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Vogel AL, Thompson KJ, Straub D, Musat F, Gutierrez T, Kleindienst S. Genetic redundancy in the naphthalene-degradation pathway of Cycloclasticus pugetii strain PS-1 enables response to varying substrate concentrations. FEMS Microbiol Ecol 2024; 100:fiae060. [PMID: 38614960 PMCID: PMC11099662 DOI: 10.1093/femsec/fiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/15/2024] Open
Abstract
Polycyclic aromatic hydrocarbon (PAH) contamination in marine environments range from low-diffusive inputs to high loads. The influence of PAH concentration on the expression of functional genes [e.g. those encoding ring-hydroxylating dioxygenases (RHDs)] has been overlooked in PAH biodegradation studies. However, understanding marker-gene expression under different PAH loads can help to monitor and predict bioremediation efficiency. Here, we followed the expression (via RNA sequencing) of Cycloclasticus pugetii strain PS-1 in cell suspension experiments under different naphthalene (100 and 30 mg L-1) concentrations. We identified genes encoding previously uncharacterized RHD subunits, termed rhdPS1α and rhdPS1β, that were highly transcribed in response to naphthalene-degradation activity. Additionally, we identified six RHD subunit-encoding genes that responded to naphthalene exposure. By contrast, four RHD subunit genes were PAH-independently expressed and three other RHD subunit genes responded to naphthalene starvation. Cycloclasticus spp. could, therefore, use genetic redundancy in key PAH-degradation genes to react to varying PAH loads. This genetic redundancy may restrict the monitoring of environmental hydrocarbon-degradation activity using single-gene expression. For Cycloclasticus pugetii strain PS-1, however, the newly identified rhdPS1α and rhdPS1β genes might be potential target genes to monitor its environmental naphthalene-degradation activity.
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Affiliation(s)
- Anjela L Vogel
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Katharine J Thompson
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
| | - Daniel Straub
- Eberhard Karls University of Tübingen, Quantitative Biology Center (QBiC), Auf der Morgenstelle 10, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Florin Musat
- Aarhus University, Department of Biology, Section for Microbiology, Ny Munkegade 116, Aarhus C 8000, Denmark
- Babeş-Bolyai University, Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Str. Republicii nr 44, Cluj-Napoca 400015, Romania
| | - Tony Gutierrez
- Heriot-Watt University, Institute of Mechanical Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Edinburgh EH14 4AS, UK
| | - Sara Kleindienst
- Eberhard Karls University of Tübingen, Department of Geosciences, Schnarrenbergstr. 94-96, Tübingen 72076, Germany
- University of Stuttgart, Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), Am Bandtäle 2, Stuttgart 70569, Germany
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Floriano B, Santero E, Reyes-Ramírez F. Biodegradation of Tetralin: Genomics, Gene Function and Regulation. Genes (Basel) 2019; 10:E339. [PMID: 31064110 DOI: 10.3390/genes10050339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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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: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Coincon M, Wang W, Sygusch J, Seah SYK. Crystal structure of reaction intermediates in pyruvate class II aldolase: substrate cleavage, enolate stabilization, and substrate specificity. J Biol Chem 2012; 287:36208-21. [PMID: 22908224 PMCID: PMC3476288 DOI: 10.1074/jbc.m112.400705] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 08/16/2012] [Indexed: 11/06/2022] Open
Abstract
Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8-2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3-C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg(70) assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg(70) stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.
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Affiliation(s)
- Mathieu Coincon
- From the Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Weijun Wang
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jurgen Sygusch
- From the Department of Biochemistry, Université de Montréal, Montréal, Québec H3C 3J7, Canada and
| | - Stephen Y. K. Seah
- the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Tomás-Gallardo L, Santero E, Camafeita E, Calvo E, Schlömann M, Floriano B. Molecular and biochemical characterization of the tetralin degradation pathway in Rhodococcus sp. strain TFB. Microb Biotechnol 2011; 2:262-73. [PMID: 21261920 PMCID: PMC3815846 DOI: 10.1111/j.1751-7915.2009.00086.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The tetralin biodegradation pathway in Rhodococcus sp. strain TFB, a Gram‐positive bacterium resistant to genetic manipulation, was characterized using a proteomic approach. Relative protein expression in cell free extracts from tetralin‐ and glucose‐grown cells was compared using the 2D‐DIGE technique. Identification of proteins specifically expressed in tetralin‐grown cells was used to characterize a complete set of genes involved in tetralin degradation by reverse genetics. We propose a tetralin degradation pathway analogous to that described for Sphingomonas macrogolitabida strain TFA. TFB thn genes are organized into three operons; two contain all of the structural genes and are transcribed in the same direction, while the third operon, thnST, is transcribed in the opposite direction and encodes a two‐component regulatory system, whose transcription is higher in tetralin‐grown cells. In addition to tetralin induction, TFB thn structural genes are subject to glucose repression. Primer extension assays and translational thnA1::gfp and thnS::gfp fusions were used to characterize putative promoter regions. A mutational analysis of the thnA1 promoter region allowed us to define nucleotides within the cis regulatory elements that are important for the control of thn gene expression.
