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Zhou XT, Jia LD, Duan MZ, Chen X, Qiao CL, Ma JQ, Zhang C, Jing FY, Zhang SS, Yang B, Zhang LY, Li JN. Genome-wide identification and expression profiling of the carotenoid cleavage dioxygenase (CCD) gene family in Brassica napus L. PLoS One 2020; 15:e0238179. [PMID: 32881902 PMCID: PMC7470270 DOI: 10.1371/journal.pone.0238179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/12/2020] [Indexed: 11/19/2022] Open
Abstract
Carotenoid cleavage dioxygenase (CCD), a key enzyme in carotenoid metabolism, cleaves carotenoids to form apo-carotenoids, which play a major role in plant growth and stress responses. CCD genes had not previously been systematically characterized in Brassica napus (rapeseed), an important oil crop worldwide. In this study, we identified 30 BnCCD genes and classified them into nine subgroups based on a phylogenetic analysis. We identified the chromosomal locations, gene structures, and cis-promoter elements of each of these genes and performed a selection pressure analysis to identify residues under selection. Furthermore, we determined the subcellular localization, physicochemical properties, and conserved protein motifs of the encoded proteins. All the CCD proteins contained a retinal pigment epithelial membrane protein (RPE65) domain. qRT-PCR analysis of expression of 20 representative BnCCD genes in 16 tissues of the B. napus cultivar Zhong Shuang 11 ('ZS11') revealed that members of the BnCCD gene family possess a broad range of expression patterns. This work lays the foundation for functional studies of the BnCCD gene family.
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Affiliation(s)
- Xin-Tong Zhou
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Le-Dong Jia
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Mou-Zheng Duan
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xue Chen
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Cai-Lin Qiao
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Qi Ma
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chao Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Fu-Yu Jing
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Sheng-Sen Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bo Yang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Li-Yuan Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jia-Na Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Loewen PC, Switala J, Wells JP, Huang F, Zara AT, Allingham JS, Loewen MC. Structure and function of a lignostilbene-α,β-dioxygenase orthologue from Pseudomonas brassicacearum. BMC Biochem 2018; 19:8. [PMID: 30115012 PMCID: PMC6097328 DOI: 10.1186/s12858-018-0098-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/02/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND Stilbene cleaving oxygenases (SCOs), also known as lignostilbene-α,β-dioxygenases (LSDs) mediate the oxidative cleavage of the olefinic double bonds of lignin-derived intermediate phenolic stilbenes, yielding small modified benzaldehyde compounds. SCOs represent one branch of the larger carotenoid cleavage oxygenases family. Here, we describe the structural and functional characterization of an SCO-like enzyme from the soil-born, bio-control agent Pseudomonas brassicacearum. METHODS In vitro and in vivo assays relying on visual inspection, spectrophotometric quantification, as well as liquid-chormatographic and mass spectrometric characterization were applied for functional evaluation of the enzyme. X-ray crystallographic analyses and in silico modeling were applied for structural investigations. RESULTS In vitro assays demonstrated preferential cleavage of resveratrol, while in vivo analyses detected putative cleavage of the straight chain carotenoid, lycopene. A high-resolution structure containing the seven-bladed β-propeller fold and conserved 4-His-Fe unit at the catalytic site, was obtained. Comparative structural alignments, as well as in silico modelling and docking, highlight potential molecular factors contributing to both the primary in vitro activity against resveratrol, as well as the putative subsidiary activities against carotenoids in vivo, for future validation. CONCLUSIONS The findings reported here provide validation of the SCO structure, and highlight enigmatic points with respect to the potential effect of the enzyme's molecular environment on substrate specificities for future investigation.
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Affiliation(s)
- Peter C Loewen
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Jacek Switala
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - James P Wells
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Fang Huang
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada
| | - Anthony T Zara
- Department of BioMedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - John S Allingham
- Department of BioMedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Michele C Loewen
- National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6, Canada.
