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Yang L, Wang C, Lai X, Jin S, Wang X, Wen Z, Yang M, Fazal A, Ding Y, Li Z, Cai J, Lu G, Lin H, Han H, Yang Y, Qi J. In vivo transgenic studies confirm the critical acylation function of LeBAHD56 for shikonin in Lithospermum erythrorhizon. PLANT CELL REPORTS 2024; 43:160. [PMID: 38825616 DOI: 10.1007/s00299-024-03242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
KEY MESSAGE LeBAHD56 is preferentially expressed in tissues where shikonin and its derivatives are biosynthesized, and it confers shikonin acylation in vivo. Two WRKY transcriptional factors might regulate LeBAHD56's expression. Shikonin and its derivatives, found in the roots of Lithospermum erythrorhizon, have extensive application in the field of medicine, cosmetics, and other industries. Prior research has demonstrated that LeBAHD1(LeSAT1) is responsible for the biochemical process of shikonin acylation both in vitro and in vivo. However, with the exception of its documented in vitro biochemical function, there is no in vivo genetic evidence supporting the acylation function of the highly homologous gene of LeSAT1, LeBAHD56(LeSAT2), apart from its reported role. Here, we validated the critical acylation function of LeBAHD56 for shikonin using overexpression (OE) and CRISPR/Cas9-based knockout (KO) strategies. The results showed that the OE lines had a significantly higher ratio of acetylshikonin, isobutyrylshikonin or isovalerylshikonin to shikonin than the control. In contrast, the KO lines had a significantly lower ratio of acetylshikonin, isobutyrylshikonin or isovalerylshikonin to shikonin than controls. As for its detailed expression patterns, we found that LeBAHD56 is preferentially expressed in roots and callus cells, which are the biosynthesis sites for shikonin and its derivatives. In addition, we anticipated that a wide range of putative transcription factors might control its transcription and verified the direct binding of two crucial WRKY members to the LeBAHD56 promoter's W-box. Our results not only confirmed the in vivo function of LeBAHD56 in shikonin acylation, but also shed light on its transcriptional regulation.
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Affiliation(s)
- Liu Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Changyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiaohui Lai
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- School of Biology and Geography Science, Yili Normal University, Yining, 835000, China
| | - Suo Jin
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuhang Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhongyi Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinfeng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Hongyan Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Hongwei Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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Shen L, Zhang LH, Xia X, Yang SX, Yang X. Cytochrome P450 SmCYP78A7a positively functions in eggplant response to salt stress via forming a positive feedback loop with SmWRKY11. Int J Biol Macromol 2024; 269:132139. [PMID: 38719008 DOI: 10.1016/j.ijbiomac.2024.132139] [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] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/12/2024]
Abstract
Accumulating salinity in soil critically affected growth, development, and yield in plant. However, the mechanisms of plant against salt stress largely remain unknown. Herein, we identified a gene named SmCYP78A7a, which encoded a cytochrome P450 monooxygenase and belonged to the CYP78A sub-family, and its transcript level was significantly up-regulated by salt stress and down-regulated by dehydration stress. SmCYP78A7a located in the endoplasmic reticulum. Silencing of SmCYP78A7a enhanced susceptibility of eggplant to salt stress, and significantly down-regulated the transcript levels of salt stress defense related genes SmGSTU10 and SmWRKY11 as well as increased hydrogen peroxide (H2O2) content and decreased catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) enzyme activities. In addition, SmCYP78A7a transient expression enhanced eggplant tolerance to salt stress. By chromatin immunoprecipitation PCR (ChIP-PCR), luciferase reporter assay, and electrophoretic mobility shift assay (EMSA), SmWRKY11 activated SmCYP78A7a expression by directly binding to the W-box 6-8 (W-box 6, W-box 7, and W-box 8) within SmCYP78A7a promoter to confer eggplant tolerance to salt stress. In summary, our finds reveal that SmCYP78A7a positively functions in eggplant response to salt stress via forming a positive feedback loop with SmWRKY11, and provide a new insight into regulatory mechanisms of eggplant to salt stress.
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Affiliation(s)
- Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
| | - Long-Hao Zhang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xin Xia
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Shi-Xin Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
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Oshikiri H, Li H, Manabe M, Yamamoto H, Yazaki K, Takanashi K. Comparative Analysis of Shikonin and Alkannin Acyltransferases Reveals Their Functional Conservation in Boraginaceae. PLANT & CELL PHYSIOLOGY 2024; 65:362-371. [PMID: 38181221 DOI: 10.1093/pcp/pcad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Shikonin and its enantiomer, alkannin, are bioactive naphthoquinones produced in several plants of the family Boraginaceae. The structures of these acylated derivatives, which have various short-chain acyl moieties, differ among plant species. The acylation of shikonin and alkannin in Lithospermum erythrorhizon was previously reported to be catalyzed by two enantioselective BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1). However, the mechanisms by which various shikonin and alkannin derivatives are produced in Boraginaceae plants remain to be determined. In the present study, evaluation of six Boraginaceae plants identified 23 homologs of LeSAT1 and LeAAT1, with 15 of these enzymes found to catalyze the acylation of shikonin or alkannin, utilizing acetyl-CoA, isobutyryl-CoA or isovaleryl-CoA as an acyl donor. Analyses of substrate specificities of these enzymes for both acyl donors and acyl acceptors and determination of their subcellular localization using Nicotiana benthamiana revealed a distinct functional differentiation of BAHD acyltransferases in Boraginaceae plants. Gene expression of these acyltransferases correlated with the enantiomeric ratio of produced shikonin/alkannin derivatives in L. erythrorhizon and Echium plantagineum. These enzymes showed conserved substrate specificities for acyl donors among plant species, indicating that the diversity in acyl moieties of shikonin/alkannin derivatives involved factors other than the differentiation of acyltransferases. These findings provide insight into the chemical diversification and evolutionary processes of shikonin/alkannin derivatives.
