1S by Azospirillum brasilense. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101839] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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39
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Lo Sciuto A, Cervoni M, Stefanelli R, Spinnato MC, Di Giamberardino A, Mancone C, Imperi F. Genetic Basis and Physiological Effects of Lipid A Hydroxylation in Pseudomonas aeruginosa PAO1. Pathogens 2019; 8:E291. [PMID: 31835493 PMCID: PMC6963906 DOI: 10.3390/pathogens8040291] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 01/09/2023] Open
Abstract
Modifications of the lipid A moiety of lipopolysaccharide influence the physicochemical properties of the outer membrane of Gram-negative bacteria. Some bacteria produce lipid A with a single hydroxylated secondary acyl chain. This hydroxylation is catalyzed by the dioxygenase LpxO, and is important for resistance to cationic antimicrobial peptides (e.g., polymyxins), survival in human blood, and pathogenicity in animal models. The lipid A of the human pathogen Pseudomonas aeruginosa can be hydroxylated in both secondary acyl chains, but the genetic basis and physiological role of these hydroxylations are still unknown. Through the generation of single and double deletion mutants in the lpxO1 and lpxO2 homologs of P. aeruginosa PAO1 and lipid A analysis by mass spectrometry, we demonstrate that both LpxO1 and LpxO2 are responsible for lipid A hydroxylation, likely acting on different secondary acyl chains. Lipid A hydroxylation does not appear to affect in vitro growth, cell wall stability, and resistance to human blood or antibiotics in P. aeruginosa. In contrast, it is required for infectivity in the Galleria mellonella infection model, without relevantly affecting in vivo persistence. Overall, these findings suggest a role for lipid A hydroxylation in P. aeruginosa virulence that could not be directly related to outer membrane integrity.
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Affiliation(s)
| | - Matteo Cervoni
- Department of Science, Roma Tre University, 00146 Roma, Italy (M.C.S.)
| | - Roberta Stefanelli
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, 00185 Roma, Italy;
| | | | | | - Carmine Mancone
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Roma, Italy; (A.D.G.); (C.M.)
| | - Francesco Imperi
- Department of Science, Roma Tre University, 00146 Roma, Italy (M.C.S.)
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40
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Study of the sRNA RsmY involved in the genetic regulation of the synthesis of alginate and alkyl resorcinols in Azotobacter vinelandii. Arch Microbiol 2019; 202:579-589. [DOI: 10.1007/s00203-019-01769-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 12/21/2022]
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A CsrA-Binding, trans-Acting sRNA of Coxiella burnetii Is Necessary for Optimal Intracellular Growth and Vacuole Formation during Early Infection of Host Cells. J Bacteriol 2019; 201:JB.00524-19. [PMID: 31451541 DOI: 10.1128/jb.00524-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 08/17/2019] [Indexed: 11/20/2022] Open
Abstract
Coxiella burnetii is an obligate intracellular gammaproteobacterium and zoonotic agent of Q fever. We previously identified 15 small noncoding RNAs (sRNAs) of C. burnetii One of them, CbsR12 (Coxiella burnetii small RNA 12), is highly transcribed during axenic growth and becomes more prominent during infection of cultured mammalian cells. Secondary structure predictions of CbsR12 revealed four putative CsrA-binding sites in stem loops with consensus AGGA/ANGGA motifs. We subsequently determined that CbsR12 binds to recombinant C. burnetii CsrA-2, but not CsrA-1, proteins in vitro Moreover, through a combination of in vitro and cell culture assays, we identified several in trans mRNA targets of CbsR12. Of these, we determined that CbsR12 binds and upregulates translation of carA transcripts coding for carbamoyl phosphate synthetase A, an enzyme that catalyzes the first step of pyrimidine biosynthesis. In addition, CbsR12 binds and downregulates translation of metK transcripts coding for S-adenosylmethionine synthetase, a component of the methionine cycle. Furthermore, we found that CbsR12 binds to and downregulates the quantity of cvpD transcripts, coding for a type IVB effector protein, in mammalian cell culture. Finally, we found that CbsR12 is necessary for expansion of Coxiella-containing vacuoles and affects growth rates in a dose-dependent manner in the early phase of infecting THP-1 cells. This is the first characterization of a trans-acting sRNA of C. burnetii and the first example of a bacterial sRNA that regulates both CarA and MetK synthesis. CbsR12 is one of only a few identified trans-acting sRNAs that interacts with CsrA.IMPORTANCE Regulation of metabolism and virulence in C. burnetii is not well understood. Here, we show that C. burnetii small RNA 12 (CbsR12) is highly transcribed in the metabolically active large-cell variant compared to the nonreplicative small-cell variant. We show that CbsR12 directly regulates several genes involved in metabolism, along with a type IV effector gene, in trans In addition, we demonstrate that CbsR12 binds to CsrA-2 in vitro and induces autoaggregation and biofilm formation when transcribed ectopically in Escherichia coli, consistent with other CsrA-sequestering sRNAs. These results implicate CbsR12 in the indirect regulation of a number of genes via CsrA-mediated regulatory activities. The results also support CbsR12 as a crucial regulatory component early on in a mammalian cell infection.
