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Solano YJ, Everett MP, Dang KS, Abueg J, Kiser PD. Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore. Nat Chem Biol 2024; 20:779-788. [PMID: 38355721 PMCID: PMC11142922 DOI: 10.1038/s41589-024-01554-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans-cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65-an evolutionary convergence that deepens our understanding of visual system diversity.
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Affiliation(s)
- Yasmeen J Solano
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Michael P Everett
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA
| | - Kelly S Dang
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Jude Abueg
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California Irvine School of Medicine, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine School of Medicine, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California Irvine School of Pharmacy and Pharmaceutical Sciences, Irvine, CA, USA.
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2
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Wang Q, Li H, Bujupi U, Gröning J, Stolz A, Bongiorno A, Gupta R. Oxygen Activation in Aromatic Ring Cleaving Salicylate Dioxygenase: Detection of Reaction Intermediates with a Nitro-substituted Substrate Analog. Chembiochem 2024; 25:e202400023. [PMID: 38363551 DOI: 10.1002/cbic.202400023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Cupin dioxygenases such as salicylate 1,2-dioxygense (SDO) perform aromatic C-C bond scission via a 3-His motif tethered iron cofactor. Here, transient kinetics measurements are used to monitor the catalytic cycle of SDO by using a nitro-substituted substrate analog, 3-nitrogentisate. Compared to the natural substrate, the nitro group reduces the enzymatic kcat by 500-fold, thereby facilitating the detection and kinetic characterization of reaction intermediates. Sums and products of reciprocal relaxation times derived from kinetic measurements were found to be linearly dependent on O2 concentration, suggesting reversible formation of two distinct intermediates. Dioxygen binding to the metal cofactor takes place with a forward rate of 5.9×103 M-1 s-1: two orders of magnitude slower than other comparable ring-cleaving dioxygenses. Optical chromophore of the first intermediate is distinct from the in situ generated SDO Fe(III)-O2⋅- complex but closer to the enzyme-substrate precursor.
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Affiliation(s)
- Qian Wang
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Hanbin Li
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Uran Bujupi
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
| | - Janosch Gröning
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andreas Stolz
- Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Angelo Bongiorno
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
| | - Rupal Gupta
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Blvd. Staten Island, New York, 10314, United States
- Ph.D. Programs in Biochemistry, The Graduate Center of the City University of New York, New York, 10016, United States
- Ph.D. Programs in Chemistry and Physics, The Graduate Center of the City University of New York, New York, 10016, United States
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3
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Mu G, Gaynor RB, McIntyre BN, Donnadieu B, Creutz SE. Synthesis and Characterization of Bipyridyl-(Imidazole) n Mn(II) Compounds and Their Evaluation as Potential Precatalysts for Water Oxidation. Molecules 2023; 28:7221. [PMID: 37894706 PMCID: PMC10608871 DOI: 10.3390/molecules28207221] [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: 09/29/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
Metalloenzymes make extensive use of manganese centers for oxidative catalysis, including water oxidation; the need to develop improved synthetic catalysts for these processes has long motivated the development of bioinspired manganese complexes. Herein, we report a series of bpy-(imidazole)n (n = 1 or 2) (bpy = 2,2'-bipyridyl) ligands and their Mn2+ complexes. Four Mn2+ complexes are structurally characterized using single-crystal X-ray diffraction, revealing different tridentate and tetradentate ligand coordination modes. Cyclic voltammetry of the complexes is consistent with ligand-centered reductions and metal-centered oxidations, and UV-vis spectroscopy complemented by TD-DFT calculations shows primarily ligand-centered transitions with minor contributions from charge-transfer type transitions at higher energies. In solution, ESI-MS studies provide evidence for ligand reorganization, suggesting complex speciation behavior. The oxidation of the complexes in the presence of water is probed using cyclic voltammetry, but the low stability of the complexes in aqueous solution leads to decomposition and precludes their ultimate application as aqueous electrocatalysts. Possible reasons for the low stability and suggestions for improvement are discussed.
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Affiliation(s)
| | | | | | | | - Sidney E. Creutz
- Department of Chemistry, Mississippi State University, Mississippi State, Starkville, MS 39762, USA; (G.M.); (R.B.G.); (B.N.M.); (B.D.)
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4
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Wang Y, Li S, Zhou Z, Sun L, Sun J, Shen C, Gao R, Song J, Pu X. The Functional Characteristics and Soluble Expression of Saffron CsCCD2. Int J Mol Sci 2023; 24:15090. [PMID: 37894770 PMCID: PMC10606151 DOI: 10.3390/ijms242015090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Crocins are important natural products predominantly obtained from the stigma of saffron, and that can be utilized as a medicinal compound, spice, and colorant with significant promise in the pharmaceutical, food, and cosmetic industries. Carotenoid cleavage dioxygenase 2 (CsCCD2) is a crucial limiting enzyme that has been reported to be responsible for the cleavage of zeaxanthin in the crocin biosynthetic pathway. However, the catalytic activity of CsCCD2 on β-carotene/lycopene remains elusive, and the soluble expression of CsCCD2 remains a big challenge. In this study, we reported the functional characteristics of CsCCD2, that can catalyze not only zeaxanthin cleavage but also β-carotene and lycopene cleavage. The molecular basis of the divergent functionality of CsCCD2 was elucidated using bioinformatic analysis and truncation studies. The protein expression optimization results demonstrated that the use of a maltose-binding protein (MBP) tag and the optimization of the induction conditions resulted in the production of more soluble protein. Correspondingly, the catalytic efficiency of soluble CsCCD2 was higher than that of the insoluble one, and the results further validated its functional verification. This study not only broadened the substrate profile of CsCCD2, but also achieved the soluble expression of CsCCD2. It provides a firm platform for CsCCD2 crystal structure resolution and facilitates the synthesis of crocetin and crocins.
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Affiliation(s)
- Ying Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Siqi Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Ze Zhou
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Lifen Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Jing Sun
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Chuanpu Shen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
| | - Ranran Gao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People’s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xiangdong Pu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei 230032, China
- Center of Traditional Chinese Medicine Formula Granule, Anhui Medical University, Hefei 230032, China
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5
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Ding A, Bao F, Yuan X, Wang J, Cheng T, Zhang Q. Integrative Analysis of Metabolome and Transcriptome Revealed Lutein Metabolism Contributed to Yellow Flower Formation in Prunus mume. PLANTS (BASEL, SWITZERLAND) 2023; 12:3333. [PMID: 37765497 PMCID: PMC10537319 DOI: 10.3390/plants12183333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
Prunus mume is a famous ornamental woody tree with colorful flowers. P. mume with yellow flowers is one of the most precious varieties. Regretfully, metabolites and regulatory mechanisms of yellow flowers in P. mume are still unclear. This hinders innovation of flower color breeding in P. mume. To elucidate the metabolic components and molecular mechanisms of yellow flowers, we analyzed transcriptome and metabolome between 'HJH' with yellow flowers and 'ZLE' with white flowers. Comparing the metabolome of the two varieties, we determined that carotenoids made contributions to the yellow flowers rather than flavonoids. Lutein was the key differential metabolite to cause yellow coloration of 'HJH'. Transcriptome analysis revealed significant differences in the expression of carotenoid cleavage dioxygenase (CCD) between the two varieties. Specifically, the expression level of PmCCD4 was higher in 'ZLE' than that in 'HJH'. Moreover, we identified six major transcription factors that probably regulated PmCCD4 to affect lutein accumulation. We speculated that carotenoid cleavage genes might be closely related to the yellow flower phenotype in P. mume. Further, the coding sequence of PmCCD4 has been cloned from the 'HJH' petals, and bioinformatics analysis revealed that PmCCD4 possessed conserved histidine residues, ensuring its enzymatic activity. PmCCD4 was closely related to PpCCD4, with a homology of 98.16%. Instantaneous transformation analysis in petal protoplasts of P. mume revealed PmCCD4 localization in the plastid. The overexpression of PmCCD4 significantly reduced the carotenoid content in tobacco plants, especially the lutein content, indicating that lutein might be the primary substrate for PmCCD4. We speculated that PmCCD4 might be involved in the cleavage of lutein in plastids, thereby affecting the formation of yellow flowers in P. mume. This work could establish a material and molecular basis of molecular breeding in P. mume for improving the flower color.