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Affiliation(s)
- Haruka Oshikiri
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hao Li
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Misaki Manabe
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hirobumi Yamamoto
- Department of Applied Biology, Faculty of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Oru-gun, Gunma, 374-0193 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
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Wang X, Wang C, Yang M, Jie W, Fazal A, Fu J, Yin T, Cai J, Liu B, Lu G, Lin H, Han H, Wen Z, Qi J, Yang Y. Genome-Wide Comparison and Functional Characterization of HMGR Gene Family Associated with Shikonin Biosynthesis in Lithospermum erythrorhizon. Int J Mol Sci 2023; 24:12532. [PMID: 37569907 PMCID: PMC10419935 DOI: 10.3390/ijms241512532] [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: 05/25/2023] [Revised: 07/16/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), as the rate-limiting enzyme in the mevalonate pathway, is essential for the biosynthesis of shikonin in Lithospermum erythrorhizon. However, in the absence of sufficient data, the principles of a genome-wide in-depth evolutionary exploration of HMGR family members in plants, as well as key members related to shikonin biosynthesis, remain unidentified. In this study, 124 HMGRs were identified and characterized from 36 representative plants, including L. erythrorhizon. Vascular plants were found to have more HMGR family genes than nonvascular plants. The phylogenetic tree revealed that during lineage and species diversification, the HMGRs evolved independently and intronless LerHMGRs emerged from multi-intron HMGR in land plants. Among them, Pinus tabuliformis and L. erythrorhizon had the most HMGR gene duplications, with 11 LerHMGRs most likely expanded through WGD/segmental and tandem duplications. In seedling roots and M9 cultured cells/hairy roots, where shikonin biosynthesis occurs, LerHMGR1 and LerHMGR2 were expressed significantly more than other genes. The enzymatic activities of LerHMGR1 and LerHMGR2 further supported their roles in catalyzing the conversion of HMG-CoA to mevalonate. Our findings provide insight into the molecular evolutionary properties and function of the HMGR family in plants and a basis for the genetic improvement of efficiently produced secondary metabolites in L. erythrorhizon.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Changyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Wencai Jie
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jiangyan Fu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinfeng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Guihua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- School of Life Sciences, Huaiyin Normal University, Huaian 223300, China
| | - Hongyan Lin
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hongwei Han
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Wang R, Liu C, Lyu C, Sun J, Kang C, Ma Y, Wan X, Guo J, Shi L, Wang J, Huang L, Wang S, Guo L. The discovery and characterization of AeHGO in the branching route from shikonin biosynthesis to shikonofuran in Arnebia euchroma. FRONTIERS IN PLANT SCIENCE 2023; 14:1160571. [PMID: 37180378 PMCID: PMC10167036 DOI: 10.3389/fpls.2023.1160571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023]
Abstract
Shikonin derivatives are natural naphthoquinone compounds and the main bioactive components produced by several boraginaceous plants, such as Lithospermum erythrorhizon and Arnebia euchroma. Phytochemical studies utilizing both L. erythrorhizon and A. euchroma cultured cells indicate the existence of a competing route branching out from the shikonin biosynthetic pathway to shikonofuran. A previous study has shown that the branch point is the transformation from (Z)-3''-hydroxy-geranylhydroquinone to an aldehyde intermediate (E)-3''-oxo-geranylhydroquinone. However, the gene encoding the oxidoreductase that catalyzes the branch reaction remains unidentified. In this study, we discovered a candidate gene belonging to the cinnamyl alcohol dehydrogenase family, AeHGO, through coexpression analysis of transcriptome data sets of shikonin-proficient and shikonin-deficient cell lines of A. euchroma. In biochemical assays, purified AeHGO protein reversibly oxidized (Z)-3''-hydroxy-geranylhydroquinone to produce (E)-3''-oxo-geranylhydroquinone followed by reversibly reducing (E)-3''-oxo-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone, resulting in an equilibrium mixture of the three compounds. Time course analysis and kinetic parameters showed that the reduction of (E)-3''-oxo-geranylhydroquinone was stereoselective and efficient in presence of NADPH, which determined that the overall reaction proceeded from (Z)-3''-hydroxy-geranylhydroquinone to (E)-3''-hydroxy-geranylhydroquinone. Considering that there is a competition between the accumulation of shikonin and shikonofuran derivatives in cultured plant cells, AeHGO is supposed to play an important role in the metabolic regulation of the shikonin biosynthetic pathway. Characterization of AeHGO should help expedite the development of metabolic engineering and synthetic biology toward production of shikonin derivatives.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Luqi Huang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Sheng Wang
- *Correspondence: Luqi Huang, ; Sheng Wang, ; Lanping Guo,
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Li P, Ren G, Wu F, Chen J, Jiang D, Liu C. Root-specific flavones and critical enzyme genes involved in their synthesis changes due to drought stress on Scutellaria baicalensis. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
IntroductionScutellaria baicalensis is rich in bioactive flavonoid, which are widely used in clinical therapy. Many environmental factors, such as water and temperature, affect gene expression and secondary metabolites accumulation in plants.MethodsIn this study, to explore the effect of drought stress on the accumulation of flavonoids and gene expression in S. baicalensis seedlings, 4-week-old Scutellaria baicalensis seedlings were treated with different concentrations of PEG6000 to simulate drought stress. The contents of four root-specific flavones (baicalein, wogonin, baicalin, and wogonoside) in samples under different treatments were quantitatively analyzed by high performance liquid chromatography (HPLC). The expression levels of flavonoid biosynthesis-related genes (PAL1, PAL2, CHS, and UBGAT) were determined by real-time quantitative PCR (qRT-PCR). Also, a correlation analysis between flavonoid contents and gene expression levels was made.ResultsThe HPLC results revealed that 5 and 10% PEG6000 treatments significantly increased the content of four flavonoids, with 5% PEG 6000 treatment being the most beneficial to the flavonoids accumulation. The qRT-PCR results showed that PAL2 and CHS gene expressions differed significantly in different organs, while PAL1 and UBGAT had poor organ-specific. For genes in roots, the expression of PAL1 and UBGAT was the highest in 5% PEG6000 treatment, and PAL2 and CHS were the highest in 10% PEG6000 treatment. Compared with other concentrations of PEG6000, 5 and 10% PEG6000 were more advantageous for gene expression. Collectively, PEG6000 at a low concentration promoted the accumulation of flavonoids and the expression of related genes. Additionally, the correlation results demonstrated that PAL1, PAL2, CHS, and UBGAT genes in roots stimulated the formation and accumulation of the four flavonoids to varying degrees, while the exception of PAL2 gene expression in roots was negatively correlated with wogonin content.DiscussionThis study for the first time investigated the effect of drought stress on the downstream gene UBGAT in S.baicalensis seedlings as well as the correlation between gene expression and flavonoid content in S. baicalensis seedlings under drought stress, providing a new sight for studying the effects of drought stress on flavonoid accumulation and related gene expression in S. baicalensis.
