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Gonzalo L, Giudicatti AJ, Manavella PA. HYL1's multiverse: A journey through miRNA biogenesis and beyond canonical and non-canonical functions of HYL1. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102546. [PMID: 38718678 DOI: 10.1016/j.pbi.2024.102546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
A delicate balance in gene expression, a process highly controlled by post-transcriptional gene silencing mediated by miRNAs, is vital during plant growth and responses to stress. Within the miRNA biogenesis pathway, HYL1 is one of the most important proteins, initially recognized for its role as a cofactor of DCL1. Yet, HYL1's functions extend beyond miRNA processing, encompassing transcriptional regulation and protein translation between other recently discovered functions. This review comprehensively examines our current knowledge of HYL1 functions in plants, looking at its structure, the complex biochemistry behind it, and its involvement in a variety of cellular processes. We also explored the most compelling open questions regarding HYL1 biology and the further perspectives in its study. Unraveling HYL1 functional details could better understand how plants grow, face environmental stresses, and how the miRNA pathway adapts its outcome to the plant growing conditions.
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Affiliation(s)
- Lucia Gonzalo
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina; Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM "La Mayora"), Universidad de Málaga-Consejo Superior de Investigaciones Cientificas (UMA-CSIC), Campus Teatinos, 29010 Málaga, Spain.
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Singh K, Sharma D, Bhagat PK, Tayyeba S, Noryang S, Sinha AK. Phosphorylation of AGO1a by MAP kinases is required for miRNA mediated resistance against Xanthomonas oryzae pv. oryzae infection in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111967. [PMID: 38154578 DOI: 10.1016/j.plantsci.2023.111967] [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: 10/11/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 12/30/2023]
Abstract
Bacterial leaf blight is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which causes severe crop loss in rice. The molecular mechanism that initiates defense against such pathogens remains unexplored. Reports have suggested crucial role of several miRNAs in regulating immune responses in plants. Argonaute (AGO) proteins have been implicated in imparting immunity against pathogens by using small RNAs as guide molecules. Here, we show that phosphorylation of rice AGO1a by MAP kinases is required for miRNA expression regulation during Xoo infection. AGO1a is induced in response to pathogen infection and is under the control of SA signaling pathway. The pathogen responsive MAP kinases MPK3, MPK4 and MPK6, interact with AGO1a in planta and can phosphorylate the protein in vitro. Overexpression of AGO1a extends disease resistance against Xoo in rice and leads to a higher accumulation of miRNAs. Conversely, overexpression of a non phosphorylatable mutant protein aggravates disease susceptibility and remarkably suppresses the miRNA expression levels. At a molecular level, phosphorylation of AGO1a by MAP kinase is required for increased accumulation of miRNAs during pathogen challenge. Taken together, the data suggests that OsAGO1a is a direct phosphorylation target of MAP kinases and this phosphorylation is crucial for its role in imparting disease resistance.
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Affiliation(s)
- Kirti Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepika Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prakash Kumar Bhagat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Sumaira Tayyeba
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA
| | - Stanzin Noryang
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; Biochemistry Department, Elizer Joldan Memorial College, UT Ladakh 194101, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Singh D, Banerjee G, Verma N, Sinha AK. MAP kinases may mediate regulation of the cell cycle in rice by E2F2 phosphorylation. FEBS Lett 2023; 597:2993-3009. [PMID: 37843487 DOI: 10.1002/1873-3468.14753] [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: 05/21/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023]
Abstract
E2F is the key transcription factor that determines the proliferative status of cells by regulating the G1/S phase of the cell cycle. In this study, we show that in rice (Oryza sativa), OsE2F2 is a phosphorylation target of MAP kinases. The MAP kinases OsMPK3, OsMPK4, and OsMPK6 interact with and phosphorylate OsE2F2. Next, we determined the serine and threonine residues that could play a role in the phosphorylation of OsE2F2. Subsequently, our study suggests a possible link between MAP kinase-mediated OsE2F2 phosphorylation and its impact on DNA proliferation in the roots of rice seedlings. Finally, we found positive feedback regulation of OsMPK4 by OsE2F2. Therefore, our study hints at the potential impact of MAP kinase signaling on the cell cycle of rice plants.
