1
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Zhang J, Pang Q, Wang Q, Qi Q, Wang Q. Modular tuning engineering and versatile applications of genetically encoded biosensors. Crit Rev Biotechnol 2021; 42:1010-1027. [PMID: 34615431 DOI: 10.1080/07388551.2021.1982858] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Genetically encoded biosensors have a diverse range of detectable signals and potential applications in many fields, including metabolism control and high-throughput screening. Their ability to be used in situ with minimal interference to the bioprocess of interest could revolutionize synthetic biology and microbial cell factories. The performance and functions of these biosensors have been extensively studied and have been rapidly improved. We review here current biosensor tuning strategies and attempt to unravel how to obtain ideal biosensor functions through experimental adjustments. Strategies for expanding the biosensor input signals that increases the number of detectable compounds have also been summarized. Finally, different output signals and their practical requirements for biotechnology and biomedical applications and environmental safety concerns have been analyzed. This in-depth review of the responses and regulation mechanisms of genetically encoded biosensors will assist to improve their design and optimization in various application scenarios.
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Affiliation(s)
- Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingxiao Pang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qi Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.,CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, P. R. China
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2
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Dvořák P, Alvarez-Carreño C, Ciordia S, Paradela A, de Lorenzo V. An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors. Environ Microbiol 2021; 23:4418-4433. [PMID: 34097798 DOI: 10.1111/1462-2920.15628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/16/2021] [Accepted: 06/06/2021] [Indexed: 01/14/2023]
Abstract
A revised model of the aromatic binding A domain of the σ54 -dependent regulator XylR of Pseudomonas putida mt-2 was produced based on the known 3D structures of homologous regulators PoxR, MopR and DmpR. The resulting frame was instrumental for mapping a number of mutations known to alter effector specificity, which were then reinterpreted under a dependable spatial reference. Some of these changes involved the predicted aromatic binding pocket but others occurred in distant locations, including dimerization interfaces and putative zinc binding site. The effector pocket was buried within the protein structure and accessible from the outside only through a narrow tunnel. Yet, several loop regions of the A domain could provide the flexibility required for widening such a tunnel for passage of aromatic ligands. The model was experimentally validated by treating the cells in vivo and the purified protein in vitro with benzyl bromide, which reacts with accessible nucleophilic residues on the protein surface. Structural and proteomic analyses confirmed the predicted in/out distribution of residues but also supported two additional possible scenarios of interaction of the A domain with aromatic effectors: a dynamic interaction of the fully structured yet flexible protein with the aromatic partner and/or inducer-assisted folding of the A domain.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Brno, Kamenice 753/5, 62500, Czech Republic
| | - Carlos Alvarez-Carreño
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain.,Centro Tecnológico José Lladó, División de Desarrollo de Tecnologías Propias, Técnicas Reunidas, Calle Sierra Nevada, 16, San Fernando de Henares, Madrid, 28830, Spain
| | - Sergio Ciordia
- Proteomics Core Facilit, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Alberto Paradela
- Proteomics Core Facilit, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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3
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Liu X, Gupta STP, Bhimsaria D, Reed JL, Rodríguez-Martínez JA, Ansari AZ, Raman S. De novo design of programmable inducible promoters. Nucleic Acids Res 2019; 47:10452-10463. [PMID: 31552424 PMCID: PMC6821364 DOI: 10.1093/nar/gkz772] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/16/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023] Open
Abstract
Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.
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Affiliation(s)
- Xiangyang Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sanjan T P Gupta
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer L Reed
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.,The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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4
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Seibt H, Sauer UH, Shingler V. The Y233 gatekeeper of DmpR modulates effector-responsive transcriptional control of σ 54 -RNA polymerase. Environ Microbiol 2019; 21:1321-1330. [PMID: 30773776 DOI: 10.1111/1462-2920.14567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 11/28/2022]
Abstract
DmpR is the obligate transcriptional activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR belongs to the AAA+ class of mechano-transcriptional regulators that employ ATP-hydrolysis to engage and remodel σ54 -RNA polymerase to allow transcriptional initiation. Previous work has established that binding of phenolic effectors by DmpR is a prerequisite to relieve interdomain repression and allow ATP-binding to trigger transition to its active multimeric conformation, and further that a structured interdomain linker between the effector- and ATP-binding domains is involved in coupling these processes. Here, we present evidence from ATPase and in vivo and in vitro transcription assays that a tyrosine residue of the interdomain linker (Y233) serves as a gatekeeper to constrain ATP-hydrolysis and aromatic effector-responsive transcriptional activation by DmpR. An alanine substitution of Y233A results in both increased ATPase activity and enhanced sensitivity to aromatic effectors. We propose a model in which effector-binding relocates Y233 to synchronize signal-reception with multimerisation to provide physiologically appropriate sensitivity of the transcriptional response. Given that Y233 counterparts are present in many ligand-responsive mechano-transcriptional regulators, the model is likely to be pertinent for numerous members of this family and has implications for development of enhanced sensitivity of biosensor used to detect pollutants.
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Affiliation(s)
- Henrik Seibt
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Uwe H Sauer
- Deparment of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
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5
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De Paepe B, Maertens J, Vanholme B, De Mey M. Chimeric LysR-Type Transcriptional Biosensors for Customizing Ligand Specificity Profiles toward Flavonoids. ACS Synth Biol 2019; 8:318-331. [PMID: 30563319 DOI: 10.1021/acssynbio.8b00326] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Transcriptional biosensors enable key applications in both metabolic engineering and synthetic biology. Due to nature's immense variety of metabolites, these applications require biosensors with a ligand specificity profile customized to the researcher's needs. In this work, chimeric biosensors were created by introducing parts of a donor regulatory circuit from Sinorhizobium meliloti, delivering the desired luteolin-specific response, into a nonspecific biosensor chassis from Herbaspirillum seropedicae. Two strategies were evaluated for the development of chimeric LysR-type biosensors with customized ligand specificity profiles toward three closely related flavonoids, naringenin, apigenin, and luteolin. In the first strategy, chimeric promoter regions were constructed at the biosensor effector module, while in the second strategy, chimeric transcription factors were created at the biosensor detector module. Via both strategies, the biosensor repertoire was expanded with luteolin-specific chimeric biosensors demonstrating a variety of response curves and ligand specificity profiles. Starting from the nonspecific biosensor chassis, a shift from 27.5% to 95.3% luteolin specificity was achieved with the created chimeric biosensors. Both strategies provide a compelling, faster, and more accessible route for the customization of biosensor ligand specificity, compared to de novo design and construction of each biosensor circuit for every desired ligand specificity.
