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Rao R, Huang X, Wang X, Li X, Liao H, Abuduwaili N, Wei X, Li D, Huang G. Genome-wide identification and analysis of DEAD-box RNA helicases in Gossypium hirsutum. Gene 2024; 920:148495. [PMID: 38663690 DOI: 10.1016/j.gene.2024.148495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
DEAD-box RNA helicases, a prominent subfamily within the RNA helicase superfamily 2 (SF2), play crucial roles in the growth, development, and abiotic stress responses of plants. This study identifies 146 DEAD-box RNA helicase genes (GhDEADs) and categorizes them into four Clades (Clade A-D) through phylogenetic analysis. Promoter analysis reveals cis-acting elements linked to plant responses to light, methyl jasmonate (MeJA), abscisic acid (ABA), low temperature, and drought. RNA-seq data demonstrate that Clade C GhDEADs exhibit elevated and ubiquitous expression across different tissues, validating their connection to leaf development through real-time quantitative polymerase chain reaction (RT-qPCR) analysis. Notably, over half of GhDEADs display up-regulation in the leaves of virus-induced gene silencing (VIGS) plants of GhVIR-A/D (members of m6A methyltransferase complex, which regulate leaf morphogenesis). In conclusion, this study offers a comprehensive insight into GhDEADs, emphasizing their potential involvement in leaf development.
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Affiliation(s)
- Ruotong Rao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Xiaoyu Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xinting Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuelong Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Huiping Liao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
| | - Nigara Abuduwaili
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Xiuzhen Wei
- Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China
| | - Dengdi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China.
| | - Gengqing Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, College of Life Science, Xinjiang Normal University, Urumqi 830017, Xinjiang Autonomous Region, China.
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2
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Wang G, Li H, Ye C, He K, Liu S, Jiang B, Ge R, Gao B, Wei J, Zhao Y, Li A, Zhang D, Zhang J, He C. Quantitative profiling of m 6A at single base resolution across the life cycle of rice and Arabidopsis. Nat Commun 2024; 15:4881. [PMID: 38849358 PMCID: PMC11161662 DOI: 10.1038/s41467-024-48941-7] [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: 01/19/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
N6-methyladenosine (m6A) plays critical roles in regulating mRNA metabolism. However, comprehensive m6A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m6A maps at single-base resolution in different tissues of rice and Arabidopsis using m6A-SAC-seq. Our analysis uncovers a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m6A sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR m6A sites in certain plant tissues. Like in mammals, a positive correlation between the m6A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m6A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m6A sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution m6A sites with functions in plants and uncover a suppression-activation model controlling m6A biogenesis across species.
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Affiliation(s)
- Guanqun Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Haoxuan Li
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Kayla He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Bochen Jiang
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Boyang Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
- Department of Chemistry and Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yutao Zhao
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Aixuan Li
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University and School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA.
- Howard Hughes Medical Institute, Chicago, IL, 60637, USA.
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3
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Cai Z, Tang Q, Song P, Tian E, Yang J, Jia G. The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis. THE PLANT CELL 2024:koae149. [PMID: 38835286 DOI: 10.1093/plcell/koae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
N 6-methyladenosine (m6A) is the most abundant mRNA modification and plays diverse roles in eukaryotes, including plants. It regulates various processes, including plant growth, development, and responses to external or internal stress responses. However, the mechanisms underlying how m6A is related to environmental stresses in both mammals and plants remain elusive. Here, we identified EVOLUTIONARILY CONSERVED C-TERMINAL REGION 8 (ECT8) as an m6A reader protein and showed that its m6A-binding capability is required for salt stress responses in Arabidopsis (Arabidopsis thaliana). ECT8 accelerates the degradation of its target transcripts through direct interaction with the decapping protein DECAPPING 5 within processing bodies. We observed a significant increase in the ECT8 expression level under various environmental stresses. Using salt stress as a representative stressor, we found that the transcript and protein levels of ECT8 rise in response to salt stress. The increased abundance of ECT8 protein results in the enhanced binding capability to m6A-modified mRNAs, thereby accelerating their degradation, especially those of negative regulators of salt stress responses. Our results demonstrated that ECT8 acts as an abiotic stress sensor, facilitating mRNA decay, which is vital for maintaining transcriptome homeostasis and enhancing stress tolerance in plants. Our findings not only advance the understanding of epitranscriptomic gene regulation but also offer potential applications for breeding more resilient crops in the face of rapidly changing environmental conditions.