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Wang S, Shi L, Wang R, Liu C, Wang J, Shen Y, Tatsumi K, Navrot N, Liu T, Guo L. Characterization of Arnebia euchroma PGT homologs involved in the biosynthesis of shikonin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:587-595. [PMID: 36780721 DOI: 10.1016/j.plaphy.2023.02.012] [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: 09/20/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Shikonin is a red naphthoquinone natural product from plants with high economical and medical values. The para-hydroxybenzoic acid geranyltransferase (PGT) catalyzes the key regulatory step of shikonin biosynthesis. PGTs from Lithospermum erythrorhizon have been well-characterized and used in industrial shikonin production. However, its perennial medicinal plant Arnebia euchroma accumulates much more pigment and the underlying mechanism remains obscure. Here, we discovered and characterized the different isoforms of AePGTs. Phylogenetic study and structure modeling suggested that the N-terminal of AePGT6 contributed to its highest activity among 7 AePGTs. Indeed, AePGT2 and AePGT3 fused with 60 amino acids from the N-terminal of AePGT6 showed even higher activity than AePGT6, while native AePGT2 and AePGT3 don't have catalytic activity. Our result not only provided a mechanistic explanation of high shikonin contents in Arnebia euchroma but also engineered a best-performing PGT to achieve the highest-to-date production of 3-geranyl-4-hydroxybenzoate acid, an intermedium of shikonin.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Linyuan Shi
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ruishan Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Changzheng Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jinye Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ye Shen
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Kanade Tatsumi
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Nicolas Navrot
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, 67084, France
| | - Tan Liu
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Suttiyut T, Benzinger SW, McCoy RM, Widhalm JR. Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones. Methods Enzymol 2023; 680:217-246. [PMID: 36710012 DOI: 10.1016/bs.mie.2022.08.020] [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: 02/01/2023]
Abstract
One of the hallmarks of specialized plant metabolites is that they are produced using precursors from central metabolism. Therefore, in addition to identifying and characterizing the pathway genes and enzymes involved in synthesizing a specialized compound, it is critical to study its metabolic origins. Identifying what primary metabolic pathways supply precursors to specialized metabolism and how primary metabolism has diversified to sustain fluxes to specialized metabolite pathways is imperative to optimizing synthetic biology strategies for producing high-value plant natural products in crops and microbial systems. Improved understanding of the metabolic origins of specialized plant metabolites has also revealed instances of recurrent evolution of the same compound, or nearly identical compounds, with similar ecological functions, thereby expanding knowledge about the factors driving the chemical diversity in the plant kingdom. In this chapter, we describe detailed methods for performing tracer studies, chemical inhibitor experiments, and reverse genetics. We use examples from investigations of the metabolic origins of specialized plant 1,4-naphthoquinones (1,4-NQs). The plant 1,4-NQs provide an excellent case study for illustrating the importance of investigating the metabolic origins of specialized metabolites. Over half a century of research by many groups has revealed that the pathways to synthesize plant 1,4-NQs are the result of multiple events of convergent evolution across several disparate plant lineages and that plant 1,4-NQ pathways are supported by extraordinary events of metabolic innovation and by various primary metabolic sources.
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Affiliation(s)
- Thiti Suttiyut
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Scott W Benzinger
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Rachel M McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States.
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Tatsumi K, Ichino T, Isaka N, Sugiyama A, Moriyoshi E, Okazaki Y, Higashi Y, Kajikawa M, Tsuji Y, Fukuzawa H, Toyooka K, Sato M, Ichi I, Shimomura K, Ohta H, Saito K, Yazaki K. Excretion of triacylglycerol as a matrix lipid facilitating apoplastic accumulation of a lipophilic metabolite shikonin. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:104-117. [PMID: 36223279 DOI: 10.1093/jxb/erac405] [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: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Plants produce a large variety of lipophilic metabolites, many of which are secreted by cells and accumulated in apoplasts. These compounds often play a role to protect plants from environmental stresses. However, little is known about how these lipophilic compounds are secreted into apoplastic spaces. In this study, we used shikonin-producing cultured cells of Lithospermum erythrorhizon as an experimental model system to analyze the secretion of lipophilic metabolites, taking advantage of its high production rate and the clear inducibility in culture. Shikonin derivatives are lipophilic red naphthoquinone compounds that accumulate exclusively in apoplastic spaces of these cells and also in the root epidermis of intact plants. Microscopic analysis showed that shikonin is accumulated in the form of numerous particles on the cell wall. Lipidomic analysis showed that L. erythrorhizon cultured cells secrete an appreciable portion of triacylglycerol (24-38% of total triacylglycerol), composed predominantly of saturated fatty acids. Moreover, in vitro reconstitution assay showed that triacylglycerol encapsulates shikonin derivatives with phospholipids to form lipid droplet-like structures. These findings suggest a novel role for triacylglycerol as a matrix lipid, a molecular component involved in the secretion of specialized lipophilic metabolites.
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Affiliation(s)
- Kanade Tatsumi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | - Takuji Ichino
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | - Natsumi Isaka
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | - Eiko Moriyoshi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yasuhiro Higashi
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masataka Kajikawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yoshinori Tsuji
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Mayuko Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Ikuyo Ichi
- Institute for Human Life Innovation, Ochanomizu University, Tokyo 112-8610, Japan
| | - Koichiro Shimomura
- Graduate School of Life Sciences, Toyo University, Gunma, 374-0193, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Plant Molecular Science Center, Chiba University, Chiba, 260-8675, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
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10
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Wang X, He Z, Yang H, He C, Wang C, Fazal A, Lai X, Yang L, Wen Z, Yang M, Ma S, Jie W, Cai J, Yin T, Liu B, Yang Y, Qi J. Genome-Wide Identification of LeBAHDs in Lithospermum erythrorhizon and In Vivo Transgenic Studies Confirm the Critical Roles of LeBAHD1/LeSAT1 in the Conversion of Shikonin to Acetylshikonin. Life (Basel) 2022; 12:life12111775. [PMID: 36362930 PMCID: PMC9694994 DOI: 10.3390/life12111775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/29/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
The BAHD acyltransferase family is a unique class of plant proteins that acylates plant metabolites and participates in plant secondary metabolic processes. However, the BAHD members in Lithospermum erythrorhizon remain unknown and uncharacterized. Although the heterologously expressed L. erythrorhizon BAHD family member LeSAT1 in Escherichia coli has been shown to catalyze the conversion of shikonin to acetylshikonin in vitro, its in vivo role remains unknown. In this study, the characterization, evolution, expression patterns, and gene function of LeBAHDs in L. erythrorhizon were explored by bioinformatics and transgenic analysis. We totally identified 73 LeBAHDs in the reference genome of L. erythrorhizon. All LeBAHDs were phylogenetically classified into five clades likely to perform different functions, and were mainly expanded by dispersed and WGD/segmental duplication. The in vivo functional investigation of the key member LeBAHD1/LeSAT1 revealed that overexpression of LeBAHD1 in hairy roots significantly increased the content of acetylshikonin as well as the conversion rate of shikonin to acetylshikonin, whereas the CRISPR/Cas9-based knockout of LeBAHD1 in hairy roots displayed the opposite trend. Our results not only confirm the in vivo function of LeBAHD1/LeSAT1 in the biosynthesis of acetylshikonin, but also provide new insights for the biosynthetic pathway of shikonin and its derivatives.