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Affiliation(s)
- Brecht De Paepe
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University − VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
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6
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Reimer A, Maffenbeier V, Dubey M, Sentchilo V, Tavares D, Gil MH, Beggah S, van der Meer JR. Complete alanine scanning of the Escherichia coli RbsB ribose binding protein reveals residues important for chemoreceptor signaling and periplasmic abundance. Sci Rep 2017; 7:8245. [PMID: 28811596 PMCID: PMC5557919 DOI: 10.1038/s41598-017-08035-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/05/2017] [Indexed: 11/27/2022] Open
Abstract
The Escherichia coli RbsB ribose binding protein has been used as a scaffold for predicting new ligand binding functions through in silico modeling, yet with limited success and reproducibility. In order to possibly improve the success of predictive modeling on RbsB, we study here the influence of individual residues on RbsB-mediated signaling in a near complete library of alanine-substituted RbsB mutants. Among a total of 232 tested mutants, we found 10 which no longer activated GFPmut2 reporter expression in E. coli from a ribose-RbsB hybrid receptor signaling chain, and 13 with significantly lower GFPmut2 induction than wild-type. Quantitative mass spectrometry abundance measurements of 25 mutants and wild-type RbsB in periplasmic space showed four categories of effects. Some (such as D89A) seem correctly produced and translocated but fail to be induced with ribose. Others (such as N190A) show lower induction probably as a result of less efficient production, folding and translocation. The third (such as N41A or K29A) have defects in both induction and abundance. The fourth category consists of semi-constitutive mutants with increased periplasmic abundance but maintenance of ribose induction. Our data show how RbsB modeling should include ligand-binding as well as folding, translocation and receptor binding.
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Affiliation(s)
- Artur Reimer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Vitali Maffenbeier
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Diogo Tavares
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Manuel Hernandez Gil
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland.
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7
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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8
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De Paepe B, Peters G, Coussement P, Maertens J, De Mey M. Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol 2016; 44:623-645. [PMID: 27837353 DOI: 10.1007/s10295-016-1862-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/30/2016] [Indexed: 12/24/2022]
Abstract
Monitoring cellular behavior and eventually properly adapting cellular processes is key to handle the enormous complexity of today's metabolic engineering questions. Hence, transcriptional biosensors bear the potential to augment and accelerate current metabolic engineering strategies, catalyzing vital advances in industrial biotechnology. The development of such transcriptional biosensors typically starts with exploring nature's richness. Hence, in a first part, the transcriptional biosensor architecture and the various modi operandi are briefly discussed, as well as experimental and computational methods and relevant ontologies to search for natural transcription factors and their corresponding binding sites. In the second part of this review, various engineering approaches are reviewed to tune the main characteristics of these (natural) transcriptional biosensors, i.e., the response curve and ligand specificity, in view of specific industrial biotechnology applications, which is illustrated using success stories of transcriptional biosensor engineering.
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Affiliation(s)
- Brecht De Paepe
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Gert Peters
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Pieter Coussement
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jo Maertens
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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9
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Ray S, Gunzburg MJ, Wilce M, Panjikar S, Anand R. Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator. ACS Chem Biol 2016; 11:2357-65. [PMID: 27362503 DOI: 10.1021/acschembio.6b00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivo biosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopR(AB)) from Acinetobacter calcoaceticus in complex with phenol and its derivatives to a maximum resolution of 2.5 Å. The structure reveals that the N-terminal residues 21-47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the "nitric oxide signaling and golgi transport" fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopR(AB) nests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.
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Affiliation(s)
- Shamayeeta Ray
- IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - Menachem J. Gunzburg
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Matthew Wilce
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Santosh Panjikar
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Australian Synchrotron, Clayton, Victoria 3168, Australia
| | - Ruchi Anand
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
- Wadhwani
Research Center for Bioengineering, IIT Bombay, Mumbai 400076, India
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10
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Büsing I, Kant M, Dörries M, Wöhlbrand L, Rabus R. The predicted σ(54)-dependent regulator EtpR is essential for expression of genes for anaerobic p-ethylphenol and p-hydroxyacetophenone degradation in "Aromatoleum aromaticum" EbN1. BMC Microbiol 2015; 15:251. [PMID: 26526497 PMCID: PMC4630880 DOI: 10.1186/s12866-015-0571-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/15/2015] [Indexed: 02/05/2023] Open
Abstract
Background The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 anaerobically utilizes a multitude of aromatic compounds via specific peripheral degradation routes. Compound-specific formation of these catabolic modules is assumed to be mediated by specific transcriptional activators. In case of the recently elucidated p-ethylphenol/p-hydroxyacetophenone pathway, the highly substrate-specific regulation was implicated to involve the predicted σ54-dependent, NtrC-type regulator EbA324. The latter was suggested to control the expression of the two neighboring gene clusters encoding the catabolic enzymes as well as a corresponding putative solvent efflux system. In the present study, a molecular genetic approach was used to study the predicted function of EbA324. Results An unmarked in frame ΔebA324 (here renamed as ΔetpR; p-ethylphenol regulator) deletion mutation was generated. The ΔetpR mutant was unable to grow anaerobically with either p-ethylphenol or p-hydroxyacetophenone. Growth similar to the wild type was restored in the ΔetpR mutant background by in trans expression of plasmid-born etpR. Furthermore, expression of the "p-ethylphenol" gene clusters as well as corresponding protein formation was shown to depend on the presence of both, EtpR and either p-ethylphenol or p-hydroxyacetophenone. In the wild type, the etpR gene appears to be constitutively expressed and its expression level not to be modulated upon effector presence. Comparison with the regulatory domains of known phenol- and alkylbenzene-responsive NtrC-type regulators of Pseudomonas spp. and Thauera aromatica allowed identifying >60 amino acid residues in the regulatory domain (in particular positions 149 to 192 of EtpR) that may contribute to the effector specificity viz. presumptively restricted effector spectrum of EtpR. Conclusions This study provides experimental evidence for the genome predicted σ54-dependent regulator EtpR (formerly EbA324) of "A. aromaticum" EbN1 to be responsive to p-ethylphenol, as well as its degradation intermediate p-hydroxyacetophenone, and to control the expression of genes involved in the anaerobic degradation of these two aromatic growth substrates. Overall, the presented results advance our understanding on the regulation of anaerobic aromatic compound catabolism, foremost based on the sensory discrimination of structurally similar substrates. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0571-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imke Büsing
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Mirjam Kant
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Marvin Dörries
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany. .,Max Planck Institute for Marine Microbiology, Bremen, Germany.
