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Wang Y, Sun X, Peng J, Li F, Ali F, Wang Z. Regulation of seed germination: ROS, epigenetic, and hormonal aspects. J Adv Res 2024:S2090-1232(24)00225-X. [PMID: 38838783 DOI: 10.1016/j.jare.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus. AIM of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement. KEY SCIENTIFIC CONCEPTS OF REVIEW We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.
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Affiliation(s)
- Yakong Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangyang Sun
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
| | - Jun Peng
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China
| | - Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, Hainan, China; State Key Laboratory of Cotton Bio‑breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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2
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Willig JJ, Guarneri N, van Loon T, Wahyuni S, Astudillo-Estévez IE, Xu L, Willemsen V, Goverse A, Sterken MG, Lozano-Torres JL, Bakker J, Smant G. Transcription factor WOX11 modulates tolerance to cyst nematodes via adventitious lateral root formation. PLANT PHYSIOLOGY 2024; 195:799-811. [PMID: 38330218 PMCID: PMC11060680 DOI: 10.1093/plphys/kiae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/28/2023] [Accepted: 12/29/2023] [Indexed: 02/10/2024]
Abstract
The transcription factor WUSCHEL-RELATED HOMEOBOX 11 (WOX11) in Arabidopsis (Arabidopsis thaliana) initiates the formation of adventitious lateral roots upon mechanical injury in primary roots. Root-invading nematodes also induce de novo root organogenesis leading to excessive root branching, but it is not known if this symptom of disease involves mediation by WOX11 and if it benefits the plant. Here, we show with targeted transcriptional repression and reporter gene analyses in Arabidopsis that the beet cyst nematode Heterodera schachtii activates WOX11-mediated adventitious lateral rooting from primary roots close to infection sites. The activation of WOX11 in nematode-infected roots occurs downstream of jasmonic acid-dependent damage signaling via ETHYLENE RESPONSE FACTOR109, linking adventitious lateral root formation to nematode damage to host tissues. By measuring different root system components, we found that WOX11-mediated formation of adventitious lateral roots compensates for nematode-induced inhibition of primary root growth. Our observations further demonstrate that WOX11-mediated rooting reduces the impact of nematode infections on aboveground plant development and growth. Altogether, we conclude that the transcriptional regulation by WOX11 modulates root system plasticity under biotic stress, which is one of the key mechanisms underlying the tolerance of Arabidopsis to cyst nematode infections.
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Affiliation(s)
- Jaap-Jan Willig
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Nina Guarneri
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Thomas van Loon
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Sri Wahyuni
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | | | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Viola Willemsen
- Cluster of Plant Developmental Biology, Cell and Developmental Biology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - José L Lozano-Torres
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
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3
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Qiao J, Quan R, Wang J, Li Y, Xiao D, Zhao Z, Huang R, Qin H. OsEIL1 and OsEIL2, two master regulators of rice ethylene signaling, promote the expression of ROS scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. PLANT COMMUNICATIONS 2024; 5:100771. [PMID: 37994014 PMCID: PMC10943563 DOI: 10.1016/j.xplc.2023.100771] [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: 06/19/2023] [Revised: 10/21/2023] [Accepted: 11/20/2023] [Indexed: 11/24/2023]
Abstract
Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural environment. In rice, coleoptile elongation facilitates seedling emergence and establishment, and ethylene plays an important role in this process. However, the underlying regulatory mechanism remains largely unclear. Here, we report that ethylene promotes cell elongation and inhibits cell expansion in rice coleoptiles, resulting in longer and thinner coleoptiles that facilitate seedlings emergence from the soil. Transcriptome analysis showed that genes related to reactive oxygen species (ROS) generation are upregulated and genes involved in ROS scavenging are downregulated in the coleoptiles of ethylene-signaling mutants. Further investigations showed that soil coverage promotes accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) and OsEIL2 in the upper region of the coleoptile, and both OsEIL1 and OsEIL2 can bind directly to the promoters of the GDP-mannose pyrophosphorylase (VTC1) gene OsVTC1-3 and the peroxidase (PRX) genes OsPRX37, OsPRX81, OsPRX82, and OsPRX88 to activate their expression. This leads to increased ascorbic acid content, greater peroxidase activity, and decreased ROS accumulation in the upper region of the coleoptile. Disruption of ROS accumulation promotes coleoptile growth and seedling emergence from soil. These findings deepen our understanding of the roles of ethylene and ROS in controlling coleoptile growth, and this information can be used by breeders to produce rice varieties suitable for direct seeding.