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Affiliation(s)
- Aiqin Ding
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Fei Bao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Xi Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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6
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Yoo HJ, Chung MY, Lee HA, Lee SB, Grandillo S, Giovannoni JJ, Lee JM. Natural overexpression of CAROTENOID CLEAVAGE DIOXYGENASE 4 in tomato alters carotenoid flux. PLANT PHYSIOLOGY 2023; 192:1289-1306. [PMID: 36715630 PMCID: PMC10231392 DOI: 10.1093/plphys/kiad049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 06/01/2023]
Abstract
Carotenoids and apocarotenoids function as pigments and flavor volatiles in plants that enhance consumer appeal and offer health benefits. Tomato (Solanum lycopersicum.) fruit, especially those of wild species, exhibit a high degree of natural variation in carotenoid and apocarotenoid contents. Using positional cloning and an introgression line (IL) of Solanum habrochaites "LA1777', IL8A, we identified carotenoid cleavage dioxygenase 4 (CCD4) as the factor responsible for controlling the dark orange fruit color. CCD4b expression in ripe fruit of IL8A plants was ∼8,000 times greater than that in the wild type, presumably due to 5' cis-regulatory changes. The ShCCD4b-GFP fusion protein localized in the plastid. Phytoene, ζ-carotene, and neurosporene levels increased in ShCCD4b-overexpressing ripe fruit, whereas trans-lycopene, β-carotene, and lutein levels were reduced, suggestive of feedback regulation in the carotenoid pathway by an unknown apocarotenoid. Solid-phase microextraction-gas chromatography-mass spectrometry analysis showed increased levels of geranylacetone and β-ionone in ShCCD4b-overexpressing ripe fruit coupled with a β-cyclocitral deficiency. In carotenoid-accumulating Escherichia coli strains, ShCCD4b cleaved both ζ-carotene and β-carotene at the C9-C10 (C9'-C10') positions to produce geranylacetone and β-ionone, respectively. Exogenous β-cyclocitral decreased carotenoid synthesis in the ripening fruit of tomato and pepper (Capsicum annuum), suggesting feedback inhibition in the pathway. Our findings will be helpful for enhancing the aesthetic and nutritional value of tomato and for understanding the complex regulatory mechanisms of carotenoid and apocarotenoid biogenesis.
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Affiliation(s)
- Hee Ju Yoo
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Mi-Young Chung
- Department of Agricultural Education, Sunchon National University, Suncheon 57922, Korea
| | - Hyun-Ah Lee
- Division of Eco-Friendly Horticulture, Yonam College, Cheonan 31005, Korea
| | - Soo-Bin Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
| | - Silvana Grandillo
- CNR-Institute of Bioscience and Bioresources (IBBR), Via Università 133, 80055 Portici, Italy
| | - James J Giovannoni
- Boyce Thompson Institute and USDA-ARS Robert W. Holley Center, Tower Rd., Cornell University Campus, Ithaca, NY 14853, USA
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, Korea
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Morote L, Rubio-Moraga Á, López-Jiménez AJ, Argandoña J, Niza E, Ahrazem O, Gómez-Gómez L. A carotenoid cleavage dioxygenase 4 from Paulownia tomentosa determines visual and aroma signals in flowers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 329:111609. [PMID: 36737005 DOI: 10.1016/j.plantsci.2023.111609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Paulownia tomentosa is an economically important fast-growing tree, and its flowers and fruits are a rich source of biologically active secondary metabolites. In addition, the flowers of P. tomentosa are distinguished by a strong aroma and are also excellent nectariferous plants. The flowers are pale lilac and characterized by the presence of yellow nectar guides, whose color changes during the development of the flower, representing reliable signals to pollinators while enhancing reproductive success. The chemical analyses of the nectar guides revealed the presence of carotenoids as the pigments responsible for the observed coloration, with β-carotene levels determining the color changes observed after anthesis, with a reduction at anthesis and further increase and accumulation in post anthesis. To understand how β-carotene accumulation was controlled in the nectar guides, the expression of genes related to carotenoid biosynthesis and metabolism was analyzed. Carotenogenic gene expression was not associated with the observed changes in β-carotene during flower development. However, the expression of a gene encoding a carotenoid cleavage dioxygenase, CCD4-4, was co-related with the levels of β-carotene in the nectar guides. In addition, CCD4-4 cleavage β-carotene at C9-C10 and C9'-C10' positions, resulting in the generation of β-ionone, which was detected in flowers at anthesis. The obtained results indicated a developmental stage specific regulation of apocarotenoid formation through β-carotene cleavage, resulting in color changes and volatile production as key traits for plant-pollinator interactions. DATA AVAILABILITY: Data will be made available on request.
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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
| | - Javier Argandoña
- 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
| | - Enrique Niza
- 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, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - 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
| | - 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, Departamento de Ciencia y Tecnología Agroforestal y Genética, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
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8
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Bandara S, von Lintig J. Aster la vista: Unraveling the biochemical basis of carotenoid homeostasis in the human retina. Bioessays 2022; 44:e2200133. [PMID: 36127289 PMCID: PMC10044510 DOI: 10.1002/bies.202200133] [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: 07/05/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022]
Abstract
Carotenoids play pivotal roles in vision as light filters and precursor of chromophore. Many vertebrates also display the colorful pigments as ornaments in bare skin parts and feathers. Proteins involved in the transport and metabolism of these lipids have been identified including class B scavenger receptors and carotenoid cleavage dioxygenases. Recent research implicates members of the Aster protein family, also known as GRAM domain-containing (GRAMD), in carotenoid metabolism. These multi-domain proteins facilitate the intracellular movement of carotenoids from their site of cellular uptake by scavenger receptors to the site of their metabolic processing by carotenoid cleavage dioxygenases. We provide a model how the coordinated interplay of these proteins and their differential expression establishes carotenoid distribution patterns and function in tissues, with particular emphasis on the human retina.
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Affiliation(s)
- Sepalika Bandara
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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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: 0.5] [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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10
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Ren D, Lee YH, Wang SA, Liu HW. Characterization of the Oxazinomycin Biosynthetic Pathway Revealing the Key Role of a Nonheme Iron-Dependent Mono-oxygenase. J Am Chem Soc 2022; 144:10968-10977. [PMID: 35687050 DOI: 10.1021/jacs.2c04080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oxazinomycin is a C-nucleoside natural product with antibacterial and antitumor activities. In addition to the characteristic C-glycosidic linkage shared with other C-nucleosides, oxazinomycin also features a structurally unusual 1,3-oxazine moiety, the biosynthesis of which had previously been unknown. Herein, complete in vitro reconstitution of the oxazinomycin biosynthetic pathway is described. Construction of the C-glycosidic bond between ribose 5-phosphate and an oxygen-labile pyridine heterocycle is catalyzed by the C-glycosidase OzmB and involves formation of an enzyme-substrate Schiff base intermediate. The DUF4243 family protein OzmD is shown to catalyze oxygen insertion and rearrangement of the pyridine C-nucleoside intermediate to generate the 1,3-oxazine moiety along with the elimination of cyanide. Spectroscopic analysis and mutagenesis studies indicate that OzmD is a novel nonheme iron-dependent enzyme in which the catalytic iron center is likely coordinated by four histidine residues. These results provide the first example of 1,3-oxazine biosynthesis catalyzed by an unprecedented iron-dependent mono-oxygenase.
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Affiliation(s)
- Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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11
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Shin KC, Seo MJ, Kim YS, Yeom SJ. Molecular Properties of β-Carotene Oxygenases and Their Potential in Industrial Production of Vitamin A and Its Derivatives. Antioxidants (Basel) 2022; 11:1180. [PMID: 35740077 PMCID: PMC9227343 DOI: 10.3390/antiox11061180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
β-Carotene 15,15'-oxygenase (BCO1) and β-carotene 9',10'-oxygenase (BCO2) are potential producers of vitamin A derivatives, since they can catalyze the oxidative cleavage of dietary provitamin A carotenoids to retinoids and derivative such as apocarotenal. Retinoids are a class of chemical compounds that are vitamers of vitamin A or are chemically related to it, and are essential nutrients for humans and highly valuable in the food and cosmetics industries. β-carotene oxygenases (BCOs) from various organisms have been overexpressed in heterogeneous bacteria, such as Escherichia coli, and their biochemical properties have been studied. For the industrial production of retinal, there is a need for increased production of a retinal producer and biosynthesis of retinal using biocatalyst systems improved by enzyme engineering. The current review aims to discuss BCOs from animal, plants, and bacteria, and to elaborate on the recent progress in our understanding of their functions, biochemical properties, substrate specificity, and enzyme activities with respect to the production of retinoids in whole-cell conditions. Moreover, we specifically propose ways to integrate BCOs into retinal biosynthetic bacterial systems to improve the performance of retinal production.
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Affiliation(s)
- Kyung-Chul Shin
- Department of Integrative Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea;
| | - Min-Ju Seo
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
| | - Yeong-Su Kim
- Wild Plants Industrialization Research Division, Baekdudaegan National Arboretum, Bonghwa 36209, Korea
| | - Soo-Jin Yeom
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea
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12
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Abstract
Here, the choice of the first coordination shell of the metal center is analyzed from the perspective of charge maintenance in a binary enzyme-substrate complex and an O2-bound ternary complex in the nonheme iron oxygenases. Comparing homogentisate 1,2-dioxygenase and gentisate dioxygenase highlights the significance of charge maintenance after substrate binding as an important factor that drives the reaction coordinate. We then extend the charge analysis to several common types of nonheme iron oxygenases containing either a 2-His-1-carboxylate facial triad or a 3-His or 4-His ligand motif, including extradiol and intradiol ring-cleavage dioxygenases, thiol dioxygenases, α-ketoglutarate-dependent oxygenases, and carotenoid cleavage oxygenases. After forming the productive enzyme-substrate complex, the overall charge of the iron complex at the 0, +1, or +2 state is maintained in the remaining catalytic steps. Hence, maintaining a constant charge is crucial to promote the reaction of the iron center beginning from the formation of the Michaelis or ternary complex. The charge compensation to the iron ion is tuned not only by protein-derived carboxylate ligands but also by substrates. Overall, these analyses indicate that charge maintenance at the iron center is significant when all the necessary components form a productive complex. This charge maintenance concept may apply to most oxygen-activating metalloenzymes systems that do not draw electrons and protons step-by-step from a separate reactant, such as NADH, via a reductase. The charge maintenance perception may also be useful in proposing catalytic pathways or designing prototypical reactions using artificial or engineered enzymes for biotechnological applications.
