1
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Yang Y, Liang Y, Wang C, Wang Y. MicroRNAs as potent regulators in nitrogen and phosphorus signaling transduction and their applications. STRESS BIOLOGY 2024; 4:38. [PMID: 39264517 PMCID: PMC11393275 DOI: 10.1007/s44154-024-00181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 06/18/2024] [Indexed: 09/13/2024]
Abstract
Nitrogen (N) and phosphorus (Pi) are essential macronutrients that affect plant growth and development by influencing the molecular, metabolic, biochemical, and physiological responses at the local and whole levels in plants. N and Pi stresses suppress the physiological activities of plants, resulting in agricultural productivity losses and severely threatening food security. Accordingly, plants have elaborated diverse strategies to cope with N and Pi stresses through maintaining N and Pi homeostasis. MicroRNAs (miRNAs) as potent regulators fine-tune N and Pi signaling transduction that are distinct and indivisible from each other. Specific signals, such as noncoding RNAs (ncRNAs), interact with miRNAs and add to the complexity of regulation. Elucidation of the mechanisms by which miRNAs regulate N and Pi signaling transduction aids in the breeding of plants with strong tolerance to N and Pi stresses and high N and Pi use efficiency by fine-tuning MIR genes or miRNAs. However, to date, there has been no detailed and systematic introduction and comparison of the functions of miRNAs in N and Pi signaling transduction from the perspective of miRNAs and their applications. Here, we summarized and discussed current advances in the involvement of miRNAs in N and Pi signaling transduction and highlighted that fine-tuning the MIR genes or miRNAs involved in maintaining N and Pi homeostasis might provide valuable sights for sustainable agriculture.
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Affiliation(s)
- Yuzhang Yang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanting Liang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Chun Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanwei Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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2
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El Arbi N, Schürholz AK, Handl MU, Schiffner A, Hidalgo Prados I, Schnurbusch L, Wenzl C, Zhao X, Zeng J, Lohmann JU, Wolf S. ARGONAUTE10 controls cell fate specification and formative cell divisions in the Arabidopsis root. EMBO J 2024; 43:1822-1842. [PMID: 38565947 PMCID: PMC11066080 DOI: 10.1038/s44318-024-00072-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
A key question in plant biology is how oriented cell divisions are integrated with patterning mechanisms to generate organs with adequate cell type allocation. In the root vasculature, a gradient of miRNA165/6 controls the abundance of HD-ZIP III transcription factors, which in turn control cell fate and spatially restrict vascular cell proliferation to specific cells. Here, we show that vascular development requires the presence of ARGONAUTE10, which is thought to sequester miRNA165/6 and protect HD-ZIP III transcripts from degradation. Our results suggest that the miR165/6-AGO10-HDZIP III module acts by buffering cytokinin responses and restricting xylem differentiation. Mutants of AGO10 show faster growth rates and strongly enhanced survival under severe drought conditions. However, this superior performance is offset by markedly increased variation and phenotypic plasticity in sub-optimal carbon supply conditions. Thus, AGO10 is required for the control of formative cell division and coordination of robust cell fate specification of the vasculature, while altering its expression provides a means to adjust phenotypic plasticity.
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Affiliation(s)
- Nabila El Arbi
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Department of Plant Physiology, Umea Plant Science Centre, Umea, Sweden
| | - Ann-Kathrin Schürholz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Corden Pharma, Heidelberg, Germany
| | - Marlene U Handl
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Alexei Schiffner
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Inés Hidalgo Prados
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Liese Schnurbusch
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Christian Wenzl
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Xin'Ai Zhao
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jian Zeng
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Sebastian Wolf
- Centre for Organismal Studies Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany.
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3
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Scacchi E, Paszkiewicz G, Thi Nguyen K, Meda S, Burian A, de Back W, Timmermans MCP. A diffusible small-RNA-based Turing system dynamically coordinates organ polarity. NATURE PLANTS 2024; 10:412-422. [PMID: 38409292 DOI: 10.1038/s41477-024-01634-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: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
The formation of a flat and thin leaf presents a developmentally challenging problem, requiring intricate regulation of adaxial-abaxial (top-bottom) polarity. The patterning principles controlling the spatial arrangement of these domains during organ growth have remained unclear. Here we show that this regulation in Arabidopsis thaliana is achieved by an organ-autonomous Turing reaction-diffusion system centred on mobile small RNAs. The data illustrate how Turing dynamics transiently instructed by prepatterned information is sufficient to self-sustain properly oriented polarity in a dynamic, growing organ, presenting intriguing parallels to left-right patterning in the vertebrate embryo. Computational modelling demonstrates that this self-organizing system continuously adapts to coordinate the robust planar polarity of a flat leaf while affording flexibility to generate the tissue patterns of evolutionarily diverse organ shapes. Our findings identify a small-RNA-based Turing network as a dynamic regulator of organ polarity that accounts for leaf shape diversity at the level of the individual organ, plant or species.
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Affiliation(s)
- Emanuele Scacchi
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany.
| | - Gael Paszkiewicz
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Khoa Thi Nguyen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Shreyas Meda
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Walter de Back
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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4
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Vaucheret H, Voinnet O. The plant siRNA landscape. THE PLANT CELL 2024; 36:246-275. [PMID: 37772967 PMCID: PMC10827316 DOI: 10.1093/plcell/koad253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Whereas micro (mi)RNAs are considered the clean, noble side of the small RNA world, small interfering (si)RNAs are often seen as a noisy set of molecules whose barbarian acronyms reflect a large diversity of often elusive origins and functions. Twenty-five years after their discovery in plants, however, new classes of siRNAs are still being identified, sometimes in discrete tissues or at particular developmental stages, making the plant siRNA world substantially more complex and subtle than originally anticipated. Focusing primarily on the model Arabidopsis, we review here the plant siRNA landscape, including transposable elements (TE)-derived siRNAs, a vast array of non-TE-derived endogenous siRNAs, as well as exogenous siRNAs produced in response to invading nucleic acids such as viruses or transgenes. We primarily emphasize the extraordinary sophistication and diversity of their biogenesis and, secondarily, the variety of their known or presumed functions, including via non-cell autonomous activities, in the sporophyte, gametophyte, and shortly after fertilization.
