1
|
Guo C, Qin L, Ma Y, Qin J. Integrated metabolomic and transcriptomic analyses of the parasitic plant Cuscuta japonica Choisy on host and non-host plants. BMC PLANT BIOLOGY 2022; 22:393. [PMID: 35934696 PMCID: PMC9358843 DOI: 10.1186/s12870-022-03773-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cuscuta japonica Choisy (Japanese dodder) is a parasitic weed that damages many plants and affects agricultural production. The haustorium of C. japonica plays a key role during parasitism in host plants; in contrast, some non-host plants effectively inhibit its formation. However, the metabolic differences between normal dodder in host plants and dodder inhibition in non-host plants are largely unknown. Here, we utilized an integrative analysis of transcriptomes and metabolomes to compare the differential regulatory mechanisms between C. japonica interacting with the host plant Ficus microcarpa and the non-host plant Mangifera indica. RESULTS After parasitization for 24 h and 72 h, the differentially abundant metabolites between these two treatments were enriched in pathways associated with α-linolenic acid metabolism, linoleic acid metabolism, phenylpropanoid biosynthesis, and pyrimidine metabolism. At the transcriptome level, the flavor biosynthesis pathway was significantly enriched at 24 h, whereas the plant-pathogen interaction, arginine and proline metabolism, and MARK signaling-plant pathways were significantly enriched at 72 h, based on the differentially expressed genes between these two treatments. Subsequent temporal analyses identified multiple genes and metabolites that showed different trends in dodder interactions between the host and non-host plants. In particular, the phenylpropanoid biosynthesis pathway showed significant differential regulation between C. japonica in host and non-host plants. CONCLUSIONS These results provide insights into the metabolic mechanisms of dodder-host interactions, which will facilitate future plant protection from C. japonica parasitism.
Collapse
Affiliation(s)
- Chenglin Guo
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science/ Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, 530007, China.
| | - Liuyan Qin
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Yongling Ma
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science/ Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, 530007, China
| | - Jianlin Qin
- Plant Protection Research Institute, Guangxi Academy of Agricultural Science/ Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Nanning, 530007, China
| |
Collapse
|
2
|
|
3
|
Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds. J CHEM-NY 2014. [DOI: 10.1155/2014/157974] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This review was conducted to provide an overview of dehalogenases involved in aerobic biodegradation of chlorinated aromatic compounds. Additionally, biochemical and molecular characterization of hydrolytic, reductive, and oxygenolytic dehalogenases was reviewed. This review will increase our understanding of the process of dehalogenation of chlorinated aromatic compounds.
Collapse
|
4
|
Xie D, Xu D, Zhang L, Guo H. Theoretical study of general base-catalyzed hydrolysis of aryl esters and implications for enzymatic reactions. J Phys Chem B 2007; 109:5259-66. [PMID: 16863192 DOI: 10.1021/jp0506181] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, the mechanism of general base-catalyzed hydrolysis of aryl esters is investigated in vacuo with density functional theory and in solutions with a polarized continuum model. The hydrolysis is found to proceed via a concerted mechanism featuring simultaneous addition and elimination steps accompanied by proton transfers, consistent with experimental evidence. Reasonable agreement with measured kinetic isotope effects provides additional validation. It is found that solvation substantially lowers the transition state energy, but has a small effect on the reaction exothermicity. An enzyme oxyanion hole, modeled by an ammonia molecule hydrogen bonded to the acyl carbonyl oxygen, is found to stabilize the near-tetrahedral transition state. Implications of these findings for the hydrolysis step of the dehalogenation reaction catalyzed by 4-chlorobenzoyl-CoA dehalogenase are discussed.