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Affiliation(s)
- Xuan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Zhuoyu He
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Huan Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Cong He
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Changyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Aliya Fazal
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiaohui Lai
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Liangjie Yang
- Yili Key Laboratory of Applied Research and Development on Active Ingredients of Chinese Herbal Medicine, Yili National Agricultural Science and Technology Park at Xinjiang, Yili 835600, China
| | - Zhongling Wen
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Minkai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Shenglin Ma
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wencai Jie
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jinfeng Cai
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yonghua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (Y.Y.); (J.Q.)
| | - Jinliang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute for Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Correspondence: (Y.Y.); (J.Q.)
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11
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Vasav AP, Godbole RC, Darshetkar AM, Pable AA, Barvkar VT. Functional genomics-enabled characterization of CYP81B140 and CYP81B141 from Plumbago zeylanica L. substantiates their involvement in plumbagin biosynthesis. PLANTA 2022; 256:102. [PMID: 36282353 DOI: 10.1007/s00425-022-04014-x] [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: 05/09/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Novel cytochrome P450s, CYP81B140 and CYP81B141 from Plumbago zeylanica were functionally characterized to understand their involvement in polyketide plumbagin biosynthesis. Further, we propose 3-methyl-1-8-naphthalenediol and isoshinanolone as intermediates for plumbagin biosynthesis. Plumbago zeylanica L. (P. zeylanica) is a medicinally important plant belonging to the family Plumbaginaceae. It comprises the most abundant naphthoquinone plumbagin having anti-cancer activity. Only the polyketide synthase (PKS) enzyme has been identified from the biosynthetic pathway which catalyzes iterative condensation of acetyl-CoA and malonyl-CoA molecules. The plumbagin biosynthesis involves hydroxylation, oxidation, hydration and dehydration of intermediate compounds which are expected to be catalyzed by cytochrome P450s (CYPs). To identify the CYPs, co-expression analysis was carried out using PKS as a candidate gene. Out of the eight identified CYPs, CYP81B140 and CYP81B141 have similar expression with PKS and belong to the CYP81 family. Phylogenetic analysis suggested that CYP81B140 and CYP81B141 cluster with CYPs from CYP81B, CYP81D, CYP81E and CYP81AA subfamilies which are known to be involved in the hydroxylation and oxidation reactions. Moreover, artificial microRNA-mediated transient individual silencing and co-silencing of CYP81B140 and CYP81B141 significantly reduced plumbagin and increased the 3-methyl-1-8-naphthalenediol and isoshinanolone content. Based on metabolite analysis, we proposed that 3-methyl-1-8-naphthalenediol and isoshinanolone function as intermediates for plumbagin biosynthesis. Transient silencing, over-expression and docking analysis revealed that CYP81B140 is involved in C-1 oxidation, C-4 hydroxylation and [C2-C3] hydration of 3-methyl-1-8-naphthalenediol to form isoshinanolone, whereas CYP81B141 is catalyzing [C2-C3] dehydration and C-4 oxidation of isoshinanolone to form plumbagin. Our results indicated that both CYP81B140 and CYP81B141 are promiscuous and necessary for plumbagin biosynthesis. This is the first report of identification and functional characterization of P. zeylanica-specific CYPs involved in plumbagin biosynthetic pathway and in general hexaketide synthesis in plants.
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Affiliation(s)
- Arati P Vasav
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | - Rucha C Godbole
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India
| | | | - Anupama A Pable
- Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Vitthal T Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, 411007, India.
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12
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Ahmad M, Varela Alonso A, Koletti AE, Assimopoulou AN, Declerck S, Schneider C, Molin EM. Transcriptional dynamics of Chitinophaga sp. strain R-73072-mediated alkannin/shikonin biosynthesis in Lithospermum officinale. Front Microbiol 2022; 13:978021. [PMID: 36071973 PMCID: PMC9441710 DOI: 10.3389/fmicb.2022.978021] [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: 06/25/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023] Open
Abstract
Plants are colonized by a wide range of bacteria, several of which are known to confer benefits to their hosts such as enhancing plant growth and the biosynthesis of secondary metabolites (SMs). Recently, it has been shown that Chitinophaga sp. strain R-73072 enhances the production of alkannin/shikonin, SMs of pharmaceutical and ecological importance. However, the mechanisms by which this bacterial strain increases these SMs in plants are not yet understood. To gain insight into these mechanisms, we analyzed the molecular responses of Lithospermum officinale, an alkannin/shikonin producing member of Boraginaceae, to inoculation with R-73072 in a gnotobiotic system using comparative transcriptomics and targeted metabolite profiling of root samples. We found that R-73072 modulated the expression of 1,328 genes, of which the majority appeared to be involved in plant defense and SMs biosynthesis including alkannin/shikonin derivatives. Importantly, bacterial inoculation induced the expression of genes that predominately participate in jasmonate and ethylene biosynthesis and signaling, suggesting an important role of these phytohormones in R-73072-mediated alkannin/shikonin biosynthesis. A detached leaf bioassay further showed that R-73072 confers systemic protection against Botrytis cinerea. Finally, R-73072-mediated coregulation of genes involved in plant defense and the enhanced production of alkannin/shikonin esters further suggest that these SMs could be important components of the plant defense machinery in alkannin/shikonin producing species.
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Affiliation(s)
- Muhammad Ahmad
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Alicia Varela Alonso
- Institut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany,Earth and Life Institute, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antigoni E. Koletti
- School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation of AUTh, Natural Products, Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreana N. Assimopoulou
- School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation of AUTh, Natural Products, Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stéphane Declerck
- Earth and Life Institute, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Eva M. Molin
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria,*Correspondence: Eva M. Molin,
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13
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Yadav S, Sharma A, Nayik GA, Cooper R, Bhardwaj G, Sohal HS, Mutreja V, Kaur R, Areche FO, AlOudat M, Shaikh AM, Kovács B, Mohamed Ahmed AE. Review of Shikonin and Derivatives: Isolation, Chemistry, Biosynthesis, Pharmacology and Toxicology. Front Pharmacol 2022; 13:905755. [PMID: 35847041 PMCID: PMC9283906 DOI: 10.3389/fphar.2022.905755] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/30/2022] [Indexed: 12/19/2022] Open
Abstract
Shikonin and its derivatives, isolated from traditional medicinal plant species of the genus Lithospermum, Alkanna, Arnebia, Anchusa, Onosma, and Echium belonging to the Boraginaceae family, have numerous applications in foods, cosmetics, and textiles. Shikonin, a potent bioactive red pigment, has been used in traditional medicinal systems to cure various ailments and is well known for its diverse pharmacological potential such as anticancer, antithrombotic, neuroprotective, antidiabetic, antiviral, anti-inflammatory, anti-gonadotropic, antioxidants, antimicrobial and insecticidal. Herein, updated research on the natural sources, pharmacology, toxicity studies, and various patents filed worldwide related to shikonin and approaches to shikonin’s biogenic and chemical synthesis are reviewed. Furthermore, recent studies to establish reliable production systems to meet market demand, functional identification, and future clinical development of shikonin and its derivatives against various diseases are presented.
