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Suman J, Sredlova K, Fraraccio S, Jerabkova M, Strejcek M, Kabickova H, Cajthaml T, Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. CHEMOSPHERE 2024; 349:140909. [PMID: 38070605 DOI: 10.1016/j.chemosphere.2023.140909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Monohydroxylated PCBs (OH-PCBs) are an (eco)toxicologically significant group of compounds, as they arise from the oxidation of polychlorinated biphenyls (PCBs) and, at the same time, may exert even more severe toxic effects than their parent PCB molecules. Despite having been widely detected in environmental samples, plants, and animals, information on the fate of OH-PCBs in the environment is scarce, including on the enzymatic machinery behind their degradation. To date, only a few bacterial taxa capable of OH-PCB transformation have been reported. In this study, we aimed to obtain a deeper insight into the transformation of OH-PCBs in soil bacteria and isolated a Pseudomonas sp. strain P1B16 based on its ability to use o-phenylphenol (2-PP) which, when exposed to the Delor 103-derived OH-PCB mixture, depleted a wide spectrum of mono-, di, and trichlorinated OH-PCBs. In the P1B16 genome, a region designated as hbp was identified, which bears a set of putative genes involved in the transformation of OH-PCBs, namely hbpA encoding for a putative flavin-dependent 2-hydroxybiphenyl monooxygenase, hbpC (2,3-dihydroxybiphenyl-1,2-dioxygenase), hbpD (2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase), and the transcriptional activator-encoding gene hbpR. The hbpA coding sequence was heterologously expressed, purified, and its substrate specificity was investigated towards the Delor 103-derived OH-PCB mixture, individual OH-PCBs, and multiple (chlorinated) phenolics. Apart from 2-PP and 2-chlorophenol, HbpA was also demonstrated to transform a range of OH-PCBs, including a 3-hydroxy-2,2',4',5,5'-pentachlorobiphenyl. Importantly, this is the first direct evidence of HbpA homologs being involved in the degradation of OH-PCBs. Moreover, using a P1B16-based biosensor strain, the specific induction of hbp genes by 2-PP, 3-phenylphenol, 4-phenylphenol, and the OH-PCB mixture was demonstrated. This study provides direct evidence on the specific enzymatic machinery responsible for the transformation of OH-PCBs in bacteria, with many implications in ecotoxicology, environmental restoration, and microbial ecology in habitats burdened with PCB contamination.
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Affiliation(s)
- Jachym Suman
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
| | - Kamila Sredlova
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Serena Fraraccio
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Martina Jerabkova
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Michal Strejcek
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic
| | - Hana Kabickova
- Military Health Institute, Ministry of Defence of the Czech Republic, U Vojenske Nemocnice 1200, 169 02, Prague, Czech Republic
| | - Tomas Cajthaml
- Institute for Environmental Studies, Faculty of Science, Charles University, Benatska 2, 128 01, Prague 2, Czech Republic; Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 162 08, Prague, Czech Republic.
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Martínez I, Mohamed MES, García JL, Díaz E. Enhancing biodesulfurization by engineering a synthetic dibenzothiophene mineralization pathway. Front Microbiol 2022; 13:987084. [PMID: 36274708 PMCID: PMC9579287 DOI: 10.3389/fmicb.2022.987084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
A synthetic dibenzothiophene (DBT) mineralization pathway has been engineered in recombinant cells of Pseudomonas azelaica Aramco J strain for its use in biodesulfurization of thiophenic compounds and crude oil. This functional pathway consists of a combination of a recombinant 4S pathway responsible for the conversion of DBT into 2-hydroxybiphenyl (2HBP) and a 2HBP mineralization pathway that is naturally present in the parental P. azelaica Aramco J strain. This novel approach allows overcoming one of the major bottlenecks of the biodesulfurization process, i.e., the feedback inhibitory effect of 2HBP on the 4S pathway enzymes. Resting cells-based biodesulfurization assays using DBT as a sulfur source showed that the 2HBP generated from the 4S pathway is subsequently metabolized by the cell, yielding an increase of 100% in DBT removal with respect to previously optimized Pseudomonas putida biodesulfurizing strains. Moreover, the recombinant P. azelaica Aramco J strain was able to use DBT as a carbon source, representing the best characterized biocatalyst harboring a DBT mineralization pathway and constituting a suitable candidate to develop future bioremediation/bioconversion strategies for oil-contaminated sites.
