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Lu Z, Li W, Xin Y, Huang Y. The stringent response gene rsh plays multiple roles in Novosphingobium pentaromativorans US6-1's accommodation to different environmental pollutants: Phenanthrene, copper and nZVI. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121315. [PMID: 36813102 DOI: 10.1016/j.envpol.2023.121315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/27/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The rsh based stringent response system is widely employed by bacteria to cope with environmental stresses. However, how does the stringent response involve in bacterial accommodation to environmental pollutant is largely unexplored. In this study, to comprehensively understand the roles of rsh in Novosphingobium pentaromativorans US6-1's metabolism and accommodation to different pollutants, three distinct pollutants, phenanthrene, copper and nanoparticulated zero valent iron (nZVI) were selected as exposure substances. Results indicated that rsh played important roles in US6-1's multiplication and metabolism, including survival rate at stationary phase, amino acid and nucleotide metabolism, extracellular polymeric substance (EPS) production, redox homeostasis, etc. The deletion of rsh affected phenanthrene removal rates through regulating the multiplication of US6-1 and increasing the expression of degradation related genes. The rsh mutant showed higher resistance to copper than the wild type, largely due to higher EPS production and enhanced expression of copper resistance related genes. Finally, the rsh based stringent response helped maintain the redox homeostasis when US6-1 confronted nZVI particles that exerted oxidative stress, thereby improving the survival rate. Overall, this study provides firsthand data that rsh plays multiple roles in US6-1's accommodation to environmental pollutants. The stringent response system could be a powerful tool for environmental scientists and engineers to harness bacterial activities for bioremediation purposes.
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Affiliation(s)
- Zejia Lu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Weiqi Li
- Department of Resources Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yiding Xin
- Department of Resources Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yili Huang
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
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2
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Moreno R, Yuste L, Rojo F. The acetoin assimilation pathway of Pseudomonas putida KT2440 is regulated by overlapping global regulatory elements that respond to nutritional cues. Environ Microbiol 2023; 25:515-531. [PMID: 36482024 PMCID: PMC10107126 DOI: 10.1111/1462-2920.16304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Many microorganisms produce and excrete acetoin (3-hydroxy-2-butanone) when growing in environments that contain glucose or other fermentable carbon sources. This excreted compound can then be assimilated by other bacterial species such as pseudomonads. This work shows that acetoin is not a preferred carbon source of Pseudomonas putida, and that the induction of genes required for its assimilation is down-modulated by different, independent, global regulatory systems when succinate, glucose or components of the LB medium are also present. The expression of the acetoin degradation genes was found to rely on the RpoN alternative sigma factor and to be modulated by the Crc/Hfq, Cyo and PTSNtr regulatory elements, with the impact of the latter three varying according to the carbon source present in addition to acetoin. Pyruvate, a poor carbon source for P. putida, did not repress acetoin assimilation. Indeed, the presence of acetoin significantly improved growth on pyruvate, revealing these compounds to have a synergistic effect. This would provide a clear competitive advantage to P. putida when growing in environments in which all the preferred carbon sources have been depleted and pyruvate and acetoin remain as leftovers from the fermentation of sugars by other microorganisms.
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Affiliation(s)
- Renata Moreno
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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3
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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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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Roy R, Ray S, Chowdhury A, Anand R. Tunable Multiplexed Whole-Cell Biosensors as Environmental Diagnostics for ppb-Level Detection of Aromatic Pollutants. ACS Sens 2021; 6:1933-1939. [PMID: 33973468 DOI: 10.1021/acssensors.1c00329] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aromatics such as phenols, benzene, and toluene are carcinogenic xenobiotics which are known to pollute water resources. By employing synthetic biology approaches combined with a structure-guided design, we created a tunable array of whole-cell biosensors (WCBs). The MopR genetic system that has the natural ability to sense and degrade phenol was adapted to detect phenol down to ∼1 ppb, making this sensor capable of directly detecting phenol in permissible limits in drinking water. Importantly, by using a single WCB design, we engineered mutations into the MopR gene that enabled generation of a battery of sensors for a wide array of pollutants. The engineered WCBs were able to sense inert compounds like benzene and xylene which lack active functional groups, without any loss in sensitivity. Overall, this universal programmable biosensor platform can be used to create WCBs that can be deployed on field for rapid testing and screening of suitable drinking water sources.
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Affiliation(s)
- Rohita Roy
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Shamayeeta Ray
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
- DBT-Welcome Trust India Alliance Senior Fellow, Mumbai 400076, India
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Mohapatra B, Phale PS. Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation. Front Bioeng Biotechnol 2021; 9:602445. [PMID: 33791281 PMCID: PMC8006333 DOI: 10.3389/fbioe.2021.602445] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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7
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Phale PS, Malhotra H, Shah BA. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2020; 112:1-65. [PMID: 32762865 DOI: 10.1016/bs.aambs.2020.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As a result of anthropogenic activity, large number of recalcitrant aromatic compounds have been released into the environment. Consequently, microbial communities have adapted and evolved to utilize these compounds as sole carbon source, under both aerobic and anaerobic conditions. The constitutive expression of enzymes necessary for metabolism imposes a heavy energy load on the microbe which is overcome by arrangement of degradative genes as operons which are induced by specific inducers. The segmentation of pathways into upper, middle and/or lower operons has allowed microbes to funnel multiple compounds into common key aromatic intermediates which are further metabolized through central carbon pathway. Various proteins belonging to diverse families have evolved to regulate the transcription of individual operons participating in aromatic catabolism. These proteins, complemented with global regulatory mechanisms, carry out the regulation of aromatic compound metabolic pathways in a concerted manner. Additionally, characteristics like chemotaxis, preferential utilization, pathway compartmentalization and biosurfactant production confer an advantage to the microbe, thus making bioremediation of the aromatic pollutants more efficient and effective.
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Affiliation(s)
- Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India.
| | - Harshit Malhotra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
| | - Bhavik A Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Mumbai, India
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8
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Abstract
Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
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9
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Biodegradation of Tetralin: Genomics, Gene Function and Regulation. Genes (Basel) 2019; 10:genes10050339. [PMID: 31064110 PMCID: PMC6563040 DOI: 10.3390/genes10050339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 01/18/2023] Open
Abstract
Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.
