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Genetic Diversity in Pseudomonas syringae pv. maculicola Strains. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.3.24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tiso T, Zauter R, Tulke H, Leuchtle B, Li WJ, Behrens B, Wittgens A, Rosenau F, Hayen H, Blank LM. Designer rhamnolipids by reduction of congener diversity: production and characterization. Microb Cell Fact 2017; 16:225. [PMID: 29241456 PMCID: PMC5729600 DOI: 10.1186/s12934-017-0838-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 12/05/2017] [Indexed: 01/19/2023] Open
Abstract
Background Rhamnolipids are biosurfactants featuring surface-active properties that render them suitable for a broad range of industrial applications. These properties include their emulsification and foaming capacity, critical micelle concentration, and ability to lower surface tension. Further, aspects like biocompatibility and environmental friendliness are becoming increasingly important. Rhamnolipids are mainly produced by pathogenic bacteria like Pseudomonas aeruginosa. We previously designed and constructed a recombinant Pseudomonas putida KT2440, which synthesizes rhamnolipids by decoupling production from host-intrinsic regulations and cell growth. Results Here, the molecular structure of the rhamnolipids, i.e., different congeners produced by engineered P. putida are reported. Natural rhamnolipid producers can synthesize mono- and di-rhamnolipids, containing one or two rhamnose molecules, respectively. Of each type of rhamnolipid four main congeners are produced, deviating in the chain lengths of the β-hydroxy-fatty acids. The resulting eight main rhamnolipid congeners with variable numbers of hydrophobic/hydrophilic residues and their mixtures feature different physico-chemical properties that might lead to diverse applications. We engineered a microbial cell factory to specifically produce three different biosurfactant mixtures: a mixture of di- and mono-rhamnolipids, mono-rhamnolipids only, and hydroxyalkanoyloxy alkanoates, the precursors of rhamnolipid synthesis, consisting only of β-hydroxy-fatty acids. To support the possibility of second generation biosurfactant production with our engineered microbial cell factory, we demonstrate rhamnolipid production from sustainable carbon sources, including glycerol and xylose. A simple purification procedure resulted in biosurfactants with purities of up to 90%. Finally, through determination of properties specific for surface active compounds, we were able to show that the different mixtures indeed feature different physico-chemical characteristics. Conclusions The approach demonstrated here is a first step towards the production of designer biosurfactants, tailor-made for specific applications by purposely adjusting the congener composition of the mixtures. Not only were we able to genetically engineer our cell factory to produce specific biosurfactant mixtures, but we also showed that the products are suited for different applications. These designer biosurfactants can be produced as part of a biorefinery from second generation carbon sources such as xylose. Electronic supplementary material The online version of this article (10.1186/s12934-017-0838-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Till Tiso
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Rabea Zauter
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Hannah Tulke
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Bernd Leuchtle
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Wing-Jin Li
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Beate Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany.,Doehler GmbH, Riedstraße 7-9, 64295, Darmstadt, Germany
| | - Andreas Wittgens
- Ulm Center for Peptide Pharmaceuticals (U-PEP), Ulm-University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank Rosenau
- Ulm Center for Peptide Pharmaceuticals (U-PEP), Ulm-University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
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The Two-Component Monooxygenase MeaXY Initiates the Downstream Pathway of Chloroacetanilide Herbicide Catabolism in Sphingomonads. Appl Environ Microbiol 2017; 83:AEM.03241-16. [PMID: 28115384 DOI: 10.1128/aem.03241-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/18/2017] [Indexed: 11/20/2022] Open
Abstract
Due to the extensive use of chloroacetanilide herbicides over the past 60 years, bacteria have evolved catabolic pathways to mineralize these compounds. In the upstream catabolic pathway, chloroacetanilide herbicides are transformed into the two common metabolites 2-methyl-6-ethylaniline (MEA) and 2,6-diethylaniline (DEA) through N-dealkylation and amide hydrolysis. The pathway downstream of MEA is initiated by the hydroxylation of aromatic rings, followed by its conversion to a substrate for ring cleavage after several steps. Most of the key genes in the pathway have been identified. However, the genes involved in the initial hydroxylation step of MEA are still unknown. As a special aniline derivative, MEA cannot be transformed by the aniline dioxygenases that have been characterized. Sphingobium baderi DE-13 can completely degrade MEA and use it as a sole carbon source for growth. In this work, an MEA degradation-deficient mutant of S. baderi DE-13 was isolated. MEA catabolism genes were predicted through comparative genomic analysis. The results of genetic complementation and heterologous expression demonstrated that the products of meaX and meaY are responsible for the initial step of MEA degradation in S. baderi DE-13. MeaXY is a two-component flavoprotein monooxygenase system that catalyzes the hydroxylation of MEA and DEA using NADH and flavin mononucleotide (FMN) as cofactors. Nuclear magnetic resonance (NMR) analysis confirmed that MeaXY hydroxylates MEA and DEA at the para-position. Transcription of meaX was enhanced remarkably upon induction of MEA or DEA in S. baderi DE-13. Additionally, meaX and meaY were highly conserved among other MEA-degrading sphingomonads. This study fills a gap in our knowledge of the biochemical pathway that carries out mineralization of chloroacetanilide herbicides in sphingomonads.IMPORTANCE Much attention has been paid to the environmental fate of chloroacetanilide herbicides used for the past 60 years. Microbial degradation is considered an important mechanism in the degradation of these compounds. Bacterial degradation of chloroacetanilide herbicides has been investigated in many recent studies. Pure cultures or consortia able to mineralize these herbicides have been obtained. The catabolic pathway has been proposed, and most key genes involved have been identified. However, the genes responsible for the initiation step (from MEA to hydroxylated MEA or from DEA to hydroxylated DEA) of the downstream pathway have not been reported. The present study demonstrates that a two-component flavin-dependent monooxygenase system, MeaXY, catalyzes the para-hydroxylation of MEA or DEA in sphingomonads. Therefore, this work finds a missing link in the biochemical pathway that carries out the mineralization of chloroacetanilide herbicides in sphingomonads. Additionally, the results expand our understanding of the degradation of a special kind of aniline derivative.
