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Chen W, Wang J, Wang Z, Zhu T, Zheng Y, Hawar A, Chang Y, Wang X, Li D, Wang G, Yang W, Zhao Y, Chen D, Yuan YA, Sun B. Capture of regulatory factors via CRISPR-dCas9 for mechanistic analysis of fine-tuned SERRATE expression in Arabidopsis. NATURE PLANTS 2024; 10:86-99. [PMID: 38168608 DOI: 10.1038/s41477-023-01575-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/29/2023] [Indexed: 01/05/2024]
Abstract
SERRATE (SE) plays an important role in many biological processes and under biotic stress resistance. However, little about the control of SE has been clarified. Here we present a method named native chromatin-associated proteome affinity by CRISPR-dCas9 (CASPA-dCas9) to holistically capture native regulators of the SE locus. Several key regulatory factors including PHYTOCHROME RAPIDLY REGULATED 2 (PAR2), WRKY DNA-binding protein 19 (WRKY19) and the MYB-family protein MYB27 of SE are identified. MYB27 recruits the long non-coding RNA-PRC2 (SEAIR-PRC2) complex for H3K27me3 deposition on exon 1 of SE and subsequently represses SE expression, while PAR2-MYB27 interaction inhibits both the binding of MYB27 on the SE promoter and the recruitment of SEAIR-PRC2 by MYB27. The interaction between PAR2 and MYB27 fine-tunes the SE expression level at different developmental stages. In addition, PAR2 and WRKY19 synergistically promote SE expression for pathogen resistance. Collectively, our results demonstrate an efficient method to capture key regulators of target genes and uncover the precise regulatory mechanism for SE.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Jingyi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zijing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yuchen Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Amangul Hawar
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yongsheng Chang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dongbao Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guangling Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wen Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanjie Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yuren Adam Yuan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Bo Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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2
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Shang B, Wang L, Yan X, Li Y, Li C, Wu C, Wang T, Guo X, Choi SW, Zhang T, Wang Z, Tong CY, Oh T, Zhang X, Wang Z, Peng X, Zhang X. Intrinsically disordered proteins SAID1/2 condensate on SERRATE for dual inhibition of miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci U S A 2023; 120:e2216006120. [PMID: 36972460 PMCID: PMC10083546 DOI: 10.1073/pnas.2216006120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) SAID1/2 are hypothetic dentin sialophosphoprotein-like proteins, but their true functions are unknown. Here, we identified SAID1/2 as negative regulators of SERRATE (SE), a core factor in miRNA biogenesis complex (microprocessor). Loss-of-function double mutants of said1; said2 caused pleiotropic developmental defects and thousands of differentially expressed genes that partially overlapped with those in se. said1; said2 also displayed increased assembly of microprocessor and elevated accumulation of microRNAs (miRNAs). Mechanistically, SAID1/2 promote pre-mRNA processing 4 kinase A-mediated phosphorylation of SE, causing its degradation in vivo. Unexpectedly, SAID1/2 have strong binding affinity to hairpin-structured pri-miRNAs and can sequester them from SE. Moreover, SAID1/2 directly inhibit pri-miRNA processing by microprocessor in vitro. Whereas SAID1/2 did not impact SE subcellular compartmentation, the proteins themselves exhibited liquid-liquid phase condensation that is nucleated on SE. Thus, we propose that SAID1/2 reduce miRNA production through hijacking pri-miRNAs to prevent microprocessor activity while promoting SE phosphorylation and its destabilization in Arabidopsis.
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Affiliation(s)
- Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, College of Life Sciences, Ningbo University, Ningbo315211, China
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Chaohua Wu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Tian Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- College of Life Science, Shandong Normal University, Jinan, Shandong250014, China
| | - Xiang Guo
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng475004, China
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Tianru Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Ziying Wang
- Department of Biology, Texas A&M University, College Station, TX77843
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Taerin Oh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
| | - Xiao Zhang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng475004, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Xu Peng
- Department of Medical Physiology, School of Medicine, Texas A&M University, Bryan, TX77807
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX77843
- Department of Biology, Texas A&M University, College Station, TX77843
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3
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Gong Q, Wang Y, Jin Z, Hong Y, Liu Y. Transcriptional and post-transcriptional regulation of RNAi-related gene expression during plant-virus interactions. STRESS BIOLOGY 2022; 2:33. [PMID: 37676459 PMCID: PMC10441928 DOI: 10.1007/s44154-022-00057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 08/14/2022] [Indexed: 09/08/2023]
Abstract
As sessile organisms, plants encounter diverse invasions from pathogens including viruses. To survive and thrive, plants have evolved multilayered defense mechanisms to combat virus infection. RNAi, also known as RNA silencing, is an across-kingdom innate immunity and gene regulatory machinery. Molecular framework and crucial roles of RNAi in antiviral defense have been well-characterized. However, it is largely unknown that how RNAi is transcriptionally regulated to initiate, maintain and enhance cellular silencing under normal or stress conditions. Recently, insights into the transcriptional and post-transcriptional regulation of RNAi-related genes in different physiological processes have been emerging. In this review, we integrate these new findings to provide updated views on how plants modulate RNAi machinery at the (post-) transcriptional level to respond to virus infection.
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Affiliation(s)
- Qian Gong
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yunjing Wang
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Zhenhui Jin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
- School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
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4
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Jeena GS, Singh N, Shukla RK. An insight into microRNA biogenesis and its regulatory role in plant secondary metabolism. PLANT CELL REPORTS 2022; 41:1651-1671. [PMID: 35579713 DOI: 10.1007/s00299-022-02877-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
The present review highlights the regulatory roles of microRNAs in plant secondary metabolism and focuses on different bioengineering strategies to modulate secondary metabolite content in plants. MicroRNAs (miRNAs) are the class of small endogenous, essential, non-coding RNAs that riboregulate the gene expression involved in various biological processes in most eukaryotes. MiRNAs has emerged as important regulators in plants that function by silencing target genes through cleavage or translational inhibition. These miRNAs plays an important role in a wide range of plant biological and metabolic processes, including plant development and various environmental response controls. Several important plant secondary metabolites like alkaloids, terpenoids, and phenolics are well studied for their function in plant defense against different types of pests and herbivores. Due to the presence of a wide range of biological and pharmaceutical properties of plant secondary metabolites, it is important to study the regulation of their biosynthetic pathways. The contribution of miRNAs in regulating plant secondary metabolism is not well explored. Recent advancements in molecular techniques have improved our knowledge in understanding the molecular function of genes, proteins, enzymes, and small RNAs involved in different steps of secondary metabolic pathways. In the present review, we have discussed the recent progress made on miRNA biogenesis, its regulation, and highlighted the current research developed in the field of identification, analysis, and characterizations of various miRNAs that regulate plant secondary metabolism. We have also discussed how different bioengineering strategies such as artificial miRNA (amiRNA), endogenous target mimicry, and CRISPR/Cas9 could be utilized to enhance the secondary metabolite production in plants.
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Affiliation(s)
- Gajendra Singh Jeena
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Neeti Singh
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Rakesh Kumar Shukla
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Near Kukrail Picnic Spot, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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5
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Wang L, Yan X, Li Y, Wang Z, Chhajed S, Shang B, Wang Z, Choi SW, Zhao H, Chen S, Zhang X. PRP4KA phosphorylates SERRATE for degradation via 20 S proteasome to fine-tune miRNA production in Arabidopsis. SCIENCE ADVANCES 2022; 8:eabm8435. [PMID: 35333566 PMCID: PMC8956257 DOI: 10.1126/sciadv.abm8435] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphorylation can quickly switch on/off protein functions. Here, we reported pre-mRNA processing 4 kinase A (PRP4KA), and its paralogs interact with Serrate (SE), a key factor in RNA processing. PRP4KA phosphorylates at least five residues of SE in vitro and in vivo. Hypophosphorylated, but not hyperphosphorylated, SE variants could readily rescue se phenotypes in vivo. Moreover, hypophosphorylated SE variants had stronger binding affinity to microprocessor component HYL1 and were more resistant to degradation by 20S proteasome than hyperphosphorylated counterparts. Knockdown of the kinases enhanced the accumulation of hypophosphorylated SE. However, the excessive SE interfered with the assembly and function of SE-scaffolded macromolecule complexes, causing the se-like defects in the mutant and wild-type backgrounds. Thus, phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates miRNA metabolism through controlling homeostasis of SE accumulation in plants.
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Affiliation(s)
- Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shweta Chhajed
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Suk Won Choi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Hongwei Zhao
- Laboratory of Bio-interactions and Crop Health, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Sixue Chen
- Department of Biology, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Corresponding author.
