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Oliva G, Pahunang RR, Vigliotta G, Zarra T, Ballesteros FC, Mariniello A, Buonerba A, Belgiorno V, Naddeo V. Advanced treatment of toluene emissions with a cutting-edge algal bacterial photo-bioreactor: Performance assessment in a circular economy perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163005. [PMID: 36965731 DOI: 10.1016/j.scitotenv.2023.163005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 05/13/2023]
Abstract
A novel approach for the treatment of VOCs (by using toluene used as a model compound) and the simultaneous conversion of carbon dioxide into valuable biomass has been investigated by using a combination of an activated sludge moving bed bioreactor (MBBR) and an algal photo-bioreactor (PBR). The first unit (MBBR, R1) promoted toluene removal up to 99.9 % for inlet load (IL) of 119.91 g m-3 d-1. The CO2 resulting from the degradation of toluene was then fixed in PBR (R2), with a fixation rate up to 95.8 %. The CO2 uptake was promoted by algae, with average production of algal biomass in Stage VI of 1.3 g L-1 d-1. In the contest of the circular economy, alternative sources of nutrients have been assessed, using synthetic urban wastewater (UWW) and dairy wastewater (DWW) for liquid renewal. The produced biomass with DWW showed a high lipid content, with a maximum productivity of 450.25 mg of lipids L-1 d-1. The solution proposed may be thus regarded as a sustainable and profitable strategy for VOCs treatment in a circular economy perspective.
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Affiliation(s)
- Giuseppina Oliva
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Rekich R Pahunang
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, Diliman, Quezon City, Philippines; Department of Environmental Engineering, Western Mindanao State University, Normal Rd., Zamboanga, 7000, Zamboanga del Sur, Philippines
| | - Giovanni Vigliotta
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy.
| | - Florencio C Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, Diliman, Quezon City, Philippines
| | - Aniello Mariniello
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Antonio Buonerba
- Department of Chemistry and Biology "Adolfo Zambelli", University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
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2
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Durante-Rodríguez G, Gutiérrez-Del-Arroyo P, Vélez M, Díaz E, Carmona M. Further Insights into the Architecture of the PN Promoter That Controls the Expression of the bzd Genes in Azoarcus. Genes (Basel) 2019; 10:genes10070489. [PMID: 31252700 PMCID: PMC6678401 DOI: 10.3390/genes10070489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/12/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
The anaerobic degradation of benzoate in bacteria involves the benzoyl-CoA central pathway. Azoarcus/Aromatoleum strains are a major group of anaerobic benzoate degraders, and the transcriptional regulation of the bzd genes was extensively studied in Azoarcus sp. CIB. In this work, we show that the bzdR regulatory gene and the PN promoter can also be identified upstream of the catabolic bzd operon in all benzoate-degrader Azoarcus/Aromatoleum strains whose genome sequences are currently available. All the PN promoters from Azoarcus/Aromatoleum strains described here show a conserved architecture including three operator regions (ORs), i.e., OR1 to OR3, for binding to the BzdR transcriptional repressor. Here, we demonstrate that, whereas OR1 is sufficient for the BzdR-mediated repression of the PN promoter, the presence of OR2 and OR3 is required for de-repression promoted by the benzoyl-CoA inducer molecule. Our results reveal that BzdR binds to the PN promoter in the form of four dimers, two of them binding to OR1. The BzdR/PN complex formed induces a DNA loop that wraps around the BzdR dimers and generates a superstructure that was observed by atomic force microscopy. This work provides further insights into the existence of a conserved BzdR-dependent mechanism to control the expression of the bzd genes in Azoarcus strains.
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Affiliation(s)
- Gonzalo Durante-Rodríguez
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Paloma Gutiérrez-Del-Arroyo
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Marisela Vélez
- Biocatalysis Department. Institute of Catalysis and Petrochemistry-CSIC. Marie Curie, 2, Cantoblanco. 28049 Madrid, Spain
| | - Eduardo Díaz
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain
| | - Manuel Carmona
- Microbial and Plant Biotechnology Department. Centro de Investigaciones Biológicas-CSIC. Ramiro de Maeztu, 9. 28040 Madrid, Spain.