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Affiliation(s)
- Igor Martínez
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - José Luis García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- *Correspondence: Eduardo Díaz,
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Carraro N, Sentchilo V, Polák L, Bertelli C, van der Meer JR. Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium Pseudomonas nitroreducens HBP-1. Genes (Basel) 2020; 11:genes11080930. [PMID: 32806781 PMCID: PMC7466150 DOI: 10.3390/genes11080930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 02/07/2023] Open
Abstract
The sewage sludge isolate Pseudomonas nitroreducens HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1's chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). P. nitroreducens carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICEclc of Pseudomonas knackmussii B13. The variable regions of ICEPni1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICEPni2 (171 kb) encodes complete meta-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10-6-10-8 per P. nitroreducens HBP-1 donor into Pseudomonas putida, where they integrated site specifically into tRNAGly-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.
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Affiliation(s)
- Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
- Correspondence:
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
| | - Lenka Polák
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
| | - Claire Bertelli
- Institute for Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland;
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland; (V.S.); (L.P.); (J.R.v.d.M.)
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Patel R, Chudasama R, Solanki R, Patel P, Parmar K, Munshi NS. Structure prediction and molecular docking studies of aromatic hydrocarbon sensing proteins TbuT, HbpR and PhnR to detect priority pollutants. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2019; 55:126-141. [PMID: 31566066 DOI: 10.1080/10934529.2019.1672457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
On-line detection of aromatic hydrocarbon pollutants in aqueous environments can be achieved by biosensing strains having fusion of gene responsible for pollutant sensing protein with a reporter gene. Regulatory proteins TbuT, HbpR and PhnR are such proteins for recognizing one-, two-and three-ring aromatic hydrocarbon pollutants respectively, for which the structure is not known till date. Aim of the present study was to predict the structure of proteins and to determine their in-silico interaction with array of pollutants. Structure prediction of proteins was performed using I-TASSER and Phyre2 and refined with ModRefiner and 3DRefine. Total 14 models were obtained for each protein and the best model had more than 95% coverage in Ramachandran plot region. After successful structure prediction, molecular interaction of proteins with respective aromatic hydrocarbon pollutants categorized by United States Environmental Protection Agency was studied using AutoDockVina where the binding energy was found to fall in range of -4.6 to -8.4 kcal/mol. The types of protein-pollutant interaction were analyzed by LigPlus and Discovery Studio 2017 R2 Client which were found to be similar for standard and pollutant compounds. This study enables us to predict the range of pollutants possible to be detected using these regulatory protein-based biosensors.
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Affiliation(s)
- Rushika Patel
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Rajesh Chudasama
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | | | - Priya Patel
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Krupali Parmar
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
| | - Nasreen S Munshi
- Institute of Science, Nirma University, Ahmedabad, Gujarat, India
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Suvorova IA, Gelfand MS. Comparative Genomic Analysis of the Regulation of Aromatic Metabolism in Betaproteobacteria. Front Microbiol 2019; 10:642. [PMID: 30984152 PMCID: PMC6449761 DOI: 10.3389/fmicb.2019.00642] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/14/2019] [Indexed: 01/23/2023] Open
Abstract
Aromatic compounds are a common carbon and energy source for many microorganisms, some of which can even degrade toxic chloroaromatic xenobiotics. This comparative study of aromatic metabolism in 32 Betaproteobacteria species describes the links between several transcription factors (TFs) that control benzoate (BenR, BenM, BoxR, BzdR), catechol (CatR, CatM, BenM), chlorocatechol (ClcR), methylcatechol (MmlR), 2,4-dichlorophenoxyacetate (TfdR, TfdS), phenol (AphS, AphR, AphT), biphenyl (BphS), and toluene (TbuT) metabolism. We characterize the complexity and variability in the organization of aromatic metabolism operons and the structure of regulatory networks that may differ even between closely related species. Generally, the upper parts of pathways, rare pathway variants, and degradative pathways of exotic and complex, in particular, xenobiotic compounds are often controlled by a single TF, while the regulation of more common and/or central parts of the aromatic metabolism may vary widely and often involves several TFs with shared and/or dual, or cascade regulation. The most frequent and at the same time variable connections exist between AphS, AphR, AphT, and BenR. We have identified a novel LysR-family TF that regulates the metabolism of catechol (or some catechol derivative) and either substitutes CatR(M)/BenM, or shares functions with it. We have also predicted several new members of aromatic metabolism regulons, in particular, some COGs regulated by several different TFs.
