mRNA ADENOSINE METHYLASE promotes drought tolerance through N
Arabidopsis thaliana
MTA
N6‐methyladenosine
drought
mRNA ADENOSINE METHYLASE
mRNA stability
translation
Journal
The New phytologist
ISSN: 1469-8137
Titre abrégé: New Phytol
Pays: England
ID NLM: 9882884
Informations de publication
Date de publication:
27 Oct 2024
27 Oct 2024
Historique:
received:
15
07
2024
accepted:
05
10
2024
medline:
28
10
2024
pubmed:
28
10
2024
entrez:
27
10
2024
Statut:
aheadofprint
Résumé
Among many mRNA modifications, adenine methylation at the N
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Division of Integrative Organismal Systems
ID : 1849708
Organisme : Division of Integrative Organismal Systems
ID : 2023310
Organisme : Directorate for Biological Sciences
ID : EPSCoR RII Track-2 FEC - 1826836
Informations de copyright
© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.
Références
Anderson SJ, Kramer MC, Gosai SJ, Yu X, Vandivier LE, Nelson ADL, Anderson ZD, Beilstein MA, Fray RG, Lyons E et al. 2018. N‐methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis. Cell Reports 25: 1146–1157.
Arribas‐Hernández L, Bressendorff S, Hansen MH, Poulsen C, Erdmann S, Brodersen P. 2018. An mA‐YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell 30: 952–967.
Arribas‐Hernández L, Brodersen P. 2020. Occurrence and functions of mA and other covalent modifications in plant mRNA. Plant Physiology 182: 79–96.
Bartels D, Sunkar R. 2005. Drought and salt tolerance in plants. Critical Reviews in Plant Sciences 24: 23–58.
Bechtold U, Field B. 2018. Molecular mechanisms controlling plant growth during abiotic stress. Journal of Experimental Botany 69: 2753–2758.
Bhat SS, Bielewicz D, Gulanicz T, Bodi Z, Yu X, Anderson SJ, Szewc L, Bajczyk M, Dolata J, Grzelak N et al. 2020. mRNA adenosine methylase (MTA) deposits mA on pri‐miRNAs to modulate miRNA biogenesis in. Proceedings of the National Academy of Sciences, USA 117: 21785–21795.
Bhat SS, Bielewicz D, Kindgren P. 2023. MTA influences RNA polymerase II transcription dynamics and regulates the cold response in Arabidopsis. bioRxiv. doi: 10.1101/2023.05.10.540235.
Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, May S, Fray RG. 2012. Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Frontiers in Plant Science 3: 48.
Cai J, Hu J, Xu T, Kang H. 2024. FIONA1‐mediated mRNA mA methylation regulates the response of Arabidopsis to salt stress. Plant, Cell & Environment 47: 900–912.
Carillo P, Yves G. 2011. Extraction and determination of proline. PrometheusWiki. [WWW document] URL https://prometheusprotocols.net/ [accessed 28 August 2023].
Chan KX, Phua SY, Crisp P, McQuinn R, Pogson BJ. 2016. Learning the languages of the chloroplast: retrograde signaling and beyond. Annual Review of Plant Biology 67: 25–53.
Chattopadhyay S, Garcia‐Martinez J, Haimovich G, Fischer J, Khwaja A, Barkai O, Chuartzman SG, Schuldiner M, Elran R, Rosenberg MI et al. 2022. RNA‐controlled nucleocytoplasmic shuttling of mRNA decay factors regulates mRNA synthesis and a novel mRNA decay pathway. Nature Communications 13: 7184.
Chen X, Ding Y, Yang Y, Song C, Wang B, Yang S, Guo Y, Gong Z. 2021. Protein kinases in plant responses to drought, salt, and cold stress. Journal of Integrative Plant Biology 63: 53–78.
Crisp PA, Smith AB, Ganguly DR, Murray KD, Eichten SR, Millar AA, Pogson BJ. 2018. RNA polymerase II read‐through promotes expression of neighboring genes in SAL1‐PAP‐XRN retrograde signaling. Plant Physiology 178: 1614–1630.
Dahan N, Choder M. 2013. The eukaryotic transcriptional machinery regulates mRNA translation and decay in the cytoplasm. Biochimica et Biophysica Acta 1829: 169–173.
Duan H‐C, Wei L‐H, Zhang C, Wang Y, Chen L, Lu Z, Chen PR, He C, Jia G. 2017. ALKBH10B is an RNA‐methyladenosine demethylase affecting Arabidopsis floral transition. Plant Cell 29: 2995–3011.
Ganguly DR, Hickey LT, Crisp PA. 2022. Harnessing genetic variation at regulatory regions to fine‐tune traits for climate‐resilient crops. Molecular Plant 15: 222–224.