- Department of BioMedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
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Puente-Sánchez F, Díaz S, Penacho V, Aguilera A, Olsson S. Basis of genetic adaptation to heavy metal stress in the acidophilic green alga Chlamydomonas acidophila. Aquat Toxicol 2018; 200:62-72. [PMID: 29727772 DOI: 10.1016/j.aquatox.2018.04.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 05/26/2023]
Abstract
To better understand heavy metal tolerance in Chlamydomonas acidophila, an extremophilic green alga, we assembled its transcriptome and measured transcriptomic expression before and after Cd exposure in this and the neutrophilic model microalga Chlamydomonas reinhardtii. Genes possibly related to heavy metal tolerance and detoxification were identified and analyzed as potential key innovations that enable this species to live in an extremely acid habitat with high levels of heavy metals. In addition we provide a data set of single orthologous genes from eight green algal species as a valuable resource for comparative studies including eukaryotic extremophiles. Our results based on differential gene expression, detection of unique genes and analyses of codon usage all indicate that there are important genetic differences in C. acidophila compared to C. reinhardtii. Several efflux family proteins were identified as candidate key genes for adaptation to acid environments. This study suggests for the first time that exposure to cadmium strongly increases transposon expression in green algae, and that oil biosynthesis genes are induced in Chlamydomonas under heavy metal stress. Finally, the comparison of the transcriptomes of several acidophilic and non-acidophilic algae showed that the Chlamydomonas genus is polyphyletic and that acidophilic algae have distinctive aminoacid usage patterns.
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MESH Headings
- Actins/genetics
- Actins/metabolism
- Adaptation, Physiological/drug effects
- Cadmium/metabolism
- Cadmium/toxicity
- Carboxylic Ester Hydrolases/classification
- Carboxylic Ester Hydrolases/genetics
- Chlamydomonas/classification
- Chlamydomonas/drug effects
- Chlamydomonas/metabolism
- Dioxygenases/classification
- Dioxygenases/genetics
- Drug Tolerance/genetics
- Metals, Heavy/metabolism
- Metals, Heavy/toxicity
- Phylogeny
- Plant Proteins/classification
- Plant Proteins/genetics
- RNA, Plant/chemistry
- RNA, Plant/isolation & purification
- RNA, Plant/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- Sequence Analysis, RNA
- Transcriptome/drug effects
- Water Pollutants, Chemical/chemistry
- Water Pollutants, Chemical/metabolism
- Water Pollutants, Chemical/toxicity
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Affiliation(s)
- Fernando Puente-Sánchez
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Calle Darwin 3, 28049, Madrid, Spain
| | - Silvia Díaz
- Department of Physiology, Genetics and Microbiology, Complutense University of Madrid (UCM), Calle José Antonio Novais 12, 28040 Madrid, Spain
| | - Vanessa Penacho
- Bioarray, S.L. Parque Científico y Empresarial de la UMH, Edificio Quorum III, Avenida de la Universidad s/n, 03202 Elche, Alicante, Spain
| | - Angeles Aguilera
- Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sanna Olsson
- INIA Forest Research Centre (INIA-CIFOR), Department Forest Ecology and Genetics, Carretera de la Coruña km 7.5, 28040 Madrid, Spain; Department Agricultural Sciences, P.O. Box 27, 00014 University of Helsinki, Finland.
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Kakizaki T, Kitashiba H, Zou Z, Li F, Fukino N, Ohara T, Nishio T, Ishida M. A 2-Oxoglutarate-Dependent Dioxygenase Mediates the Biosynthesis of Glucoraphasatin in Radish. Plant Physiol 2017; 173:1583-1593. [PMID: 28100450 PMCID: PMC5338677 DOI: 10.1104/pp.16.01814] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/16/2017] [Indexed: 05/22/2023]
Abstract
Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis (Arabidopsis thaliana). GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL composition even within individual species. However, in radish (Raphanus sativus), glucoraphasatin (4-methylthio-3-butenyl glucosinolate) accounts for more than 90% of the total GSLs, and little compositional variation is observed. Because glucoraphasatin is not contained in other members of the Brassicaceae, like Arabidopsis and cabbage (Brassica oleracea), the biosynthetic pathways for glucoraphasatin remain unclear. In this report, we identified and characterized a gene encoding GLUCORAPHASATIN SYNTHASE 1 (GRS1) by genetic mapping using a mutant that genetically lacks glucoraphasatin. Transgenic Arabidopsis, which overexpressed GRS1 cDNA, accumulated glucoraphasatin in the leaves. GRS1 encodes a 2-oxoglutarate-dependent dioxygenase, and it is abundantly expressed in the leaf. To further investigate the biosynthesis and transportation of GSLs in radish, we grafted a grs1 plant onto a wild-type plant. The grafting experiment revealed a leaf-to-root long-distance glucoraphasatin transport system in radish and showed that the composition of GSLs differed among the organs. Based on these observations, we propose a characteristic biosynthesis pathway for glucoraphasatin in radish. Our results should be useful in metabolite engineering for breeding of high-value vegetables.