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Affiliation(s)
- Snehlata Yadav
- Department of Chemistry, Chandigarh University, Mohali, India
| | - Ajay Sharma
- Department of Chemistry, Chandigarh University, Mohali, India
- University Centre for Research and Development, Department of Chemistry, Chandigarh University, Chandigarh- Ludhiana Highway, Mohali, India
| | - Gulzar Ahmad Nayik
- Department of Food Science & Technology, Govt. Degree College Shopian, Srinagar, India
| | - Raymond Cooper
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Garima Bhardwaj
- Department of Chemistry, Sant Longowal Institute of Engineering and Technology, Longowal, Sangrur, India
| | | | - Vishal Mutreja
- Department of Chemistry, Chandigarh University, Mohali, India
| | - Ramandeep Kaur
- Department of Chemistry, Punjab Agricultural University, Ludhiana, India
| | - Franklin Ore Areche
- Professional School of Agroindustrial Engineering, National University of Huancavelica, Huancavelica, Peru
| | - Mohannad AlOudat
- Doctoral School of Food Science, Hungarian University of Agriculture and Life Sciences, Budapset, Hungary
| | | | - Béla Kovács
- Institute of Food Science, University of Debrecen, Debrecen, Hungary
| | - Abdelhakam Esmaeil Mohamed Ahmed
- Institute of Food Science, University of Debrecen, Debrecen, Hungary
- Faculty of Forestry, University of Khartoum, Khartoum North, Sudan
- *Correspondence: Abdelhakam Esmaeil Mohamed Ahmed,
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14
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Using genome and transcriptome analysis to elucidate biosynthetic pathways. Curr Opin Biotechnol 2022; 75:102708. [DOI: 10.1016/j.copbio.2022.102708] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/19/2022] [Accepted: 02/23/2022] [Indexed: 12/21/2022]
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15
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Li H, Matsuda H, Tsuboyama A, Munakata R, Sugiyama A, Yazaki K. Inventory of ATP-binding cassette proteins in Lithospermum erythrorhizon as a model plant producing divergent secondary metabolites. DNA Res 2022; 29:6596041. [PMID: 35640979 PMCID: PMC9195045 DOI: 10.1093/dnares/dsac016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/26/2022] [Indexed: 02/07/2023] Open
Abstract
ATP-binding cassette (ABC) proteins are the largest membrane transporter family in plants. In addition to transporting organic substances, these proteins function as ion channels and molecular switches. The development of multiple genes encoding ABC proteins has been associated with their various biological roles. Plants utilize many secondary metabolites to adapt to environmental stresses and to communicate with other organisms, with many ABC proteins thought to be involved in metabolite transport. Lithospermum erythrorhizon is regarded as a model plant for studying secondary metabolism, as cells in culture yielded high concentrations of meroterpenes and phenylpropanoids. Analysis of the genome and transcriptomes of L. erythrorhizon showed expression of genes encoding 118 ABC proteins, similar to other plant species. The number of expressed proteins in the half-size ABCA and full-size ABCB subfamilies was ca. 50% lower in L. erythrorhizon than in Arabidopsis, whereas there was no significant difference in the numbers of other expressed ABC proteins. Because many ABCG proteins are involved in the export of organic substances, members of this subfamily may play important roles in the transport of secondary metabolites that are secreted into apoplasts.
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Affiliation(s)
- Hao Li
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Hinako Matsuda
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Ai Tsuboyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Ryosuke Munakata
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan
| | - Kazufumi Yazaki
- To whom correspondence should be addressed. Tel. +81 774 38 3617.
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16
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Suttiyut T, Auber RP, Ghaste M, Kane CN, McAdam SAM, Wisecaver JH, Widhalm JR. Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis. HORTICULTURE RESEARCH 2022; 9:uhab087. [PMID: 35048120 PMCID: PMC8969065 DOI: 10.1093/hr/uhab087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/07/2021] [Indexed: 05/28/2023]
Abstract
Plant specialized 1,4-naphthoquinones present a remarkable case of convergent evolution. Species across multiple discrete orders of vascular plants produce diverse 1,4-naphthoquinones via one of several pathways using different metabolic precursors. Evolution of these pathways was preceded by events of metabolic innovation and many appear to share connections with biosynthesis of photosynthetic or respiratory quinones. Here, we sought to shed light on the metabolic connections linking shikonin biosynthesis with its precursor pathways and on the origins of shiknoin metabolic genes. Downregulation of Lithospermum erythrorhizon geranyl diphosphate synthase (LeGPPS), recently shown to have been recruited from a cytoplasmic farnesyl diphosphate synthase (FPPS), resulted in reduced shikonin production and a decrease in expression of mevalonic acid and phenylpropanoid pathway genes. Next, we used LeGPPS and other known shikonin pathway genes to build a coexpression network model for identifying new gene connections to shikonin metabolism. Integrative in silico analyses of network genes revealed candidates for biochemical steps in the shikonin pathway arising from Boraginales-specific gene family expansion. Multiple genes in the shikonin coexpression network were also discovered to have originated from duplication of ubiquinone pathway genes. Taken together, our study provides evidence for transcriptional crosstalk between shikonin biosynthesis and its precursor pathways, identifies several shikonin pathway gene candidates and their evolutionary histories, and establishes additional evolutionary links between shikonin and ubiquinone metabolism. Moreover, we demonstrate that global coexpression analysis using limited transcriptomic data obtained from targeted experiments is effective for identifying gene connections within a defined metabolic network.
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Affiliation(s)
- Thiti Suttiyut
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Robert P Auber
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Manoj Ghaste
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Cade N Kane
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Scott A M McAdam
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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17
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Peng LH, Gu TW, Xu Y, Dad HA, Liu JX, Lian JZ, Huang LQ. Gene delivery strategies for therapeutic proteins production in plants: Emerging opportunities and challenges. Biotechnol Adv 2021; 54:107845. [PMID: 34627952 DOI: 10.1016/j.biotechadv.2021.107845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/07/2021] [Accepted: 10/04/2021] [Indexed: 12/19/2022]
Abstract
There are sharply rising demands for pharmaceutical proteins, however shortcomings associated with traditional protein production methods are obvious. Genetic engineering of plant cells has gained importance as a new strategy for protein production. But most current genetic manipulation techniques for plant components, such as gene gun bombardment and Agrobacterium mediated transformation are associated with irreversible tissue damage, species-range limitation, high risk of integrating foreign DNAs into the host genome, and complicated handling procedures. Thus, there is urgent expectation for innovative gene delivery strategies with higher efficiency, fewer side effect, and more practice convenience. Materials based nanovectors have established themselves as novel vehicles for gene delivery to plant cells due to their large specific surface areas, adjustable particle sizes, cationic surface potentials, and modifiability. In this review, multiple techniques employed for plant cell-based genetic engineering and the applications of nanovectors are reviewed. Moreover, different strategies associated with the fusion of nanotechnology and physical techniques are outlined, which immensely augment delivery efficiency and protein yields. Finally, approaches that may overcome the associated challenges of these strategies to optimize plant bioreactors for protein production are discussed.
