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Yan Y, Luo H, Qin Y, Yan T, Jia J, Hou Y, Liu Z, Zhai J, Long Y, Deng X, Cao X. Light controls mesophyll-specific post-transcriptional splicing of photoregulatory genes by AtPRMT5. Proc Natl Acad Sci U S A 2024; 121:e2317408121. [PMID: 38285953 PMCID: PMC10861865 DOI: 10.1073/pnas.2317408121] [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: 10/14/2023] [Accepted: 12/29/2023] [Indexed: 01/31/2024] Open
Abstract
Light plays a central role in plant growth and development, providing an energy source and governing various aspects of plant morphology. Previous study showed that many polyadenylated full-length RNA molecules within the nucleus contain unspliced introns (post-transcriptionally spliced introns, PTS introns), which may play a role in rapidly responding to changes in environmental signals. However, the mechanism underlying post-transcriptional regulation during initial light exposure of young, etiolated seedlings remains elusive. In this study, we used FLEP-seq2, a Nanopore-based sequencing technique, to analyze nuclear RNAs in Arabidopsis (Arabidopsis thaliana) seedlings under different light conditions and found numerous light-responsive PTS introns. We also used single-nucleus RNA sequencing (snRNA-seq) to profile transcripts in single nucleus and investigate the distribution of light-responsive PTS introns across distinct cell types. We established that light-induced PTS introns are predominant in mesophyll cells during seedling de-etiolation following exposure of etiolated seedlings to light. We further demonstrated the involvement of the splicing-related factor A. thaliana PROTEIN ARGININE METHYLTRANSFERASE 5 (AtPRMT5), working in concert with the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), a critical repressor of light signaling pathways. We showed that these two proteins orchestrate light-induced PTS events in mesophyll cells and facilitate chloroplast development, photosynthesis, and morphogenesis in response to ever-changing light conditions. These findings provide crucial insights into the intricate mechanisms underlying plant acclimation to light at the cell-type level.
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Affiliation(s)
- Yan Yan
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Haofei Luo
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Yuwei Qin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Tingting Yan
- Key Laboratory of Tropical Fruit Tree Biology of Hainan Province, Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences, Haikou571100, China
| | - Jinbu Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yifeng Hou
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Zhijian Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Yanping Long
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen518055, China
| | - Xian Deng
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
| | - Xiaofeng Cao
- Key Laboratory of Seed Innovation, State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
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Zheng B, Li YT, Wu QP, Zhao W, Ren TH, Zhang XH, Li G, Ning TY, Zhang ZS. Maize (Zea mays L.) planted at higher density utilizes dynamic light more efficiently. PLANT, CELL & ENVIRONMENT 2023; 46:3305-3322. [PMID: 37485705 DOI: 10.1111/pce.14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
In nature, plants are exposed to a dynamic light environment. Fluctuations in light decreased the photosynthetic light utilization efficiency (PLUE) of leaves, and much more severely in C4 species than in C3 species. However, little is known about the plasticity of PLUE under dynamic light in C4 species. Present study focused on the influence of planting density to the photosynthesis under dynamic light in maize (Zea mays L.), a most important C4 crop. In addition, the molecular mechanism behind photosynthetic adaptation to planting density were also explored by quantitative proteomics analysis. Results revealed that as planting density increases, maize leaves receive less light that fluctuates more. The maize planted at high density (HD) improved the PLUE under dynamic light, especially in the middle and later growth stages. Quantitative proteomics analysis showed that the transfer of nitrogen from Rubisco to RuBP regeneration and C4 pathway related enzymes contributes to the photosynthetic adaptation to lower and more fluctuating light environment in HD maize. This study provides potential ways to further improve the light energy utilization efficiency of maize in HD.