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Affiliation(s)
- Dhanraj Singh
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Gopal Banerjee
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Delhi, New Delhi, India
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Huang X, Wei JM, Feng WZ, Luo Q, Tan GF, Li YZ. Interaction between SlMAPK3 and SlASR4 regulates drought resistance in tomato ( Solanum lycopersicum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:73. [PMID: 37795156 PMCID: PMC10545654 DOI: 10.1007/s11032-023-01418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023]
Abstract
Tomato is a leading vegetable in modern agriculture, and with global warming, drought has become an important factor threatening tomato production. Mitogen-activated protein kinase 3 (MAPK3) plays an important role in plant disease and stress resistance. To clarify the downstream target proteins of SlMAPK3 and the mechanism of stress resistance in tomato, this study was conducted with the SlMAPK3-overexpressing lines OE-1 and OE-2 and the CRISPR/Cas9-mediated mutant lines slmapk3-1 and slmapk3-2 under PEG 6000-simulated drought. The results of yeast two-hybrid (Y2H), pull-down, and coimmunoprecipitation (Co-IP) assays confirmed that SlASR4 (NP_001269248.1) interacted with SlMAPK3. Analyses of the SlASR4 protein structure and SlASR4 expression under PEG 6000 and BTH stress revealed that SlASR4 has a highly conserved protein structural domain involved in the drought stress response under PEG 6000 treatment. The function of the SlASR4 and SlMAPK3 downstream target protein, in drought resistance in tomato plants, was identified by virus-induced gene silencing (VIGS). This study clarified that SlMAPK3 interacts with SlASR4 to positively regulate drought resistance in tomato plants.
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Affiliation(s)
- Xin Huang
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025 Guizhou China
| | - Jian-Ming Wei
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025 Guizhou China
| | - Wen-Zhuo Feng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025 Guizhou China
| | - Qing Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou China
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou China
| | - Yun-Zhou Li
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, 550025 Guizhou China
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Fletcher CE, Taylor MA, Bevan CL. PLK1 Regulates MicroRNA Biogenesis through Drosha Phosphorylation. Int J Mol Sci 2023; 24:14290. [PMID: 37762595 PMCID: PMC10531876 DOI: 10.3390/ijms241814290] [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: 08/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Polo-Like Kinase 1 (PLK1), a key mediator of cell-cycle progression, is associated with poor prognosis and is a therapeutic target in a number of malignancies. Putative phosphorylation sites for PLK1 have been identified on Drosha, the main catalytic component of the microprocessor responsible for miR biogenesis. Several kinases, including GSK3β, p70 S6 kinase, ABL, PAK5, p38 MAPK, CSNK1A1 and ANKRD52-PPP6C, have been shown to phosphorylate components of the miR biogenesis machinery, altering their activity and/or localisation, and therefore the biogenesis of distinct miR subsets. We hypothesised that PLK1 regulates miR biogenesis through Drosha phosphorylation. In vitro kinase assays confirmed PLK1 phosphorylation of Drosha at S300 and/or S302. PLK1 inhibition reduced serine-phosphorylated levels of Drosha and its RNA-dependent association with DGCR8. In contrast, a "phospho-mimic" Drosha mutant showed increased association with DGCR8. PLK1 phosphorylation of Drosha alters Drosha Microprocessor complex subcellular localisation, since PLK1 inhibition increased cytosolic protein levels of both DGCR8 and Drosha, whilst nuclear levels were decreased. Importantly, the above effects are independent of PLK1's cell cycle-regulatory role, since altered Drosha:DGCR8 localisation upon PLK1 inhibition occurred prior to significant accumulation of cells in M-phase, and PLK1-regulated miRs were not increased in M-phase-arrested cells. Small RNA sequencing and qPCR validation were used to assess downstream consequences of PLK1 activity on miR biogenesis, identifying a set of ten miRs (miR-1248, miR-1306-5p, miR-2277-5p, miR-29c-5p, miR-93-3p, miR-152-3p, miR-509-3-5p, miR-511-5p, miR-891a-5p and miR-892a) whose expression levels were statistically significantly downregulated by two pharmacological PLK1 kinase domain inhibitors, RO-5203280 and GSK461364. Opposingly, increased levels of these miRs were observed upon transfection of wild-type or constitutively active PLK1. Importantly, pre-miR levels were reduced upon PLK1 inhibition, and pri-miR levels decreased upon PLK1 activation, and hence, PLK1 Drosha phosphorylation regulates MiR biogenesis at the level of pri-miR-to-pre-miR processing. In combination with prior studies, this work identifies Drosha S300 and S302 as major integration points for signalling by several kinases, whose relative activities will determine the relative biogenesis efficiency of different miR subsets. Identified kinase-regulated miRs have potential for use as kinase inhibitor response-predictive biomarkers, in cancer and other diseases.