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Affiliation(s)
- Ephrahime S. Traore
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, Texas 78249, United States
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13
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Zhang QW, Kong CL, Tao YS. Fate of carotenoids in yeasts: synthesis and cleavage. Crit Rev Food Sci Nutr 2022; 63:7638-7652. [PMID: 35275506 DOI: 10.1080/10408398.2022.2048352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Carotenoids and their cleavage products (norisoprenoids) have excellent functional properties with diverse applications in foods, medicaments, cosmetics, etc. Carotenoids can be oxidatively cleaved through nonspecific reactions or by carotenoid cleavage oxygenases (CCOs), the product of which could further modify food flavor. This review provides comprehensive information on both carotenoid synthesis and cleavage processes with emphasis on enzyme characterization and biosynthetic pathway optimization. The use of interdisciplinary approaches of bioengineering and computer-aided experimental technology for key enzyme modification and systematic pathway design is beneficial to monitor metabolic pathways and assess pathway bottlenecks, which could efficiently lead to accumulation of carotenoids in microorganisms. The identification of CCOs spatial structures isolated from different species has made a significant contribution to the current state of knowledge. Current trends in carotenoid-related flavor modification are also discussed. In particular, we propose the carotenoid-synthesizing yeast Rhodotorula spp. for the production of food bioactive compounds. Understanding the behavior underlying the formation of norisoprenoids from carotenoids using interdisciplinary approaches may point toward other areas of investigation that could lead to better exploiting the potential use of autochthonous yeast in flavor enhancement.
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Affiliation(s)
- Qian-Wei Zhang
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Cai-Lin Kong
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong-Sheng Tao
- College of Enology, Northwest A&F University, Yangling, Shaanxi, China
- Ningxia Helan Mountain's East Foothill Wine Experiment and Demonstration Station of Northwest A&F University, Yongning, Ningxia, China
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14
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Pan W, Zhou YL, Wang J, Dai HE, Wang X, Liu L. Structural and Functional Analysis of Nonheme Iron Enzymes BCMO-1 and BCMO-2 from Caenorhabditis elegans. Front Mol Biosci 2022; 9:844453. [PMID: 35223999 PMCID: PMC8866865 DOI: 10.3389/fmolb.2022.844453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 12/27/2022] Open
Abstract
Carotenoid metabolism is critical for diverse physiological processes. The nematode Caenorhabditis elegans has two genes that are annotated as β-carotene 15,15′-monooxygenase (BCMO) and are 17 centimorgan apart on chromosome II, but the function of BCMO-1 and BCMO-2 remains uncharacterized. Sequence homology indicates that the two enzymes belong to the carotenoid cleavage dioxygenase family that share a seven-bladed β-propeller fold with a nonheme iron center. Here we determined crystal structures of BCMO-1 and BCMO-2 at resolutions of 1.8 and 1.9 Å, respectively. Structural analysis reveals that BCMO-1 and BCMO-2 are strikingly similar to each other. We also characterized their β-carotene cleavage activity, but the results suggest that they may not act as β-carotene 15,15′-oxygenases.
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Affiliation(s)
- Weimin Pan
- School of Life Sciences, Anhui University, Hefei, China
| | | | - Jian Wang
- School of Life Sciences, Anhui University, Hefei, China
| | - Huai-En Dai
- School of Life Sciences, Anhui University, Hefei, China
| | - Xiao Wang
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei, China
- Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, China
- *Correspondence: Lin Liu,
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15
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Otani Y, Maoka T, Kawai-Noma S, Saito K, Umeno D. A novel carotenoid biosynthetic route via oxidosqualene. Biochem Biophys Res Commun 2022; 599:75-80. [PMID: 35176628 DOI: 10.1016/j.bbrc.2022.01.105] [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: 11/16/2021] [Revised: 01/04/2022] [Accepted: 01/26/2022] [Indexed: 11/02/2022]
Abstract
Over 800 known carotenoids are synthesized from phytoene or 4,4'-diapophytoene (dehydrosqualene) characterized by three conjugated double bonds. In this paper, we report that carotenoid desaturase CrtN from Staphylococcus aureus and Methylomonas can accept oxidosqualene, which is the precursor for plant- or animal-type triterpenoids, yielding the yellow carotenoid pigments with 8, 9, or 10 conjugated double bonds. The resulting pathway is the second nonnatural route for carotenoid pigments and the first pathway for carotenoid pigments not biosynthesized via (diapo)phytoene.
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Affiliation(s)
- Yusuke Otani
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Takashi Maoka
- Research Institute for Production Development, Kyoto, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Chiba University, Chiba, Japan; Department of Applied Chemistry, Waseda University, Tokyo, Japan.
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16
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Comprehensive Analysis of Carotenoid Cleavage Dioxygenases Gene Family and Its Expression in Response to Abiotic Stress in Poplar. Int J Mol Sci 2022; 23:ijms23031418. [PMID: 35163346 PMCID: PMC8836127 DOI: 10.3390/ijms23031418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 02/06/2023] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) catalyzes the cleavage of various carotenoids into smaller apocarotenoids which are essential for plant growth and development and response to abiotic stresses. CCD family is divided into two subfamilies: 9-cis epoxycarotenoid dioxygenases (NCED) family and CCD family. A better knowledge of carotenoid biosynthesis and degradation could be useful for regulating carotenoid contents. Here, 23 CCD genes were identified from the Populus trichocarpa genome, and their characterizations and expression profiling were validated. The PtCCD members were divided into PtCCD and PtNCED subfamilies. The PtCCD family contained the PtCCD1, 4, 7, and 8 classes. The PtCCDs clustered in the same clade shared similar intron/exon structures and motif compositions and distributions. In addition, the tandem and segmental duplications resulted in the PtCCD gene expansion based on the collinearity analysis. An additional integrated collinearity analysis among poplar, Arabidopsis, rice, and willow revealed the gene pairs between poplar and willow more than that between poplar and rice. Identifying tissue-special expression patterns indicated that PtCCD genes display different expression patterns in leaves, stems, and roots. Abscisic acid (ABA) treatment and abiotic stress suggested that many PtCCD genes are responsive to osmotic stress regarding the comprehensive regulation networks. The genome-wide identification of PtCCD genes may provide the foundation for further exploring the putative regulation mechanism on osmotic stress and benefit poplar molecular breeding.
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17
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Hernandez BY, Zhu X, Risch HA, Lu L, Ma X, Irwin ML, Lim JK, Taddei TH, Pawlish KS, Stroup AM, Brown R, Wang Z, Wong LL, Yu H. Oral Cyanobacteria and Hepatocellular Carcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:221-229. [PMID: 34697061 PMCID: PMC8755591 DOI: 10.1158/1055-9965.epi-21-0804] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/22/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Gut microbial alterations have been linked to chronic liver disease and hepatocellular carcinoma (HCC). The role of the oral microbiome in liver cancer development has not been widely investigated. METHODS Bacterial 16S rRNA sequences were evaluated in oral samples from 90 HCC cases and 90 controls who were a part of a larger U.S. case-control study of HCC among patients diagnosed from 2011 to 2016. RESULTS The oral microbiome of HCC cases showed significantly reduced alpha diversity compared with controls (Shannon P = 0.002; Simpson P = 0.049), and beta diversity significantly differed (weighted Unifrac P = 0.004). The relative abundance of 30 taxa significantly varied including Cyanobacteria, which was enriched in cases compared with controls (P = 0.018). Cyanobacteria was positively associated with HCC [OR, 8.71; 95% confidence interval (CI), 1.22-62.00; P = 0.031] after adjustment for age, race, birthplace, education, smoking, alcohol, obesity, type 2 diabetes, Hepatitis C virus (HCV), Hepatitis B virus (HBV), fatty liver disease, aspirin use, other NSAID use, laboratory batch, and other significant taxa. When stratified by HCC risk factors, significant associations of Cyanobacteria with HCC were exclusively observed among individuals with negative histories of established risk factors as well as females and college graduates. Cyanobacterial genes positively associated with HCC were specific to taxa producing microcystin, the hepatotoxic tumor promotor, and other genes known to be upregulated with microcystin exposure. CONCLUSIONS Our study provides novel evidence that oral Cyanobacteria may be an independent risk factor for HCC. IMPACT These findings support future studies to further examine the causal relationship between oral Cyanobacteria and HCC risk.