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Affiliation(s)
- Tomohiro Kakizaki
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.);
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Hiroyasu Kitashiba
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Zhongwei Zou
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Feng Li
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Nobuko Fukino
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Takayoshi Ohara
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Takeshi Nishio
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Masahiko Ishida
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
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Priya R, Siva R. Analysis of phylogenetic and functional diverge in plant nine-cis epoxycarotenoid dioxygenase gene family. J Plant Res 2015; 128:519-34. [PMID: 25929830 DOI: 10.1007/s10265-015-0726-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/15/2014] [Indexed: 05/27/2023]
Abstract
During different environmental stress conditions, plant growth is regulated by the hormone abscisic acid (an apocarotenoid). In the biosynthesis of abscisic acid, the oxidative cleavage of cis-epoxycarotenoid catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED) is the crucial step. The NCED genes were isolated in numerous plant species and those genes were phylogenetically investigated to understand the evolution of NCED genes in various plant lineages comprising lycophyte, gymnosperm, dicot and monocot. A total of 93 genes were obtained from 48 plant species to statistically estimate their sequence conservation and functional divergence. Selaginella moellendorffii appeared to be evolutionarily distinct from those of the angiosperms, insisting the substantial influence of natural selection pressure on NCED genes. Further, using exon-intron structure analysis, the gene structures of NCED were found to be conserved across some species. In addition, the substitution rate ratio of non-synonymous (Ka) versus synonymous (Ks) mutations using the Bayesian inference approach, depicted the critical amino acid residues for functional divergence. A significant functional divergence was found between some subgroups through the co-efficient of type-I functional divergence. Our results suggest that the evolution of NCED genes occurred by duplication, diversification and exon intron loss events. The site-specific profile and functional diverge analysis revealed NCED genes might facilitate the tissue-specific functional divergence in NCED sub-families, that could combat different environmental stress conditions aiding plant survival.
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Affiliation(s)
- R Priya
- School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India
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Rubio-Moraga A, Rambla JL, Fernández-de-Carmen A, Trapero-Mozos A, Ahrazem O, Orzáez D, Granell A, Gómez-Gómez L. New target carotenoids for CCD4 enzymes are revealed with the characterization of a novel stress-induced carotenoid cleavage dioxygenase gene from Crocus sativus. Plant Mol Biol 2014; 86:555-69. [PMID: 25204497 DOI: 10.1007/s11103-014-0250-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/03/2014] [Indexed: 05/04/2023]
Abstract
Apocarotenoid compounds play diverse communication functions in plants, some of them being as hormones, pigments and volatiles. Apocarotenoids are the result of enzymatic cleavage of carotenoids catalyzed by carotenoid cleavage dioxygenase (CCD). The CCD4 family is the largest family of plant CCDs, only present in flowering plants, suggesting a functional diversification associated to the adaptation for specific physiological capacities unique to them. In saffron, two CCD4 genes have been previously isolated from the stigma tissue and related with the generation of specific volatiles involved in the attraction of pollinators. The aim of this study was to identify additional CCD4 members associated with the generation of other carotenoid-derived volatiles during the development of the stigma. The expression of CsCCD4c appears to be restricted to the stigma tissue in saffron and other Crocus species and was correlated with the generation of megastigma-4,6,8-triene. Further, CsCCD4c was up-regulated by wounding, heat, and osmotic stress, suggesting an involvement of its apocarotenoid products in the adaptation of saffron to environmental stresses. The enzymatic activity of CsCCD4c was determined in vivo in Escherichia coli and subsequently in Nicotiana benthamiana by analyzing carotenoids by HPLC-DAD and the volatile products by GC/MS. β-Carotene was shown to be the preferred substrate, being cleaved at the 9,10 (9',10') bonds and generating β-ionone, although β-cyclocitral resulting from a 7,8 (7',8') cleavage activity was also detected at lower levels. Lutein, neoxanthin and violaxanthin levels in Nicotiana leaves were markedly reduced when CsCCD4c is over expressed, suggesting that CsCCD4c recognizes these carotenoids as substrates.