Govindan G, Sharma B, Li Y‐F, Armstrong CD, Merum P, Rohila JS, Gregory BD, Sunkar R. 2022. mRNA N‐methyladenosine is critical for cold tolerance in Arabidopsis. The Plant Journal 111: 1052–1068.
Hou C‐Y, Lee W‐C, Chou H‐C, Chen A‐P, Chou S‐J, Chen H‐M. 2016. Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants. Plant Cell 28: 2398–2416.
Hu J, Cai J, Park SJ, Lee K, Li Y, Chen Y, Yun J‐Y, Xu T, Kang H. 2021. N‐methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. The Plant Journal 106: 1759–1775.
Kierzek E, Kierzek R. 2003. The thermodynamic stability of RNA duplexes and hairpins containing N6‐alkyladenosines and 2‐methylthio‐N6‐alkyladenosines. Nucleic Acids Research 31: 4472–4480.
Kramer MC, Janssen KA, Palos K, Nelson ADL, Vandivier LE, Garcia BA, Lyons E, Beilstein MA, Gregory BD. 2020. N‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. Plant Direct 4: e00239.
Lee W‐C, Hou B‐H, Hou C‐Y, Tsao S‐M, Kao P, Chen H‐M. 2020. Widespread exon junction complex footprints in the RNA degradome mark mRNA degradation before steady state translation. Plant Cell 32: 904–922.
Li Y‐F, Mahalingam R, Sunkar R. 2017. Isolation of polysomal RNA for analyzing stress‐responsive genes regulated at the translational level in plants. Methods in Molecular Biology 1631: 151–161.
Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. 2015. N(6)‐methyladenosine‐dependent RNA structural switches regulate RNA‐protein interactions. Nature 518: 560–564.
Liu N, Zhou KI, Parisien M, Dai Q, Diatchenko L, Pan T. 2017. N6‐methyladenosine alters RNA structure to regulate binding of a low‐complexity protein. Nucleic Acids Research 45: 6051–6063.
Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real‐time quantitative PCR and the 2(‐Delta Delta C(T)) method. Methods 25: 402–408.
Luo G‐Z, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, Liu J, Chen K, Jia G, Bergelson J et al. 2014. Unique features of the m6A methylome in Arabidopsis thaliana. Nature Communications 5: 5630.
Luo J‐H, Wang Y, Wang M, Zhang L‐Y, Peng H‐R, Zhou Y‐Y, Jia G‐F, He Y. 2020. Natural variation in RNA mA methylation and its relationship with translational status. Plant Physiology 182: 332–344.
Martínez‐Pérez M, Gómez‐Mena C, Alvarado‐Marchena L, Nadi R, Micol JL, Pallas V, Aparicio F. 2021. The mA RNA demethylase ALKBH9B plays a critical role for vascular movement of alfalfa mosaic virus in Arabidopsis. Frontiers in Microbiology 12: 745576.
Mi H, Muruganujan A, Huang X, Ebert D, Mills C, Guo X, Thomas PD. 2019. Protocol update for large‐scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nature Protocols 14: 703–721.
Mickelbart MV, Hasegawa PM, Bailey‐Serres J. 2015. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nature Reviews. Genetics 16: 237–251.
Mielecki D, Zugaj DŁ, Muszewska A, Piwowarski J, Chojnacka A, Mielecki M, Nieminuszczy J, Grynberg M, Grzesiuk E. 2012. Novel AlkB dioxygenases—alternative models for in silico and in vivo studies. PLoS ONE 7: e30588.
Prall W, Ganguly DR, Gregory BD. 2023a. The covalent nucleotide modifications within plant mRNAs: what we know, how we find them, and what should be done in the future. Plant Cell 35: 1801–1816.
Prall W, Sheikh AH, Bazin J, Bigeard J, Almeida‐Trapp M, Crespi M, Hirt H, Gregory BD. 2023b. Pathogen‐induced m6A dynamics affect plant immunity. Plant Cell 35: 4155–4172.
Ramanjulu S, Bartels D. 2002. Drought‐ and desiccation‐induced modulation of gene expression in plants. Plant, Cell & Environment 25: 141–151.
Ramanjulu S, Sudhakar C. 2000. Proline metabolism during dehydration in two mulberry genotypes with contrasting drought tolerance. Journal of Plant Physiology 157: 81–85.
Razzaq A, Wani SH, Saleem F, Yu M, Zhou M, Shabala S. 2021. Rewilding crops for climate resilience: economic analysis and de novo domestication strategies. Journal of Experimental Botany 72: 6123–6139.
Reichel M, Köster T, Staiger D. 2019. Marking RNA: m6A writers, readers, and functions in Arabidopsis. Journal of Molecular Cell Biology 11: 899–910.
Růžička K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, Eeckhout D, El‐Showk S, Li H, Zhong S et al. 2017. Identification of factors required for m A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytologist 215: 157–172.