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Affiliation(s)
- Li-Hua Peng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Ting-Wei Gu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haseeb Anwar Dad
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jia-Zhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lu-Qi Huang
- National Resource Centre for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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18
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Song W, Zhuang Y, Liu T. CYP82AR Subfamily Proteins Catalyze C-1' Hydroxylations of Deoxyshikonin in the Biosynthesis of Shikonin and Alkannin. Org Lett 2021; 23:2455-2459. [PMID: 33728922 DOI: 10.1021/acs.orglett.1c00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Shikonin and S-enantiomer alkannin are important naphthoquinone derivatives present in many Boraginaceae species. We report that cytochrome P450 monooxygenases (CYPs) from a new CYP82AR subfamily catalyzed hydroxylations of deoxyshikonin at C-1' position of isoprenoid side chain. Two homologues were discovered from each species of the four Boraginaceae plants. One CYP preferred converting deoxyshikonin into shikonin, and the other stereoselectively hydroxylated deoxyshikonin into alkannin. The discovery might be a general feature of shikonin/alkannin-producing Boraginaceae plants.
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Affiliation(s)
- Wan Song
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yibin Zhuang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Tao Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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19
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Meyer GW, Bahamon Naranjo MA, Widhalm JR. Convergent evolution of plant specialized 1,4-naphthoquinones: metabolism, trafficking, and resistance to their allelopathic effects. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:167-176. [PMID: 33258472 PMCID: PMC7853596 DOI: 10.1093/jxb/eraa462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/03/2020] [Indexed: 05/08/2023]
Abstract
Plant 1,4-naphthoquinones encompass a class of specialized metabolites known to mediate numerous plant-biotic interactions. This class of compounds also presents a remarkable case of convergent evolution. The 1,4-naphthoquinones are synthesized by species belonging to nearly 20 disparate orders spread throughout vascular plants, and their production occurs via one of four known biochemically distinct pathways. Recent developments from large-scale biology and genetic studies corroborate the existence of multiple pathways to synthesize plant 1,4-naphthoquinones and indicate that extraordinary events of metabolic innovation and links to respiratory and photosynthetic quinone metabolism probably contributed to their independent evolution. Moreover, because many 1,4-naphthoquinones are excreted into the rhizosphere and they are highly reactive in biological systems, plants that synthesize these compounds also needed to independently evolve strategies to deploy them and to resist their effects. In this review, we highlight new progress made in understanding specialized 1,4-naphthoquinone biosynthesis and trafficking with a focus on how these discoveries have shed light on the convergent evolution and diversification of this class of compounds in plants. We also discuss how emerging themes in metabolism-based herbicide resistance may provide clues to mechanisms plants employ to tolerate allelopathic 1,4-naphthoquinones.
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Affiliation(s)
- George W Meyer
- Department of Horticulture and Landscape Architecture, Purdue University, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Maria A Bahamon Naranjo
- Department of Horticulture and Landscape Architecture, Purdue University, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture, Purdue University, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
- Correspondence:
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20
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Oshikiri H, Watanabe B, Yamamoto H, Yazaki K, Takanashi K. Two BAHD Acyltransferases Catalyze the Last Step in the Shikonin/Alkannin Biosynthetic Pathway. PLANT PHYSIOLOGY 2020; 184:753-761. [PMID: 32727911 PMCID: PMC7536692 DOI: 10.1104/pp.20.00207] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/24/2020] [Indexed: 05/28/2023]
Abstract
Several Boraginaceae plants produce biologically active red naphthoquinone pigments, derivatives of the enantiomers shikonin and alkannin, which vary in acyl groups on their side chains. Compositions of shikonin/alkannin derivatives vary in plant species, but the mechanisms generating the diversity of shikonin/alkannin derivatives are largely unknown. This study describes the identification and characterization of two BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1), from Lithospermum erythrorhizon, a medicinal plant in the family Boraginaceae that primarily produces the shikonin/alkannin derivatives acetylshikonin and β-hydroxyisovalerylshikonin. Enzyme assays using Escherichia coli showed that the acylation activity of LeSAT1 was specific to shikonin, whereas the acylation activity of LeAAT1 was specific to alkannin. Both enzymes recognized acetyl-CoA, isobutyryl-CoA, and isovaleryl-CoA as acyl donors to produce their corresponding shikonin/alkannin derivatives, with both enzymes showing the highest activity for acetyl-CoA. These findings were consistent with the composition of shikonin/alkannin derivatives in intact L erythrorhizon plants and cell cultures. Genes encoding both enzymes were preferentially expressed in the roots and cell cultures in the dark in pigment production medium M9, conditions associated with shikonin/alkannin production. These results indicated that LeSAT1 and LeAAT1 are enantiomer-specific acyltransferases that generate various shikonin/alkannin derivatives.