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Abdallah K, Hartman K, Pletzer D, Zhurina D, Ullrich MS. The bacteriophage-derived transcriptional regulator, LscR, activates the expression of levansucrase genes in Pseudomonas syringae. Mol Microbiol 2016; 102:1062-1074. [PMID: 27664099 DOI: 10.1111/mmi.13536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 11/30/2022]
Abstract
Synthesis of the exopolysaccharide levan occurs in the bacterial blight pathogen of soybean, Pseudomonas syringae pv. glycinea PG4180, when this bacterium encounters moderate to high concentrations of sucrose inside its host plant. The process is mediated by the temperature-dependent expression and secretion of two levansucrases, LscB and LscC. Previous studies showed the importance of a prophage-associated promoter element in driving the expression of levansucrase genes. Herein, heterologous screening for transcriptional activators revealed that the prophage-borne transcriptional regulator, LscR, from P. syringae mediates expression of levansucrase. A lscR-deficient mutant was generated and exhibited a levan-negative phenotype when grown on a sucrose-rich medium. This phenotype was confirmed by zymographic analysis and Western blots which demonstrated absence of levansucrase in the supernatant and total cell lysates. Transcriptional analysis showed a down-regulation of expression levels of levansucrase and glycosyl hydrolase genes in the lscR-deficient mutant. Ultimately, a direct binding of LscR to the promoter region of levansucrase was demonstrated using electrophoretic mobility shift assays allowing to conclude that a bacteriophage-derived regulator dictates expression of bacterial genes involved in in planta fitness.
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Affiliation(s)
- Khaled Abdallah
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Katharina Hartman
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Daniel Pletzer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Daria Zhurina
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Matthias S Ullrich
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
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The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part III. {[Fe2S2](Cys)3(X)} (X=Asp, Arg, His) and {[Fe2S2](Cys)2(His)2} proteins. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.07.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Udaondo Z, Molina L, Segura A, Duque E, Ramos JL. Analysis of the core genome and pangenome ofPseudomonas putida. Environ Microbiol 2015; 18:3268-3283. [DOI: 10.1111/1462-2920.13015] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 08/04/2015] [Accepted: 08/06/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Zulema Udaondo
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Lázaro Molina
- Department of Environmental Protection; Estación Experimental del Zaidín; Consejo Superior de Investigaciones Científicas. C/ Profesor Albareda 1 18008 Granada Spain
| | - Ana Segura
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Estrella Duque
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
| | - Juan L. Ramos
- Biotechnology Technological Area; Abengoa Research; Calle Energía Solar 1, Building E, Campus Palmas Altas 41014 Sevilla Spain
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Liu Y, Liu K, Yu X, Li B, Cao B. Identification and control of a Pseudomonas spp (P. fulva and P. putida) bloodstream infection outbreak in a teaching hospital in Beijing, China. Int J Infect Dis 2014; 23:105-8. [PMID: 24747963 DOI: 10.1016/j.ijid.2014.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 02/04/2014] [Accepted: 02/12/2014] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES An outbreak of bacteremia caused by Pseudomonas spp (P. fulva and P. putida) was first identified in our hospital in the summer of 2010 and reoccurred in the following year. Based on the epidemiological data collected in these 2 years, we initiated an investigation on the source of the outbreak. The aim of this study was to report the results of the investigation, as well as the intervention strategies that resulted in successful control of the outbreak. METHODS An infection control team was set up consisting of infectious disease specialists, microbiologists, infection control practitioners, and head nurses. The microbiology and medical records of case-patients with P. fulva or P. putida bloodstream infections were reviewed. Environmental samples and intravenous (IV) solutions from the wards and the pharmacy center were collected for culturing. The molecular characteristics of the bacterial isolates were studied by pulsed-field gel electrophoresis (PFGE). Strict infection control strategies were implemented. RESULTS A total of 20 case-patients from five inpatient wards were identified during three summer seasons from 2010 to 2012. Nineteen of them recovered with proper antibiotics. Unfortunately one died from complications of heart failure. A total of 19 isolates of P. fulva and four of P. putida were identified, of which 20 were from blood, two from environmental surface samples from the hospital pharmacy, and one from an in-use compounded solution from a case-patient in the cardiology ward. Molecular analysis revealed that the P. fulva isolated from the in-use compounded solution (5% glucose solution containing insulin, isosorbide dinitrate, and potassium magnesium aspartate) and the environmental samples had the same PFGE type as the clinical isolates. CONCLUSIONS The investigation identified that contaminated IV solution was the source of the P. fulva bacteremia, which prompted us to implement intensified control measures that resulted in successful control of the outbreak.
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Affiliation(s)
- Yingmei Liu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Gongren Tiyuchang South Road, Chaoyang District, Beijing 100020, People's Republic of China; Beijing Institute of Respiratory Medicine, Beijing, People's Republic of China; Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Beijing, People's Republic of China
| | - Kun Liu
- Department of Infection Control, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Xiaomin Yu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Gongren Tiyuchang South Road, Chaoyang District, Beijing 100020, People's Republic of China; Beijing Institute of Respiratory Medicine, Beijing, People's Republic of China; Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Beijing, People's Republic of China
| | - Binbin Li
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Gongren Tiyuchang South Road, Chaoyang District, Beijing 100020, People's Republic of China; Beijing Institute of Respiratory Medicine, Beijing, People's Republic of China; Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Beijing, People's Republic of China
| | - Bin Cao
- Department of Infectious Diseases and Clinical Microbiology, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Gongren Tiyuchang South Road, Chaoyang District, Beijing 100020, People's Republic of China; Beijing Institute of Respiratory Medicine, Beijing, People's Republic of China; Beijing Key Laboratory of Respiratory and Pulmonary Circulation, Beijing, People's Republic of China.
