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Ahn CS, Lee DH, Pai HS. Characterization of Maf1 in Arabidopsis: function under stress conditions and regulation by the TOR signaling pathway. PLANTA 2019; 249:527-542. [PMID: 30293201 DOI: 10.1007/s00425-018-3024-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/30/2018] [Indexed: 06/08/2023]
Abstract
Maf1 repressor activity is critical for plant survival during environmental stresses, and is regulated by its phosphorylation/dephosphorylation through the activity of TOR and PP4/PP2A phosphatases. Maf1 is a global repressor of RNA polymerase III (Pol III), and is conserved in eukaryotes. Pol III synthesizes small RNAs, 5S rRNA, and tRNAs that are essential for protein translation and cell growth. Maf1 is a phosphoprotein and dephosphorylation of Maf1 promotes its repressor activity in yeast and mammals. Plant Maf1 was identified in citrus plants as a canker elicitor-binding protein, and citrus Maf1 represses cell growth associated with canker development. However, functions of plant Maf1 under diverse stress conditions and its regulation by the target of rapamycin (TOR) signaling components are poorly understood. In this study, the Arabidopsis maf1 mutants were more susceptible to diverse stresses and treatment with the TOR inhibitor Torin-1 than wild-type plants. The maf1 mutants expressed higher levels of Maf1 target RNAs, including 5S rRNA and pre-tRNAs in leaf cells, supporting Pol III repressor activity of Arabidopsis Maf1. Cellular stresses and Torin-1 treatment induced dephosphorylation of Maf1, suggesting Maf1 activation under diverse stress conditions. TOR silencing also stimulated Maf1 dephosphorylation, while silencing of catalytic subunit genes of PP4 and PP2A repressed it. Thus, TOR kinase and PP4/PP2A phosphatases appeared to oppositely modulate the Maf1 phosphorylation status. TOR silencing decreased the abundance of the target RNAs, while silencing of the PP4 and PP2A subunit genes increased it, supporting the positive correlation between Maf1 dephosphorylation and its repressor activity. Taken together, these results suggest that repressor activity of Maf1, regulated by the TOR signaling pathway, is critical for plant cell survival during environmental stresses.
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Affiliation(s)
- Chang Sook Ahn
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
- Future Technology Research Center, Corporate R&D, LG Chem/LG Science Park, Seoul, 07796, Korea
| | - Du-Hwa Lee
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul, 03722, Korea.
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52
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Pegler JL, Grof CPL, Eamens AL. The Plant microRNA Pathway: The Production and Action Stages. Methods Mol Biol 2019; 1932:15-39. [PMID: 30701489 DOI: 10.1007/978-1-4939-9042-9_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Plant microRNAs are an endogenous class of small regulatory RNA central to the posttranscriptional regulation of gene expression in plant development and environmental stress adaptation or in response to pathogen challenge. The plant microRNA pathway is readily separated into two distinct stages: (1) the production stage, which is localized to the plant cell nucleus and where the microRNA small RNA is processed from a double-stranded RNA precursor transcript, and (2) the action stage, which is localized to the plant cell cytoplasm and where the mature microRNA small RNA is loaded into an effector complex and is used by the complex as a sequence specificity guide to direct expression repression of target genes harboring highly complementary microRNA target sequences. Historical research indicated that the plant microRNA pathway was a highly structured, almost linear pathway requiring a small set of core machinery proteins. However, contemporary research has demonstrated that the plant microRNA pathway is highly dynamic, and to allow for this flexibility, a large and highly functionally diverse set of machinery proteins is now known to be required. For example, recent research has shown that plant microRNAs can regulate target gene expression via a translational repression mechanism of RNA silencing in addition to the standard messenger RNA cleavage-based mechanism of RNA silencing: a mode of RNA silencing originally assigned to all plant microRNAs. Using Arabidopsis thaliana as our model system, here we report on both the core and auxiliary sets of machinery proteins now known to be required for both microRNA production and microRNA action in plants.
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Affiliation(s)
- Joseph L Pegler
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P L Grof
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Andrew L Eamens
- Faculty of Science, Centre for Plant Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia.
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53
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Achkar NP, Cho SK, Poulsen C, Arce AL, Re DA, Giudicatti AJ, Karayekov E, Ryu MY, Choi SW, Harholt J, Casal JJ, Yang SW, Manavella PA. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation. Dev Cell 2018; 46:236-247.e6. [PMID: 30016624 DOI: 10.1016/j.devcel.2018.06.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 03/14/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
Abstract
Light is the most influential environmental stimulus for plant growth. In response to deficient light, plants reprogram their development to adjust their growth in search for a light source. A fine reprogramming of gene expression orchestrates this adaptive trait. Here we show that plants alter microRNA (miRNA) biogenesis in response to light transition. When plants suffer an unusual extended period of light deprivation, the miRNA biogenesis factor HYPONASTIC LEAVES 1 (HYL1) is degraded but an inactive pool of phosphorylated protein remains stable inside the nucleus. Degradation of HYL1 leads to the release of gene silencing, triggering a proper response to dark and shade. Upon light restoration, a quick dephosphorylation of HYL1 leads to the reactivation of miRNA biogenesis and a switch toward a developmental program that maximizes the light uptake. Our findings define a unique and fast regulatory mechanism controlling the plant silencing machinery during plant light response.
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Affiliation(s)
- Natalia P Achkar
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Seok Keun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | | | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Delfina A Re
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina
| | - Elizabeth Karayekov
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina
| | - Moon Young Ryu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Suk Won Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Jesper Harholt
- Carlsberg Research Laboratory, Copenhagen V 1799, Denmark
| | - Jorge J Casal
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires 1417, Argentina; Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET, Buenos Aires 1405, Argentina
| | - Seong Wook Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea; Department of Plant and Environmental Science, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL-FBCB), Santa Fe 3000, Argentina.
