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Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes (Basel) 2024; 15:1072. [PMID: 39202430 PMCID: PMC11353317 DOI: 10.3390/genes15081072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 2024; 95:101287. [PMID: 38906423 DOI: 10.1016/j.plipres.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Terpenoids constitute one of the largest and most chemically diverse classes of primary and secondary metabolites in nature with an exceptional breadth of functional roles in plants. Biosynthesis of all terpenoids begins with the universal five‑carbon building blocks, isopentenyl diphosphate (IPP) and its allylic isomer dimethylallyl diphosphate (DMAPP), which in plants are derived from two compartmentally separated but metabolically crosstalking routes, the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways. Here, we review the current knowledge on the terpenoid precursor pathways and highlight the critical hidden constraints as well as multiple regulatory mechanisms that coordinate and homeostatically govern carbon flux through the terpenoid biosynthetic network in plants.
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Affiliation(s)
- Matthew E Bergman
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Ruy W J Kortbeek
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Michael Gutensohn
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, United States; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States.
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Cheng Y, Xiang N, Chen H, Zhao Y, Wang L, Cheng X, Guo X. The modulation of light quality on carotenoid and tocochromanol biosynthesis in mung bean ( Vigna radiata) sprouts. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 6:100170. [PMID: 36950347 PMCID: PMC10025981 DOI: 10.1016/j.fochms.2023.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023]
Abstract
This study aimed to identify the regulatory mechanisms of white, blue, red lights on carotenoid and tocochromanol biosynthesis in mung bean sprouts. Results showed that three lights stimulated the increase of the predominated lutein (3.2-8.1 folds) and violaxanthin (2.1-6.1 folds) in sprouts as compared with dark control, as well as β-carotene (20-36 folds), with the best yield observed under white light. Light signals also promoted α- and γ-tocopherol accumulation (up to 1.8 folds) as compared with dark control. The CRTISO, LUT5 and DXS (1.24-6.34 folds) exhibited high expression levels under light quality conditions, resulting in an overaccumulation of carotenoids. The MPBQ-MT, TC and TMT were decisive genes in tocochromanol biosynthesis, and were expressed up to 4.19 folds as compared with control. Overall, the results could provide novel insights into light-mediated regulation and fortification of carotenoids and tocopherols, as well as guide future agricultural cultivation of mung bean sprouts.
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Key Words
- BL, blue light
- Biofortification
- Biosynthesis
- CK, dark control
- Carotenoids
- HPLC, high performance liquid chromatography
- LEDs, light-emitting diodes
- LHCII, light-harvesting complex of PSII
- LQ, light quality
- Light quality
- MEP, methylerythritol phosphate
- Mung bean
- NASH, nonalcoholic steatohepatitis
- PS, photosynthesis
- PSII, photosystem II
- PSs, photosystems
- RL, red light
- Tocopherols
- VAD, vitamin A deficiency
- WL, white light
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Affiliation(s)
- Yaoyao Cheng
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China
| | - Nan Xiang
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China
| | - Honglin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yihan Zhao
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China
| | - Lixia Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuzhen Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding authors.
| | - Xinbo Guo
- School of Food Science and Engineering, Ministry of Education Engineering Research Centre of Starch & Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou 510640, China
- Corresponding authors.
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Hou Z, Xu D, Deng N, Li Y, Yang L, Li S, Zhou H, Huang Q, Wang X. Comparative Proteomics of Mulberry Leaves at Different Developmental Stages Identify Novel Proteins Function Related to Photosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:797631. [PMID: 35003187 PMCID: PMC8739898 DOI: 10.3389/fpls.2021.797631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Mulberry leaves at different positions are different in photosynthetic rate, nutrient substance and feeding impact to silkworms. Here, we investigated the proteomic differences of the first (L1), sixth (L6), and twentieth (L20) mulberry leaves at different stem positions (from top to the base) using a label-free quantitative proteomics approach. L1 contained less developed photosynthetic apparatus but was more active in protein synthesis. L20 has more channel proteins and oxidoreductases relative to L6. Proteins that detected in all measured leaves were classified into three groups according to their expression patterns in L1, L6, and L20. The protein group that displayed the maximum amount in L6 has the highest possibility that function related to photosynthesis. Nine function unknown proteins belong to this group were further analyzed in the light responsive expression, evolutionary tree and sub-cellular localization analysis. Based on the results, five proteins were suggested to be involved in photosynthesis. Taken together, these results reveal the molecular details of different roles of mulberry leaves at different developmental stages and contribute to the identification of five proteins that might function related to photosynthesis.
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Affiliation(s)
- Zhiwei Hou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Dashun Xu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Na Deng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yan Li
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Luoling Yang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Shuxuan Li
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Hong Zhou
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Qintao Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xiling Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
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