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Romaniuk K, Golec P, Dziewit L. Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. Front Microbiol 2018; 9:3144. [PMID: 30619210 PMCID: PMC6305408 DOI: 10.3389/fmicb.2018.03144] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/04/2018] [Indexed: 11/13/2022] Open
Abstract
Arthrobacter spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.
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Affiliation(s)
- Krzysztof Romaniuk
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Piotr Golec
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
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Niu H, Yang W, Zhuang K, Chen X, Chen Y, Liu D, Wu J, Zhu C, Ying H. Screening of promoters from Arthrobacter sp. CGMCC 3584 using a green fluorescent protein reporter system. World J Microbiol Biotechnol 2017; 33:208. [DOI: 10.1007/s11274-017-2375-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/29/2017] [Indexed: 11/29/2022]
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Abstract
The survival capacity of microorganisms in a contaminated environment is limited by the concentration and/or toxicity of the pollutant. Through evolutionary processes, some bacteria have developed or acquired mechanisms to cope with the deleterious effects of toxic compounds, a phenomenon known as tolerance. Common mechanisms of tolerance include the extrusion of contaminants to the outer media and, when concentrations of pollutants are low, the degradation of the toxic compound. For both of these approaches, plasmids that encode genes for the degradation of contaminants such as toluene, naphthalene, phenol, nitrobenzene, and triazine or are involved in tolerance toward organic solvents and heavy metals, play an important role in the evolution and dissemination of these catabolic pathways and efflux pumps. Environmental plasmids are often conjugative and can transfer their genes between different strains; furthermore, many catabolic or efflux pump genes are often associated with transposable elements, making them one of the major players in bacterial evolution. In this review, we will briefly describe catabolic and tolerance plasmids and advances in the knowledge and biotechnological applications of these plasmids.
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Dib JR, Wagenknecht M, Farías ME, Meinhardt F. Strategies and approaches in plasmidome studies-uncovering plasmid diversity disregarding of linear elements? Front Microbiol 2015; 6:463. [PMID: 26074886 PMCID: PMC4443254 DOI: 10.3389/fmicb.2015.00463] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/28/2015] [Indexed: 01/01/2023] Open
Abstract
The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions.
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Affiliation(s)
- Julián R Dib
- Planta Piloto de Procesos Industriales Microbiológicos-Consejo Nacional de Investigaciones Científicas y Técnicas , Tucumán, Argentina ; Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany ; Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán , Tucumán, Argentina
| | - Martin Wagenknecht
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany ; Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster , Münster, Germany
| | - María E Farías
- Planta Piloto de Procesos Industriales Microbiológicos-Consejo Nacional de Investigaciones Científicas y Técnicas , Tucumán, Argentina
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany
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Soh EYC, Chhabra SR, Halliday N, Heeb S, Müller C, Birmes FS, Fetzner S, Cámara M, Chan KG, Williams P. Biotic inactivation of the Pseudomonas aeruginosa quinolone signal molecule. Environ Microbiol 2015; 17:4352-65. [PMID: 25809238 DOI: 10.1111/1462-2920.12857] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Abstract
In Pseudomonas aeruginosa, quorum sensing (QS) regulates the production of secondary metabolites, many of which are antimicrobials that impact on polymicrobial community composition. Consequently, quenching QS modulates the environmental impact of P. aeruginosa. To identify bacteria capable of inactivating the QS signal molecule 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), a minimal medium containing PQS as the sole carbon source was used to enrich a Malaysian rainforest soil sample. This yielded an Achromobacter xylosoxidans strain (Q19) that inactivated PQS, yielding a new fluorescent compound (I-PQS) confirmed as PQS-derived using deuterated PQS. The I-PQS structure was elucidated using mass spectrometry and nuclear magnetic resonance spectroscopy as 2-heptyl-2-hydroxy-1,2-dihydroquinoline-3,4-dione (HHQD). Achromobacter xylosoxidans Q19 oxidized PQS congeners with alkyl chains ranging from C1 to C5 and also N-methyl PQS, yielding the corresponding 2-hydroxy-1,2-dihydroquinoline-3,4-diones, but was unable to inactivate the PQS precursor HHQ. This indicates that the hydroxyl group at position 3 in PQS is essential and that A. xylosoxidans inactivates PQS via a pathway involving the incorporation of oxygen at C2 of the heterocyclic ring. The conversion of PQS to HHQD also occurred on incubation with 12/17 A. xylosoxidans strains recovered from cystic fibrosis patients, with P. aeruginosa and with Arthrobacter, suggesting that formation of hydroxylated PQS may be a common mechanism of inactivation.