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Zhang B, Zhang Y, Liang F, Ma Y, Wu X. An Extract Produced by Bacillus sp. BR3 Influences the Function of the GacS/GacA Two-Component System in Pseudomonas syringae pv. tomato DC3000. Front Microbiol 2019; 10:2005. [PMID: 31572307 PMCID: PMC6749012 DOI: 10.3389/fmicb.2019.02005] [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: 04/15/2019] [Accepted: 08/15/2019] [Indexed: 12/03/2022] Open
Abstract
The GacS/GacA two-component system is essential for virulence in many plant pathogenic bacteria, and thus represents a promising anti-virulence target. In the present study, we isolated and screened rhizobacteria that were capable of inhibiting the expression of the gacS gene in the phytopathogenic bacterium Pseudomonas syringae pv. tomato (Pto) DC3000. One candidate inhibitor bacterium, BR3 was obtained and identified as a Bacillus sp. strain based on 16s rRNA gene sequence analysis. Besides the gacS gene, the GacA-dependent small RNA genes rsmZ and rsmY were repressed transcriptionally when DC3000 was treated with an extract from strain BR3. Importantly, the extract also influenced bacterial motility, the expression of type three secretion system effector AvrPto, and the plant hypersensitive response triggered by strain DC3000. The results suggested that the extract from strain BR3 might offer an alternative method to control bacterial diseases in plants by targeting the GacS/GacA system.
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Affiliation(s)
- Bo Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Fei Liang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yinan Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Xiaogang Wu
- College of Agriculture, Guangxi University, Nanning, China
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Remigi P, Ferguson GC, McConnell E, De Monte S, Rogers DW, Rainey PB. Ribosome Provisioning Activates a Bistable Switch Coupled to Fast Exit from Stationary Phase. Mol Biol Evol 2019; 36:1056-1070. [PMID: 30835283 PMCID: PMC6501884 DOI: 10.1093/molbev/msz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Observations of bacteria at the single-cell level have revealed many instances of phenotypic heterogeneity within otherwise clonal populations, but the selective causes, molecular bases, and broader ecological relevance remain poorly understood. In an earlier experiment in which the bacterium Pseudomonas fluorescens SBW25 was propagated under a selective regime that mimicked the host immune response, a genotype evolved that stochastically switched between capsulation states. The genetic cause was a mutation in carB that decreased the pyrimidine pool (and growth rate), lowering the activation threshold of a preexisting but hitherto unrecognized phenotypic switch. Genetic components surrounding bifurcation of UTP flux toward DNA/RNA or UDP-glucose (a precursor of colanic acid forming the capsules) were implicated as key components. Extending these molecular analyses-and based on a combination of genetics, transcriptomics, biochemistry, and mathematical modeling-we show that pyrimidine limitation triggers an increase in ribosome biosynthesis and that switching is caused by competition between ribosomes and CsrA/RsmA proteins for the mRNA transcript of a positively autoregulated activator of colanic acid biosynthesis. We additionally show that in the ancestral bacterium the switch is part of a program that determines stochastic entry into a semiquiescent capsulated state, ensures that such cells are provisioned with excess ribosomes, and enables provisioned cells to exit rapidly from stationary phase under permissive conditions.