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Affiliation(s)
- Hervé Vaucheret
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Olivier Voinnet
- Department of Biology, Swiss Federal Institute of Technology (ETH-Zurich), 8092 Zürich, Switzerland
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5
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Huang NC, Tien HC, Yu TS. Arabidopsis leaf-expressed AGAMOUS-LIKE 24 mRNA systemically specifies floral meristem differentiation. THE NEW PHYTOLOGIST 2024; 241:504-515. [PMID: 37766487 DOI: 10.1111/nph.19293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023]
Abstract
Plants can record external stimuli in mobile mRNAs and systemically deliver them to distal tissues to adjust development. Despite the identification of thousands of mobile mRNAs, the functional relevance of mobile mRNAs remains limited. Many mobile mRNAs are synthesized in the source cells that perceive environmental stimuli, but specifically exert their functions upon transportation to the recipient cells. However, the translation of mobile mRNA-encoded protein in the source cells could locally activate downstream target genes. How plants avoid ectopic functions of mobile mRNAs in the source cells to achieve tissue specificity remains to be elucidated. Here, we show that Arabidopsis AGAMOUS-LIKE 24 (AGL24) is a mobile mRNA whose movement is necessary and sufficient to specify floral organ identity. Although AGL24 mRNA is expressed in vegetative tissues, AGL24 protein exclusively accumulates in the shoot apex. In leaves, AGL24 proteins are degraded to avoid ectopically activating its downstream target genes. Our results reveal how selective protein degradation in source cells provides a strategy to limit the local effects associated with proteins encoded by mobile mRNAs, which ensures that mobile mRNAs specifically trigger systemic responses only in recipient tissues.
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Affiliation(s)
- Nien-Chen Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Huan-Chi Tien
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
| | - Tien-Shin Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
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6
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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7
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Xu C, Zhang Z, He J, Bai Y, Cui J, Liu L, Tang J, Tang G, Chen X, Mo B. The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:144-160. [PMID: 37415266 DOI: 10.1111/tpj.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
RCF1 is a highly conserved DEAD-box RNA helicase found in yeast, plants, and mammals. Studies about the functions of RCF1 in plants are limited. Here, we uncovered the functions of RCF1 in Arabidopsis thaliana as a player in pri-miRNA processing and splicing, as well as in pre-mRNA splicing. A mutant with miRNA biogenesis defects was isolated, and the defect was traced to a recessive point mutation in RCF1 (rcf1-4). We show that RCF1 promotes D-body formation and facilitates the interaction between pri-miRNAs and HYL1. Finally, we show that intron-containing pri-miRNAs and pre-mRNAs exhibit a global splicing defect in rcf1-4. Together, this work uncovers roles for RCF1 in miRNA biogenesis and RNA splicing in Arabidopsis.
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Affiliation(s)
- Chi Xu
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Zhanhui Zhang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Yongsheng Bai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guiliang Tang
- National Key Laboratory of Wheat and Maize Crop Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biological Sciences and Biotechnology Research Center, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Xuemei Chen
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
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8
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Yan Y. Insights into Mobile Small-RNAs Mediated Signaling in Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:3155. [PMID: 36432884 PMCID: PMC9698838 DOI: 10.3390/plants11223155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, small RNA (sRNA)-mediated RNA interfering (RNAi) is involved in a broad range of biological processes. Growing evidence supports the model that sRNAs are mobile signaling agents that move intercellularly, systemically and cross-species. Recently, considerable progress has been made in terms of characterization of the mobile sRNAs population and their function. In this review, recent progress in identification of new mobile sRNAs is assessed. Here, critical questions related to the function of these mobile sRNAs in coordinating developmental, physiological and defense-related processes is discussed. The forms of mobile sRNAs and the underlying mechanisms mediating sRNA trafficking are discussed next. A concerted effort has been made to integrate these new findings into a comprehensive overview of mobile sRNAs signaling in plants. Finally, potential important areas for both basic science and potential applications are highlighted for future research.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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9
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Arabidopsis AAR2, a conserved splicing factor in eukaryotes, acts in microRNA biogenesis. Proc Natl Acad Sci U S A 2022; 119:e2208415119. [PMID: 36191209 PMCID: PMC9565372 DOI: 10.1073/pnas.2208415119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In yeast and humans, AAR2 is involved in pre-messenger RNA (pre-mRNA) splicing through regulating U5 snRNP assembly. This study shows that Arabidopsis AAR2 promotes microRNA (miRNA) accumulation in addition to its conserved role in pre-mRNA splicing. AAR2 is associated with the microprocessor component HYL1 and promotes its dephosphorylation to produce the active form in miRNA biogenesis. The study also reveals a previously unknown role of HYL1 in causing the degradation of the primary precursors to miRNAs (pri-miRNAs) and a role of AAR2 in protecting pri-miRNAs from HYL1-depedent degradation. Taken together, our findings provide insights into the role of a conserved splicing factor in miRNA biogenesis in plants. MicroRNAs (miRNAs) play an essential role in plant growth and development, and as such, their biogenesis is fine-tuned via regulation of the core microprocessor components. Here, we report that Arabidopsis AAR2, a homolog of a U5 snRNP assembly factor in yeast and humans, not only acts in splicing but also promotes miRNA biogenesis. AAR2 interacts with the microprocessor component hyponastic leaves 1 (HYL1) in the cytoplasm, nucleus, and dicing bodies. In aar2 mutants, abundance of nonphosphorylated HYL1, the active form of HYL1, and the number of HYL1-labeled dicing bodies are reduced. Primary miRNA (pri-miRNA) accumulation is compromised despite normal promoter activities of MIR genes in aar2 mutants. RNA decay assays show that the aar2-1 mutation leads to faster degradation of pri-miRNAs in a HYL1-dependent manner, which reveals a previously unknown and negative role of HYL1 in miRNA biogenesis. Taken together, our findings reveal a dual role of AAR2 in miRNA biogenesis and pre-messenger RNA splicing.