Collapse
Affiliation(s)
- Daiqian Xie
- Department of Chemistry, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | | | | | | |
Collapse
|
5
|
Zhou L, Poh RPC, Marks TS, Chowdhry BZ, Smith ARW. Structure and denaturation of 4-chlorobenzoyl coenzyme A dehalogenase from Arthrobacter sp. strain TM-1. Biodegradation 2007; 19:65-75. [PMID: 17431803 DOI: 10.1007/s10532-007-9115-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 03/09/2007] [Indexed: 11/27/2022]
Abstract
The secondary structure of the trimeric protein 4-chlorobenzoyl coenzyme A dehalogenase from Arthrobacter sp. strain TM-1, the second of three enzymes involved in the dechlorination of 4-chlorobenzoate to form 4-hydroxybenzoate, has been examined. E(mM) for the enzyme was 12.59. Analysis by circular dichroism spectrometry in the far uv indicated that 4-chlorobenzoyl coenzyme A dehalogenase was composed mostly of alpha-helix (56%) with lesser amounts of random coil (21%), beta-turn (13%) and beta-sheet (9%). These data are in close agreement with a computational prediction of secondary structure from the primary amino acid sequence, which indicated 55.8% alpha-helix, 33.7% random coil and 10.5% beta-sheet; the enzyme is, therefore, similar to the 4-chlorobenzoyl coenzyme A dehalogenase from Pseudomonas sp. CBS-3. The three-dimensional structure, including that of the presumed active site, predicted by computational analysis, is also closely similar to that of the Pseudomonas dehalogenase. Study of the stability and physicochemical properties revealed that at room temperature, the enzyme was stable for 24 h but was completely inactivated by heating to 60 degrees C for 5 min; thereafter by cooling at 1 degrees C min(-1) to 45 degrees C, 20.6% of the activity could be recovered. Mildly acidic (pH 5.2) or alkaline (pH 10.1) conditions caused complete inactivation, but activity was fully recovered on returning the enzyme to pH 7.4. Circular dichroism studies also indicated that secondary structure was little altered by heating to 60 degrees C, or by changing the pH from 7.4 to 6.0 or 9.2. Complete, irreversible destruction of, and maximal decrease in the fluorescence yield of the protein at 330-350 nm were brought about by 4.5 M urea or 1.1 M guanidinium chloride. Evidence was obtained to support the hypothetical three-dimensional model, that residues W140 and W167 are buried in a non-polar environment, whereas W182 appears at or close to the surface of the protein. At least one of the enzymes of the dehalogenase system (the combined 4-chlorobenzoate:CoA ligase, the dehalogenase and 4-hydroxybenzoyl coenzyme A thioesterase) appears to be capable of association with the cell membrane.
Collapse
Affiliation(s)
- Lihong Zhou
- Department of Life Science, School of Science, University of Greenwich, Medway Campus, Pembroke, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | | | | | | |
Collapse
|
6
|
Pieper DH. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 2004; 67:170-91. [PMID: 15614564 DOI: 10.1007/s00253-004-1810-4] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 10/10/2004] [Accepted: 10/19/2004] [Indexed: 10/26/2022]
Abstract
The microbial degradation of polychlorinated biphenyls (PCBs) has been extensively studied in recent years. The genetic organization of biphenyl catabolic genes has been elucidated in various groups of microorganisms, their structures have been analyzed with respect to their evolutionary relationships, and new information on mobile elements has become available. Key enzymes, specifically biphenyl 2,3-dioxygenases, have been intensively characterized, structure/sequence relationships have been determined and enzymes optimized for PCB transformation. However, due to the complex metabolic network responsible for PCB degradation, optimizing degradation by single bacterial species is necessarily limited. As PCBs are usually not mineralized by biphenyl-degrading organisms, and cometabolism can result in the formation of toxic metabolites, the degradation of chlorobenzoates has received special attention. A broad set of bacterial strategies to degrade chlorobenzoates has recently been elucidated, including new pathways for the degradation of chlorocatechols as central intermediates of various chloroaromatic catabolic pathways. To optimize PCB degradation in the environment beyond these metabolic limitations, enhancing degradation in the rhizosphere has been suggested, in addition to the application of surfactants to overcome bioavailability barriers. However, further research is necessary to understand the complex interactions between soil/sediment, pollutant, surfactant and microorganisms in different environments.
