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Letizia M, Mellini M, Fortuna A, Visca P, Imperi F, Leoni L, Rampioni G. PqsE Expands and Differentially Modulates the RhlR Quorum Sensing Regulon in Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0096122. [PMID: 35604161 PMCID: PMC9241726 DOI: 10.1128/spectrum.00961-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 12/22/2022] Open
Abstract
In the opportunistic pathogen Pseudomonas aeruginosa, many virulence traits are finely regulated by quorum sensing (QS), an intercellular communication system that allows the cells of a population to coordinate gene expression in response to cell density. The key aspects underlying the functionality of the complex regulatory network governing QS in P. aeruginosa are still poorly understood, including the interplay between the effector protein PqsE and the transcriptional regulator RhlR in controlling the QS regulon. Different studies have focused on the characterization of PqsE- and RhlR-controlled genes in genetic backgrounds in which RhlR activity can be modulated by PqsE and pqsE expression is controlled by RhlR, thus hampering identification of the distinct regulons controlled by PqsE and RhlR. In this study, a P. aeruginosa PAO1 mutant strain with deletion of multiple QS elements and inducible expression of pqsE and/or rhlR was generated and validated. Transcriptomic analyses performed on this genetic background allowed us to unambiguously define the regulons controlled by PqsE and RhlR when produced alone or in combination. Transcriptomic data were validated via reverse transcription-quantitative PCR (RT-qPCR) and transcriptional fusions. Overall, our results showed that PqsE has a negligible effect on the P. aeruginosa transcriptome in the absence of RhlR, and that multiple RhlR subregulons exist with distinct dependency on PqsE. Overall, this study contributes to untangling the regulatory link between the pqs and rhl QS systems mediated by PqsE and RhlR and clarifying the impact of these QS elements on the P. aeruginosa transcriptome. IMPORTANCE The ability of Pseudomonas aeruginosa to cause difficult-to-treat infections relies on its capacity to fine-tune the expression of multiple virulence traits via the las, rhl, and pqs QS systems. Both the pqs effector protein PqsE and the rhl transcriptional regulator RhlR are required for full production of key virulence factors in vitro and pathogenicity in vivo. While it is known that PqsE can stimulate the ability of RhlR to control some virulence factors, no data are available to allow clear discrimination of the PqsE and RhlR regulons. The data produced in this study demonstrate that PqsE mainly impacts the P. aeruginosa transcriptome via an RhlR-dependent pathway and splits the RhlR regulon into PqsE-dependent and PqsE-independent subregulons. Besides contributing to untangling of the complex QS network of P. aeruginosa, our data confirm that both PqsE and RhlR are suitable targets for the development of antivirulence drugs.
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Affiliation(s)
| | - Marta Mellini
- Department of Science, Roma Tre University, Rome, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Livia Leoni
- Department of Science, Roma Tre University, Rome, Italy
| | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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Dhankhar R, Kumar A, Kumar S, Chhabra D, Shukla P, Gulati P. Multilevel algorithms and evolutionary hybrid tools for enhanced production of arginine deiminase from Pseudomonas furukawaii RS3. BIORESOURCE TECHNOLOGY 2019; 290:121789. [PMID: 31326652 DOI: 10.1016/j.biortech.2019.121789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
In the present study a high arginine deiminase (ADI) yielding bacterium was isolated from soil samples of Haryana, India and identified as Pseudomonas furukawaii. The specific enzyme activity was optimized to 1.420 IU/ml by OFAT and further enhanced to 2.708 IU/ml (an increase of 90.7%) with the help of statistical parametric optimization approaches using GA-ANN and GA-ANFIS. The obtained value of the coefficient of correlation (R = 0.88) for ANN and epoch error (0.12) for ANFIS, indicates the prediction accuracy and strength of these data training models. ADI production was improved significantly in simple super broth media supplemented with 1.5% fructose and 1.75% arginine at pH 7 at 37 °C using multilevel algorithms and evolutionary hybrid tools. The native enzyme was partially purified (ten-fold) up to a specific enzyme activity of 29.559 IU/mg.