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10
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Yan Y, Ham BK. The Mobile Small RNAs: Important Messengers for Long-Distance Communication in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:928729. [PMID: 35783973 PMCID: PMC9247610 DOI: 10.3389/fpls.2022.928729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/25/2022] [Indexed: 06/06/2023]
Abstract
Various species of small RNAs (sRNAs), notably microRNAs and small interfering RNAs (siRNAs), have been characterized as the major effectors of RNA interference in plants. Growing evidence supports a model in which sRNAs move, intercellularly, systemically, and between cross-species. These non-coding sRNAs can traffic cell-to-cell through plasmodesmata (PD), in a symplasmic manner, as well as from source to sink tissues, via the phloem, to trigger gene silencing in their target cells. Such mobile sRNAs function in non-cell-autonomous communication pathways, to regulate various biological processes, such as plant development, reproduction, and plant defense. In this review, we summarize recent progress supporting the roles of mobile sRNA in plants, and discuss mechanisms of sRNA transport, signal amplification, and the plant's response, in terms of RNAi activity, within the recipient tissues. We also discuss potential research directions and their likely impact on engineering of crops with traits for achieving food security.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Byung-Kook Ham
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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11
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Shen C, Huang YY, Xin JL, He CT, Yang ZY. A novel microRNA IamiR-4-3p from water spinach (Ipomoea aquatica Forsk.) increased Cd uptake and translocation in Arabidopsis thaliana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:41375-41385. [PMID: 35089521 DOI: 10.1007/s11356-022-18875-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) play important roles in plant response to Cd stress. In our previous study, we observed significant differences in the expression levels of IamiR-4-3p between high-Cd and low-Cd cultivars of water spinach. The function of IamiR-4-3p was investigated by using wild type Arabidopsis (WT), Arabidopsis transfected with empty vector pCambia1302 (CK), and Arabidopsis transfected with IamiR-4-3p + vector pCambia1302 (p35S::miR-4-3p) in this study. In p35S::miR-4-3p Arabidopsis, the expression levels of GST3 and AWPM19-like were reduced by 20% and 24%. Under Cd treatment, higher root and shoot Cd concentrations were detected in the transgenic p35S::miR-4-3p Arabidopsis. MDA and H2O2 concentrations were positively correlated with the Cd concentrations in all Arabidopsis. The elevated GSH pool in p35S::miR-4-3p Arabidopsis should compensate for its restricted GST3 expression in response to Cd-induced oxidative stress. Lower F1 (cell wall) and higher F2 (organelle) and F3 (soluble fraction) Cd concentrations were observed along with the reduced ABA level in p35S::miR-4-3p Arabidopsis, which could induce a weakened apoplastic barrier and higher Cd accumulation and translocation in roots. It is suggested that IamiR-4-3p is able to reduce the expression levels of GST3 and AWPM19-like, resulting in higher Cd uptake and translocation in Arabidopsis.
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Affiliation(s)
- Chuang Shen
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Ying-Ying Huang
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Jun-Liang Xin
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Chun-Tao He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou, 510275, China.
| | - Zhong-Yi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou, 510275, China.
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12
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Cisneros AE, de la Torre‐Montaña A, Carbonell A. Systemic silencing of an endogenous plant gene by two classes of mobile 21-nucleotide artificial small RNAs. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1166-1181. [PMID: 35277899 PMCID: PMC9310713 DOI: 10.1111/tpj.15730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
Artificial small RNAs (art-sRNAs) are 21-nucleotide small RNAs (sRNAs) computationally designed to silence plant genes or pathogenic RNAs with high efficacy and specificity. They are typically produced in transgenic plants to induce silencing at the whole-organism level, although their expression in selected tissues for inactivating genes in distal tissues has not been reported. Here, art-sRNAs designed against the magnesium chelatase subunit CHLI-encoding SULFUR gene (NbSu) were agroinfiltrated in Nicotiana benthamiana leaves, and the induction of local and systemic silencing was analyzed phenotypically by monitoring the appearance of the characteristic bleached phenotype, as well as molecularly by analyzing art-sRNA processing, accumulation and targeting activity and efficacy. We found that the two classes of art-sRNAs, artificial microRNAs (amiRNAs) and synthetic trans-acting small interfering RNAs (syn-tasiRNAs), are able to induce systemic silencing of NbSu, which requires high art-sRNA expression in the vicinity of the leaf petiole but is independent on the production of secondary sRNAs from NbSu mRNAs. Moreover, we revealed that 21-nucleotide amiRNA and syn-tasiRNA duplexes, and not their precursors, are the molecules moving between cells and through the phloem to systemically silence NbSu in upper leaves. In sum, our results indicate that 21-nucleotide art-sRNAs can move throughout the plant to silence plant genes in tissues different from where they are produced. This highlights the biotechnological potential of art-sRNAs, which might be applied locally for triggering whole-plant and highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops. The present study demonstrates that artificial small RNAs, such as artificial microRNAs and synthetic trans-acting small interfering RNAs, can move long distances in plants as 21-nucleotide duplexes, specifically silencing endogenous genes in tissues different from where they are applied. This highlights the biotechnological potential of artificial small RNAs, which might be applied locally for triggering whole-plant, highly specific silencing to regulate gene expression or induce resistance against pathogenic RNAs in next-generation crops.
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Affiliation(s)
- Adriana E. Cisneros
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Ainhoa de la Torre‐Montaña
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universitat Politècnica de València)46022ValenciaSpain
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13
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Fan L, Zhang C, Gao B, Zhang Y, Stewart E, Jez J, Nakajima K, Chen X. Microtubules promote the non-cell autonomous action of microRNAs by inhibiting their cytoplasmic loading onto ARGONAUTE1 in Arabidopsis. Dev Cell 2022; 57:995-1008.e5. [PMID: 35429434 PMCID: PMC9056376 DOI: 10.1016/j.devcel.2022.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/22/2021] [Accepted: 03/24/2022] [Indexed: 01/03/2023]
Abstract
Mobile microRNAs (miRNAs) serve as local and long-distance signals in the developmental patterning and stress responses in plants. However, mechanisms governing the non-cell autonomous activities of miRNAs remain elusive. Here, we show that mutations that disrupt microtubule dynamics are specifically defective for the non-cell autonomous actions of mobile miRNAs, including miR165/6 that is produced in the endodermis and moves to the vasculature to pattern xylem cell fates in Arabidopsis roots. We show that KTN1, a subunit of a microtubule-severing enzyme, is required in source cells to inhibit the loading of miR165/6 into ARGONUATE1 (AGO1), which is cell autonomous, to enable the miRNA to exit the cell. Microtubule disruption enhances the association of miR165/6 with AGO1 in the cytoplasm. These findings suggest that although cell-autonomous miRNAs load onto AGO1 in the nucleus, the cytoplasmic AGO1 loading of mobile miRNAs is a key step regulated by microtubules to promote the range of miRNA cell-to-cell movement.