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Affiliation(s)
- Philippe Remigi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Laboratoire des Interactions Plantes-Microorganismes (LIPM), Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gayle C Ferguson
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Ellen McConnell
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Silvia De Monte
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - David W Rogers
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris Tech), CNRS UMR 8231, PSL Research University, Paris, France
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Vibrio cholerae CsrA Directly Regulates varA To Increase Expression of the Three Nonredundant Csr Small RNAs. mBio 2019; 10:mBio.01042-19. [PMID: 31164471 PMCID: PMC6550530 DOI: 10.1128/mbio.01042-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
CsrA, an RNA-binding global regulator, is an essential protein in Vibrio choleraeV. cholerae CsrA is regulated by three small RNAs (sRNAs), namely, CsrB, CsrC, and CsrD, which act to sequester and antagonize the activity of CsrA. Although the sRNAs were considered to be largely redundant, we found that they differ in expression, half-life, and the ability to regulate CsrA. Further, we identified a feedback loop in the Csr system in which CsrA increases the synthesis of these antagonistic sRNAs. Because the Csr sRNAs are positively regulated by VarA, we determined the effects of CsrA on VarA levels. The level of VarA was reduced in a csrA mutant, and we found that CsrA directly bound to varA mRNA in an electrophoretic mobility shift assay in vitro and in an CsrA-RNA immunoprecipitation assay in vivo Thus, varA mRNA is an in vivo-verified direct target of CsrA in V. cholerae, and this is the first demonstration of CsrA directly binding to a varA/uvrY/gacA homolog. Additionally, we demonstrated that a varA translational fusion was less active in a csrA mutant than in wild-type V. cholerae, suggesting that CsrA enhances varA translation. We propose that this autoregulatory feedback loop, in which CsrA increases the production of the nonredundant Csr sRNAs by regulating the amount of VarA, provides a mechanism for fine-tuning the availability of CsrA and, thus, of its downstream targets.IMPORTANCEVibrio cholerae is a major human pathogen, causing epidemics and pandemics of cholera. V. cholerae persists in the aquatic environment, providing a constant source for human infection. Success in transitioning from the environment to the human host and back requires the bacterium to rapidly respond and to adjust its gene expression and metabolism to these two very different habitats. Our findings show that CsrA, an RNA-binding regulatory protein, plays a central role in regulating these transitions. CsrA activity is controlled by the antagonistic sRNAs CsrB, CsrC, and CsrD, and these sRNAs respond to changes in the availability of nutrients. CsrA autoregulates its own activity by controlling these sRNAs via their primary regulator VarA. Thus, the change in CsrA availability in response to nutrient availability allows V. cholerae to alter gene expression in response to environmental cues.
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Kumar SS, Penesyan A, Elbourne LDH, Gillings MR, Paulsen IT. Catabolism of Nucleic Acids by a Cystic Fibrosis Pseudomonas aeruginosa Isolate: An Adaptive Pathway to Cystic Fibrosis Sputum Environment. Front Microbiol 2019; 10:1199. [PMID: 31214142 PMCID: PMC6555301 DOI: 10.3389/fmicb.2019.01199] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We undertook Biolog Phenotype Microarray testing of P. aeruginosa CF isolates to investigate their catabolic capabilities compared to P. aeruginosa laboratory strains PAO1 and PA14. One strain, PASS4, displayed an unusual phenotype, only showing strong respiration on adenosine and inosine. Further testing indicated that PASS4 could grow on DNA as a sole carbon source, with a higher biomass production than PAO1. This suggested that PASS4 was specifically adapted to metabolize extracellular DNA, a substrate present at high concentrations in the CF lung. Transcriptomic and proteomic profiling of PASS4 and PAO1 when grown with DNA as a sole carbon source identified a set of upregulated genes, including virulence and host-adaptation genes. PASS4 was unable to utilize N-Acetyl-D-glucosamine, and when we selected PASS4 mutants able to grow on this carbon source, they also displayed a gain in ability to catabolize a broad range of other carbon sources. Genome sequencing of the mutants revealed they all contained mutations within the purK gene, encoding a key protein in the de novo purine biosynthesis pathway. This suggested that PASS4 was a purine auxotroph. Growth assays in the presence of 2 mM adenosine and the complementation of PASS4 with an intact purK gene confirmed this conclusion. Purine auxotrophy may represent a viable microbial strategy for adaptation to DNA-rich environments such as the CF lung.