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Affiliation(s)
- Brenda Y Hernandez
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii.
| | - Xuemei Zhu
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale School of Medicine, New Haven, Connecticut
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale School of Medicine, New Haven, Connecticut
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale School of Medicine, New Haven, Connecticut
| | - Melinda L Irwin
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale School of Medicine, New Haven, Connecticut
| | - Joseph K Lim
- Yale Liver Center and Section of Digestive Diseases, Department if Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Tamar H Taddei
- Yale Liver Center and Section of Digestive Diseases, Department if Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Karen S Pawlish
- New Jersey State Cancer Registry, New Jersey Department of Health, Trenton, New Jersey
| | - Antoinette M Stroup
- New Jersey State Cancer Registry, New Jersey Department of Health, Trenton, New Jersey
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, The State University of New Jersey, Piscataway, New Jersey
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Robert Brown
- Department of Medicine, Joan & Sanford I. Weill Medical College of Cornell University, New York, New York
- Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, New York
| | - Zhanwei Wang
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Linda L Wong
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
- Department of Surgery, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Herbert Yu
- University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
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18
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Modelling of the Citrus CCD4 Family Members: In Silico Analysis of Membrane Binding and Substrate Preference. Int J Mol Sci 2021; 22:ijms222413616. [PMID: 34948418 PMCID: PMC8708828 DOI: 10.3390/ijms222413616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/26/2022] Open
Abstract
Coloring is one of the most important characteristics in commercial flowers and fruits, generally due to the accumulation of carotenoid pigments. Enzymes of the CCD4 family in citrus intervene in the generation of β-citraurin, an apocarotenoid responsible for the reddish-orange color of mandarins. Citrus CCD4s enzymes could be capable of interacting with the thylakoid membrane inside chloroplasts. However, to date, this interaction has not been studied in detail. In this work, we present three new complete models of the CCD4 family members (CCD4a, CCD4b, and CCD4c), modeled with a lipid membrane. To identify the preference for substrates, typical carotenoids were inserted in the active site of the receptors and the protein–ligand interaction energy was evaluated. The results show a clear preference of CCD4s for xanthophylls over aliphatic carotenes. Our findings indicate the ability to penetrate the membrane and maintain a stable interaction through the N-terminal α-helical domain, spanning a contact surface of 2250 to 3250 Å2. The orientation and depth of penetration at the membrane surface suggest that CCD4s have the ability to extract carotenoids directly from the membrane through a tunnel consisting mainly of hydrophobic residues that extends up to the catalytic center of the enzyme.
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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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20
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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: 6] [Impact Index Per Article: 2.0] [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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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: 37] [Impact Index Per Article: 12.3] [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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22
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Cai X, Jiang Z, Tang L, Zhang S, Li X, Wang H, Liu C, Chi J, Zhang X, Zhang J. Genome-wide characterization of carotenoid oxygenase gene family in three cotton species and functional identification of GaNCED3 in drought and salt stress. J Appl Genet 2021; 62:527-543. [PMID: 34109531 DOI: 10.1007/s13353-021-00634-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Cotton that serves natural fiber for the textile industry is an important industrial crop. However, abiotic stress imposed a significant negative impact on yield and quality of cotton fiber. Carotenoid cleavage oxygenases (CCOs) that specifically catalyze the cleavage of carotenoid are essential for plant growth and development and abiotic stress response. While information of cotton CCOs and their potential functions in abiotic stress is still far from satisfactory, which imposes restrictions on application in genetic breeding for stress resistance. In this study, 15, 15, and 30 CCOs were identified from Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively. Phylogenetic relationship indicated that CCO genes could be classified into two groups (NCEDs and CCDs). Cis-elements prediction showed that there were 18 types of stress-related cis-elements in promoter regions. Analysis with transcriptome data revealed tissue-specific expression pattern of cotton CCOs. qRT-PCR analysis revealed only that GhNCED3a_A/D and GhNCED3c_A/D had strong response to drought, salt, and cold stress, while GhCCD1_A/D and GhCCD4_A showed relatively slight expression changes. Virus-induced gene silencing of GaNCED3a, the ortholog gene of GhNCED3a_A/D, suggested that silenced plants exhibited decreased resistance not only to drought but also to salt, with significantly reduced proline content, and high malondialdehyde content and water loss rate. In addition, stress response genes RD29A, DREB1A, and SOS1 significantly downregulated under drought and salt stress in silenced plants compared to control plants, indicating that GaNCED3a played an important role in drought and salt response. The results provided valuable insights into function analysis of cotton CCOs in abiotic stress response, and suggested potential benefit genes for stress-resistant breeding.
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Affiliation(s)
- Xiao Cai
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | | | - Liyuan Tang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Sujun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Xinghe Li
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Haitao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Cunjing Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Jina Chi
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China.,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China
| | - Xiangyun Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China. .,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China.
| | - Jianhong Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, 050051, Hebei, China. .,National Cotton Improvement Center Hebei Branch, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, 050051, Hebei, China.
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23
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Blum E, Zhang J, Zaluski J, Einstein DE, Korshin EE, Kubas A, Gruzman A, Tochtrop GP, Kiser PD, Palczewski K. Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy. J Med Chem 2021; 64:8287-8302. [PMID: 34081480 DOI: 10.1021/acs.jmedchem.1c00279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recycling of all-trans-retinal to 11-cis-retinal through the visual cycle is a fundamental metabolic pathway in the eye. A potent retinoid isomerase (RPE65) inhibitor, (R)-emixustat, has been developed and tested in several clinical trials; however, it has not received regulatory approval for use in any specific retinopathy. Rapid clearance of this drug presents challenges to maintaining concentrations in eyes within a therapeutic window. To address this pharmacokinetic inadequacy, we rationally designed and synthesized a series of emixustat derivatives with strategically placed fluorine and deuterium atoms to slow down the key metabolic transformations known for emixustat. Crystal structures and quantum chemical analysis of RPE65 in complex with the most potent emixustat derivatives revealed the structural and electronic bases for how fluoro substituents can be favorably accommodated within the active site pocket of RPE65. We found a close (∼3.0 Å) F-π interaction that is predicted to contribute ∼2.4 kcal/mol to the overall binding energy.
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Affiliation(s)
- Eliav Blum
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Jianye Zhang
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States
| | - Jordan Zaluski
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - David E Einstein
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Research Service, VA Long Beach Healthcare System, Long Beach, California 90822, United States
| | - Edward E Korshin
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Adam Kubas
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Arie Gruzman
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Gregory P Tochtrop
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States.,Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Research Service, VA Long Beach Healthcare System, Long Beach, California 90822, United States
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, California 92697, United States.,Department of Physiology and Biophysics, University of California, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, California 92697, United States
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24
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Challenges and Potential in Increasing Lutein Content in Microalgae. Microorganisms 2021; 9:microorganisms9051068. [PMID: 34063406 PMCID: PMC8156089 DOI: 10.3390/microorganisms9051068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 02/08/2023] Open
Abstract
Research on enhancing lutein content in microalgae has made significant progress in recent years. However, strategies are needed to address the possible limitations of microalgae as practical lutein producers. The capacity of lutein sequestration may determine the upper limit of cellular lutein content. The preliminary estimation presented in this work suggests that the lutein sequestration capacity of the light-harvesting complex (LHC) of microalgae is most likely below 2% on the basis of dry cell weight (DCW). Due to its nature as a structural pigment, higher lutein content might interfere with the LHC in fulfilling photosynthetic functions. Storing lutein in a lipophilic environment is a mechanism for achieving high lutein content but several critical barriers must be overcome such as lutein degradation and access to lipid droplet to be stored through esterification. Understanding the mechanisms underlying lipid droplet biogenesis in chloroplasts, as well as carotenoid trafficking through chloroplast membranes and carotenoid esterification, may provide insight for new approaches to achieve high lutein contents in algae. In the meantime, building the machinery for esterification and sequestration of lutein and other hydroxyl-carotenoids in model microorganisms, such as yeast, with synthetic biology technology provides a promising option.
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25
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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: 5.3] [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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26
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Gazda MA, Toomey MB, Araújo PM, Lopes RJ, Afonso S, Myers CA, Serres K, Kiser PD, Hill GE, Corbo JC, Carneiro M. Genetic Basis of De Novo Appearance of Carotenoid Ornamentation in Bare Parts of Canaries. Mol Biol Evol 2021; 37:1317-1328. [PMID: 31930402 DOI: 10.1093/molbev/msaa006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Unlike wild and domestic canaries (Serinus canaria), or any of the three dozen species of finches in genus Serinus, the domestic urucum breed of canaries exhibits bright red bills and legs. This novel trait offers a unique opportunity to understand the mechanisms of bare-part coloration in birds. To identify the mutation producing the colorful phenotype, we resequenced the genome of urucum canaries and performed a range of analyses to search for genotype-to-phenotype associations across the genome. We identified a nonsynonymous mutation in the gene BCO2 (beta-carotene oxygenase 2, also known as BCDO2), an enzyme involved in the cleavage and breakdown of full-length carotenoids into short apocarotenoids. Protein structural models and in vitro functional assays indicate that the urucum mutation abrogates the carotenoid-cleavage activity of BCO2. Consistent with the predicted loss of carotenoid-cleavage activity, urucum canaries tended to have increased levels of full-length carotenoid pigments in bill tissue and reduced levels of carotenoid-cleavage products (apocarotenoids) in retinal tissue compared with other breeds of canaries. We hypothesize that carotenoid-based bare-part coloration might be readily gained, modified, or lost through simple switches in the enzymatic activity or regulation of BCO2 and this gene may be an important mediator in the evolution of bare-part coloration among bird species.