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6
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Jin L, Chen M, Xiang M, Guo Z. RNAi-Based Antiviral Innate Immunity in Plants. Viruses 2022; 14:v14020432. [PMID: 35216025 PMCID: PMC8875485 DOI: 10.3390/v14020432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/13/2022] Open
Abstract
Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.
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7
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Arif MA, Top O, Csicsely E, Lichtenstern M, Beheshti H, Adjabi K, Frank W. DICER-LIKE1a autoregulation based on intronic microRNA processing is required for stress adaptation in Physcomitrium patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:227-240. [PMID: 34743365 DOI: 10.1111/tpj.15570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/27/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
The Physcomitrium patens DICER-LIKE1a (PpDCL1a) mRNA encoding the essential Dicer protein for microRNA (miRNA) biogenesis harbors an intronic miRNA (miR1047). An autoregulatory mechanism to control PpDCL1a abundance that is based on competitive processing of the intronic miRNA and proper PpDCL1a mRNA splicing has previously been proposed. If intron splicing occurs first the mRNA can be translated into the functional PpDCL1a protein, whereas the processing of the intronic miRNA catalyzed by PpDCL1a itself, prior to pre-mRNA splicing, generates a truncated transcript unable to produce a functional protein. This proposed autoregulation of DCL1 has not been functionally analyzed in any plant species, and the existence of this autoregulatory control is expected to have a general impact on the overall miRNA biogenesis pathway and the transcriptome that is under miRNA control. We abolished PpDCL1a autoregulatory feedback control by the precise deletion of the MIR1047-containing intron. The generated line displayed hypersensitivity to salt stress and hyposensitivity to the plant hormone ABA, accompanied by the disturbed expression of miRNAs and mRNAs, revealed by transcriptome analyses. The feedback control together with the phenotypic abnormalities and molecular changes in the intron-less line can be rescued by the re-insertion of a modified intron harboring a sequence-unrelated artificial miRNA. Our findings indicate the physiological importance of miR1047-based feedback control of PpDCL1a transcript abundance, which controls the expression of miRNAs, and their cognate target RNAs during salt stress adaptation, and suggests a key role for this autoregulation in the molecular adaptation of land plants to terrestrial habitats.
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Affiliation(s)
- M Asif Arif
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Oguz Top
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Erika Csicsely
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Myriam Lichtenstern
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Hossein Beheshti
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Kaoutar Adjabi
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, LMU Biocenter, Großhaderner Straße 2-4, Planegg-Martinsried, 82152, Germany
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8
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Abstract
Phytohormones mediate plant development and responses to stresses caused by biotic agents or abiotic factors. The functions of phytohormones in responses to viral infection have been intensively studied, and the emerging picture of complex mechanisms provides insights into the roles that phytohormones play in defense regulation as a whole. These hormone signaling pathways are not simple linear or isolated cascades, but exhibit crosstalk with each other. Here, we summarized the current understanding of recent advances for the classical defense hormones salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) and also the roles of abscisic acid (ABA), auxin, gibberellic acid (GA), cytokinins (CKs), and brassinosteroids (BRs) in modulating plant–virus interactions.
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9
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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10
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Li Y, Sun D, Ma Z, Yamaguchi K, Wang L, Zhong S, Yan X, Shang B, Nagashima Y, Koiwa H, Han J, Xie Q, Zhou M, Wang Z, Zhang X. Degradation of SERRATE via ubiquitin-independent 20S proteasome to survey RNA metabolism. NATURE PLANTS 2020; 6:970-982. [PMID: 32690892 PMCID: PMC7426255 DOI: 10.1038/s41477-020-0721-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/16/2020] [Indexed: 05/18/2023]
Abstract
SERRATE (SE) is a key factor in RNA metabolism. Here, we report that SE binds 20S core proteasome α subunit G1 (PAG1) among other components and is accumulated in their mutants. Purified PAG1-containing 20S proteasome degrades recombinant SE via an ATP- and ubiquitin-independent manner in vitro. Nevertheless, PAG1 is a positive regulator for SE in vivo, as pag1 shows comparable molecular and/or developmental defects relative to se. Furthermore, SE is poorly assembled into macromolecular complexes, exemplified by the microprocessor in pag1 compared with Col-0. SE overexpression triggered the destruction of both transgenic and endogenous protein, leading to similar phenotypes of se and SE overexpression lines. We therefore propose that PAG1 degrades the intrinsically disordered portion of SE to secure the functionality of folded SE that is assembled and protected in macromolecular complexes. This study provides insight into how the 20S proteasome regulates RNA metabolism through controlling its key factor in eukaryotes.
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Affiliation(s)
- Yanjun Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Karissa Yamaguchi
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Lin Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Xingxing Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Baoshuan Shang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA
| | - Yukihiro Nagashima
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
| | - Jiajia Han
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China.
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX, USA.
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11
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Sacnun JM, Crespo R, Palatnik J, Rasia R, González-Schain N. Dual function of HYPONASTIC LEAVES 1 during early skotomorphogenic growth in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:977-991. [PMID: 31922639 DOI: 10.1111/tpj.14681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Seeds germinating underground display a specific developmental programme, termed skotomorphogenesis, to ensure survival of the emerging seedlings until they reach the light. They rapidly elongate the hypocotyl and maintain the cotyledons closed, forming a hook with the hypocotyl in order to protect apical meristematic cells from mechanical damage. Such crucial events for the fate of the seedling are tightly regulated and although some transcriptional regulators and phytohormones are known to be implicated in this regulation, we are still far from a complete understanding of these biological processes. Our work provides information on the diverse roles in skotomorphogenesis of the core components of microRNA biogenesis in Arabidopsis, HYL1, DCL1, and SE. We show that hypocotyl elongation is promoted by all these components, probably through the action of specific miRNAs. Hook development also depends on these proteins however, remarkably, HYL1 exerts its role in an opposite way to DCL1 and SE. Interestingly, we found that a specific HYL1 domain involved in protein-protein interaction is required for this function. Genetic evidences also point to the phosphorylation status of HYL1 as important for this function. We propose that HYL1 help maintain the hook closed during early skotomorphogenesis in a microprocessor-independent manner by repressing the activity of HY5, the transcriptional master regulator that triggers light responses. This work uncovers a previously unnoticed link between components of the miRNA biogenesis machinery, the skotomorphogenic growth, and hook development in Arabidopsis.
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Affiliation(s)
- Juan Manuel Sacnun
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Roberta Crespo
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Javier Palatnik
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Rodolfo Rasia
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Nahuel González-Schain
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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12
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Katsarou K, Mitta E, Bardani E, Oulas A, Dadami E, Kalantidis K. DCL-suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology. MOLECULAR PLANT PATHOLOGY 2019; 20:432-446. [PMID: 30343523 PMCID: PMC6637889 DOI: 10.1111/mpp.12761] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RNA silencing is a universal mechanism involved in development, epigenetic modifications and responses to biotic and abiotic stresses. The major components of this mechanism are Dicer-like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) proteins. Understanding the role of each component is of great scientific and agronomic importance. Plants, including Nicotiana benthamiana, an important plant model, usually possess four DCL proteins, each of which has a specific role, namely being responsible for the production of an exclusive small RNA population. Here, we used RNA interference (RNAi) technology to target DCL proteins and produced single and combinatorial mutants for DCL. We analysed the phenotype for each DCL knockdown plant, together with the small RNA profile, by next-generation sequencing (NGS). We also investigated transgene expression, as well as viral infections, and were able to show that DCL suppression results in distinct developmental defects, changes in small RNA populations, increases in transgene expression and, finally, higher susceptibility in certain RNA viruses. Therefore, these plants are excellent tools for the following: (i) to study the role of DCL enzymes; (ii) to overexpress proteins of interest; and (iii) to understand the complex relationship between the plant silencing mechanism and biotic or abiotic stresses.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
| | - Eleni Mitta
- Department of BiologyUniversity of CreteHeraklionGreece
| | | | - Anastasis Oulas
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Present address:
Bioinformatics Group, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Elena Dadami
- Department of BiologyUniversity of CreteHeraklionGreece
- Present address:
RLP AgroScience, AlPlantaNeustadtGermany
| | - Kriton Kalantidis
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology‐HellasHeraklionGreece
- Department of BiologyUniversity of CreteHeraklionGreece
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13
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Speth C, Szabo EX, Martinho C, Collani S, Zur Oven-Krockhaus S, Richter S, Droste-Borel I, Macek B, Stierhof YD, Schmid M, Liu C, Laubinger S. Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. eLife 2018; 7:37078. [PMID: 30152752 PMCID: PMC6135607 DOI: 10.7554/elife.37078] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/22/2018] [Indexed: 01/16/2023] Open
Abstract
Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.