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Affiliation(s)
- Inna A Suvorova
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems RAS (The Kharkevich Institute), Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
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6
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Perruchon C, Vasileiadis S, Rousidou C, Papadopoulou ES, Tanou G, Samiotaki M, Garagounis C, Molassiotis A, Papadopoulou KK, Karpouzas DG. Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol. Sci Rep 2017; 7:6449. [PMID: 28743883 PMCID: PMC5527002 DOI: 10.1038/s41598-017-06727-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Ortho-phenylphenol (OPP) is a fungicide contained in agro-industrial effluents produced by fruit-packaging plants. Within the frame of developing bio-strategies to detoxify these effluents, an OPP-degrading Sphingomonas haloaromaticamans strain was isolated. Proteins/genes with a putative catabolic role and bacterium adaptation mechanisms during OPP degradation were identified via genomic and proteomic analysis. Transcription analysis of all putative catabolic genes established their role in the metabolism of OPP. The formation of key transformation products was verified by chromatographic analysis. Genomic analysis identified two orthologous operons encoding the ortho-cleavage of benzoic acid (BA) (ben/cat). The second ben/cat operon was located in a 92-kb scaffold along with (i) an operon (opp) comprising genes for the transformation of OPP to BA and 2-hydroxypenta-2,4-dienoate (and genes for its transformation) and (ii) an incomplete biphenyl catabolic operon (bph). Proteomics identified 13 up-regulated catabolic proteins when S. haloaromaticamans was growing on OPP and/or BA. Transcription analysis verified the key role of the catabolic operons located in the 92-kb scaffold, and flanked by transposases, on the transformation of OPP by S. haloaromaticamans. A flavin-dependent monoxygenase (OppA1), one of the most up-regulated proteins in the OPP-growing cells, was isolated via heterologous expression and its catabolic activity was verified in vitro.
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Affiliation(s)
- Chiara Perruchon
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Sotirios Vasileiadis
- University of South Australia, Future Industries Institute, Mawson Lakes, Australia
| | - Constantina Rousidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Evangelia S Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Georgia Tanou
- Aristotle University of Thessaloniki, School of Agriculture, Thessaloniki, Greece
| | - Martina Samiotaki
- Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Greece
| | - Constantinos Garagounis
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | | | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, Laboratory of Plant and Environmental Biotechnology, Viopolis, 41500, Larissa, Greece.
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7
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Merulla D, van der Meer JR. Regulatable and Modulable Background Expression Control in Prokaryotic Synthetic Circuits by Auxiliary Repressor Binding Sites. ACS Synth Biol 2016; 5:36-45. [PMID: 26348795 DOI: 10.1021/acssynbio.5b00111] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Expression control in synthetic genetic circuitry, for example, for construction of sensitive biosensors, is hampered by the lack of DNA parts that maintain ultralow background yet achieve high output upon signal integration by the cells. Here, we demonstrate how placement of auxiliary transcription factor binding sites within a regulatable promoter context can yield an important gain in signal-to-noise output ratios from prokaryotic biosensor circuits. As a proof of principle, we use the arsenite-responsive ArsR repressor protein from Escherichia coli and its cognate operator. Additional ArsR operators placed downstream of its target promoter can act as a transcription roadblock in a distance-dependent manner and reduce background expression of downstream-placed reporter genes. We show that the transcription roadblock functions both in cognate and heterologous promoter contexts. Secondary ArsR operators placed upstream of their promoter can also improve signal-to-noise output while maintaining effector dependency. Importantly, background control can be released through the addition of micromolar concentrations of arsenite. The ArsR-operator system thus provides a flexible system for additional gene expression control, which, given the extreme sensitivity to micrograms per liter effector concentrations, could be applicable in more general contexts.
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Affiliation(s)
- Davide Merulla
- Department of Fundamental
Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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8
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Perruchon C, Patsioura V, Vasileiadis S, Karpouzas DG. Isolation and characterisation of a Sphingomonas strain able to degrade the fungicide ortho-phenylphenol. PEST MANAGEMENT SCIENCE 2016; 72:113-124. [PMID: 25556554 DOI: 10.1002/ps.3970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/16/2014] [Accepted: 12/28/2014] [Indexed: 06/04/2023]
Abstract
BACKGROUND Ortho-phenylphenol (OPP) is a fungicide used in fruit packaging plants for the control of fungal infestations during storage. Its application leads to the production of large wastewater volumes which according to the European legislation should be treated on site. In spite of this, no efficient treatment systems are currently available, and the development of biological systems based on tailored-made pesticide-degrading inocula for the treatment of these wastewaters is an appealing solution. RESULTS Enrichment cultures from a soil collected from a wastewater disposal site resulted in the isolation of a pure Sphingomonas haloaromaticamans strain P3 able to degrade rapidly OPP and use it as an energy source. Its degrading capacity was dependent on the external supply of amino acids or on the presence of other bacteria that did not contribute to fungicide degradation. The isolated S. haloaromaticamans strain was able to metabolise up to 150 mg L(-1) of OPP within 7 days, in a wide range of pH (4.5-9) and temperatures (4-37 °C), and in the presence of other pesticides (thiabendazole and diphenylamine) co-used in the fruit packaging industry. CONCLUSION Overall, the OPP-degrading bacterium isolated showed high potential for use in future biodepuration treatment systems and bioremediation strategies.
