1
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DeWeese DE, Everett MP, Babicz JT, Daruwalla A, Solomon EI, Kiser PD. Spectroscopy and crystallography define carotenoid oxygenases as a new subclass of mononuclear non-heme Fe II enzymes. J Biol Chem 2025; 301:108444. [PMID: 40147775 PMCID: PMC12051055 DOI: 10.1016/j.jbc.2025.108444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Revised: 03/14/2025] [Accepted: 03/20/2025] [Indexed: 03/29/2025] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) are non-heme FeII enzymes that catalyze the oxidative cleavage of alkene bonds in carotenoids, stilbenoids, and related compounds. How these enzymes control the reaction of dioxygen (O2) with their alkene substrates is unclear. Here, we apply spectroscopy in conjunction with X-ray crystallography to define the iron coordination geometry of a model CCD, CAO1 (Neurospora crassa carotenoid oxygenase 1), in its resting state and following substrate binding and coordination sphere substitutions. Resting CAO1 exhibits a five-coordinate (5C), square pyramidal FeII center that undergoes steric distortion toward a trigonal bipyramidal geometry in the presence of piceatannol. Titrations with the O2-analog, nitric oxide, show a >100-fold increase in iron-nitric oxide affinity upon substrate binding, defining a crucial role for the substrate in activating the FeII site for O2 reactivity. The importance of the 5C FeII structure for reactivity was probed through mutagenesis of the second-sphere Thr151 residue of CAO1, which occludes ligand binding at the sixth coordination position. A T151G substitution resulted in the conversion of the iron center to a six-coordinate state and a 135-fold reduction in apparent catalytic efficiency toward piceatannol compared with the wildtype enzyme. Substrate complexation resulted in partial six-coordinate to 5C conversion, indicating solvent dissociation from the iron center. Additional substitutions at this site demonstrated a general functional importance of the occluding residue within the CCD superfamily. Taken together, these data suggest an ordered mechanism of CCD catalysis occurring via substrate-promoted solvent replacement by O2. CCDs thus represent a new class of mononuclear non-heme FeII enzymes.
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Affiliation(s)
- Dory E DeWeese
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Michael P Everett
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, California, USA
| | - Jeffrey T Babicz
- Department of Chemistry, Stanford University, Stanford, California, USA; SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA
| | - Anahita Daruwalla
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, California, USA
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California, USA; SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California, USA.
| | - Philip D Kiser
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, California, USA; Research Service, VA Long Beach Healthcare System, Long Beach, California, USA.
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2
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Wang J, Ouyang X, Meng S, Li J, Liu L, Li C, Li H, Zheng H, Liao C, Zhao YL, Ni J. Semi-rational design of an aromatic dioxygenase by substrate tunnel redirection. iScience 2025; 28:111570. [PMID: 39811656 PMCID: PMC11731282 DOI: 10.1016/j.isci.2024.111570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 11/08/2024] [Accepted: 12/06/2024] [Indexed: 01/16/2025] Open
Abstract
Lignin valorization is crucial for achieving economic and sustainable biorefinery processes. However, the enzyme substrate preferences involved in lignin degradation remain poorly understood, and low activity toward specific substrates presents a significant challenge to the efficient utilization of lignin. In this study, we investigated the substrate promiscuity of ThAdo, a key enzyme involved in lignin valorization. Pre-reaction state analysis revealed that a hydrogen bond network is critical in determining substrate selectivity. By performing targeted saturation mutagenesis on residues surrounding the substrate tunnels, we identified the Y205W and Y205Q mutants, which demonstrated 0.73-fold and 0.72-fold enhancements in activity, respectively. Structural analysis indicated that the redirection of the original substrate tunnel may be responsible for the improved activity. Our study provides essential insights into the substrate preference mechanisms of lignin degrading enzymes and suggests that this tunnel-redirection strategy can be extended to other promiscuous enzymes.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xingyu Ouyang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyu Meng
- Innovation Center for Synthetic Biotechnology, Lumy Biotechnology, Changzhou 213200, Jiangsu, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liangxu Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chaofeng Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hengrun Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haotian Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Liao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jun Ni
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- Innovation Center for Synthetic Biotechnology, Lumy Biotechnology, Changzhou 213200, Jiangsu, China
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3
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Tian Q, Han W, Zhou S, Yang L, Wang D, Zhou W, Wang Z. Carotenoid Cleavage Dioxygenase Gene CCD4 Enhances Tanshinone Accumulation and Drought Resistance in Salvia miltiorrhiza. Int J Mol Sci 2024; 25:13223. [PMID: 39684932 DOI: 10.3390/ijms252313223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Revised: 12/02/2024] [Accepted: 12/04/2024] [Indexed: 12/18/2024] Open
Abstract
Danshen (Salvia miltiorrhiza Bunge) is a perennial herbaceous plant of the Salvia genus in the family Lamiaceae. Its dry root is one of the important traditional Chinese herbal medicines with a long officinal history. The yield and quality of S. miltiorrhiza are influenced by various factors, among which drought is one of the most significant types of abiotic stress. Based on the transcriptome database of S. miltiorrhiza, our research group discovered a carotenoid cleavage dioxygenase gene, SmCCD4, belonging to the carotenoid cleavage oxygenase (CCO) gene family which is highly responsive to drought stress on the basis of our preceding work. Here, we identified 26 CCO genes according to the whole-genome database of S. miltiorrhiza. The expression pattern of SmCCD4 showed that this gene is strongly overexpressed in the aboveground tissue of S. miltiorrhiza. And by constructing SmCCD4 overexpression strains, it was shown that the overexpression of SmCCD4 not only promotes the synthesis of abscisic acid and increases plant antioxidant activity but also regulates the synthesis of the secondary metabolites tanshinone and phenolic acids in S. miltiorrhiza. In summary, this study is the first in-depth and systematic identification and investigation of the CCO gene family in S. miltiorrhiza. The results provide useful information for further systematic research on the function of CCO genes and provide a theoretical basis for improving the yield and quality of S. miltiorrhiza.