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Affiliation(s)
- Jinzhu Qiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
| | - Yuxiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dinglin Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zihan Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China.
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China.
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4
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Yu Y, Zhao F, Yue Y, Zhao Y, Zhou DX. Lysine acetylation of histone acetyltransferase adaptor protein ADA2 is a mechanism of metabolic control of chromatin modification in plants. NATURE PLANTS 2024; 10:439-452. [PMID: 38326652 DOI: 10.1038/s41477-024-01623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
Histone acetylation is a predominant active chromatin mark deposited by histone acetyltransferases (HATs) that transfer the acetyl group from acetyl coenzyme A (acetyl-CoA) to lysine ε-amino groups in histones. GENERAL CONTROL NON-REPRESSED PROTEIN 5 (GCN5) is one of the best-characterized HATs and functions in association with several adaptor proteins such as ADA2 within multiprotein HAT complexes. ADA2-GCN5 interaction increases GCN5 binding to acetyl-CoA and stimulates its HAT activity. It remains unclear whether the HAT activity of GCN5 (which acetylates not only histones but also cellular proteins) is regulated by acetyl-CoA levels, which vary greatly in cells under different metabolic and nutrition conditions. Here we show that the ADA2 protein itself is acetylated by GCN5 in rice cells. Lysine acetylation exposes ADA2 to a specific E3 ubiquitin ligase and reduces its protein stability. In rice plants, ADA2 protein accumulation reversely parallels its lysine acetylation and acetyl-CoA levels, both of which are dynamically regulated under varying growth conditions. Stress-induced ADA2 accumulation could stimulate GCN5 HAT activity to compensate for the reduced acetyl-CoA levels for histone acetylation. These results indicate that ADA2 lysine acetylation that senses cellular acetyl-CoA variations is a mechanism to regulate HAT activity and histone acetylation homeostasis in plants under changing environments.
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Affiliation(s)
- Yue Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Feng Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, France.
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5
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Meng Y, Ni Y, Li Z, Jiang T, Sun T, Li Y, Gao X, Li H, Suo C, Li C, Yang S, Lan T, Liao G, Liu T, Wang P, Ding C. Interplay between acetylation and ubiquitination of imitation switch chromatin remodeler Isw1 confers multidrug resistance in Cryptococcus neoformans. eLife 2024; 13:e85728. [PMID: 38251723 PMCID: PMC10834027 DOI: 10.7554/elife.85728] [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: 12/21/2022] [Accepted: 01/21/2024] [Indexed: 01/23/2024] Open
Abstract
Cryptococcus neoformans poses a threat to human health, but anticryptococcal therapy is hampered by the emergence of drug resistance, whose underlying mechanisms remain poorly understood. Herein, we discovered that Isw1, an imitation switch chromatin remodeling ATPase, functions as a master modulator of genes responsible for in vivo and in vitro multidrug resistance in C. neoformans. Cells with the disrupted ISW1 gene exhibited profound resistance to multiple antifungal drugs. Mass spectrometry analysis revealed that Isw1 is both acetylated and ubiquitinated, suggesting that an interplay between these two modification events exists to govern Isw1 function. Mutagenesis studies of acetylation and ubiquitination sites revealed that the acetylation status of Isw1K97 coordinates with its ubiquitination processes at Isw1K113 and Isw1K441 through modulating the interaction between Isw1 and Cdc4, an E3 ligase. Additionally, clinical isolates of C. neoformans overexpressing the degradation-resistant ISW1K97Q allele showed impaired drug-resistant phenotypes. Collectively, our studies revealed a sophisticated acetylation-Isw1-ubiquitination regulation axis that controls multidrug resistance in C. neoformans.