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11
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Shemer B, Palevsky N, Yagur-Kroll S, Belkin S. Genetically engineered microorganisms for the detection of explosives' residues. Front Microbiol 2015; 6:1175. [PMID: 26579085 PMCID: PMC4625088 DOI: 10.3389/fmicb.2015.01175] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/12/2015] [Indexed: 01/14/2023] Open
Abstract
The manufacture and use of explosives throughout the past century has resulted in the extensive pollution of soils and groundwater, and the widespread interment of landmines imposes a major humanitarian risk and prevents civil development of large areas. As most current landmine detection technologies require actual presence at the surveyed areas, thus posing a significant risk to personnel, diverse research efforts are aimed at the development of remote detection solutions. One possible means proposed to fulfill this objective is the use of microbial bioreporters: genetically engineered microorganisms “tailored” to generate an optical signal in the presence of explosives’ vapors. The use of such sensor bacteria will allow to pinpoint the locations of explosive devices in a minefield. While no study has yet resulted in a commercially operational system, significant progress has been made in the design and construction of explosives-sensing bacterial strains. In this article we review the attempts to construct microbial bioreporters for the detection of explosives, and analyze the steps that need to be undertaken for this strategy to be applicable for landmine detection.
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Affiliation(s)
- Benjamin Shemer
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Noa Palevsky
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Sharon Yagur-Kroll
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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12
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Jha RK, Chakraborti S, Kern TL, Fox DT, Strauss CEM. Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor. Proteins 2015; 83:1327-40. [DOI: 10.1002/prot.24828] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/09/2015] [Accepted: 05/02/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory; Los Alamos New Mexico 87545
| | - Subhendu Chakraborti
- Bioscience Division, Los Alamos National Laboratory; Los Alamos New Mexico 87545
| | - Theresa L. Kern
- Bioscience Division, Los Alamos National Laboratory; Los Alamos New Mexico 87545
| | - David T. Fox
- Bioscience Division, Los Alamos National Laboratory; Los Alamos New Mexico 87545
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13
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Reimer A, Yagur-Kroll S, Belkin S, Roy S, van der Meer JR. Escherichia [corrected] coli ribose binding protein based bioreporters revisited. Sci Rep 2014; 4:5626. [PMID: 25005019 PMCID: PMC4088097 DOI: 10.1038/srep05626] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/17/2014] [Indexed: 01/09/2023] Open
Abstract
Bioreporter bacteria, i.e., strains engineered to respond to chemical exposure by production of reporter proteins, have attracted wide interest because of their potential to offer cheap and simple alternative analytics for specified compounds or conditions. Bioreporter construction has mostly exploited the natural variation of sensory proteins, but it has been proposed that computational design of new substrate binding properties could lead to completely novel detection specificities at very low affinities. Here we reconstruct a bioreporter system based on the native Escherichia coli ribose binding protein RbsB and one of its computationally designed variants, reported to be capable of binding 2,4,6-trinitrotoluene (TNT). Our results show in vivo reporter induction at 50 nM ribose, and a 125 nM affinity constant for in vitro ribose binding to RbsB. In contrast, the purified published TNT-binding variant did not bind TNT nor did TNT cause induction of the E. coli reporter system.
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Affiliation(s)
- Artur Reimer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge 1015 Lausanne, Switzerland
| | - Sharon Yagur-Kroll
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shimshon Belkin
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Shantanu Roy
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge 1015 Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge 1015 Lausanne, Switzerland
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14
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Hynninen A, Virta M. Whole-cell bioreporters for the detection of bioavailable metals. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 118:31-63. [PMID: 19543702 DOI: 10.1007/10_2009_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Whole-cell bioreporters are living microorganisms that produce a specific, quantifiable output in response to target chemicals. Typically, whole-cell bioreporters combine a sensor element for the substance of interest and a reporter element coding for an easily detectable protein. The sensor element is responsible for recognizing the presence of an analyte. In the case of metal bioreporters, the sensor element consists of a DNA promoter region for a metal-binding transcription factor fused to a promoterless reporter gene that encodes a signal-producing protein. In this review, we provide an overview of specific whole-cell bioreporters for heavy metals. Because the sensing of metals by bioreporter microorganisms is usually based on heavy metal resistance/homeostasis mechanisms, the basis of these mechanisms will also be discussed. The goal here is not to present a comprehensive summary of individual metal-specific bioreporters that have been constructed, but rather to express views on the theory and applications of metal-specific bioreporters and identify some directions for future research and development.