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Affiliation(s)
- Corinna Speth
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Emese Xochitl Szabo
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany.,Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
| | - Claudia Martinho
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Silvio Collani
- Department of Plant Physiology, Umea Plant Science Centre, Umeå University, Umea, Sweden
| | | | - Sandra Richter
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | | | - Boris Macek
- Proteome Centre, University of Tuebingen, Tuebingen, Germany
| | - York-Dieter Stierhof
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | - Markus Schmid
- Department of Plant Physiology, Umea Plant Science Centre, Umeå University, Umea, Sweden
| | - Chang Liu
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany.,Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
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14
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Ma Z, Castillo-González C, Wang Z, Sun D, Hu X, Shen X, Potok ME, Zhang X. Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression. Dev Cell 2018; 45:769-784.e6. [PMID: 29920280 DOI: 10.1016/j.devcel.2018.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/04/2018] [Accepted: 05/20/2018] [Indexed: 12/25/2022]
Abstract
Serrate (SE) is a key component in RNA metabolism. Little is known about whether and how it can regulate epigenetic silencing. Here, we report histone methyltransferases ATXR5 and ATXR6 (ATXR5/6) as novel partners of SE. ATXR5/6 deposit histone 3 lysine 27 monomethylation (H3K27me1) to promote heterochromatin formation, repress transposable elements (TEs), and control genome stability in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions. Furthermore, SE directly enhances ATXR5 enzymatic activity in vitro. Unexpectedly, se mutation suppresses the TE reactivation and DNA re-replication phenotypes in the atxr5 atxr6 mutant. The suppression of TE expression results from triggering RNA-dependent RNA polymerase 6 (RDR6)-dependent RNA silencing in the se atxr5 atxr6 mutant. We propose that SE facilitates ATXR5/6-mediated deposition of the H3K27me1 mark while inhibiting RDR6-mediated RNA silencing to protect TE transcripts. Hence, SE coordinates epigenetic silencing and RNA processing machineries to fine-tune the TE expression.
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Affiliation(s)
- Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaomei Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xuefeng Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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15
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Alazem M, He MH, Moffett P, Lin NS. Abscisic Acid Induces Resistance against Bamboo Mosaic Virus through Argonaute2 and 3. PLANT PHYSIOLOGY 2017; 174:339-355. [PMID: 28270624 PMCID: PMC5411131 DOI: 10.1104/pp.16.00015] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/03/2017] [Indexed: 05/21/2023]
Abstract
Plant resistance to pathogens is tuned by defense-related hormones. Of these, abscisic acid (ABA) is well documented to moderate resistance against fungi and bacteria. However, ABA's contribution to resistance against viruses is pleiotropic. ABA affects callose deposition at plasmodesmata (therefore hindering the viral cell-to-cell movement), but here, we show that when callose synthase is down-regulated, ABA still induces resistance against infection with Bamboo mosaic virus (BaMV). By examining the potential connections between the ABA and RNA-silencing pathways in Arabidopsis (Arabidopsis thaliana), we showed that ABA regulates the expression of almost the whole ARGONAUTE (AGO) gene family, of which some are required for plant resistance against BaMV Our data show that BaMV infection and ABA treatment regulate the same set of AGOs, with positive effects on AGO1, AGO2, and AGO3, no effect on AGO7, and negative effects on AGO4 and AGO10 The BaMV-mediated regulation of AGO1, AGO2, and AGO3 is ABA dependent, because the accumulation of these AGOs in BaMV-infected ABA mutants did not reach the levels observed in infected wild-type plants. In addition, the AGO1-miR168a complex is dispensable for BaMV resistance, while AGO2 and AGO3 were important for ABA-mediated resistance. While most ago mutants showed increased susceptibility to BaMV infection (except ago10), ago1-27 showed reduced BaMV titers, which was attributed to the up-regulated levels of AGO2, AGO3, and AGO4 We have established that ABA regulates the expression of several members of the AGO family, and this regulation partially contributes to ABA-mediated resistance against BaMV These findings reveal another role for ABA in plants.
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Affiliation(s)
- Mazen Alazem
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Meng-Hsun He
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Peter Moffett
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China (M.A., M.-H.H., N.-S.L.); and
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1K 2R1 (P.M.)
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16
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Katsarou K, Mavrothalassiti E, Dermauw W, Van Leeuwen T, Kalantidis K. Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid. PLoS Pathog 2016; 12:e1005936. [PMID: 27732664 PMCID: PMC5061435 DOI: 10.1371/journal.ppat.1005936] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022] Open
Abstract
Viroids are self replicating non-coding RNAs capable of infecting a wide range of plant hosts. They do not encode any proteins, thus the mechanism by which they escape plant defenses remains unclear. RNAi silencing is a major defense mechanism against virus infections, with the four DCL proteins being principal components of the pathway. We have used Nicotiana benthamiana as a model to study Potato spindle tuber viroid infection. This viroid is a member of the Pospiviroidae family and replicates in the nucleus via an asymmetric rolling circle mechanism. We have created knock-down plants for all four DCL genes and their combinations. Previously, we showed that DCL4 has a positive effect on PSTVd infectivity since viroid levels drop when DCL4 is suppressed. Here, we show that PSTVd levels remain decreased throughout infection in DCL4 knockdown plants, and that simultaneous knockdown of DCL1, DCL2 or DCL3 together with DCL4 cannot reverse this effect. Through infection of plants suppressed for multiple DCLs we further show that a combined suppression of DCL2 and DCL3 has a major effect in succumbing plant antiviral defense. Based on our results, we further suggest that Pospoviroids may have evolved to be primarily processed by DCL4 as it seems to be a DCL protein with less detrimental effects on viroid infectivity. These findings pave the way to delineate the complexity of the relationship between viroids and plant RNA silencing response.
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Affiliation(s)
- Konstantina Katsarou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | | | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Belgium
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, The Netherlands
| | - Kriton Kalantidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
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17
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Abstract
RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous gene expression, controls invading transposable elements (TEs), and protects the cell against viruses. Key components of the mechanism are small RNAs (sRNAs) of 21-24 nt that guide the silencing machinery to their nucleic acid targets in a nucleotide sequence-specific manner. Transcriptional gene silencing is associated with 24-nt sRNAs and RNA-directed DNA methylation (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH). We previously demonstrated that 24-nt sRNAs are mobile from shoot to root in Arabidopsis thaliana and confirmed that they mediate DNA methylation at three sites in recipient cells. In this study, we extend this finding by demonstrating that RdDM of thousands of loci in root tissues is dependent upon mobile sRNAs from the shoot and that mobile sRNA-dependent DNA methylation occurs predominantly in non-CG contexts. Mobile sRNA-dependent non-CG methylation is largely dependent on the DOMAINS REARRANGED METHYLTRANSFERASES 1/2 (DRM1/DRM2) RdDM pathway but is independent of the CHROMOMETHYLASE (CMT)2/3 DNA methyltransferases. Specific superfamilies of TEs, including those typically found in gene-rich euchromatic regions, lose DNA methylation in a mutant lacking 22- to 24-nt sRNAs (dicer-like 2, 3, 4 triple mutant). Transcriptome analyses identified a small number of genes whose expression in roots is associated with mobile sRNAs and connected to DNA methylation directly or indirectly. Finally, we demonstrate that sRNAs from shoots of one accession move across a graft union and target DNA methylation de novo at normally unmethylated sites in the genomes of root cells from a different accession.
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18
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Deng S, Xu J, Liu J, Kim SH, Shi S, Chua NH. JMJ24 binds to RDR2 and is required for the basal level transcription of silenced loci in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:770-82. [PMID: 26119694 DOI: 10.1111/tpj.12924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/29/2015] [Accepted: 06/23/2015] [Indexed: 05/09/2023]
Abstract
Transposable elements (TEs) and repetitive sequences are ubiquitously present in eukaryotic genomes which are in general epigenetically silenced by DNA methylation and/or histone 3 lysine 9 methylation (H3K9me). RNA-directed DNA methylation (RdDM) is the major pathway that initiates de novo DNA methylation in Arabidopsis and sets up a self-reinforcing silencing loop between DNA methylation and H3K9me. However, a key issue is the requirement of a basal level transcript from the target loci to initiate the RNA-based silencing. How the heterochromatic silenced loci are transcribed remains largely unknown. Here, we show that JMJ24, a JmjC domain-containing protein counteracts H3K9me to promote basal level transcription of endogenous silenced loci in Arabidopsis. JMJ24 functionally resembles the fission yeast JmjC protein Epe1. The transcript promoted by JMJ24 is, at least in part, processed to small RNA to initiate the RdDM. Genome-wide transcriptome profiling indicates that transcript levels of TEs are more likely regulated by JMJ24, compared with protein-coding genes. Our data suggest that JMJ24 plays a conserved role in promoting basal level transcription of endogenous silenced loci to reinforce the silencing. We also provide evidence of a physical association between JMJ24 and RNA-dependent RNA polymerase 2 (RDR2), which represents an evolved property of the RNA silencing pathway.