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Towards the Response Threshold for p-Hydroxyacetophenone in the Denitrifying Bacterium "Aromatoleum aromaticum" EbN1. Appl Environ Microbiol 2018; 84:AEM.01018-18. [PMID: 29959253 DOI: 10.1128/aem.01018-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 06/26/2018] [Indexed: 01/21/2023] Open
Abstract
The denitrifying betaproteobacterium "Aromatoleum aromaticum" EbN1 regulates the capacity to anaerobically degrade p-ethylphenol (via p-hydroxyacetophenone) with high substrate specificity. This process is mediated by the σ54-dependent transcriptional regulator EtpR, which apparently recognizes both aromatic compounds, yielding congruent expression profiles. The responsiveness of this regulatory system was studied with p-hydroxyacetophenone, which is more easily administered to cultures and traced analytically. Cultures of A. aromaticum EbN1 were initially cultivated under nitrate-reducing conditions with a growth-limiting supply of benzoate, upon the complete depletion of which p-hydroxyacetophenone was added at various concentrations (from 500 μM down to 0.1 nM). Depletion profiles of this aromatic substrate and presumptive effector were determined by highly sensitive micro-high-performance liquid chromatography (microHPLC). Irrespective of the added concentration of p-hydroxyacetophenone, depletion commenced after less than 5 min and suggested a response threshold of below 10 nM. This approximation was corroborated by time-resolved transcript profiles (quantitative reverse transcription-PCR) of selected degradation and efflux relevant genes (e.g., pchF, encoding a subunit of predicted p-ethylphenol methylenehydroxylase) and narrowed down to a range of 10 to 1 nM. The most pronounced transcriptional response was observed, as expected, for genes located at the beginning of the two operon-like structures, related to catabolism (i.e., acsA) and potential efflux (i.e., ebA335).IMPORTANCE Aromatic compounds are widespread microbial growth substrates with natural as well as anthropogenic sources, albeit with their in situ concentrations and their bioavailabilities varying over several orders of magnitude. Even though degradation pathways and underlying regulatory systems have long been studied with aerobic and, to a lesser extent, with anaerobic bacteria, comparatively little is known about the effector concentration-dependent responsiveness. A. aromaticum EbN1 is a model organism for the anaerobic degradation of aromatic compounds with the architecture of the catabolic network and its substrate-specific regulation having been intensively studied by means of differential proteogenomics. The present study aims at unraveling the minimal concentration of an aromatic growth substrate (p-hydroxyacetophenone here) required to initiate gene expression for its degradation pathway and to learn in principle about the lower limit of catabolic responsiveness of an anaerobic degradation specialist.
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Koh S, Hwang J, Guchhait K, Lee EG, Kim SY, Kim S, Lee S, Chung JM, Jung HS, Lee SJ, Ryu CM, Lee SG, Oh TK, Kwon O, Kim MH. Molecular Insights into Toluene Sensing in the TodS/TodT Signal Transduction System. J Biol Chem 2016; 291:8575-90. [PMID: 26903514 PMCID: PMC4861429 DOI: 10.1074/jbc.m116.718841] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 11/17/2022] Open
Abstract
TodS is a sensor kinase that responds to various monoaromatic compounds, which either cause an agonistic or antagonistic effect on phosphorylation of its cognate response regulator TodT, and controls tod operon expression in Pseudomonas putida strains. We describe a molecular sensing mechanism of TodS that is activated in response to toluene. The crystal structures of the TodS Per-Arnt-Sim (PAS) 1 sensor domain (residues 43–164) and its complex with toluene (agonist) or 1,2,4-trimethylbenzene (antagonist) show a typical β2α3β3 PAS fold structure (residues 45–149), forming a hydrophobic ligand-binding site. A signal transfer region (residues 150–163) located immediately after the canonical PAS fold may be intrinsically flexible and disordered in both apo-PAS1 and antagonist-bound forms and dramatically adapt an α-helix upon toluene binding. This structural change in the signal transfer region is proposed to result in signal transmission to activate the TodS/TodT two-component signal transduction system. Site-directed mutagenesis and β-galactosidase assays using a P. putida reporter strain system verified the essential residues involved in ligand sensing and signal transfer and suggest that the Phe46 residue acts as a ligand-specific switch.