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Affiliation(s)
- Yang Meng
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Yue Ni
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Zhuoran Li
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Tianhang Jiang
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Tianshu Sun
- Department of Scientific Research, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yanjian Li
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Xindi Gao
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Hailong Li
- NHC Key Laboratory of AIDS Immunology, The First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Chenhao Suo
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Chao Li
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Sheng Yang
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Tian Lan
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest UniversityChongqingChina
| | - Tongbao Liu
- Medical Research Institute, Southwest UniversityChongqingChina
| | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center New OrleansNew OrleansUnited States
| | - Chen Ding
- College of Life and Health Sciences, Northeastern UniversityShenyangChina
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6
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Yang S, Chen N, Qi J, Salam A, Khan AR, Azhar W, Yang C, Xu N, Wu J, Liu Y, Liu B, Gan Y. OsUGE2 Regulates Plant Growth through Affecting ROS Homeostasis and Iron Level in Rice. RICE (NEW YORK, N.Y.) 2024; 17:6. [PMID: 38212485 PMCID: PMC10784444 DOI: 10.1186/s12284-024-00685-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND The growth and development of rice (Oryza sativa L.) are affected by multiple factors, such as ROS homeostasis and utilization of iron. Here, we demonstrate that OsUGE2, a gene encoding a UDP-glucose 4-epimerase, controls growth and development by regulating reactive oxygen species (ROS) and iron (Fe) level in rice. Knockout of this gene resulted in impaired growth, such as dwarf phenotype, weakened root growth and pale yellow leaves. Biochemical analysis showed that loss of function of OsUGE2 significantly altered the proportion and content of UDP-Glucose (UDP-Glc) and UDP-Galactose (UDP-Gal). Cellular observation indicates that the impaired growth may result from decreased cell length. More importantly, RNA-sequencing analysis showed that knockout of OsUGE2 significantly influenced the expression of genes related to oxidoreductase process and iron ion homeostasis. Consistently, the content of ROS and Fe are significantly decreased in OsUGE2 knockout mutant. Furthermore, knockout mutants of OsUGE2 are insensitive to both Fe deficiency and hydrogen peroxide (H2O2) treatment, which further confirmed that OsUGE2 control rice growth possibly through Fe and H2O2 signal. Collectively, these results reveal a new pathway that OsUGE2 could affect growth and development via influencing ROS homeostasis and Fe level in rice.
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Affiliation(s)
- Shuaiqi Yang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Nana Chen
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Jiaxuan Qi
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Abdul Salam
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Ali Raza Khan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Wardah Azhar
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Chunyan Yang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Nuo Xu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Junyu Wu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, Shandong, China
| | - Bohan Liu
- College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China.
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7
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Tarigholizadeh S, Sushkova S, Rajput VD, Ranjan A, Arora J, Dudnikova T, Barbashev A, Mandzhieva S, Minkina T, Wong MH. Transfer and Degradation of PAHs in the Soil-Plant System: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:46-64. [PMID: 38108272 DOI: 10.1021/acs.jafc.3c05589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are highly toxic, persistent organic pollutants that threaten ecosystems and human health. Consistent monitoring is essential to minimize the entry of PAHs into plants and reduce food chain contamination. PAHs infiltrate plants through multiple pathways, causing detrimental effects and triggering diverse plant responses, ultimately increasing either toxicity or tolerance. Primary plant detoxification processes include enzymatic transformation, conjugation, and accumulation of contaminants in cell walls/vacuoles. Plants also play a crucial role in stimulating microbial PAHs degradation by producing root exudates, enhancing bioavailability, supplying nutrients, and promoting soil microbial diversity and activity. Thus, synergistic plant-microbe interactions efficiently decrease PAHs uptake by plants and, thereby, their accumulation along the food chain. This review highlights PAHs uptake pathways and their overall fate as contaminants of emerging concern (CEC). Understanding plant uptake mechanisms, responses to contaminants, and interactions with rhizosphere microbiota is vital for addressing PAH pollution in soil and ensuring food safety and quality.