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Affiliation(s)
- Małgorzata Anna Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Matthew B Toomey
- Department of Biological Science, University of Tulsa, Tulsa, OK
| | - Pedro M Araújo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ricardo J Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Kyla Serres
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Philip D Kiser
- Department of Physiology & Biophysics, School of Medicine, Gillespie Neuroscience Research Facility, University of California, Irvine, Irvine, CA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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27
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Triflumizole as a Novel Lead Compound for Strigolactone Biosynthesis Inhibitor. Molecules 2020; 25:molecules25235525. [PMID: 33255720 PMCID: PMC7728069 DOI: 10.3390/molecules25235525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Strigolactones (SLs) are carotenoid-derived plant hormones involved in the development of various plants. SLs also stimulate seed germination of the root parasitic plants, Striga spp. and Orobanche spp., which reduce crop yield. Therefore, regulating SL biosynthesis may lessen the damage of root parasitic plants. Biosynthetic inhibitors effectively control biological processes by targeted regulation of biologically active compounds. In addition, biosynthetic inhibitors regulate endogenous levels in developmental stage- and tissue-specific manners. To date, although some chemicals have been found as SL biosynthesis inhibitor, these are derived from only three lead chemicals. In this study, to find a novel lead chemical for SL biosynthesis inhibitor, 27 nitrogen-containing heterocyclic derivatives were screened for inhibition of SL biosynthesis. Triflumizole most effectively reduced the levels of rice SL, 4-deoxyorobanchol (4DO), in root exudates. In addition, triflumizole inhibited endogenous 4DO biosynthesis in rice roots by inhibiting the enzymatic activity of Os900, a rice enzyme that converts the SL intermediate carlactone to 4DO. A Striga germination assay revealed that triflumizole-treated rice displayed a reduced level of germination stimulation for Striga. These results identify triflumizole as a novel lead compound for inhibition of SL biosynthesis.
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28
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Widjaja-Adhi MAK, Golczak M. The molecular aspects of absorption and metabolism of carotenoids and retinoids in vertebrates. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158571. [PMID: 31770587 PMCID: PMC7244374 DOI: 10.1016/j.bbalip.2019.158571] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/08/2023]
Abstract
Vitamin A is an essential nutrient necessary for numerous basic physiological functions, including reproduction and development, immune cell differentiation and communication, as well as the perception of light. To evade the dire consequences of vitamin A deficiency, vertebrates have evolved specialized metabolic pathways that enable the absorption, transport, and storage of vitamin A acquired from dietary sources as preformed retinoids or provitamin A carotenoids. This evolutionary advantage requires a complex interplay between numerous specialized retinoid-transport proteins, receptors, and enzymes. Recent advances in molecular and structural biology resulted in a rapid expansion of our understanding of these processes at the molecular level. This progress opened new avenues for the therapeutic manipulation of retinoid homeostasis. In this review, we summarize current research related to the biochemistry of carotenoid and retinoid-processing proteins with special emphasis on the structural aspects of their physiological actions. 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)
- Made Airanthi K Widjaja-Adhi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America.
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29
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von Lintig J, Moon J, Lee J, Ramkumar S. Carotenoid metabolism at the intestinal barrier. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158580. [PMID: 31794861 PMCID: PMC7987234 DOI: 10.1016/j.bbalip.2019.158580] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Carotenoids exert a rich variety of physiological functions in mammals and are beneficial for human health. These lipids are acquired from the diet and metabolized to apocarotenoids, including retinoids (vitamin A and its metabolites). The small intestine is a major site for their absorption and bioconversion. From here, carotenoids and their metabolites are distributed within the body in triacylglycerol-rich lipoproteins to support retinoid signaling in peripheral tissues and photoreceptor function in the eyes. In recent years, much progress has been made in identifying carotenoid metabolizing enzymes, transporters, and binding proteins. A diet-responsive regulatory network controls the activity of these components and adapts carotenoid absorption and bioconversion to the bodily requirements of these lipids. Genetic variability in the genes encoding these components alters carotenoid homeostasis and is associated with pathologies. We here summarize the advanced state of knowledge about intestinal carotenoid metabolism and its impact on carotenoid and retinoid homeostasis of other organ systems, including the eyes, liver, and immune system. The implication of the findings for science-based intake recommendations for these essential dietary lipids is discussed. 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)
- Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America.
| | - Jean Moon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America
| | - Joan Lee
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America
| | - Srinivasagan Ramkumar
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States of America
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30
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Poliakov E, Uppal S, Rogozin IB, Gentleman S, Redmond TM. Evolutionary aspects and enzymology of metazoan carotenoid cleavage oxygenases. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158665. [PMID: 32061750 PMCID: PMC7423639 DOI: 10.1016/j.bbalip.2020.158665] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/25/2020] [Accepted: 02/05/2020] [Indexed: 12/18/2022]
Abstract
The carotenoids are terpenoid fat-soluble pigments produced by plants, algae, and several bacteria and fungi. They are ubiquitous components of animal diets. Carotenoid cleavage oxygenase (CCO) superfamily members are involved in carotenoid metabolism and are present in all kingdoms of life. Throughout the animal kingdom, carotenoid oxygenases are widely distributed and they are completely absent only in two unicellular organisms, Monosiga and Leishmania. Mammals have three paralogs 15,15'-β-carotene oxygenase (BCO1), 9',10'-β-carotene oxygenase (BCO2) and RPE65. The first two enzymes are classical carotenoid oxygenases: they cleave carbon‑carbon double bonds and incorporate two atoms of oxygen in the substrate at the site of cleavage. The third, RPE65, is an unusual family member, it is the retinoid isomerohydrolase in the visual cycle that converts all-trans-retinyl ester into 11-cis-retinol. Here we discuss evolutionary aspects of the carotenoid cleavage oxygenase superfamily and their enzymology to deduce what insight we can obtain from their evolutionary conservation.
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Affiliation(s)
- Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sheetal Uppal
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Susan Gentleman
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - T Michael Redmond
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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31
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Liu T, Yu S, Xu Z, Tan J, Wang B, Liu YG, Zhu Q. Prospects and progress on crocin biosynthetic pathway and metabolic engineering. Comput Struct Biotechnol J 2020; 18:3278-3286. [PMID: 33209212 PMCID: PMC7653203 DOI: 10.1016/j.csbj.2020.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/22/2022] Open
Abstract
Crocins are a group of highly valuable apocarotenoid-derived pigments mainly produced in Crocus sativus stigmas and Gardenia jasminoides fruits, which display great pharmacological activities for human health, such as anticancer, reducing the risk of atherosclerosis, and preventing Alzheimer's disease. However, traditional sources of crocins are no longer sufficient to meet current demands. The recent clarification of the crocin biosynthetic pathway opens up the possibility of large-scale production of crocins by synthetic metabolic engineering methods. In this review, we mainly introduce the crocin biosynthetic pathway, subcellular route, related key enzymes, and its synthetic metabolic engineering, as well as its challenges and prospects, with a view to providing useful references for further studies on the synthetic metabolic engineering of crocins.
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Affiliation(s)
- Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Suize Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Bin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Fang Q, Li Y, Liu B, Meng X, Yang Z, Yang S, Bao T, Kimani S, Gao X, Wang L. Cloning and functional characterization of a carotenoid cleavage dioxygenase 2 gene in safranal and crocin biosynthesis from Freesia hybrida. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 154:439-450. [PMID: 32912484 DOI: 10.1016/j.plaphy.2020.06.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Safranal and crocin, commonly derived from the oxidative cleavage reaction of zeaxanthin in plants, are two kinds of apocarotenoids with versatile functions, which were only found in limited number of plant species. In this study, both metabolites were detected and varied concomitantly with the expression of carotenoid cleavage dioxygenase (CCD) genes in Freesia hybrida, Red River® and Ambiance cultivars. The newly isolated CCD, denoted here as FhCCD2, was phylogenetically clustered with other reported saffron CCD2s. Besides, ten introns were also observed in the genomic DNA sequence of FhCCD2 and the presence of N-terminal transporter peptide suggested its plastidial sub-localization. Biochemical analysis showed that the FhCCD2 cleaved zeaxanthin at the 7, 8 and 7', 8' double bonds to generate intermediates prerequisite for the biosynthesis of safranal and crocin. Further, gene transient expression analysis showed that the promoter of FhCCD2 was functional in Ambiance as well as Red River® cultivars, even with slight variation in their promoter sequence. At present, CCD2 proteins have only been found in Freesia and Crocus genus of Iridaceae family. Phylogenetic and intron position analysis infer that CCD2 perhaps emerged after the intron loss during evolutionary process of CCD1 or their shared ancestry.