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Affiliation(s)
- Angela Rubio-Moraga
- Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Instituto Botánico, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
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Baboshin MA, Golovleva LA. [Biodegradation of polycyclic aromatic hydrocarbons (PAH) by aerobic bacteria and its kinetics aspects]. Mikrobiologiia 2012; 81:695-706. [PMID: 23610919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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8
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Jiang J, Wang H, Gao JS, Song L, Ning DL. [Cloning and sequence analysis of 1,2,4-trichlorobenzene dioxygenase and dehydrogenase genes]. Huan Jing Ke Xue 2008; 29:1655-1659. [PMID: 18763518] [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] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Pseudomonas nitroreducens J5-1 is able to use monochlorobenzene, 1,2-dichlorobenzene, 1,3-dichlorobenzene and 1,2,4-trichlorobenzene as sole carbon and energy sources, and it differs from those 1,2,4-trichlorobenzene degrading bacteria reported in substrate utilizing characters. PCR technique was used to amplify the genes of chlorobenzene dioxygenase and dehydrogenase of J5-1, and they were named as tcbA and tcbB, respectively. Homology analysis indicated that these genes and gene products were most closely related to those of Burkholderia sp. PS12. By alignment of the amino acid sequences of the a subunits of TcbAa (from J5-1) and TecA1 (from PS12), four amino acid residues from site 307 to site 310 were found to be different (I307L, M308T, I309V, Q310E), which probably retarded the preference for the substrate 1,2,4,5-tetrachlorobenzene. Furthermore, the phylogenetic analysis of the dioxygenase alpha subunits showed that TcbAa was belong to the toluene/diphenyl subfamily, and was most closely related to the poly-chlorinated benzene dioxygenase alpha subunit.
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Affiliation(s)
- Jian Jiang
- Institute of Environmental Biology, Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China.
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Song L, Wang H, Jiang J, Gao JS, Shi HC. [Isolation, idetification of 1,2, 4-trichlorobenzene-degrading strain Pseudomonas nitroreducens J5-1 and cloning of chlorocatechol 1,2-dioxygenase gene]. Huan Jing Ke Xue 2007; 28:1878-1881. [PMID: 17926427] [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] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A bacterium capable of utilizing 1,2,4-trichlorobenzene as sole carbon source was isolated from the polluted soil sample. This baterium was identified as Pseudomonas nitroreducens according to its physiological & biochemical analysis and its 16S rDNA sequence (GenBank Accession No. EF107515). When the initial concentration of 1,2,4-TCB is 400 mg/L, J5-1 can achieve a maximum degradation rate of 90%. When the initial concentration of 1,2,4-TCB is 20 mg/L, the effect of degradation is the best. Degradation of 1,2,4-TCB by strain J5-1 obeys the first order dynamics. The total gene of chlorocatechol 1,2-dioxygenase was cloned from genomic DNA of J5-1.
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Affiliation(s)
- Lei Song
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084, China.
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Abstract
The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases.
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Affiliation(s)
- Tomasz Borowski
- Department of Physics, Stockholm Center for Physics, Astronomy and Biotechnology, Stockholm University, S-10691 Stockholm, Sweden.
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Witzig R, Aly HAH, Strömpl C, Wray V, Junca H, Pieper DH. Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples. Environ Microbiol 2007; 9:1202-18. [PMID: 17472635 DOI: 10.1111/j.1462-2920.2007.01242.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [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: 11/26/2022]
Abstract
Resin acids are tricyclic diterpenoids naturally synthesized by trees that are released from wood during pulping processes. Using a newly designed primer set, genes similar to that encoding the DitA1 catalytic alpha-subunit of the diterpenoid dioxygenase, a key enzyme in abietane resin acid degradation by Pseudomonas abietaniphila BKME-9, could be amplified from different Pseudomonas strains, whereas ditA1 gene sequence types representing distinct branches in the evolutionary tree were amplified from Burkholderia and Cupriavidus isolates. All isolates harbouring a ditA1-homologue were capable of growth on dehydroabietic acid as the sole source of carbon and energy and reverse transcription polymerase chain reaction analysis in three strains confirmed that ditA1 was expressed constitutively or in response to DhA, demonstrating its involvement in DhA-degradation. Evolutionary analyses indicate that gyrB (as a phylogenetic marker) and ditA1 genes have coevolved under purifying selection from their ancestral variants present in the most recent common ancestor of the genera Pseudomonas, Cupriavidus and Burkholderia. A polymerase chain reaction-single-strand conformation poylmorphism fingerprinting method was established to monitor the diversity of ditA1 genes in environmental samples. The molecular fingerprints indicated the presence ofa broad, previously unrecognized diversity of diterpenoid dioxygenase genes in soils, and suggest that other bacterial phyla may also harbour the genetic potential for DhA-degradation.