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Affiliation(s)
- Qian Tian
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Wei Han
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Shuai Zhou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Liu Yang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Donghao Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Wen Zhou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
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Morote L, Rubio-Moraga Á, López Jiménez AJ, Aragonés V, Diretto G, Demurtas OC, Frusciante S, Ahrazem O, Daròs JA, Gómez-Gómez L. Verbascum species as a new source of saffron apocarotenoids and molecular tools for the biotechnological production of crocins and picrocrocin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:58-72. [PMID: 38100533 DOI: 10.1111/tpj.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Crocins are glucosylated apocarotenoids present in flowers and fruits of a few plant species, including saffron, gardenia, and Buddleja. The biosynthesis of crocins in these plants has been unraveled, and the enzymes engineered for the production of crocins in heterologous systems. Mullein (Verbascum sp.) has been identified as a new source of crocins and picrocrocin. In this work, we have identified eight enzymes involved in the cleavage of carotenoids in two Verbascum species, V. giganteum and V. sinuatum. Four of them were homologous to the previously identified BdCCD4.1 and BdCCD4.3 from Buddleja, involved in the biosynthesis of crocins. These enzymes were analyzed for apocarotenogenic activity in bacteria and Nicotiana benthamiana plants using a virus-driven system. Metabolic analyses of bacterial extracts and N. benthamiana leaves showed the efficient activity of these enzymes to produce crocins using β-carotene and zeaxanthin as substrates. Accumulations of 0.17% of crocins in N. benthamiana dry leaves were reached in only 2 weeks using a recombinant virus expressing VgCCD4.1, similar to the amounts previously produced using the canonical saffron CsCCD2L. The identification of these enzymes, which display a particularly broad substrate spectrum, opens new avenues for apocarotenoid biotechnological production.
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Affiliation(s)
- Lucía Morote
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
| | - Ángela Rubio-Moraga
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
| | - Alberto José López Jiménez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022, Valencia, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123, Rome, Italy
| | - Olivia Costantina Demurtas
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123, Rome, Italy
| | - Sarah Frusciante
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123, Rome, Italy
| | - Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022, Valencia, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
- Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071, Albacete, Spain
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5
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Li F, Gong X, Liang Y, Peng L, Han X, Wen M. Characteristics of a new carotenoid cleavage dioxygenase NtCCD10 derived from Nicotiana tabacum. PLANTA 2022; 256:100. [PMID: 36251100 DOI: 10.1007/s00425-022-04013-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
A new carotenoid cleavage dioxygenase NtCCD10 from tobacco was characterized. There is some difference between NtCCD10 and CCD1 in structure. NtCCD10 can cleave the C5-C6 (C5'-C6') and C9-C10 (C9'-C10') double bonds of carotenoids and has high catalytic activity. Carotenoid cleavage dioxygenases (CCDs) cleave carotenoids to produce a variety of apocarotenoids, which have important biological functions for organisms in nature. There are eleven CCDs subfamilies in the plant kingdom, many of which have been extensively characterized in their functions. However, as a newly classified subfamily, the function of CCD10 has rarely been studied. In this work, the function of an NtCCD10 gene from dicotyledonous Nicotiana tabacum was cloned and characterized, and its phylogeny, molecular structural modeling and protein structure were also systematically analyzed. Like other CCDs, NtCCD10 also possesses a seven bladed β-propeller with Fe2+ cofactor in its center constituting the active site of the enzyme. The Fe2+ is also coordinated bonding with four conserved histidine residues. Meanwhile, NtCCD10 also has many unique features, such as its α1 and α3 helixes are not anti-parallel, a special β-sheet and a longer access tunnel for substrates. When expressed in engineered Escherichia coli (producing phytoene, lycopene, β-carotene, and zeaxanthin) and Saccharomyces cerevisiae (producing β-carotene), NtCCD10 could symmetrically cleave phytoene and β-carotene at the C9-C10 and C9'-C10' positions to produce geranylacetone and β-ionone, respectively. In addition, NtCCD10 could also cleave the C5-C6 and C5'-C6' double bonds of lycopene to generate 6-methyl-5-heptene-2-one (MHO). NtCCD10 has higher catalytic activity than PhCCD1 in yeast, which provides a good candidate CCD for biosynthesis of β-ionone and has potential applications in biotechnological industry. This study identified the taxonomic position and catalytic activity of the first NtCCD10 in dicotyledonous plants. This will provide a reference for the discovery and functional identification of CCD10 enzymes in dicotyledons.
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Affiliation(s)
- Fan Li
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, China
| | - Xiaowei Gong
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, China
- R & D Center of China Tobacco Yunnan Industrial Co., Ltd, Kunming, 650231, Yunnan, China
| | - Yupeng Liang
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lijuan Peng
- Yunnan Tobacco Quality Supervision and Test Station, Kunming, 650106, Yunnan, China
| | - Xiulin Han
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, China.
| | - Mengliang Wen
- National Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, Yunnan, China.