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Affiliation(s)
- Chiara Perruchon
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Vasiliki Patsioura
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Sotirios Vasileiadis
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, Australia
| | - Dimitrios G Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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9
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Coronado E, Valtat A, van der Meer JR. Sphingomonas wittichii RW1 gene reporters interrogating the dibenzofuran metabolic network highlight conditions for early successful development in contaminated microcosms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:480-488. [PMID: 25683238 DOI: 10.1111/1758-2229.12276] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/31/2015] [Indexed: 06/04/2023]
Abstract
In order to better understand the fate and activity of bacteria introduced into contaminated material for the purpose of enhancing biodegradation rates, we constructed Sphingomonas wittichii RW1 variants with gene reporters interrogating dibenzofuran metabolic activity. Three potential promoters from the dibenzofuran metabolic network were selected and fused to the gene for enhanced green fluorescent protein (EGFP). The stability of the resulting genetic constructions in RW1 was examined, with plasmids based on the broad-host range vector pME6012 being the most reliable. One of the selected promoters, upstream of the gene Swit_4925 for a putative 2-hydroxy-2,4-pentadienoate hydratase, was inducible by growth on dibenzofuran. Sphingomonas wittichii RW1 equipped with the Swit_4925 promoter egfp fusion grew in a variety of non-sterile sandy microcosms contaminated with dibenzofuran and material from a former gasification site. The strain also grew in microcosms without added dibenzofuran but to a very limited extent, and EGFP expression indicated the formation of consistent small subpopulations of cells with an active inferred dibenzofuran metabolic network. Evidence was obtained for competition for dibenzofuran metabolites scavenged by resident bacteria in the gasification site material, which resulted in a more rapid decline of the RW1 population. Our results show the importance of low inoculation densities in order to observe the population development of the introduced bacteria and further illustrate that the limited availability of unique carbon substrate may be the most important factor impinging growth.
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Affiliation(s)
- Edith Coronado
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Annabelle Valtat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, 1015, Switzerland
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10
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García JL, Rozas D, del Cerro C, Nogales J, El-Said Mohamed M, Díaz E. Genome Sequence of Pseudomonas azelaica HBP1, Which Catabolizes 2-Hydroxybiphenyl Fungicide. GENOME ANNOUNCEMENTS 2014; 2:e01248-13. [PMID: 24526653 PMCID: PMC3924385 DOI: 10.1128/genomea.01248-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/27/2014] [Indexed: 11/20/2022]
Abstract
Pseudomonas azelaica HBP1 (DSM 8897) is one of the few bacteria able to completely mineralize the 2-hydroxybiphenyl biocide. Here, we report the draft genome sequence of this strain (7.4 Mbp; G+C content, 63.5%) and the findings obtained from its genome annotation.
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Affiliation(s)
- José L. García
- Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Daniel Rozas
- Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carlos del Cerro
- Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Nogales
- Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Eduardo Díaz
- Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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11
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Czechowska K, Reimmann C, van der Meer JR. Characterization of a MexAB-OprM efflux system necessary for productive metabolism of Pseudomonas azelaica HBP1 on 2-hydroxybiphenyl. Front Microbiol 2013; 4:203. [PMID: 23882265 PMCID: PMC3715732 DOI: 10.3389/fmicb.2013.00203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/28/2013] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas azelaica HBP1 is one of the few bacteria known to completely mineralize the biocide and toxic compound 2-hydroxybiphenyl (2-HBP), but the mechanisms of its tolerance to the toxicity are unknown. By transposon mutant analysis and screening for absence of growth on water saturating concentrations of 2-HBP (2.7 mM) we preferentially found insertions in three genes with high homology to the mexA, mexB, and oprM efflux system. Mutants could grow at 2-HBP concentrations below 100 μM but at lower growth rates than the wild-type. Exposure of the wild-type to increasing 2-HBP concentrations resulted in acute cell growth arrest and loss of membrane potential, to which the cells adapt after a few hours. By using ethidium bromide (EB) as proxy we could show that the mutants are unable to expel EB effectively. Inclusion of a 2-HBP reporter plasmid revealed that the wild-type combines efflux with metabolism at all 2-HBP concentrations, whereas the mutants cannot remove the compound and arrest metabolism at concentrations above 24 μM. The analysis thus showed the importance of the MexAB-OprM system for productive metabolism of 2-HBP.
