1
|
Long Q, Zhang C, Zhu H, Zhou Y, Liu S, Liu Y, Ma X, An W, Zhou J, Zhao J, Zhang Y, Jin C. Comparative metabolomics combined with genome sequencing provides insights into novel wolfberry-specific metabolites and their formation mechanisms. FRONTIERS IN PLANT SCIENCE 2024; 15:1392175. [PMID: 38736439 PMCID: PMC11082402 DOI: 10.3389/fpls.2024.1392175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
Wolfberry (Lycium, of the family Solanaceae) has special nutritional benefits due to its valuable metabolites. Here, 16 wolfberry-specific metabolites were identified by comparing the metabolome of wolfberry with those of six species, including maize, rice, wheat, soybean, tomato and grape. The copy numbers of the riboflavin and phenyllactate degradation genes riboflavin kinase (RFK) and phenyllactate UDP-glycosyltransferase (UGT1) were lower in wolfberry than in other species, while the copy number of the phenyllactate synthesis gene hydroxyphenyl-pyruvate reductase (HPPR) was higher in wolfberry, suggesting that the copy number variation of these genes among species may be the main reason for the specific accumulation of riboflavin and phenyllactate in wolfberry. Moreover, the metabolome-based neighbor-joining tree revealed distinct clustering of monocots and dicots, suggesting that metabolites could reflect the evolutionary relationship among those species. Taken together, we identified 16 specific metabolites in wolfberry and provided new insight into the accumulation mechanism of species-specific metabolites at the genomic level.
Collapse
Affiliation(s)
- Qiyuan Long
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Changjian Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Hui Zhu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Yutong Zhou
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Shuo Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Yanchen Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Xuemin Ma
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Wei An
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Jun Zhou
- College of Biological Science and Engineering, North Minzu University, Yinchuan, China
| | - Jianhua Zhao
- National Wolfberry Engineering Research Center, Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yuanyuan Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Cheng Jin
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| |
Collapse
|
2
|
Zhao J, Xu Y, Li H, Zhu X, Yin Y, Zhang X, Qin X, Zhou J, Duan L, Liang X, Huang T, Zhang B, Wan R, Shi Z, Cao Y, An W. ERF5.1 modulates carotenoid accumulation by interacting with CCD4.1 in Lycium. HORTICULTURE RESEARCH 2023; 10:uhad230. [PMID: 38143484 PMCID: PMC10745278 DOI: 10.1093/hr/uhad230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/01/2023] [Indexed: 12/26/2023]
Abstract
Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (CCD4) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in Lycium have not been discovered. Here, we annotated LbCCDs from the Lycium reference genome and found that LbCCD4.1 expression was significantly correlated with the carotenoid metabolites during Lycium five fruit developmental stages. Over-expression of LbCCD4.1 in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, LbERF5.1, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing ERF5.1 transgenic NQ's leaves. Over-expression or virus-induced gene silencing of LbERF5.1 in NQ's leaves induced a consistent up- or down-expression, respectively, of LbCCD4.1. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that ERF5.1 interacted with the promoter of CCD4.1 to increase its expression, and LbERF5.1 could bind to any one of the three predicted binding sites in the promoter of LbCCD4.1. A transcriptome analysis of LbERF5.1 and LbCCD4.1 over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between ERF5.1 and CCD4.1, which may be used to enhance carotenoid in Lycium.
Collapse
Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yuhui Xu
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Haoxia Li
- Institute of Forestry and Grassland Ecology, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xinlei Zhu
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Yue Yin
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xiyan Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | | | - Jun Zhou
- College of Biological Science & Engineering, North Minzu University, Yinchuan 750021, China
| | - Linyuan Duan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Ting Huang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Bo Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Ru Wan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Zhigang Shi
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Wei An
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| |
Collapse
|
3
|
Varghese R, S UK, C GPD, Ramamoorthy S. Unraveling the versatility of CCD4: Metabolic engineering, transcriptomic and computational approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110991. [PMID: 34315605 DOI: 10.1016/j.plantsci.2021.110991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/16/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Carotenoids are economically valuable isoprenoids synthesized by plants and microorganisms, which play a paramount role in their overall growth and development. Carotenoid cleavage dioxygenases are a vast group of enzymes that specifically cleave thecarotenoids to produce apocarotenoids. Recently, CCDs are a subject of talk because of their contributions to different aspects of plant growth and due to their significance in the production of economically valuable apocarotenoids. Among them, CCD4 stands unique because of its versatility in performing metabolic roles. This review focuses on the multiple functionalities of CCD4 like pigmentation, volatile apocarotenoid production, stress responses, etc. Interestingly, through our literature survey we arrived at a conclusion that CCD4 could perform functions of other carotenoid cleaving enzymes.The metabolic engineering, transcriptomic, and computational approaches adopted to reveal the contributions of CCD4 were also considered here for the study.Phylogenetic analysis was performed to delve into the evolutionary relationships of CCD4 in different plant groups. A tree of 81CCD genes from 64 plant species was constructed, signifying the presence of well-conserved families. Gene structures were illustrated and the difference in the number and position of exons could be considered as a factor behind functional versatility and substrate tolerance of CCD4 in different plants.
Collapse
Affiliation(s)
- Ressin Varghese
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Udhaya Kumar S
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - George Priya Doss C
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Siva Ramamoorthy
- School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
4
|
Gao J, Liu J, Jiang C, Chen S, Huang L. Identification of suitable reference genes for studies of Syringa pinnatifolia Hemsl. FEBS Open Bio 2021; 11:1041-1053. [PMID: 33484622 PMCID: PMC8016119 DOI: 10.1002/2211-5463.13097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
Syringa pinnatifolia Hemsl. (Oleaceae) is a species of shrub with a limited distribution in China. Several chemical compounds with pharmacological effects have been isolated from S. pinnatifolia, including new lignans and sesquiterpenes. Studies of gene expression in this species require the identification of suitable reference genes that are stably expressed under different conditions and in different tissues. To identify candidate reference genes, here we used the geNorm, NormFinder, and BestKeeper algorithms to analyze the stability of 12 candidate genes. The geometric mean of the rankings generated with these algorithms was used to obtain a comprehensive ranking. TBP and PP2A were found to be appropriate reference genes for calli treated with different external stimuli, and TIP41 and TBP were found to be appropriate reference genes in differentiated tissues. When calli and differentiated tissues were considered together, TBP and TIP41 were found to be the most reliable reference genes. The selected genes were validated by analysis of HMGR expression in calli and differentiated tissues. This study is the first to screen candidate reference genes in the genus Syringa and could help guide future molecular studies in this genus.
Collapse
Affiliation(s)
- Jiaqi Gao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Suyile Chen
- Alashan Mongolian Hospital, Alashan East Banner of Alashan, Inner Mongolia, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmacy, Jiangsu University, Zhenjiang, China
| |
Collapse
|