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Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
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Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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Msomi NN, Padayachee T, Nzuza N, Syed PR, Kryś JD, Chen W, Gront D, Nelson DR, Syed K. In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria. Molecules 2021; 26:1538. [PMID: 33799696 PMCID: PMC7998510 DOI: 10.3390/molecules26061538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The impact of lifestyle on shaping the genome content of an organism is a well-known phenomenon and cytochrome P450 enzymes (CYPs/P450s), heme-thiolate proteins that are ubiquitously present in organisms, are no exception. Recent studies focusing on a few bacterial species such as Streptomyces, Mycobacterium, Cyanobacteria and Firmicutes revealed that the impact of lifestyle affected the P450 repertoire in these species. However, this phenomenon needs to be understood in other bacterial species. We therefore performed genome data mining, annotation, phylogenetic analysis of P450s and their role in secondary metabolism in the bacterial class Gammaproteobacteria. Genome-wide data mining for P450s in 1261 Gammaproteobacterial species belonging to 161 genera revealed that only 169 species belonging to 41 genera have P450s. A total of 277 P450s found in 169 species grouped into 84 P450 families and 105 P450 subfamilies, where 38 new P450 families were found. Only 18% of P450s were found to be involved in secondary metabolism in Gammaproteobacterial species, as observed in Firmicutes as well. The pathogenic or commensal lifestyle of Gammaproteobacterial species influences them to such an extent that they have the lowest number of P450s compared to other bacterial species, indicating the impact of lifestyle on shaping the P450 repertoire. This study is the first report on comprehensive analysis of P450s in Gammaproteobacteria.
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Affiliation(s)
- Ntombizethu Nokuphiwa Msomi
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
| | - Puleng Rosinah Syed
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Justyna Dorota Kryś
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077 Göttingen, Germany;
| | - Dominik Gront
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
| | - David R. Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa; (N.N.M.); (T.P.); (N.N.)
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Luchnikova NA, Ivanova KM, Tarasova EV, Grishko VV, Ivshina IB. Microbial Conversion of Toxic Resin Acids. Molecules 2019; 24:molecules24224121. [PMID: 31739575 PMCID: PMC6891630 DOI: 10.3390/molecules24224121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/03/2022] Open
Abstract
Organic wood extractives—resin acids—significantly contribute to an increase in the toxicity level of pulp and paper industry effluents. Entering open ecosystems, resin acids accumulate and have toxic effects on living organisms, which can lead to the ecological imbalance. Among the most effective methods applied to neutralize these ecotoxicants is enzymatic detoxification using microorganisms. A fundamental interest in the in-depth study of the oxidation mechanisms of resin acids and the search for their key biodegraders is increasing every year. Compounds from this group receive attention because of the need to develop highly effective procedures of resin acid removal from pulp and paper effluents and also the possibility to obtain their derivatives with pronounced pharmacological effects. Over the past fifteen years, this is the first report analyzing the data on distribution, the impacts on living organisms, and the microbial transformation of resin acids. Using the example of dehydroabietic acid—the dominant compound of resin acids in effluents—the review discusses the features of interactions between microorganisms and this pollutant and also highlights the pathways and main products of resin acid bioconversion.
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Affiliation(s)
- Natalia A. Luchnikova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Kseniya M. Ivanova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Ekaterina V. Tarasova
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
| | - Victoria V. Grishko
- Institute of Technical Chemistry, Ural Branch of the Russian Academy of Sciences, 614013 Perm, Russia;
| | - Irina B. Ivshina
- Institute of Ecology and Genetics of Microorganisms, Ural Branch of the Russian Academy of Sciences, 614081 Perm, Russia; (N.A.L.); (K.M.I.); (E.V.T.)
- Department of Microbiology and Immunology, Perm State National Research University, 614990 Perm, Russia
- Correspondence: ; Tel.: +7-342-2808114
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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Gomes TG, Hadi SIIA, Costa Alves GS, Mendonça S, De Siqueira FG, Miller RNG. Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review. J Agric Food Chem 2018; 66:2510-2522. [PMID: 29498277 DOI: 10.1021/acs.jafc.7b05691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.