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Affiliation(s)
- Qiang Fang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China; School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China.
| | - Baofeng Liu
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Xiangyu Meng
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Zhongzhou Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Song Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China; School of Pure and Applied Sciences, Karatina University, Karatina, Kenya
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China; National Demonstration Center for Experimental Biology Education, Northeast Normal University, Changchun, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China.
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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: 3.3] [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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Ernst DA, Fitak RR, Schmidt M, Derby CD, Johnsen S, Lohmann KJ. Pulse magnetization elicits differential gene expression in the central nervous system of the Caribbean spiny lobster, Panulirus argus. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:725-742. [PMID: 32607762 DOI: 10.1007/s00359-020-01433-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 05/18/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
Diverse animals use Earth's magnetic field to guide their movements, but the neural and molecular mechanisms underlying the magnetic sense remain enigmatic. One hypothesis is that particles of the mineral magnetite (Fe3O4) provide the basis of magnetoreception. Here we examined gene expression in the central nervous system of a magnetically sensitive invertebrate, the Caribbean spiny lobster (Panulirus argus), after applying a magnetic pulse known to alter magnetic orientation behavior. Numerous genes were differentially expressed in response to the pulse, including 647 in the brain, 1256 in the subesophageal ganglion, and 712 in the thoracic ganglia. Many such genes encode proteins linked to iron regulation, oxidative stress, and immune response, consistent with possible impacts of a magnetic pulse on magnetite-based magnetoreceptors. Additionally, however, altered expression also occurred for numerous genes with no apparent link to magnetoreception, including genes encoding proteins linked to photoreception, carbohydrate and hormone metabolism, and other physiological processes. Overall, the results are consistent with the magnetite hypothesis of magnetoreception, yet also reveal that in spiny lobsters, a strong pulse altered expression of > 10% of all expressed genes, including many seemingly unrelated to sensory processes. Thus, caution is required when interpreting the effects of magnetic pulses on animal behavior.
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Affiliation(s)
- David A Ernst
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA. .,Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Robert R Fitak
- Genomics and Bioinformatics Cluster, Department of Biology, University of Central Florida, Orlando, FL, 32816, USA
| | - Manfred Schmidt
- Neuroscience Institute and Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Charles D Derby
- Neuroscience Institute and Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Sönke Johnsen
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Kenneth J Lohmann
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
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Timmins JJB, Kroukamp H, Paulsen IT, Pretorius IS. The Sensory Significance of Apocarotenoids in Wine: Importance of Carotenoid Cleavage Dioxygenase 1 (CCD1) in the Production of β-Ionone. Molecules 2020; 25:E2779. [PMID: 32560189 PMCID: PMC7356381 DOI: 10.3390/molecules25122779] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 02/07/2023] Open
Abstract
Olfactory cues are key drivers of our multisensory experiences of food and drink. For example, our perception and enjoyment of the flavour and taste of a wine is primarily steered by its aroma. Making sense of the underlying smells that drive consumer preferences is integral to product innovation as a vital source of competitive advantage in the marketplace, which explains the intense interest in the olfactory component of flavour and the sensory significance of individual compounds, such as one of the most important apocarotenoids for the bouquet of wine, β-ionone (violet and woody notes). β-Ionone is formed directly from β-carotene as a by-product of the actions of carotenoid cleavage dioxygenases (CCDs). The biological production of CCDs in microbial cell factories is one way that important aroma compounds can be generated on a large scale and with reduced costs, while retaining the 'natural' moniker. The CCD family includes the CCD1, CCD2, CCD4, CCD7 and CCD8; however, the functions, co-dependency and interactions of these CCDs remain to be fully elucidated. Here, we review the classification, actions and biotechnology of CCDs, particularly CCD1 and its action on β-carotene to produce the aromatic apocarotenoid β-ionone.
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Affiliation(s)
- John J. B. Timmins
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.J.B.T.); (I.T.P.)
| | - Heinrich Kroukamp
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.J.B.T.); (I.T.P.)
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Ian T. Paulsen
- Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (J.J.B.T.); (I.T.P.)
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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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: 30] [Impact Index Per Article: 7.5] [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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Uppal S, Rogozin IB, Redmond T, Poliakov E. Palmitoylation of Metazoan Carotenoid Oxygenases. Molecules 2020; 25:E1942. [PMID: 32331396 PMCID: PMC7221588 DOI: 10.3390/molecules25081942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 11/16/2022] Open
Abstract
Abundant in nature, carotenoids are a class of fat-soluble pigments with a polyene tetraterpenoid structure. They possess antioxidant properties and their consumption leads to certain health benefits in humans. Carotenoid cleavage oxygenases (CCOs) are a superfamily of enzymes which oxidatively cleave carotenoids and they are present in all kingdoms of life. Complexity of CCO evolution is high. For example, in this study we serendipitously found a new family of eukaryotic CCOs, the apocarotenoid oxygenase-like (ACOL) family. This family has several members in animal genomes and lacks the animal-specific amino acid motif PDPCK. This motif is likely to be associated with palmitoylation of some animal CCOs. We recently demonstrated that two mammalian members of the carotenoid oxygenase family retinal pigment epithelial-specific 65 kDa protein (RPE65) and beta-carotene oxygenase 2 (BCO2) are palmitoylated proteins. Here we used the acyl-resin-assisted capture (acyl-RAC) method to demonstrate protein palmitoylation and immunochemistry to localize mouse BCO2 (mBCO2) in COS7 cell line in the absence and presence of its substrate β-carotene. We demonstrate that mBCO2 palmitoylation depends on the evolutionarily conserved motif PDPCK and that metazoan family members lacking the motif (Lancelet beta-carotene oxygenase-like protein (BCOL) and Acropora ACOL) are not palmitoylated. Additionally, we observed that the palmitoylation status of mBCO2 and its membrane association depend on the presence of its substrate β-carotene. Based on our results we conclude that most metazoan carotenoid oxygenases retain the evolutionarily conserved palmitoylation PDPCK motif to target proteins to internal membranes depending on substrate status. Exceptions are in the secreted BCOL subfamily and the strictly cytosolic ancient ACOL subfamily of carotenoid oxygenases.
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Affiliation(s)
- Sheetal Uppal
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.U.); (T.M.R.)
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA;
| | - T.Michael Redmond
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.U.); (T.M.R.)
| | - Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.U.); (T.M.R.)
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Helgeland H, Sodeland M, Zoric N, Torgersen JS, Grammes F, von Lintig J, Moen T, Kjøglum S, Lien S, Våge DI. Genomic and functional gene studies suggest a key role of beta-carotene oxygenase 1 like (bco1l) gene in salmon flesh color. Sci Rep 2019; 9:20061. [PMID: 31882713 PMCID: PMC6934663 DOI: 10.1038/s41598-019-56438-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Red coloration of muscle tissue (flesh) is a unique trait in several salmonid genera, including Atlantic salmon. The color results from dietary carotenoids deposited in the flesh, whereas the color intensity is affected both by diet and genetic components. Herein we report on a genome-wide association study (GWAS) to identify genetic variation underlying this trait. Two SNPs on ssa26 showed strong associations to the flesh color in salmon. Two genes known to be involved in carotenoid metabolism were located in this QTL- region: beta-carotene oxygenase 1 (bco1) and beta-carotene oxygenase 1 like (bco1l). To determine whether flesh color variation is caused by one, or both, of these genes, functional studies were carried out including mRNA and protein expression in fish with red and pale flesh color. The catalytic abilities of these two genes were also tested with different carotenoids. Our results suggest bco1l to be the most likely gene to explain the flesh color variation observed in this population.
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Affiliation(s)
- Hanna Helgeland
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Oslo University Hospital, Department of Radiation Biology, Institute for Cancer Research, N-0310, Oslo, Norway
| | - Marte Sodeland
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Institute of Marine research, N-4817, His, Norway.,University of Agder, Department of Natural Sciences, Faculty of Engineering and Science, N-4604, Kristiansand, Norway
| | - Nina Zoric
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway
| | | | - Fabian Grammes
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway
| | - Johannes von Lintig
- Case Western Reserve University, Department of Pharmacology, 2109 Adelbert Rd. Wood Bldg. 341, Cleveland, OH, 44106, USA
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway
| | - Dag Inge Våge
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, NO-1432, Ås, Norway.