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Bodilis J, Nsigue-Meilo S, Besaury L, Quillet L. Variable copy number, intra-genomic heterogeneities and lateral transfers of the 16S rRNA gene in Pseudomonas. PLoS One 2012; 7:e35647. [PMID: 22545126 PMCID: PMC3335818 DOI: 10.1371/journal.pone.0035647] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 03/19/2012] [Indexed: 11/18/2022] Open
Abstract
Even though the 16S rRNA gene is the most commonly used taxonomic marker in microbial ecology, its poor resolution is still not fully understood at the intra-genus level. In this work, the number of rRNA gene operons, intra-genomic heterogeneities and lateral transfers were investigated at a fine-scale resolution, throughout the Pseudomonas genus. In addition to nineteen sequenced Pseudomonas strains, we determined the 16S rRNA copy number in four other Pseudomonas strains by Southern hybridization and Pulsed-Field Gel Electrophoresis, and studied the intra-genomic heterogeneities by Denaturing Gradient Gel Electrophoresis and sequencing. Although the variable copy number (from four to seven) seems to be correlated with the evolutionary distance, some close strains in the P. fluorescens lineage showed a different number of 16S rRNA genes, whereas all the strains in the P. aeruginosa lineage displayed the same number of genes (four copies). Further study of the intra-genomic heterogeneities revealed that most of the Pseudomonas strains (15 out of 19 strains) had at least two different 16S rRNA alleles. A great difference (5 or 19 nucleotides, essentially grouped near the V1 hypervariable region) was observed only in two sequenced strains. In one of our strains studied (MFY30 strain), we found a difference of 12 nucleotides (grouped in the V3 hypervariable region) between copies of the 16S rRNA gene. Finally, occurrence of partial lateral transfers of the 16S rRNA gene was further investigated in 1803 full-length sequences of Pseudomonas available in the databases. Remarkably, we found that the two most variable regions (the V1 and V3 hypervariable regions) had probably been laterally transferred from another evolutionary distant Pseudomonas strain for at least 48.3 and 41.6% of the 16S rRNA sequences, respectively. In conclusion, we strongly recommend removing these regions of the 16S rRNA gene during the intra-genus diversity studies.
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Affiliation(s)
- Josselin Bodilis
- Laboratoire M2C, Université de Rouen, UMR CNRS 6143, Mont Saint Aignan, France.
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Rühl J, Hein EM, Hayen H, Schmid A, Blank LM. The glycerophospholipid inventory of Pseudomonas putida is conserved between strains and enables growth condition-related alterations. Microb Biotechnol 2012; 5:45-58. [PMID: 21895997 PMCID: PMC3815271 DOI: 10.1111/j.1751-7915.2011.00286.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/28/2022] Open
Abstract
Microorganisms, such as Pseudomonas putida, utilize specific physical properties of cellular membrane constituents, mainly glycerophospholipids, to (re-)adjust the membrane barrier to environmental stresses. Building a basis for membrane composition/function studies, we inventoried the glycerophospholipids of different Pseudomonas and challenged membranes of growing cells with n-butanol. Using a new high-resolution liquid chromatography/mass spectrometry (LC/MS) method, 127 glycerophospholipid species [e.g. phosphatidylethanolamine PE(32:1)] with up to five fatty acid combinations were detected. The glycerophospholipid inventory consists of 305 distinct glycerophospholipids [e.g. PE(16:0/16:1)], thereof 14 lyso-glycerophospholipids, revealing conserved compositions within the four investigated pseudomonads P. putida KT2440, DOT-T1E, S12 and Pseudomonas sp. strain VLB120. Furthermore, we addressed the influence of environmental conditions on the glycerophospholipid composition of Pseudomonas via long-time exposure to the sublethal n-butanol concentration of 1% (v/v), focusing on: (i) relative amounts of glycerophospholipid species, (ii) glycerophospholipid head group composition, (iii) fatty acid chain length, (iv) degree of saturation and (v) cis/trans isomerization of unsaturated fatty acids. Observed alterations consist of changing head group compositions and for the solvent-sensitive strain KT2440 diminished fatty acid saturation degrees. Minor changes in the glycerophospholipid composition of the solvent-tolerant strains P. putida S12 and Pseudomonas sp. VLB120 suggest different strategies of the investigated Pseudomonas to maintain the barrier function of cellular membranes.
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Affiliation(s)
- Jana Rühl
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund, Emil-Figge-Str. 66, 44221 Dortmund, Germany
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Wittgens A, Tiso T, Arndt TT, Wenk P, Hemmerich J, Müller C, Wichmann R, Küpper B, Zwick M, Wilhelm S, Hausmann R, Syldatk C, Rosenau F, Blank LM. Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440. Microb Cell Fact 2011; 10:80. [PMID: 21999513 PMCID: PMC3258213 DOI: 10.1186/1475-2859-10-80] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 10/17/2011] [Indexed: 01/29/2023] Open
Abstract
Background Rhamnolipids are potent biosurfactants with high potential for industrial applications. However, rhamnolipids are currently produced with the opportunistic pathogen Pseudomonas aeruginosa during growth on hydrophobic substrates such as plant oils. The heterologous production of rhamnolipids entails two essential advantages: Disconnecting the rhamnolipid biosynthesis from the complex quorum sensing regulation and the opportunity of avoiding pathogenic production strains, in particular P. aeruginosa. In addition, separation of rhamnolipids from fatty acids is difficult and hence costly. Results Here, the metabolic engineering of a rhamnolipid producing Pseudomonas putida KT2440, a strain certified as safety strain using glucose as carbon source to avoid cumbersome product purification, is reported. Notably, P. putida KT2440 features almost no changes in growth rate and lag-phase in the presence of high concentrations of rhamnolipids (> 90 g/L) in contrast to the industrially important bacteria Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli. P. putida KT2440 expressing the rhlAB-genes from P. aeruginosa PAO1 produces mono-rhamnolipids of P. aeruginosa PAO1 type (mainly C10:C10). The metabolic network was optimized in silico for rhamnolipid synthesis from glucose. In addition, a first genetic optimization, the removal of polyhydroxyalkanoate formation as competing pathway, was implemented. The final strain had production rates in the range of P. aeruginosa PAO1 at yields of about 0.15 g/gglucose corresponding to 32% of the theoretical optimum. What's more, rhamnolipid production was independent from biomass formation, a trait that can be exploited for high rhamnolipid production without high biomass formation. Conclusions A functional alternative to the pathogenic rhamnolipid producer P. aeruginosa was constructed and characterized. P. putida KT24C1 pVLT31_rhlAB featured the highest yield and titer reported from heterologous rhamnolipid producers with glucose as carbon source. Notably, rhamnolipid production was uncoupled from biomass formation, which allows optimal distribution of resources towards rhamnolipid synthesis. The results are discussed in the context of rational strain engineering by using the concepts of synthetic biology like chassis cells and orthogonality, thereby avoiding the complex regulatory programs of rhamnolipid production existing in the natural producer P. aeruginosa.