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Affiliation(s)
- Anu Hynninen
- Department of Applied Chemistry and Microbiology, University of Helsinki, 56, 00014, Helsinki, Finland
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15
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de las Heras A, Fraile S, de Lorenzo V. Increasing signal specificity of the TOL network of Pseudomonas putida mt-2 by rewiring the connectivity of the master regulator XylR. PLoS Genet 2012; 8:e1002963. [PMID: 23071444 PMCID: PMC3469447 DOI: 10.1371/journal.pgen.1002963] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/07/2012] [Indexed: 11/28/2022] Open
Abstract
Prokaryotic transcription factors (TFs) that bind small xenobiotic molecules (e.g., TFs that drive genes that respond to environmental pollutants) often display a promiscuous effector profile for analogs of the bona fide chemical signals. XylR, the master TF for expression of the m-xylene biodegradation operons encoded in the TOL plasmid pWW0 of Pseudomonas putida, responds not only to the aromatic compound but also, albeit to a lesser extent, to many other aromatic compounds, such as 3-methylbenzylalcohol (3MBA). We have examined whether such a relaxed regulatory scenario can be reshaped into a high-capacity/high-specificity regime by changing the connectivity of this effector-sensing TF within the rest of the circuit rather than modifying XylR structure itself. To this end, the natural negative feedback loop that operates on xylR transcription was modified with a translational attenuator that brings down the response to 3MBA while maintaining the transcriptional output induced by m-xylene (as measured with a luxCDABE reporter system). XylR expression was then subject to a positive feedback loop in which the TF was transcribed from its own target promoters, each known to hold different input/output transfer functions. In the first case (xylR under the strong promoter of the upper TOL operon, Pu), the reporter system displayed an increased transcriptional capacity in the resulting network for both the optimal and the suboptimal XylR effectors. In contrast, when xylR was expressed under the weaker Ps promoter, the resulting circuit unmistakably discriminated m-xylene from 3MBA. The non-natural connectivity engineered in the network resulted both in a higher promoter activity and also in a much-increased signal-to-background ratio. These results indicate that the working regimes of given genetic circuits can be dramatically altered through simple changes in the way upstream transcription factors are self-regulated by positive or negative feedback loops. It is generally taken for granted that promoters regulated by transcriptional factors (TFs) that respond to small molecules control their specificity to given effectors by tightening or relaxing the intrinsic dual interaction between the TF and the particular inducer. One such promoter is Pu, which drives expression of an operon for the biodegradation of m-xylene by the soil bacterium P. putida mt-2. While XylR, the chief TF of this system, binds this substrate and activates Pu, the same regulator responds, to a lesser extent, to 3-methylbenzylalcohol and thus also activates the promoter. This work provides evidence that such natural effector promiscuity of the system can be altogether suppressed by replacing the naturally occurring negative autoregulation loop that governs XylR expression with an equivalent positive feedback loop. Based on this result, we argue that signal specificity of a given regulatory device depends not only on the TF involved but also on TF connectivity to upstream signals and downstream targets.
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Affiliation(s)
| | | | - Victor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
- * E-mail:
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16
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Gredell JA, Frei CS, Cirino PC. Protein and RNA engineering to customize microbial molecular reporting. Biotechnol J 2011; 7:477-99. [PMID: 22031507 DOI: 10.1002/biot.201100266] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/20/2011] [Accepted: 08/23/2011] [Indexed: 12/19/2022]
Abstract
Nature takes advantage of the malleability of protein and RNA sequence and structure to employ these macromolecules as molecular reporters whose conformation and functional roles depend on the presence of a specific ligand (an "effector" molecule). By following nature's example, ligand-responsive proteins and RNA molecules are now routinely engineered and incorporated into customized molecular reporting systems (biosensors). Microbial small-molecule biosensors and endogenous molecular reporters based on these sensing components find a variety of applications that include high-throughput screening of biosynthesis libraries, environmental monitoring, and novel gene regulation in synthetic biology. Here, we review recent advances in engineering small-molecule recognition by proteins and RNA and in coupling in vivo ligand binding to reporter-gene expression or to allosteric activation of a protein conferring a detectable phenotype. Emphasis is placed on microbial screening systems that serve as molecular reporters and facilitate engineering the ligand-binding component to recognize new molecules.
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Affiliation(s)
- Joseph A Gredell
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
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17
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Garmendia J, de las Heras A, Galvão TC, de Lorenzo V. Tracing explosives in soil with transcriptional regulators of Pseudomonas putida evolved for responding to nitrotoluenes. Microb Biotechnol 2011; 1:236-46. [PMID: 21261843 PMCID: PMC3815885 DOI: 10.1111/j.1751-7915.2008.00027.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Although different biological approaches for detection of anti-personnel mines and other unexploded ordnance (UXO) have been entertained, none of them has been rigorously documented thus far in the scientific literature. The industrial 2,4,6 trinitrotoluene (TNT) habitually employed in the manufacturing of mines is at all times tainted with a small but significant proportion of the more volatile 2,4 dinitrotoluene (2,4 DNT) and other nitroaromatic compounds. By using mutation-prone PCR and DNA sequence shuffling we have evolved in vitro and selected in vivo variants of the effector recognition domain of the toluene-responsive XylR regulator of the soil bacterium Pseudomonas putida that responds to mono-, bi- and trinitro substituted toluenes. Re-introduction of such variants in P. putida settled the transcriptional activity of the cognate promoters (Po and Pu) as a function of the presence of nitrotoluenes in the medium. When strains bearing transcriptional fusions to reporters with an optical output (luxAB, GFP) were spread on soil spotted with nitrotoluenes, the signal triggered by promoter activation allowed localization of the target compounds on the soil surface. Our data provide a proof of concept that non-natural transcription factors evolved to respond to nitroaromatics can be engineered in soil bacteria and inoculated on a target site to pinpoint the presence of explosives. This approach thus opens new ways to tackle this gigantic humanitarian problem.
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Affiliation(s)
- Junkal Garmendia
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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18
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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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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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de las Heras A, de Lorenzo V. Cooperative amino acid changes shift the response of the σ54-dependent regulator XylR from natural m-xylene towards xenobiotic 2,4-dinitrotoluene. Mol Microbiol 2011; 79:1248-59. [DOI: 10.1111/j.1365-2958.2010.07518.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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In situ detection of aromatic compounds with biosensor Pseudomonas putida cells preserved and delivered to soil in water-soluble gelatin capsules. Anal Bioanal Chem 2010; 400:1093-104. [DOI: 10.1007/s00216-010-4558-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/21/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
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22
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23
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Bhaganna P, Volkers RJM, Bell ANW, Kluge K, Timson DJ, McGrath JW, Ruijssenaars HJ, Hallsworth JE. Hydrophobic substances induce water stress in microbial cells. Microb Biotechnol 2010; 3:701-16. [PMID: 21255365 PMCID: PMC3815343 DOI: 10.1111/j.1751-7915.2010.00203.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Ubiquitous noxious hydrophobic substances, such as hydrocarbons, pesticides and diverse industrial chemicals, stress biological systems and thereby affect their ability to mediate biosphere functions like element and energy cycling vital to biosphere health. Such chemically diverse compounds may have distinct toxic activities for cellular systems; they may also share a common mechanism of stress induction mediated by their hydrophobicity. We hypothesized that the stressful effects of, and cellular adaptations to, hydrophobic stressors operate at the level of water : macromolecule interactions. Here, we present evidence that: (i) hydrocarbons reduce structural interactions within and between cellular macromolecules, (ii) organic compatible solutes – metabolites that protect against osmotic and chaotrope‐induced stresses – ameliorate this effect, (iii) toxic hydrophobic substances induce a potent form of water stress in macromolecular and cellular systems, and (iv) the stress mechanism of, and cellular responses to, hydrophobic substances are remarkably similar to those associated with chaotrope‐induced water stress. These findings suggest that it may be possible to devise new interventions for microbial processes in both natural environments and industrial reactors to expand microbial tolerance of hydrophobic substances, and hence the biotic windows for such processes.