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6
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Abstract
Carotenoid cleavage dioxygenases (CCDs) constitute a superfamily of enzymes that are found in all domains of life where they play key roles in the metabolism of carotenoids and apocarotenoids as well as certain phenylpropanoids such as resveratrol. Interest in these enzymes stems not only from their biological importance but also from their remarkable catalytic properties including their regioselectivity, their ability to accommodate diverse substrates, and the additional activities (e.g., isomerase) that some of these enzyme possess. X-ray crystallography is a key experimental approach that has allowed detailed investigation into the structural basis behind the interesting biochemical features of these enzymes. Here, we describe approaches used by our lab that have proven successful in generating single crystals of these enzymes in resting or ligand-bound states for high-resolution X-ray diffraction analysis.
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Affiliation(s)
- Anahita Daruwalla
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, United States
| | - Xuewu Sui
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, United States; Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Philip D Kiser
- Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, United States; Department of Ophthalmology, Center for Translational Vision Research, University of California, Irvine School of Medicine, Irvine, CA, United States; Research Service, VA Long Beach Healthcare System, Long Beach, CA, United States.
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7
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Long Z, Zhao Y, Xue Y, Wang M, Li J, Su Z, Sun J, Liu Q, Liu H, Mao D, Wei T. A novel thermophilic β-carotene 15,15'-monooxygenase with broad substrate specificity from the marine bacterium Candidatus Pelagibacter sp. HTCC7211. Biotechnol Lett 2021; 43:2233-2241. [PMID: 34618272 DOI: 10.1007/s10529-021-03188-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/13/2021] [Indexed: 10/20/2022]
Abstract
To characterize a novel thermophilic β-carotene 15,15'-monooxygenase BCMO7211 isolated from the marine bacterium Candidatus Pelagibacter sp. HTCC7211. BCMO7211 was functionally overexpressed in Escherichia coli and purified to homogeneity by Ni-NTA affinity chromatography and Superdex-200 gel filtration chromatography. Labeling experiments with H218O demonstrated that the oxygen atom in the terminal aldehyde group of the produced retinal molecules was provided from both molecular oxygen and water, indicating that BCMO7211 is the first characterized bacterial β-carotene 15,15'-monooxygenase. BCMO7211 exhibited broad carotenoid substrate specificity toward α-carotene, β-cryptoxanthin, β-carotene, zeaxanthin, and lutein. The optimum temperature, pH, and concentrations of the substrate and enzyme for retinal production were 60 °C, 9.0, 500 mg β-carotene/L, and 2.5 U/ml, respectively. Under optimum conditions, 888.3 mg/L retinal was produced in 60 min with a conversion rate of 89.0% (w/w). BCMO7211 is a potential candidate for the enzymatic synthesis of retinal in biotechnological applications.
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Affiliation(s)
- Zhangde Long
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China.,School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China
| | - Yuzhe Zhao
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China
| | - Yun Xue
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China.,School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China
| | - Min Wang
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China
| | - Jigang Li
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China
| | - Zan Su
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China
| | - Jiansheng Sun
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China
| | - Qibin Liu
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China
| | - Hong Liu
- China Tobacco Guangxi Industrial Co., Ltd., Nanning, 530001, China
| | - Duobin Mao
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China
| | - Tao Wei
- School of Food and Biological Engineering, Zhengzhou University of Light Industry, 5 Dongfeng Rd, Zhengzhou, 450002, China.
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8
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Liang N, Yao MD, Wang Y, Liu J, Feng L, Wang ZM, Li XY, Xiao WH, Yuan YJ. CsCCD2 Access Tunnel Design for a Broader Substrate Profile in Crocetin Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11626-11636. [PMID: 34554747 DOI: 10.1021/acs.jafc.1c04588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Crocetin, a high-value apocarotenoid in saffron, is widely applied to the fields of food and medicine. However, the existing method of obtaining crocetin through large-scale cultivation is far from meeting the market demand. Microbial synthesis of crocetin is a potential alternative to traditional resources, and it is found that carotenoid cleavage dioxygenase (CCD) is the critical enzyme to synthesize crocetin. So, in this study, we used "hybrid-tunnel" engineering to obtain variants of Crocus sativus-derived CsCCD2, essential for zeaxanthin conversion into crocetin, with a broader substrate specificity and higher catalytic efficiency. Variants including S323A, with a lower charge bias and a larger tunnel size than the wild-type, showed a 5-fold higher crocetin titer in yeast-based fermentations. S323A could also convert the β-carotene substrate to crocetin dialdehyde and exhibited a 12.83-fold greater catalytic efficiency (kcat/Km) toward zeaxanthin than the wild-type in vitro. This strategy enabled the production of 107 mg/L crocetin in 5 L fed-batch fermentation, higher than that previously reported. Our findings demonstrate that engineering access tunnels to expand the substrate profile by in silico protein design represents a viable strategy to refine the catalytic properties of enzymes across a range of applications.