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Affiliation(s)
- Taisa G Gomes
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Sámed I I A Hadi
- Universidade Federal de Minas Gerais , Instituto de Ciências Biológicas - ICB , Av. Pres. Antônio Carlos, 6627 , 31270-010 , Belo Horizonte , MG , Brazil
| | - Gabriel S Costa Alves
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
| | - Simone Mendonça
- Embrapa Agroenergia, STN-70297-400 , 70297-400 , Brasília , DF , Brazil
| | | | - Robert N G Miller
- Instituto de Ciências Biológicas, Departamento de Biologia Celular , Universidade de Brasília , Campus Universitário Darcy Ribeiro, Asa Norte , 70910-900 , Brasília , DF , Brazil
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Berasategui A, Salem H, Paetz C, Santoro M, Gershenzon J, Kaltenpoth M, Schmidt A. Gut microbiota of the pine weevil degrades conifer diterpenes and increases insect fitness. Mol Ecol 2017; 26:4099-4110. [DOI: 10.1111/mec.14186] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/02/2017] [Accepted: 05/05/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Aileen Berasategui
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
- Insect Symbiosis Research Group; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Hassan Salem
- Insect Symbiosis Research Group; Max Planck Institute for Chemical Ecology; Jena Germany
- Department of Biology; Emory University; Atlanta GA USA
| | - Christian Paetz
- NMR Department; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Maricel Santoro
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
- Departamento de Biología Molecular; Universidad Nacional de Río Cuarto; Río Cuarto Argentina
| | - Jonathan Gershenzon
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology; Johannes Gutenberg University Mainz; Mainz Germany
| | - Axel Schmidt
- Biochemistry Department; Max Planck Institute for Chemical Ecology; Jena Germany
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Dorado-Morales P, Vilanova C, P Garay C, Martí JM, Porcar M. Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling. Sci Rep 2015; 5:18396. [PMID: 26671778 PMCID: PMC4680887 DOI: 10.1038/srep18396] [Citation(s) in RCA: 7] [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: 05/06/2015] [Accepted: 11/17/2015] [Indexed: 01/29/2023] Open
Abstract
We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia.
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Affiliation(s)
- Pedro Dorado-Morales
- Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), 46020 Valencia, Spain
| | - Cristina Vilanova
- Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), 46020 Valencia, Spain
| | - Carlos P Garay
- Instituto de Física Corpuscular, CSIC-UVEG, 46071, Valencia, Spain
| | | | - Manuel Porcar
- Cavanilles Institute of Biodiversity and Evolutionary Biology (Universitat de València), 46020 Valencia, Spain.,Fundació General de la Universitat de València, Spain
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Chanda A, Gummadidala PM, Gomaa OM. Mycoremediation with mycotoxin producers: a critical perspective. Appl Microbiol Biotechnol 2016; 100:17-29. [DOI: 10.1007/s00253-015-7032-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/08/2015] [Accepted: 09/10/2015] [Indexed: 12/18/2022]
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Janocha S, Bernhardt R. Design and characterization of an efficient CYP105A1-based whole-cell biocatalyst for the conversion of resin acid diterpenoids in permeabilized Escherichia coli. Appl Microbiol Biotechnol 2013; 97:7639-49. [PMID: 23793341 DOI: 10.1007/s00253-013-5008-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/02/2013] [Accepted: 05/19/2013] [Indexed: 10/26/2022]
Abstract
Cytochrome P450 enzymes exhibit a tremendous potential for biotechnological applications due to their ability to introduce oxygen into non-activated carbon atoms. Their catalytic diversity is complemented by a broad substrate range covering many natural compounds. Especially the functionalization of terpenoids by P450s becomes increasingly interesting due to the diverse biological effects of these compounds. The bacterial CYP105A1 from Streptomyces griseolus was recently identified to carry out a one-step hydroxylation of several abietane-type resin acids. In this work, a whole-cell system for CYP105A1 with its heterologous electron transfer proteins Arh1 and Etp1(fd) from Schizosaccharomyces pombe was designed in Escherichia coli JM109 cells. Additionally, an enzyme-coupled cofactor regeneration system was integrated by co-expression of alcohol dehydrogenase from Lactobacillus brevis. In order to overcome mass transfer limitations of substrate into the cell, different agents were tested towards their permeabilizing activity on the E. coli membrane. The peptide antibiotic polymyxin B proved to be the most effective permeabilizer. After optimising the expression and conversion conditions, the cells were able to completely convert 200 μM of abietic acid into 15-hydroxyabietic acid within 2 h, exhibiting an initial conversion rate of 125 μM/h. These results demonstrate the high potential of this whole-cell system for the synthesis of functionalized resin acid diterpenoids.
