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Wu W, Wang X, Liang X, Huang X, Nawaz MA, Jing C, Fan Y, Niu J, Wu J, Feng X. Characterization of the m 6A Regulatory Gene Family in Phaseolus vulgaris L. and Functional Analysis of PvMTA in Response to BCMV Infection. Int J Mol Sci 2025; 26:2748. [PMID: 40141390 PMCID: PMC11942742 DOI: 10.3390/ijms26062748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/13/2025] [Accepted: 03/15/2025] [Indexed: 03/28/2025] Open
Abstract
Common bean (Phaseolus vulgaris L.) is known for its high protein, dietary fiber, and various trace element contents, making it a widely grown leguminous crop globally. The bean common mosaic virus (BCMV) poses a significant threat to leguminous crop production, causing substantial yield reductions when common beans are infected. Widely occurring in mRNA, the m6A modification is vital for maintaining mRNA stability, facilitating splicing, enabling nuclear export, supporting polyadenylation, and initiating translation. Recent studies have identified the m6A regulatory gene family in various plant species, and its ability to regulate plant virus infection has been confirmed. There is currently insufficient information regarding the m6A regulatory gene family in beans and how it responds to BCMV infection. Consequently, we carried out a genome-wide characterization of the m6A regulatory gene family in common bean, which led to the identification of 31 potential regulatory gene members associated with m6A. According to evolutionary analysis, the increase in the bean m6A regulatory gene family appears to be linked to either whole-genome duplication or segmental duplication events. Subsequent investigations into the expression levels of these genes throughout different phases of BCMV infection showed that all candidate genes responded to the infection with various changes in expression. Moreover, we characterized the methyltransferase activity of PvMTA and validated the interactive relationship between mRNA adenosine methyltransferase A (MTA) and mRNA adenosine methyltransferase B (MTB) in common beans. Through overexpressing and silencing PvMTA, we further ascertained that this particular gene has a detrimental impact on the regulation of BCMV infection. This research provides fresh perspectives on the molecular processes that govern the interaction between the common bean and BCMV and aids progress in molecular bean breeding.
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Affiliation(s)
- Wenyan Wu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Xinhua Wang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Xingrui Liang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Xinqi Huang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Muhammad Amjad Nawaz
- Advanced Engineering School (Agrobiotek), National Research Tomsk State University, Lenin Ave, 36, 634050 Tomsk, Tomsk Oblast, Russia;
- Centre for Research in the Field of Materials and Technologies, National Research Tomsk State University, Lenin Ave, 36, 634050 Tomsk, Tomsk Oblast, Russia
| | - Chenchen Jing
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Yaru Fan
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Jingya Niu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
| | - Jing Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xue Feng
- College of Plant Protection, Shanxi Agricultural University, Jinzhong 030801, China; (W.W.); (X.W.); (X.L.); (X.H.); (C.J.); (Y.F.); (J.N.)
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Xiang Y, Zhang D, Li L, Xue YX, Zhang CY, Meng QF, Wang J, Tan XL, Li YL. Detection, distribution, and functions of RNA N 6-methyladenosine (m 6A) in plant development and environmental signal responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1429011. [PMID: 39081522 PMCID: PMC11286456 DOI: 10.3389/fpls.2024.1429011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.
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Cerav EN, Wu N, Akkaya MS. Transcriptome-Wide N6-Methyladenosine (m 6A) Methylation Analyses in a Compatible Wheat- Puccinia striiformis f. sp. tritici Interaction. PLANTS (BASEL, SWITZERLAND) 2024; 13:982. [PMID: 38611510 PMCID: PMC11013425 DOI: 10.3390/plants13070982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant-pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat's response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens.
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Affiliation(s)
| | | | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China; (E.N.C.); (N.W.)
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Shen L, Ma J, Li P, Wu Y, Yu H. Recent advances in the plant epitranscriptome. Genome Biol 2023; 24:43. [PMID: 36882788 PMCID: PMC9990323 DOI: 10.1186/s13059-023-02872-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/12/2023] [Indexed: 03/09/2023] Open
Abstract
Chemical modifications of RNAs, known as the epitranscriptome, are emerging as widespread regulatory mechanisms underlying gene regulation. The field of epitranscriptomics advances recently due to improved transcriptome-wide sequencing strategies for mapping RNA modifications and intensive characterization of writers, erasers, and readers that deposit, remove, and recognize RNA modifications, respectively. Herein, we review recent advances in characterizing plant epitranscriptome and its regulatory mechanisms in post-transcriptional gene regulation and diverse physiological processes, with main emphasis on N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We also discuss the potential and challenges for utilization of epitranscriptome editing in crop improvement.
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Affiliation(s)
- Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
| | - Jinqi Ma
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Ping Li
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Yujin Wu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Hao Yu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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