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Affiliation(s)
- Robert Witzig
- Department of Environmental Microbiology, HZI--Helmholtz Centre for Infection Research, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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Yu Z, Genest PA, ter Riet B, Sweeney K, DiPaolo C, Kieft R, Christodoulou E, Perrakis A, Simmons JM, Hausinger RP, van Luenen HG, Rigden DJ, Sabatini R, Borst P. The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res 2007; 35:2107-15. [PMID: 17389644 PMCID: PMC1874643 DOI: 10.1093/nar/gkm049] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trypanosomatids contain an unusual DNA base J (beta-d-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe(2+) and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe(2+) and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
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Affiliation(s)
- Zhong Yu
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Paul-André Genest
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bas ter Riet
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Kate Sweeney
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Courtney DiPaolo
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Rudo Kieft
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Evangelos Christodoulou
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Anastassis Perrakis
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jana M. Simmons
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert P. Hausinger
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Henri G.A.M. van Luenen
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Daniel J. Rigden
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Robert Sabatini
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Piet Borst
- Division of Molecular Biology and Centre of Biomedical Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Global Infectious Diseases Program Marine Biological Laboratory, Woods Hole, MA 02543, USA, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands, Department of Biochemistry & Molecular Biology and Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, USA and School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
- *To whom correspondence should be addressed. +31 20 512 2880+31 20 669 1383
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Khomenkov VG, Shevelev AB, Zhukov VG, Kurlovich AE, Zagustina NA, Popov VO. [Metabolic pathways responsible for consumption of aromatic hydrocarbons by microbial associations: molecular-genetic characterization]. Prikl Biokhim Mikrobiol 2005; 41:298-302. [PMID: 15977790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Genes for catechol 1,2- and 2,3-dioxygenases were cloned. These enzymes hold important positions in the ortho and meta pathways of the metabolism of aromatic carbons by microbial associations that consume the following volatile organic compounds in pilot minireactors: toluene, styrene, ethyl benzene, o-xylene, m-xylene, and naphthalene. Genes of both pathways were found in an association consuming m-xylene; only genes of the ortho pathway were found in associations consuming o-xylene, styrene, and ethyl benzene, and only genes of the meta pathway were found in associations consuming naphthalene and toluene. Genes of the ortho pathway (C120) cloned from associations consuming o-xylene and ethyl benzene were similar to corresponding genes located on the pND6 plasmid of Pseudomonas putida. Genes of the ortho pathway from associations consuming o-xylene and m-xylene were similar to chromosomal genes of P. putida. Genes of the meta pathway (C230) from associations consuming toluene and naphthalene were similar to corresponding genes formerly found in plasmids pWWO and pTOL.
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Taylor PM, Janssen PH. Variations in the abundance and identity of class II aromatic ring-hydroxylating dioxygenase genes in groundwater at an aromatic hydrocarbon-contaminated site. Environ Microbiol 2005; 7:140-6. [PMID: 15643944 DOI: 10.1111/j.1462-2920.2004.00679.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [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: 11/29/2022]
Abstract
The abundance of genes encoding aromatic ring-hydroxylating dioxygenases (RHDs) in the groundwater at an aromatic hydrocarbon-contaminated landfill near Sydney, Australia, was determined by quantitative DNA-DNA hybridization using class II RHD genes as probes. There were marked differences in hybridization signal intensity against DNA extracted from the groundwater at seven different locations across this heterogeneous site. This was interpreted as indicating variation in RHD gene abundance. Clone libraries of polymerase chain reaction (PCR)-amplified RHD gene fragments were constructed from DNA from each of the groundwater samples. The libraries from the samples with greater RHD gene abundance were dominated by a group of bacterial class II RHD genes, designated the S-cluster, that has yet to be found in cultured isolates. These groundwater samples contained no detectable petroleum hydrocarbons. A second group of class II RHD gene sequences, designated the T-cluster, dominated RHD gene clone libraries prepared from groundwater samples that contained detectable levels of total petroleum and aromatic hydrocarbons but lower RHD gene abundance. The hosts and in situ expression of these novel genes, and the substrates of the enzymes they encode, remain unknown. The scarcity of genes from known aromatic hydrocarbon-degrading bacteria and the numerical dominance of the novel genes suggest that the hosts of these novel genes may play an important role in aromatic hydrocarbon degradation at this site.
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Affiliation(s)
- Paul M Taylor
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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