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Affiliation(s)
- Haruka Oshikiri
- Department of Biology, Faculty of Science, Shinshu University, Nagano 390-8621, Japan
| | - Bunta Watanabe
- Institute for Chemical Research, Kyoto University, Kyoto 611-0011, Japan
| | - Hirobumi Yamamoto
- Department of Applied Biology, Faculty of Life Sciences, Toyo University, Gunma 374-0193, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 611-0011, Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Nagano 390-8621, Japan
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21
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Yamamoto H, Tsukahara M, Yamano Y, Wada A, Yazaki K. Alcohol Dehydrogenase Activity Converts 3″-Hydroxy-geranylhydroquinone to an Aldehyde Intermediate for Shikonin and Benzoquinone Derivatives in Lithospermum erythrorhizon. PLANT & CELL PHYSIOLOGY 2020; 61:1798-1806. [PMID: 32810231 DOI: 10.1093/pcp/pcaa108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Shikonin derivatives are red naphthoquinone pigments produced by several boraginaceous plants, such as Lithospermum erythrorhizon. These compounds are biosynthesized from p-hydroxybenzoic acid and geranyl diphosphate. The coupling reaction that yields m-geranyl-p-hydroxybenzoic acid has been actively characterized, but little is known about later biosynthetic reactions. Although 3″-hydroxy-geranylhydroquinone produced from geranylhydroquinone by CYP76B74 has been regarded as an intermediate of shikonin derivatives, the next intermediate has not yet been identified. This study describes a novel alcohol dehydrogenase activity in L. erythrorhizon cell cultures. This enzyme was shown to oxidize the 3″-alcoholic group of (Z)-3″-hydroxy-geranylhydroquinone to an aldehyde moiety concomitant with the isomerization at the C2'-C3' double bond from the Z-form to the E-form. An enzyme oxidizing this substrate was not detected in other plant cell cultures, suggesting that this enzyme is specific to L. erythrorhizon. The reaction product, (E)-3″-oxo-geranylhydroquinone, was further converted to deoxyshikonofuran, another meroterpenoid metabolite produced in L. erythrorhizon cells. Although nonenzymatic cyclization occurred slowly, it was more efficient in the presence of crude enzymes of L. erythrorhizon cells. This activity was detected in both shikonin-producing and nonproducing cells, suggesting that the aldehyde intermediate at the biosynthetic branch point between naphthalene and benzo/hydroquinone ring formation likely constitutes a key common intermediate in the synthesis of shikonin and benzoquinone products, respectively.
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Affiliation(s)
- Hirobumi Yamamoto
- Department of Applied Biosciences, Faculty of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Ora-gun, Gunma, 374-0193 Japan
- Graduate School of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Ora-gun, Gunma, 374-0193 Japan
| | - Mika Tsukahara
- Graduate School of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Ora-gun, Gunma, 374-0193 Japan
| | - Yumiko Yamano
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe, Hyogo, 658-8558 Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Higashinada-ku, Kobe, Hyogo, 658-8558 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
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22
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Kaur D, Alkhder D, Corre C, Alberti F. Engineering Isoprenoid Quinone Production in Yeast. ACS Synth Biol 2020; 9:2239-2245. [PMID: 32786347 DOI: 10.1021/acssynbio.0c00081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isoprenoid quinones are bioactive molecules that include an isoprenoid chain and a quinone head. They are traditionally found to be involved in primary metabolism, where they act as electron transporters, but specialized isoprenoid quinones are also produced by all domains of life. Here, we report the engineering of a baker's yeast strain, Saccharomyces cerevisiae EPYFA3, for the production of isoprenoid quinones. Our yeast strain was developed through overexpression of the shikimate pathway in a well-established recipient strain (S. cerevisiae EPY300) where the mevalonate pathway is overexpressed. As a proof of concept, our new host strain was used to overproduce the endogenous isoprenoid quinone coenzyme Q6, resulting in a nearly 3-fold production increase. EPYFA3 represents a valuable platform for the heterologous production of high value isoprenoid quinones. EPYFA3 will also facilitate the elucidation of isoprenoid quinone biosynthetic pathways.
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Affiliation(s)
- Divjot Kaur
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Duha Alkhder
- Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Christophe Corre
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Fabrizio Alberti
- School of Life Sciences and Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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23
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Izuishi Y, Isaka N, Li H, Nakanishi K, Kageyama J, Ishikawa K, Shimada T, Masuta C, Yoshikawa N, Kusano H, Yazaki K. Apple latent spherical virus (ALSV)-induced gene silencing in a medicinal plant, Lithospermum erythrorhizon. Sci Rep 2020; 10:13555. [PMID: 32782359 PMCID: PMC7421898 DOI: 10.1038/s41598-020-70469-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/27/2020] [Indexed: 11/12/2022] Open
Abstract
Lithospermum erythrorhizon is a medicinal plant that produces shikonin, a red lipophilic naphthoquinone derivative that accumulates exclusively in roots. The biosynthetic steps required to complete the naphthalene ring of shikonin and its mechanism of secretion remain unclear. Multiple omics studies identified several candidate genes involved in shikonin production. The functions of these genes can be evaluated using virus-induced gene silencing (VIGS) systems, which have been shown advantageous in introducing iRNA genes into non-model plants. This study describes the development of a VIGS system using an apple latent spherical virus (ALSV) vector and a target gene, phytoene desaturase (LePDS1). Virus particles packaged in Nicotiana benthamiana were inoculated into L. erythrorhizon seedlings, yielding new leaves with albino phenotype but without disease symptoms. The levels of LePDS1 mRNAs were significantly lower in the albino plants than in mock control or escape plants. Virus-derived mRNA was detected in infected plants but not in escape and mock plants. Quantitative PCR and deep sequencing analysis indicated that transcription of another hypothetical PDS gene (LePDS2) also decreased in the defective leaves. Virus infection, however, had no effect on shikonin production. These results suggest that virus-based genetic transformation and the VIGS system silence target genes in soil-grown L. erythrorhizon.
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Affiliation(s)
- Yuki Izuishi
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Natsumi Isaka
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Hao Li
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Kohei Nakanishi
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Joji Kageyama
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Kazuya Ishikawa
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoo Shimada
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo, 060-8589, Japan
| | - Nobuyuki Yoshikawa
- Agri-Innovation Center, Iwate University, Morioka 3-18-8, Iwate, 020-8550, Japan
| | - Hiroaki Kusano
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan
| | - Kazufumi Yazaki
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011, Japan.
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24
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Song W, Zhuang Y, Liu T. Potential role of two cytochrome P450s obtained from Lithospermum erythrorhizon in catalyzing the oxidation of geranylhydroquinone during Shikonin biosynthesis. PHYTOCHEMISTRY 2020; 175:112375. [PMID: 32305685 DOI: 10.1016/j.phytochem.2020.112375] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Shikonin is a natural naphthoquinone derivative that specifically occurs in boraginaceous plants, and the major active ingredient of the medicinal plant Lithospermum erythrorhizon. Previously, a cytochrome P450 oxygenase (CYP) CYP76B74 catalyzing 3″-hydroxylation of geranylhydroquinone (GHQ) - a key intermediate of shikonin biosynthesis, was identified from cultured cells of Arnebia euchroma. However, the enzymes catalyzing oxidation of the geranyl side-chain of GHQ from L. erythrorhizon remain unknown. In this study, we performed transcriptome analysis of different tissues (red roots and green leaves/stems) from L. erythrorhizon using RNA sequencing technology. Highly expressed CYP genes found in the roots were then heterologously expressed in Saccharomyces cerevisiae and functionally screened with GHQ as the substrate. As the result, two CYPs of CYP76B subfamily catalyzing the oxidation of GHQ were characterized. CYP76B100 catalyzed the hydroxylation of the geranyl side-chain of GHQ at the C-3″ position to form 3″-hydroxyl geranylhydroquinone (GHQ-3″-OH). The enzyme CYP76B101 carried out oxidation reaction of GHQ at the C-3″ position to produce a 3″-carboxylic acid derivative of GHQ (GHQ-3″-COOH) as well as GHQ-3″-OH. This enzyme-catalyzed oxidation reaction with GHQ as the substrate is reported for the first time. This study implicates CYP76B100 and CYP76B101 as having a potential role in shikonin biosynthesis in L. erythrorhizon.