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10
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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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11
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Lallement A, Vinatier V, Brigante M, Deguillaume L, Delort AM, Mailhot G. First evaluation of the effect of microorganisms on steady state hydroxyl radical concentrations in atmospheric waters. CHEMOSPHERE 2018; 212:715-722. [PMID: 30179836 DOI: 10.1016/j.chemosphere.2018.08.128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
Clouds are complex multiphasic media where efficient chemical reactions take place and where microorganisms have been found to be metabolically active. Hydroxyl radical is the main oxidant in cloud water, and more generally in the atmosphere, during the day and drives the cloud oxidative capacity. However, only one measurement of the steady state hydroxyl radical concentrations in cloud water has been reported so far. Cloud chemistry models are used to estimate the hydroxyl radical concentrations with values ranging from 10-12 to 10-15 M that are surely overestimated due to a lack of knowledge about the speciation of the organic matter acting as a sink for hydroxyl radicals. The aim of this work is to quantify the concentration of hydroxyl radicals at steady state in rain and cloud waters and to measure the impact of native microflora on this concentration. First, the non-toxicity of terephthalic acid as probe is controlled before the analysis in real atmospheric water samples. Higher concentrations of hydroxyl radicals are found in cloud waters than in rain waters, with a mean value "1.6 ± 1.5" × 10-16 M and "7.2 ± 5.0" × 10-16 M for rain and cloud waters respectively and no real impact of microorganisms was observed. This method allows the measurement of steady state hydroxyl radical levels at very low concentrations (down to 10-17 M) and it is biocompatible, fast and easy to handle. It is a useful tool, complementary to other methods, to give a better overview of atmospheric water oxidant capacity.
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Affiliation(s)
- A Lallement
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - V Vinatier
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - M Brigante
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - L Deguillaume
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie Physique, 63000, Clermont-Ferrand, France
| | - A M Delort
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France.
| | - G Mailhot
- Université Clermont Auvergne, CNRS, SIGMA Clermont, Institut de Chimie de Clermont-Ferrand, 63000, Clermont-Ferrand, France.
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12
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Sánchez-Hevia DL, Yuste L, Moreno R, Rojo F. Influence of the Hfq and Crc global regulators on the control of iron homeostasis inPseudomonas putida. Environ Microbiol 2018; 20:3484-3503. [DOI: 10.1111/1462-2920.14263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Dione L. Sánchez-Hevia
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Renata Moreno
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana; Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco; Madrid, 28049 Spain
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13
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Transcriptional control of the phenol hydroxylase gene phe of Corynebacterium glutamicum by the AraC-type regulator PheR. Microbiol Res 2018; 209:14-20. [DOI: 10.1016/j.micres.2018.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/23/2018] [Accepted: 02/03/2018] [Indexed: 11/20/2022]
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14
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Wirebrand L, Madhushani AWK, Irie Y, Shingler V. Multiple Hfq-Crc target sites are required to impose catabolite repression on (methyl)phenol metabolism in Pseudomonas putida CF600. Environ Microbiol 2017; 20:186-199. [PMID: 29076626 DOI: 10.1111/1462-2920.13966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/17/2017] [Accepted: 10/19/2017] [Indexed: 12/11/2022]
Abstract
The dmp-system encoded on the IncP-2 pVI150 plasmid of Pseudomonas putida CF600 confers the ability to assimilate (methyl)phenols. Regulation of the dmp-genes is subject to sophisticated control, which includes global regulatory input to subvert expression of the pathway in the presence of preferred carbon sources. Previously we have shown that in P. putida, translational inhibition exerted by the carbon repression control protein Crc operates hand-in-hand with the RNA chaperon protein Hfq to reduce translation of the DmpR regulator of the Dmp-pathway. Here, we show that Crc and Hfq co-target four additional sites to form riboprotein complexes within the proximity of the translational initiation sites of genes encoding the first two steps of the Dmp-pathway to mediate two-layered control in the face of selection of preferred substrates. Furthermore, we present evidence that Crc plays a hitherto unsuspected role in maintaining the pVI150 plasmid within a bacterial population, which has implications for (methyl)phenol degradation and a wide variety of other physiological processes encoded by the IncP-2 group of Pseudomonas-specific mega-plasmids.
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Affiliation(s)
- Lisa Wirebrand
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
| | | | - Yasuhiko Irie
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
| | - Victoria Shingler
- Department of Molecular Biology, Umeå University, Umeå SE 90187, Sweden
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15
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Wang JP, Zhang WM, Chao HJ, Zhou NY. PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3. Front Microbiol 2017; 8:1714. [PMID: 28959240 PMCID: PMC5603801 DOI: 10.3389/fmicb.2017.01714] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/24/2017] [Indexed: 11/17/2022] Open
Abstract
A LysR-type transcriptional regulator (LTTR), PnpR, has previously been shown to activate the transcription of operons pnpA, pnpB, and pnpCDEFG for para-nitrophenol (PNP) degradation in Pseudomonas sp. strain WBC-3. Further preliminary evidence suggested the possible presence of an LTTR additional binding site in the promoter region of pnpCDEFG. In this study, an additional LTTR PnpM, which shows 44% homology to PnpR, was determined to activate the expression of pnpCDEFG. Interestingly, a pnpM-deleted WBC-3 strain was unable to grow on PNP but accumulating hydroquinone (HQ), which is the catabolic product from PNP degradation by PnpAB and the substrate for PnpCD. Through electrophoretic mobility shift assays (EMSAs) and promoter activity detection, only PnpR was involved in the activation of pnpA and pnpB, but both PnpR and PnpM were involved in the activation of pnpCDEFG. DNase I footprinting analysis suggested that PnpR and PnpM shared the same DNA-binding regions of 27 bp in the pnpCDEFG promoter. In the presence of PNP, the protection region increased to 39 bp by PnpR and to 38 bp by PnpM. Our data suggested that both PnpR and PnpM were involved in activating pnpCDEFG expression, in which PNP rather than the substrate hydroquinone for PnpCD is the inducer. Thus, during the PNP catabolism in Pseudomonas sp. strain WBC-3, pnpA and pnpB operons for the initial two reactions were controlled by PnpR, while the third operon (pnpCDEFG) for HQ degradation was activated by PnpM and PnpR. This study builds upon our previous findings and shows that two LTTRs PnpR and PnpM are involved in the transcriptional activation of these three catabolic operons. Specifically, our identification that an LTTR, PnpM, regulates pnpCDEFG expression provides new insights in an intriguing regulation system of PNP catabolism that is controlled by two regulators.