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Redondo-Nieto M, Barret M, Morrissey J, Germaine K, Martínez-Granero F, Barahona E, Navazo A, Sánchez-Contreras M, Moynihan JA, Muriel C, Dowling D, O'Gara F, Martín M, Rivilla R. Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics 2013; 14:54. [PMID: 23350846 PMCID: PMC3570484 DOI: 10.1186/1471-2164-14-54] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [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] [Received: 07/17/2012] [Accepted: 01/23/2013] [Indexed: 01/04/2023] Open
Abstract
Background Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. Results Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. Conclusions The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.
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Affiliation(s)
- Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin, 2, Madrid, 28049, Spain
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Khatri Y, Hannemann F, Perlova O, Müller R, Bernhardt R. Investigation of cytochromes P450 in myxobacteria: Excavation of cytochromes P450 from the genome ofSorangium cellulosumSo ce56. FEBS Lett 2011; 585:1506-13. [DOI: 10.1016/j.febslet.2011.04.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 04/13/2011] [Accepted: 04/14/2011] [Indexed: 10/18/2022]
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Smith DJ, Patrauchan MA, Florizone C, Eltis LD, Mohn WW. Distinct roles for two CYP226 family cytochromes P450 in abietane diterpenoid catabolism by Burkholderia xenovorans LB400. J Bacteriol 2008; 190:1575-83. [PMID: 18156276 DOI: 10.1128/JB.01530-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [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
The 80-kb dit cluster of Burkholderia xenovorans LB400 encodes the catabolism of abietane diterpenoids. This cluster includes ditQ and ditU, predicted to encode cytochromes P450 (P450s) belonging to the poorly characterized CYP226A subfamily. Using proteomics, we identified 16 dit-encoded proteins that were significantly more abundant in LB400 cells grown on dehydroabietic acid (DhA) or abietic acid (AbA) than in succinate-grown cells. A key difference in the catabolism of DhA and AbA lies in the differential expression of the P450s; DitU was detected only in the AbA-grown cells, whereas DitQ was expressed both during growth on DhA and during growth on AbA. Analyses of insertion mutants showed that ditQ was required for growth on DhA, ditU was required for growth on AbA, and neither gene was required for growth on the central intermediate, 7-oxo-DhA. In cell suspension assays, patterns of substrate removal and metabolite accumulation confirmed the role of DitU in AbA transformation and the role of DitQ in DhA transformation. Spectral assays revealed that DitQ binds both DhA (dissociation constant, 0.98 +/- 0.01 microM) and palustric acid. Finally, DitQ transformed DhA to 7-hydroxy-DhA in vitro. These results demonstrate the distinct roles of the P450s DitQ and DitU in the transformation of DhA and AbA, respectively, to 7-oxo-DhA in a convergent degradation pathway.