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Affiliation(s)
| | - Anahit Penesyan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | | | - Michael R Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Muriel C, Blanco-Romero E, Trampari E, Arrebola E, Durán D, Redondo-Nieto M, Malone JG, Martín M, Rivilla R. The diguanylate cyclase AdrA regulates flagellar biosynthesis in Pseudomonas fluorescens F113 through SadB. Sci Rep 2019; 9:8096. [PMID: 31147571 PMCID: PMC6543031 DOI: 10.1038/s41598-019-44554-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/14/2019] [Indexed: 11/23/2022] Open
Abstract
Flagellum mediated motility is an essential trait for rhizosphere colonization by pseudomonads. Flagella synthesis is a complex and energetically expensive process that is tightly regulated. In Pseudomonas fluorescens, the regulatory cascade starts with the master regulatory protein FleQ that is in turn regulated by environmental signals through the Gac/Rsm and SadB pathways, which converge in the sigma factor AlgU. AlgU is required for the expression of amrZ, encoding a FleQ repressor. AmrZ itself has been shown to modulate c-di-GMP levels through the control of many genes encoding enzymes implicated in c-di-GMP turnover. This cyclic nucleotide regulates flagellar function and besides, the master regulator of the flagellar synthesis signaling pathway, FleQ, has been shown to bind c-di-GMP. Here we show that AdrA, a diguanylate cyclase regulated by AmrZ participates in this signaling pathway. Epistasis analysis has shown that AdrA acts upstream of SadB, linking SadB with environmental signaling. We also show that SadB binds c-di-GMP with higher affinity than FleQ and propose that c-di-GMP produced by AdrA modulates flagella synthesis through SadB.
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Affiliation(s)
- Candela Muriel
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Esther Blanco-Romero
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Eleftheria Trampari
- Department of Molecular Microbiology, John Innes Centre. Colney Lane, Norwich, UK.,Quadram Institute, Norwich, UK
| | - Eva Arrebola
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.,Department of Microbiology, University of Málaga, Málaga, Spain
| | - David Durán
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Miguel Redondo-Nieto
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre. Colney Lane, Norwich, UK
| | - Marta Martín
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049, Madrid, Spain.
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47
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Francis VI, Porter SL. Multikinase Networks: Two-Component Signaling Networks Integrating Multiple Stimuli. Annu Rev Microbiol 2019; 73:199-223. [PMID: 31112439 DOI: 10.1146/annurev-micro-020518-115846] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacteria depend on two-component systems to detect and respond to threats. Simple pathways comprise a single sensor kinase (SK) that detects a signal and activates a response regulator protein to mediate an appropriate output. These simple pathways with only a single SK are not well suited to making complex decisions where multiple different stimuli need to be evaluated. A recently emerging theme is the existence of multikinase networks (MKNs) where multiple SKs collaborate to detect and integrate numerous different signals to regulate a major lifestyle switch, e.g., between virulence, sporulation, biofilm formation, and cell division. In this review, the role of MKNs and the phosphosignaling mechanisms underpinning their signal integration and decision making are explored.
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Affiliation(s)
- Vanessa I Francis
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom; ,
| | - Steven L Porter
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom; ,
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48
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Methionine Limitation Impairs Pathogen Expansion and Biofilm Formation Capacity. Appl Environ Microbiol 2019; 85:AEM.00177-19. [PMID: 30824455 DOI: 10.1128/aem.00177-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 02/23/2019] [Indexed: 02/01/2023] Open
Abstract
Multidrug-resistant bacterial pathogens are becoming increasingly prevalent, and novel strategies to treat bacterial infections caused by these organisms are desperately needed. Bacterial central metabolism is crucial for catabolic processes and provides precursors for anabolic pathways, such as the biosynthesis of essential biomolecules like amino acids or vitamins. However, most essential pathways are not regarded as good targets for antibiotic therapy since their products might be acquired from the environment. This issue raises doubts about the essentiality of such targets during infection. A putative target in bacterial anabolism is the methionine biosynthesis pathway. In contrast to humans, almost all bacteria carry methionine biosynthesis pathways which have often been suggested as putative targets for novel anti-infectives. While the growth of methionine auxotrophic strains can be stimulated by exogenous methionine, the extracellular concentrations required by most bacterial species are unknown. Furthermore, several phenotypic characteristics of methionine auxotrophs are only partly reversed by exogenous methionine. We investigated methionine auxotrophic mutants of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli (all differing in methionine biosynthesis enzymes) and found that each needed concentrations of exogenous methionine far exceeding that reported for human serum (∼30 µM). Accordingly, these methionine auxotrophs showed a reduced ability to proliferate in human serum. Additionally, S. aureus and P. aeruginosa methionine auxotrophs were significantly impaired in their ability to form and maintain biofilms. Altogether, our data show intrinsic defects of methionine auxotrophs. This result suggests that the pathway should be considered for further studies validating the therapeutic potential of inhibitors.IMPORTANCE New antibiotics that attack novel targets are needed to circumvent widespread resistance to conventional drugs. Bacterial anabolic pathways, such as the enzymes for biosynthesis of the essential amino acid methionine, have been proposed as potential targets. However, the eligibility of enzymes in these pathways as drug targets is unclear because metabolites might be acquired from the environment to overcome inhibition. We investigated the nutritional needs of methionine auxotrophs of the pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli We found that each auxotrophic strain retained a growth disadvantage at methionine concentrations mimicking those available in vivo and showed that biofilm biomass was strongly influenced by endogenous methionine biosynthesis. Our experiments suggest that inhibition of the methionine biosynthesis pathway has deleterious effects even in the presence of external methionine. Therefore, additional efforts to validate the effects of methionine biosynthesis inhibitors in vivo are warranted.