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Affiliation(s)
- Andreas Wittgens
- Institute for Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52426 Jülich, Germany
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Selected Pseudomonas putida strains able to grow in the presence of high butanol concentrations. Appl Environ Microbiol 2009; 75:4653-6. [PMID: 19411419 DOI: 10.1128/aem.00225-09] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adapted Pseudomonas putida strains grew in the presence of up to 6% (vol/vol) butanol, the highest reported butanol concentration tolerated by a microbe. P. putida might be an alternative host for biobutanol production, overcoming the primary limitation of currently used strains-insufficient product titers due to low butanol tolerance.
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Reva ON, Weinel C, Weinel M, Böhm K, Stjepandic D, Hoheisel JD, Tümmler B. Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 2006; 188:4079-92. [PMID: 16707699 PMCID: PMC1482902 DOI: 10.1128/jb.00101-06] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 03/15/2006] [Indexed: 11/20/2022] Open
Abstract
The metabolically versatile soil bacterium Pseudomonas putida has to cope with numerous abiotic stresses in its habitats. The stress responses of P. putida KT2440 to 4 degrees C, pH 4.5, 0.8 M urea, and 45 mM sodium benzoate were analyzed by determining the global mRNA expression profiles and screening for stress-intolerant nonauxotrophic Tn5 transposon mutants. In 392 regulated genes or operons, 36 gene regions were differentially expressed by more than 2.5-fold, and 32 genes in 23 operons were found to be indispensable for growth during exposure to one of the abiotic stresses. The transcriptomes of the responses to urea, benzoate, and 4 degrees C correlated positively with each other but negatively with the transcriptome of the mineral acid response. The CbrAB sensor kinase, the cysteine synthase CysM, PcnB and VacB, which control mRNA stability, and BipA, which exerts transcript-specific translational control, were essential to cope with cold stress. The cyo operon was required to cope with acid stress. A functional PhoP, PtsP, RelA/SpoT modulon, and adhesion protein LapA were necessary for growth in the presence of urea, and the outer membrane proteins OmlA and FepA and the phosphate transporter PstBACS were indispensable for growth in the presence of benzoate. A lipid A acyltransferase (PP0063) was a mandatory component of the stress responses to cold, mineral acid, and benzoate. Adaptation of the membrane barrier, uptake of phosphate, maintenance of the intracellular pH and redox status, and translational control of metabolism are key mechanisms of the response of P. putida to abiotic stresses.
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Affiliation(s)
- Oleg N Reva
- Klinische Forschergruppe, OE 6710, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30623 Hannover, Germany
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Park W, Peña-Llopis S, Lee Y, Demple B. Regulation of superoxide stress in Pseudomonas putida KT2440 is different from the SoxR paradigm in Escherichia coli. Biochem Biophys Res Commun 2006; 341:51-6. [PMID: 16412384 DOI: 10.1016/j.bbrc.2005.12.142] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 12/20/2005] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, the SoxR regulon orchestrates genes for defense against certain types of oxidative stress through the SoxR-regulated synthesis of the SoxS transcription activator. The Pseudomonas putida genome did not reveal a clear soxS homolog. The P. putida SoxR protein appears to be functional: its expression in an E. coli DeltasoxR strain restored the paraquat inducibility of soxS. Of nine candidate P. putida oxidative stress genes, which are known to be SoxR regulon in E. coli, tested for response to superoxide or nitric oxide, fumC-1, sodA, zwf-1, and particularly fpr, encoding ferredoxin:NADP(+) reductase, were induced, all independent of P. putida soxR. Disruption of the fpr and finR, a regulatory protein that is required for paraquat-dependent expression of the fpr, resulted in more oxidative stress sensitivity. However, a P. putida soxR-deletion strain had normal resistance to the superoxide-generating agent paraquat. The data presented here show that the genetic responses to superoxide stress in P. putida differ markedly from those seen in E. coli and Salmonella, and the role of P. putida soxR remains to be established.
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Affiliation(s)
- Woojun Park
- Division of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seoul.
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Niu C, Gilbert ES. Colorimetric method for identifying plant essential oil components that affect biofilm formation and structure. Appl Environ Microbiol 2004; 70:6951-6. [PMID: 15574886 PMCID: PMC535164 DOI: 10.1128/aem.70.12.6951-6956.2004] [Citation(s) in RCA: 195] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2004] [Accepted: 07/12/2004] [Indexed: 11/20/2022] Open
Abstract
The specific biofilm formation (SBF) assay, a technique based on crystal violet staining, was developed to locate plant essential oils and their components that affect biofilm formation. SBF analysis determined that cinnamon, cassia, and citronella oils differentially affected growth-normalized biofilm formation by Escherichia coli. Examination of the corresponding essential oil principal components by the SBF assay revealed that cinnamaldehyde decreased biofilm formation compared to biofilms grown in Luria-Bertani broth, eugenol did not result in a change, and citronellol increased the SBF. To evaluate these results, two microscopy-based assays were employed. First, confocal laser scanning microscopy (CLSM) was used to examine E. coli biofilms cultivated in flow cells, which were quantitatively analyzed by COMSTAT, an image analysis program. The overall trend for five parameters that characterize biofilm development corroborated the findings of the SBF assay. Second, the results of an assay measuring growth-normalized adhesion by direct microscopy concurred with the results of the SBF assay and CLSM imaging. Viability staining indicated that there was reduced toxicity of the essential oil components to cells in biofilms compared to the toxicity to planktonic cells but revealed morphological damage to E. coli after cinnamaldehyde exposure. Cinnamaldehyde also inhibited the swimming motility of E. coli. SBF analysis of three Pseudomonas species exposed to cinnamaldehyde, eugenol, or citronellol revealed diverse responses. The SBF assay could be useful as an initial step for finding plant essential oils and their components that affect biofilm formation and structure.