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Affiliation(s)
- Lusheng Fan
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Cui Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Bin Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Yong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Ethan Stewart
- Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Jakub Jez
- Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
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14
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Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading. Nat Commun 2022; 13:1217. [PMID: 35260568 PMCID: PMC8904849 DOI: 10.1038/s41467-022-28872-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene expression regulation through RNA cleavage or translation repression. Here, we report the identification of an evolutionarily conserved WD40 domain protein as a player in miRNA biogenesis in Arabidopsis thaliana. A mutation in the REDUCTION IN BLEACHED VEIN AREA (RBV) gene encoding a WD40 domain protein led to the suppression of leaf bleaching caused by an artificial miRNA; the mutation also led to a global reduction in the accumulation of endogenous miRNAs. The nuclear protein RBV promotes the transcription of MIR genes into pri-miRNAs by enhancing the occupancy of RNA polymerase II (Pol II) at MIR gene promoters. RBV also promotes the loading of miRNAs into AGO1. In addition, RNA-seq revealed a global splicing defect in the mutant. Thus, this evolutionarily conserved, nuclear WD40 domain protein acts in miRNA biogenesis and RNA splicing. MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.
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15
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Chen X, Rechavi O. Plant and animal small RNA communications between cells and organisms. Nat Rev Mol Cell Biol 2022; 23:185-203. [PMID: 34707241 PMCID: PMC9208737 DOI: 10.1038/s41580-021-00425-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Since the discovery of eukaryotic small RNAs as the main effectors of RNA interference in the late 1990s, diverse types of endogenous small RNAs have been characterized, most notably microRNAs, small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). These small RNAs associate with Argonaute proteins and, through sequence-specific gene regulation, affect almost every major biological process. Intriguing features of small RNAs, such as their mechanisms of amplification, rapid evolution and non-cell-autonomous function, bestow upon them the capacity to function as agents of intercellular communications in development, reproduction and immunity, and even in transgenerational inheritance. Although there are many types of extracellular small RNAs, and despite decades of research, the capacity of these molecules to transmit signals between cells and between organisms is still highly controversial. In this Review, we discuss evidence from different plants and animals that small RNAs can act in a non-cell-autonomous manner and even exchange information between species. We also discuss mechanistic insights into small RNA communications, such as the nature of the mobile agents, small RNA signal amplification during transit, signal perception and small RNA activity at the destination.
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Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Oded Rechavi
- Department of Neurobiology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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16
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Vigh ML, Bressendorff S, Thieffry A, Arribas-Hernández L, Brodersen P. Nuclear and cytoplasmic RNA exosomes and PELOTA1 prevent miRNA-induced secondary siRNA production in Arabidopsis. Nucleic Acids Res 2022; 50:1396-1415. [PMID: 35037064 PMCID: PMC8860578 DOI: 10.1093/nar/gkab1289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/13/2021] [Accepted: 01/03/2022] [Indexed: 11/14/2022] Open
Abstract
Amplification of short interfering RNA (siRNAs) via RNA-dependent RNA polymerases (RdRPs) is of fundamental importance in RNA silencing. Plant microRNA (miRNA) action generally does not involve engagement of RdRPs, in part thanks to a poorly understood activity of the cytoplasmic exosome adaptor SKI2. Here, we show that inactivation of the exosome subunit RRP45B and SKI2 results in similar patterns of miRNA-induced siRNA production. Furthermore, loss of the nuclear exosome adaptor HEN2 leads to secondary siRNA production from miRNA targets largely distinct from those producing siRNAs in ski2. Importantly, mutation of the Release Factor paralogue PELOTA1 required for subunit dissociation of stalled ribosomes causes siRNA production from miRNA targets overlapping with, but distinct from, those affected in ski2 and rrp45b mutants. We also show that in exosome mutants, miRNA targets can be sorted into producers and non-producers of illicit secondary siRNAs based on trigger miRNA levels and miRNA:target affinity rather than on presence of 5′-cleavage fragments. We propose that stalled RNA-Induced Silencing Complex (RISC) and ribosomes, but not mRNA cleavage fragments released from RISC, trigger siRNA production, and that the exosome limits siRNA amplification by reducing RISC dwell time on miRNA target mRNAs while PELOTA1 does so by reducing ribosome stalling.
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Affiliation(s)
- Maria L Vigh
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simon Bressendorff
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Axel Thieffry
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Laura Arribas-Hernández
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Peter Brodersen
- University of Copenhagen, Copenhagen Plant Science Center, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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17
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Hajieghrari B, Farrokhi N. Plant RNA-mediated gene regulatory network. Genomics 2021; 114:409-442. [PMID: 34954000 DOI: 10.1016/j.ygeno.2021.12.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/21/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
Abstract
Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.
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Affiliation(s)
- Behzad Hajieghrari
- Department of Agricultural Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran.
| | - Naser Farrokhi
- Department of Cell, Molecular Biology Faculty of Life Sciences, Biotechnology, Shahid Beheshti University, G. C Evin, Tehran, Iran.