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Affiliation(s)
- Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qian Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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4
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Song P, Cai Z, Jia G. Principles, functions, and biological implications of m 6A in plants. RNA (NEW YORK, N.Y.) 2024; 30:491-499. [PMID: 38531642 PMCID: PMC11019739 DOI: 10.1261/rna.079951.124] [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: 01/14/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- PKU-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology, Peking University, Beijing 100871, China
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5
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Dai X, Xiang S, Zhang Y, Yang S, Hu Q, Wu Z, Zhou T, Xiang J, Chen G, Tan X, Wang J, Ding J. Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis. HORTICULTURE RESEARCH 2024; 11:uhad215. [PMID: 38689695 PMCID: PMC11059793 DOI: 10.1093/hr/uhad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/16/2023] [Indexed: 05/02/2024]
Abstract
Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.
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Affiliation(s)
- Xiaokang Dai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Songzhu Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Yulin Zhang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Siting Yang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Qianqian Hu
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Tingting Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Jingsong Xiang
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Gongyou Chen
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Xiaohua Tan
- Shennongjia Academy of Forestry, 442499, Shennongjia Forestry District, Hubei, China
| | - Jing Wang
- Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, China
| | - Jihua Ding
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Hubei Hongshan Laboratory, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
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6
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Liang J, Yi Q, Liu Y, Li J, Yang Z, Sun W, Sun W. Recent advances of m6A methylation in skeletal system disease. J Transl Med 2024; 22:153. [PMID: 38355483 PMCID: PMC10868056 DOI: 10.1186/s12967-024-04944-y] [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: 11/17/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Skeletal system disease (SSD) is defined as a class of chronic disorders of skeletal system with poor prognosis and causes heavy economic burden. m6A, methylation at the N6 position of adenosine in RNA, is a reversible and dynamic modification in posttranscriptional mRNA. Evidences suggest that m6A modifications play a crucial role in regulating biological processes of all kinds of diseases, such as malignancy. Recently studies have revealed that as the most abundant epigentic modification, m6A is involved in the progression of SSD. However, the function of m6A modification in SSD is not fully illustrated. Therefore, make clear the relationship between m6A modification and SSD pathogenesis might provide novel sights for prevention and targeted treatment of SSD. This article will summarize the recent advances of m6A regulation in the biological processes of SSD, including osteoporosis, osteosarcoma, rheumatoid arthritis and osteoarthritis, and discuss the potential clinical value, research challenge and future prospect of m6A modification in SSD.
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Affiliation(s)
- Jianhui Liang
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
- Shantou University Medical College, Shantou, 515000, China
| | - Qian Yi
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, 646099, Sichuan, China
| | - Yang Liu
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
| | - Jiachen Li
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
- Shantou University Medical College, Shantou, 515000, China
| | - Zecheng Yang
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
| | - Wei Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China.
| | - Weichao Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China.
- The Central Laboratory, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China.
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7
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Jiang B, Zhong Z, Gu L, Zhang X, Wei J, Ye C, Lin G, Qu G, Xiang X, Wen C, Hummel M, Bailey-Serres J, Wang Q, He C, Wang X, Lin C. Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis. NATURE PLANTS 2023; 9:2042-2058. [PMID: 38066290 PMCID: PMC10724061 DOI: 10.1038/s41477-023-01580-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023]
Abstract
Light regulates chlorophyll homeostasis and photosynthesis via various molecular mechanisms in plants. The light regulation of transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how light regulation of mRNA metabolism affects abundance of nuclear-encoded chloroplast proteins and chlorophyll homeostasis remains poorly understood. Here we show that the blue light receptor cryptochrome 2 (CRY2) and the METTL16-type m6A writer FIONA1 (FIO1) regulate chlorophyll homeostasis in response to blue light. In contrast to the CRY2-mediated photo-condensation of the mRNA adenosine methylase (MTA), photoexcited CRY2 co-condenses FIO1 only in the presence of the CRY2-signalling protein SUPPRESSOR of PHYTOCHROME A (SPA1). CRY2 and SPA1 synergistically or additively activate the RNA methyltransferase activity of FIO1 in vitro, whereas CRY2 and FIO1, but not MTA, are required for the light-induced methylation and translation of the mRNAs encoding multiple chlorophyll homeostasis regulators in vivo. Our study demonstrates that the light-induced liquid-liquid phase separation of the photoreceptor/writer complexes is commonly involved in the regulation of photoresponsive changes of mRNA methylation, whereas the different photo-condensation mechanisms of the CRY/FIO1 and CRY/MTA complexes explain, at least partially, the writer-specific functions in plant photomorphogenesis.
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Affiliation(s)
- Bochen Jiang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
| | - Zhenhui Zhong
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueyang Zhang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Guifang Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gaoping Qu
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xian Xiang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenjin Wen
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maureen Hummel
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Qin Wang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Xu Wang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, China.