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Affiliation(s)
- Jin-Pei Wang
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China.,University of Chinese Academy of SciencesBeijing, China
| | - Wen-Mao Zhang
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Hong-Jun Chao
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Ning-Yi Zhou
- Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China.,State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong UniversityShanghai, China
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16
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Biodegradation of phenol and its derivatives by engineered bacteria: current knowledge and perspectives. World J Microbiol Biotechnol 2017; 33:174. [DOI: 10.1007/s11274-017-2339-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/01/2017] [Indexed: 11/26/2022]
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17
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The Azoarcus anaerobius 1,3-Dihydroxybenzene (Resorcinol) Anaerobic Degradation Pathway Is Controlled by the Coordinated Activity of Two Enhancer-Binding Proteins. Appl Environ Microbiol 2017; 83:AEM.03042-16. [PMID: 28258136 DOI: 10.1128/aem.03042-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 02/22/2017] [Indexed: 11/20/2022] Open
Abstract
The anaerobic resorcinol degradation pathway in Azoarcus anaerobius is unique in that it uses an oxidative rather than a reductive strategy to overcome the aromatic ring stability in degradation of this compound, in a process that is dependent on nitrate respiration. We show that the pathway is organized in five transcriptional units, three of which are inducible by the presence of the substrate. Three σ54-dependent promoters located upstream from the three operons coding for the main pathway enzymes were identified, which shared a similar structure with conserved upstream activating sequences (UASs) located at 103 to 111 bp from the transcription start site. Expression of the pathway is controlled by the bacterial enhancer-binding proteins (bEBPs) RedR1 and RedR2, two homologous regulators that, despite their high sequence identity (97%), have nonredundant functions: RedR2, the master regulator which also controls RedR1 expression, is itself able to promote transcription from two of the promoters, while RedR1 activity is strictly dependent on the presence of RedR2. The two regulators were shown to interact with each other, suggesting that the natural mode of activation is by forming heterodimers, which become active in the presence of the substrate after its metabolization to hydroxybenzoquinone through the pathway enzymes. The model structure of the N-terminal domain of the proteins is composed of tandem GAF and PAS motifs; the possible mechanisms controlling the activity of the regulators are discussed.IMPORTANCEAzoarcus anaerobius is a strict anaerobe that is able to use 1,3-dihydroxybenzene as the sole carbon source in a process that is dependent on nitrate respiration. We have shown that expression of the pathway is controlled by two regulators of almost identical sequences: the bEBPs RedR1 and RedR2, which share 97% identity. These regulators control three promoters with similar structure. Despite their sequence identity, the two bEBPs are not redundant and are both required for maximum pathway expression. In fact, the two proteins function as heterodimers and require activation by the pathway intermediate hydroxyhydroquinone. The structure of the domain sensing the activation signal resembles that of regulators that are known to interact with other proteins.
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18
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Fazli M, Rybtke M, Steiner E, Weidel E, Berthelsen J, Groizeleau J, Bin W, Zhi BZ, Yaming Z, Kaever V, Givskov M, Hartmann RW, Eberl L, Tolker-Nielsen T. Regulation of Burkholderia cenocepacia biofilm formation by RpoN and the c-di-GMP effector BerB. Microbiologyopen 2017; 6. [PMID: 28419759 PMCID: PMC5552954 DOI: 10.1002/mbo3.480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022] Open
Abstract
Knowledge about the molecular mechanisms that are involved in the regulation of biofilm formation is essential for the development of biofilm‐control measures. It is well established that the nucleotide second messenger cyclic diguanosine monophosphate (c‐di‐GMP) is a positive regulator of biofilm formation in many bacteria, but more knowledge about c‐di‐GMP effectors is needed. We provide evidence that c‐di‐GMP, the alternative sigma factor RpoN (σ54), and the enhancer‐binding protein BerB play a role in biofilm formation of Burkholderia cenocepacia by regulating the production of a biofilm‐stabilizing exopolysaccharide. Our findings suggest that BerB binds c‐di‐GMP, and activates RpoN‐dependent transcription of the berA gene coding for a c‐di‐GMP‐responsive transcriptional regulator. An increased level of the BerA protein in turn induces the production of biofilm‐stabilizing exopolysaccharide in response to high c‐di‐GMP levels. Our findings imply that the production of biofilm exopolysaccharide in B. cenocepacia is regulated through a cascade involving two consecutive transcription events that are both activated by c‐di‐GMP. This type of regulation may allow tight control of the expenditure of cellular resources.
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Affiliation(s)
- Mustafa Fazli
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Steiner
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Elisabeth Weidel
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Jens Berthelsen
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie Groizeleau
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wu Bin
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Boo Zhao Zhi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhang Yaming
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Michael Givskov
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rolf W Hartmann
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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19
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Abstract
Phenolic aromatic compounds are a major source of environmental pollution. Currently there are no in situ methods for specifically and selectively detecting these pollutants. Here, we exploit the nature's biosensory machinery by employing Acinetobacter calcoaceticus NCIB8250 protein, MopR, as a model system to develop biosensors for selective detection of a spectrum of these pollutants. The X-ray structure of the sensor domain of MopR was used as a scaffold for logic-based tunable biosensor design. By employing a combination of in silico structure guided approaches, mutagenesis and isothermal calorimetric studies, we were able to generate biosensor templates, that can selectively and specifically sense harmful compounds like chlorophenols, cresols, catechol, and xylenols. Furthermore, the ability of native protein to selectively sense phenol as the primary ligand was also enhanced. Overall, this methodology can be extended as a suitable framework for development of a series of exclusive biosensors for accurate and selective detection of aromatic pollutants from real time environmental samples.
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Affiliation(s)
- Shamayeeta Ray
- IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India
| | - 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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20
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Svenningsen NB, Nicolaisen MH, Hansen HCB, de Lorenzo V, Nybroe O. Nitrogen regulation of the xyl genes of Pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil. Microb Biotechnol 2016; 9:814-823. [PMID: 27561962 PMCID: PMC5072197 DOI: 10.1111/1751-7915.12404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/18/2016] [Accepted: 07/22/2016] [Indexed: 11/29/2022] Open
Abstract
The nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by Pseudomonas putida. Nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m‐xylene in soil, the natural habitat of this bacterium. To address this issue, we have developed a test‐tube‐to‐soil model system that exposes the end‐effects of remediation practices influencing gene expression of P. putida mt‐2. We found that NO3− compared with NH4+ had a stimulating effect on xyl gene expression in pure culture as well as in soil, and that this stimulation was translated into increased m‐xylene mineralization in soil. Furthermore, expression analysis of the nitrogen‐regulated genes amtB and gdhA allowed us to monitor nitrogen sensing status in both experimental systems. Hence, for nitrogen sources, regulatory patterns that emerge in soil reflect those observed in liquid cultures. The current study shows how distinct regulatory traits can lead to discrete environmental consequences; and it underpins that attempts to improve bioremediation by nitrogen amendment should integrate knowledge on their effects on growth and on catabolic gene regulation under natural conditions.