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Affiliation(s)
- Eliza Ye-Chen Soh
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Siri R Chhabra
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Nigel Halliday
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Stephan Heeb
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Christine Müller
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, D-48149, Muenster, Germany
| | - Franziska S Birmes
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, D-48149, Muenster, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Muenster, D-48149, Muenster, Germany
| | - Miguel Cámara
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Paul Williams
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Conversion of the Pseudomonas aeruginosa Quinolone Signal and Related Alkylhydroxyquinolines by Rhodococcus sp. Strain BG43. Appl Environ Microbiol 2014; 80:7266-74. [PMID: 25239889 DOI: 10.1128/aem.02342-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/11/2014] [Indexed: 11/20/2022] Open
Abstract
A bacterial strain, which based on the sequences of its 16S rRNA, gyrB, catA, and qsdA genes, was identified as a Rhodococcus sp. closely related to Rhodococcus erythropolis, was isolated from soil by enrichment on the Pseudomonas quinolone signal [PQS; 2-heptyl-3-hydroxy-4(1H)-quinolone], a quorum sensing signal employed by the opportunistic pathogen Pseudomonas aeruginosa. The isolate, termed Rhodococcus sp. strain BG43, cometabolically degraded PQS and its biosynthetic precursor 2-heptyl-4(1H)-quinolone (HHQ) to anthranilic acid. HHQ degradation was accompanied by transient formation of PQS, and HHQ hydroxylation by cell extracts required NADH, indicating that strain BG43 has a HHQ monooxygenase isofunctional to the biosynthetic enzyme PqsH of P. aeruginosa. The enzymes catalyzing HHQ hydroxylation and PQS degradation were inducible by PQS, suggesting a specific pathway. Remarkably, Rhodococcus sp. BG43 is also capable of transforming 2-heptyl-4-hydroxyquinoline-N-oxide to PQS. It thus converts an antibacterial secondary metabolite of P. aeruginosa to a quorum sensing signal molecule.
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Thierbach S, Bui N, Zapp J, Chhabra SR, Kappl R, Fetzner S. Substrate-assisted O2 activation in a cofactor-independent dioxygenase. ACTA ACUST UNITED AC 2014; 21:217-25. [PMID: 24388758 DOI: 10.1016/j.chembiol.2013.11.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
In contrast to the majority of O2-activating enzymes, which depend on an organic cofactor or a metal ion for catalysis, a particular group of structurally unrelated oxygenases is functional without any cofactor. In this study, we characterized the mechanism of O2 activation in the reaction pathway of a cofactor-independent dioxygenase with an α/β-hydrolase fold, which catalyzes the oxygenolytic cleavage of 2-alkyl-3-hydroxy-4(1H)-quinolones. Chemical analysis and electron paramagnetic resonance spectroscopic data revealed that O2 activation in the enzyme's active site is substrate-assisted, relying on single electron transfer from the bound substrate anion to O2 to form a radical pair, which recombines to a C2-peroxide intermediate. Thus, an oxygenase can function without a cofactor, if the organic substrate itself, after activation to a (carb)anion by an active-site base, is intrinsically reactive toward molecular oxygen.
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Affiliation(s)
- Sven Thierbach
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany
| | - Nguyen Bui
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Campus, Building C2, 66123 Saarbrücken, Germany
| | - Siri Ram Chhabra
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Reinhard Kappl
- Department of Biophysics, School of Medicine, Saarland University, Clinical Center, Building 76, 66421 Homburg, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149 Münster, Germany.