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Affiliation(s)
- Claire Emily Fletcher
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | | | - Charlotte Lynne Bevan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
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Bielewicz D, Dolata J, Bajczyk M, Szewc L, Gulanicz T, Bhat SS, Karlik A, Jozwiak M, Jarmolowski A, Szweykowska-Kulinska Z. Hyponastic Leaves 1 Interacts with RNA Pol II to Ensure Proper Transcription of MicroRNA Genes. PLANT & CELL PHYSIOLOGY 2023; 64:571-582. [PMID: 37040378 DOI: 10.1093/pcp/pcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 06/16/2023]
Abstract
Hyponastic Leaves 1 (HYL1) [also known as Double-stranded RNA-Binding protein 1 (DRB1)] is a double-stranded RNA-binding protein involved in microRNA (miRNA) processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by the Dicer-Like 1 protein. In this work, we report a novel function of the HYL1 protein in the transcription of miRNA (MIR) genes. HYL1 colocalizes with RNA polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that the HYL1 protein interacts with many transcription factors. Finally, we show that the action of HYL1 is not limited to MIR genes and impacts the expression of many other genes, a majority of which are involved in plastid organization. These discoveries indicate HYL1 as an additional player in gene regulation at the transcriptional level, independent of its role in miRNA biogenesis.
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Affiliation(s)
- Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Advanced Technologies, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Lukasz Szewc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Tomasz Gulanicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun 87-100, Poland
| | - Susheel S Bhat
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Anna Karlik
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan 61-614, Poland
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Lakatos L, Groma G, Silhavy D, Nagy F. In Arabidopsis thaliana, RNA-Induced Silencing Complex-Loading of MicroRNAs Plays a Minor Regulatory Role During Photomorphogenesis Except for miR163. FRONTIERS IN PLANT SCIENCE 2022; 13:854869. [PMID: 35909792 PMCID: PMC9326452 DOI: 10.3389/fpls.2022.854869] [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: 01/14/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
The shift of dark-grown seedlings to the light leads to substantial reprogramming of gene expression, which results in dramatic developmental changes (referred to as de-etiolation or photomorphogenesis). MicroRNAs (miRNAs) regulate most steps of plant development, thus miRNAs might play important role in transcriptional reprogramming during de-etiolation. Indeed, miRNA biogenesis mutants show aberrant de-etiolation. Previous works showed that the total miRNA expression pattern (total miRNAome) is only moderately altered during photomorphogenesis. However, a recent study has shown that plant miRNAs are present in two pools, biologically active miRNAs loaded to RISC (RNA-induced silencing complex-loaded) form while inactive miRNAs accumulate in duplex form upon organ formation. To test if RISC-loading efficiency is changed during photomorphogenesis. we compared the total miRNAome and the RISC-loaded miRNAome of dark-grown and de-etiolated Arabidopsis thaliana seedlings. miRNA sequencing has revealed that although regulated RISC-loading is involved in the control of active miRNAome formation during de-etiolation, this effect is moderate. The total miRNAomes and the RISC-loaded miRNAomes of dark-grown and de-etiolated plants are similar indicating that most miRNAs are loaded onto RISC with similar efficiency in dark and light. Few miRNAs were loaded onto RISC with different efficiency and one miRNA, miR163, was RISC-loaded much more effectively in light than in dark. Thus, our results suggest that although RISC-loading contributes significantly to the control of the formation of organ-specific active miRNA pools, it plays a limited role in the regulation of active miRNA pool formation during de-etiolation. Regulated RISC-loading strongly modifies the expression of miRNA163, could play a role in the fine-tuning of a few other miRNAs, and do not modify the expression of most miRNAs.
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Affiliation(s)
- Lóránt Lakatos
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gergely Groma
- Dermatological Research Group, University of Szeged, Szeged, Hungary
| | - Daniel Silhavy
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferenc Nagy
- Laboratory of Photo and Chronobiology, Biological Research Centre, Institute of Plant Biology, Eötvös Loránd Research Network, Szeged, Hungary
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