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Affiliation(s)
- Nanna B Svenningsen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Mette H Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Hans Christian B Hansen
- Section for Environmental Chemistry and Physics, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| | - Victor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, 28049, Spain
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark.
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21
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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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22
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George KW, Hay AG. Bacterial strategies for growth on aromatic compounds. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:1-33. [PMID: 21459192 DOI: 10.1016/b978-0-12-387022-3.00005-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Although the biodegradation of aromatic compounds has been studied for over 40 years, there is still much to learn about the strategies bacteria employ for growth on novel substrates. Elucidation of these strategies is crucial for predicting the environmental fate of aromatic pollutants and will provide a framework for the development of engineered bacteria and degradation pathways. In this chapter, we provide an overview of studies that have advanced our knowledge of bacterial adaptation to aromatic compounds. We have divided these strategies into three broad categories: (1) recruitment of catabolic genes, (2) expression of "repair" or detoxification proteins, and (3) direct alteration of enzymatic properties. Specific examples from the literature are discussed, with an eye toward the molecular mechanisms that underlie each strategy.
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Affiliation(s)
- Kevin W George
- Field of Environmental Toxicology, Cornell University Ithaca, New York, USA; Department of Microbiology, Wing Hall, Cornell University Ithaca, New York, USA
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23
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Xiao X, Si M, Yang Z, Zhang Y, Guan J, Chaudhry MT, Wang Y, Shen X. Molecular characterization of a eukaryotic-like phenol hydroxylase from Corynebacterium glutamicum. J GEN APPL MICROBIOL 2016; 61:99-107. [PMID: 26377129 DOI: 10.2323/jgam.61.99] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study focuses on the genetic and biochemical characterization of phenol hydroxylase (Phe, NCgl2588) from Corynebacterium glutamicum that shares 31% identity in amino acids with phenol hydroxylase from yeast Trichosporon cutaneum but less similarity with that from bacteria. The phe deletion mutant significantly reduced its ability to grow with phenol as the sole carbon and energy source. Expression of the phe gene was strongly induced with phenol and also subject to the control of carbon catabolite repression (CCR). The molecular weight of purified Phe protein determined by gel filtration chromatography was 70 kDa, indicating that Phe exists as a monomer in the purification condition. However, Phe protein pre-incubated with phenol showed a molecular weight of 140 kDa, suggesting that Phe is likely active as a dimer. In addition to phenol, the Phe protein could utilize various other phenolic compounds as substrates. Site-directed mutagenesis revealed that D75, P261, R262, R269, C349 and C476 are key amino acid residues closely related to the enzyme activity of Phe.
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Affiliation(s)
- Xiao Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University
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24
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Ledesma-García L, Sánchez-Azqueta A, Medina M, Reyes-Ramírez F, Santero E. Redox proteins of hydroxylating bacterial dioxygenases establish a regulatory cascade that prevents gratuitous induction of tetralin biodegradation genes. Sci Rep 2016; 6:23848. [PMID: 27030382 PMCID: PMC4814904 DOI: 10.1038/srep23848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/09/2016] [Indexed: 11/21/2022] Open
Abstract
Bacterial dioxygenase systems are multicomponent enzymes that catalyze the initial degradation of many environmentally hazardous compounds. In Sphingopyxis granuli strain TFA tetralin dioxygenase hydroxylates tetralin, an organic contaminant. It consists of a ferredoxin reductase (ThnA4), a ferredoxin (ThnA3) and a oxygenase (ThnA1/ThnA2), forming a NAD(P)H–ThnA4–ThnA3–ThnA1/ThnA2 electron transport chain. ThnA3 has also a regulatory function since it prevents expression of tetralin degradation genes (thn) in the presence of non-metabolizable substrates of the catabolic pathway. This role is of physiological relevance since avoids gratuitous and wasteful production of catabolic enzymes. Our hypothesis for thn regulation implies that ThnA3 exerts its action by diverting electrons towards the regulator ThnY, an iron-sulfur flavoprotein that together with the transcriptional activator ThnR is necessary for thn gene expression. Here we analyze electron transfer among ThnA4, ThnA3 and ThnY by using stopped-flow spectrophotometry and determination of midpoint reduction potentials. Our results indicate that when accumulated in its reduced form ThnA3 is able to fully reduce ThnY. In addition, we have reproduced in vitro the regulatory circuit in the proposed physiological direction, NAD(P)H–ThnA4–ThnA3–ThnY. ThnA3 represents an unprecedented way of communication between a catabolic pathway and its regulatory system to prevent gratuitous induction.
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Affiliation(s)
- Laura Ledesma-García
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, and Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Ana Sánchez-Azqueta
- Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - Francisca Reyes-Ramírez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, and Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
| | - Eduardo Santero
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía, and Departamento de Biología Molecular e Ingeniería Bioquímica, Seville, Spain
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25
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Herath A, Wawrik B, Qin Y, Zhou J, Callaghan AV. Transcriptional response of Desulfatibacillum alkenivorans AK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses. FEMS Microbiol Ecol 2016; 92:fiw062. [PMID: 27009900 DOI: 10.1093/femsec/fiw062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2016] [Indexed: 12/16/2022] Open
Abstract
Microbial transformation of n-alkanes in anaerobic ecosystems plays a pivotal role in biogeochemical carbon cycling and bioremediation, but the requisite genetic machinery is not well elucidated.Desulfatibacillum alkenivorans AK-01 utilizes n-alkanes (C13 to C18) and contains two genomic loci encoding alkylsuccinate synthase (ASS) gene clusters. ASS catalyzes alkane addition to fumarate to form methylalkylsuccinic acids. We hypothesized that the genes in the two clusters would be differentially expressed depending on the alkane substrate utilized for growth. RT-qPCR was used to investigate ass-gene expression across AK-01's known substrate range, and microarray-based transcriptomic analysis served to investigate whole-cell responses to growth on n-hexadecane versus hexadecanoate. RT-qPCR revealed induction of ass gene cluster 1 during growth on all tested alkane substrates, and the transcriptional start sites in cluster 1 were determined via 5'RACE. Induction of ass gene cluster 2 was not observed under the tested conditions. Transcriptomic analysis indicated that the upregulation of genes potentially involved in methylalkylsuccinate metabolism, including methylmalonyl-CoA mutase and a putative carboxyl transferase. These findings provide new directions for studying the transcriptional regulation of genes involved in alkane addition to fumarate, fumarate recycling and the processing of methylalkylsuccinates with regard to isolates, enrichment cultures and ecological datasets.