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The PaaX-type repressor MeqR2 of Arthrobacter sp. strain Rue61a, involved in the regulation of quinaldine catabolism, binds to its own promoter and to catabolic promoters and specifically responds to anthraniloyl coenzyme A. J Bacteriol 2012; 195:1068-80. [PMID: 23275246 DOI: 10.1128/jb.01547-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The genes coding for quinaldine catabolism in Arthrobacter sp. strain Rue61a are clustered on the linear plasmid pAL1 in two upper pathway operons (meqABC and meqDEF) coding for quinaldine conversion to anthranilate and a lower pathway operon encoding anthranilate degradation via coenzyme A (CoA) thioester intermediates. The meqR2 gene, located immediately downstream of the catabolic genes, codes for a PaaX-type transcriptional repressor. MeqR2, purified as recombinant fusion protein, forms a dimer in solution and shows specific and cooperative binding to promoter DNA in vitro. DNA fragments recognized by MeqR2 contained a highly conserved palindromic motif, 5'-TGACGNNCGTcA-3', which is located at positions -35 to -24 of the two promoters that control the upper pathway operons, at positions +4 to +15 of the promoter of the lower pathway genes and at positions +53 to +64 of the meqR2 promoter. Disruption of the palindrome abolished MeqR2 binding. The dissociation constants (K(D)) of MeqR2-DNA complexes as deduced from electrophoretic mobility shift assays were very similar for the four promoters tested (23 nM to 28 nM). Anthraniloyl-CoA was identified as the specific effector of MeqR2, which impairs MeqR2-DNA complex formation in vitro. A binding stoichiometry of one effector molecule per MeqR2 monomer and a K(D) of 22 nM were determined for the effector-protein complex by isothermal titration calorimetry (ITC). Quantitative reverse transcriptase PCR analyses suggested that MeqR2 is a potent regulator of the meqDEF operon; however, additional regulatory systems have a major impact on transcriptional control of the catabolic operons and of meqR2.
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Niewerth H, Schuldes J, Parschat K, Kiefer P, Vorholt JA, Daniel R, Fetzner S. Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a. BMC Genomics 2012; 13:534. [PMID: 23039946 PMCID: PMC3534580 DOI: 10.1186/1471-2164-13-534] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Accepted: 10/01/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-methylquinoline) as sole carbon and energy source. The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain. RESULTS The genome of Arthrobacter sp. Rue61a consists of a single circular chromosome of 4,736,495 bp with an average G + C content of 62.32%, the circular 231,551-bp plasmid pARUE232, and the linear 112,992-bp plasmid pARUE113 that was already published. Plasmid pARUE232 is proposed to contribute to the resistance of Arthrobacter sp. Rue61a to arsenate and Pb2+, whereas the linear plasmid confers the ability to convert quinaldine to anthranilate. Remarkably, degradation of anthranilate exclusively proceeds via a CoA-thioester pathway. Apart from quinaldine utilization, strain Rue61a has a limited set of aromatic degradation pathways, enabling the utilization of 4-hydroxy-substituted aromatic carboxylic acids, which are characteristic products of lignin depolymerization, via ortho cleavage of protocatechuate. However, 4-hydroxyphenylacetate degradation likely proceeds via meta cleavage of homoprotocatechuate. The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. It encodes a broad spectrum of enzymes for the uptake and utilization of various sugars and organic nitrogen compounds. A. aurescens TC-1 is the closest sequenced relative of strain Rue61a. CONCLUSIONS The genome of Arthrobacter sp. Rue61a reflects the saprophytic lifestyle and nutritional versatility of the organism and a strong adaptive potential to environmental stress. The circular plasmid pARUE232 and the linear plasmid pARUE113 contribute to heavy metal resistance and to the ability to degrade quinaldine, respectively.