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Affiliation(s)
- Prashanth Bhaganna
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
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24
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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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25
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Peng Z, Yan Y, Xu Y, Takeo M, Yu H, Zhao Z, Zhan Y, Zhang W, Lin M, Chen M. Improvement of an E. coli bioreporter for monitoring trace amounts of phenol by deletion of the inducible σ54-dependent promoter. Biotechnol Lett 2010; 32:1265-70. [DOI: 10.1007/s10529-010-0317-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 04/07/2010] [Accepted: 04/13/2010] [Indexed: 11/24/2022]
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26
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de Lorenzo V. Recombinant bacteria for environmental release: what went wrong and what we have learnt from it. Clin Microbiol Infect 2009; 15 Suppl 1:63-5. [DOI: 10.1111/j.1469-0691.2008.02683.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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de las Heras A, Carreño CA, de Lorenzo V. Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 2008; 10:3305-16. [DOI: 10.1111/j.1462-2920.2008.01722.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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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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Silva-Rocha R, de Lorenzo V. Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett 2008; 582:1237-44. [PMID: 18275855 DOI: 10.1016/j.febslet.2008.01.060] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
Abstract
Prokaryotic transcriptional networks possess a large number of regulatory modules that formally implement many of the logic gates that are typical of digital, Boolean circuits. Yet, natural regulatory elements appear most often compressed and exaggeratedly context-dependent for any reliable circuit engineering barely comparable to electronic counterparts. To overcome this impasse, we argue that designing new functions with biological parts requires (i) the recognition of logic gates not yet assigned but surely present in the meta-genome, (ii) the orthogonalization and disambiguation of natural regulatory modules and (iii) the development of ways to tackle the connectivity and the definition of boundaries between minimal biological components.
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Affiliation(s)
- Rafael Silva-Rocha
- Centro Nacional de Biotecnología, CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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Abstract
Metagenomics--the application of the genomics suit of technologies to uncultivated microorganisms--is coming of age. Sophisticated technologies are being developed and adapted to this promising genetic resource to make increasing use of the seemingly boundless molecular and functional diversity. Particular progress has been made in the areas of randomly proliferating limited-source DNA, massively parallel sequencing without cloning, isolating specific target sequences from highly complex template mixtures, high-throughput assay systems targeting metabolic pathways, artificial transcriptional regulators activating reporter genes to indicate enzymatic substrate conversion and cDNA cloning from extracted mRNA to directly clone actively expressed genes from a microbial consortium. However, challenges still lie ahead. Most prominently, the efficient heterologous expression of a plethora of potentially interesting enzymes from unknown source organisms is not readily achieved.
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Galvão TC, Mencía M, de Lorenzo V. Emergence of novel functions in transcriptional regulators by regression to stem protein types. Mol Microbiol 2007; 65:907-19. [PMID: 17645451 DOI: 10.1111/j.1365-2958.2007.05832.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Evolutionary expansion of metabolic networks entails the emergence of regulatory factors that become sensitive to new chemical species. A dedicated genetic system was developed for the soil bacterium Pseudomonas putida aimed at deciphering the steps involved in the gain of responsiveness of the toluene-activated prokaryotic regulator XylR to the xenobiotic chemical 2,4 dinitrotoluene (DNT). A mutant library of the A domain of XylR was screened in vivo for those variants activated by DNT through coupling the cognate promoter Pu to the P. putida yeast URA3 homologue, pyrF. All DNT-responsive clones maintained their sensitivity to ordinary effectors of XylR and broadened the range of inducers to unrelated aromatics. Yet, none of the altered amino acids lay in the recognizable effector binding pocket of the polypeptide. Instead, mutations appeared in protein surfaces believed to engage in the conformational shifts that follow effector binding and modulate signal transmission between XylR domains. It thus seems that transcriptional factors are likely to regress into functionally multipotent forms (i.e. stem protein types) as a first step towards the divergence of a new specificity.
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Affiliation(s)
- Teca Calcagno Galvão
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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Schilling O, Herzberg C, Hertrich T, Vörsmann H, Jessen D, Hübner S, Titgemeyer F, Stülke J. Keeping signals straight in transcription regulation: specificity determinants for the interaction of a family of conserved bacterial RNA-protein couples. Nucleic Acids Res 2006; 34:6102-15. [PMID: 17074746 PMCID: PMC1635312 DOI: 10.1093/nar/gkl733] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Regulatory systems often evolve by duplication of ancestral systems and subsequent specialization of the components of the novel signal transduction systems. In the Gram-positive soil bacterium Bacillus subtilis, four homologous antitermination systems control the expression of genes involved in the metabolism of glucose, sucrose and β-glucosides. Each of these systems is made up of a sensory sugar permease that does also act as phosphotransferase, an antitermination protein, and a RNA switch that is composed of two mutually exclusive structures, a RNA antiterminator (RAT) and a transcriptional terminator. We have studied the contributions of sugar specificity of the permeases, carbon catabolite repression, and protein–RAT recognition for the straightness of the signalling chains. We found that the β-glucoside permease BglP does also have a minor activity in glucose transport. However, this activity is irrelevant under physiological conditions since carbon catabolite repression in the presence of glucose prevents the synthesis of the β-glucoside permease. Reporter gene studies, in vitro RNA–protein interaction analyzes and northern blot transcript analyzes revealed that the interactions between the antiterminator proteins and their RNA targets are the major factor contributing to regulatory specificity. Both structural features in the RATs and individual bases are important specificity determinants. Our study revealed that the specificity of protein–RNA interactions, substrate specificity of the permeases as well as the general mechanism of carbon catabolite repression together allow to keep the signalling chains straight and to avoid excessive cross-talk between the systems.