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Affiliation(s)
- Shulin Deng
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jun Xu
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Jun Liu
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Sang-Hee Kim
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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19
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Alazem M, Lin NS. Roles of plant hormones in the regulation of host-virus interactions. MOLECULAR PLANT PATHOLOGY 2015; 16:529-40. [PMID: 25220680 PMCID: PMC6638471 DOI: 10.1111/mpp.12204] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Hormones are tuners of plant responses to biotic and abiotic stresses. They are involved in various complicated networks, through which they modulate responses to different stimuli. Four hormones primarily regulate plant defence to pathogens: salicylic acid (SA), jasmonic acid (JA), ethylene (Et) and abscisic acid (ABA). In susceptible plants, viral infections result in hormonal disruption, which manifests as the simultaneous induction of several antagonistic hormones. However, these antagonistic hormones may exhibit some sequential accumulation in resistant lines. Virus propagation is usually restricted by the activation of the small interfering RNA (siRNA) antiviral machinery and/or SA signalling pathway. Several studies have investigated these two systems, using different model viruses. However, the roles of hormones other than SA, especially those with antagonistic properties, such as ABA, have been neglected. Increasing evidence indicates that hormones control components of the small RNA system, which regulates many processes (including the siRNA antiviral machinery and the microRNA system) at the transcriptional or post-transcriptional level. Consequently, cross-talk between the antagonistic SA and ABA pathways modulates plant responses at multiple levels. In this review, we summarize recent findings on the different roles of hormones in the regulation of plant-virus interactions, which are helping us to elucidate the fine tuning of viral and plant systems by hormones.
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Affiliation(s)
- Mazen Alazem
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan
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20
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New opportunities for the regulation of secondary metabolism in plants: focus on microRNAs. Biotechnol Lett 2015; 37:1719-27. [PMID: 26003096 DOI: 10.1007/s10529-015-1863-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/14/2015] [Indexed: 12/22/2022]
Abstract
Plant cell cultures are of particular interest in industrial applications as a source of biologically active substances. It is difficult, however, to achieve stable production of secondary metabolites for many plant cell cultures using classical techniques. Novel approaches should be developed for removal of the inhibitor blocks that prevent pathway activation and shift the regulatory balance to the activation of entire biosynthetic pathways. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. Only recently miRNAs have been demonstrated as active in secondary metabolism regulation. In this work, we summarize recent data on the emerging approaches based on regulation of secondary metabolism by miRNAs.
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21
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Martinho C, Confraria A, Elias CA, Crozet P, Rubio-Somoza I, Weigel D, Baena-González E. Dissection of miRNA pathways using arabidopsis mesophyll protoplasts. MOLECULAR PLANT 2015; 8:261-75. [PMID: 25680775 DOI: 10.1016/j.molp.2014.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/10/2014] [Accepted: 10/10/2014] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this article, we describe a transient expression system in Arabidopsis mesophyll protoplasts, which is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, by either overexpression or the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up, and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.
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Affiliation(s)
- Cláudia Martinho
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Carlos Alexandre Elias
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Pierre Crozet
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal
| | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de Ciência, Rua da Quinta Grande - 6, 2780-156 Oeiras, Portugal.
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22
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Abstract
DNA methylation is a type of epigenetic modification where a methyl group is added to the cytosine or adenine residue of a given DNA sequence. It has been observed that DNA methylation is achieved by some collaborative agglomeration of certain proteins and non-coding RNAs. The assembly of IDN2 and its homologous proteins with siRNAs recruits the enzyme DRM2, which adds a methyl group at certain cytosine residues within the DNA sequence. In this study, it was found that de novo DNA methylation might be regulated by miRNAs through systematic targeting of the genes involved in DNA methylation. A comprehensive genome-wide and system-level study of miRNA targeting, transcription factors, DNA-methylation-causing genes and their target genes has provided a clear picture of an interconnected relationship of all these factors which regulate DNA methylation in Arabidopsis. The study has identified a DNA methylation system that is controlled by four different genes: IDN2, IDNl1, IDNl2 and DRM2. These four genes along with various critical transcription factors appear to be controlled by five different miRNAs. Altogether, DNA methylation appears to be a finely tuned process of opposite control systems of DNAmethylation- causing genes and certain miRNAs pitted against each other.
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Affiliation(s)
- Ashwani Jha
- Studio of Computational Biology and Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176 061, India
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23
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Xie M, Zhang S, Yu B. microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 2015; 72:87-99. [PMID: 25209320 PMCID: PMC11113746 DOI: 10.1007/s00018-014-1728-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/13/2014] [Accepted: 09/04/2014] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and guide their effector protein named argonaute 1 (AGO1) to silence the expression of target RNAs containing their complementary sequences in plants. miRNA levels and activities are tightly controlled to ensure their functions in various biological processes such as development, metabolism and responses to abiotic and biotic stresses. Studies have identified many factors that involve in miRNA accumulation and activities. Characterization of these factors in turn greatly improves our understanding of the processes related to miRNAs. Here, we review recent progress of mechanisms underlying miRNA expression and functions in plants.
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Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Shuxin Zhang
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
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24
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Thompson BE, Basham C, Hammond R, Ding Q, Kakrana A, Lee TF, Simon SA, Meeley R, Meyers BC, Hake S. The dicer-like1 homolog fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize. THE PLANT CELL 2014; 26:4702-17. [PMID: 25465405 PMCID: PMC4311206 DOI: 10.1105/tpc.114.132670] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant architecture is determined by meristems that initiate leaves during vegetative development and flowers during reproductive development. Maize (Zea mays) inflorescences are patterned by a series of branching events, culminating in floral meristems that produce sexual organs. The maize fuzzy tassel (fzt) mutant has striking inflorescence defects with indeterminate meristems, fasciation, and alterations in sex determination. fzt plants have dramatically reduced plant height and shorter, narrower leaves with leaf polarity and phase change defects. We positionally cloned fzt and discovered that it contains a mutation in a dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. miRNAs are small noncoding RNAs that reduce target mRNA levels and are key regulators of plant development and physiology. Small RNA sequencing analysis showed that most miRNAs are moderately reduced in fzt plants and a few miRNAs are dramatically reduced. Some aspects of the fzt phenotype can be explained by reduced levels of known miRNAs, including miRNAs that influence meristem determinacy, phase change, and leaf polarity. miRNAs responsible for other aspects of the fzt phenotype are unknown and likely to be those miRNAs most severely reduced in fzt mutants. The fzt mutation provides a tool to link specific miRNAs and targets to discrete phenotypes and developmental roles.
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Affiliation(s)
- Beth E Thompson
- Department of Biology, East Carolina University, Greenville, North Carolina 27858
| | - Christine Basham
- Department of Biology, East Carolina University, Greenville, North Carolina 27858
| | - Reza Hammond
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714 Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Queying Ding
- Department of Biology, East Carolina University, Greenville, North Carolina 27858
| | - Atul Kakrana
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19714 Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Tzuu-Fen Lee
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Stacey A Simon
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | | | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Sarah Hake
- Plant Gene Expression Center and University of California-Berkeley, Albany, California 94710
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Baev V, Milev I, Naydenov M, Vachev T, Apostolova E, Mehterov N, Gozmanva M, Minkov G, Sablok G, Yahubyan G. Insight into small RNA abundance and expression in high- and low-temperature stress response using deep sequencing in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:105-114. [PMID: 25261853 DOI: 10.1016/j.plaphy.2014.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/15/2014] [Indexed: 05/25/2023]
Abstract
Small RNA profiling and assessing its dependence on changing environmental factors have expanded our understanding of the transcriptional and post-transcriptional regulation of plant stress responses. Insufficient data have been documented earlier to depict the profiling of small RNA classes in temperature-associated stress which has a wide implication for climate change biology. In the present study, we report a comparative assessment of the genome-wide profiling of small RNAs in Arabidopsis thaliana using two conditional responses, induced by high- and low-temperature. Genome-wide profiling of small RNAs revealed an abundance of 21 nt small RNAs at low temperature, while high temperature showed an abundance of 21 nt and 24 nt small RNAs. The two temperature treatments altered the expression of a specific subset of mature miRNAs and displayed differential expression of a number of miRNA isoforms (isomiRs). Comparative analysis demonstrated that a large number of protein-coding genes can give rise to differentially expressed small RNAs following temperature shifts. Low temperature caused accumulation of small RNAs, corresponding to the sense strand of a number of cold-responsive genes. In contrast, high temperature stimulated the production of small RNAs of both polarities from genes encoding functionally diverse proteins.