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Affiliation(s)
- Nan Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Ming-Dong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lu Feng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Xiang-Yu Li
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan 436070, China
| | - Wen-Hai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen 518071, China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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9
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Kiser PD. Retinal pigment epithelium 65 kDa protein (RPE65): An update. Prog Retin Eye Res 2021; 88:101013. [PMID: 34607013 PMCID: PMC8975950 DOI: 10.1016/j.preteyeres.2021.101013] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Vertebrate vision critically depends on an 11-cis-retinoid renewal system known as the visual cycle. At the heart of this metabolic pathway is an enzyme known as retinal pigment epithelium 65 kDa protein (RPE65), which catalyzes an unusual, possibly biochemically unique, reaction consisting of a coupled all-trans-retinyl ester hydrolysis and alkene geometric isomerization to produce 11-cis-retinol. Early work on this isomerohydrolase demonstrated its membership to the carotenoid cleavage dioxygenase superfamily and its essentiality for 11-cis-retinal production in the vertebrate retina. Three independent studies published in 2005 established RPE65 as the actual isomerohydrolase instead of a retinoid-binding protein as previously believed. Since the last devoted review of RPE65 enzymology appeared in this journal, major advances have been made in a number of areas including our understanding of the mechanistic details of RPE65 isomerohydrolase activity, its phylogenetic origins, the relationship of its membrane binding affinity to its catalytic activity, its role in visual chromophore production for rods and cones, its modulation by macromolecules and small molecules, and the involvement of RPE65 mutations in the development of retinal diseases. In this article, I will review these areas of progress with the goal of integrating results from the varied experimental approaches to provide a comprehensive picture of RPE65 biochemistry. Key outstanding questions that may prove to be fruitful future research pursuits will also be highlighted.
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Affiliation(s)
- Philip D Kiser
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, 90822, USA; Department of Physiology & Biophysics, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA; Department of Ophthalmology and Center for Translational Vision Research, Gavin Herbert Eye Institute, University of California, Irvine School of Medicine, Irvine, CA, 92697, USA.
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10
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Yu S, Tian L. Assessing the Role of Carotenoid Cleavage Dioxygenase 4 Homoeologs in Carotenoid Accumulation and Plant Growth in Tetraploid Wheat. Front Nutr 2021; 8:740286. [PMID: 34568408 PMCID: PMC8455956 DOI: 10.3389/fnut.2021.740286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
The dietary needs of humans for provitamin A carotenoids arise from their inability to synthesize vitamin A de novo. To improve the status of this essential micronutrient, special attention has been given to biofortification of staple foods, such as wheat grains, which are consumed in large quantities but contain low levels of provitamin A carotenoids. However, there remains an unclear contribution of metabolic genes and homoeologs to the turnover of carotenoids in wheat grains. To better understand carotenoid catabolism in tetraploid wheat, Targeting Induced Local Lesions in Genomes (TILLING) mutants of CCD4, encoding a Carotenoid Cleavage Dioxygenase (CCD) that cleaves carotenoids into smaller apocarotenoid molecules, were isolated and characterized. Our analysis showed that ccd4 mutations co-segregated with Poltergeist-like (pll) mutations in the TILLING mutants of A and B subgenomes, hence the ccd-A4 pll-A, ccd-B4 pll-B, and ccd-A4 ccd-B4 pll-A pll-B mutants were analyzed in this study. Carotenoid profiles are comparable in mature grains of the mutant and control plants, indicating that CCD4 homoeologs do not have a major impact on carotenoid accumulation in grains. However, the neoxanthin content was increased in leaves of ccd-A4 ccd-B4 pll-A pll-B relative to the control. In addition, four unidentified carotenoids showed a unique presence in leaves of ccd-A4 ccd-B4 pll-A pll-B plants. These results suggested that CCD4 homoeologs may contribute to the turnover of neoxanthin and the unidentified carotenoids in leaves. Interestingly, abnormal spike, grain, and seminal root phenotypes were also observed for ccd-A4 pll-A, ccd-B4 pll-B, and ccd-A4 ccd-B4 pll-A pll-B plants, suggesting that CCD4 and/or PLL homoeologs could function toward these traits. Overall, this study not only reveals the role of CCD4 in cleavage of carotenoids in leaves and grains, but also uncovers several critical growth traits that are controlled by CCD4, PLL, or the CCD4-PLL interaction.
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Affiliation(s)
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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11
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Kuatsjah E, Chan ACK, Katahira R, Haugen SJ, Beckham GT, Murphy MEP, Eltis LD. Structural and functional analysis of lignostilbene dioxygenases from Sphingobium sp. SYK-6. J Biol Chem 2021; 296:100758. [PMID: 33965373 PMCID: PMC8191317 DOI: 10.1016/j.jbc.2021.100758] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 11/27/2022] Open
Abstract
Lignostilbene-α,β-dioxygenases (LSDs) are iron-dependent oxygenases involved in the catabolism of lignin-derived stilbenes. Sphingobium sp. SYK-6 contains eight LSD homologs with undetermined physiological roles. To investigate which homologs are involved in the catabolism of dehydrodiconiferyl alcohol (DCA), derived from β-5 linked lignin subunits, we heterologously produced the enzymes and screened their activities in lysates. The seven soluble enzymes all cleaved lignostilbene, but only LSD2, LSD3, and LSD4 exhibited high specific activity for 3-(4-hydroxy-3-(4-hydroxy-3-methoxystyryl)-5-methoxyphenyl) acrylate (DCA-S) relative to lignostilbene. LSD4 catalyzed the cleavage of DCA-S to 5-formylferulate and vanillin and cleaved lignostilbene and DCA-S (∼106 M−1 s−1) with tenfold greater specificity than pterostilbene and resveratrol. X-ray crystal structures of native LSD4 and the catalytically inactive cobalt-substituted Co-LSD4 at 1.45 Å resolution revealed the same fold, metal ion coordination, and edge-to-edge dimeric structure as observed in related enzymes. Key catalytic residues, Phe-59, Tyr-101, and Lys-134, were also conserved. Structures of Co-LSD4·vanillin, Co-LSD4·lignostilbene, and Co-LSD4·DCA-S complexes revealed that Ser-283 forms a hydrogen bond with the hydroxyl group of the ferulyl portion of DCA-S. This residue is conserved in LSD2 and LSD4 but is alanine in LSD3. Substitution of Ser-283 with Ala minimally affected the specificity of LSD4 for either lignostilbene or DCA-S. By contrast, substitution with phenylalanine, as occurs in LSD5 and LSD6, reduced the specificity of the enzyme for both substrates by an order of magnitude. This study expands our understanding of an LSD critical to DCA catabolism as well as the physiological roles of other LSDs and their determinants of substrate specificity.