Collapse
Affiliation(s)
- Dietmar H Pieper
- Department of Environmental Microbiology, German Research Center for Biotechnology, Mascheroder Weg 1, 38124, Braunschweig, Germany.
| |
Collapse
|
7
|
Xu D, Wei Y, Wu J, Dunaway-Mariano D, Guo H, Cui Q, Gao J. QM/MM studies of the enzyme-catalyzed dechlorination of 4-chlorobenzoyl-CoA provide insight into reaction energetics. J Am Chem Soc 2004; 126:13649-58. [PMID: 15493922 DOI: 10.1021/ja0460211] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA catalyzed by 4-chlorobenzoyl-CoA dehalogenase is investigated using combined QM/MM approaches. The calculated potential of mean force at the PM3/CHARMM level supports the proposed nucleophilic aromatic substitution mechanism. In particular, a Meisenheimer intermediate was found, stabilized by hydrogen bonds between the benzoyl carbonyl of the ligand and two backbone amide NHs at positions 64 and 114. Mutation of Gly113 to Ala significantly increases the barrier by disrupting the hydrogen bond with the Gly114 backbone. The formation of the Meisenheimer complex is accompanied by significant charge redistribution and structural changes in the substrate benzoyl moiety, consistent with experimental observations. Theoretical results suggest that the reaction rate is limited by the formation of the Meisenheimer complex, rather than by its decomposition. A kinetic model based on the calculated free energy profile is found to be consistent with the experimental time course data.
Collapse
Affiliation(s)
- Dingguo Xu
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | | | | | | | | | | |
Collapse
|
8
|
Zaar A, Eisenreich W, Bacher A, Fuchs G. A novel pathway of aerobic benzoate catabolism in the bacteria Azoarcus evansii and Bacillus stearothermophilus. J Biol Chem 2001; 276:24997-5004. [PMID: 11306574 DOI: 10.1074/jbc.m100291200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aerobic catabolism of benzoate was studied in the Gram-negative proteobacterium Azoarcus evansii and in the Gram-positive bacterium Bacillus stearothermophilus. In contrast to earlier proposals, benzoate was not converted into hydroxybenzoate or gentisate. Rather, benzoyl-CoA was a product of benzoate catabolism in both microbial species under aerobic conditions in vivo. Benzoyl-CoA was converted into various CoA thioesters by cell extracts of both species in oxygen- and NADPH-dependent reactions. Using [ring-(13)C(6)]benzoyl-CoA as substrate, cis-3,4-[2,3,4,5,6-(13)C(5)]dehydroadipyl-CoA, trans-2,3-[2,3,4,5,6-(13)C(5)]dehydroadipyl-CoA, the 3,6-lactone of 3-[2,3,4,5,6-(13)C(5)]hydroxyadipyl-CoA, and 3-[2,3,4,5,6-(13)C(5)]hydroxyadipyl-CoA were identified as products by NMR spectroscopy. A protein mixture of A. evansii transformed [ring-(13)C(6)]benzoyl-CoA in an NADPH- and oxygen-dependent reaction into 6-[2,3,4,5,6-(13)C(5)]hydroxy-3-hexenoyl-CoA. The data suggest a novel aerobic pathway of benzoate catabolism via CoA intermediates leading to beta-ketoadipyl-CoA, an intermediate of the known beta-ketoadipate pathway.