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Affiliation(s)
- Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
| | - Ivan Milev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Mladen Naydenov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Tihomir Vachev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Nikolay Mehterov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanva
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Georgi Minkov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, San Michele 38010, Italy
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
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Secco D, Shou H, Whelan J, Berkowitz O. RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin. BMC Genomics 2014; 15:230. [PMID: 24666749 PMCID: PMC4028058 DOI: 10.1186/1471-2164-15-230] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/18/2014] [Indexed: 01/03/2023] Open
Abstract
Background Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dense lateral roots formed by several plant species for the effective mining of nutrient rich soil patches through a combination of increased surface area and exudation of carboxylates. White lupin is becoming a model-species allowing for the discovery of gene networks involved in CR development. A greater understanding of the underlying molecular mechanisms driving these developmental processes is important for the generation of smarter plants for a world with diminishing resources to improve food security. Results RNA-seq analyses for three developmental stages of the CR formed under phosphorus-limited conditions and two of non-cluster roots have been performed for white lupin. In total 133,045,174 high-quality paired-end reads were used for a de novo assembly of the root transcriptome and merged with LAGI01 (Lupinus albus gene index) to generate an improved LAGI02 with 65,097 functionally annotated contigs. This was followed by comparative gene expression analysis. We show marked differences in the transcriptional response across the various cluster root stages to adjust to phosphate limitation by increasing uptake capacity and adjusting metabolic pathways. Several transcription factors such as PLT, SCR, PHB, PHV or AUX/IAA with a known role in the control of meristem activity and developmental processes show an increased expression in the tip of the CR. Genes involved in hormonal responses (PIN, LAX, YUC) and cell cycle control (CYCA/B, CDK) are also differentially expressed. In addition, we identify primary transcripts of miRNAs with established function in the root meristem. Conclusions Our gene expression analysis shows an intricate network of transcription factors and plant hormones controlling CR initiation and formation. In addition, functional differences between the different CR developmental stages in the acclimation to phosphorus starvation have been identified.
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Affiliation(s)
| | | | | | - Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009, Australia.
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27
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Speth C, Laubinger S. RACK1 and the microRNA pathway: is it déjà-vu all over again? PLANT SIGNALING & BEHAVIOR 2014; 9:e27909. [PMID: 24521556 PMCID: PMC4091593 DOI: 10.4161/psb.27909] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 01/19/2014] [Indexed: 05/30/2023]
Abstract
MicroRNAs (miRNAs) control many aspects of development and adaption in plants and in animals by post-transcriptional control of mRNA stability and translatability. Over the last years numerous proteins have been identified in the miRNA pathway. The versatile scaffold protein RACK1 has been associated with efficient miRNA production and function in plants and metazoans. Here, we briefly summarize the differences of RACK1 function in the plant and animal miRNA pathways and discuss putative mechanisms and functional roles of RACK1 in miRNA biogenesis and action.
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Affiliation(s)
- Corinna Speth
- Center for Plant Molecular Biology (ZMBP); University of Tübingen; Tübingen, Germany
- Chemical Genomics Centre (CGC) of the Max Planck Society; Dortmund, Germany, & MPI for Developmental Biology; Tübingen, Germany
| | - Sascha Laubinger
- Center for Plant Molecular Biology (ZMBP); University of Tübingen; Tübingen, Germany
- Chemical Genomics Centre (CGC) of the Max Planck Society; Dortmund, Germany, & MPI for Developmental Biology; Tübingen, Germany
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Kravchik M, Sunkar R, Damodharan S, Stav R, Zohar M, Isaacson T, Arazi T. Global and local perturbation of the tomato microRNA pathway by a trans-activated DICER-LIKE 1 mutant. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:725-39. [PMID: 24376253 PMCID: PMC3904720 DOI: 10.1093/jxb/ert428] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DICER-like 1 (DCL1) is a major player in microRNA (miRNA) biogenesis and accordingly, its few known loss-of-function mutants are either lethal or display arrested development. Consequently, generation of dcl1 mutants by reverse genetics and functional analysis of DCL1 in late-developing organs are challenging. Here, these challenges were resolved through the unique use of trans-activated RNA interference. Global, as well as organ-specific tomato DCL1 (SlDCL1) silencing was induced by crossing the generated responder line (OP:SlDCL1IR) with the appropriate driver line. Constitutive trans-activation knocked down SlDCL1 levels by ~95%, resulting in severe abnormalities including post-germination growth arrest accompanied by decreased miRNA and 21-nucleotide small RNA levels, but prominently elevated levels of 22-nucleotide small RNAs. The increase in the 22-nucleotide small RNAs was correlated with specific up-regulation of SlDCL2b and SlDCL2d, which are probably involved in their biogenesis. Leaf- and flower-specific OP:SlDCL1IR trans-activation inhibited blade outgrowth, induced premature bud senescence and produced pale petals, respectively, emphasizing the importance of SlDCL1-dependent small RNAs in these processes. Together, these results establish OP:SlDCL1IR as an efficient tool for analysing processes regulated by SlDCL1-mediated gene regulation in tomato.
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Affiliation(s)
- Michael Kravchik
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan 50250, Israel
| | - Ramanjulu Sunkar
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Subha Damodharan
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan 50250, Israel
| | - Ran Stav
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan 50250, Israel
| | - Matat Zohar
- Unit of Deciduous Fruit Tree Sciences, Newe Ya’ar Research Center, Agricultural Research Organization, PO Box 1021, Ramat Yishay 30095, Israel
| | - Tal Isaacson
- Unit of Deciduous Fruit Tree Sciences, Newe Ya’ar Research Center, Agricultural Research Organization, PO Box 1021, Ramat Yishay 30095, Israel
| | - Tzahi Arazi
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan 50250, Israel
- * To whom correspondence should be addressed. E-mail:
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Speth C, Willing EM, Rausch S, Schneeberger K, Laubinger S. RACK1 scaffold proteins influence miRNA abundance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:433-45. [PMID: 23941160 DOI: 10.1111/tpj.12308] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1 to facilitate efficient and precise pri-miRNA processing and miRNA loading, respectively. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein that is found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants, and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to over-accumulation of miRNA target mRNAs, which are important for ABA responses and phyllotaxy, for example. In conclusion, our study identified complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway; these proteins are important for miRNA production and therefore plant development.
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Affiliation(s)
- Corinna Speth
- Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany; Chemical Genomics Centre of the Max Planck Society, 44227, Dortmund, Germany; Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
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30
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Jeong IS, Aksoy E, Fukudome A, Akhter S, Hiraguri A, Fukuhara T, Bahk JD, Koiwa H. Arabidopsis C-terminal domain phosphatase-like 1 functions in miRNA accumulation and DNA methylation. PLoS One 2013; 8:e74739. [PMID: 24058624 PMCID: PMC3776750 DOI: 10.1371/journal.pone.0074739] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 08/02/2013] [Indexed: 11/19/2022] Open
Abstract
Arabidopsis CTD-PHOSPHATASE-LIKE 1 (CPL1) is a protein phosphatase that can dephosphorylate RNA polymerase II C-terminal domain (CTD). Unlike typical CTD-phosphatases, CPL1 contains a double-stranded (ds) RNA-binding motif (dsRBM) and has been implicated for gene regulation mediated by dsRNA-dependent pathways. We investigated the role of CPL1 and its dsRBMs in various gene silencing pathways. Genetic interaction analyses revealed that cpl1 was able to partially suppress transcriptional gene silencing and DNA hypermethylation phenotype of ros1 suggesting CPL1 is involved in the RNA-directed DNA methylation pathway without reducing siRNA production. By contrast, cpl1 reduced some miRNA levels at the level of processing. Indeed, CPL1 protein interacted with proteins important for miRNA biogenesis, suggesting that CPL1 regulates miRNA processing. These results suggest that CPL1 regulates DNA methylation via a miRNA-dependent pathway.