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Affiliation(s)
- Eugene Kuatsjah
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge Tennessee, USA
| | - Anson C K Chan
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Rui Katahira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Stefan J Haugen
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge Tennessee, USA
| | - Michael E P Murphy
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada
| | - Lindsay D Eltis
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, Canada; BioProducts Institute, The University of British Columbia, Vancouver, Canada.
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12
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Gao J, Yang S, Tang K, Li G, Gao X, Liu B, Wang S, Feng X. GmCCD4 controls carotenoid content in soybeans. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:801-813. [PMID: 33131209 PMCID: PMC8051601 DOI: 10.1111/pbi.13506] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 10/06/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
To better understand the mechanisms regulating plant carotenoid metabolism in staple crop, we report the map-based cloning and functional characterization of the Glycine max carotenoid cleavage dioxygenase 4 (GmCCD4) gene, which encodes a carotenoid cleavage dioxygenase enzyme involved in metabolizing carotenoids into volatile β-ionone. Loss of GmCCD4 protein function in four Glycine max increased carotenoid content (gmicc) mutants resulted in yellow flowers due to excessive accumulation of carotenoids in flower petals. The carotenoid contents also increase three times in gmicc1 seeds. A genome-wide association study indicated that the GmCCD4 locus was one major locus associated with carotenoid content in natural population. Further analysis indicated that the haplotype-1 of GmCCD4 gene was positively associated with higher carotenoid levels in soybean cultivars and accumulated more β-carotene in engineered E. coli with ectopic expression of different GmCCD4 haplotypes. These observations uncovered that GmCCD4 was a negative regulator of carotenoid content in soybean, and its various haplotypes provide useful resources for future soybean breeding practice.
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Affiliation(s)
- Jinshan Gao
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Guang Li
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE)Northeast Normal UniversityChangchunChina
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE)Northeast Normal UniversityChangchunChina
| | - Shaodong Wang
- Key Laboratory of Soybean Biology of Education MinistryNortheast Agricultural UniversityHarbinChina
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design BreedingNortheast Institute of Geography and AgroecologyChinese Academy of SciencesChangchunChina
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13
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Dhar MK, Mishra S, Bhat A, Chib S, Kaul S. Plant carotenoid cleavage oxygenases: structure-function relationships and role in development and metabolism. Brief Funct Genomics 2020; 19:1-9. [PMID: 31875900 DOI: 10.1093/bfgp/elz037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of 'carotenoids and apocarotenoids' is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide representation among organisms. Their biosynthesis occurs by oxidative cleavage of carotenoids, a high-value reaction, mediated by carotenoid cleavage oxygenases or carotenoid cleavage dioxygenases (CCDs)-a family of non-heme iron enzymes. Structurally, this protein family displays wide diversity but is limited in its distribution among plants. Functionally, this protein family has been recognized to offer a role in phytohormones, volatiles and signal production. Further, their wide presence and clade-specific functional disparity demands a comprehensive account. This review focuses on the critical assessment of CCDs of higher plants, describing recent progress in their functional aspects and regulatory mechanisms, domain architecture, classification and localization. The work also highlights the relevant discussion for further exploration of this multi-prospective protein family for the betterment of its functional understanding and improvement of crops.
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Affiliation(s)
- Manoj Kumar Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sonal Mishra
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Archana Bhat
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sudha Chib
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu 180006, India
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14
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Song T, Wu N, Wang C, Wang Y, Chai F, Ding M, Li X, Yao M, Xiao W, Yuan Y. Crocetin Overproduction in Engineered Saccharomyces cerevisiae via Tuning Key Enzymes Coupled With Precursor Engineering. Front Bioeng Biotechnol 2020; 8:578005. [PMID: 33015027 PMCID: PMC7500066 DOI: 10.3389/fbioe.2020.578005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022] Open
Abstract
Crocetin, an important natural carotenoid dicarboxylic acid with high pharmaceutical values, has been successfully generated from glucose by engineered Saccharomyces cerevisiae in our previous study. Here, a systematic optimization was executed for crocetin overproduction in yeast. The effects of precursor enhancement on crocetin production were investigated by blocking the genes involved in glyoxylate cycle [citric acid synthase (CIT2) and malic acid synthase (MLS1)]. Crocetin titer was promoted by 50% by ΔCIT2 compared to that of the starting strain. Then, the crocetin production was further increased by 44% through introducing the forward fusion enzymes of PsCrtZ (CrtZ from Pantoea stewartii)-CsCCD2 (CCD2 from Crocus sativus). Consequently, the crocetin titer reached to 1.95 ± 0.23 mg/L by overexpression of PsCrtZ-CsCCD2 followed by medium optimization. Eventually, a titer of 12.43 ± 0.62 mg/L crocetin was achieved in 5-L bioreactor, which is the highest crocetin titer reported in micro-organisms.