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Affiliation(s)
- Laura Tomás-Gallardo
- Centro Andaluz de Biología del Desarrollo-CSIC, Universidad Pablo de Olavide Carretera de Utrera, Km 1. 41013-Seville, Spain
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López-Sánchez A, Floriano B, Andújar E, Hernáez MJ, Santero E. Tetralin-induced and ThnR-regulated aldehyde dehydrogenase and beta-oxidation genes in Sphingomonas macrogolitabida strain TFA. Appl Environ Microbiol 2010; 76:110-8. [PMID: 19897762 DOI: 10.1128/AEM.01846-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new cluster of genes has been found downstream of the previously identified thnA2 gene. The gene products are similar to nonacylating aldehyde dehydrogenases (ThnG) and to proteins representing a complete beta-oxidation pathway (ThnH to ThnP). ThnG has a nonacylating NAD-dependent pimelic semialdehyde dehydrogenase activity that renders pimelic acid a seven-carbon dicarboxylic acid. For further metabolism via beta-oxidation, pimelic acid could be acylated by a constitutive acyl coenzyme A (acyl-CoA) ligase found in Sphingomonas macrogolitabida strain TFA or by ThnH, which would transfer CoA from a previously acylated molecule. The first round of beta-oxidation is expected to render glutaryl-CoA and acetyl-CoA. Glutaryl-CoA dehydrogenase (ThnN) would catalyze the oxidation and decarboxylation of glutaryl-CoA and yield crotonyl-CoA, which enters the central metabolism via acetyl-CoA. Mutagenesis studies have shown that these genes are not essential for growth on tetralin or fatty acids, although a thnG disruption mutant showed threefold less pimelic semialdehyde dehydrogenase activity. Transcriptional analysis indicated that these genes are induced by tetralin, subjected to catabolite repression, and regulated by the same regulatory factors previously identified to regulate other thn structural genes. In the present study, transcription initiation upstream of thnH and thnM has been detected by primer extension analysis, and putative promoters were identified by sequence analysis. In addition, binding of the activator ThnR to its putative binding sites at the PH and PM promoter regions has been characterized. These results provide a complete characterization of the biodegradation pathway of tetralin to central metabolites and describe the transcriptional organization of the thn operons in S. macrogolitabida strain TFA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang W, Seah SY. The role of a conserved histidine residue in a pyruvate-specific Class II aldolase. FEBS Lett 2008; 582:3385-8. [DOI: 10.1016/j.febslet.2008.08.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 08/19/2008] [Accepted: 08/27/2008] [Indexed: 11/20/2022]
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Serafimov JM, Gillingham D, Kuster S, Hilvert D. The Putative Diels−Alderase Macrophomate Synthase is an Efficient Aldolase. J Am Chem Soc 2008; 130:7798-9. [DOI: 10.1021/ja8017994] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jörg M. Serafimov
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Dennis Gillingham
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Simon Kuster
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland
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Martínez-Pérez O, López-Sánchez A, Reyes-Ramírez F, Floriano B, Santero E. Integrated response to inducers by communication between a catabolic pathway and its regulatory system. J Bacteriol 2007; 189:3768-75. [PMID: 17351041 PMCID: PMC1913338 DOI: 10.1128/jb.00057-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient gene regulation of metabolic pathways implies that the profile of molecules inducing the pathway matches that of the molecules that are metabolized. Gratuitous induction, a well-known phenomenon in catabolic pathways, is the consequence of differences in the substrate and inducer profiles. This phenomenon is particularly evident in pathways for biodegradation of organic contaminants that can be induced by a variety of molecules similar to the real substrates. Analysis of the regulation of tetralin biodegradation genes in mutant strains with mutations that affect each component of the initial dioxygenase enzymatic complex indicated that the response of the regulatory system to potential inducers is altered differently depending on the mutated component. Based on the expression phenotypes of a number of single or double mutants, we propose a model that represents an unprecedented way of communication between a catabolic pathway and its regulatory system to prevent efficient induction by a molecule that is not a real substrate. This communication allows a better fit of the substrate and inducer profiles, thus minimizing gratuitous induction, without a requirement for optimal coevolution to match the specificity of catabolic enzymes and their regulatory systems. Modulation of the regulatory system in this way not only provides a more appropriate response to potential inducers recognized by the regulatory system but also may properly adjust the levels of gene expression to the substrate availability.