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Affiliation(s)
- Serry Koh
- From the Infection and Immunity Research Center,
| | | | - Koushik Guchhait
- From the Infection and Immunity Research Center, the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea
| | - Eun-Gyeong Lee
- the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea the Biochemicals and Synthetic Biology Research Center, and
| | - Sang-Yoon Kim
- the Biochemicals and Synthetic Biology Research Center, and
| | - Sujin Kim
- the Biochemicals and Synthetic Biology Research Center, and
| | - Sangmin Lee
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do 200-701, Korea, and
| | - Jeong Min Chung
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do 200-701, Korea, and
| | - Hyun Suk Jung
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon-do 200-701, Korea, and
| | - Sang Jun Lee
- From the Infection and Immunity Research Center, the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea
| | - Choong-Min Ryu
- the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea the Molecular Phytobacteriology Laboratory, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
| | - Seung-Goo Lee
- the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea the Biochemicals and Synthetic Biology Research Center, and
| | - Tae-Kwang Oh
- From the Infection and Immunity Research Center, the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea
| | - Ohsuk Kwon
- the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea the Biochemicals and Synthetic Biology Research Center, and
| | - Myung Hee Kim
- From the Infection and Immunity Research Center, the Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Korea
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Katsir G, Jarvis M, Phillips M, Ma Z, Gunsalus RP. The Escherichia coli NarL receiver domain regulates transcription through promoter specific functions. BMC Microbiol 2015; 15:174. [PMID: 26307095 PMCID: PMC4549865 DOI: 10.1186/s12866-015-0502-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/06/2015] [Indexed: 12/20/2022] Open
Abstract
Background The Escherichia coli response regulator NarL controls transcription of genes involved in nitrate respiration during anaerobiosis. NarL consists of two domains joined by a linker that wraps around the interdomain interface. Phosphorylation of the NarL N-terminal receiver domain (RD) releases the, otherwise sequestered, C-terminal output domain (OD) that subsequently binds specific DNA promoter sites to repress or activate gene expression. The aim of this study is to investigate the extent to which the NarL OD and RD function independently to regulate transcription, and the affect of the linker on OD function. Results NarL OD constructs containing different linker segments were examined for their ability to repress frdA-lacZ or activate narG-lacZ reporter fusion genes. These in vivo expression assays revealed that the NarL OD, in the absence or presence of linker helix α6, constitutively repressed frdA-lacZ expression regardless of nitrate availability. However, the presence of the linker loop α5-α6 reversed this repression and also showed impaired DNA binding in vitro. The OD alone could not activate narG-lacZ expression; this activity required the presence of the NarL RD. A footprint assay demonstrated that the NarL OD only partially bound recognition sites at the narG promoter, and the binding affinity was increased by the presence of the phosphorylated RD. Analytical ultracentrifugation used to examine domain oligomerization showed that the NarL RD forms dimers in solution while the OD is monomeric. Conclusions The NarL RD operates as an on-off switch to occlude or release the OD in a nitrate-responsive manner, but has additional roles to directly stimulate transcription at promoters for which the OD lacks independent function. One such role of the RD is to enhance the DNA binding affinity of the OD to target promoter sites. The data also imply that NarL phosphorylation results in RD dimerization and in the separation of the entire linker region from the OD. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0502-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Galit Katsir
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA.,Molecular Biology Institute, University of California, Los Angeles, USA.,Present address: San Jose City College, San Jose, CA, USA
| | - Michael Jarvis
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA.,Present address: Ambry Genetics, Aliso Viejo, CA, USA
| | - Martin Phillips
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Zhongcai Ma
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA.,Present address: NeuroInDx, Inc, Signal Hill, CA, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA. .,Molecular Biology Institute, University of California, Los Angeles, USA.
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Krell T, Lacal J, García-Fontana C, Silva-Jiménez H, Rico-Jiménez M, Lugo AC, Darias JAR, Ramos JL. Characterization of molecular interactions using isothermal titration calorimetry. Methods Mol Biol 2014; 1149:193-203. [PMID: 24818906 DOI: 10.1007/978-1-4939-0473-0_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Isothermal titration calorimetry (ITC) is based on a simple titration of one ligand with another and the small heat changes caused by the molecular interaction are detected. From one ITC experiment the complete set of thermodynamic parameters of binding including association and dissociation constants as well as changes in enthalpy, entropy, and free energy can be derived. Using this technique almost any type of molecular interaction can be analyzed. Both ligands are in solution, and there is no need for their chemical derivatization. There are no limits as to the choice of the analysis buffer, and the analysis temperature can be set between 4 and 80 °C. This technique has been primarily applied to study the interaction between various proteins of Pseudomonas with small molecule ligands. In addition, ITC has been used to study the binding of Pseudomonas proteins to target DNA fragments.