Scutenaire J, Deragon J‐M, Jean V, Benhamed M, Raynaud C, Favory J‐J, Merret R, Bousquet‐Antonelli C. 2018. The YTH domain protein ECT2 is an mA reader required for normal trichome branching in Arabidopsis. Plant Cell 30: 986–1005.
Sharma B, Govindan G, Li Y, Sunkar R, Gregory BD. 2024. RNA N6‐methyladenosine affects copper‐induced oxidative stress response in Arabidopsis thaliana. Non‐Coding RNA 10: 8.
Shen L, Liang Z, Gu X, Chen Y, Teo ZWN, Hou X, Cai WM, Dedon PC, Liu L, Yu H. 2016. N(6)‐methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Developmental Cell 38: 186–200.
Slobodin B, Han R, Calderone V, Vrielink JAFO, Loayza‐Puch F, Elkon R, Agami R. 2017. Transcription impacts the efficiency of mRNA translation via co‐transcriptional N6‐adenosine methylation. Cell 169: 326–337.
Song P, Wei L, Chen Z, Cai Z, Lu Q, Wang C, Tian E, Jia G. 2023. mA readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis. Genome Biology 24: 103.
Song Y, Zhang X, Li M, Yang H, Fu D, Lv J, Ding Y, Gong Z, Shi Y, Yang S. 2021. The direct targets of CBFs: in cold stress response and beyond. Journal of Integrative Plant Biology 63: 1874–1887.
Sun B, Bhati KK, Song P, Edwards A, Petri L, Kruusvee V, Blaakmeer A, Dolde U, Rodrigues V, Straub D et al. 2022. FIONA1‐mediated methylation of the 3′UTR of FLC affects FLC transcript levels and flowering in Arabidopsis. PLoS Genetics 18: e1010386.
Sunkar R, Li Y‐F, Jagadeeswaran G. 2012. Functions of microRNAs in plant stress responses. Trends in Plant Science 17: 196–203.
Vandivier LE, Campos R, Kuksa PP, Silverman IM, Wang L‐S, Gregory BD. 2015. Chemical modifications mark alternatively spliced and uncapped messenger RNAs in Arabidopsis. Plant Cell 27: 3024–3037.
Vandivier LE, Gregory BD. 2018. New insights into the plant epitranscriptome. Journal of Experimental Botany 69: 4659–4665.
Wang C, Yang J, Song P, Zhang W, Lu Q, Yu Q, Jia G. 2022. FIONA1 is an RNA N‐methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. Genome Biology 23: 40.
Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G et al. 2014. N6‐methyladenosine‐dependent regulation of messenger RNA stability. Nature 505: 117–120.
Wei L‐H, Song P, Wang Y, Lu Z, Tang Q, Yu Q, Xiao Y, Zhang X, Duan H‐C, Jia G. 2018. The mA reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis. Plant Cell 30: 968–985.
Willmann MR, Berkowitz ND, Gregory BD. 2014. Improved genome‐wide mapping of uncapped and cleaved transcripts in eukaryotes – GMUCT 2.0. Methods 67: 64–73.
Wu X, Su T, Zhang S, Zhang Y, Wong CE, Ma J, Shao Y, Hua C, Shen L, Yu H. 2024. N‐methyladenosine‐mediated feedback regulation of abscisic acid perception via phase‐separated ECT8 condensates in Arabidopsis. Nature Plants 10: 469–482.
Xu T, Wu X, Wong CE, Fan S, Zhang Y, Zhang S, Liang Z, Yu H, Shen L. 2022. FIONA1‐mediated mA modification regulates the floral transition in Arabidopsis. Advancement of Science 9: e2103628.
Yamaguchi‐Shinozaki K, Shinozaki K. 2006. Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses. Annual Review of Plant Biology 57: 781–803.
Yu X, Willmann MR, Anderson SJ, Gregory BD. 2016. Genome‐wide mapping of uncapped and cleaved transcripts reveals a role for the nuclear mRNA cap‐binding complex in cotranslational RNA decay in Arabidopsis. Plant Cell 28: 2385–2397.
Zhang M, Zeng Y, Peng R, Dong J, Lan Y, Duan S, Chang Z, Ren J, Luo G, Liu B et al. 2022. N‐methyladenosine RNA modification regulates photosynthesis during photodamage in plants. Nature Communications 13: 7441.
Zhou L, Tang R, Li X, Tian S, Li B, Qin G. 2021. N‐methyladenosine RNA modification regulates strawberry fruit ripening in an ABA‐dependent manner. Genome Biology 22: 168.
Zhu J‐K. 2016. Abiotic stress signaling and responses in plants. Cell 167: 313–324.
Zhu T, Roundtree IA, Wang P, Wang X, Wang L, Sun C, Tian Y, Li J, He C, Xu Y. 2014. Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6‐methyladenosine. Cell Research 24: 1493–1496.