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Ezeduru V, Shao ARQ, Venegas FA, McKay G, Rich J, Nguyen D, Thibodeaux CJ. Defining the Functional Properties of Cyclopropane Fatty Acid Synthase from Pseudomonas aeruginosa PAO1. J Biol Chem 2024:107618. [PMID: 39095026 DOI: 10.1016/j.jbc.2024.107618] [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: 06/26/2024] [Revised: 07/20/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Cyclopropane fatty acid synthases (CFAS) catalyze the conversion of unsaturated fatty acids to cyclopropane fatty acids (CFAs) within bacterial membranes. This modification alters the biophysical properties of membranes and has been correlated with virulence in several human pathogens. Despite the central role played by CFAS enzymes in regulating bacterial stress responses, the mechanistic properties of the CFAS enzyme family and the consequences of CFA biosynthesis remain largely uncharacterized in most bacteria. We report the first characterization of the CFAS enzyme from Pseudomonas aeruginosa (PA) - an opportunistic human pathogen with complex membrane biology that is frequently associated with antimicrobial resistance and high tolerance to various external stressors. We demonstrate that CFAs are produced by a single enzyme in PA and that cfas gene expression is upregulated during the transition to stationary phase and in response to oxidative stress. Analysis of PA lipid extracts reveal a massive increase in CFA production as PA cells enter stationary phase and help define the optimal membrane composition for in vitro assays. The purified PA-CFAS enzyme forms a stable homodimer and preferentially modifies phosphatidylglycerol lipid substrates and membranes with a higher content of unsaturated acyl chains. Bioinformatic analysis across bacterial phyla shows highly divergent amino acid sequences within the lipid binding domain of CFAS enzymes, perhaps suggesting distinct membrane binding properties among different orthologues. This work lays an important foundation for further characterization of CFAS in Pseudomonas aeruginosa and for examining the functional differences between CFAS enzymes from different bacteria.
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Affiliation(s)
| | | | | | - Geoffrey McKay
- Research Institute of the McGill University Health Center, McGill University
| | - Jacquelyn Rich
- Research Institute of the McGill University Health Center, McGill University; Department of Microbiology and Immunology, McGill University
| | - Dao Nguyen
- Research Institute of the McGill University Health Center, McGill University; Department of Microbiology and Immunology, McGill University; Department of Medicine, McGill University
| | - Christopher J Thibodeaux
- Department of Chemistry, McGill University; Centre de Recherche en Biologie Structurale, McGill University.
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2
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Bernal P, Civantos C, Pacheco-Sánchez D, Quesada JM, Filloux A, Llamas MA. Transcriptional organization and regulation of the Pseudomonas putida K1 type VI secretion system gene cluster. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001295. [PMID: 36748579 PMCID: PMC9993120 DOI: 10.1099/mic.0.001295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The type VI secretion system (T6SS) is an antimicrobial molecular weapon that is widespread in Proteobacteria and offers competitive advantages to T6SS-positive micro-organisms. Three T6SSs have recently been described in Pseudomonas putida KT2440 and it has been shown that one, K1-T6SS, is used to outcompete a wide range of phytopathogens, protecting plants from pathogen infections. Given the relevance of this system as a powerful and innovative mechanism of biological control, it is critical to understand the processes that govern its expression. Here, we experimentally defined two transcriptional units in the K1-T6SS cluster. One encodes the structural components of the system and is transcribed from two adjacent promoters. The other encodes two hypothetical proteins, the tip of the system and the associated adapters, and effectors and cognate immunity proteins, and it is also transcribed from two adjacent promoters. The four identified promoters contain the typical features of σ70-dependent promoters. We have studied the expression of the system under different conditions and in a number of mutants lacking global regulators. P. putida K1-T6SS expression is induced in the stationary phase, but its transcription does not depend on the stationary σ factor RpoS. In fact, the expression of the system is indirectly repressed by RpoS. Furthermore, it is also repressed by RpoN and the transcriptional regulator FleQ, an enhancer-binding protein typically acting in conjunction with RpoN. Importantly, expression of the K1-T6SS gene cluster is positively regulated by the GacS-GacA two-component regulatory system (TCS) and repressed by the RetS sensor kinase, which inhibits this TCS. Our findings identified a complex regulatory network that governs T6SS expression in general and P. putida K1-T6SS in particular, with implications for controlling and manipulating a bacterial agent that is highly relevant in biological control.