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Affiliation(s)
- Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain,
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Krell T, Lacal J, Guazzaroni ME, Busch A, Silva-Jiménez H, Fillet S, Reyes-Darías JA, Muñoz-Martínez F, Rico-Jiménez M, García-Fontana C, Duque E, Segura A, Ramos JL. Responses of Pseudomonas putida to toxic aromatic carbon sources. J Biotechnol 2012; 160:25-32. [DOI: 10.1016/j.jbiotec.2012.01.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 10/14/2022]
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Silva-Jiménez H, Ramos JL, Krell T. Construction of a prototype two-component system from the phosphorelay system TodS/TodT. Protein Eng Des Sel 2012; 25:159-69. [PMID: 22308529 DOI: 10.1093/protein/gzs001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two-component systems (TCSs) play key roles in the adaptation of bacteria to environmental changes. In prototype TCSs a single phosphoryl transfer between the sensor kinase and response regulator occurs, whereas phosphorelay TCSs are characterised by a His1-Asp1-His2-Asp2 phosphorylation cascade. The TodS/TodT TCS controls the expression of a toluene degradation pathway and the TodS sensor kinase operates by a three-step internal phosphorelay. Based on TodS we report the construction of a minimal form of TodS, termed as Min-TodS, that contains only three of the seven TodS domains. Min-TodS is composed of the N-terminal PAS sensor domain as well as the C-terminal dimerisation/phosphotransfer domain and catalytic domain of TodS. We have conducted a comparative analysis of the phosphorelay TCS with its prototypal derivative. We demonstrate that Min-TodS binds effector molecules with affinities comparable with those observed for TodS. Min-TodS forms a TCS with TodT and toluene increases the amount of TodT-P. In contrast to TodS, toluene does not stimulate Min-TodS autophosphorylation. The half-life of Min-TodS-P was significantly increased as compared with TodS. Analysis of TodSD500A revealed that the hydrolysis of the acylphosphate of the receiver domain is responsible for the reduced half-life of TodS. The regulation of P(todX) expression by Min-TodS/TodT and TodS/TodT in response to different effectors are compared. The Min-TodS/TodT system was characterized by a higher basal activity but a lower magnitude of response. Data will be discussed in the context that the phosphorelay system appears to be better suited for the control of a degradation pathway for toxic compounds.
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Affiliation(s)
- Hortencia Silva-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda, 1, 18008 Granada, Spain
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Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites. PLoS One 2012; 7:e30102. [PMID: 22291906 PMCID: PMC3264566 DOI: 10.1371/journal.pone.0030102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 12/13/2011] [Indexed: 12/04/2022] Open
Abstract
Expression of KdpFABC, a K+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABCBS) via the winged helix-turn-helix type DNA binding domain (KdpEDBD). Exploration of E. coli KdpEDBD and kdpFABCBS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpEDBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpEDBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpEDBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.
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Silva-Jiménez H, García-Fontana C, Cadirci BH, Ramos-González MI, Ramos JL, Krell T. Study of the TmoS/TmoT two-component system: towards the functional characterization of the family of TodS/TodT like systems. Microb Biotechnol 2011; 5:489-500. [PMID: 22212183 PMCID: PMC3815326 DOI: 10.1111/j.1751-7915.2011.00322.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The two‐component system TmoS/TmoT controls the expression of the toluene‐4‐monooxygenase pathway in Pseudomonas mendocina RK1 via modulation of PtmoX activity. The TmoS/TmoT system belongs to the family of TodS/TodT like proteins. The sensor kinase TmoS is a 108 kDa protein composed of seven different domains. Using isothermal titration calorimetry we show that purified TmoS binds a wide range of aromatic compounds with high affinities. Tightest ligand binding was observed for toluene (KD = 150 nM), which corresponds to the highest affinity measured between an effector and a sensor kinase. Other compounds with affinities in the nanomolar range include benzene, the 3 xylene isomers, styrene, nitrobenzene or p‐chlorotoluene. We demonstrate that only part of the ligands that bind to TmoS increase protein autophosphorylation in vitro and consequently pathway expression in vivo. These compounds are referred to as agonists. Other TmoS ligands, termed antagonists, failed to increase TmoS autophosphorylation, which resulted in their incapacity to stimulate gene expression in vivo. We also show that TmoS saturated with different agonists differs in their autokinase activities. The effector screening of gene expression showed that promoter activity of PtmoX and PtodX (controlled by the TodS/TodT system) is mediated by the same set of 22 compounds. The common structural feature of these compounds is the presence of a single aromatic ring. Among these ligands, toluene was the most potent inducer of both promoter activities. Information on the TmoS/TmoT and TodS/TodT system combined with a sequence analysis of family members permits to identify distinct features that define this protein family.
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Affiliation(s)
- Hortencia Silva-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Prof. Albareda 1, Granada, Spain.