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, China.
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA, USA.
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8
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Vicente AM, Manavski N, Rohn PT, Schmid LM, Garcia-Molina A, Leister D, Seydel C, Bellin L, Möhlmann T, Ammann G, Kaiser S, Meurer J. The plant cytosolic m 6A RNA methylome stabilizes photosynthesis in the cold. PLANT COMMUNICATIONS 2023; 4:100634. [PMID: 37287225 PMCID: PMC10721483 DOI: 10.1016/j.xplc.2023.100634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/10/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
The sessile lifestyle of plants requires an immediate response to environmental stressors that affect photosynthesis, growth, and crop yield. Here, we showed that three abiotic perturbations-heat, cold, and high light-triggered considerable changes in the expression signatures of 42 epitranscriptomic factors (writers, erasers, and readers) with putative chloroplast-associated functions that formed clusters of commonly expressed genes in Arabidopsis. The expression changes under all conditions were reversible upon deacclimation, identifying epitranscriptomic players as modulators in acclimation processes. Chloroplast dysfunctions, particularly those induced by the oxidative stress-inducing norflurazon in a largely GENOME UNCOUPLED-independent manner, triggered retrograde signals to remodel chloroplast-associated epitranscriptomic expression patterns. N6-methyladenosine (m6A) is known as the most prevalent RNA modification and impacts numerous developmental and physiological functions in living organisms. During cold treatment, expression of components of the primary nuclear m6A methyltransferase complex was upregulated, accompanied by a significant increase in cellular m6A mRNA marks. In the cold, the presence of FIP37, a core component of the writer complex, played an important role in positive regulation of thylakoid structure, photosynthetic functions, and accumulation of photosystem I, the Cytb6f complex, cyclic electron transport proteins, and Curvature Thylakoid1 but not that of photosystem II components and the chloroplast ATP synthase. Downregulation of FIP37 affected abundance, polysomal loading, and translation of cytosolic transcripts related to photosynthesis in the cold, suggesting m6A-dependent translational regulation of chloroplast functions. In summary, we identified multifaceted roles of the cellular m6A RNA methylome in coping with cold; these were predominantly associated with chloroplasts and served to stabilize photosynthesis.
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Affiliation(s)
- Alexandre Magno Vicente
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Nikolay Manavski
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Paul Torben Rohn
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Lisa-Marie Schmid
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Antoni Garcia-Molina
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Charlotte Seydel
- Plant Development, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany
| | - Leo Bellin
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Erwin-Schrödinger-Street, 7, 67663 Kaiserslautern, Germany
| | - Torsten Möhlmann
- Plant Physiology, Faculty of Biology, University of Kaiserslautern, Erwin-Schrödinger-Street, 7, 67663 Kaiserslautern, Germany
| | - Gregor Ammann
- Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Stefanie Kaiser
- Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-University Munich, Großhaderner Street 2-4, 82152 Planegg-Martinsried, Germany.
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9
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Li J, Wang J, Pang Q, Yan X. Analysis of N 6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sugar beet (Beta vulgaris). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111794. [PMID: 37459955 DOI: 10.1016/j.plantsci.2023.111794] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/31/2023]
Abstract
Salinity is an important environmental factor in crop growth and development. N6-methyladenosine (m6A) is an essential epigenetic modification that regulates plant-environment interaction. Sugar beet is a major sugar-yielding crop that has a certain tolerance to salt, but the dynamic response elicited by the m6A modification of transcripts under salt stress remains unknown. In this study, sugar beet was exposed to 300 mM NaCl to investigate its physiological response to high salinity and transcriptome-wide m6A modification profile. After the salt treatment, 7737 significantly modified m6A sites and 4981 differentially expressed genes (DEGs) were identified. Among the 312 m6A-modified DEGs, 113 hypomethylated DEGs were up-regulated and 99 hypermethylated DEGs were down-regulated, indicating a negative correlation between m6A modification and gene expression. Well-known salt tolerance genes (e.g., sodium/hydrogen exchanger 1, choline monooxygenase, and nucleoredoxin 2) and phospholipid signaling pathway genes (phosphoinositol-specific phospholipase C, phospholipase D, diacylglycerol kinase 1, etc.) were also among the m6A-modified genes. Further analysis showed that m6A modification may regulate salt-tolerant related gene expression by controlling mRNA stability. Therefore, changes in m6A modification may negatively regulate the expression of the salt-resistant genes in sugar beet, at least in part by modulating the stability of the mRNA via demethylase BvAlkbh10B. These findings could provide a better understanding of the epigenetic mechanisms of salt tolerance in sugar beets and uncover new candidate genes for improving the production of sugar beets planted in high-salinity soil.