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Affiliation(s)
- Anjumala Herath
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Yujia Qin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA Institute of Environmental Genomics, Stephenson Research Center, 101 David L. Boren Blvd, Norman, OK 73019, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA Institute of Environmental Genomics, Stephenson Research Center, 101 David L. Boren Blvd, Norman, OK 73019, USA Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94270, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
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26
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Nešvera J, Rucká L, Pátek M. Catabolism of Phenol and Its Derivatives in Bacteria: Genes, Their Regulation, and Use in the Biodegradation of Toxic Pollutants. ADVANCES IN APPLIED MICROBIOLOGY 2015; 93:107-60. [PMID: 26505690 DOI: 10.1016/bs.aambs.2015.06.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Phenol and its derivatives (alkylphenols, halogenated phenols, nitrophenols) are natural or man-made aromatic compounds that are ubiquitous in nature and in human-polluted environments. Many of these substances are toxic and/or suspected of mutagenic, carcinogenic, and teratogenic effects. Bioremediation of the polluted soil and water using various bacteria has proved to be a promising option for the removal of these compounds. In this review, we describe a number of peripheral pathways of aerobic and anaerobic catabolism of various natural and xenobiotic phenolic compounds, which funnel these substances into a smaller number of central catabolic pathways. Finally, the metabolites are used as carbon and energy sources in the citric acid cycle. We provide here the characteristics of the enzymes that convert the phenolic compounds and their catabolites, show their genes, and describe regulatory features. The genes, which encode these enzymes, are organized on chromosomes and plasmids of the natural bacterial degraders in various patterns. The accumulated data on similarities and the differences of the genes, their varied organization, and particularly, an astonishingly broad range of intricate regulatory mechanism may be read as an exciting adventurous book on divergent evolutionary processes and horizontal gene transfer events inscribed in the bacterial genomes. In the end, the use of this wealth of bacterial biodegradation potential and the manipulation of its genetic basis for purposes of bioremediation is exemplified. It is envisioned that the integrated high-throughput techniques and genome-level approaches will enable us to manipulate systems rather than separated genes, which will give birth to systems biotechnology.
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Affiliation(s)
- Jan Nešvera
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Lenka Rucká
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
| | - Miroslav Pátek
- Institute of Microbiology CAS, v. v. i., Prague, Czech Republic
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27
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Parales RE, Luu RA, Hughes JG, Ditty JL. Bacterial chemotaxis to xenobiotic chemicals and naturally-occurring analogs. Curr Opin Biotechnol 2015; 33:318-26. [DOI: 10.1016/j.copbio.2015.03.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
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28
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Madhushani A, del Peso-Santos T, Moreno R, Rojo F, Shingler V. Transcriptional and translational control through the 5′-leader region of thedmpRmaster regulatory gene of phenol metabolism. Environ Microbiol 2014; 17:119-33. [DOI: 10.1111/1462-2920.12511] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/11/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Anjana Madhushani
- Department of Molecular Biology; Umeå University; Umeå SE 90187 Sweden
| | | | - Renata Moreno
- Departamento de Biotecnologia Microbiana; Centro Nacional de Biotecnologia; CSIC; Madrid Spain
| | - Fernando Rojo
- Departamento de Biotecnologia Microbiana; Centro Nacional de Biotecnologia; CSIC; Madrid Spain
| | - Victoria Shingler
- Department of Molecular Biology; Umeå University; Umeå SE 90187 Sweden
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29
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Induction and carbon catabolite repression of phenol degradation genes in Rhodococcus erythropolis and Rhodococcus jostii. Appl Microbiol Biotechnol 2014; 98:8267-79. [DOI: 10.1007/s00253-014-5881-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 06/04/2014] [Indexed: 10/25/2022]
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30
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Valderrama JA, Shingler V, Carmona M, Díaz E. AccR is a master regulator involved in carbon catabolite repression of the anaerobic catabolism of aromatic compounds in Azoarcus sp. CIB. J Biol Chem 2013; 289:1892-904. [PMID: 24302740 DOI: 10.1074/jbc.m113.517714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we characterized the first known transcriptional regulator that accounts for carbon catabolite repression (CCR) control of the anaerobic catabolism of aromatic compounds in bacteria. The AccR response regulator of Azoarcus sp. CIB controls succinate-responsive CCR of the central pathways for the anaerobic catabolism of aromatics by this strain. Phosphorylation of AccR to AccR-P triggers a monomer-to-dimer transition as well as the ability to bind to the target promoter and causes repression both in vivo and in vitro. Substitution of the Asp(60) phosphorylation target residue of the N-terminal receiver motif of AccR to a phosphomimic Glu residue generates a constitutively active derivative that behaves as a superrepressor of the target genes. AccR-P binds in vitro to a conserved inverted repeat (ATGCA-N6-TGCAT) present at two different locations within the PN promoter of the bzd genes for anaerobic benzoate degradation. Because the DNA binding-proficient C-terminal domain of AccR is monomeric, we propose an activation mechanism in which phosphorylation of Asp(60) of AccR alleviates interdomain repression mediated by the N-terminal domain. The presence of AccR-like proteins encoded in the genomes of other β-proteobacteria of the Azoarcus/Thauera group further suggests that AccR constitutes a master regulator that controls anaerobic CCR in these bacteria.