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Affiliation(s)
- Bin Zheng
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Yu-Ting Li
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Qiu-Ping Wu
- Jining Academy of Agricultural Sciences, Shandong, P. R. China
| | - Wei Zhao
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Ting-Hu Ren
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Xing-Hui Zhang
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Geng Li
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Tang-Yuan Ning
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, P. R. China
| | - Zi-Shan Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, P. R. China
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Chen W, Zhang J, Li D, Wang Y. Application of Isothermal Signal Amplification Technique in the Etiological Diagnosis of Gonorrhea and Drug Resistance Gene Detection. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5989889. [PMID: 35813416 PMCID: PMC9270114 DOI: 10.1155/2022/5989889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/18/2022]
Abstract
Background: Isothermal signal amplification technique is developed based on the rolling ring amplification mechanism of cyclic DNA molecules in nature. This technique plays an extremely beneficial role in gonorrhea pathogen identification and drug resistance gene detection. Aims: This study analyzes the isothermal signal amplification techniques in the etiological diagnosis of gonorrhea and drug resistance gene detection. Materials and Methods: Urethral, cervical secretion, or prostatic fluid samples from 322 cases of gonorrhea collected from January 2018 to December 2021 at the STD clinic of our hospital dermatology department were selected for direct smear examination and gonococcal culture examination; DNA was extracted from urethral, cervical secretion, or prostatic fluid samples and then used for pathogen identification by SAT assay and rolling loop nucleic acid amplification technique, smear examination and pathogen culture examination methods, SAT assay, and isothermal signal amplification technique for comparative sensitivity and specificity analysis. Results: The highest rate of gonorrhea positivity was for the urine rolling loop nucleic acid amplification technique, followed by the swab rolling loop nucleic acid amplification technique, and the lowest rate of gonorrhea positivity was for the urine SAT test. The difference in the positivity rate between the two urine testing methods was statistically significant (P < 0.05). The highest sensitivity of the urine rolling loop nucleic acid amplification technique method for the detection of gonorrhea pathogens and the lowest sensitivity of the urine SAT method were statistically significant (P < 0.01). The differences in sensitivity and specificity between the swab rolling loop nucleic acid amplification technique and the swab SAT method were not statistically significant (P > 0.05). ROC curves were plotted based on sensitivity and specificity, with swab SAT assay (AUC = 0.998) > rolling loop nucleic acid amplification technique (AUC = 0.981). Comparing the negative rates of urine and swab rolling loop nucleic acid amplification technique and urine SAT assay, the differences were not statistically significant (P > 0.05). Conclusion: The isothermal signal amplification technique improves the shortcomings of gonorrhea pathogen identification means and drug resistance gene detection methods, with good detection sensitivity and specificity, simple operation, low price, and easy promotion, which has obvious advantages in clinical applications and epidemiological studies.
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Affiliation(s)
- Wei Chen
- Wuhan Fourth Hospital, Oncology Department, China
| | | | - Dongsheng Li
- Wuhan No.1 Hospital, Department of Dermatology, China
| | - Yue Wang
- Wuhan No.1 Hospital, Department of Dermatology, China
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Yokochi Y, Yoshida K, Hahn F, Miyagi A, Wakabayashi KI, Kawai-Yamada M, Weber APM, Hisabori T. Redox regulation of NADP-malate dehydrogenase is vital for land plants under fluctuating light environment. Proc Natl Acad Sci U S A 2021; 118:e2016903118. [PMID: 33531363 PMCID: PMC8017969 DOI: 10.1073/pnas.2016903118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Many enzymes involved in photosynthesis possess highly conserved cysteine residues that serve as redox switches in chloroplasts. These redox switches function to activate or deactivate enzymes during light-dark transitions and have the function of fine-tuning their activities according to the intensity of light. Accordingly, many studies on chloroplast redox regulation have been conducted under the hypothesis that "fine regulation of the activities of these enzymes is crucial for efficient photosynthesis." However, the impact of the regulatory system on plant metabolism is still unclear. To test this hypothesis, we here studied the impact of the ablation of a redox switch in chloroplast NADP-malate dehydrogenase (MDH). By genome editing, we generated a mutant plant whose MDH lacks one of its redox switches and is active even in dark conditions. Although NADPH consumption by MDH in the dark is expected to be harmful to plant growth, the mutant line did not show any phenotypic differences under standard long-day conditions. In contrast, the mutant line showed severe growth retardation under short-day or fluctuating light conditions. These results indicate that thiol-switch redox regulation of MDH activity is crucial for maintaining NADPH homeostasis in chloroplasts under these conditions.
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Affiliation(s)
- Yuichi Yokochi
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
| | - Keisuke Yoshida
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
| | - Florian Hahn
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Center for Synthetic Life Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Atsuko Miyagi
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 338-8570 Saitama, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
| | - Maki Kawai-Yamada
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, 338-8570 Saitama, Japan
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences, Center for Synthetic Life Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Toru Hisabori
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 226-8503 Yokohama, Japan;
- School of Life Science and Technology, Tokyo Institute of Technology, 226-8503 Yokohama, Japan
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