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Affiliation(s)
- Tianqing Song
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Nan Wu
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Chen Wang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Fenghua Chai
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Xia Li
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, China
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15
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Structural basis for carotenoid cleavage by an archaeal carotenoid dioxygenase. Proc Natl Acad Sci U S A 2020; 117:19914-19925. [PMID: 32747548 DOI: 10.1073/pnas.2004116117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Apocarotenoids are important signaling molecules generated from carotenoids through the action of carotenoid cleavage dioxygenases (CCDs). These enzymes have a remarkable ability to cleave carotenoids at specific alkene bonds while leaving chemically similar sites within the polyene intact. Although several bacterial and eukaryotic CCDs have been characterized, the long-standing goal of experimentally visualizing a CCD-carotenoid complex at high resolution to explain this exquisite regioselectivity remains unfulfilled. CCD genes are also present in some archaeal genomes, but the encoded enzymes remain uninvestigated. Here, we address this knowledge gap through analysis of a metazoan-like archaeal CCD from Candidatus Nitrosotalea devanaterra (NdCCD). NdCCD was active toward β-apocarotenoids but did not cleave bicyclic carotenoids. It exhibited an unusual regiospecificity, cleaving apocarotenoids solely at the C14'-C13' alkene bond to produce β-apo-14'-carotenals. The structure of NdCCD revealed a tapered active site cavity markedly different from the broad active site observed for the retinal-forming Synechocystis apocarotenoid oxygenase (SynACO) but similar to the vertebrate retinoid isomerase RPE65. The structure of NdCCD in complex with its apocarotenoid product demonstrated that the site of cleavage is defined by interactions along the substrate binding cleft as well as selective stabilization of reaction intermediates at the scissile alkene. These data on the molecular basis of CCD catalysis shed light on the origins of the varied catalytic activities found in metazoan CCDs, opening the possibility of modifying their activity through rational chemical or genetic approaches.
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16
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von Lintig J, Moon J, Babino D. Molecular components affecting ocular carotenoid and retinoid homeostasis. Prog Retin Eye Res 2020; 80:100864. [PMID: 32339666 DOI: 10.1016/j.preteyeres.2020.100864] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 12/15/2022]
Abstract
The photochemistry of vision employs opsins and geometric isomerization of their covalently bound retinylidine chromophores. In different animal classes, these light receptors associate with distinct G proteins that either hyperpolarize or depolarize photoreceptor membranes. Vertebrates also use the acidic form of chromophore, retinoic acid, as the ligand of nuclear hormone receptors that orchestrate eye development. To establish and sustain these processes, animals must acquire carotenoids from the diet, transport them, and metabolize them to chromophore and retinoic acid. The understanding of carotenoid metabolism, however, lagged behind our knowledge about the biology of their receptor molecules. In the past decades, much progress has been made in identifying the genes encoding proteins that mediate the transport and enzymatic transformations of carotenoids and their retinoid metabolites. Comparative analysis in different animal classes revealed how evolutionary tinkering with a limited number of genes evolved different biochemical strategies to supply photoreceptors with chromophore. Mutations in these genes impair carotenoid metabolism and induce various ocular pathologies. This review summarizes this advancement and introduces the involved proteins, including the homeostatic regulation of their activities.
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Affiliation(s)
- Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Jean Moon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Darwin Babino
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, USA
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17
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Daruwalla A, Kiser PD. Structural and mechanistic aspects of carotenoid cleavage dioxygenases (CCDs). Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158590. [PMID: 31874225 DOI: 10.1016/j.bbalip.2019.158590] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/03/2023]
Abstract
Carotenoid cleavage dioxygenases (CCDs) comprise a superfamily of mononuclear non-heme iron proteins that catalyze the oxygenolytic fission of alkene bonds in carotenoids to generate apocarotenoid products. Some of these enzymes exhibit additional activities such as carbon skeleton rearrangement and trans-cis isomerization. The group also includes a subfamily of enzymes that split the interphenyl alkene bond in molecules such as resveratrol and lignostilbene. CCDs are involved in numerous biological processes ranging from production of light-sensing chromophores to degradation of lignin derivatives in pulping waste sludge. These enzymes exhibit unique features that distinguish them from other families of non-heme iron enzymes. The distinctive properties and biological importance of CCDs have stimulated interest in their modes of catalysis. Recent structural, spectroscopic, and computational studies have helped clarify mechanistic aspects of CCD catalysis. Here, we review these findings emphasizing common and unique properties of CCDs that enable their variable substrate specificity and regioselectivity. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Anahita Daruwalla
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, United States of America; Department of Physiology & Biophysics, University of California, Irvine, CA 92697, United States of America
| | - Philip D Kiser
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697, United States of America; Research Service, VA Long Beach Healthcare System, Long Beach, CA 90822, United States of America.
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18
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Kuatsjah E, Verstraete MM, Kobylarz MJ, Liu AKN, Murphy MEP, Eltis LD. Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase. J Biol Chem 2019; 294:12911-12920. [PMID: 31292192 DOI: 10.1074/jbc.ra119.009428] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/03/2019] [Indexed: 01/21/2023] Open
Abstract
Lignostilbene-α,β-dioxygenase A (LsdA) from the bacterium Sphingomonas paucimobilis TMY1009 is a nonheme iron oxygenase that catalyzes the cleavage of lignostilbene, a compound arising in lignin transformation, to two vanillin molecules. To examine LsdA's substrate specificity, we heterologously produced the dimeric enzyme with the help of chaperones. When tested on several substituted stilbenes, LsdA exhibited the greatest specificity for lignostilbene (k cat app = 1.00 ± 0.04 × 106 m-1 s-1). These experiments further indicated that the substrate's 4-hydroxy moiety is required for catalysis and that this moiety cannot be replaced with a methoxy group. Phenylazophenol inhibited the LsdA-catalyzed cleavage of lignostilbene in a reversible, mixed fashion (Kic = 6 ± 1 μm, Kiu = 24 ± 4 μm). An X-ray crystal structure of LsdA at 2.3 Å resolution revealed a seven-bladed β-propeller fold with an iron cofactor coordinated by four histidines, in agreement with previous observations on related carotenoid cleavage oxygenases. We noted that residues at the dimer interface are also present in LsdB, another lignostilbene dioxygenase in S. paucimobilis TMY1009, rationalizing LsdA and LsdB homo- and heterodimerization in vivo A structure of an LsdA·phenylazophenol complex identified Phe59, Tyr101, and Lys134 as contacting the 4-hydroxyphenyl moiety of the inhibitor. Phe59 and Tyr101 substitutions with His and Phe, respectively, reduced LsdA activity (k cat app) ∼15- and 10-fold. The K134M variant did not detectably cleave lignostilbene, indicating that Lys134 plays a key catalytic role. This study expands our mechanistic understanding of LsdA and related stilbene-cleaving dioxygenases.