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Affiliation(s)
| | | | - Tina Hertrich
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | | | | | | | - Fritz Titgemeyer
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-NürnbergErlangen, Germany
| | - Jörg Stülke
- To whom correspondence should be addressed. Tel: +49 551 393781; Fax: +49 551 393808;
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Jurado P, Fernández LA, de Lorenzo V. In vivo drafting of single-chain antibodies for regulatory duty on the sigma54-promoter Pu of the TOL plasmid. Mol Microbiol 2006; 60:1218-27. [PMID: 16689797 DOI: 10.1111/j.1365-2958.2006.05183.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The identification of single-chain antibodies (scFvs) that interfere in vivo with the building of the complex that activate the prokaryotic, sigma54-dependent promoter Pu of the catabolic TOL plasmid pWW0 is reported. To this end, a phage M13 library of scFvs was raised against the cognate prokaryotic enhancer-binding activator, XylR. The scFv pool was then expressed intracellularly in a reporter Pu-lacZ strain of Escherichia coli designed to permit formation of intramolecular disulphide bonds in cytoplasmic proteins. This strain allowed the assembly of functional scFvs and the direct testing of their activity on the Pu promoter in vivo. Specifically, genetic screening for lacZ-minus colonies yielded a number of scFvs able to downregulate transcriptional output in live cells. Two antibody clones were purified and shown to inhibit the activity of the same promoter in vitro as well. These scFvs targeted the DNA-binding domain of XylR and its ATP binding site respectively. This work provides a proof of principle that mimetic regulatory factors can be derived from an antibody repertoire that specifically interact with given transcriptional activators. As assembly of initiation complexes is stimulated or inhibited by regulatory proteins we argue that anti-XylR scFvs operate as bona fide transcriptional inhibitors of the Pu promoter.
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Affiliation(s)
- Paola Jurado
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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Mohn WW, Garmendia J, Galvao TC, de Lorenzo V. Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 2006; 8:546-55. [PMID: 16478460 DOI: 10.1111/j.1462-2920.2006.00983.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a DNA clone into a selectable/scorable phenotype. We established this strategy with a system to expose the activity of dehydrochlorinases acting upon gamma-hexachlorocyclohexane (gamma-HCH or lindane). To this end, the effector-binding protein, XylR, was evolved by gene shuffling plus mutagenic polymerase chain reaction to be optimally responsive to the major product of gamma-HCH dehydrochlorination, 1,2,4-trichlorobenzene (TCB). We then derived Escherichia coli strains that constitutively expressed the modified XylR variant (named XylR5) and had lacZ under control of the Pu promoter, which is activated by XylR. A robotic beta-galactosidase assay indicated that when the resulting strain was transformed with a linA+ clone (expressing a gamma-HCH dehydrochlorinase from Sphingomonas paucimobilis UT26), it had levels of beta-galactosidase that were dependent on the gamma-HCH concentration. This à la carte host thus translated the conversion of gamma-HCH to TCB into upregulation of lacZ. An alternate host additionally expressing LacY grew efficiently on lactose only when LacZ was upregulated in a fashion dependent on TCB or other effectors of XylR5. These results demonstrated the power of deriving a host for the genetic scrutiny, rather than enzymatic screening, of clones expressing a given catabolic enzyme.
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Affiliation(s)
- William W Mohn
- Department of Microbiology and Immunology, University of British Columbia, 300-6174 University Blvd., Vancouver, BC V6T 1Z3, Canada
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35
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Galvão TC, de Lorenzo V. Transcriptional regulators à la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 2006; 17:34-42. [PMID: 16359854 DOI: 10.1016/j.copbio.2005.12.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 11/15/2005] [Accepted: 12/05/2005] [Indexed: 11/27/2022]
Abstract
For many regulators of bacterial biodegradation pathways, small molecule/effector binding is the signal for triggering transcriptional activation. Thus, regulation results from a cross-talk between chemicals sensed by transcriptional factors and operon expression status. These features can be utilised in the construction of biosensors for a wide range of target compounds as, in principle, any regulatory protein whose activity is modulated by binding to a small molecule can have its effector/inducer profile artificially altered. The cognate specificities of a number of regulatory proteins have been modified as an astute approach to developing, among others, bacterial biosensors for environmentally relevant compounds.
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Affiliation(s)
- Teca Calcagno Galvão
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología-CSIC, Madrid 28049, Spain.
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36
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Tecon R, van der Meer JR. Information from single-cell bacterial biosensors: what is it good for? Curr Opin Biotechnol 2006; 17:4-10. [PMID: 16326092 DOI: 10.1016/j.copbio.2005.11.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 11/10/2005] [Accepted: 11/23/2005] [Indexed: 11/26/2022]
Abstract
Bacterial reporter cells (i.e. strains engineered to produce easily measurable signals in response to one or more chemical targets) can principally be used to quantify chemical signals and analytes, physicochemical conditions and gradients on a microscale (i.e. micrometer to submillimeter distances), when the reporter signal is determined in individual cells. This makes sense, as bacterial life essentially thrives in microheterogenic environments and single-cell reporter information can help us to understand the microphysiology of bacterial cells and its importance for macroscale processes like pollutant biodegradation, beneficial bacteria-eukaryote interactions, and infection. Recent findings, however, showed that clonal bacterial populations are essentially always physiologically, phenotypically and genotypically heterogeneous, thus emphasizing the need for sound statistical approaches for the interpretation of reporter response in individual bacterial cells. Serious attempts have been made to measure and interpret single-cell reporter gene expression and to understand variability in reporter expression among individuals in a population.
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Affiliation(s)
- Robin Tecon
- Department of Fundamental Microbiology, Bâtiment Biophore, Quartier UNIL-Sorge, University of Lausanne, CH 1015 Lausanne, Switzerland
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37
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van Sint Fiet S, van Beilen JB, Witholt B. Selection of biocatalysts for chemical synthesis. Proc Natl Acad Sci U S A 2006; 103:1693-8. [PMID: 16446453 PMCID: PMC1413619 DOI: 10.1073/pnas.0504733102] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To determine whether microbial chemosensors can be used to find new or better biocatalysts, we constructed Escherichia coli hosts that recognize the product of a biocatalytic conversion through the transcriptional activator NahR and respond by expression of a lacZ or tetA reporter gene. Equipped with a benzaldehyde dehydrogenase (XylC from Pseudomonas putida), the lacZ-based host responded to the oxidation of benzaldehyde and 2-hydroxybenzaldehyde to the corresponding benzoic acids by forming blue colonies, whereas XylC- cells did not. Similarly, the tetA-based host was able to grow under selective conditions only when equipped with XylC, enabling selection of biocatalytically active cells in inactive populations at frequencies as low as 10(-6).