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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: 26] [Impact Index Per Article: 5.2] [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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40
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Han Z, Long L, Ding S. Expression and Characterization of Carotenoid Cleavage Oxygenases From Herbaspirillum seropedicae and Rhodobacteraceae bacterium Capable of Biotransforming Isoeugenol and 4-Vinylguaiacol to Vanillin. Front Microbiol 2019; 10:1869. [PMID: 31456782 PMCID: PMC6700365 DOI: 10.3389/fmicb.2019.01869] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/29/2019] [Indexed: 11/13/2022] Open
Abstract
HsCCO and RbCCO from Herbaspirillum seropedicae and Rhodobacteraceae bacterium were selected and characterized from five putative bacterial carotenoid cleavage oxygenase gene sequences, due to merits in expression solubility and catalytic properties. Both enzymes can convert 4-vinylguaiacol and isoeugenol to vanillin. HsCCO showed maximum activity at 40°C and pH 7.0 and was stable at pH 6.5-10 and temperature around 25°C, retaining over 90 and 80% of initial activity, respectively. RbCCO showed maximum activity at 35°C and pH 9.0 and was stable at pH 6-11 and temperatures of 25-30°C, retaining over 80% of initial activity. The kinetic constants K m of HsCCO for isoeugenol and 4-vinylguaiacol were 1.55 and 1.65 mM and V max were 74.09 and 27.91 nmol min-1 mg-1, respectively. The kinetic constants K m of RbCCO for isoeugenol and 4-vinylguaiacol were 2.24 and 0.85 mM and V max were 76.48 and 19.96 nmol min-1 mg-1, respectively. The transformed Escherichia coli cells harboring HsCCO converted isoeugenol and 4-vinylguaiacol at molar conversion yields of 80 and 55% and the maximum vanillin concentrations were up to 1.22 and 0.84 g L-1, respectively. Comparably, the molar conversion yields of the transformed E. coli cells harboring RbCCO against isoeugenol 4-vinylguaiacol were 75 and 58%, and the maximum vanillin yields were up to 1.14 and 0.88 g L-1, respectively.
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Affiliation(s)
- Zichun Han
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Liangkun Long
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Shaojun Ding
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
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41
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Khadka N, Farquhar ER, Hill HE, Shi W, von Lintig J, Kiser PD. Evidence for distinct rate-limiting steps in the cleavage of alkenes by carotenoid cleavage dioxygenases. J Biol Chem 2019; 294:10596-10606. [PMID: 31138651 DOI: 10.1074/jbc.ra119.007535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/24/2019] [Indexed: 11/06/2022] Open
Abstract
Carotenoid cleavage dioxygenases (CCDs) use a nonheme Fe(II) cofactor to split alkene bonds of carotenoid and stilbenoid substrates. The iron centers of CCDs are typically five-coordinate in their resting states, with solvent occupying an exchangeable site. The involvement of this iron-bound solvent in CCD catalysis has not been experimentally addressed, but computational studies suggest two possible roles. 1) Solvent dissociation provides a coordination site for O2, or 2) solvent remains bound to iron but changes its equilibrium position to allow O2 binding and potentially acts as a proton source. To test these predictions, we investigated isotope effects (H2O versus D2O) on two stilbenoid-cleaving CCDs, Novosphingobium aromaticivorans oxygenase 2 (NOV2) and Neurospora crassa carotenoid oxygenase 1 (CAO1), using piceatannol as a substrate. NOV2 exhibited an inverse isotope effect (k H/k D ∼ 0.6) in an air-saturated buffer, suggesting that solvent dissociates from iron during the catalytic cycle. By contrast, CAO1 displayed a normal isotope effect (k H/k D ∼ 1.7), suggesting proton transfer in the rate-limiting step. X-ray absorption spectroscopy on NOV2 and CAO1 indicated that the protonation states of the iron ligands are unchanged within pH 6.5-8.5 and that the Fe(II)-aquo bond is minimally altered by substrate binding. We pinpointed the origin of the differential kinetic behaviors of NOV2 and CAO1 to a single amino acid difference near the solvent-binding site of iron, and X-ray crystallography revealed that the substitution alters binding of diffusible ligands to the iron center. We conclude that solvent-iron dissociation and proton transfer are both associated with the CCD catalytic mechanism.
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Affiliation(s)
- Nimesh Khadka
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Erik R Farquhar
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973.,Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4988, and
| | - Hannah E Hill
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, New York 11973.,Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106-4988, and
| | - Johannes von Lintig
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Philip D Kiser
- From the Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, .,Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio 44106
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Vega-Teijido M, Cantero J, Rodrigo MJ, López C, Zunini MP. An in silicostudy of the citrus dioxygenases CCD4 family substrates. J Biomol Struct Dyn 2019; 37:2086-2097. [DOI: 10.1080/07391102.2018.1477619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Mauricio Vega-Teijido
- Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones (DETEMA), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Computational Chemistry and Biology Group (CCBG), DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Jorge Cantero
- Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones (DETEMA), Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Departamento de Investigación, Facultad de Agronomía, Universidad Nacional del Este, Ciudad del Este, Paraguay
| | - Maria J. Rodrigo
- Laboratorio Fisiología y Biotecnología Postcosecha, Instituto de Agroquímica y Tecnología de Alimentos, IATA-CSIC, Valencia, Spain
| | - Carolina López
- Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones (DETEMA), Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Margot Paulino Zunini
- Centro de Bioinformática Estructural (CeBioInfo), Departamento de Experimentación y Teoría de la Estructura de la Materia y sus Aplicaciones (DETEMA), Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Batra R, Agarwal P, Tyagi S, Saini DK, Kumar V, Kumar A, Kumar S, Balyan HS, Pandey R, Gupta PK. A study of CCD8 genes/proteins in seven monocots and eight dicots. PLoS One 2019; 14:e0213531. [PMID: 30861026 PMCID: PMC6413960 DOI: 10.1371/journal.pone.0213531] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/23/2019] [Indexed: 02/08/2023] Open
Abstract
In plants, the enzyme CCD8 (carotenoid cleavage dioxygenase 8) is involved in the synthesis of an important hormone, strigolactone, and therefore, plays an important role in controlling growth and development. Using cDNA and protein sequence derived from the gene ZmCCD8 from maize, we identified putative orthologs of the gene encoding CCD8 in six other monocots and eight dicots; the sequence similarity ranged from 52–75.9% at the gene level and 60.9–93.7% at the protein level. The average length of the gene was ~3.3 kb (range: 2.08 to 3.98 kb), although the number of introns within the genes differed (4 or 5 in dicots and 3 or 4 in monocots, except in T. urartu with 6 introns). Several cis-acting regulatory elements were identified in the promoters of CCD8 genes, which are known to respond to biotic and abiotic stresses. The N-terminal end (up to ~70 amino acids) of CCD8 proteins was highly variable due to insertions, deletions and mismatches. The variation in genes and proteins were particularly conspicuous in T. urartu and Ae. tauschii among the monocots and A. thaliana and P. persica among the dicots. In CCD8 proteins, 12 motifs were also identified, of which 6 were novel; 4 of these novel motifs occurred in all the 15 species. The 3D structures of proteins had the characteristic features of the related enzyme apocarotenoid oxygenase (ACO) of Synechocystis (a representative of cyanobacteria). The results of qRT-PCR in wheat revealed that under phosphorous (P)-starved condition (relative to expression under optimum P used as control), the expression of TaCCD8 genes increased ~37 fold in root tissue of the cultivar C306 and ~33 fold in shoot tissue of the cultivar HUW468 (the two cultivars differed in their P-use efficiency). This suggested that expression of TaCCD8 genes is genotype-dependent and tissue-specific and is regulated under different levels of P supply.
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Affiliation(s)
- Ritu Batra
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Sandhya Tyagi
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Dinesh Kumar Saini
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Vikas Kumar
- Department of Genetics and Plant Breeding, CCS University, Meerut, India
| | - Anuj Kumar
- Advance Center for Computational & Applied Biotechnology, Uttarakhand Council for Biotechnology (UCB), Dehradun, India
| | - Sanjay Kumar
- Bioinformatics Centre, Biotech Park, Lucknow, India
| | | | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Choi EH, Suh S, Sander CL, Hernandez CJO, Bulman ER, Khadka N, Dong Z, Shi W, Palczewski K, Kiser PD. Insights into the pathogenesis of dominant retinitis pigmentosa associated with a D477G mutation in RPE65. Hum Mol Genet 2019; 27:2225-2243. [PMID: 29659842 DOI: 10.1093/hmg/ddy128] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/06/2018] [Indexed: 12/31/2022] Open
Abstract
RPE65 is the essential trans-cis isomerase of the classical retinoid (visual) cycle. Mutations in RPE65 give rise to severe retinal dystrophies, most of which are associated with loss of protein function and recessive inheritance. The only known exception is a c.1430G>A (D477G) mutation that gives rise to dominant retinitis pigmentosa with delayed onset and choroidal and macular involvement. Position 477 is distant from functionally critical regions of RPE65. Hence, the mechanism of D477G pathogenicity remains unclear, although protein misfolding and aggregation mechanisms have been suggested. We characterized a D477G knock-in mouse model which exhibited mild age-dependent changes in retinal structure and function. Immunoblot analysis of protein extracts from the eyes of these knock-in mice demonstrated the presence of ubiquitinated RPE65 and reduced RPE65 expression. We observed an accumulation of retinyl esters in the knock-in mice as well as a delay in rhodopsin regeneration kinetics and diminished electroretinography responses, indicative of RPE65 functional impairment induced by the D477G mutation in vivo. However, a cell line expressing D477G RPE65 revealed protein expression levels, cellular localization and retinoid isomerase activity comparable to cells expressing wild-type protein. Structural analysis of an RPE65 chimera suggested that the D477G mutation does not perturb protein folding or tertiary structure. Instead, the mutation generates an aggregation-prone surface that could induce cellular toxicity through abnormal complex formation as suggested by crystal packing analysis. These results indicate that a toxic gain-of-function induced by the D477G RPE65 substitution may play a role in the pathogenesis of this form of dominant retinitis pigmentosa.