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18
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Susila H, Jurić S, Liu L, Gawarecka K, Chung KS, Jin S, Kim SJ, Nasim Z, Youn G, Suh MC, Yu H, Ahn JH. Florigen sequestration in cellular membranes modulates temperature-responsive flowering. Science 2021; 373:1137-1142. [PMID: 34516842 DOI: 10.1126/science.abh4054] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Snježana Jurić
- Department of Life Sciences, Korea University, Seoul 02841, Korea.,Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lu Liu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore.,Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Kyung Sook Chung
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Suhyun Jin
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Soo-Jin Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Geummin Youn
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Mi Chung Suh
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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19
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Hendrix B, Zheng W, Bauer MJ, Havecker ER, Mai JT, Hoffer PH, Sanders RA, Eads BD, Caruano-Yzermans A, Taylor DN, Hresko C, Oakes J, Iandolino AB, Bennett MJ, Deikman J. Topically delivered 22 nt siRNAs enhance RNAi silencing of endogenous genes in two species. PLANTA 2021; 254:60. [PMID: 34448043 PMCID: PMC8390415 DOI: 10.1007/s00425-021-03708-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 08/16/2021] [Indexed: 05/23/2023]
Abstract
MAIN CONCLUSION 22 nt siRNAs applied to leaves induce production of transitive sRNAs for targeted genes and can enhance local silencing. Systemic silencing was only observed for a GFP transgene. RNA interference (RNAi) is a gene silencing mechanism important in regulating gene expression during plant development, response to the environment and defense. Better understanding of the molecular mechanisms of this pathway may lead to future strategies to improve crop traits of value. An abrasion method to deliver siRNAs into leaf cells of intact plants was used to investigate the activities of 21 and 22 nt siRNAs in silencing genes in Nicotiana benthamiana and Amaranthus cruentus. We confirmed that both 21 and 22 nt siRNAs were able to silence a green fluorescent protein (GFP) transgene in treated leaves of N. benthamiana, but systemic silencing of GFP occurred only when the guide strand contained 22 nt. Silencing in the treated leaves of N. benthamiana was demonstrated for three endogenous genes: magnesium cheletase subunit I (CHL-I), magnesium cheletase subunit H (CHL-H), and GENOMES UNCOUPLED4 (GUN4). However, systemic silencing of these endogenous genes was not observed. Very high levels of transitive siRNAs were produced for GFP in response to treatment with 22 nt siRNAs but only low levels were produced in response to a 21 nt siRNA. The endogenous genes tested also produced transitive siRNAs in response to 22 nt siRNAs. 22 nt siRNAs produced greater local silencing phenotypes than 21 nt siRNAs for three of the genes. These special properties of 22 nt siRNAs were also observed for the CHL-H gene in A. cruentus. These experiments suggest a functional role for transitive siRNAs in amplifying the RNAi response.
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Affiliation(s)
- Bill Hendrix
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
- Bayer U.S. LLC, Research and Development, Crop Science, Biologics Pest Control, 890 Embarcadero Drive, West Sacramento, CA, 95605, USA
| | - Wei Zheng
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
| | - Matthew J Bauer
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Ericka R Havecker
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Jennifer T Mai
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
| | - Paul H Hoffer
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
- California Governor's Office of Emergency Services, 3650 Schriever Avenue, Mather, CA, 95655, USA
| | - Rick A Sanders
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
| | - Brian D Eads
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | | | - Danielle N Taylor
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Chelly Hresko
- Bayer Crop Science, 700 Chesterfield Parkway West, Chesterfield, MO, 63017, USA
| | - Janette Oakes
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
| | | | - Michael J Bennett
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA
| | - Jill Deikman
- Bayer Crop Science, 37437 State Highway 16, Woodland, CA, 95695, USA.
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20
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Qiao Y, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W. Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:265-288. [PMID: 34077241 DOI: 10.1146/annurev-phyto-121520-023514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host-pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of trans-species gene silencing at the host-pathogen interface are discussed.
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Affiliation(s)
- Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China
| | - Jixian Zhai
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Li Feng
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi Zhai
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK;
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21
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Brioudes F, Jay F, Sarazin A, Grentzinger T, Devers EA, Voinnet O. HASTY, the Arabidopsis EXPORTIN5 ortholog, regulates cell-to-cell and vascular microRNA movement. EMBO J 2021; 40:e107455. [PMID: 34152631 PMCID: PMC8327949 DOI: 10.15252/embj.2020107455] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/04/2023] Open
Abstract
Plant microRNAs (miRNAs) guide cytosolic post-transcriptional gene silencing of sequence-complementary transcripts within the producing cells, as well as in distant cells and tissues. Here, we used an artificial miRNA-based system (amiRSUL) in Arabidopsis thaliana to explore the still elusive mechanisms of inter-cellular miRNA movement via forward genetics. This screen identified many mutant alleles of HASTY (HST), the ortholog of mammalian EXPORTIN5 (XPO5) with a recently reported role in miRNA biogenesis in Arabidopsis. In both epidermis-peeling and grafting assays, amiRSUL levels were reduced much more substantially in miRNA-recipient tissues than in silencing-emitting tissues. We ascribe this effect to HST controlling cell-to-cell and phloem-mediated movement of the processed amiRSUL, in addition to regulating its biogenesis. While HST is not required for the movement of free GFP or siRNAs, its cell-autonomous expression in amiRSUL-emitting tissues suffices to restore amiRSUL movement independently of its nucleo-cytosolic shuttling activity. By contrast, HST is dispensable for the movement and activity of amiRSUL within recipient tissues. Finally, HST enables movement of endogenous miRNAs that display mostly unaltered steady-state levels in hst mutant tissues. We discuss a role for HST as a hitherto unrecognized regulator of miRNA movement in relation to its recently assigned nuclear function at the nexus of MIRNA transcription and miRNA processing.
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Affiliation(s)
| | - Florence Jay
- Department of BiologyETH ZürichZürichSwitzerland
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22
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Cataloguing the small RNA content of honey using next generation sequencing. FOOD CHEMISTRY. MOLECULAR SCIENCES 2021; 2:100014. [PMID: 35415639 PMCID: PMC8991712 DOI: 10.1016/j.fochms.2021.100014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/09/2021] [Accepted: 02/12/2021] [Indexed: 12/02/2022]
Abstract
Plant miRNAs are present in Australian polyfloral and Leptospermum scoparium honey. Sequencing shows that honey contains a diverse range of small, non-coding RNAs. Honey RNA comes from different phylogenies including invertebrates and prokaryotes. Unique small RNA profiles can provide insight into honey production conditions.