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Affiliation(s)
- In Sil Jeong
- Division of Applied Life Science (BK21 Program), Graduate School of Gyeongsang National University, Jinju, Gyeongsangnam-do, Korea
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Emre Aksoy
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Akihito Fukudome
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Salina Akhter
- Division of Applied Life Science (BK21 Program), Graduate School of Gyeongsang National University, Jinju, Gyeongsangnam-do, Korea
| | - Akihiro Hiraguri
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Jeong Dong Bahk
- Division of Applied Life Science (BK21 Program), Graduate School of Gyeongsang National University, Jinju, Gyeongsangnam-do, Korea
- * E-mail: (HK); (JDB)
| | - Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (HK); (JDB)
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31
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Lin JS, Lin CC, Li YC, Wu MT, Tsai MH, Hsing YIC, Jeng ST. Interaction of small RNA-8105 and the intron of IbMYB1 RNA regulates IbMYB1 family genes through secondary siRNAs and DNA methylation after wounding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:781-794. [PMID: 23663233 DOI: 10.1111/tpj.12238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 06/02/2023]
Abstract
Small RNAs (sRNAs) play important roles in plants under stress conditions. However, limited research has been performed on the sRNAs involved in plant wound responses. In the present study, a novel wounding-induced sRNA, sRNA8105, was identified in sweet potato (Ipomoea batatas cv. Tainung 57) using microarray analysis. It was found that expression of sRNA8105 increased after mechanical wounding. Furthermore, Dicer-like 1 (DCL1) is required for the sRNA8105 precursor (pre-sRNA8105) to generate 22 and 24 nt mature sRNA8105. sRNA8105 targeted the first intron of IbMYB1 (MYB domain protein 1) before RNA splicing, and mediated RNA cleavage and DNA methylation of IbMYB1. The interaction between sRNA8105 and IbMYB1 was confirmed by cleavage site mapping, agro-infiltration analyses, and use of a transgenic sweet potato over-expressing pre-sRNA8105 gene. Induction of IbMYB1-siRNA was observed in the wild-type upon wounding and in transgenic sweet potato over-expressing pre-sRNA8105 gene without wounding, resulting in decreased expression of the whole IbMYB1 gene family, i.e. IbMYB1 and the IbMYB2 genes, and thus directing metabolic flux toward biosynthesis of lignin in the phenylpropanoid pathway. In conclusion, sRNA8105 induced by wounding binds to the first intron of IbMYB1 RNA to methylate IbMYB1, cleave IbMYB1 RNA, and trigger production of secondary siRNAs, further repressing the expression of the IbMYB1 family genes and regulating the phenylpropanoid pathway.
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Affiliation(s)
- Jeng-Shane Lin
- Institute of Plant Biology and Department of Life Science, National Taiwan University, Roosevelt Road, Taipei, 106, Taiwan
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32
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Panda K, Slotkin RK. Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway. PLANT SIGNALING & BEHAVIOR 2013; 8:25206. [PMID: 23759554 PMCID: PMC3999056 DOI: 10.4161/psb.25206] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/29/2013] [Indexed: 05/18/2023]
Abstract
The activity of transposable elements is epigenetically suppressed by both transcriptional and post-transcriptional mechanisms. We recently identified a direct connection between the small RNA-mediated post-transcriptional mRNA degradation of actively transcribing transposable elements and the de novo methylation of transposable element DNA, providing a mechanistic link between these two established pathways of transposable element silencing. Here we provide a model for the initiation, establishment and epigenetic maintenance of transposable element silencing that incorporates recent data in this rapidly emerging field.
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Rogers K, Chen X. Biogenesis, turnover, and mode of action of plant microRNAs. THE PLANT CELL 2013; 25:2383-99. [PMID: 23881412 PMCID: PMC3753372 DOI: 10.1105/tpc.113.113159] [Citation(s) in RCA: 584] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 04/25/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs that control gene expression through silencing of target mRNAs. Mature miRNAs are processed from primary miRNA transcripts by the endonuclease activity of the DICER-LIKE1 (DCL1) protein complex. Mechanisms exist that allow the DCL1 complex to precisely excise the miRNA from its precursor. Our understanding of miRNA biogenesis, particularly its intersection with transcription and other aspects of RNA metabolism such as splicing, is still evolving. Mature miRNAs are incorporated into an ARGONAUTE (AGO) effector complex competent for target gene silencing but are also subjected to turnover through a degradation mechanism that is beginning to be understood. The mechanisms of miRNA target silencing in plants are no longer limited to AGO-catalyzed slicing, and the contribution of translational inhibition is increasingly appreciated. Here, we review the mechanisms underlying the biogenesis, turnover, and activities of plant miRNAs.
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Affiliation(s)
- Kestrel Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- Howard Hughes Medical Institute, University of California, Riverside, California 92521
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Carreras-Villaseñor N, Esquivel-Naranjo EU, Villalobos-Escobedo JM, Abreu-Goodger C, Herrera-Estrella A. The RNAi machinery regulates growth and development in the filamentous fungusTrichoderma atroviride. Mol Microbiol 2013; 89:96-112. [DOI: 10.1111/mmi.12261] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Nohemi Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Edgardo U. Esquivel-Naranjo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - J. Manuel Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad; Cinvestav Sede Irapuato; Km 9.6 Libramiento Norte Carretera Irapuato-León; 36821; Irapuato; Gto.; Mexico
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35
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Rogers K, Chen X. microRNA biogenesis and turnover in plants. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2013; 77:183-94. [PMID: 23439913 DOI: 10.1101/sqb.2013.77.014530] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
microRNAs (miRNAs) are short RNAs that regulate gene expression in eukaryotes. The biogenesis and turnover of miRNAs determine their spatiotemporal accumulation within tissues. miRNA biogenesis is a multistep process that entails transcription, processing, nuclear export, and formation of the miRNA-ARGONAUTE complex. Factors that perform each of these steps have been identified. Generation of mature miRNAs from primary transcripts, i.e., miRNA processing, is a key step in miRNA biogenesis. Our understanding of miRNA processing has expanded beyond the enzyme that performs the reactions, as more and more additional factors that impact the efficiency and accuracy of miRNA processing are uncovered. In contrast to miRNA biogenesis, miRNA turnover is an important but poorly understood process that contributes to the steady-state levels of miRNAs. Enzymes responsible for miRNA degradation have only recently been identified. This review describes the processes of miRNA maturation and degradation in plants.
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Affiliation(s)
- K Rogers
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
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36
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Confraria A, Martinho C, Elias A, Rubio-Somoza I, Baena-González E. miRNAs mediate SnRK1-dependent energy signaling in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:197. [PMID: 23802004 PMCID: PMC3687772 DOI: 10.3389/fpls.2013.00197] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/27/2013] [Indexed: 05/17/2023]
Abstract
The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24 nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to their role in plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1. By comparing the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis, we identified 831 starvation genes misregulated in the dcl1-9 mutant, out of which 155 are validated or predicted miRNA targets. Functional clustering analysis revealed that the main cellular processes potentially co-regulated by SnRK1 and miRNAs are translation and organelle function and uncover TCP transcription factors as one of the most highly enriched functional clusters. TCP repression during energy deprivation was impaired in miR319 knockdown (MIM319) plants, demonstrating the involvement of miR319 in the stress-dependent regulation of TCPs. Altogether, our data indicates that miRNAs are components of the SnRK1 signaling cascade contributing to the regulation of specific mRNA targets and possibly tuning down particular cellular processes during the stress response.
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Affiliation(s)
- Ana Confraria
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Cláudia Martinho
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Alexandre Elias
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Ignacio Rubio-Somoza
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingen, Germany
| | - Elena Baena-González
- Plant Stress Signaling, Instituto Gulbenkian de CiênciaOeiras, Portugal
- *Correspondence: Elena Baena-González, Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal e-mail:
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Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D. Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 2012; 151:859-870. [PMID: 23141542 DOI: 10.1016/j.cell.2012.09.039] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/08/2012] [Accepted: 09/30/2012] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are processed from primary transcripts that contain partially self-complementary foldbacks. As in animals, the core microprocessor in plants is a Dicer protein, DICER-LIKE1 (DCL1). Processing accuracy and strand selection is greatly enhanced through the RNA binding protein HYPONASTIC LEAVES 1 (HYL1) and the zinc finger protein SERRATE (SE). We have combined a luciferase-based genetic screen with whole-genome sequencing for rapid identification of new regulators of miRNA biogenesis and action. Among the first six mutants analyzed were three alleles of C-TERMINAL DOMAIN PHOSPHATASE-LIKE 1 (CPL1)/FIERY2 (FRY2). In the miRNA processing complex, SE functions as a scaffold to mediate CPL1 interaction with HYL1, which needs to be dephosphorylated for optimal activity. In the absence of CPL1, HYL1 dephosphorylation and hence accurate processing and strand selection from miRNA duplexes are compromised. Our findings thus define a new regulatory step in plant miRNA biogenesis.