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Affiliation(s)
- Heiko Niewerth
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077, Göttingen, Germany
| | - Katja Parschat
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
- Present address: Jennewein Biotechnologie GmbH, 53619, Rheinbreitbach, Germany
| | - Patrick Kiefer
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077, Göttingen, Germany
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Corrensstrasse 3, 48149, Münster, Germany
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Falcone-Dias MF, Vaz-Moreira I, Manaia CM. Bottled mineral water as a potential source of antibiotic resistant bacteria. WATER RESEARCH 2012; 46:3612-3622. [PMID: 22534119 DOI: 10.1016/j.watres.2012.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/26/2012] [Accepted: 04/03/2012] [Indexed: 05/31/2023]
Abstract
The antibiotic resistance phenotypes of the cultivable bacteria present in nine batches of two Portuguese and one French brands of commercially available mineral waters were examined. Most of the 238 isolates recovered on R2A, Pseudomonas Isolation agar or on these culture media supplemented with amoxicillin or ciprofloxacin, were identified (based on 16S rRNA gene sequence analysis) as Proteobacteria of the divisions Beta, Gamma and Alpha. Bacteria resistant to more than three distinct classes of antibiotics were detected in all the batches of the three water brands in counts up to 10² CFU/ml. In the whole set of isolates, it was observed resistance against all the 22 antimicrobials tested (ATB, bioMérieux and disc diffusion), with most of the bacteria showing resistance to three or more classes of antibiotics. Bacteria with the highest multi-resistance indices were members of the genera Variovorax, Bosea, Ralstonia, Curvibacter, Afipia and Pedobacter. Some of these bacteria are related with confirmed or suspected nosocomial agents. Presumable acquired resistance may be suggested by the observation of bacteria taxonomically related but isolated from different brands, exhibiting distinct antibiotic resistance profiles. Bottled mineral water was confirmed as a possible source of antibiotic resistant bacteria, with the potential to be transmitted to humans.
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Affiliation(s)
- Maria Fernanda Falcone-Dias
- CBQF/Escola Superior de Biotecnologia, Universidade Católica Portuguesa, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
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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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12
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Francis I, De Keyser A, De Backer P, Simón-Mateo C, Kalkus J, Pertry I, Ardiles-Diaz W, De Rycke R, Vandeputte OM, El Jaziri M, Holsters M, Vereecke D. pFiD188, the linear virulence plasmid of Rhodococcus fascians D188. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:637-47. [PMID: 22482837 DOI: 10.1094/mpmi-08-11-0215] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the 198,917 bp revealed four syntenic regions with linear plasmids of R. erythropolis, R. jostii, and R. opacus, suggesting a common origin of these replicons. Mutational analysis of pFi_086 and pFi_102, similar to cutinases and type IV peptidases, respectively, showed that conserved region R2 was involved in plasmid dispersal and pointed toward a novel function for actinobacterial cutinases in conjugation. Additionally, pFiD188 had three regions that were unique for R. fascians. Functional analysis of the stk and nrp loci of regions U2 and U3, respectively, indicated that their role in symptom development was limited compared with that of the previously identified fas, att, and hyp virulence loci situated in region U1. Thus, pFiD188 is a typical rhodococcal linear plasmid with a composite structure that encodes core functions involved in plasmid maintenance and accessory functions, some possibly acquired through horizontal gene transfer, implicated in virulence and the interaction with the host.
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Affiliation(s)
- Isolde Francis
- Department of Plant Biotechnology and Bioinformatics, VIB, 9052 Gent, Belgium
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Genome Sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614. J Bacteriol 2011; 193:3399-400. [PMID: 21551312 DOI: 10.1128/jb.05109-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.