Honey adulteration is a problem that effects the global honey industry and specifically, has been discovered in the Australian market. Common methods of adulteration include dilution with sugar syrup substitutes and the mislabelling of the floral and geographic origin(s) of honey. Current authentication tools rely on the molecular variability between different honeys, identifying unique chemical profiles and/or DNA signatures characteristic of a particular honey. Honey is known to contain plant miRNAs derived from its floral source. To explore the composition and variability of honey RNA molecules, this is the first study to catalogue the small RNA content of Australian polyfloral table honey and New Zealand Leptospermum scoparium honey using next generation sequencing. The data shows that in addition to miRNAs, honey contains a variety of small non-coding RNAs including tRNA-derived fragments. Moreover, the honey small RNAs are derived from a range of phylogenetic sources, including from plant, invertebrate, and prokaryotic species. The data indicates that different honeys contain unique small RNA profiles, which suggests a novel avenue in developing molecular-based honey authentication tools.
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23
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Dukowic-Schulze S, van der Linde K. Oxygen, secreted proteins and small RNAs: mobile elements that govern anther development. PLANT REPRODUCTION 2021; 34:1-19. [PMID: 33492519 PMCID: PMC7902584 DOI: 10.1007/s00497-020-00401-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/24/2020] [Indexed: 05/24/2023]
Abstract
Correct anther development is essential for male fertility and subsequently agricultural yield. Defects in anther development range from the early stage of stamen formation until the late stage of tapetum degeneration. In particular, the specification of the four distinct somatic layers and the inner sporogenous cells need perfect orchestration relying on precise cell-cell communication. Up to now, several signals, which coordinate the anther´s developmental program, have been identified. Among the known signals are phytohormones, environmental conditions sensed via glutaredoxins, several receptor-like kinases triggered by ligands like MAC1, and small RNAs such as miRNAs and the monocot-prevalent reproductive phasiRNAs. Rather than giving a full review on anther development, here we discuss anther development with an emphasis on mobile elements like ROS/oxygen, secreted proteins and small RNAs (only briefly touching on phytohormones), how they might act and interact, and what the future of this research area might reveal.
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Affiliation(s)
- Stefanie Dukowic-Schulze
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
| | - Karina van der Linde
- Department of Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany.
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24
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Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. FRONTIERS IN PLANT SCIENCE 2021; 12:610283. [PMID: 33737942 PMCID: PMC7960677 DOI: 10.3389/fpls.2021.610283] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - A. Abdul Kader Jailani
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Mukherjee
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sunil K. Mukherjee,
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Liu Y, Teng C, Xia R, Meyers BC. PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. THE PLANT CELL 2020; 32:3059-3080. [PMID: 32817252 PMCID: PMC7534485 DOI: 10.1105/tpc.20.00335] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 05/08/2023]
Abstract
Phased secondary small interfering RNAs (phasiRNAs) constitute a major category of small RNAs in plants, but most of their functions are still poorly defined. Some phasiRNAs, known as trans-acting siRNAs, are known to target complementary mRNAs for degradation and to function in development. However, the targets or biological roles of other phasiRNAs remain speculative. New insights into phasiRNA biogenesis, their conservation, and their variation across the flowering plants continue to emerge due to the increased availability of plant genomic sequences, deeper and more sophisticated sequencing approaches, and improvements in computational biology and biochemical/molecular/genetic analyses. In this review, we survey recent progress in phasiRNA biology, with a particular focus on two classes associated with male reproduction: 21-nucleotide (accumulate early in anther ontogeny) and 24-nucloetide (produced in somatic cells during meiosis) phasiRNAs. We describe phasiRNA biogenesis, function, and evolution and define the unanswered questions that represent topics for future research.
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Affiliation(s)
- Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510640, China
- College of Horticulture, South China Agricultural University, Guangzhou 510640, Guangdong, China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri 65211
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Maizel A, Markmann K, Timmermans M, Wachter A. To move or not to move: roles and specificity of plant RNA mobility. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:52-60. [PMID: 32634685 DOI: 10.1016/j.pbi.2020.05.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/07/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Intercellular communication in plants coordinates cellular functions during growth and development, and in response to environmental cues. RNAs figure prominently among the mobile signaling molecules used. Many hundreds of RNA species move over short and long distances, and can be mutually exchanged in biotic interactions. Understanding the specificity determinants of RNA mobility and the physiological relevance of this phenomenon are areas of active research. Here, we highlight the recent progress in our knowledge of small RNA and messenger RNA movement. Particular emphasis is given to novel insight into the specificity determinants of messenger RNA mobility, the role of small RNA movement in development, and the specificity of RNA exchange in plant-plant and plant-microbe interactions.
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Affiliation(s)
- Alexis Maizel
- Center for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Katharina Markmann
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Marja Timmermans
- Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Johannes von Müller-Weg 6, 55128 Mainz, Germany
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Zhang B, You C, Zhang Y, Zeng L, Hu J, Zhao M, Chen X. Linking key steps of microRNA biogenesis by TREX-2 and the nuclear pore complex in Arabidopsis. NATURE PLANTS 2020; 6:957-969. [PMID: 32690891 PMCID: PMC7426256 DOI: 10.1038/s41477-020-0726-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 06/18/2020] [Indexed: 05/03/2023]
Abstract
Unlike in metazoans, the stepwise biogenesis of microRNAs (miRNAs) in plants occurs within the nucleus. Whether or how the major steps in miRNA biogenesis are coordinated is largely unknown. Here we show that the plant TREX-2 complex promotes multiple steps in miRNA biogenesis, including transcription, processing and nuclear export. THP1 and SAC3A-the core subunits of TREX-2-interact and colocalize with RNA polymerase II to promote the transcription of MIR genes in the nucleoplasm. TREX-2 interacts with the microprocessor component SERRATE and promotes the formation of dicing bodies in the nucleoplasm. THP1 also interacts and colocalizes with the nucleoporin protein NUP1 at the nuclear envelope. NUP1 and THP1 promote the nuclear export of miRNAs and ARGONAUTE1. These results suggest that TREX-2 coordinates the transcription, processing and export steps in miRNA biogenesis to ensure efficient miRNA production.