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Affiliation(s)
| | - Svetlana Sushkova
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Vishnu D Rajput
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Anuj Ranjan
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Jayati Arora
- Amity Institute of Environmental Science, Amity University, Noida 201301, India
| | - Tamara Dudnikova
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Andrey Barbashev
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | | | - Tatiana Minkina
- Southern Federal University, Rostov-on-Don, 344090, Russian Federation
| | - Ming Hung Wong
- Consortium on Health, Environment, Education, and Research (CHEER), The Education University of Hong Kong, Hong Kong, China; Southern Federal University, Rostov-on-Don, 344090, Russian Federation
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8
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Kumar A, Verma K, Kashyap R, Joshi VJ, Sircar D, Yadav SR. Auxin-responsive ROS homeostasis genes display dynamic expression pattern during rice crown root primordia morphogenesis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108307. [PMID: 38159549 DOI: 10.1016/j.plaphy.2023.108307] [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: 09/24/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Reactive oxygen species (ROS) are generated continuously as a by-product of aerobic metabolism in plants. While excessive ROS cause oxidative stresses in cells, they act as signaling molecules when maintained at an optimum concentration through the dynamic equilibrium of ROS metabolizing mechanisms to regulate growth, development and response to environmental stress. Auxin and its crosstalk with other signaling cascades are crucial for maintaining ROS homeostasis and orchestrating root architecture but dissecting the underlying mechanism requires detailed investigation at the molecular level. Rice fibrous root system is primarily composed of shoot-derived adventitious roots (also called crown roots). Here, we uncover auxin-ROS cross-talk during initiation and growth of rice roots. Potassium iodide treatment changes ROS levels that results in an altered rice root architecture. We reveal that auxin induction recover root growth and development defects by recouping level of hydrogen peroxide. By comparing global datasets previously generated by auxin induction and laser capture microdissection-RNA sequencing, we identify the redox-related antioxidants genes from peroxidase, glutathione reductase, glutathione S-transferase, and thioredoxin reductase families whose expression is regulated by the auxin signaling and also display dynamic expression patterns during crown root primordia morphogenesis. The auxin-mediated differential transcriptome data were validated by quantifying expression levels of a set of genes upon auxin induction. Further, in-depth spatio-temporal expression pattern analysis by RNA in situ hybridization shows the spatially restricted expression of selected genes in the developing crown root primordia. Together, our findings uncover molecular components of auxin-ROS crosstalk involved in root organogenesis.
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Affiliation(s)
- Akshay Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Komal Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Rohan Kashyap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Vedika Jayant Joshi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Debabrata Sircar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India
| | - Shri Ram Yadav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India.
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9
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Qin Q. ROS: Important factor in plant stem cell fate regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 289:154082. [PMID: 37690340 DOI: 10.1016/j.jplph.2023.154082] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Reactive oxygen species (ROS) are initially considered to be toxic byproducts of aerobic metabolic reactions. However, increasing evidence has shown that they have emerged as signaling molecules involved in several basic biological processes. Recent studies highlight the pivotal role of ROS in the maintenance of shoot and root stem cell niche. In this review, we discuss the impact of ROS distribution and their gradients on the stability of the stem cell niches (SCN) in shoot apical meristem (SAM) and root apical meristem (RAM) by determining the balance between stemness and differentiation. We also summarize several important transcription factors that are involved in the regulation of ROS balance in SAM and RAM, regulating key enzymes in ROS metabolism, especially SOD and peroxidase. ROS are also tightly interconnected with phytohormones in the control of the stem cell fate. Besides, ROS are also important regulators of the cell cycle in controlling the size of the stem cells. Understanding the regulation mechanisms of ROS production, polarization gradient distribution, homeostasis, and downstream signal transduction in cells will open exciting new perspectives for plant developmental biology.