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Affiliation(s)
- Rakhi Dhankhar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Ashwani Kumar
- Optimization and Mechatronics Laboratory, Department of Mechanical Engineering, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Deepak Chhabra
- Optimization and Mechatronics Laboratory, Department of Mechanical Engineering, University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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Karishma M, Trivedi VD, Choudhary A, Mhatre A, Kambli P, Desai J, Phale PS. Analysis of preference for carbon source utilization among three strains of aromatic compounds degradingPseudomonas. FEMS Microbiol Lett 2015; 362:fnv139. [DOI: 10.1093/femsle/fnv139] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2015] [Indexed: 01/07/2023] Open
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Styrene is sensed by the N-terminal PAS sensor domain of StyS, a double sensor kinase from the styrene-degrading bacterium Pseudomonas fluorescens ST. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0931-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Silva-Jiménez H, García-Fontana C, Cadirci BH, Ramos-González MI, Ramos JL, Krell T. Study of the TmoS/TmoT two-component system: towards the functional characterization of the family of TodS/TodT like systems. Microb Biotechnol 2011; 5:489-500. [PMID: 22212183 PMCID: PMC3815326 DOI: 10.1111/j.1751-7915.2011.00322.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The two‐component system TmoS/TmoT controls the expression of the toluene‐4‐monooxygenase pathway in Pseudomonas mendocina RK1 via modulation of PtmoX activity. The TmoS/TmoT system belongs to the family of TodS/TodT like proteins. The sensor kinase TmoS is a 108 kDa protein composed of seven different domains. Using isothermal titration calorimetry we show that purified TmoS binds a wide range of aromatic compounds with high affinities. Tightest ligand binding was observed for toluene (KD = 150 nM), which corresponds to the highest affinity measured between an effector and a sensor kinase. Other compounds with affinities in the nanomolar range include benzene, the 3 xylene isomers, styrene, nitrobenzene or p‐chlorotoluene. We demonstrate that only part of the ligands that bind to TmoS increase protein autophosphorylation in vitro and consequently pathway expression in vivo. These compounds are referred to as agonists. Other TmoS ligands, termed antagonists, failed to increase TmoS autophosphorylation, which resulted in their incapacity to stimulate gene expression in vivo. We also show that TmoS saturated with different agonists differs in their autokinase activities. The effector screening of gene expression showed that promoter activity of PtmoX and PtodX (controlled by the TodS/TodT system) is mediated by the same set of 22 compounds. The common structural feature of these compounds is the presence of a single aromatic ring. Among these ligands, toluene was the most potent inducer of both promoter activities. Information on the TmoS/TmoT and TodS/TodT system combined with a sequence analysis of family members permits to identify distinct features that define this protein family.
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Affiliation(s)
- Hortencia Silva-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda 1, Granada, Spain.
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Anuchin AM, Goncharenko AV, Demidenok OI, Kaprelyants AS. Histone-like proteins of bacteria (review). APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811060020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Rojo F. Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 2010; 34:658-84. [PMID: 20412307 DOI: 10.1111/j.1574-6976.2010.00218.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.
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Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
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Krell T, Busch A, Lacal J, Silva-Jiménez H, Ramos JL. The enigma of cytosolic two-component systems: a hypothesis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:171-176. [PMID: 23765790 DOI: 10.1111/j.1758-2229.2009.00020.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
One-component systems (OCSs) and cytosolic two-component regulatory systems (TCSs) appear to share the same biological function, which consists in the transcriptional control in response to the cellular concentration of signal molecules. However, cytosolic TCSs as compared with OCSs represent a genetic and metabolic burden to the cell: the genetic information encoding a TCS is significantly larger than that of an OCS, two or more proteins instead of one need to be synthesized for a TCS and operation of the latter system requires the expense of ATP which is not the case for most OCSs. The evolutionary advantages of cytosolic TCSs over OCSs are thus not obvious. We hypothesize here that the increased capacity of cytosolic TCSs to respond to multiple signals is a major advantage over OCSs. Different mechanisms for the incorporation of additional signals into the regulatory circuit are discussed. The inclusion of several signals into the definition of the final regulatory response is proposed to result in a better adaptation of the host to given environmental conditions.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008 Granada, Spain
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Busch A, Guazzaroni ME, Lacal J, Ramos JL, Krell T. The sensor kinase TodS operates by a multiple step phosphorelay mechanism involving two autokinase domains. J Biol Chem 2009; 284:10353-60. [PMID: 19240030 DOI: 10.1074/jbc.m900521200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Expression of the Pseudomonas putida tod operon, which encodes enzymes for toluene metabolism, takes place from the P(todX) promoter and is mediated by the TodS/TodT two component system. The sensor kinase TodS has a complex domain arrangement containing two functional modules, each harboring a sensor- and an autokinase domain and separated by a receiver domain. Based on site-directed mutagenesis of phosphoaccepting His-190, Asp-500, and His-760 and in vitro transphosphorylation experiments with recombinant TodS fragments, we show that TodS uses a multiple step phosphorelay mechanism to activate TodT. Toluene binding stimulates exclusively phosphorylation of His-190, which is followed by phosphotransfer to Asp-500 and subsequently to His-760 prior to phosphorylation of TodT Asp-57. Mutation of His-190, Asp-500, and H760A prevented up-regulation of toluene-mediated stimulation of TodT transphosphorylation in vitro and reduced in vivo expression of P(todX) to the basal level. Calorimetric studies support that TodT binds to the C-terminal kinase module with a K(D) of approximately 200 nm and 1:1 stoichiometry. This is the first report of a multiple step phosphorelay mechanism of a sensor kinase that involves two autokinase domains.
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Affiliation(s)
- Andreas Busch
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008 Granada, Spain
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