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Affiliation(s)
- Eugene Kuatsjah
- Genome Science and Technology Program, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Meghan M Verstraete
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Marek J Kobylarz
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Alvin K N Liu
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Michael E P Murphy
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Lindsay D Eltis
- Genome Science and Technology Program, The University of British Columbia, Vancouver V6T 1Z3, Canada; Department of Microbiology and Immunology, The University of British Columbia, Vancouver V6T 1Z3, Canada.
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19
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Werner N, Ramirez-Sarmiento CA, Agosin E. Protein engineering of carotenoid cleavage dioxygenases to optimize β-ionone biosynthesis in yeast cell factories. Food Chem 2019; 299:125089. [PMID: 31319343 DOI: 10.1016/j.foodchem.2019.125089] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Synthesis of β-ionone in recombinant Saccharomyces cerevisiae is limited by the efficiency of Carotenoid Cleavage Dioxygenases (CCD), membrane-tethered enzymes catalyzing the last step in the pathway. We performed in silico design and membrane affinity analysis, focused on single-point mutations of PhCCD1 to improve membrane anchoring. The resulting constructs were tested in a β-carotene hyper-producing strain by comparing colony pigmentation against colonies transformed with native PhCCD1 and further analyzed by β-ionone quantification via RP-HPLC. Two single-point mutants increased β-ionone yields almost 3-fold when compared to native PhCCD1. We also aimed to improve substrate accessibility of PhCCD1 through the amino-terminal addition of membrane destination peptides directed towards the endoplasmic reticulum or plasma membrane. Yeast strains expressing peptide-PhCCD1 constructs showed β-ionone yields up to 4-fold higher than the strain carrying the native enzyme. Our results demonstrate that protein engineering of CCDs significantly increases the yield of β-ionone synthesized by metabolically engineered yeast.
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Affiliation(s)
- Nicole Werner
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
| | - César A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
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20
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Gluck‐Thaler E, Vijayakumar V, Slot JC. Fungal adaptation to plant defences through convergent assembly of metabolic modules. Mol Ecol 2018; 27:5120-5136. [DOI: 10.1111/mec.14943] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Emile Gluck‐Thaler
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
| | - Vinod Vijayakumar
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
| | - Jason C. Slot
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences The Ohio State University Columbus Ohio
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21
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Sui X, Farquhar ER, Hill HE, von Lintig J, Shi W, Kiser PD. Preparation and characterization of metal-substituted carotenoid cleavage oxygenases. J Biol Inorg Chem 2018; 23:887-901. [PMID: 29946976 PMCID: PMC6060882 DOI: 10.1007/s00775-018-1586-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/20/2018] [Indexed: 11/26/2022]
Abstract
Carotenoid cleavage oxygenases (CCO) are non-heme iron enzymes that catalyze oxidative cleavage of alkene bonds in carotenoid and stilbenoid substrates. Previously, we showed that the iron cofactor of CAO1, a resveratrol-cleaving member of this family, can be substituted with cobalt to yield a catalytically inert enzyme useful for trapping active site-bound stilbenoid substrates for structural characterization. Metal substitution may provide a general method for identifying the natural substrates for CCOs in addition to facilitating structural and biophysical characterization of CCO-carotenoid complexes under normal aerobic conditions. Here, we demonstrate the general applicability of cobalt substitution in a prototypical carotenoid cleaving CCO, apocarotenoid oxygenase (ACO) from Synechocystis. Among the non-native divalent metals investigated, cobalt was uniquely able to stably occupy the ACO metal binding site and inhibit catalysis. Analysis by X-ray crystallography and X-ray absorption spectroscopy demonstrate that the Co(II) forms of both ACO and CAO1 exhibit a close structural correspondence to the native Fe(II) enzyme forms. Hence, cobalt substitution is an effective strategy for generating catalytically inert but structurally intact forms of CCOs.
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Affiliation(s)
- Xuewu Sui
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106-4988, USA
| | - Hannah E Hill
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106-4988, USA
| | - Philip D Kiser
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E 101st Street, Cleveland, OH, 44106, USA.
- Research Service, Louis Stokes Cleveland VA Medical Center, 10701 East Boulevard, Cleveland, OH, 44106, USA.