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Smith DJ, Park J, Tiedje JM, Mohn WW. A large gene cluster in Burkholderia xenovorans encoding abietane diterpenoid catabolism. J Bacteriol 2007; 189:6195-204. [PMID: 17586638 PMCID: PMC1951937 DOI: 10.1128/jb.00179-07] [Citation(s) in RCA: 23] [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: 02/02/2007] [Accepted: 06/14/2007] [Indexed: 11/20/2022] Open
Abstract
Abietane diterpenoids are defense compounds synthesized by trees that are abundant in natural environments and occur as significant pollutants from pulp and paper production. Burkholderia xenovorans LB400 has diverse catabolic capabilities and represents an important group of heterotrophic bacteria in soil environments. The genome sequence of LB400 revealed homologs of the dit genes of Pseudomonas abietaniphila BKME-9, which encode abietane diterpenoid degradation. LB400 grew on abietic acid (AbA), dehydroabietic acid (DhA), palustric acid (PaA), and 7-oxo-DhA. A Xeotron microarray set, with probes for 8450 of the estimated 9000 LB400 genes, was used to compare the transcriptomes of LB400 growing on DhA versus on succinate. On DhA, 97 genes were upregulated, 43 of which were within an 80-kb cluster located on the 1.47-Mbp megaplasmid of LB400. Upregulated genes in this cluster encode a permease, a ring-hydroxylating dioxygenase system (DitA), a ring-cleavage dioxygenase (DitC), a P450 monooxygenase (DitQ), and enzymes catalyzing beta-oxidation-type reactions. Disruption of the ditA1 gene, encoding the alpha-subunit of DitA, abolished growth on these abietanes. Analyses of the metabolism of abietanes by cell suspensions of wild-type LB400 and the ditA1 mutant indicate a convergent pathway, with 7-oxo-DhA as a common intermediate for ring hydroxylation by DitA. Also, 7-oxo-PaA was identified as a metabolite of both AbA and PaA. Sequence analysis indicates that genes encoding this pathway have been horizontally transferred among Betaproteobacteria and Gammaproteobacteria.
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Affiliation(s)
- Daryl J Smith
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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Smith DJ, Martin VJJ, Mohn WW. A cytochrome P450 involved in the metabolism of abietane diterpenoids by Pseudomonas abietaniphila BKME-9. J Bacteriol 2004; 186:3631-9. [PMID: 15150251 PMCID: PMC415779 DOI: 10.1128/jb.186.11.3631-3639.2004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [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: 12/11/2003] [Accepted: 02/26/2004] [Indexed: 11/20/2022] Open
Abstract
Diterpenoids are naturally occurring plant compounds which have pharmaceutical properties. We have sequenced a 10.4-kbp extension of the dit cluster in Pseudomonas abietaniphila BKME-9, containing genes involved in abietane diterpenoid biodegradation. The ditQ gene was found to encode a cytochrome P450 monooxygenase, P450dit, and to be homologous to the tdtD gene of Pseudomonas diterpeniphila A19-6a. Knocking out ditQ had little effect on growth of BKME-9 on abietic acid but severely impaired growth on dehydroabietic acid (DhA) and palustric acid (PaA), increasing doubling times from 3.8 to 15 h on DhA and from 5.6 to 18.5 h on PaA. A xylE transcriptional fusion showed that transcription of ditQ was induced by a range of diterpenoids. Substrate binding assays of P450dit expressed in Escherichia coli revealed that DhA binds to the enzyme and yields a type I binding spectrum with a Kd of 0.4 microM. These results indicate that P450dit is involved in the metabolism of DhA and PaA and are consistent with its putative role in converting DhA to 7-hydroxy-DhA. Finally, an amino acid sequence identity of greater than 72% and conserved gene arrangement support the hypothesis that the dit gene cluster of P. abietaniphila BKME-9 and the tdt cluster of P. diterpeniphila A19-6a contain functional homologues.
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Affiliation(s)
- Daryl J Smith
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Abstract
A DNA microarray to monitor the expression of bacterial metabolic genes within mixed microbial communities was designed and tested. Total RNA was extracted from pure and mixed cultures containing the 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterium Ralstonia eutropha JMP134, and the inducing agent 2,4-D. Induction of the 2,4-D catabolic genes present in this organism was readily detected 4, 7, and 24 h after the addition of 2,4-D. This strain was diluted into a constructed mixed microbial community derived from a laboratory scale sequencing batch reactor. Induction of two of five 2,4-D catabolic genes (tfdA and tfdC) from populations of JMP134 as low as 10(5) cells/ml was clearly detected against a background of 10(8) cells/ml. Induction of two others (tfdB and tfdE) was detected from populations of 10(6) cells/ml in the same background; however, the last gene, tfdF, showed no significant induction due to high variability. In another experiment, the induction of resin acid degradative genes was statistically detectable in sludge-fed pulp mill effluent exposed to dehydroabietic acid in batch experiments. We conclude that microarrays will be useful tools for the detection of bacterial gene expression in wastewaters and other complex systems.
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Affiliation(s)
- Philip Dennis
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada
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