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Affiliation(s)
- Patricia Bernal
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - José M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Singapore Centre for Environmental Life Sciences Engineering. Nanyang Technological University, Singapore
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
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3
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Nowak A, Żur-Pińska J, Piński A, Pacek G, Mrozik A. Adaptation of phenol-degrading Pseudomonas putida KB3 to suboptimal growth condition: A focus on degradative rate, membrane properties and expression of xylE and cfaB genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 221:112431. [PMID: 34146980 DOI: 10.1016/j.ecoenv.2021.112431] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 06/12/2023]
Abstract
Detailed characterization of new Pseudomonas strains that degrade toxic pollutants is required and utterly necessary before their potential use in environmental microbiology and biotechnology applications. Therefore, phenol degradation by Pseudomonas putida KB3 under suboptimal temperatures, pH, and salinity was examined in this study. Parallelly, adaptive mechanisms of bacteria to stressful growth conditions concerning changes in cell membrane properties during phenol exposure as well as the expression level of genes encoding catechol 2,3-dioxygenase (xylE) and cyclopropane fatty acid synthase (cfaB) were determined. It was found that high salinity and the low temperature had the most significant effect on the growth of bacteria and the rate of phenol utilization. Degradation of phenol (300 mg L-1) proceeded 12-fold and seven-fold longer at 10 °C and 5% NaCl compared to the optimal conditions. The ability of bacteria to degrade phenol was coupled with a relatively high activity of catechol 2,3-dioxygenase. The only factor that inhibited enzyme activity by approximately 80% compared to the control sample was salinity. Fatty acid methyl ester (FAMEs) profiling, membrane permeability measurements, and hydrophobicity tests indicated severe alterations in bacteria membrane properties during phenol degradation in suboptimal growth conditions. The highest values of pH, salinity, and temperature led to a decrease in membrane permeability. FAME analysis showed fatty acid saturation indices and cyclopropane fatty acid participation at high temperature and salinity. Genetic data showed that suboptimal growth conditions primarily resulted in down-regulation of xylE and cfaB gene expression.
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Affiliation(s)
- Agnieszka Nowak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Joanna Żur-Pińska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
| | - Gabriela Pacek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Agnieszka Mrozik
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellońska 28, 40-032 Katowice, Poland
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4
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Mauger M, Ferreri C, Chatgilialoglu C, Seemann M. The bacterial protective armor against stress: The cis-trans isomerase of unsaturated fatty acids, a cytochrome-c type enzyme. J Inorg Biochem 2021; 224:111564. [PMID: 34418715 DOI: 10.1016/j.jinorgbio.2021.111564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Accepted: 08/01/2021] [Indexed: 10/20/2022]
Abstract
Bacteria have evolved several outstanding strategies to resist to compounds or factors that compromise their survival. The first line of defense of the cell against environmental stresses is the membrane with fatty acids as fundamental building blocks of phospholipids. In this review, we focus on a periplasmic heme enzyme that catalyzes the cis-trans isomerization of unsaturated fatty acids to trigger a decrease in the fluidity of the membrane in order to rapidly counteract the danger. We particularly detailed the occurrence of such cis-trans isomerase in Nature, the different stresses that are at the origin of the double bond isomerization, the first steps in the elucidation of the mechanism of this peculiar metalloenzyme and some aspects of its regulation.