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22
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Abstract
Resveratrol is among the best-known secondary plant metabolites because of its antioxidant, anti-inflammatory, and anticancer properties. It also is an important allelopathic chemical widely credited with the protection of plants from pathogens. The ecological role of resveratrol in natural habitats is difficult to establish rigorously, because it does not seem to accumulate outside plant tissue. It is likely that bacterial degradation plays a key role in determining the persistence, and thus the ecological role, of resveratrol in soil. Here, we report the isolation of an Acinetobacter species that can use resveratrol as a sole carbon source from the rhizosphere of peanut plants. Both molecular and biochemical techniques indicate that the pathway starts with the conversion of resveratrol to 3,5-dihydroxybenzaldehyde and 4-hydroxybenzaldehyde. The aldehydes are oxidized to substituted benzoates that subsequently enter central metabolism. The gene that encodes the enzyme responsible for the oxidative cleavage of resveratrol was cloned and expressed in Escherichia coli to establish its function. Its physiological role in the resveratrol catabolic pathway was established by knockouts and by the reverse transcription-quantitative PCR (RT-qPCR) demonstration of expression during growth on resveratrol. The results establish the presence and capabilities of resveratrol-degrading bacteria in the rhizosphere of the peanut plants and set the stage for studies to evaluate the role of the bacteria in plant allelopathy.IMPORTANCE In addition to its antioxidant properties, resveratrol is representative of a broad array of allelopathic chemicals produced by plants to inhibit competitors, herbivores, and pathogens. The bacterial degradation of such chemicals in the rhizosphere would reduce the effects of the chemicals. Therefore, it is important to understand the activity and ecological role of bacteria that biodegrade resveratrol near the plants that produce it. This study describes the isolation from the peanut rhizosphere of bacteria that can grow on resveratrol. The characterization of the initial steps in the biodegradation process sets the stage for the investigation of the evolution of the catabolic pathways responsible for the biodegradation of resveratrol and its homologs.
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23
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Jia KP, Baz L, Al-Babili S. From carotenoids to strigolactones. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2189-2204. [PMID: 29253188 DOI: 10.1093/jxb/erx476] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/07/2017] [Indexed: 05/18/2023]
Abstract
Strigolactones are phytohormones that regulate various plant developmental and adaptation processes. When released into soil, strigolactones act as chemical signals, attracting symbiotic arbuscular mycorrhizal fungi and inducing seed germination in root-parasitic weeds. Strigolactones are carotenoid derivatives, characterized by the presence of a butenolide ring that is connected by an enol ether bridge to a less conserved second moiety. Carotenoids are isopenoid pigments that differ in structure, number of conjugated double bonds, and stereoconfiguration. Genetic analysis and enzymatic studies have demonstrated that strigolactones originate from all-trans-β-carotene in a pathway that involves the all-trans-/9-cis-β-carotene isomerase DWARF27 and carotenoid cleavage dioxygenase 7 and 8 (CCD7, 8). The CCD7-mediated, regiospecific and stereospecific double-bond cleavage of 9-cis-β-carotene leads to a 9-cis-configured intermediate that is converted by CCD8 via a combination of reactions into the central metabolite carlactone. By catalyzing repeated oxygenation reactions that can be coupled to ring closure, CYP711 enzymes convert carlactone into tricyclic-ring-containing canonical and non-canonical strigolactones. Modifying enzymes, which are mostly unknown, further increase the diversity of strigolactones. This review explores carotenogenesis, provides an update on strigolactone biosynthesis, with emphasis on the substrate specificity and reactions catalyzed by the different enzymes, and describes the regulation of the biosynthetic pathway.
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Affiliation(s)
- Kun-Peng Jia
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, The Bioactives Lab, Thuwal, Kingdom of Saudi Arabia
| | - Lina Baz
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, The Bioactives Lab, Thuwal, Kingdom of Saudi Arabia
| | - Salim Al-Babili
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, The Bioactives Lab, Thuwal, Kingdom of Saudi Arabia
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24
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Ma G, Zhang L, Iida K, Madono Y, Yungyuen W, Yahata M, Yamawaki K, Kato M. Identification and quantitative analysis of β-cryptoxanthin and β-citraurin esters in Satsuma mandarin fruit during the ripening process. Food Chem 2017; 234:356-364. [PMID: 28551247 DOI: 10.1016/j.foodchem.2017.05.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
In this study, to investigate the xanthophyll accumulation in citrus fruits, the major fatty acid esters of β-cryptoxanthin and β-citraurin were identified, and changes in their contents were investigated in two Satsuma mandarin varieties, 'Miyagawa-wase' and 'Yamashitabeni-wase', during the ripening process. The results showed that β-cryptoxanthin and β-citraurin were mainly esterified with lauric acid, myristic acid, and palmitic acid in citrus fruits. During the ripening process, β-cryptoxanthin laurate, myristate, and palmitate were accumulated gradually in the flavedos and juice sacs of the two varieties. In the flavedo of 'Yamashitabeni-wase', β-citraurin laurate, myristate, and palmitate were specifically accumulated, and their contents increased rapidly with a peak in November. In addition, functional analyses showed that CitCCD1 and CitCCD4 efficiently cleaved the free β-cryptoxanthin, but not the β-cryptoxanthin esters in vitro. The substrate specificity of CitCCDs towards free β-cryptoxanthin indicated that β-cryptoxanthin esters might be more stable than free β-cryptoxanthin in citrus fruits.
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Affiliation(s)
- Gang Ma
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Lancui Zhang
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Kohei Iida
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Yuki Madono
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Witchulada Yungyuen
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan; The United Graduate School of Agricultural Science, Gifu University (Shizuoka University), Yanagido, Gifu 501-1193, Japan.
| | - Masaki Yahata
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Kazuki Yamawaki
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
| | - Masaya Kato
- Department of Biological and Environmental Sciences, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga, Shizuoka 422-8529, Japan.
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