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Affiliation(s)
- Junliang Li
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China; Post-doctoral Research Stations, Northeast Forestry University, Harbin 150040, China
| | - Jiayuan Wang
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China
| | - Qiuying Pang
- Post-doctoral Research Stations, Northeast Forestry University, Harbin 150040, China; Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China.
| | - Xiufeng Yan
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Institute for Eco-environmental Research of Sanyang Wetland, College of Life and Environmental Science, Wenzhou University, Zhong-Xin Street, Wenzhou 325035, China.
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10
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Lin H, Shi T, Zhang Y, He C, Zhang Q, Mo Z, Pan W, Nie X. Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii. PLANTS (BASEL, SWITZERLAND) 2023; 12:2747. [PMID: 37514361 PMCID: PMC10385245 DOI: 10.3390/plants12142747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.
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Affiliation(s)
- Huiyuan Lin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Tingrui Shi
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Ying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Chuyang He
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Qiying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Zhiping Mo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy and Yangling Branch of China Wheat Improvement Center, Northwest A&F University, Yangling 712100, China
- Australia-China Joint Research Centre for Abiotic and Biotic Stress Management in Agriculture, Horticulture and Forestry, Yangling 712100, China
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11
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Song P, Wei L, Chen Z, Cai Z, Lu Q, Wang C, Tian E, Jia G. m 6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis. Genome Biol 2023; 24:103. [PMID: 37122016 PMCID: PMC10150487 DOI: 10.1186/s13059-023-02947-4] [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: 10/26/2022] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND RNA N6-methyladenosine (m6A) modification is critical for plant growth and crop yield. m6A reader proteins can recognize m6A modifications to facilitate the functions of m6A in gene regulation. ECT2, ECT3, and ECT4 are m6A readers that are known to redundantly regulate trichome branching and leaf growth, but their molecular functions remain unclear. RESULTS Here, we show that ECT2, ECT3, and ECT4 directly interact with each other in the cytoplasm and perform genetically redundant functions in abscisic acid (ABA) response regulation during seed germination and post-germination growth. We reveal that ECT2/ECT3/ECT4 promote the stabilization of their targeted m6A-modified mRNAs, but have no function in alternative polyadenylation and translation. We find that ECT2 directly interacts with the poly(A) binding proteins, PAB2 and PAB4, and maintains the stabilization of m6A-modified mRNAs. Disruption of ECT2/ECT3/ECT4 destabilizes mRNAs of ABA signaling-related genes, thereby promoting the accumulation of ABI5 and leading to ABA hypersensitivity. CONCLUSION Our study reveals a unified functional model of m6A mediated by m6A readers in plants. In this model, ECT2/ECT3/ECT4 promote stabilization of their target mRNAs in the cytoplasm.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Lianhuan Wei
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Zixin Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Zhihe Cai
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Chunling Wang
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Enlin Tian
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China.
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12
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Zhang L, Zhang Y, Liu J, Li H, Liu B, Zhao T. N6-methyladenosine mRNA methylation is important for the light response in soybean. FRONTIERS IN PLANT SCIENCE 2023; 14:1153840. [PMID: 37082338 PMCID: PMC10110966 DOI: 10.3389/fpls.2023.1153840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
N6-methyladenosine (m6A) modification of messenger RNA (mRNA) is the most prevalent and abundant modification in eukaryotic mRNA and posttranscriptionally modulates the transcriptome at almost all stages of mRNA metabolism. In plants, m6A is crucial for embryonic-phase growth, flowering time control, microspore generation and fruit maturation. However, the role of m6A in plant responses to light, the most important environmental stimulus, remains unexplored. Here, we profile the m6A transcriptome of Williams 82, a soybean cultivar, and reveal that m6A is highly conserved and plays an important role in the response to light stimuli in soybean. Similar to the case in Arabidopsis, m6A in soybean is enriched not only around the stop codon and within the 3'UTR but also around the start codon. Moreover, genes with methylation occurring in the 3'UTR have higher expression levels and are more prone to alternative splicing. The core genes in the light signaling pathway, GmSPA1a, GmPRR5e and GmBIC2b, undergo changes in methylation modification and transcription levels in response to light. KEGG pathway analysis revealed that differentially expressed genes with differential m6A peaks were involved in the "photosynthesis" and "circadian rhythm" pathways. Our results highlight the important role played by epitranscriptomic mRNA methylation in the light response in soybean and provide a solid basis for determining the functional role of light on RNA m6A modification in this plant.
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