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Affiliation(s)
- Mickaël Mauger
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg/CNRS 4, rue Blaise Pascal, 67070 Strasbourg, France
| | - Carla Ferreri
- Consiglio Nazionale delle Ricerche - ISOF, Via Piero Gobetti 101, 40129 Bologna, Italy
| | | | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg/CNRS 4, rue Blaise Pascal, 67070 Strasbourg, France.
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5
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Dolke F, Dong C, Bandi S, Paetz C, Glauser G, von Reuß SH. Ascaroside Signaling in the Bacterivorous Nematode Caenorhabditis remanei Encodes the Growth Phase of Its Bacterial Food Source. Org Lett 2019; 21:5832-5837. [PMID: 31305087 DOI: 10.1021/acs.orglett.9b01914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel class of species-specific modular ascarosides that integrate additional fatty acid building blocks was characterized in the nematode Caenorhabditis remanei using a combination of HPLC-ESI-(-)-MS/MS precursor ion scanning, microreactions, HR-MS/MS, MSn, and NMR techniques. The structure of the dominating component carrying a cyclopropyl fatty acid moiety was established by total synthesis. Biogenesis of this female-produced male attractant depends on cyclopropyl fatty acid synthase (cfa), which is expressed in bacteria upon entering their stationary phase.
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Affiliation(s)
- Franziska Dolke
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Chuanfu Dong
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Siva Bandi
- Laboratory for Bioanalytical Chemistry, Institute of Chemistry , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| | - Christian Paetz
- Research Group Biosynthesis/NMR , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany
| | - Gaétan Glauser
- Neuchâtel Platform for Analytical Chemistry (NPAC) , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
| | - Stephan H von Reuß
- Department of Bioorganic Chemistry , Max Planck Institute for Chemical Ecology , Hans-Knöll Straße 8 , D-07745 Jena , Germany.,Laboratory for Bioanalytical Chemistry, Institute of Chemistry , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland.,Neuchâtel Platform for Analytical Chemistry (NPAC) , University of Neuchâtel , Avenue de Bellevaux 51 , CH-2000 Neuchâtel , Switzerland
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6
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Kondakova T, Cronan JE. Transcriptional regulation of fatty acid cis-trans isomerization in the solvent-tolerant soil bacterium, Pseudomonas putida F1. Environ Microbiol 2019; 21:1659-1676. [PMID: 30702193 PMCID: PMC7357427 DOI: 10.1111/1462-2920.14546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/21/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022]
Abstract
One key to the success of Pseudomonas spp. is their ability to reside in hostile environments. Pseudomonas spp. possess a cis-trans isomerase (Cti) an enzyme that converts the cis-unsaturated fatty acids (FAs) of the membrane lipids to their trans-isomers to rigidify the membrane and thereby resist stresses. Whereas the posttranslational Cti regulation has been previously reported, transcriptional cti regulation remains to be studied in more details. Here, we have studied cti transcriptional regulation in the solvent-tolerant strain Pseudomonas putida F1. Two cti transcriptional start sites (cti-279 and cti-77) were identified with cti-279 transcript being dominant. Expression of cti was found to increase with temperature increase, addition of the organic solvent, octanol and in the stationary growth phase. We found that cti expression was repressed by the cyclic-AMP receptor protein (Crp) and repression required the cyclic-AMP ligand of Crp. Production of trans-unsaturated FAs was found to decrease after 24 h of growth. Although this decrease was accompanied by an increase in cyclopropane FA content, this was not at the expense of trans-unsaturated FAs demonstrating the absence of competition between Cti and Cfa in FA modification.