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Affiliation(s)
- Olga Martínez-Pérez
- Departamento de Biología Molecular e Ingeniería Bioquímica and Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, Ctra. Utrera, Km. 1, 41013 Sevilla, Spain
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11
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Samland AK, Sprenger GA. Microbial aldolases as C-C bonding enzymes--unknown treasures and new developments. Appl Microbiol Biotechnol 2006; 71:253-64. [PMID: 16614860 DOI: 10.1007/s00253-006-0422-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2006] [Revised: 03/10/2006] [Accepted: 03/10/2006] [Indexed: 11/26/2022]
Abstract
Aldolases are a specific group of lyases that catalyze the reversible stereoselective addition of a donor compound (nucleophile) onto an acceptor compound (electrophile). Whereas most aldolases are specific for their donor compound in the aldolization reaction, they often tolerate a wide range of aldehydes as acceptor compounds. C-C bonding by aldolases creates stereocenters in the resulting aldol products. This makes aldolases interesting tools for asymmetric syntheses of rare sugars or sugar-derived compounds as iminocyclitols, statins, epothilones, and sialic acids. Besides the well-known fructose 1,6-bisphosphate aldolase, other aldolases of microbial origin have attracted the interest of synthetic bio-organic chemists in recent years. These are either other dihydroxyacetone phosphate aldolases or aldolases depending on pyruvate/phosphoenolpyruvate, glycine, or acetaldehyde as donor substrate. Recently, an aldolase that accepts dihydroxyacetone or hydroxyacetone as a donor was described. A further enlargement of the arsenal of available chemoenzymatic tools can be achieved through screening for novel aldolase activities and directed evolution of existing aldolases to alter their substrate- or stereospecifities. We give an update of work on aldolases, with an emphasis on microbial aldolases.
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Affiliation(s)
- Anne K Samland
- Institut für Mikrobiologie, Universität Stuttgart, Germany
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12
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Martínez-Pérez O, Moreno-Ruiz E, Floriano B, Santero E. Regulation of tetralin biodegradation and identification of genes essential for expression of thn operons. J Bacteriol 2004; 186:6101-9. [PMID: 15342579 PMCID: PMC515167 DOI: 10.1128/jb.186.18.6101-6109.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 06/17/2004] [Indexed: 11/20/2022] Open
Abstract
The tetralin biodegradation genes of Sphingomonas macrogolitabida strain TFA are clustered in two closely linked and divergent operons. To analyze expression of both operons under different growth conditions, transcriptional and translational gene fusions of the first genes of each operon to lacZ have been constructed in plasmids unable to replicate in Sphingomonas and integrated by recombination into the genome of strain TFA. Expression analysis indicated that the transcription of both genes is induced in similar ways by the presence of tetralin. Gene expression in both operons is also subjected to overimposed catabolic repression. Two additional genes named thnR and thnY have been identified downstream of thnCA3A4 genes. ThnR is similar to LysR-type regulators, and mutational analysis indicated that ThnR is strictly required for expression of the thn operons. Unlike other LysR-type regulators, ThnR does not repress its own synthesis. In fact, ThnR activates its own expression, since thnR is cotranscribed with the thnCA3A4 genes. ThnY is similar to the ferredoxin reductase components of dioxygenase systems and shows the fer2 domain, binding a Cys4[2Fe-2S] iron sulfur center, and the FAD-binding domain, common to those reductases. However, it lacks the NAD-binding domain. Intriguingly, ThnY has a regulatory role, since it is also strictly required for expression of the thn operons. Given the similarity of ThnY to reductases and the possibility of its being present in the two redox states, it is tempting to speculate that ThnY is a regulatory component connecting expression of the thn operons to the physiological status of the cell.
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MESH Headings
- Artificial Gene Fusion
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Biodegradation, Environmental
- DNA, Bacterial/chemistry
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genes, Regulator
- Genes, Reporter
- Molecular Sequence Data
- Mutation
- Operon
- Oxidoreductases/genetics
- Oxidoreductases/physiology
- Phylogeny
- RNA, Bacterial/analysis
- RNA, Messenger/analysis
- Recombinant Fusion Proteins/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Sphingomonas/genetics
- Sphingomonas/metabolism
- Tetrahydronaphthalenes/metabolism
- Transcription Factors/genetics
- Transcription Factors/physiology
- Transcription, Genetic
- beta-Galactosidase/genetics
- beta-Galactosidase/metabolism
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Affiliation(s)
- O Martínez-Pérez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, ctra. Utrera Km 1, 41013 Sevilla, Spain
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13
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Moreno-Ruiz E, Hernáez MJ, Martínez-Pérez O, Santero E. Identification and functional characterization of Sphingomonas macrogolitabida strain TFA genes involved in the first two steps of the tetralin catabolic pathway. J Bacteriol 2003; 185:2026-30. [PMID: 12618469 PMCID: PMC150124 DOI: 10.1128/jb.185.6.2026-2030.2003] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2002] [Accepted: 12/19/2002] [Indexed: 11/20/2022] Open
Abstract
Five genes involved in the two initial steps of the tetralin biodegradation pathway of Sphingomonas macrogolitabida strain TFA have been characterized. ThnA1A2 and ThnA3A4, components of the ring-hydroxylating dioxygenase, were encoded in divergently transcribed operons. ThnA1, ThnA2, and ThnA3 were essential for tetralin ring-hydroxylating dioxygenase activity. ThnB was identified as a dehydrogenase required for tetralin biodegradation.
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Affiliation(s)
- Emilia Moreno-Ruiz
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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