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Affiliation(s)
- J Andrés Valderrama
- From the Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain and
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31
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Ni B, Huang Z, Fan Z, Jiang CY, Liu SJ. Comamonas testosteroniuses a chemoreceptor for tricarboxylic acid cycle intermediates to trigger chemotactic responses towards aromatic compounds. Mol Microbiol 2013; 90:813-23. [DOI: 10.1111/mmi.12400] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Bin Ni
- State Key Laboratory of Microbial Resources; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Zhou Huang
- State Key Laboratory of Microbial Resources; Chinese Academy of Sciences; Beijing 100101 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Zheng Fan
- Core facility at Institute of Microbiology; Chinese Academy of Sciences; Beijing 100101 China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Microbiology Research Center; Chinese Academy of Sciences; Beijing 100101 China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources; Chinese Academy of Sciences; Beijing 100101 China
- Environmental Microbiology Research Center; Chinese Academy of Sciences; Beijing 100101 China
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Tilston EL, Collins CD, Mitchell GR, Princivalle J, Shaw LJ. Nanoscale zerovalent iron alters soil bacterial community structure and inhibits chloroaromatic biodegradation potential in Aroclor 1242-contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 173:38-46. [PMID: 23202280 DOI: 10.1016/j.envpol.2012.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 05/20/2023]
Abstract
Nanoscale zerovalent iron (nZVI) has potential for the remediation of organochlorine-contaminated environments. Environmental safety concerns associated with in situ deployment of nZVI include potential negative impacts on indigenous microbes whose biodegradative functions could contribute to contaminant remediation. With respect to a two-step polychlorinated biphenyl remediation scenario comprising nZVI dechlorination followed by aerobic biodegradation, we examined the effect of polyacrylic acid (PAA)-coated nZVI (mean diameter = 12.5 nm) applied at 10 g nZVI kg(-1) to Aroclor-1242 contaminated and uncontaminated soil over 28 days. nZVI had a limited effect on Aroclor congener profiles, but, either directly or indirectly via changes to soil physico-chemical conditions (pH, Eh), nZVI addition caused perturbation to soil bacterial community composition, and reduced the activity of chloroaromatic mineralizing microorganisms. We conclude that nZVI addition has the potential to inhibit microbial functions that could be important for PCB remediation strategies combining nZVI treatment and biodegradation.
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Affiliation(s)
- Emma L Tilston
- Soil Research Centre, Department of Geography and Environmental Science, University of Reading, Whiteknights, Reading RG6 6DW, UK
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Valderrama JA, Durante-Rodríguez G, Blázquez B, García JL, Carmona M, Díaz E. Bacterial degradation of benzoate: cross-regulation between aerobic and anaerobic pathways. J Biol Chem 2012; 287:10494-10508. [PMID: 22303008 DOI: 10.1074/jbc.m111.309005] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have studied for the first time the transcriptional regulatory circuit that controls the expression of the box genes encoding the aerobic hybrid pathway used to assimilate benzoate via coenzyme A (CoA) derivatives in bacteria. The promoters responsible for the expression of the box cluster in the β-proteobacterium Azoarcus sp., their cognate transcriptional repressor, the BoxR protein, and the inducer molecule (benzoyl-CoA) have been characterized. The BoxR protein shows a significant sequence identity to the BzdR transcriptional repressor that controls the bzd genes involved in the anaerobic degradation of benzoate. Because the boxR gene is present in all box clusters so far identified in bacteria, the BoxR/benzoyl-CoA regulatory system appears to be a widespread strategy to control this aerobic hybrid pathway. Interestingly, the paralogous BoxR and BzdR regulators act synergistically to control the expression of the box and bzd genes. This cross-regulation between anaerobic and aerobic pathways for the catabolism of aromatic compounds has never been shown before, and it may reflect a biological strategy to increase the cell fitness in organisms that survive in environments subject to changing oxygen concentrations.
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Affiliation(s)
- J Andrés Valderrama
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Gonzalo Durante-Rodríguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Blas Blázquez
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - José Luis García
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Manuel Carmona
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Eduardo Díaz
- Department of Environmental Biology, Centro de Investigaciones Biológicas-Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.
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Identification of a transcriptional repressor involved in benzoate metabolism in Geobacter bemidjiensis. Appl Environ Microbiol 2011; 77:7058-62. [PMID: 21821763 DOI: 10.1128/aem.05516-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species. A transcription factor that represses expression of bamA, a benzoate-inducible gene, in Geobacter bemidjiensis during growth with acetate was identified. It is likely that this repressor also regulates other genes involved in aromatic compound metabolism.
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Koutinas M, Kiparissides A, Silva-Rocha R, Lam MC, Martins dos Santos VA, de Lorenzo V, Pistikopoulos EN, Mantalaris A. Linking genes to microbial growth kinetics—An integrated biochemical systems engineering approach. Metab Eng 2011; 13:401-13. [DOI: 10.1016/j.ymben.2011.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 01/31/2011] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
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Del Peso-Santos T, Bernardo LMD, Skärfstad E, Holmfeldt L, Togneri P, Shingler V. A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation. Nucleic Acids Res 2011; 39:5853-65. [PMID: 21447563 PMCID: PMC3152329 DOI: 10.1093/nar/gkr167] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The activities of promoters can be temporally and conditionally regulated by mechanisms other than classical DNA-binding repressors and activators. One example is the inherently weak σ70-dependent Pr promoter that ultimately controls catabolism of phenolic compounds. The activity of Pr is up-regulated through the joint action of ppGpp and DksA that enhance the performance of RNA polymerase at this promoter. Here, we report a mutagenesis analysis that revealed substantial differences between Pr and other ppGpp/DksA co-stimulated promoters. In vitro transcription and RNA polymerase binding assays show that it is the T at the −11 position of the extremely suboptimal −10 element of Pr that underlies both poor binding of σ70-RNAP and a slow rate of open complex formation—the process that is accelerated by ppGpp and DksA. Our findings support the idea that collaborative action of ppGpp and DksA lowers the rate-limiting transition energy required for conversion between intermediates on the road to open complex formation.
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38
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Yu H, Peng Z, Zhan Y, Wang J, Yan Y, Chen M, Lu W, Ping S, Zhang W, Zhao Z, Li S, Takeo M, Lin M. Novel regulator MphX represses activation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR in Acinetobacter calcoaceticus. PLoS One 2011; 6:e17350. [PMID: 21455294 PMCID: PMC3063778 DOI: 10.1371/journal.pone.0017350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/31/2011] [Indexed: 11/18/2022] Open
Abstract
Acinetobacter calcoaceticus PHEA-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphKLMNOP) for phenol degradation. Two additional genes, mphR and mphX, were found upstream and downstream of mphKLMNOP, respectively. The mphR gene encodes a XylR/DmpR-type regulator-like protein and is transcribed in the opposite direction to mphKLMNOP. The mphX gene is transcribed in the same direction as mphKLMNOP and encodes a protein with 293 amino acid residues showing weak identity with some unknown proteins encoded in the meta-cleavage pathway gene clusters for aromatic compound degradation. Disruption of mphR by homologous recombination resulted in the loss of phenol degradation while disruption of mphX caused significantly faster phenol degradation than in the wild type strain. Transcriptional assays for mphK, mphR, and mphX revealed that mphR activated mphKLMNOP transcription in the presence of phenol, but mphX partially repressed this activation. Gel mobility-shift assay demonstrated a direct interaction of MphR with the mphK promoter region. These results indicate the involvement of a novel repressor protein MphX in transcriptional regulation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR.