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54
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Badmi R, Sheikh AH, Bhagat PK, Verma D, Noryang S, Sinha AK. Possible role of plant MAP kinases in the biogenesis and transcription regulation of rice microRNA pathway factors. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:238-243. [PMID: 29902676 DOI: 10.1016/j.plaphy.2018.06.005] [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: 03/09/2018] [Revised: 05/19/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Signalling pathways play vital roles as determinants of almost all the molecular processes inside a eukaryotic cell. They are more often considered to be the link between extracellular and intracellular environmental cues. Gene silencing pathways have emerged to be involved in regulation of stress responses and developmental processes. However, very little is known about the crosstalk between signalling and silencing pathways and their influence on each other. The present work describes the effects of general protein kinase inhibitors and specific mitogen activated protein kinase (MAPK) pathway inhibitors on the components of microRNA pathway in rice. The kinase inhibitors significantly reduced the activities of miRNA biogenesis complex and changed the transcript expression of miRNA pathway factors. This study suggests a possible regulation of microRNA machinery by plant kinases and MAP kinases in particular.
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Affiliation(s)
- Raghuram Badmi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India.
| | - Arsheed Hussain Sheikh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India
| | - Prakash Kumar Bhagat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India
| | - Deepanjali Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India
| | - Stanzin Noryang
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India
| | - Alok Krishna Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110065, India
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Dolata J, Taube M, Bajczyk M, Jarmolowski A, Szweykowska-Kulinska Z, Bielewicz D. Regulation of Plant Microprocessor Function in Shaping microRNA Landscape. FRONTIERS IN PLANT SCIENCE 2018; 9:753. [PMID: 29922322 PMCID: PMC5996484 DOI: 10.3389/fpls.2018.00753] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/16/2018] [Indexed: 05/19/2023]
Abstract
MicroRNAs are small molecules (∼21 nucleotides long) that are key regulators of gene expression. They originate from long stem-loop RNAs as a product of cleavage by a protein complex called Microprocessor. The core components of the plant Microprocessor are the RNase type III enzyme Dicer-Like 1 (DCL1), the zinc finger protein Serrate (SE), and the double-stranded RNA binding protein Hyponastic Leaves 1 (HYL1). Microprocessor assembly and its processing of microRNA precursors have been reported to occur in discrete nuclear bodies called Dicing bodies. The accessibility of and modifications to Microprocessor components affect microRNA levels and may have dramatic consequences in plant development. Currently, numerous lines of evidence indicate that plant Microprocessor activity is tightly regulated. The cellular localization of HYL1 is dependent on a specific KETCH1 importin, and the E3 ubiquitin ligase COP1 indirectly protects HYL1 from degradation in a light-dependent manner. Furthermore, proper localization of HYL1 in Dicing bodies is regulated by MOS2. On the other hand, the Dicing body localization of DCL1 is regulated by NOT2b, which also interacts with SE in the nucleus. Post-translational modifications are substantial factors that contribute to protein functional diversity and provide a fine-tuning system for the regulation of protein activity. The phosphorylation status of HYL1 is crucial for its activity/stability and is a result of the interplay between kinases (MPK3 and SnRK2) and phosphatases (CPL1 and PP4). Additionally, MPK3 and SnRK2 are known to phosphorylate SE. Several other proteins (e.g., TGH, CDF2, SIC, and RCF3) that interact with Microprocessor have been found to influence its RNA-binding and processing activities. In this minireview, recent findings on the various modes of Microprocessor activity regulation are discussed.
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Affiliation(s)
| | | | | | | | | | - Dawid Bielewicz
- *Correspondence: Zofia Szweykowska-Kulinska, Dawid Bielewicz,
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Zhang X, Jayaweera D, Peters JL, Szecsi J, Bendahmane M, Roberts JA, González-Carranza ZH. The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT is a new player in the microRNA pathway. PLoS One 2017; 12:e0189788. [PMID: 29244865 PMCID: PMC5731758 DOI: 10.1371/journal.pone.0189788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/03/2017] [Indexed: 11/26/2022] Open
Abstract
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport. Genetic crosses between hws-1 and mutant lines for genes in the miRNA pathway also suppress the phenotypes associated with HWS loss of function, corroborating epistatic relations between the miRNA pathway genes and HWS. In agreement with these data, accumulation of miRNA is modified in HWS loss or gain of function mutants. Our data propose HWS as a new player in the miRNA pathway, important for plant growth.
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Affiliation(s)
- Xuebin Zhang
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Dasuni Jayaweera
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Janny L. Peters
- Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Jeremy A. Roberts
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
| | - Zinnia H. González-Carranza
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, United Kingdom
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57
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Yu Y, Jia T, Chen X. The 'how' and 'where' of plant microRNAs. THE NEW PHYTOLOGIST 2017; 216:1002-1017. [PMID: 29048752 PMCID: PMC6040672 DOI: 10.1111/nph.14834] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/21/2017] [Indexed: 05/18/2023]
Abstract
Contents 1002 I. 1002 II. 1007 III. 1010 IV. 1013 1013 References 1013 SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation. Studies have implicated restricted and surprising subcellular locations in which miRNA biogenesis or activity takes place. In this article, we summarize the current knowledge on how plant miRNAs are made and degraded, and how they repress target gene expression. We discuss not only the players involved in these processes, but also the subcellular sites in which these processes are known or implicated to take place. We hope to raise awareness that the cell biology of miRNAs holds the key to a full understanding of these enigmatic molecules.
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Affiliation(s)
- Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Tianran Jia
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, Howard Hughes Medical Institute, University of California, Riverside, CA 92521, USA
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