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Affiliation(s)
- Qianqian Qin
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Key Laboratory of Gene Editing for Breeding, Gansu Province, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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10
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Suga N, Ikeda Y, Yoshikawa S, Taniguchi K, Sawamura H, Matsuda S. In Search of a Function for the N6-Methyladenosine in Epitranscriptome, Autophagy and Neurodegenerative Diseases. Neurol Int 2023; 15:967-979. [PMID: 37606395 PMCID: PMC10443253 DOI: 10.3390/neurolint15030062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/23/2023] Open
Abstract
Changes in epitranscriptome with N6-methyladenine (m6A) modification could be involved in the development of multiple diseases, which might be a prevalent modification of messenger RNAs (mRNAs) in eukaryotes. The m6A modification might be performed through the action of methyltransferases, demethylases, and methylation-binding proteins. Importantly, the m6A methylation may be associated with various neurological disorders including Alzheimer's disease (AD), Parkinson's disease (PD), depression, aging-related diseases, and/or aging itself. In addition, the m6A methylation might functionally regulate the eukaryotic transcriptome by influencing the splicing, export, subcellular localization, translation, stability, and decay of mRNAs. Neurodegenerative diseases may possess a wide variety of phenotypes, depending on the neurons that degenerate on occasion. Interestingly, an increasing amount of evidence has indicated that m6A modification could modulate the expression of autophagy-related genes and promote autophagy in neuronal cells. Oxidative stresses such as reactive oxygen species (ROS) could stimulate the m6A RNA methylation, which may also be related to the regulation of autophagy and/or the development of neurodegenerative diseases. Both m6A modification and autophagy could also play critical roles in regulating the health condition of neurons. Therefore, a comprehensive understanding of the m6A and autophagy relationship in human diseases may benefit in developing therapeutic strategies in the future. This paper reviews advances in the understanding of the regulatory mechanisms of m6A modification in the occurrence and development of neurodegenerative diseases and/or aging, discussing the possible therapeutic procedures related to mechanisms of m6A RNA methylation and autophagy.
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Affiliation(s)
| | | | | | | | | | - Satoru Matsuda
- Department of Food Science and Nutrition, Nara Women’s University, Kita-Uoya Nishimachi, Nara 630-8506, Japan
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Lu Y, Bu Q, Chuan M, Cui X, Zhao Y, Zhou DX. Metabolic regulation of the plant epigenome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1001-1013. [PMID: 36705504 DOI: 10.1111/tpj.16122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 05/31/2023]
Abstract
Chromatin modifications shape the epigenome and are essential for gene expression reprogramming during plant development and adaptation to the changing environment. Chromatin modification enzymes require primary metabolic intermediates such as S-adenosyl-methionine, acetyl-CoA, alpha-ketoglutarate, and NAD+ as substrates or cofactors. The availability of the metabolites depends on cellular nutrients, energy and reduction/oxidation (redox) states, and affects the activity of chromatin regulators and the epigenomic landscape. The changes in the plant epigenome and the activity of epigenetic regulators in turn control cellular metabolism through transcriptional and post-translational regulation of metabolic enzymes. The interplay between metabolism and the epigenome constitutes a basis for metabolic control of plant growth and response to environmental changes. This review summarizes recent advances regarding the metabolic control of plant chromatin regulators and epigenomes, which are involved in plant adaption to environmental stresses.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Qing Bu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoyun Cui
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dao-Xiu Zhou
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris-Saclay, Orsay, 91405, France
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
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Xu Q, Wang Y, Yue Y, Chen Z, Zhou DX, Zhao Y. Transcription factor WOX11 regulates protein translation via ribosome protein acetylation in rice roots. PLANT PHYSIOLOGY 2023; 191:2224-2228. [PMID: 36715652 PMCID: PMC10069905 DOI: 10.1093/plphys/kiad025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/03/2023] [Indexed: 06/18/2023]
Abstract
WUSCHEL-related Homeobox 11 regulates protein translation via lysine acetylation of ribosome protein mediated by ROS in rice root meristem.