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Affiliation(s)
- Tatiana Kondakova
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E. Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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7
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Sandoval NR, Papoutsakis ET. Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes. Curr Opin Microbiol 2016; 33:56-66. [PMID: 27376665 DOI: 10.1016/j.mib.2016.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
Abstract
Metabolite toxicity in microbes, particularly at the membrane, remains a bottleneck in the production of fuels and chemicals. Under chemical stress, native adaptation mechanisms combat hyper-fluidization by modifying the phospholipids in the membrane. Recent work in fluxomics reveals the mechanism of how membrane damage negatively affects energy metabolism while lipidomic and transcriptomic analyses show that strains evolved to be tolerant maintain membrane fluidity under stress through a variety of mechanisms such as incorporation of cyclopropanated fatty acids, trans-unsaturated fatty acids, and upregulation of cell wall biosynthesis genes. Engineered strains with modifications made in the biosynthesis of fatty acids, peptidoglycan, and lipopolysaccharide have shown increased tolerance to exogenous stress as well as increased production of desired metabolites of industrial importance. We review recent advances in elucidation of mechanisms or toxicity and tolerance as well as efforts to engineer the bacterial membrane and cell wall.
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Affiliation(s)
- Nicholas R Sandoval
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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8
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Ramos JL, Sol Cuenca M, Molina-Santiago C, Segura A, Duque E, Gómez-García MR, Udaondo Z, Roca A. Mechanisms of solvent resistance mediated by interplay of cellular factors inPseudomonas putida. FEMS Microbiol Rev 2015; 39:555-66. [DOI: 10.1093/femsre/fuv006] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2015] [Indexed: 11/14/2022] Open
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9
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Analysis of solvent tolerance inPseudomonas putidaDOT-T1E based on its genome sequence and a collection of mutants. FEBS Lett 2012; 586:2932-8. [DOI: 10.1016/j.febslet.2012.07.031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 07/09/2012] [Accepted: 07/09/2012] [Indexed: 11/19/2022]
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10
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Müller C, Fetzner S. A Pseudomonas putida bioreporter for the detection of enzymes active on 2-alkyl-4(1H)-quinolone signalling molecules. Appl Microbiol Biotechnol 2012; 97:751-60. [PMID: 22740050 DOI: 10.1007/s00253-012-4236-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 10/28/2022]
Abstract
The quorum sensing signalling molecules 2-heptyl-3-hydroxy-4(1H)-quinolone, termed the "Pseudomonas quinolone signal" (PQS), and 2-heptyl-4(1H)-quinolone (HHQ) play an important role in the control of virulence gene expression in Pseudomonas aeruginosa. To construct a bioreporter for the specific and sensitive detection of these compounds, a plasmid with the pqsR gene encoding the PQS- and HHQ-responsive transcriptional regulator PqsR, and with the PqsR-controlled pqsA promoter fused to the lacZ gene, was established in Pseudomonas putida KT2440. The bioreporter responds to HHQ and PQS at concentrations in the range of 0.1-10 and 0.01-5 μM, respectively, with EC(50) values of 1.50 ± 0.25 μM for HHQ and 0.15 ± 0.02 μM for PQS. 2,4-Dihydroxyquinoline, a metabolite produced abundantly by P. aeruginosa, did not elicit an increase in reporter enzyme activity. To test whether the bioreporter can be used for the detection of enzymes active on AQ signalling molecules, the hodC gene coding for 2-methyl-3-hydroxy-4(1H)-quinolone 2,4-dioxygenase was expressed in the reporter strain. This dioxygenase catalyses the cleavage of PQS, albeit with very low activity. The response of the bioreporter to PQS was significantly quenched by co-expression of the hodC gene, and HPLC analysis of culture extracts verified that the PQS levels decreased during cultivation. The bioreporter can be applied to screen for AQ-converting enzymes, which will be useful tools to interfere with quorum sensing and thus virulence in P. aeruginosa.
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Affiliation(s)
- Christine Müller
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstraße 3, 48149 Münster, Germany
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11
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Segura A, Molina L, Fillet S, Krell T, Bernal P, Muñoz-Rojas J, Ramos JL. Solvent tolerance in Gram-negative bacteria. Curr Opin Biotechnol 2012; 23:415-21. [DOI: 10.1016/j.copbio.2011.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/29/2011] [Accepted: 11/11/2011] [Indexed: 10/14/2022]
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