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Affiliation(s)
- Elliot H Choi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susie Suh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christopher L Sander
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Christian J Ortiz Hernandez
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,University of Puerto Rico at Humacao, Humacao, PR, USA
| | - Elizabeth R Bulman
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA
| | - Nimesh Khadka
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Zhiqian Dong
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Polgenix Inc., Cleveland, OH 44106, USA
| | - Wuxian Shi
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Philip D Kiser
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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45
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Photosynthetic adaptation to low iron, light, and temperature in Southern Ocean phytoplankton. Proc Natl Acad Sci U S A 2019; 116:4388-4393. [PMID: 30787187 DOI: 10.1073/pnas.1810886116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytoplankton productivity in the polar Southern Ocean (SO) plays an important role in the transfer of carbon from the atmosphere to the ocean's interior, a process called the biological carbon pump, which helps regulate global climate. SO productivity in turn is limited by low iron, light, and temperature, which restrict the efficiency of the carbon pump. Iron and light can colimit productivity due to the high iron content of the photosynthetic photosystems and the need for increased photosystems for low-light acclimation in many phytoplankton. Here we show that SO phytoplankton have evolved critical adaptations to enhance photosynthetic rates under the joint constraints of low iron, light, and temperature. Under growth-limiting iron and light levels, three SO species had up to sixfold higher photosynthetic rates per photosystem II and similar or higher rates per mol of photosynthetic iron than temperate species, despite their lower growth temperature (3 vs. 18 °C) and light intensity (30 vs. 40 μmol quanta⋅m2⋅s-1), which should have decreased photosynthetic rates. These unexpectedly high rates in the SO species are partly explained by their unusually large photosynthetic antennae, which are among the largest ever recorded in marine phytoplankton. Large antennae are disadvantageous at low light intensities because they increase excitation energy loss as heat, but this loss may be mitigated by the low SO temperatures. Such adaptations point to higher SO production rates than environmental conditions should otherwise permit, with implications for regional ecology and biogeochemistry.
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Biodegradation of the Allelopathic Chemical Pterostilbene by a Sphingobium sp. Strain from the Peanut Rhizosphere. Appl Environ Microbiol 2019; 85:AEM.02154-18. [PMID: 30578258 DOI: 10.1128/aem.02154-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Many plants produce allelopathic chemicals, such as stilbenes, to inhibit pathogenic fungi. The degradation of allelopathic compounds by bacteria associated with the plants would limit their effectiveness, but little is known about the extent of biodegradation or the bacteria involved. Screening of tissues and rhizosphere of peanut (Arachis hypogaea) plants revealed substantial enrichment of bacteria able to grow on resveratrol and pterostilbene, the most common stilbenes produced by the plants. Investigation of the catabolic pathway in Sphingobium sp. strain JS1018, isolated from the rhizosphere, indicated that the initial cleavage of pterostilbene was catalyzed by a carotenoid cleavage oxygenase (CCO), which led to the transient accumulation of 4-hydroxybenzaldehyde and 3,5-dimethoxybenzaldehyde. 4-Hydroxybenzaldehyde was subsequently used for the growth of the isolate, while 3,5-dimethoxybenzaldehyde was further converted to a dead-end metabolite with a molecular weight of 414 (C24H31O6). The gene that encodes the initial oxygenase was identified in the genome of strain JS1018, and its function was confirmed by heterologous expression in Escherichia coli This study reveals the biodegradation pathway of pterostilbene by plant-associated bacteria. The prevalence of such bacteria in the rhizosphere and plant tissues suggests a potential role of bacterial interference in plant allelopathy.IMPORTANCE Pterostilbene, an analog of resveratrol, is a stilbene allelochemical produced by plants to inhibit microbial infection. As a potent antioxidant, pterostilbene acts more effectively than resveratrol as an antifungal agent. Bacterial degradation of this plant natural product would affect the allelopathic efficacy and fate of pterostilbene and thus its ecological role. This study explores the isolation and abundance of bacteria that degrade resveratrol and pterostilbene in peanut tissues and rhizosphere, the catabolic pathway for pterostilbene, and the molecular basis for the initial cleavage of pterostilbene. If plant allelopathy is an important process in agriculture and management of invasive plants, the ecological role of bacteria that degrade the allelopathic chemicals must be equally important.
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Bai J, Hou Q, Zhu W, Liu Y. Mechanical insights into the oxidative cleavage of resveratrol catalyzed by dioxygenase NOV1 from Novosphingobium aromaticivorans: confirmation of dioxygenase mechanism by QM/MM calculations. Catal Sci Technol 2019. [DOI: 10.1039/c8cy01885e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM calculations confirm that the oxidative cleavage of resveratrol catalyzed by dioxygenase NOV1 follows the dioxygenase mechanism.
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Affiliation(s)
- Jie Bai
- Key Lab of Colloid and Interface Chemistry, Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Qianqian Hou
- Shandong Non-metallic Materials Institute
- Jinan
- China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering
- Xuzhou Institute of Technology
- Xuzhou
- China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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48
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Allen KN, Entova S, Ray LC, Imperiali B. Monotopic Membrane Proteins Join the Fold. Trends Biochem Sci 2019; 44:7-20. [PMID: 30337134 PMCID: PMC6309722 DOI: 10.1016/j.tibs.2018.09.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sonya Entova
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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49
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Butt H, Jamil M, Wang JY, Al-Babili S, Mahfouz M. Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis. BMC PLANT BIOLOGY 2018; 18:174. [PMID: 30157762 PMCID: PMC6116466 DOI: 10.1186/s12870-018-1387-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 08/07/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Precision plant genome engineering holds much promise for targeted improvement of crop traits via unprecedented single-base level control over the genetic material. Strigolactones (SLs) are a key determinant of plant architecture, known for their role in inhibiting shoot branching (tillering). RESULTS We used CRISPR/Cas9 in rice (Oryza sativa) for targeted disruption of CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), which controls a key step in SL biosynthesis. The ccd7 mutants exhibited a striking increase in tillering, combined with a reduced height, which could be rescued by application of the synthetic SL analog GR24. Striga germination assays and liquid chromatography-mass spectrometry analysis showed that root exudates of ccd7 mutants were also SL deficient. CONCLUSIONS Taken together, our results show the potential and feasibility of the use of the CRISPR/Cas9 system for targeted engineering of plant architecture and for elucidating the molecular underpinnings of architecture-related traits.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Muhammad Jamil
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Jian You Wang
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Salim Al-Babili
- The Bioactives Lab, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
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50
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Kelly ME, Ramkumar S, Sun W, Colon Ortiz C, Kiser PD, Golczak M, von Lintig J. The Biochemical Basis of Vitamin A Production from the Asymmetric Carotenoid β-Cryptoxanthin. ACS Chem Biol 2018; 13:2121-2129. [PMID: 29883100 PMCID: PMC6158786 DOI: 10.1021/acschembio.8b00290] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vitamin A serves essential functions in mammalian biology as a signaling molecule and chromophore. This lipid can be synthesized from more than 50 putative dietary provitamin A precursor molecules which contain at least one unsubstituted β-ionone ring. We here scrutinized the enzymatic properties and substrate specificities of the two structurally related carotenoid cleavage dioxygenases (CCDs) which catalyze this synthesis. Recombinant BCO1 split substrates across the C15,C15' double bond adjacent to a canonical β-ionone ring site to vitamin A aldehyde. Substitution of the ring with a hydroxyl group prevented this conversion. The removal of methyl groups from the polyene carbon backbone of the substrate did not impede enzyme activity. Homology modeling and site-directed mutagenesis identified amino acid residues at the entrance of the substrate tunnel, which determined BCO1's specificity for the canonical β-ionone ring site. In contrast, BCO2 split substrates across the C9,C10 double bond adjacent to assorted ionone ring sites. Kinetic analysis revealed a higher catalytic efficiency of BCO2 with substrates bearing 3-hydroxy-β-ionone rings. In the mouse intestine, the asymmetric carotenoid β-cryptoxanthin with one canonical and one 3-hydroxy-β-ionone ring site was meticulously converted to vitamin A. The tailoring of this asymmetric substrate occurred by a stepwise processing of the carotenoid substrate by both CCDs and involved a β-apo-10'-carotenal intermediate. Thus, opposite selectivity for ionone ring sites of the two mammalian CCDs complement each other in the metabolic challenge of vitamin A production from a chemically diverse set of precursor molecules.
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Affiliation(s)
- Mary E. Kelly
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Srinivasagan Ramkumar
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Weizhong Sun
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Crystal Colon Ortiz
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Philip D. Kiser
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
| | - Johannes von Lintig
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106
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