Collapse
Affiliation(s)
- A Zaar
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | | | | | | |
Collapse
|
9
|
Zheng YJ, Bruice TC. On the Dehalogenation Mechanism of 4-Chlorobenzoyl CoA by 4-Chlorobenzoyl CoA Dehalogenase: Insights from Study Based on the Nonenzymatic Reaction. J Am Chem Soc 1997. [DOI: 10.1021/ja970114j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ya-Jun Zheng
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| | - Thomas C. Bruice
- Contribution from the Department of Chemistry, University of California at Santa Barbara, Santa Barbara, California 93106
| |
Collapse
|
10
|
Yang G, Liu RQ, Taylor KL, Xiang H, Price J, Dunaway-Mariano D. Identification of active site residues essential to 4-chlorobenzoyl-coenzyme A dehalogenase catalysis by chemical modification and site directed mutagenesis. Biochemistry 1996; 35:10879-85. [PMID: 8718880 DOI: 10.1021/bi9609533] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
4-Chlorobenzoyl-coenzyme A (4-CBA-CoA) dehalogenase catalyzes the hydrolysis of 4-CBA-CoA to 4-hydroxybenzoyl-coenzyme A (4-HBA-CoA) via a nucleophilic aromatic substitution pathway involving the participation of an active site carboxylate side chain in covalent catalysis. In this paper we report on the identification of conserved aspartate, histidine, and tryptophan residues essential to 4-CBA-CoA catalysis using chemical modification and site-directed mutagenesis techniques. Treatment of the dehalogenase with diethyl pyrocarbonate resulted in complete loss of catalytic activity (Kinact = 0.17 mM-1 min-1 at pH 6.5, 25 degrees C) that was fully regained by subsequent treatment with hydroxylamine. The protection from inactivation afforded by enzyme bound 4-HBA-CoA indicated that the essential histidine residues are located at the active site. Replacement of conserved histidine residues 81, 90, 94, and 208 with glutamine residues resulted in a significant loss of catalytic activity only in the cases of the histidine 81 and 90 mutants. Substrate and product ligand binding studies showed that binding is not significantly inhibited in these mutants. Site directed mutagenesis of a selection of conserved aspartate and glutamate residues, identified aspartate 145 as being essential to dehalogenase catalysis. Ligand binding studies showed that this residue is not required for tight substrate/product binding. Chemical modification of the dehalogenase with N-bromosuccinimide resulted in full loss of catalytic activity that was prevented by saturation of the active site with product ligand, providing evidence favoring an essential active site tryptophan. Phenylalanine replacement of conserved tryptophan residues 179 and 137 reduced catalytic activity only in the latter (Kcat = 0.03% of wild-type dehalogenase). On the basis of these results and the recently determined X-ray crystal structure of the complex of 4-CBA-CoA dehalogenase and 4-HBA-CoA [Benning, M. M., Taylor, K.L., Liu, R.-Q., Yang, G., Xiang, H., Wesenberg, G., Dunaway-Mariano, D., Holden, H.M. (1996) Biochemistry 35,8103-8109] we propose that aspartate 145 functions as the active site nucleophile, that tryptophan 137 serves as a hydrogen bond donor to the aspartate 145 C = O, and that histidine 90 serves to deprotonate the bound H2O molecule.
Collapse
Affiliation(s)
- G Yang
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA
| | | | | | | | | | | |
Collapse
|
11
|
Seibold B, Matthes M, Eppink MH, Lingens F, Van Berkel WJ, Müller R. 4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3. Purification, characterization, gene cloning, sequence analysis and assignment of structural features determining the coenzyme specificity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 239:469-78. [PMID: 8706756 DOI: 10.1111/j.1432-1033.1996.0469u.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 was purified by five consecutive steps to apparent homogeneity. The enrichment was 50-fold with a yield of about 20%. The enzyme is a homodimeric flavoprotein monooxygenase with each 44-kDa polypeptide chain containing one FAD molecule as a rather weakly bound prosthetic group. In contrast to other 4-hydroxybenzoate hydroxylases of known primary structure, the enzyme preferred NADH over NADPH as electron donor. The pH optimum for catalysis was pH 8.0 with a maximum turnover rate around 45 degrees C. Chloride ions were inhibitory, and competitive with respect to NADH. 4-Hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 has a narrow substrate specificity. In addition to the transformation of 4-hydroxybenzoate to 3,4-dihydroxybenzoate, the enzyme converted 2-fluoro-4-hydroxybenzoate, 2-chloro-4-hydroxybenzoate, and 2,4-dihydroxybenzoate. With all aromatic substrates, no uncoupling of hydroxylation was observed. The gene encoding 4-hydroxybenzoate hydroxylase from Pseudomonas sp. CBS3 was cloned in Escherichia coli. Nucleotide sequence analysis revealed an open reading frame of 1182 bp that corresponded to a protein of 394 amino acid residues. Upstream of the pobA gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli TG1. The deduced amino acid sequence of Pseudomonas sp. CBS3 4-hydroxybenzoate hydroxylase revealed 53% identity with that of the pobA enzyme from Pseudomonas fluorescens for which a three-dimensional structure is known. The active-site residues and the fingerprint sequences associated with FAD binding are strictly conserved. This and the conservation of secondary structures implies that the enzymes share a similar three-dimensional fold. Based on an isolated region of sequence divergence and site-directed mutagenesis data of 4-hydroxybenzoate hydroxylase from P. fluorescens, it is proposed that helix H2 is involved in determining the coenzyme specificity.