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Affiliation(s)
- Haiying Yu
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Zixin Peng
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
| | - Yuhua Zhan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Jin Wang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Yongliang Yan
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Ming Chen
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Lu
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuzhen Ping
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Wei Zhang
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- National Centre for Plant Gene Research, Beijing, China
| | - Zhonglin Zhao
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Shuying Li
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
| | - Masahiro Takeo
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan
- * E-mail: (MT); (ML)
| | - Min Lin
- College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Crop Biotechnology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, China
- * E-mail: (MT); (ML)
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Silva-Rocha R, Tamames J, dos Santos VM, de Lorenzo V. The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol 2011; 13:2389-402. [PMID: 21410625 DOI: 10.1111/j.1462-2920.2011.02455.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulatory and metabolic networks that rule biodegradation of pollutants by environmental bacteria are wired to the rest of the cellular physiology through both transcriptional factors and intermediary signal molecules. In this review, we examine some formalisms for describing catalytic/regulatory circuits of this sort and advocate the adoption of Boolean logic for combining transcriptional and enzymatic occurrences in the same biological system. As an example, we show how known regulatory and metabolic actions that bring about biodegradation of m-xylene by Pseudomonas putida mt-2 can be represented as clusters of binary operations and then reconstructed as a digital network. Despite the many simplifications, Boolean tools still capture the gross behaviour of the system even in the absence of kinetic constants determined experimentally. On this basis, we argue that still with a limited volume of data binary formalisms allow us to penetrate the raison d'être of extant regulatory and metabolic architectures.
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Affiliation(s)
- Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, 28049, Spain
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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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Abstract
Alternative σ-factors of bacteria bind core RNA polymerase to program the specific promoter selectivity of the holoenzyme. Signal-responsive changes in the availability of different σ-factors redistribute the RNA polymerase among the distinct promoter classes in the genome for appropriate adaptive, developmental and survival responses. The σ(54) -factor is structurally and functionally distinct from all other σ-factors. Consequently, binding of σ(54) to RNA polymerase confers unique features on the cognate holoenzyme, which requires activation by an unusual class of mechano-transcriptional activators, whose activities are highly regulated in response to environmental cues. This review summarizes the current understanding of the mechanisms of transcriptional activation by σ(54) -RNA polymerase and highlights the impact of global regulatory factors on transcriptional efficiency from σ(54) -dependent promoters. These global factors include the DNA-bending proteins IHF and CRP, the nucleotide alarmone ppGpp, and the RNA polymerase-targeting protein DksA.
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42
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Rojo F. Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 2010; 34:658-84. [PMID: 20412307 DOI: 10.1111/j.1574-6976.2010.00218.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Metabolically versatile free-living bacteria have global regulation systems that allow cells to selectively assimilate a preferred compound among a mixture of several potential carbon sources. This process is known as carbon catabolite repression (CCR). CCR optimizes metabolism, improving the ability of bacteria to compete in their natural habitats. This review summarizes the regulatory mechanisms responsible for CCR in the bacteria of the genus Pseudomonas, which can live in many different habitats. Although the information available is still limited, the molecular mechanisms responsible for CCR in Pseudomonas are clearly different from those of Enterobacteriaceae or Firmicutes. An understanding of the molecular mechanisms underlying CCR is important to know how metabolism is regulated and how bacteria degrade compounds in the environment. This is particularly relevant for compounds that are degraded slowly and accumulate, creating environmental problems. CCR has a major impact on the genes involved in the transport and metabolism of nonpreferred carbon sources, but also affects the expression of virulence factors in several bacterial species, genes that are frequently directed to allow the bacterium to gain access to new sources of nutrients. Finally, CCR has implications in the optimization of biotechnological processes such as biotransformations or bioremediation strategies.
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Affiliation(s)
- Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
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43
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Li D, Yan Y, Ping S, Chen M, Zhang W, Li L, Lin W, Geng L, Liu W, Lu W, Lin M. Genome-wide investigation and functional characterization of the beta-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC Microbiol 2010; 10:36. [PMID: 20137101 PMCID: PMC2907835 DOI: 10.1186/1471-2180-10-36] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs. Results In this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of Pseudomonas stutzeri A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The P. stutzeri A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the catR and pcaK genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the ben operon, while transcription from the catBC promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate. Conclusions The expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.
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Affiliation(s)
- Danhua Li
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
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Ju KS, Parales JV, Parales RE. Reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator NtdR. Mol Microbiol 2009; 74:826-43. [PMID: 19849778 PMCID: PMC10423642 DOI: 10.1111/j.1365-2958.2009.06904.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many toxic man-made compounds have been introduced into the environment, and bacterial strains that are able to grow on them are ideal model systems for studying the evolution of metabolic pathways and regulatory systems. Acidovorax sp. strain JS42 is unique in its ability to use 2-nitrotoluene as a sole carbon, nitrogen, and energy source for growth. The LysR-type transcriptional regulator NtdR activates expression of the 2-nitrotoluene degradation genes not only when nitroaromatic compounds are present, but also in the presence of a wide range of aromatic acids and analogues. The molecular determinants of inducer specificity were identified through comparative analysis with NagR, the activator of the naphthalene degradation pathway genes in Ralstonia sp. strain U2. Although NagR is 98% identical to NtdR, it does not respond to nitrotoluenes. Exchange of residues that differ between NagR and NtdR revealed that residues at positions 227 and 232 were key for the recognition of nitroaromatic compounds, while the amino acid at position 169 determined the range of aromatic acids recognized. Structural modelling of NtdR suggests that these residues are near the predicted inducer binding pocket. Based on these results, an evolutionary model is presented that depicts the stepwise evolution of NtdR.