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Affiliation(s)
- K Czechowska
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge Lausanne, Switzerland
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12
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Geng S, Fang J, Turner KB, Daunert S, Wei Y. Accumulation and efflux of polychlorinated biphenyls in Escherichia coli. Anal Bioanal Chem 2012; 403:2403-9. [PMID: 22349406 DOI: 10.1007/s00216-012-5835-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/01/2012] [Accepted: 02/02/2012] [Indexed: 01/23/2023]
Abstract
Polychlorinated biphenyls (PCBs) are environmental pollutants that have been associated with numerous adverse health effects in human and animals. Hydroxylated PCBs (HPCBs) are the product of the oxidative metabolism of PCBs. The presence of hydroxyl groups in HPCBs makes these compounds more hydrophilic than the parent PCBs. One of the best approaches to break down and remove these contaminants is bioremediation; an environmentally friendly process that uses microorganisms to degrade hazardous chemicals into non-toxic ones. In this study, we investigated the cellular accumulation and toxicity of selected PCBs and HPCBs in Gram-negative bacteria, using Escherichia coli as a model organism. We found that none of the five PCBs tested were toxic to E. coli, presumably due to their limited bioavailability. Nevertheless, different HPCBs tested showed different levels of toxicity. Furthermore, we demonstrated that the primary multidrug efflux system in E. coli, AcrAB-TolC, facilitated the efflux of HPCBs out of the cell. Since AcrAB-TolC is constitutively expressed in E. coli and is conserved in all sequenced Gram-negative bacterial genomes, our results suggest that the efflux activities of multidrug resistant pumps may affect the accumulation and degradation of PCBs in Gram-negative bacteria.
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Affiliation(s)
- Shen Geng
- Department of Chemistry, University of Kentucky, Lexington, KY 40506-0055, USA
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Raut N, O'Connor G, Pasini P, Daunert S. Engineered cells as biosensing systems in biomedical analysis. Anal Bioanal Chem 2012; 402:3147-59. [PMID: 22311427 DOI: 10.1007/s00216-012-5756-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/07/2012] [Accepted: 01/16/2012] [Indexed: 01/08/2023]
Abstract
Over the past two decades there have been great advances in biotechnology, including use of nucleic acids, proteins, and whole cells to develop a variety of molecular analytical tools for diagnostic, screening, and pharmaceutical applications. Through manipulation of bacterial plasmids and genomes, bacterial whole-cell sensing systems have been engineered that can serve as novel methods for analyte detection and characterization, and as more efficient and cost-effective alternatives to traditional analytical techniques. Bacterial cell-based sensing systems are typically sensitive, specific and selective, rapid, easy to use, low-cost, and amenable to multiplexing, high-throughput, and miniaturization for incorporation into portable devices. This critical review is intended to provide an overview of available bacterial whole-cell sensing systems for assessment of a variety of clinically relevant analytes. Specifically, we examine whole-cell sensing systems for detection of bacterial quorum sensing molecules, organic and inorganic toxic compounds, and drugs, and for screening of antibacterial compounds for identification of their mechanisms of action. Methods used in the design and development of whole-cell sensing systems are also reviewed.
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Affiliation(s)
- Nilesh Raut
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA
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Beggah S, Vogne C, Zenaro E, Van Der Meer JR. Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting. Microb Biotechnol 2011; 1:68-78. [PMID: 21261823 PMCID: PMC3864433 DOI: 10.1111/j.1751-7915.2007.00008.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutants were produced in the A-domain of HbpR, a protein belonging to the XylR family of σ(54)-dependent transcription activators, with the purpose of changing its effector recognition specificity from 2-hydroxybiphenyl (2-HBP, the cognate effector) to 2-chlorobiphenyl (2-CBP). Mutations were introduced in the hbpR gene part for the A-domain via error-prone polymerase chain reaction, and assembled on a gene circuitry plasmid in Escherichia coli, permitting HbpR-dependent induction of the enhanced green fluorescent protein (egfp). Cells with mutant HbpR proteins responsive to 2-CBP were enriched and separated in a flow cytometry-assisted cell-sorting procedure. Some 70 mutants were isolated and the A-domain mutations mapped. One of these had acquired true 2-CBP recognition but reacted hypersensitively to 2-HBP (20-fold more than the wild type), whereas others had reduced sensitivity to 2-HBP but a gain of 2-CBP recognition. Sequencing showed that most mutants carried double or triple mutations in the A-domain gene part, and were not located in previously recognized conserved residues within the XylR family members. Further selection from a new mutant pool prepared of the hypersensitive mutant did not result in increased 2-CBP or reduced 2-HBP recognition. Our data thus demonstrate that a one-step in vitro 'evolutionary' adaptation of the HbpR protein can result in both enhancement and reduction of the native effector recognition.
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Affiliation(s)
- Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, 1015 Lausanne, Switzerland
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15
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Abstract
In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored simultaneously. This critical review will discuss the paradigm shift associated with cellular heterogeneity, speak to the key developments that have lead to our better understanding of systems biology, and detail the future directions of the discipline (281 references).