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Affiliation(s)
- C Niu
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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17
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Hirkala DLM, Germida JJ. Field and soil microcosm studies on the survival and conjugation of aPseudomonas putidastrain bearing a recombinant plasmid, pADPTel. Can J Microbiol 2004; 50:595-604. [PMID: 15467785 DOI: 10.1139/w04-045] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pseudomonas putida CR30RNS (pADPTel) is an antibiotic-resistant strain with a recombinant plasmid that confers resistance to tellurite and the ability to catabolize atrazine. The survival of this strain as well as its ability to transfer genes for atrazine degradation and tellurite resistance to indigenous soil bacteria were tested in both fallow soil and canola (Brassica napus) rhizosphere by the use of parallel field and laboratory releases. Culturable CR30RNS (pADPTel) were enumerated in field and microcosm soils at 7- to 14-day intervals over 49 d. Strain CR30RNS (pADPTel) survived for up to 7 weeks in microcosm soils at a density of 104CFU/g soil, whereas in field soils the population declined to 103CFU/g soil by the fourth week. In contrast, when CR30RNS (pADPTel) was introduced into the soil as a seed coating of canola (B. napus 'Karoo'), the bacterium established at higher cell densities in the rhizosphere (106–105CFU/g fresh root mass), with no subsequent decrease in numbers. The presence of selective pressure (i.e., atrazine) had no significant effect on the survival of CR30RNS (pADPTel) in either field or microcosm soils. One year postinoculation field sites were examined for the presence of CR30RNS (pADPTel) and no evidence of culturable parental cells was observed when samples were plated onto selective media. However, the atzC and telAB gene segments were amplified from the field soils at that time. Under laboratory conditions, indigenous soil bacteria were capable of receiving and expressing the engineered plasmid construct at frequencies ranging from 1 to 10-3transconjugants per donor. However, no plasmid transfer to indigenous soil bacteria was detected in the field or microcosm soils regardless of the presence of canola rhizosphere and (or) the application of atrazine. Our results show that the survival and population size of P. putida CR30RNS (pADPTel) might be sufficient for degradation of environmental pollutants but that the transfer frequency was too low to be detected under the conditions of this study.Key words: Pseudomonas putida CR30RNS (pADPTel), survival, gene transfer, field, microcosm.
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Affiliation(s)
- Danielle L M Hirkala
- Department of Applied Microbiology and Food Science, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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Yomoda S, Okubo T, Takahashi A, Murakami M, Iyobe S. Presence of Pseudomonas putida strains harboring plasmids bearing the metallo-beta-lactamase gene bla(IMP) in a hospital in Japan. J Clin Microbiol 2003; 41:4246-51. [PMID: 12958252 PMCID: PMC193810 DOI: 10.1128/jcm.41.9.4246-4251.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To determine the persistence and spread of antibiotic-resistant strains in Gunma University Hospital, 83 Pseudomonas putida strains (each from a different patient) were isolated from January 1997 through December 2001. Of the 83 strains isolated, 27 were resistant to carbapenems. All 27 produced metallo-beta-lactamase and were found to be PCR positive for the bla(IMP) gene. Most (22 strains) were primarily isolated from the wards (W7 [9 strains] and W4 [8 strains]). Another five bla(IMP)-positive P. putida strains from wards W7 and W4 were obtained by swabbing around the water pipes. A total of 32 bla(IMP)-positive P. putida strains were assessed by pulsed-field gel electrophoresis (PFGE) and testing of drug susceptibility to 10 chemotherapeutic agents. Both PFGE and MIC patterns revealed that there were long-term resident strains among inpatients and hospital environments. The bla(IMP) genes of 22 of 32 strains were all transferable to a recipient strain of Pseudomonas aeruginosa by conjugation or transformation and conferred resistance to carbapenems and cephems. The bla(IMP) plasmids were conjugally transmissible among P. aeruginosa strains and mediated resistance to amikacin as well as beta-lactams. Ten of the 22 plasmids mediated additional resistance to gentamicin and tobramycin. Plasmids with identical DNA and drug resistance patterns were found in P. putida strains with identical PFGE patterns and with different PFGE patterns. We presumed that P. putida was one of the resident species in inpatients and especially in hospital environments, spreading drug resistance genes via plasmids among P. putida strains and supplying them to more pathogenically important species, such as P. aeruginosa.
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Affiliation(s)
- Sachie Yomoda
- Department of Laboratory Medicine and Clinical Laboratory Center, Gunma University School of Medicine, 3-39-22, Showa-machi, Maebashi 371-8511, Japan
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19
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Abu-Lail NI, Camesano TA. Role of ionic strength on the relationship of biopolymer conformation, DLVO contributions, and steric interactions to bioadhesion of Pseudomonas putida KT2442. Biomacromolecules 2003; 4:1000-12. [PMID: 12857085 DOI: 10.1021/bm034055f] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biopolymers produced extracellularly by Pseudomonas putida KT2442 were examined via atomic force microscopy (AFM) and single molecule force spectroscopy. Surface biopolymers were probed in solutions with added salt concentrations ranging from that of pure water to 1 M KCl. By studying the physicochemical properties of the polymers over this range of salt concentrations, we observed a transition in the steric and electrostatic properties and in the conformation of the biopolymers that were each directly related to bioadhesion. In low salt solutions, the electrophoretic mobility of the bacterium was negative, and large theoretical energy barriers to adhesion were predicted from soft-particle DLVO theory calculations. The brush layer in low salt solution was extended due to electrostatic repulsion, and therefore, steric repulsion was also high (polymers extended 440 nm from surface in pure water). The extended polymer brush layer was "soft", characterized by the slope of the compliance region of the AFM approach curves (-0.014 nN/nm). These properties resulted in low adhesion between biopolymers and the silicon nitride AFM tip. As the salt concentration increased to > or =0.01 M, a transition was observed toward a more rigid and compressed polymer brush layer, and the adhesion forces increased. In 1 M KCl, the polymer brush extended 120 nm from the surface and the rigidity of the outer cell surface was greater (slope of the compliance region = -0.114 nN/nm). A compressed and more rigid polymer layer, as well as a less negative electrophoretic mobility for the bacterium, resulted in higher adhesion forces between the biopolymers and the AFM tip. Scaling theories for polyelectrolyte brushes were also used to explain the behavior of the biopolymer brush layer as a function of salt concentration.
