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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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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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Sohn SI, Pandian S, Rakkammal K, Largia MJV, Thamilarasan SK, Balaji S, Zoclanclounon YAB, Shilpha J, Ramesh M. Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview. FRONTIERS IN PLANT SCIENCE 2022; 13:942789. [PMID: 36035665 PMCID: PMC9407636 DOI: 10.3389/fpls.2022.942789] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.
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Affiliation(s)
- Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | | | - Senthil Kumar Thamilarasan
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | | | - Yedomon Ange Bovys Zoclanclounon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jayabalan Shilpha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Manikandan Ramesh
- Department of Biotechnology, Alagappa University, Karaikudi, Tamil Nadu, India
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Kumar A, Shashni S, Kumar P, Pant D, Singh A, Verma RK. Phytochemical constituents, distributions and traditional usages of Arnebia euchroma: A review. JOURNAL OF ETHNOPHARMACOLOGY 2021; 271:113896. [PMID: 33524510 DOI: 10.1016/j.jep.2021.113896] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 01/02/2021] [Accepted: 01/24/2021] [Indexed: 05/20/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The present study has indicated phytochemical composition, distribution and ethno-medicinal uses of Arnebia euchroma (Royle) I.M. Johnst, which is commonly known as "Ratanjot" in the Indian subcontinent. It has widely been used in the traditional systems of the Unani, Ayurvedic and Chinese medicines recipes due to its anti-fungal and anti-microbial properties. Instead, the gap of earlier studies is well defined that will be helpful for researchers to carry out more analysis and increase medicinal importance of this plant. AIM OF STUDY The main aim of this review study is to demonstrate the phytochemical composition and traditional ethno-medicinal uses of A. euchroma all over the world. Earlier studies related to this plant have been discussed in the present study and on that basis, future perspective of A. euchroma is also proposed. MATERIALS AND METHODS The information of A. euchroma has been gathered from various electronic database, reference books and available literature. RESULTS The study has indicated that Arnebia euchroma owing to anti-microbial and anti-inflammatory properties is used in the traditional medicines and pharmaceutical industries for the treatment of hair problems, remitting, chronic diseases, burnt limbs, cough and cold, etc., and besides as a vegetable colorant and dyeing of cloths. The important phytochemical constituents viz., shikonin, acetyl-shikonin, iso-butyryl-shikonin, β,β-di-methylacryl-shikonin, isovaleryl-shikonin, β-hydroxy-isovaleryl-shikonin, deoxy-shikonin, isobutyl-shikonin, arnebinone, arnebin-7, stigmasterol, etc., isolated from the roots of Arnebia euchroma are used for curing various harmful diseases. CONCLUSIONS The earlier studies have confirmed that Arnebia euchroma is having wound healing, anti-microbial and anti-bacterial properties and thus used for the treatment of several diseases. Although, a little works is done on the experimental study regarding anti-HIV, anti-cancer diseases, etc., so there is a requirement of more exploration via analytical studies on phytochemical compounds to treat such diseases. Moreover, the information of its clinical and pharmacokinetics uses is also limited. Therefore, further research is needed to understand bioavailability and pharmacokinetics of this species. In-situ and ex-situ conservations for the management of this endangered species are also lacking in the Himalayan perspective. Such studies will emphasize to explore the possibilities for its conservation and development of agro-technological protocol.
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Affiliation(s)
- Anil Kumar
- Himalayan Forest Research Institute, Panthaganti, Shimla, Himachal Pradesh, 171013, India; G. B. Pant National Institute of Himalayan Environment Himachal Regional Centre Mohal, Kullu, 175126, India.
| | - Sarla Shashni
- G. B. Pant National Institute of Himalayan Environment Himachal Regional Centre Mohal, Kullu, 175126, India
| | - Pawan Kumar
- Department of Environmental Studies, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana, 123031, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana, 123031, India
| | - Ashok Singh
- CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Raj Kumar Verma
- Himalayan Forest Research Institute, Panthaganti, Shimla, Himachal Pradesh, 171013, India
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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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Wu FY, Tang CY, Guo YM, Bian ZW, Fu JY, Lu GH, Qi JL, Pang YJ, Yang YH. Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales' evolutionary history. Sci Rep 2017; 7:4477. [PMID: 28667265 PMCID: PMC5493674 DOI: 10.1038/s41598-017-04750-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/22/2017] [Indexed: 11/09/2022] Open
Abstract
Shikonin and its derivatives extracted from Lithospermeae plants' red roots have current applications in food and pharmaceutical industries. Previous studies have cloned some genes related to shikonin biosynthesis. However, most genes related to shikonin biosynthesis remain unclear, because the lack of the genome/transcriptome of the Lithospermeae plants. Therefore, in order to provide a new understanding of shikonin biosynthesis, we obtained transcriptome data and unigenes expression profiles in three shikonin-producing Lithospermeae plants, i.e., Lithospermum erythrorhizon, Arnebia euchroma and Echium plantagineum. As a result, two unigenes (i.e., G10H and 12OPR) that are involved in "shikonin downstream biosynthesis" and "methyl jasmonate biosynthesis" were deemed to relate to shikonin biosynthesis in this study. Furthermore, we conducted a Lamiids phylogenetic model and identified orthologous unigenes under positive selection in above three Lithospermeae plants. The results indicated Boraginales was more relative to Solanales/Gentianales than to Lamiales.
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Affiliation(s)
- Feng-Yao Wu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Cheng-Yi Tang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yu-Min Guo
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Zhuo-Wu Bian
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jiang-Yan Fu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Gui-Hua Lu
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Jin-Liang Qi
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Yan-Jun Pang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Yong-Hua Yang
- State Key Laboratory of Pharmaceutical Biotechnology, NJU-NJFU Joint Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
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Hao H, Pu GB, Lei CY, Ye HC, Wang H. Effects of ammonium ion on cell growth and biosynthesis of shikonin derivatives in callus tissues of Arnebia euchroma. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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