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Affiliation(s)
- Qiutao Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Yijie Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Yaping Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Zhengting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
- Institute of Plant Science Paris-Saclay (IPS2), CNRS, INRAE, University Paris–Saclay, Orsay 91405, Paris, France
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, Hubei Province, China
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Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a. Int J Mol Sci 2023; 24:ijms24065766. [PMID: 36982841 PMCID: PMC10057709 DOI: 10.3390/ijms24065766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized a novel lncRNA molecule through sequence alignment, Sanger sequencing, transient expression in protoplasts, and genetic transformation in poplar. lncWOX11a is a 215 bp transcript located on poplar chromosome 13, ~50 kbp upstream of PeWOX11a on the reverse strand, and the lncRNA may fold into a series of complex stem–loop structures. Despite the small open reading frame (sORF) of 51 bp within lncWOX11a, bioinformatics analysis and protoplast transfection revealed that lncWOX11a has no protein-coding ability. The overexpression of lncWOX11a led to a decrease in the quantity of adventitious roots on the cuttings of transgenic poplars. Further, cis-regulatory module prediction and CRISPR/Cas9 knockout experiments with poplar protoplasts demonstrated that lncWOX11a acts as a negative regulator of adventitious rooting by downregulating the WUSCHEL-related homeobox gene WOX11, which is supposed to activate adventitious root development in plants. Collectively, our findings imply that lncWOX11a is essential for modulating the formation and development of adventitious roots.
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M 6A RNA Methylation Mediates NOD1/NF-kB Signaling Activation in the Liver of Piglets Challenged with Lipopolysaccharide. Antioxidants (Basel) 2022; 11:antiox11101954. [PMID: 36290677 PMCID: PMC9598714 DOI: 10.3390/antiox11101954] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification that widely participates in various immune and inflammatory responses; however, its regulatory mechanisms in the inflammation of liver induced by lipopolysaccharide in piglets remain largely unknown. In the present study, piglets were intraperitoneally injected with 80 μg/kg LPS or an equal dose of sterile saline. Results indicated that LPS administration increased activities of serum alanine aminotransferase (ALT), induced M1 macrophage polarization and promoted secretion of inflammatory cytokines, and finally led to hepatic lesions in piglets. The NOD1/NF-κB signaling pathway was activated in the livers of the LPS group. Moreover, the total m6A level was significantly elevated after LPS treatment. MeRIP-seq showed that 1166 and 1344 transcripts contained m6A methylation in control and LPS groups, respectively. The m6A methylation sites of these transcripts mainly distributes in the 5′ untranslated region (5′UTR), the coding sequence (CDS), and the 3′ untranslated region (3′UTR). Interestingly, these genes were mostly enriched in the NF-κB signaling pathway, and LPS treatment significantly changed the m6A modification in NOD1, RIPK2, NFKBIA, NFKBIB, and TNFAIP3 mRNAs. In addition, knockdown of METTL3 or overexpression of FTO both changed gene levels in the NOD1/NF-κB pathway, suggesting that activation of this pathway was regulated by m6A RNA methylation. Moreover, the alteration of m6A RNA methylation profile may be associated with the increase of reactive oxygen species (ROS), HIF-1α, and MAT2A. In conclusion, LPS activated the NOD1/NF-κB pathway at post-transcriptional regulation through changing m6A RNA methylation, and then promoted the overproduction of proinflammatory cytokines, ultimately resulting in liver inflammation and damage.
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