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Affiliation(s)
- Maureen A Walling
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA
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Vogne C, Bisht H, Arias S, Fraile S, Lal R, van der Meer JR. Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis. PLoS One 2011; 6:e16539. [PMID: 21379585 PMCID: PMC3040749 DOI: 10.1371/journal.pone.0016539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 12/29/2010] [Indexed: 11/18/2022] Open
Abstract
Bacterial transcription activators of the XylR/DmpR subfamily exert their expression control via σ(54)-dependent RNA polymerase upon stimulation by a chemical effector, typically an aromatic compound. Where the chemical effector interacts with the transcription regulator protein to achieve activation is still largely unknown. Here we focus on the HbpR protein from Pseudomonas azelaica, which is a member of the XylR/DmpR subfamily and responds to biaromatic effectors such as 2-hydroxybiphenyl. We use protein structure modeling to predict folding of the effector recognition domain of HbpR and molecular docking to identify the region where 2-hydroxybiphenyl may interact with HbpR. A large number of site-directed HbpR mutants of residues in- and outside the predicted interaction area was created and their potential to induce reporter gene expression in Escherichia coli from the cognate P(C) promoter upon activation with 2-hydroxybiphenyl was studied. Mutant proteins were purified to study their conformation. Critical residues for effector stimulation indeed grouped near the predicted area, some of which are conserved among XylR/DmpR subfamily members in spite of displaying different effector specificities. This suggests that they are important for the process of effector activation, but not necessarily for effector specificity recognition.
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Affiliation(s)
- Christelle Vogne
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Hansi Bisht
- Department of Zoology, University of Delhi, Delhi, India
| | - Sagrario Arias
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sofia Fraile
- National Centre for Biotechnology, CSIC, Madrid, Spain
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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18
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De Las Heras A, Carreño CA, Martínez-García E, De Lorenzo V. Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol Rev 2010; 34:842-65. [DOI: 10.1111/j.1574-6976.2010.00238.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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19
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Bacterial Biosensors for Measuring Availability of Environmental Pollutants. SENSORS 2008; 8:4062-4080. [PMID: 27879922 PMCID: PMC3697161 DOI: 10.3390/s8074062] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/06/2008] [Accepted: 07/09/2008] [Indexed: 11/24/2022]
Abstract
Traditionally, pollution risk assessment is based on the measurement of a pollutant's total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensor-reporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.
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20
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Tropel D, van der Meer JR. Characterization of HbpR binding by site-directed mutagenesis of its DNA-binding site and by deletion of the effector domain. FEBS J 2005; 272:1756-66. [PMID: 15794762 DOI: 10.1111/j.1742-4658.2005.04607.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the presence of 2-hydroxybiphenyl, the enhancer binding protein, HbpR, activates the sigma54-dependent P(hbpC) promoter and controls the initial steps of 2-hydroxybiphenyl degradation in Pseudomonas azelaica. In the activation process, an oligomeric HbpR complex of unknown subunit composition binds to an operator region containing two imperfect palindromic sequences. Here, the HbpR-DNA binding interactions were investigated by site-directed mutagenesis of the operator region and by DNA-binding assays using purified HbpR. Mutations that disrupted the twofold symmetry in the palindromes did not affect the binding affinity of HbpR, but various mutations along a 60 bp region, and also outside the direct palindromic sequences, decreased the binding affinity. Footprints of HbpR on mutant operator fragments showed that a partial loss of binding contacts occurs, suggesting that the binding of one HbpR 'protomer' in the oligomeric complex is impaired whilst leaving the other contacts intact. An HbpR variant, devoid of its N-terminal sensing A-domain, was unable to activate transcription from the hbpC promoter while maintaining protection of the operator DNA in footprints. Wild-type HbpR was unable to activate transcription from the hbpC promoter when delta A-HbpR was expressed in the same cell, suggesting the formation of (repressing) hetero-oligomers. This model implies that HbpR can self-associate on its operator DNA without effector recognition or ATP binding. Furthermore, our findings suggest that the N-terminal sensing domain of HbpR is needed to activate the central ATPase domain rather than to repress a constitutively active C domain, as is the case for the related regulatory protein XylR.
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Affiliation(s)
- David Tropel
- Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), Dübendorf, Switzerland
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21
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Suar M, van der Meer JR, Lawlor K, Holliger C, Lal R. Dynamics of multiple lin gene expression in Sphingomonas paucimobilis B90A in response to different hexachlorocyclohexane isomers. Appl Environ Microbiol 2005; 70:6650-6. [PMID: 15528530 PMCID: PMC525160 DOI: 10.1128/aem.70.11.6650-6656.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sphingomonas paucimobilis B90A is able to degrade the alpha-, beta-, gamma-, and delta-isomers of hexachlorocyclohexane (HCH). It contains the genes linA, linB, linC, linD, linE, and linR, which have been implicated in HCH degradation. In this study, dynamic expression of the lin genes was measured in chemostat-grown S. paucimobilis B90A by RNA dot blot hybridization and real-time reverse transcriptase PCR upon exposure to a pulse of different HCH isomers. Irrespective of the addition of HCH, linA, linB, and linC were all expressed constitutively. In contrast, linD and linE were induced with alpha-HCH (2 mg/liter) and gamma-HCH (7 mg/liter). A sharp increase in mRNA levels for linD and linE was observed from 10 to 45 min after the addition of alpha- or gamma-HCH. Induction of linD and linE was not detectable upon the addition of 0.7 mg of gamma-HCH per liter, although the compound was degraded by the cells. The addition of beta-HCH (5 mg/liter) or delta-HCH (20 mg/liter) did not lead to linE and linD induction, despite the fact that 50% of the compounds were degraded. This suggests that degradation of beta- and delta-HCH proceeds by a different pathway than that of alpha- and gamma-HCH.