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Affiliation(s)
- Bailong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Liping Zeng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jun Hu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Minglei Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
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28
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Devers EA, Brosnan CA, Sarazin A, Albertini D, Amsler AC, Brioudes F, Jullien PE, Lim P, Schott G, Voinnet O. Movement and differential consumption of short interfering RNA duplexes underlie mobile RNA interference. NATURE PLANTS 2020; 6:789-799. [PMID: 32632272 DOI: 10.1038/s41477-020-0687-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 05/06/2020] [Indexed: 05/19/2023]
Abstract
In RNA interference (RNAi), the RNase III Dicer processes long double-stranded RNA (dsRNA) into short interfering RNA (siRNA), which, when loaded into ARGONAUTE (AGO) family proteins, execute gene silencing1. Remarkably, RNAi can act non-cell autonomously2,3: it is graft transmissible4-7, and plasmodesmata-associated proteins modulate its cell-to-cell spread8,9. Nonetheless, the molecular mechanisms involved remain ill defined, probably reflecting a disparity of experimental settings. Among other caveats, these almost invariably cause artificially enhanced movement via transitivity, whereby primary RNAi-target transcripts are converted into further dsRNA sources of secondary siRNA5,10,11. Whether siRNA mobility naturally requires transitivity and whether it entails the same or distinct signals for cell-to-cell versus long-distance movement remains unclear, as does the identity of the mobile signalling molecules themselves. Movement of long single-stranded RNA, dsRNA, free/AGO-bound secondary siRNA or primary siRNA have all been advocated12-15; however, an entity necessary and sufficient for all known manifestations of plant mobile RNAi remains to be ascertained. Here, we show that the same primary RNAi signal endows both vasculature-to-epidermis and long-distance silencing movement from three distinct RNAi sources. The mobile entities are AGO-free primary siRNA duplexes spreading length and sequence independently. However, their movement is accompanied by selective siRNA depletion reflecting the AGO repertoires of traversed cell types. Coupling movement with this AGO-mediated consumption process creates qualitatively distinct silencing territories, potentially enabling unlimited spatial gene regulation patterns well beyond those granted by mere gradients.
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Affiliation(s)
| | - Christopher A Brosnan
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | | | | | | | | | - Pauline E Jullien
- Department of Biology, ETH Zürich, Zurich, Switzerland
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Peiqi Lim
- Department of Biology, ETH Zürich, Zurich, Switzerland
- QIAGEN Singapore, Singapore, Singapore
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Miguel VN, Manavella PA, Chan RL, Capella MA. The AtHB1 Transcription Factor Controls the miR164-CUC2 Regulatory Node to Modulate Leaf Development. PLANT & CELL PHYSIOLOGY 2020; 61:659-670. [PMID: 31868910 DOI: 10.1093/pcp/pcz233] [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: 08/16/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The presence of small tooth-like indentations, or serrations, characterizes leaf margins of Arabidopsis thaliana plants. The NAC family member CUP-SHAPED COTYLEDON 2 (CUC2), which undergoes post-transcriptional gene silencing by three micro-RNA genes (MIR164A, B and C), controls the extension of leaf serration. Here, we analyzed the role of AtHB1, a transcription factor (TF) belonging to the homeodomain-leucine zipper subfamily I, in shaping leaf margins. Using mutants with an impaired silencing pathway as background, we obtained transgenic plants expressing AtHB1 over 100 times compared to controls. These plants presented an atypical developmental phenotype characterized by leaves with deep serration. Transcript measurements revealed that CUC2 expression was induced in plants overexpressing AtHB1 and repressed in athb1 mutants, indicating a positive regulation exerted by this TF. Moreover, molecular analyses of AtHB1 overexpressing and mutant plants revealed that AtHB1 represses MIR164 transcription. We found that overexpression of MIR164B was able to reverse the serration phenotype of plants overexpressing AtHB1. Finally, chromatin immunoprecipitation assays revealed that AtHB1 was able to bind in vivo the promoter regions of all three MIR164 encoding loci. Altogether, our results indicate that AtHB1 directly represses MIR164 expression to enhance leaf serration by increasing CUC2 levels.
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Affiliation(s)
- Virginia N Miguel
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Matï As Capella
- Instituto de Agrobiotecnolog�a del Litoral, Facultad de Bioqu�mica y Ciencias Biol�gicas, Universidad Nacional del Litoral - CONICET, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
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30
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de Felippes FF, Waterhouse PM. The Whys and Wherefores of Transitivity in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:579376. [PMID: 32983223 PMCID: PMC7488869 DOI: 10.3389/fpls.2020.579376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/14/2020] [Indexed: 05/05/2023]
Abstract
Transitivity in plants is a mechanism that produces secondary small interfering RNAs (siRNAs) from a transcript targeted by primary small RNAs (sRNAs). It expands the silencing signal to additional sequences of the transcript. The process requires RNA-dependent RNA polymerases (RDRs), which convert single-stranded RNA targets into a double-stranded (ds) RNA, the precursor of siRNAs and is critical for effective and amplified responses to virus infection. It is also important for the production of endogenous secondary siRNAs, such as phased siRNAs (phasiRNAs), which regulate several genes involved in development and adaptation. Transitivity on endogenous transcripts is very specific, utilizing special primary sRNAs, such as miRNAs with unique features, and particular ARGONAUTEs. In contrast, transitivity on transgene and virus (exogenous) transcripts is more generic. This dichotomy of responses implies the existence of a mechanism that differentiates self from non-self targets. In this work, we examine the possible mechanistic process behind the dichotomy and the intriguing counter-intuitive directionality of transitive sequence-spread in plants.
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31
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Abstract
The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.
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Affiliation(s)
- Simon Klesen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kristine Hill
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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32
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Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants. Int J Mol Sci 2019; 20:ijms20174306. [PMID: 31484348 PMCID: PMC6747330 DOI: 10.3390/ijms20174306] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/22/2023] Open
Abstract
Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications.