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Affiliation(s)
- Pablo A Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Felix Ott
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Sascha Laubinger
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Mirita Franz
- Proteome Center, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Boris Macek
- Proteome Center, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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38
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Ren G, Yu B. Critical roles of RNA-binding proteins in miRNA biogenesis in Arabidopsis. RNA Biol 2012; 9:1424-8. [PMID: 23135480 DOI: 10.4161/rna.22740] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression and play critical roles in modulating metabolism, development and physiology in animals and plants. miRNA levels are transcriptionally and post-transcriptionally controlled for their proper function. Recent studies have shown that RNA-binding proteins play important roles in producing miRNAs by affecting the accurate and/or efficient processing of precursors of miRNAs. Many of these RNA-binding proteins also have roles in general RNA metabolism, indicating potential connections between miRNA biogenesis and other RNA metabolism. Here, we focus on the function of several RNA-binding proteins in miRNA biogenesis in Arabidopsis.
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Affiliation(s)
- Guodong Ren
- Center for Plant Science Innovation & School of Biological Sciences; University of Nebraska; Lincoln, NE USA
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39
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Liu J, Jung C, Xu J, Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. THE PLANT CELL 2012; 24:4333-45. [PMID: 23136377 PMCID: PMC3531837 DOI: 10.1105/tpc.112.102855] [Citation(s) in RCA: 487] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/12/2012] [Accepted: 10/19/2012] [Indexed: 05/18/2023]
Abstract
Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of intron-containing lincRNAs.
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40
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Romanel E, Silva TF, Corrêa RL, Farinelli L, Hawkins JS, Schrago CEG, Vaslin MFS. Global alteration of microRNAs and transposon-derived small RNAs in cotton (Gossypium hirsutum) during Cotton leafroll dwarf polerovirus (CLRDV) infection. PLANT MOLECULAR BIOLOGY 2012; 80:443-60. [PMID: 22987114 DOI: 10.1007/s11103-012-9959-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 05/13/2023]
Abstract
Small RNAs (sRNAs) are a class of non-coding RNAs ranging from 20- to 40-nucleotides (nts) that are present in most eukaryotic organisms. In plants, sRNAs are involved in the regulation of development, the maintenance of genome stability and the antiviral response. Viruses, however, can interfere with and exploit the silencing-based regulatory networks, causing the deregulation of sRNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs). To understand the impact of viral infection on the plant sRNA pathway, we deep sequenced the sRNAs in cotton leaves infected with Cotton leafroll dwarf virus (CLRDV), which is a member of the economically important virus family Luteoviridae. A total of 60 putative conserved cotton miRNAs were identified, including 19 new miRNA families that had not been previously described in cotton. Some of these miRNAs were clearly misregulated during viral infection, and their possible role in symptom development and disease progression is discussed. Furthermore, we found that the 24-nt heterochromatin-associated siRNAs were quantitatively and qualitatively altered in the infected plant, leading to the reactivation of at least one cotton transposable element. This is the first study to explore the global alterations of sRNAs in virus-infected cotton plants. Our results indicate that some CLRDV-induced symptoms may be correlated with the deregulation of miRNA and/or epigenetic networks.
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Affiliation(s)
- Elisson Romanel
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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41
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Ren G, Yu B. Post-transcriptional control of miRNA abundance in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2012; 7:1443-6. [PMID: 22960761 PMCID: PMC3548868 DOI: 10.4161/psb.21956] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs (small RNAs) that are 20-24nt in length and predominantly repress gene expression at post-transcriptional levels. They regulate many biological processes including development, metabolism and physiology. Numerous studies have revealed that the steady-state levels of miRNA are under sophisticated control to ensure their proper function. In this review, we summarize recent advances on regulation of miRNA processing and stability in plants.
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Affiliation(s)
| | - Bin Yu
- Correspondence to: Bin Yu,
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42
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Zhao JP, Diao S, Zhang BY, Niu BQ, Wang QL, Wan XC, Luo YQ. Phylogenetic analysis and molecular evolution patterns in the MIR482-MIR1448 polycistron of Populus L. PLoS One 2012; 7:e47811. [PMID: 23094096 PMCID: PMC3475693 DOI: 10.1371/journal.pone.0047811] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 09/17/2012] [Indexed: 12/05/2022] Open
Abstract
The microRNAs (miRNAs) miR482 and miR1448 are disease resistance-related miRNAs; the former is ubiquitously distributed in seed plants whereas the latter has only been reported in Populus trichocarpa. The precursor and mature sequences of poplar miR1448 are highly homologous to those of poplar miR482, and these two miRNAs are located in one transcript as a polycistron. Therefore, we hypothesized that the MIR1448 gene may have evolved from the MIR482 gene in poplar. However, the molecular evolution patterns of this process remain unclear. In this study, utilizing cloning and Blast analysis in NCBI ESTs and whole-genome shotgun contigs (WGS) dataset, we determined that the MIR482-MIR1448 polycistron is a family-specific clustered miRNA in Salicaceae. Moreover, phylogenetic analysis illustrated that MIR1448 is the product of a tandem duplication event from MIR482. Nucleotide substitution analysis revealed that both MIR482 and MIR1448 have more rapid evolution ratios than ribosomal DNA (rDNA) genes, and that compensatory mutations that occurred in the stem region of the secondary structure were the main mechanisms that drove the evolution of these MIRNA genes. Furthermore, by comparing the substitution patterns in the miRNA-target complexes of miR482 and miR1448, we inferred that co-evolution between miRNAs and their targets was the major force that drove the "duplicated MIR482" evolve to MIR1448. We propose a novel miRNA-target pairing pattern called the "frameshift targeted mechanism" to explain the gain of target genes by miR1448. The results also imply that the major role of miR482 was in resistance to disease or other stresses via NBS-LRR proteins, whereas the biological functions of miR1448 are more diverse.
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Affiliation(s)
- Jia-Ping Zhao
- State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, China
| | - Shu Diao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bing-Yu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bao-Qing Niu
- Agricultural University of Hebei, Baoding, China
| | | | - Xian-Chong Wan
- State Key Laboratory of Tree Genetics and Breeding, Institute of New Forestry Technology, Chinese Academy of Forestry, Beijing, China
| | - You-Qing Luo
- Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Beijing, China
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43
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Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis. Proc Natl Acad Sci U S A 2012; 109:18198-203. [PMID: 23071326 DOI: 10.1073/pnas.1216199109] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are important for plant development and stress responses. However, factors regulating miRNA metabolism are not completely understood. SICKLE (SIC), a proline-rich protein critical for development and abiotic stress tolerance of Arabidopsis, was identified in this study. Loss-of-function sic-1 mutant plants exhibited a serrated, sickle-like leaf margin, reduced height, delayed flowering, and abnormal inflorescence phyllotaxy, which are common characteristics of mutants involved in miRNA biogenesis. The sic-1 mutant plants accumulated lower levels of a subset of miRNAs and transacting siRNAs but higher levels of corresponding primary miRNAs than the WT. The SIC protein colocalizes with the miRNA biogenesis component HYL1 in distinct subnuclear bodies. sic-1 mutant plants also accumulated higher levels of introns from hundreds of loci. In addition, sic-1 mutant plants are hypersensitive to chilling and salt stresses. These results suggest that SIC is a unique factor required for the biogenesis of some miRNAs and degradation of some spliced introns and important for plant development and abiotic stress responses.