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Affiliation(s)
- Nehal I Abu-Lail
- Department of Chemical Engineering, Worcester Polytechnic Institute, 100 Institute Rd., Worcester, Massachusetts 01609, USA
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20
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Komatsu H, Imura Y, Ohori A, Nagata Y, Tsuda M. Distribution and organization of auxotrophic genes on the multichromosomal genome of Burkholderia multivorans ATCC 17616. J Bacteriol 2003; 185:3333-43. [PMID: 12754231 PMCID: PMC155387 DOI: 10.1128/jb.185.11.3333-3343.2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Burkholderia multivorans strain ATCC 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 Mb. To determine the distribution and organization of the amino acid biosynthetic genes on the genome of this beta-proteobacterium, various auxotrophic mutations were isolated using a Tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. Analysis by pulsed-field gel electrophoresis revealed that 20 out of 23 insertion mutations were distributed on the 3.4-Mb chromosome. More detailed analysis of the his, trp, arg, and lys mutations and their flanking regions revealed the following properties of these auxotrophic genes: (i) all nine his genes were clustered on the 3.4-Mb chromosome; (ii) seven trp genes were organized within two distinct regions, i.e., a trpEGDC cluster on the 3.4-Mb chromosome and a trpFBA cluster on the 2.5-Mb chromosome; (iii) the leu gene cluster, leuCDB, was also located close to the trpFBA cluster; and (iv) lysA and argG genes were located on the 2.5-Mb chromosome, in contrast to the argH gene, which was located on the 3.4-Mb chromosome. Southern hybridization analysis, allelic exchange mutagenesis of ATCC 17616, and complementation tests demonstrated that all of the genes examined were functional and existed as a single copy within the genome. The present findings also indicated that the 2.5-Mb chromosome carried various auxotrophic genes with no structural or functional counterparts on the remaining two chromosomes.
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Affiliation(s)
- Harunobu Komatsu
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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21
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Felske A, Vandieken V, Pauling BV, von Canstein HF, Wagner-Döbler I. Molecular quantification of genes encoding for green-fluorescent proteins. J Microbiol Methods 2003; 52:297-304. [PMID: 12531498 DOI: 10.1016/s0167-7012(02)00184-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A quantitative PCR approach is presented to analyze the amount of recombinant green fluorescent protein (gfp) genes in environmental DNA samples. The quantification assay is a combination of specific PCR amplification and temperature gradient gel electrophoresis (TGGE). Gene quantification is provided by a competitively coamplified DNA standard constructed by point mutation PCR. A single base difference was introduced to achieve a suitable migration difference in TGGE between the original target DNA and the modified standard without altering the PCR amplification efficiency. This competitive PCR strategy is a highly specific and sensitive way to monitor recombinant DNA in environments like the efflux of a biotechnological plant.
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Affiliation(s)
- A Felske
- GBF (German Research Center for Biotechnology), Division of Microbiology, Mascheroder Weg 1, D-38124 Braunschweig, Germany.
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22
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23
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Stjepandić D, Weinel C, Hilbert H, Koo HL, Diehl F, Nelson KE, Tümmler B, Hoheisel JD. The genome structure of Pseudomonas putida: high-resolution mapping and microarray analysis. Environ Microbiol 2002; 4:819-23. [PMID: 12534465 DOI: 10.1046/j.1462-2920.2002.00313.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
As part of a collaborative project aimed at sequencing and functionally analysing the entire genome of Pseudomonas putida strain KT2440, a physical clone map was produced as an initial resource. To this end, a high-coverage cosmid library was arrayed and ordered by clone hybridizations. Restriction fragments generated by rare-cutting enzymes and plasmids containing the rrn operon and 23S rDNA of Pseudomonas aeruginosa were used as probes and, parts of the cosmids were end-sequenced. This provided the information necessary for merging and comparing the macro-restriction map, cosmid clone order and sequence information, thereby assuring co-linearity of the eventual sequence assembly with the actual genome. A tiling path of clones was selected, from the shotgun clones used for sequencing, for the production of DNA microarrays that represent the entire genome including its non-coding portions.
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Affiliation(s)
- Diana Stjepandić
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, D-69120 Heidelberg, Germany.
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24
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Lombardi G, Luzzaro F, Docquier JD, Riccio ML, Perilli M, Colì A, Amicosante G, Rossolini GM, Toniolo A. Nosocomial infections caused by multidrug-resistant isolates of pseudomonas putida producing VIM-1 metallo-beta-lactamase. J Clin Microbiol 2002; 40:4051-5. [PMID: 12409373 PMCID: PMC139695 DOI: 10.1128/jcm.40.11.4051-4055.2002] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Successful carbapenem-based chemotherapy for the treatment of Pseudomonas infections has been seriously hindered by the recent appearance of IMP- and VIM-type metallo-beta-lactamases, which confer high-level resistance to carbapenems and most other beta-lactams. Recently, multidrug-resistant Pseudomonas putida isolates for which carbapenem MICs were >/=32 micro g/ml were recovered from cultures of urine from three inpatients in the general intensive care unit of the Ospedale di Circolo, Varese, Italy. Enzyme assays revealed production of a metallo-beta-lactamase activity, while molecular analysis detected in each isolate a bla(VIM-1) determinant carried by an apparently identical medium-sized plasmid. Conjugation experiments were unsuccessful in transferring the beta-lactamase determinant to Escherichia coli or Pseudomonas aeruginosa. Macrorestriction analysis by pulsed-field gel electrophoresis demonstrated that the isolates were of clonal origin. PCR mapping and sequencing of the variable region of the plasmid-borne class 1 integron carrying the bla(VIM-1) determinant (named In110) showed that the bla(VIM-1)-containing cassette was identical to that previously found in strains of different species from other Italian hospitals and that the cassette array of In110 was not identical but clearly related to that of In70 (a bla(VIM-1)-containing plasmid-borne integron from an Achromobacter xylosoxidans isolate), pointing to a common origin of this cassette and to a related evolutionary history of their cognate integrons.