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Affiliation(s)
- Stephan van Sint Fiet
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
| | - Jan B. van Beilen
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
| | - Bernard Witholt
- Institute of Biotechnology, Eidgenössische Technische Hochschule Hönggerberg, HPT Building, Wolfgang-Pauli-Strasse 16, 8093 Zürich, Switzerland
- *To whom correspondence should be addressed. E-mail:
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Galvão TC, Mohn WW, de Lorenzo V. Exploring the microbial biodegradation and biotransformation gene pool. Trends Biotechnol 2005; 23:497-506. [PMID: 16125262 DOI: 10.1016/j.tibtech.2005.08.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Revised: 03/30/2005] [Accepted: 08/11/2005] [Indexed: 11/26/2022]
Abstract
Similar to the New World explorers of the 16th and 17th century, microbiologists today find themselves at the edge of unknown territory. It is estimated that only 0.1-1% of microorganisms can be cultivated using current techniques; the vastness of microbial lifestyles remains to be explored. Because the microbial metagenome is the largest reservoir of genes that determine enzymatic reactions, new techniques are being developed to identify the genes that underlie many valuable chemical biotransformations carried out by microbes, particularly in pathways for biodegradation of recalcitrant and xenobiotic molecules. Our knowledge of catabolic routes built on research during the past 40 years is a solid basis from which to venture on to the little-explored pathways that might exist in nature. However, it is clear that the vastness of information to be obtained requires astute experimental strategies for finding novel reactions.
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Affiliation(s)
- Teca Calcagno Galvão
- Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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39
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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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40
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Abstract
The delicate and dynamic balance of the physiological steady state and its maintenance is well characterized by studies of bacterial stress response. Through the use of genetic analysis, numerous stress regulons, their physiological regulators and their biochemical processes have been delineated. In particular, transcriptionally activated stress regulons are subjects of study and application. These regulons include those that respond to macromolecular damage and toxicity as well as to nutrient starvation. The convenience of reporter gene fusions has allowed the creation of biosensor strains, resulting from the fusion of stress-responsive promoters with a variety of reporter genes. Such cellular biosensors are being used for monitoring dynamic systems and can report the presence of environmental stressors in real time. They provide a greater range of sensitivity, e.g. to sub-lethal concentrations of toxicants, than the simple assessment of cell viability. The underlying physiological context of the reporter strains results in the detection of bioavailable concentrations of both toxicants and nutrients. Culture conditions and host strain genotypes can be customized so as to maximize the sensitivity of the strain for a particular application. Collections of specific strains that are grouped in panels are used to diagnose targets or mode of action for unknown toxicants. Further application in massive by parallel DNA and gene fusion arrays greatly extends the information available for diagnosis of modes of action and may lead to development of novel high-throughput screens. Future studies will include more panels, arrays, as well as single reporter cell detection for a better understanding of the population heterogeneity during stress response. New knowledge of physiology gained from further studies of novel systems, or using innovative methods of analysis, will undoubtedly yield still more useful and informative environmental biosensors.
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Affiliation(s)
- Amy Cheng Vollmer
- Department of Biology, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA.
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41
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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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42
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Tropel D, van der Meer JR. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol Mol Biol Rev 2004; 68:474-500, table of contents. [PMID: 15353566 PMCID: PMC515250 DOI: 10.1128/mmbr.68.3.474-500.2004] [Citation(s) in RCA: 285] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. The interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. In addition, regulation of catabolic pathway expression has attracted the interest of numerous different groups, and several catabolic pathway regulators have been exemplary for understanding transcription control mechanisms. More recently, information about regulatory systems has been used to construct whole-cell living bioreporters that are used to measure the quality of the aqueous, soil, and air environment. The topic of biodegradation is relatively coherent, and this review presents a coherent overview of the regulatory systems involved in the transcriptional control of catabolic pathways. This review summarizes the different regulatory systems involved in biodegradation pathways of aromatic compounds linking them to other known protein families. Specific attention has been paid to describing the genetic organization of the regulatory genes, promoters, and target operon(s) and to discussing present knowledge about signaling molecules, DNA binding properties, and operator characteristics, and evidence from regulatory mutants. For each regulator family, this information is combined with recently obtained protein structural information to arrive at a possible mechanism of transcription activation. This demonstrates the diversity of control mechanisms existing in catabolic pathways.
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Affiliation(s)
- David Tropel
- Swiss Federal Institute for Environmental Science and Technology (EAWAG), Dübendorf, Switzerland
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Shingler V. Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour. Environ Microbiol 2004; 5:1226-41. [PMID: 14641570 DOI: 10.1111/j.1462-2920.2003.00472.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deciphering the complex interconnecting bacterial responses to the presence of aromatic compounds is required to gain an integrated understanding of how aromatic catabolic processes function in relation to their genome and environmental context. In addition to the properties of the catabolic enzymes themselves, regulatory responses on at least three different levels are important. At a primary level, aromatic compounds control the activity of specific members of many families of transcriptional regulators to direct the expression of the specialized enzymes for their own catabolism. At a second level, dominant global regulation in response to environmental and physiological cues is incorporated to subvert and couple transcription levels to the energy status of the bacteria. Mediators of these global regulatory responses include the alarmone (p)ppGpp, the DNA-bending protein IHF and less well-defined systems that probably sense the energy status through the activity of the electron transport chain. At a third level, aromatic compounds can also impact on catabolic performance by provoking behavioural responses that allow the bacteria to seek out aromatic growth substrates in their environment.
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Affiliation(s)
- Victoria Shingler
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.