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Wagenknecht M, Meinhardt F. Copy number determination, expression analysis of genes potentially involved in replication, and stability assays of pAL1 – the linear megaplasmid of Arthrobacter nitroguajacolicus Rü61a. Microbiol Res 2011; 166:14-26. [DOI: 10.1016/j.micres.2009.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 12/17/2009] [Accepted: 12/30/2009] [Indexed: 10/19/2022]
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15
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Wagenknecht M, Meinhardt F. Replication-involved genes of pAL1, the linear plasmid of Arthrobacter nitroguajacolicus Rü61a--phylogenetic and transcriptional analysis. Plasmid 2010; 65:176-84. [PMID: 21185858 DOI: 10.1016/j.plasmid.2010.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 11/28/2022]
Abstract
The 113-kb pAL1 is the only Arthrobacter linear plasmid known; it has terminal inverted repeats and 5' covalently attached terminal proteins (TPs). The latter and a telomere-associated protein (Tap) are encoded by plasmid ORFs 102 and 101, respectively. As for Streptomyces linear replicons, in which both above proteins are instrumental in telomere patching, they are involved in pAL1 replication as well. However, the alignment of actinobacterial Taps and TPs revealed that pAL1 and the linear elements from Rhodococci comprise a discrete phylogenetic group, clearly delineated from the streptomycetes linear plasmids. In line with such findings is the same genetic arrangement of ORF 101 and 102 counterparts in the rhodococcal elements. Furthermore, the adjacent gene (ORF100) has matches in the rhodococcal plasmids as well. In linear elements of Streptomyces there is no ORF100 homolog. Two alternative annotations are possible for ORF100 gene products. As RT-PCR revealed cotranscription of ORFs 100-102, the ORF100 gene product is presumably involved in replicative processes. Taken also into consideration the likely absence of an internal replication origin (other than in Streptomyces linear elements), we assume a distinct replication/telomere patching mechanism for pAL1 type replicons.
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Affiliation(s)
- Martin Wagenknecht
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstr. 3, D-48149 Münster, Germany
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Ütkür FÖ, Gaykawad S, Bühler B, Schmid A. Regioselective aromatic hydroxylation of quinaldine by water using quinaldine 4-oxidase in recombinant Pseudomonas putida. J Ind Microbiol Biotechnol 2010; 38:1067-77. [DOI: 10.1007/s10295-010-0883-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 09/17/2010] [Indexed: 11/24/2022]
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A novel replicative enzyme encoded by the linear Arthrobacter plasmid pAL1. J Bacteriol 2010; 192:4935-43. [PMID: 20675469 DOI: 10.1128/jb.00614-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soil bacterium Arthrobacter nitroguajacolicus Rü61a contains the linear plasmid pAL1, which codes for the degradation of 2-methylquinoline. Like other linear replicons of actinomycetes, pAL1 is characterized by short terminal inverted-repeat sequences and terminal proteins (TPpAL1) covalently attached to its 5' ends. TPpAL1, encoded by the pAL1.102 gene, interacts in vivo with the protein encoded by pAL1.101. Bioinformatic analysis of the pAL1.101 protein, which comprises 1,707 amino acids, suggested putative zinc finger and topoisomerase-primase domains and part of a superfamily 2 helicase domain in its N-terminal and central regions, respectively. Sequence motifs characteristic of the polymerization domain of family B DNA polymerases are partially conserved in a C-terminal segment. The purified recombinant protein catalyzed the deoxycytidylation of TPpAL1 in the presence of single-stranded DNA templates comprising the 3'-terminal sequence (5'-GCAGG-3'), which in pAL1 forms the terminal inverted repeat, but also at templates with 5'-(G/T)CA(GG/GC/CG)-3' ends. Enzyme assays suggested that the protein exhibits DNA topoisomerase, DNA helicase, and DNA- and protein-primed DNA polymerase activities. The pAL1.101 protein, therefore, may act as a replicase of pAL1.