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Affiliation(s)
- Gianluigi Lombardi
- Laboratorio di Microbiologia, Ospedale di Circolo, and Università dell'Insubria, I-21100 Varese, Italy
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25
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Tobes R, Ramos JL. AraC-XylS database: a family of positive transcriptional regulators in bacteria. Nucleic Acids Res 2002; 30:318-21. [PMID: 11752325 PMCID: PMC99111 DOI: 10.1093/nar/30.1.318] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The AraC-XylS database contains information about a family of positive transcriptional regulators broadly distributed in bacteria. This specific database focuses on protein sequences and on the biological and functional features of each of the proteins that belong to this family. Each entry provides information on the protein itself, the annotated protein sequence and, when the crystal is available, a comprehensive representation of its three-dimensional structure. The organization of the database is based on an exhaustive analysis of the scientific literature. The data are interconnected and linked with other databases. Multiple alignments of the members of the family, an extensive collection of references and a tutorial about the family provide additional information. The AraC-XylS database is accessible on the World Wide Web at http://www.AraC-XylS.org.
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Affiliation(s)
- Raquel Tobes
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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26
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Weinel C, Tümmler B, Hilbert H, Nelson KE, Kiewitz C. General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440. Nucleic Acids Res 2001; 29:E110. [PMID: 11713330 PMCID: PMC92575 DOI: 10.1093/nar/29.22.e110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of SwaI- or I-CeuI-restricted chromosomes to serve as a backbone for the quick quality control of sequence and contig assemblies. The library of PCR-generated SwaI linking probes was derived from the sequence assembly after 3- and 6-fold genome coverage. In order to support gap closure in regions with ambiguous assemblies such as the repetitive sequence of the seven ribosomal operons, high-resolution Smith/Birnstiel maps were generated by Southern hybridisation of pulsed-field gel electrophoresis-separated rare-cutter complete/frequent-cutter partial digestions with rare-cutter fragment end probes. Overall 1.5 Mb of the 6.1 Mb P.putida KT2440 genome has been subjected to high-resolution physical mapping in order to align assemblies generated from shotgun sequencing.
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Affiliation(s)
- C Weinel
- Klinische Forschergruppe OE 6711, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.
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27
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Thirup L, Johnsen K, Winding A. Succession of indigenous Pseudomonas spp. and actinomycetes on barley roots affected by the antagonistic strain Pseudomonas fluorescens DR54 and the fungicide imazalil. Appl Environ Microbiol 2001; 67:1147-53. [PMID: 11229904 PMCID: PMC92707 DOI: 10.1128/aem.67.3.1147-1153.2001] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2000] [Accepted: 12/21/2000] [Indexed: 11/20/2022] Open
Abstract
In recent years, the interest in the use of bacteria for biological control of plant-pathogenic fungi has increased. We studied the possible side effects of coating barley seeds with the antagonistic strain Pseudomonas fluorescens DR54 or a commercial fungicide, imazalil. This was done by monitoring the number of indigenous Pseudomonas organisms and actinomycetes on barley roots during growth in soil, harvest after 50 days, and subsequent decomposition. Bacteria were enumerated by traditional plate spreading on Gould's S1 agar (Pseudomonas) and as filamentous colonies on Winogradsky agar (actinomycetes) and by two quantitative competitive PCR assays. For this we developed an assay targeting Streptomyces and closely related genera. DR54 constituted more than 75% of the Pseudomonas population at the root base during the first 21 days but decreased to less than 10% at day 50. DR54 was not successful in colonizing root tips. Initially, DR54 affected the number of indigenous Pseudomonas organisms negatively, whereas imazalil affected Pseudomonas numbers positively, but the effects were transient. Although plate counts were considerably lower than the number of DNA copies, the two methods correlated well for Pseudomonas during plant growth, but after plant harvest Pseudomonas-specific DNA copy numbers decreased while plate counts were in the same magnitude as before. Hence, Pseudomonas was 10-fold more culturable in a decomposition environment than in the rhizosphere. The abundance of actinomycetes was unaffected by DR54 or imazalil amendments, and CFU and quantitative PCR results correlated throughout the experiment. The abundance of actinomycetes increased gradually, mostly in numbers of DNA copies, confirming their role in colonizing old roots.
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Affiliation(s)
- L Thirup
- Department of Microbial Ecology and Biotechnology, National Environmental Research Institute, Roskilde, Denmark
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28
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Ramos C, Molina L, Mølbak L, Ramos JL, Molin S. A bioluminescent derivative of Pseudomonas putida KT2440 for deliberate release into the environment. FEMS Microbiol Ecol 2000; 34:91-102. [PMID: 11102686 DOI: 10.1111/j.1574-6941.2000.tb00758.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Recombinant derivatives of Pseudomonas putida strain KT2440 are of potential interest as microbial inoculants to be deliberately released for agricultural applications. To facilitate tracking of this strain and its derivatives after introduction into the environment, a mini-Tn5-'luxAB transposon was introduced into the chromosome of P. putida KT2440, yielding strain P. putida S1B1. Sequencing of the DNA region located upstream of the 'luxAB genes and similarity search with the P. putida KT2440 genome sequence, localized the transposon within a 3021-bp open reading frame (ORF), whose translated sequence showed significant similarity with the hypothetical YdiJ proteins from Escherichia coli and Haemophilus influenzae. A second ORF adjacent to and divergent from the ydiJ sequence was also found and showed significant homology with various LysR-type transcriptional activator proteins from several bacteria. Disruption of the ydiJ locus in P. putida S1B1 did not affect the survival of the strain in unvegetated or vegetated soils. Bioluminescent detection of P. putida S1B1 cells enriched in selective media directly from soil allowed detection of culturable cells in soil samples over a period of at least 8 months. The addition of the luxAB biomarker facilitates tracking in the root system of several plant species grown under sterile and non-sterile conditions. The correlation of the bioluminescent phenotype with the growth activity of P. putida S1B1 cells colonizing the root system of barley and corn plants was estimated by monitoring ribosomal contents using quantitative hybridization with fluorescence-labeled ribosomal RNA probes. A correlation between inoculum density, light output, and ribosomal contents was found for P. putida cells colonizing the root system of barley seedlings grown under sterile conditions. Although ribosomal contents, and therefore growth activity, of P. putida S1B1 cells extracted from the rhizosphere of corn plants grown in non-sterile soil were similar to those found in starved cells, the luminescent system permitted non-destructive in situ detection of the strain in the upper root system.