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Stafford GP, Scanlan J, McDonald IR, Murrell JC. rpoN, mmoR and mmoG, genes involved in regulating the expression of soluble methane monooxygenase in Methylosinus trichosporium OB3b. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1771-1784. [PMID: 12855729 DOI: 10.1099/mic.0.26060-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The methanotrophic bacterium Methylosinus trichosporium OB3b converts methane to methanol using two distinct forms of methane monooxygenase (MMO) enzyme: a cytoplasmic soluble form (sMMO) and a membrane-bound form (pMMO). The transcription of these two operons is known to proceed in a reciprocal fashion with sMMO expressed at low copper-to-biomass ratios and pMMO at high copper-to-biomass ratios. Transcription of the smmo operon is initiated from a sigma(N) promoter 5' of mmoX. In this study the genes encoding sigma(N) (rpoN) and a typical sigma(N)-dependent transcriptional activator (mmoR) were cloned and sequenced. mmoR, a regulatory gene, and mmoG, a gene encoding a GroEL homologue, lie 5' of the structural genes for the sMMO enzyme. Subsequent mutation of rpoN and mmoR by marker-exchange mutagenesis resulted in strains Gm1 and JS1, which were unable to express functional sMMO or initiate transcription of mmoX. An rpoN mutant was also unable to fix nitrogen or use nitrate as sole nitrogen source, indicating that sigma(N) plays a role in both nitrogen and carbon metabolism in Ms. trichosporium OB3b. The data also indicate that mmoG is transcribed in a sigma(N)- and MmoR-independent manner. Marker-exchange mutagenesis of mmoG revealed that MmoG is necessary for smmo gene transcription and activity and may be an MmoR-specific chaperone required for functional assembly of transcriptionally competent MmoR in vivo. The data presented allow the proposal of a more complete model for copper-mediated regulation of smmo gene expression.
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Affiliation(s)
- Graham P Stafford
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Julie Scanlan
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Ian R McDonald
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - J Colin Murrell
- Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
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45
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Lessner DJ, Parales RE, Narayan S, Gibson DT. Expression of the nitroarene dioxygenase genes in Comamonas sp. strain JS765 and Acidovorax sp. strain JS42 is induced by multiple aromatic compounds. J Bacteriol 2003; 185:3895-904. [PMID: 12813084 PMCID: PMC161575 DOI: 10.1128/jb.185.13.3895-3904.2003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This work reports a genetic analysis of the expression of nitrobenzene dioxygenase (NBDO) in Comamonas sp. strain JS765 and 2-nitrotoluene dioxygenase (2NTDO) in Acidovorax sp. strain JS42. Strains JS765 and JS42 possess identical LysR-type regulatory proteins, NbzR and NtdR, respectively. NbzR/NtdR is homologous to NahR, the positive salicylate-responsive transcriptional activator of the naphthalene degradation genes in Pseudomonas putida G7. The genes encoding NBDO and 2NTDO in each strain are cotranscribed, and transcription starts at the same site within identical promoter regions for each operon. Results from a lacZ reporter gene fusion demonstrated that expression of NBDO and 2NTDO is induced by multiple aromatic compounds, including an array of nitroaromatic compounds (nitrobenzene, 2-, 3-, and 4-nitrotoluene, 2,4- and 2,6-dinitrotoluene, and aminodinitrotoluenes), as well as salicylate and anthranilate. The nitroaromatic compounds appear to be the actual effector molecules. Analysis of beta-galactosidase and 2NTDO activities with strain JS42 demonstrated that NtdR was required for induction by all of the inducing compounds, high basal-level expression of 2NTDO, and complementation of a JS42 ntdR null mutant. Complementation with the closely related regulators NagR (from Ralstonia sp. strain U2) and NahR restored only induction by the archetype inducers, salicylate or salicylate and anthranilate, respectively, and did not restore the high basal level of expression of 2NTDO. The mechanism of 2NTDO gene regulation in JS42, and presumably that of NBDO gene regulation in JS765, appear similar to that of NahR-regulated genes in Pseudomonas putida G7. However, NbzR and NtdR appear to have evolved a broader specificity in JS42 and JS765, allowing for recognition of nitroaromatic compounds while retaining the ability to respond to salicylate and anthranilate. NtdR is also the first example of a nitroarene-responsive LysR-type transcriptional activator.
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Affiliation(s)
- Daniel J Lessner
- Department of Microbiology and Center for Biocatalysis and Bioprocessing, The University of Iowa, Iowa City, Iowa 52242, USA.
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Devos D, Garmendia J, de Lorenzo V, Valencia A. Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain. Environ Microbiol 2002; 4:29-41. [PMID: 11966823 DOI: 10.1046/j.1462-2920.2002.00265.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The prokaryotic enhancer-binding protein XylR is the central regulator of the toluene degradation pathway in Pseudomonas species. Copious genetic and biochemical data indicate that the N-terminal domain of the protein (domain A) interacts directly with m-xylene, which renders the protein competent as a transcriptional activator. Single-site and shuffling mutants of XylR or homologues have been reported to change or expand their effector profiles. Here, we follow a fold recognition approach to generate three-dimensional models of the domain A of XylR and DmpR with the purpose of deciphering the molecular activity of this protein family. The model is based on the crystallographic data of the rat catechol O-methyltransferase, a typical alpha/beta fold, consisting of eight alpha-helices and seven beta-strands. The fold identification is supported by physico-chemical properties of conserved amino acids, distribution of residues characteristic of the sequence families and confrontation with experimental data. The model not only provides a rationale for understanding published experimental data, but also suggests the molecular mechanism of the activation step and is a potentially useful conceptual tool for designing regulators with predefined inducer specificities.
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Affiliation(s)
- D Devos
- Protein Design Group, National Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid E-28049, Spain
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47
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Garmendia J, Devos D, Valencia A, de Lorenzo V. A la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors. Mol Microbiol 2001; 42:47-59. [PMID: 11679066 DOI: 10.1046/j.1365-2958.2001.02633.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To investigate the activation mechanism of the enhancer-binding protein XylR encoded by the TOL plasmid of Pseudomonas putida mt-2, a combinatorial library was generated composed of shuffled N-terminal A domains of the homologous regulators DmpR, XylR and TbuT, reassembled within the XylR structure. When the library was screened in vivo for responsiveness to non-effectors bulkier than one aromatic ring (such as biphenyl) or bearing an entirely different distribution of electronegative groups (e.g. nitrotoluenes), protein variants were found that displayed an expanded inducer range including the new effectors. Although the phenotypes endowed with the corresponding changes were largely similar, the modifications involved different sites within the A domain. The positions of the mutations within a structural model of the A domain suggest that expansion of the inducer profile can be brought about not only by changes in the effector pocket of the protein but also by unlocking steps of the signal transmission mechanism that follows effector binding. These results provide a rationale for evolving in vitro regulators à la carte that are responsive to predetermined, natural or xenobiotic chemical species.
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Affiliation(s)
- J Garmendia
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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