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Lo Sciuto A, Martorana AM, Fernández-Piñar R, Mancone C, Polissi A, Imperi F. Pseudomonas aeruginosa LptE is crucial for LptD assembly, cell envelope integrity, antibiotic resistance and virulence. Virulence 2019; 9:1718-1733. [PMID: 30354941 PMCID: PMC7204523 DOI: 10.1080/21505594.2018.1537730] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential structural component of the outer membrane (OM) of most Gram-negative bacteria. In the model organism Escherichia coli, LPS transport to the OM requires seven essential proteins (LptABCDEFG) that form a continuous bridge across the cell envelope. In Pseudomonas aeruginosa the recently-demonstrated essentiality of LptD and LptH, the P. aeruginosa LptA homologue, confirmed the crucial role of the Lpt system and, thus, of LPS in OM biogenesis in this species. Surprisingly, independent high-throughput transposon mutagenesis studies identified viable P. aeruginosa insertion mutants in the lptE gene, suggesting that it might be dispensable for bacterial growth. To test this hypothesis, we generated an lptE conditional mutant in P. aeruginosa PAO1. LptE depletion only slightly impairs P. aeruginosa growth in vitro. Conversely, LptE is important for cell envelope stability, antibiotic resistance and virulence in an insect model. Interestingly, the maturation and OM localization of LPS is only marginally affected in LptE-depleted cells, while the levels of the OM component LptD are strongly reduced. This suggests that P. aeruginosa LptE might not be directly involved in LPS transport, although it is clearly essential for the maturation and/or stability of LptD. While poor functionality of LptD caused by LptE depletion is somehow tolerated by P. aeruginosa, this has a high cost in terms of cell integrity, drug resistance and virulence, highlighting LptE function(s) as an interesting target to weaken P. aeruginosa defenses and reduce its infectivity.
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Affiliation(s)
- Alessandra Lo Sciuto
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Alessandra M Martorana
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Regina Fernández-Piñar
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
| | - Carmine Mancone
- c Department of Cellular Biotechnologies and Haematology , Sapienza University of Rome , Rome , Italy
| | - Alessandra Polissi
- b Department of Pharmacological and Biomolecular Sciences , University of Milan , Milan , Italy
| | - Francesco Imperi
- a Department of Biology and Biotechnology Charles Darwin , Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti , Rome , Italy
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50
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Mancl JM, Ray WK, Helm RF, Schubot FD. Helix Cracking Regulates the Critical Interaction between RetS and GacS in Pseudomonas aeruginosa. Structure 2019; 27:785-793.e5. [PMID: 30879888 DOI: 10.1016/j.str.2019.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/07/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Recent paradigm shifting discoveries have demonstrated that bacterial signaling kinases engage in unexpected regulatory crosstalk, yet the underlying molecular mechanisms remain largely uncharacterized. The Pseudomonas aeruginosa RetS/GacS system constitutes an ideal model for studying these mechanisms. The in-depth analysis of the kinase region of RetS and RetS/GacS interactions presented here refutes a longstanding model, which posited the formation of a catalytically inactive RetS/GacS heterodimer. Crystallographic studies uncovered structurally dynamic features within the RetS kinase region, suggesting that RetS uses the reversible unfolding of a helix, or helix cracking, to control interactions with GacS. The pivotal importance of this helical region for regulating GacS and, by extension, Pseudomonas aeruginosa virulence, was corroborated via in vivo assays. The implications of this work extend beyond the RetS/GacS system because the helix cracking occurs right next to a highly conserved catalytic residue histidine-424, suggesting this model could represent an emergent archetype for histidine kinase regulation.
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Affiliation(s)
- Jordan M Mancl
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - William K Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Rich F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Florian D Schubot
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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