Collapse
Affiliation(s)
- B Seibold
- Institute of Microbiology, Hohenheim University, Stuttgart, Germany
| | | | | | | | | | | |
Collapse
|
12
|
Romanov V, Hausinger RP. NADPH-dependent reductive ortho dehalogenation of 2,4-dichlorobenzoic acid in Corynebacterium sepedonicum KZ-4 and Coryneform bacterium strainNTB-1 via 2,4-dichlorobenzoyl coenzyme A. J Bacteriol 1996; 178:2656-61. [PMID: 8626335 PMCID: PMC177992 DOI: 10.1128/jb.178.9.2656-2661.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Corynebacterium sepedonicum KZ-4, described earlier as a strain capable of growth on 2,4-dichlorobenzoate (G.M. Zaitsev and Y.N. Karasevich, Mikrobiologiya 54:356-369, 1985), is known to metabolize this substrate via 4-hydroxybenzoate and protocatechuate, and evidence consistent with an initial reductive dechlorination step to form 4-chlorobenzoate was found in another coryneform bacterium, strain NTB-1 (W.J.J. van den Tweel, J.B. Kok, and J.A.M. de Bont, Appl. Environ. Microbiol. 53:810-815, 1987). 2-Chloro-4-fluorobenzoate was found to be converted stoichiometrically to 4-fluorobenzoate by resting cells of strain KZ-4, compatible with a reductive process. Experiments with cell extracts demonstrated that Mg - ATP and coenzyme A (CoA) were required to stimulate reductive dehalogenation, consistent with the intermediacy of 2-chloro-4-fluoro-benzoyl-CoA and 2,4-dichlorobenzoyl-CoA thioesters. 2,4-Dichlorobenzoyl-CoA was shown to be converted to 4-chlorobenzoyl-CoA in a novel NADPH-dependent reaction in extracts of both KZ-4 and NTB-1. In addition to the ligase and reductive dehalogenase activities, hydrolytic 4-chlorobenzoyl-CoA dehalogenase and thioesterase activities, 4-hydroxybenzoate 3-monooxygenase, and protocatechuate 3,4-dioxygenase activities were demonstrated to be present in the soluble fraction of KZ-4 extracts following ultracentrifugation. We propose that the pathway for 2,4-dichlorobenzoate catabolism in strains KZ-4 and NTB-1 involves formation of 2,4-dichlorobenzoyl-CoA, NADPH-dependent ortho dehalogenation yielding 4-chlorobenzoyl-CoA, hydrolytic removal of chlorine from the para position to generate 4-hydroxybenzoyl-CoA, hydrolysis to form 4-hydroxybenzoate, oxidation to yield protocatechuate, and oxidative ring cleavage.
Collapse
Affiliation(s)
- V Romanov
- Center for Microbial Ecology, Michigan State University, East Lansing 48824, USA
| | | |
Collapse
|