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Dellarole M, Sánchez IE, de Prat Gay G. Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site. Biochemistry 2010; 49:10277-86. [PMID: 21047141 PMCID: PMC3091369 DOI: 10.1021/bi1014908] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Binding cooperativity guides the formation of protein−nucleic acid complexes, in particular those that are highly regulated such as replication origins and transcription sites. Using the DNA binding domain of the origin binding and transcriptional regulator protein E2 from human papillomavirus type 16 as model, and through isothermal titration calorimetry analysis, we determined a positive, entropy-driven cooperativity upon binding of the protein to its cognate tandem double E2 site. This cooperativity is associated with a change in DNA structure, where the overall B conformation is maintained. Two homologous E2 domains, those of HPV18 and HPV11, showed that the enthalpic−entropic components of the reaction and DNA deformation can diverge. Because the DNA binding helix is almost identical in the three domains, the differences must lie dispersed throughout this unique dimeric β-barrel fold. This is in surprising agreement with previous results for this domain, which revealed a strong coupling between global dynamics and DNA recognition.
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Affiliation(s)
- Mariano Dellarole
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-Conicet, Patricias Argentinas 435, Buenos Aires, Argentina
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12
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Catabolite repression of the TodS/TodT two-component system and effector-dependent transphosphorylation of TodT as the basis for toluene dioxygenase catabolic pathway control. J Bacteriol 2010; 192:4246-50. [PMID: 20543072 DOI: 10.1128/jb.00379-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The TodS/TodT two-component system of Pseudomonas putida regulates the expression of the toluene dioxygenase (tod) operon for the metabolism of toluene, benzene, and ethylbenzene. The sensor kinase TodS has a complex domain arrangement containing two functional modules, each harboring a sensor and an autokinase domain separated by a receiver domain. The TodT protein is the cognate response regulator that activates transcription of the toluene dioxygenase (TOD) pathway genes at the P(todX) promoter. We report in this study that the todST operon is transcribed from a main promoter and that the +1 initiation point is located 31 nucleotides upstream from the A of the first ATG codon and is preceded by a -10/-35 canonical promoter. Expression from P(todS) is under catabolite control, and in cells growing with glucose, the level of expression from this promoter is reduced, which in turn translates to low levels of the TodS/TodT regulators and results in a decrease of transcription from the P(todX) promoter. Thus, the main underlying regulatory mechanisms of the tod structural genes are at the levels of catabolite repression control from P(todS) and transcription activation, mediated by the TodT response regulator through a regulatory cascade in which the effector enhances autophosphorylation of TodS by ATP, with subsequent transphosphorylation of TodT.
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13
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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14
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Responses of Pseudomonas to small toxic molecules by a mosaic of domains. Curr Opin Microbiol 2009; 12:215-20. [DOI: 10.1016/j.mib.2009.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/02/2009] [Accepted: 02/02/2009] [Indexed: 11/21/2022]
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15
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Busch A, Guazzaroni ME, Lacal J, Ramos JL, Krell T. The sensor kinase TodS operates by a multiple step phosphorelay mechanism involving two autokinase domains. J Biol Chem 2009; 284:10353-60. [PMID: 19240030 DOI: 10.1074/jbc.m900521200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Expression of the Pseudomonas putida tod operon, which encodes enzymes for toluene metabolism, takes place from the P(todX) promoter and is mediated by the TodS/TodT two component system. The sensor kinase TodS has a complex domain arrangement containing two functional modules, each harboring a sensor- and an autokinase domain and separated by a receiver domain. Based on site-directed mutagenesis of phosphoaccepting His-190, Asp-500, and His-760 and in vitro transphosphorylation experiments with recombinant TodS fragments, we show that TodS uses a multiple step phosphorelay mechanism to activate TodT. Toluene binding stimulates exclusively phosphorylation of His-190, which is followed by phosphotransfer to Asp-500 and subsequently to His-760 prior to phosphorylation of TodT Asp-57. Mutation of His-190, Asp-500, and H760A prevented up-regulation of toluene-mediated stimulation of TodT transphosphorylation in vitro and reduced in vivo expression of P(todX) to the basal level. Calorimetric studies support that TodT binds to the C-terminal kinase module with a K(D) of approximately 200 nm and 1:1 stoichiometry. This is the first report of a multiple step phosphorelay mechanism of a sensor kinase that involves two autokinase domains.
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Affiliation(s)
- Andreas Busch
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda, 1, 18008 Granada, Spain
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