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44
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Wu L, Mao L, Qi Y. Roles of dicer-like and argonaute proteins in TAS-derived small interfering RNA-triggered DNA methylation. PLANT PHYSIOLOGY 2012; 160:990-9. [PMID: 22846193 PMCID: PMC3461571 DOI: 10.1104/pp.112.200279] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/24/2012] [Indexed: 05/18/2023]
Abstract
Trans-acting small interfering RNAs (ta-siRNAs; TAS) emerge as a class of plant-specific small RNAs that are initiated from microRNA-mediated cleavage of TAS gene transcripts. It has been revealed that ta-siRNAs are generated by the sequential activities of SUPPRESSOR OF GENE SILENCING3 (SGS3), RNA-DEPENDENT RNA POLYMERASE6 (RDR6), and DICER-LIKE4 (DCL4), and loaded into ARGONAUTE1 (AGO1) proteins to posttranscriptionally regulate several target genes by messenger RNA cleavage in trans. Here, we showed a high cytosine DNA methylation status at ta-siRNA-generating loci in Arabidopsis (Arabidopsis thaliana), which is dependent on RDR6, SGS3, and DNA-DIRECTED RNA POLYMERASE V (PolV). More important, we found that DCL1 is the only DCL protein that is required for TAS3 loci DNA methylation, and all four DCLs exert combinatory functions in the methylation of TAS1 loci, suggesting a previously unknown role for DCL1 in directly processing TAS gene transcripts. Furthermore, we demonstrated that AGO4/6 complexes rather than AGO1 are responsible for TAS siRNA-guided DNA methylation. Based upon these findings, we propose a novel ta-siRNA pathway that acts at both the messenger RNA and chromatin level.
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Affiliation(s)
- Liang Wu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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45
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Zhang X, Xia J, Lii YE, Barrera-Figueroa BE, Zhou X, Gao S, Lu L, Niu D, Chen Z, Leung C, Wong T, Zhang H, Guo J, Li Y, Liu R, Liang W, Zhu JK, Zhang W, Jin H. Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol 2012; 13:R20. [PMID: 22439910 PMCID: PMC3439971 DOI: 10.1186/gb-2012-13-3-r20] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 03/15/2012] [Accepted: 03/22/2012] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs. RESULTS Through deep sequencing, we identified more than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 10 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice. CONCLUSIONS Our results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.
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Affiliation(s)
- Xiaoming Zhang
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
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46
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Havecker ER, Wallbridge LM, Fedito P, Hardcastle TJ, Baulcombe DC. Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts. PLoS One 2012; 7:e45242. [PMID: 23028873 PMCID: PMC3447930 DOI: 10.1371/journal.pone.0045242] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 08/17/2012] [Indexed: 01/26/2023] Open
Abstract
Individual plants within a population may vary at both genetic and epigenetic levels. The rate of genetic divergence and its underlying mechanisms is well understood. Less is known about the factors contributing to epigenetic divergence among isogenic populations except that, despite the presence of mechanisms that faithfully maintain epigenetic marks, epigenetic differences are more frequent than genetic variation. Epigenetically divergent stretches of isogenic DNA sequence are called epialleles. Currently, it is not clear why certain regions exhibit variable epigenetic status. We identified and characterised two long RNA transcripts with altered expression and DNA methylation in an ago5 mutant. However, further investigation revealed that these changes were not dependent upon AGO5. Rather, the variable transcription of these loci in Arabidopsis mutant and wild-type populations corresponds to spontaneous differential methylated regions (DMRs) or epialleles. These two DMRs are delineated by RNAs which are highly expressed when the DMR is hypomethylated. Furthermore, they control the expression of 5′ transcriptional start site mRNA variants of nearby protein coding genes. Our data support the recent observations that meiotically stable DMRs exist within inbred populations. We further demonstrate that DMR boundaries can be defined by putative non-coding promoter-associated transcripts.
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Affiliation(s)
- Ericka R. Havecker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Laura M. Wallbridge
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Paola Fedito
- BIOMAA, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Thomas J. Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - David C. Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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47
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Giacomelli JI, Weigel D, Chan RL, Manavella PA. Role of recently evolved miRNA regulation of sunflower HaWRKY6 in response to temperature damage. THE NEW PHYTOLOGIST 2012; 195:766-773. [PMID: 22846054 DOI: 10.1111/j.1469-8137.2012.04259.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
MicroRNAs (miRNAs) are small 21-nucleotide RNAs that post-transcriptionally regulate gene expression. MiR396 controls leaf development by targeting GRF and bHLH transcription factors in Arabidopsis. WRKY transcription factors, unique to plants, have been identified as mediating varied stress responses. The sunflower (Helianthus annuus) HaWRKY6 is a particularly divergent WRKY gene exhibiting a putative target site for the miR396. A possible post-transcriptional regulation of HaWRKY6 by miR396 was investigated. Here, we used expression analyses, performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and northern blots together with computational approaches to establish the regulatory interaction between HaWRKY6 and the identified sunflower miR396. Arabidopsis plants expressing a mi396-resistant version of HaWRKY6 confirmed the miRNA-dependency of the HaWRKY6 silencing. Sunflower plants exposed to high temperatures or salicylic acid presented opposite expression of HaWRKY6 and miR396. Experiments using the wildtype and miRNA-resistant versions of HaWRKY6 showed altered stress responses. Our results showed a role of the recently evolved miR396 regulation of HaWRKY6 during early responses to high temperature. Our study reveals how a miRNA that normally regulates development has been recruited for high-temperature protection in sunflower, a plant particularly well adapted to this type of stress.
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Affiliation(s)
- Jorge I Giacomelli
- Instituto de Agrobiotecnología del Litoral, Conicet-Universidad Nacional del Litoral, CC 242, 3000, Santa Fe, Argentina
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Conicet-Universidad Nacional del Litoral, CC 242, 3000, Santa Fe, Argentina
| | - Pablo A Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
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48
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Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudié M, Karlowski WM, Cooke R, Colot V, Voinnet O, Lagrange T. NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell 2012; 48:121-32. [PMID: 22940247 DOI: 10.1016/j.molcel.2012.07.027] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/21/2012] [Accepted: 07/05/2012] [Indexed: 12/31/2022]
Abstract
In Arabidopsis, transcriptional gene silencing (TGS) can be triggered by 24 nt small-interfering RNAs (siRNAs) through the RNA-directed DNA methylation (RdDM) pathway. By functional analysis of NERD, a GW repeat- and PHD finger-containing protein, we demonstrate that Arabidopsis harbors a second siRNA-dependent DNA methylation pathway targeting a subset of nonconserved genomic loci. The activity of the NERD-dependent pathway differs from RdDM by the fact that it relies both on silencing-related factors previously implicated only in posttranscriptional gene silencing (PTGS), including RNA-DEPENDENT RNA POLYMERASE1/6 and ARGONAUTE2, and most likely on 21 nt siRNAs. A central role for NERD in integrating RNA silencing and chromatin signals in transcriptional silencing is supported by data showing that it binds both to histone H3 and AGO2 proteins and contributes to siRNA accumulation at a NERD-targeted locus. Our results unravel the existence of a conserved chromatin-based RNA silencing pathway encompassing both PTGS and TGS components in plants.
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Affiliation(s)
- Dominique Pontier
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique/Université de Perpignan via Domitia, UMR5096, Perpignan, France
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49
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Garcia D, Garcia S, Pontier D, Marchais A, Renou JP, Lagrange T, Voinnet O. Ago hook and RNA helicase motifs underpin dual roles for SDE3 in antiviral defense and silencing of nonconserved intergenic regions. Mol Cell 2012; 48:109-20. [PMID: 22940249 DOI: 10.1016/j.molcel.2012.07.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 05/22/2012] [Accepted: 07/25/2012] [Indexed: 10/27/2022]
Abstract
In Arabidopsis thaliana, the putative RNA-helicase SDE3 assists posttranscriptional-gene-silencing (PTGS) amplification by RNA-dependent-RNA-polymerase-6 (RDR6). SDE3 homologs in Drosophila, worm and human contribute to silence viruses, transposons or recently duplicated genes but the underlying mechanisms remain largely unknown. Here, we demonstrate that SDE3 is present with the PTGS effectors AGO1 and AGO2 in higher-order protein complexes owing to a specialized GW-repeat-containing C-terminal domain. We uncover an essential contribution of the RNA-helicase activity and a facilitating role for AGO binding in SDE3 action, which occurs downstream of RDR6. We show that these biochemical properties underpin dual roles for SDE3 in antiviral defense and, unexpectedly, in transposon silencing via a hitherto unanticipated pathway that correlates with DNA methylation, suggesting a continuum of action between PTGS and chromatin-level silencing. We identified endogenous SDE3 targets corresponding to nonconserved intergenic regions, transposons and recently evolved pseudogenes, unraveling striking functional convergences among plant and metazoan SDE3 pathways.
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Affiliation(s)
- Damien Garcia
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Strasbourg, France
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50
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Zhang C, Li G, Wang J, Fang J. Identification of trans-acting siRNAs and their regulatory cascades in grapevine. Bioinformatics 2012; 28:2561-8. [DOI: 10.1093/bioinformatics/bts500] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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