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Tropel D, Bähler A, Globig K, van der Meer JR. Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR. Environ Microbiol 2005; 6:1186-96. [PMID: 15479251 DOI: 10.1111/j.1462-2920.2004.00645.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HbpR protein is the sigma54-dependent transcription activator for 2-hydroxybiphenyl degradation in Pseudomonas azelaica. The ability of HbpR and XylR, which share 35% amino acid sequence identity, to cross-activate the PhbpC and Pu promoters was investigated by determining HbpR- or XylR-mediated luciferase expression and by DNA binding assays. XylR measurably activated the PhbpC promoter in the presence of the effector m-xylene, both in Escherichia coli and Pseudomonas putida. HbpR weakly stimulated the Pu promoter in E. coli but not in P. azelaica. Poor HbpR-dependent activation from Pu was caused by a weak binding to the operator region. To create promoters efficiently activated by both regulators, the HbpR binding sites on PhbpC were gradually changed into the XylR binding sites of Pu by site-directed mutagenesis. Inducible luciferase expression from mutated promoters was tested in E. coli on a two plasmid system, and from mono copy gene fusions in P. azelaica and P. putida. Some mutants were efficiently activated by both HbpR and XylR, showing that promoters can be created which are permissive for both regulators. Others achieved a higher XylR-dependent transcription than from Pu itself. Mutants were also obtained which displayed a tenfold lower uninduced expression level by HbpR than the wild-type PhbpC, while keeping the same maximal induction level. On the basis of these results, a dual-responsive bioreporter strain of P. azelaica was created, containing both XylR and HbpR, and activating luciferase expression from the same single promoter independently with m-xylene and 2-hydroxybiphenyl.
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Affiliation(s)
- David Tropel
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), CH-8600 Dübendorf, Switzerland
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Abstract
Engineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically, the reasons for this are the lack of engineering principles in the detection chain in the bioreporters. Here, we dissect critical steps in the detection chain and illustrate how bioreporter design could be improved by mutagenizing specificity and selectivity of the sensing and regulatory proteins, by newer expression strategies and application of different signalling networks. Furthermore, we describe how redesigning bioreporter assays with respect to pollutant transport into the cells and application of other detection devices can decrease detection limits and increase the speed of detection.
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Affiliation(s)
- Jan Roelof van der Meer
- Department of Fundamental Microbiology, Bâtiment de Biologie, University of Lausanne, 1015 Lausanne, Switzerland.
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Fujii I, Yasuoka Y, Tsai HF, Chang YC, Kwon-Chung KJ, Ebizuka Y. Hydrolytic polyketide shortening by ayg1p, a novel enzyme involved in fungal melanin biosynthesis. J Biol Chem 2004; 279:44613-20. [PMID: 15310761 DOI: 10.1074/jbc.m406758200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pentaketide 1,3,6,8-tetrahydroxynaphthalene (T4HN) is a key precursor of 1,8-dihydroxynaphthalene-melanin, an important virulence factor in pathogenic fungi, where T4HN is believed to be the direct product of pentaketide synthases. We showed recently the involvement of a novel protein, Ayg1p, in the formation of T4HN from the heptaketide precursor YWA1 in Aspergillus fumigatus. To investigate the mechanism of its enzymatic function, Ayg1p was purified from an Aspergillus oryzae strain that overexpressed the ayg1 gene. The Ayg1p converted the naphthopyrone YWA1 to T4HN with a release of the acetoacetic acid. Although Ayg1p does not show significant homology with known enzymes, a serine protease-type hydrolytic motif is present in its sequence, and serine-specific inhibitors strongly inhibited the activity. To identify its catalytic residues, site-directed Ayg1p mutants were expressed in Escherichia coli, and their enzyme activities were examined. The single substitution mutations S257A, D352A, and H380A resulted in a complete loss of enzyme activity in Ayg1p. These results indicated that the catalytic triad Asp352-His380-Ser257 constituted the active-site of Ayg1p. From a Dixon plot analysis, 2-acetyl-1,3,6,8-tetrahydroxynaphthalene was found to be a strong mixed-type inhibitor, suggesting the involvement of an acyl-enzyme intermediate. These studies support the mechanism in which the Ser257 at the active site functions as a nucleophile to attack the YWA1 side-chain 1'-carbonyl and cleave the carbon-carbon bond between the naphthalene ring and the side chain. Acetoacetic acid is subsequently released from the Ser257-O-acetoacetylated Ayg1p by hydrolysis. An enzyme with activity similar to Ayg1p in melanin biosynthesis has not been reported in any other organism.