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29
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Heydorn A, Nielsen AT, Hentzer M, Sternberg C, Givskov M, Ersbøll BK, Molin S. Quantification of biofilm structures by the novel computer program COMSTAT. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 10):2395-2407. [PMID: 11021916 DOI: 10.1099/00221287-146-10-2395] [Citation(s) in RCA: 1587] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas: putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as substrate. Analysis by the COMSTAT program of four variables describing biofilm structure - mean thickness, roughness, substratum coverage and surface to volume ratio - showed that the four Pseudomonas: strains represent different modes of biofilm growth. P. putida had a unique developmental pattern starting with single cells on the substratum growing into micro-colonies, which were eventually succeeded by long filaments and elongated cell clusters. P. aeruginosa colonized the entire substratum, and formed flat, uniform biofilms. P. aureofaciens resembled P. aeruginosa, but had a stronger tendency to form micro-colonies. Finally, the biofilm structures of P. fluorescens had a phenotype intermediate between those of P. putida and P. aureofaciens. Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration. Moreover, biofilm roughness increased with lower citrate concentrations, whereas surface to volume ratio increased with higher citrate concentrations.
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Affiliation(s)
- Arne Heydorn
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
| | - Alex Toftgaard Nielsen
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
| | - Morten Hentzer
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
| | - Claus Sternberg
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
| | - Michael Givskov
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
| | - Bjarne Kjær Ersbøll
- Department of Mathematical Modelling, The Technical University of Denmark, DK-2800 Lyngby, Denmark2
| | - Søren Molin
- Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark1
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30
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Eberl L, Ammendola A, Rothballer MH, Givskov M, Sternberg C, Kilstrup M, Schleifer KH, Molin S. Inactivation of gltB abolishes expression of the assimilatory nitrate reductase gene (nasB) in Pseudomonas putida KT2442. J Bacteriol 2000; 182:3368-76. [PMID: 10852866 PMCID: PMC101894 DOI: 10.1128/jb.182.12.3368-3376.2000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By using mini-Tn5 transposon mutagenesis, random transcriptional fusions of promoterless bacterial luciferase, luxAB, to genes of Pseudomonas putida KT2442 were generated. Insertion mutants that responded to ammonium deficiency by induction of bioluminescence were selected. The mutant that responded most strongly was genetically analyzed and is demonstrated to bear the transposon within the assimilatory nitrate reductase gene (nasB) of P. putida KT2442. Genetic evidence as well as sequence analyses of the DNA regions flanking nasB suggest that the genes required for nitrate assimilation are not clustered. We isolated three second-site mutants in which induction of nasB expression was completely abolished under nitrogen-limiting conditions. Nucleotide sequence analysis of the chromosomal junctions revealed that in all three mutants the secondary transposon had inserted at different sites in the gltB gene of P. putida KT2442 encoding the major subunit of the glutamate synthase. A detailed physiological characterization of the gltB mutants revealed that they are unable to utilize a number of potential nitrogen sources, are defective in the ability to express nitrogen starvation proteins, display an aberrant cell morphology under nitrogen-limiting conditions, and are impaired in the capacity to survive prolonged nitrogen starvation periods.
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Affiliation(s)
- L Eberl
- Lehrstuhl für Mikrobiologie, Technische Universität München, D-85350 Freising, Germany.
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31
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Abstract
Retrotransfer of DNA refers to the phenomenon by which a plasmid travels from a host strain to a recipient one and returns to the original host, bringing with it DNA from the recipient. The resultant host strain with DNA from the recipient is called a retrotransconjugant. The retrotransfer phenomenon mediated by the TOL plasmid pWW0 and other plasmids has been documented on plates under optimal laboratory culture conditions, but never under natural conditions. In this work, we show that retrotransfer mediated by the IncP9 TOL pWW0 plasmid occurs in the rhizosphere, a niche in which the continuous supply of nutrients via root exudates allows cells to reach a high density. This suggests that this unusual sexual fertilization may be of great importance in lateral gene transfer. We also show that retrotransfer of DNA seems to require co-integration of the plasmid and the host chromosome and subsequent resolution, because a TOL plasmid with a mutation in the tnpR gene, encoding the resolvase of the Tn4653 of the TOL plasmid, was self-transferred between Pseudomonas strains, but unable to mobilize chromosome.
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Affiliation(s)
- M C Ronchel
- Department of Plant Biochemistry, CSIC-Estación Experimental del Saidín, Granada, Spain
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Smith LM, Tola E, deBoer P, O'Gara F. Signalling by the fungus Pythium ultimum represses expression of two ribosomal RNA operons with key roles in the rhizosphere ecology of Pseudomonas fluorescens F113. Environ Microbiol 1999; 1:495-502. [PMID: 11207771 DOI: 10.1046/j.1462-2920.1999.00067.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas fluorescens F113 produces antifungal metabolites that protect the roots of sugarbeet from the fungus Pythium ultimum. The phytopathogen, in turn, has the ability to downregulate the expression of genes fundamental to the rhizosphere competence of the bacterial strain. This paper describes the characterization of two of these genes, which were isolated by screening a mini-Tn5::lacZ mutant bank for differential expression of beta-galactosidase in the presence of P. ultimum. In order to identify the genes affected in reporter mutants SF3 and SF5, the transposons and flanking regions were cloned. Sequence analysis of the regions flanking the transposons in SF3 revealed that mini-Tn5::lacZ had inserted into a tRNA(Ile) gene, which maps within a ribosomal RNA (rrn) operon. In SF5, the transposon inserted between the promoter of a second rrn operon and a gene encoding a 16S rRNA. Southern blot analysis demonstrated that there are five rrn operons in P. fluorescens F113 and that the transposons in SF3 and SF5 had inserted into two different operons. Further characterization of these mutants suggests that their reduced rhizosphere competence is not the result of reduced viability in the short term but may be accounted for partly by reduced growth rates under conditions that support rapid growth. Analysis of lacZ expression in the reporter mutants indicate that the marked rrn operons are regulated differently, suggesting different physiological roles.
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Affiliation(s)
- L M Smith
- Department of Microbiology, National University of Ireland, Cork
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Frangeul L, Nelson KE, Buchrieser C, Danchin A, Glaser P, Kunst F. Cloning and assembly strategies in microbial genome projects. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 10):2625-34. [PMID: 10537184 DOI: 10.1099/00221287-145-10-2625] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L Frangeul
- Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, Paris, France
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