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Mattes TE, Alexander AK, Coleman NV. Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution. FEMS Microbiol Rev 2010; 34:445-75. [DOI: 10.1111/j.1574-6976.2010.00210.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Pustelny C, Albers A, Büldt-Karentzopoulos K, Parschat K, Chhabra SR, Cámara M, Williams P, Fetzner S. Dioxygenase-mediated quenching of quinolone-dependent quorum sensing in Pseudomonas aeruginosa. ACTA ACUST UNITED AC 2010; 16:1259-67. [PMID: 20064436 DOI: 10.1016/j.chembiol.2009.11.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 10/29/2009] [Accepted: 11/02/2009] [Indexed: 01/19/2023]
Abstract
2-Heptyl-3-hydroxy-4(1H)-quinolone (PQS) is a quorum-sensing signal molecule used by Pseudomonas aeruginosa. The structural similarity between 3-hydroxy-2-methyl-4(1H)-quinolone, the natural substrate for the 2,4-dioxygenase, Hod, and PQS prompted us to investigate whether Hod quenched PQS signaling. Hod is capable of catalyzing the conversion of PQS to N-octanoylanthranilic acid and carbon monoxide. In P. aeruginosa PAO1 cultures, exogenously supplied Hod protein reduced expression of the PQS biosynthetic gene pqsA, expression of the PQS-regulated virulence determinants lectin A, pyocyanin, and rhamnolipids, and virulence in planta. However, the proteolytic cleavage of Hod by extracellular proteases, competitive inhibition by the PQS precursor 2-heptyl-4(1H)-quinolone, and PQS binding to rhamnolipids reduced the efficiency of Hod as a quorum-quenching agent. Nevertheless, these data indicate that enzyme-mediated PQS inactivation has potential as an antivirulence strategy against P. aeruginosa.
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Affiliation(s)
- Christian Pustelny
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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Cofactor-independent oxidases and oxygenases. Appl Microbiol Biotechnol 2010; 86:791-804. [DOI: 10.1007/s00253-010-2455-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 01/14/2010] [Accepted: 01/14/2010] [Indexed: 10/19/2022]
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Kolkenbrock S, Fetzner S. Identification and in vitro deoxynucleotidylation of the terminal protein of the linear plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a. FEMS Microbiol Lett 2010; 304:169-76. [PMID: 20141532 DOI: 10.1111/j.1574-6968.2010.01900.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a is a linear replicon, characterized by inverted terminal repeats and terminal proteins (TPs) covalently bound to its 5'-ends. Previous sequence analysis and predictions of possible secondary structures formed by telomeric 3'-overhangs indicated significant differences of the 'left' and 'right' telomere of pAL1, raising the question of whether each terminus is recognized by a specific protein. The genes pAL1.102 and pAL1.103, located close to a terminus, code for possible DNA-binding proteins; however, only the pORF102 protein encoded by pAL1.102 shows a weak similarity to known TPs of Streptomyces linear replicons. pORF102, purified from recombinant A. nitroguajacolicus Rü61a as a fusion with maltose-binding protein (MBP), was specifically associated with terminal pAL1 DNA, whereas MBP-pORF103 was devoid of DNA, suggesting that pORF102 represents the protein attached to both ends of the linear plasmid. In electrophoretic mobility shift assays, the MBP-pORF102 protein was not capable of specifically recognizing telomeric DNA sequences. Consistent with its proposed role as a protein primer in DNA synthesis, pORF102 was deoxynucleotidylated in vitro with dCMP, complementary to the 3'-ends (... GCAGG) of pAL1.
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Affiliation(s)
- Stephan Kolkenbrock
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany
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Vedler E. Megaplasmids and the Degradation of Aromatic Compounds by Soil Bacteria. MICROBIAL MEGAPLASMIDS 2009. [DOI: 10.1007/978-3-540-85467-8_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Two closely related pathways of nicotine catabolism in Arthrobacter nicotinovorans and Nocardioides sp. strain JS614. Arch Microbiol 2007; 189:511-7. [PMID: 18071673 DOI: 10.1007/s00203-007-0340-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 11/16/2007] [Accepted: 11/26/2007] [Indexed: 10/22/2022]
Abstract
A virtually identical nicotine catabolic pathway including the heterotrimeric molybdenum enzyme nicotine and 6-hydroxy-pseudo-oxynicotine dehydrogenase, 6-hydroxy-L: -nicotine oxidase, 2,6-dihydroxy-pseudo-oxynicotine hydrolase, and 2,6-dihydroxypyridine hydroxylase have been identified in A. nicotinovorans and Nocardioides sp. JS614. Enzymes catalyzing the same reactions and similar protein antigens were detected in the extracts of the two microorganisms. Nicotine blue and methylamine, two end products of nicotine catabolism were detected in the growth medium of both bacterial species. Nicotine catabolic genes are clustered on pAO1 in A. nicotinovorans, but located chromosomally in Nocardioides sp. JS614.
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