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Affiliation(s)
- Isao Fujii
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Tropel D, van der Meer JR. Identification and physical characterization of the HbpR binding sites of the hbpC and hbpD promoters. J Bacteriol 2002; 184:2914-24. [PMID: 12003931 PMCID: PMC135056 DOI: 10.1128/jb.184.11.2914-2924.2002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas azelaica HBP1 can use 2-hydroxybiphenyl (2-HBP) and 2,2'-dihydroxybiphenyl as sole carbon and energy sources by means of the hbp regulon. This regulon is composed of three genes, hbpCA and hbpD, coding for enzymes of a meta-cleavage pathway and the hbpR gene, which codes for a XylR/DmpR-type transcription regulator. It was previously shown that HbpR activates transcription from two sigma(54)-dependent promoters, P(hbpC) and P(hbpD), in the presence of 2-HBP. In this study, by using gel mobility shift assays with a purified fusion protein containing calmodulin binding protein (CBP) and HbpR, we detected two binding regions for HbpR in P(hbpC) and one binding region in P(hbpD). DNase I footprints of the proximal binding region of P(hbpC) and of the binding region in P(hbpD) showed that CBP-HbpR protected a region composed of two inverted repeat sequences which were homologous to the binding sites identified for XylR. Unlike the situation in the XylR/P(u) system, we observed simultaneous binding of CBP-HbpR on the two upstream activating sequences (UASs). Fragments with only one UAS did not show an interaction with HbpR, indicating that both pairs of UASs are needed for HbpR binding. The addition of both ATP and 2-HBP increased the DNA binding affinity of HbpR. These results showed for the first time that, for regulators of the XylR/DmpR type, the effector positively affects the recruitment of the regulatory protein on the enhancer DNA.
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Affiliation(s)
- David Tropel
- Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), CH-8600 Dübendorf, Switzerland
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Jaspers MCM, Sturme M, van der Meer JR. Unusual location of two nearby pairs of upstream activating sequences for HbpR, the main regulatory protein for the 2-hydroxybiphenyl degradation pathway of "Pseudomonas azelaica" HBP1. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2183-2194. [PMID: 11495995 DOI: 10.1099/00221287-147-8-2183] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
"Pseudomonas azelaica" HBP1 degrades 2-hydroxybiphenyl (2-HBP) and 2,2'-diHBP by employing a meta-cleavage pathway encoded by the hbpCAD genes. The regulatory gene hbpR, located directly upstream of the hbpCAD genes and oriented in the opposite direction, encodes a transcription activator protein belonging to the so-called XylR/DmpR subclass within the NtrC family. HbpR activates transcription from two separate sigma(54)-dependent promoters upstream of the hbpC and the hbpD genes, in the presence of the pathway substrates 2-HBP and 2,2'-diHBP. The DNA region upstream of the hbpC gene displays an unusual organization, containing two adjacent 0.3 kb regions that share 71% sequence identity. The DNA region most proximal to the hbpC promoter harbours one pair of putative upstream activating sequences (UASs C-1/C-2) and a small cryptic ORF that shows homology to hbpR itself. The second, more distal, region contains a second pair of putative UASs (UASs C-3/4) and the 5'-part of the hbpR gene. Transcriptional fusions in Escherichia coli between different deletions of the hbpR-hbpC intergenic region and the genes for bacterial luciferase revealed that most if not all of the transcriptional output from the hbpC promoter is mediated from the proximal UASs C-1/C-2. However, when the UASs C-1/C-2 were deleted and UASs C-3/C-4 were placed in an appropriate position with respect to the promoter region, the hbpC promoter was still inducible with 2-HBP, albeit at a lower level. Transcription studies in E. coli and "P. azelaica" revealed that the divergently oriented hbpR gene is expressed constitutively from a sigma(70)-dependent promoter situated within the cryptic ORF. The presence of UAS pair C-3/C-4 mediated a slightly higher promoter activity for transcription of hbpR.
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Affiliation(s)
- Marco C M Jaspers
- Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), Postbox 611, CH-8600 Dübendorf, Switzerland1
| | - Mark Sturme
- Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), Postbox 611, CH-8600 Dübendorf, Switzerland1
| | - Jan Roelof van der Meer
- Process of Environmental Microbiology and Molecular Ecotoxicology, Swiss Federal Institute for Environmental Science and Technology (EAWAG), Postbox 611, CH-8600 Dübendorf, Switzerland1
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