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Affiliation(s)
- Kou-San Ju
- Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Juanito V. Parales
- Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Rebecca E. Parales
- Department of Microbiology, College of Biological Sciences, University of California, Davis, CA 95616
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Kivisaar M. Degradation of nitroaromatic compounds: a model to study evolution of metabolic pathways. Mol Microbiol 2009; 74:777-81. [PMID: 19818019 DOI: 10.1111/j.1365-2958.2009.06905.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although many nitroaromatic compounds have been in nature for only a few decades, bacteria have already evolved the ability to metabolize them. Both horizontal transfer of genes and mutagenesis induced under stressful conditions might facilitate evolution of new catabolic pathways. Nitrotoluene degradation pathways are supposedly derived from an ancestral naphthalene degradation pathway. The 2-nitrotoluene degradation genes in Acidovorax sp. strain JS42 are controlled by the transcriptional activator NtdR, which differs from NagR, the activator of the naphthalene degradation operon in Ralstonia sp. strain U2, by only five amino acids. Both regulators respond to salicylate, an intermediate of naphthalene degradation, but NtdR also recognizes a wide range of nitroaromatic compounds. In this issue of Molecular Microbiology, Ju et al. present results of site-directed mutagenesis of NtdR and NagR and show how the nitrotoluene-responsive regulator NtdR can be generated from a NagR-like ancestor by only a few mutations. The reconstructed hypothetical pathway for the evolution of NtdR from NagR demonstrates stepwise broadening of the effector range of the evolving protein without loss of the original activity. These results provide strong evidence for the idea that promiscuity of proteins is an important step in the evolution of new functions.
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Affiliation(s)
- Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, 23 Riia Street, 51010 Tartu, Estonia.
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López-Sánchez A, Rivas-Marín E, Martínez-Pérez O, Floriano B, Santero E. Co-ordinated regulation of two divergent promoters through higher-order complex formation by the LysR-type regulator ThnR. Mol Microbiol 2009; 73:1086-100. [PMID: 19682246 DOI: 10.1111/j.1365-2958.2009.06834.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The genes required for tetralin biodegradation by Sphingomonas macrogolitabida strain TFA are clustered in two divergent and closely linked operons. ThnR, a LysR-type regulator, activates transcription from each operon in response to tetralin. The regulatory thnR gene is co-transcribed with the catabolic genes thnC, thnA3 and thnA4, resulting in positive autoregulation. ThnR binds with different affinity to two primary binding sites, designated B and C, in the intervening region between the two operons and makes additional contact with secondary sites that extend towards the promoters. In addition, ThnR may interact with itself when bound to each site via the formation of a DNA loop, as evidenced by the distortion of the DNA between the primary binding sites and the elimination of the higher-order complexes following the introduction of a half-turn of the DNA helix between the primary binding sites. Transcription from each promoter is not fully independent since mutations in each binding site affected transcription from both promoters. Based on these results, we propose a model of transcription activation that involves the formation of a complex structure by interactions between ThnR molecules bound to distant binding sites and favours transcription from one promoter to the detriment of the other.
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Affiliation(s)
- Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC, Carretera de Utrera, Sevilla, Spain
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Porrúa O, García-González V, Santero E, Shingler V, Govantes F. Activation and repression of a sigmaN-dependent promoter naturally lacking upstream activation sequences. Mol Microbiol 2009; 73:419-33. [PMID: 19570137 DOI: 10.1111/j.1365-2958.2009.06779.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Pseudomonas sp. strain ADP protein AtzR is a LysR-type transcriptional regulator required for activation of the atzDEF operon in response to nitrogen limitation and cyanuric acid. Transcription of atzR is directed by the sigma(N)-dependent promoter PatzR, activated by NtrC and repressed by AtzR. Here we use in vivo and in vitro approaches to address the mechanisms of PatzR activation and repression. Activation by NtrC did not require any promoter sequences other than the sigma(N) recognition motif both in vivo and in vitro, suggesting that NtrC activates PatzR in an upstream activation sequences-independent fashion. Regarding AtzR-dependent autorepression, our in vitro transcription experiments show that the concentration of AtzR required for repression of the PatzR promoter in vitro correlates with AtzR affinity for its binding site. In addition, AtzR prevents transcription from PatzR when added to a preformed E-sigma(N)-PatzR closed complex, but isomerization to an open complex prevents repression. Gel mobility shift and DNase I footprint assays indicate that DNA-bound AtzR and E-sigma(N) are mutually exclusive. Taken together, these results strongly support the notion that AtzR represses transcription from PatzR by competing with E-sigma(N) for their overlapping binding sites. There are no previous reports of a similar mechanism for repression of sigma(N)-dependent transcription.
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Affiliation(s)
- Odil Porrúa
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC, Carretera de Utrera, Km. 1. 41013 Sevilla, Spain
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Moreno R, Martínez-Gomariz M, Yuste L, Gil C, Rojo F. The Pseudomonas putida
Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: Evidence from proteomic and genomic analyses. Proteomics 2009; 9:2910-28. [DOI: 10.1002/pmic.200800918] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Carmona M, Zamarro MT, Blázquez B, Durante-Rodríguez G, Juárez JF, Valderrama JA, Barragán MJL, García JL, Díaz E. Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 2009; 73:71-133. [PMID: 19258534 PMCID: PMC2650882 DOI: 10.1128/mmbr.00021-08] [Citation(s) in RCA: 267] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aromatic compounds belong to one of the most widely distributed classes of organic compounds in nature, and a significant number of xenobiotics belong to this family of compounds. Since many habitats containing large amounts of aromatic compounds are often anoxic, the anaerobic catabolism of aromatic compounds by microorganisms becomes crucial in biogeochemical cycles and in the sustainable development of the biosphere. The mineralization of aromatic compounds by facultative or obligate anaerobic bacteria can be coupled to anaerobic respiration with a variety of electron acceptors as well as to fermentation and anoxygenic photosynthesis. Since the redox potential of the electron-accepting system dictates the degradative strategy, there is wide biochemical diversity among anaerobic aromatic degraders. However, the genetic determinants of all these processes and the mechanisms involved in their regulation are much less studied. This review focuses on the recent findings that standard molecular biology approaches together with new high-throughput technologies (e.g., genome sequencing, transcriptomics, proteomics, and metagenomics) have provided regarding the genetics, regulation, ecophysiology, and evolution of anaerobic aromatic degradation pathways. These studies revealed that the anaerobic catabolism of aromatic compounds is more diverse and widespread than previously thought, and the complex metabolic and stress programs associated with the use of aromatic compounds under anaerobic conditions are starting to be unraveled. Anaerobic biotransformation processes based on unprecedented enzymes and pathways with novel metabolic capabilities, as well as the design of novel regulatory circuits and catabolic networks of great biotechnological potential in synthetic biology, are now feasible to approach.
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Affiliation(s)
- Manuel Carmona
- Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Vedler E. Megaplasmids and the Degradation of Aromatic Compounds by Soil Bacteria. MICROBIAL MEGAPLASMIDS 2009. [DOI: 10.1007/978-3-540-85467-8_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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