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Affiliation(s)
- Wan Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yibin Zhuang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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25
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Auber RP, Suttiyut T, McCoy RM, Ghaste M, Crook JW, Pendleton AL, Widhalm JR, Wisecaver JH. Hybrid de novo genome assembly of red gromwell ( Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis. HORTICULTURE RESEARCH 2020; 7:82. [PMID: 32528694 PMCID: PMC7261806 DOI: 10.1038/s41438-020-0301-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/06/2020] [Accepted: 03/31/2020] [Indexed: 05/08/2023]
Abstract
Lithospermum erythrorhizon (red gromwell; zicao) is a medicinal and economically valuable plant belonging to the Boraginaceae family. Roots from L. erythrorhizon have been used for centuries based on the antiviral and wound-healing properties produced from the bioactive compound shikonin and its derivatives. More recently, shikonin, its enantiomer alkannin, and several other shikonin/alkannin derivatives have collectively emerged as valuable natural colorants and as novel drug scaffolds. Despite several transcriptomes and proteomes having been generated from L. erythrorhizon, a reference genome is still unavailable. This has limited investigations into elucidating the shikonin/alkannin pathway and understanding its evolutionary and ecological significance. In this study, we obtained a de novo genome assembly for L. erythrorhizon using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies. The resulting genome is ∼367.41 Mb long, with a contig N50 size of 314.31 kb and 27,720 predicted protein-coding genes. Using the L. erythrorhizon genome, we identified several additional p-hydroxybenzoate:geranyltransferase (PGT) homologs and provide insight into their evolutionary history. Phylogenetic analysis of prenyltransferases suggests that PGTs originated in a common ancestor of modern shikonin/alkannin-producing Boraginaceous species, likely from a retrotransposition-derived duplication event of an ancestral prenyltransferase gene. Furthermore, knocking down expression of LePGT1 in L. erythrorhizon hairy root lines revealed that LePGT1 is predominantly responsible for shikonin production early in culture establishment. Taken together, the reference genome reported in this study and the provided analysis on the evolutionary origin of shikonin/alkannin biosynthesis will guide elucidation of the remainder of the pathway.
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Affiliation(s)
- Robert P. Auber
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
| | - Thiti Suttiyut
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Rachel M. McCoy
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Manoj Ghaste
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Joseph W. Crook
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Amanda L. Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
| | - Joshua R. Widhalm
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Jennifer H. Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907 USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907 USA
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26
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Tatsumi K, Ichino T, Onishi N, Shimomura K, Yazaki K. Highly efficient method of Lithospermum erythrorhizon transformation using domestic Rhizobium rhizogenes strain A13. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:39-46. [PMID: 32362747 PMCID: PMC7193830 DOI: 10.5511/plantbiotechnology.19.1212a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/12/2019] [Indexed: 06/11/2023]
Abstract
Lithospermum erythrorhizon, a medicinal plant growing in Asian countries, produces shikonin derivatives that are lipophilic secondary metabolites. These red naphthoquinone pigments are traditionally used as a natural drug and a dye in East Asia. In intact L. erythrorhizon plants, shikonin derivatives are produced in the root epidermal cells and secreted into extracellular spaces. The biosynthetic pathway for shikonin derivatives remains incompletely understood and the secretion mechanisms are largely unknown. Understanding the molecular mechanisms underlying shikonin biosynthesis and transport in L. erythrorhizon cells requires functional analysis of candidate genes using transgenic plants. To date, however, standard transformation methods have not yet been established. This study describes an efficient method for L. erythrorhizon transformation using hairy roots by Rhizobium rhizogenes strain A13, present domestically in Japan. Hairy roots of L. erythrorhizon were generated from explants of the axenic shoots that were infected with R. rhizogenes strain A13. Integration into the genome was assessed by PCR amplifying a transgene encoding green fluorescent protein (GFP) and by monitoring GFP expression. This method enhanced transformation efficiency 50-70%. Although methods for the systematic stable transformation of L. erythrorhizon plants have not yet been reported, the method described in this study resulted in highly efficient stable transformation using hairy roots. This method enables the functional analysis of L. erythrorhizon genes.
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Affiliation(s)
- Kanade Tatsumi
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takuji Ichino
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Noboru Onishi
- Central Laboratories for Key Technologies, Kirin Holdings Company Limited, 1-13-5 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Koichiro Shimomura
- Graduate School of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma 374-0193, Japan
| | - Kazufumi Yazaki
- Laboratory of Plant Gene Expression, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
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27
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Tang CY, Li S, Wang YT, Wang X. Comparative genome/transcriptome analysis probes Boraginales' phylogenetic position, WGDs in Boraginales, and key enzyme genes in the alkannin/shikonin core pathway. Mol Ecol Resour 2019; 20:228-241. [PMID: 31625679 DOI: 10.1111/1755-0998.13104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 12/27/2022]
Abstract
Boraginales (the forget-me-not order) is a core group within the lamiids clade. However, until now, no genome from Boraginales has been reported, and published transcriptomes are also rare. Here, we report the first Boraginales species de novo genome (i.e. Echium plantagineum genome) and seven other Boraginales species transcriptomes to probe three issues: (i) Boraginales' phylogenetic position within the lamiids clade; (ii) potential whole genome duplications (WGDs) in Boraginales; and (iii) candidate key enzyme genes in the alkannin/shikonin core pathway. The results showed that: (i) Boraginales was most probably closer to the Solanales/Gentianales clade than the Lamiales clade, at least based on the single-copy orthologous genes from genome/transcriptome data; (ii) after the gamma (γ) event, Boraginaceae (classified into the Boraginales I clade) probably underwent at least two rounds of WGD, whereas Heliotropiaceae and Ehretiaceae (classified into the Boraginales II clade) probably underwent only one round of WGD; and (iii) several candidate key enzyme genes in the alkannin/shikonin core pathway were inferred, e.g. genes corresponding to geranyl cyclase, naphthol hydroxylase and O-acyl transferase.
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Affiliation(s)
- Cheng-Yi Tang
- School of the Environment, Nanjing University, Nanjing, China
| | - Song Li
- School of the Environment, Nanjing University, Nanjing, China.,Biomarker Technologies Corporation, Beijing, China
| | | | - Xi Wang
- Biomarker Technologies Corporation, Beijing, China
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