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33
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de Felippes FF. Gene Regulation Mediated by microRNA-Triggered Secondary Small RNAs in Plants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E112. [PMID: 31035467 PMCID: PMC6572396 DOI: 10.3390/plants8050112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 01/18/2023]
Abstract
In plants, proper development and response to abiotic and biotic stimuli requires an orchestrated regulation of gene expression. Small RNAs (sRNAs) are key molecules involved in this process, leading to downregulation of their target genes. Two main classes of sRNAs exist, the small interfering RNAs (siRNAs) and microRNAs (miRNAs). The role of the latter class in plant development and physiology is well known, with many examples of how miRNAs directly impact the expression of genes in cells where they are produced, with dramatic consequences to the life of the plant. However, there is an aspect of miRNA biology that is still poorly understood. In some cases, miRNA targeting can lead to the production of secondary siRNAs from its target. These siRNAs, which display a characteristic phased production pattern, can act in cis, reinforcing the initial silencing signal set by the triggering miRNA, or in trans, affecting genes that are unrelated to the initial target. In this review, the mechanisms and implications of this process in the gene regulation mediated by miRNAs will be discussed. This work will also explore techniques for gene silencing in plants that are based on this unique pathway.
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Wang S, Quan L, Li S, You C, Zhang Y, Gao L, Zeng L, Liu L, Qi Y, Mo B, Chen X. The PROTEIN PHOSPHATASE4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis. THE PLANT CELL 2019; 31:486-501. [PMID: 30674692 PMCID: PMC6447022 DOI: 10.1105/tpc.18.00556] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/28/2018] [Accepted: 01/16/2019] [Indexed: 05/02/2023]
Abstract
PROTEIN PHOSPHATASE4 (PP4) is a highly conserved Ser/Thr protein phosphatase found in yeast, plants, and animals. The composition and functions of PP4 in plants are poorly understood. Here, we uncovered the complexity of PP4 composition and function in Arabidopsis (Arabidopsis thaliana) and identified the composition of one form of PP4 containing the regulatory subunit PP4R3A. We show that PP4R3A, together with one of two redundant catalytic subunit genes, PROTEIN PHOSPHATASE X (PPX)1 and PPX2, promotes the biogenesis of microRNAs (miRNAs). PP4R3A is a chromatin-associated protein that interacts with RNA polymerase II and recruits it to the promoters of miRNA-encoding (MIR) genes to promote their transcription. PP4R3A likely also promotes the cotranscriptional processing of miRNA precursors, because it recruits the microprocessor component HYPONASTIC LEAVES1 to MIR genes and to nuclear dicing bodies. Finally, we show that hundreds of introns exhibit splicing defects in pp4r3a mutants. Together, this study reveals roles for Arabidopsis PP4 in transcription and nuclear RNA metabolism.
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Affiliation(s)
- Suikang Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Li Quan
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi 712100, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chenjiang You
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Yong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Liping Zeng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yanhua Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
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35
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Cai Q, Liang C, Wang S, Hou Y, Gao L, Liu L, He W, Ma W, Mo B, Chen X. The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs. Nat Commun 2018; 9:5080. [PMID: 30498229 PMCID: PMC6265325 DOI: 10.1038/s41467-018-07516-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/29/2018] [Indexed: 11/21/2022] Open
Abstract
Plants evolved an array of disease resistance genes (R genes) to fight pathogens. In the absence of pathogen infection, NBS-LRR genes, which comprise a major subfamily of R genes, are suppressed by a small RNA cascade involving microRNAs (miRNAs) that trigger the biogenesis of phased siRNAs (phasiRNAs) from R gene transcripts. However, whether or how R genes influence small RNA biogenesis is unknown. In this study, we isolate a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and trace the defects to the over accumulation and nuclear localization of an R protein SNC1. We show that nuclear SNC1 represses the transcription of miRNA and phasiRNA loci, probably through the transcriptional corepressor TPR1. Intriguingly, nuclear SNC1 reduces the accumulation of phasiRNAs from three source R genes and concomitantly, the expression of a majority of the ~170R genes is up-regulated. Taken together, this study suggests an R gene-miRNA-phasiRNA regulatory module that amplifies plant immune responses. A small RNA-based signaling cascade prevents the induction of plant resistance genes (R-genes) in the absence of pathogen challenge. Here Cai et al. show that nuclear accumulation of the R protein SNC1 can activate immunity by suppressing small RNA production and releasing R-gene repression.
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Affiliation(s)
- Qiang Cai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Chao Liang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Suikang Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Wenrong He
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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36
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Liu L, Chen X. Intercellular and systemic trafficking of RNAs in plants. NATURE PLANTS 2018; 4:869-878. [PMID: 30390090 PMCID: PMC7155933 DOI: 10.1038/s41477-018-0288-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/21/2018] [Indexed: 05/14/2023]
Abstract
Plants have evolved dynamic and complex networks of cell-to-cell communication to coordinate and adapt their growth and development to a variety of environmental changes. In addition to small molecules, such as metabolites and phytohormones, macromolecules such as proteins and RNAs also act as signalling agents in plants. As information molecules, RNAs can move locally between cells through plasmodesmata, and over long distances through phloem. Non-cell-autonomous RNAs may act as mobile signals to regulate plant development, nutrient allocation, gene silencing, antiviral defence, stress responses and many other physiological processes in plants. Recent work has shed light on mobile RNAs and, in some cases, uncovered their roles in intercellular and systemic signalling networks. This review summarizes the current knowledge of local and systemic RNA movement, and discusses the potential regulatory mechanisms and biological significance of RNA trafficking in plants.
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Affiliation(s)
- Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Longhua Bioindustry and Innovation Research Institute, Shenzhen University, Shenzhen, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
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37
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Tamiru M, Hardcastle TJ, Lewsey MG. Regulation of genome-wide DNA methylation by mobile small RNAs. THE NEW PHYTOLOGIST 2018; 217:540-546. [PMID: 29105762 DOI: 10.1111/nph.14874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/20/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 540 I. Introduction 540 II. There are different types of sRNA mobility 541 III. Mechanisms of sRNA movement 541 IV. Long-distance, shoot-root, mobile siRNAs influence DNA methylation in recipient tissues 541 V. Classes of interactions between shoot-root mobile siRNAs and DNA methylation 542 VI. Loci targeted directly and indirectly by shoot-root mobile siRNAs are associated with different histone modifications 543 VII. Is mobile siRNA-regulated DNA methylation important in specific tissues or under specific conditions? 543 VIII. Mobile sRNAs can be used to modify plant traits 544 IX. Conclusions 544 Acknowledgements 544 References 544 SUMMARY: RNA-directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA-DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.
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Affiliation(s)
- Muluneh Tamiru
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Science, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
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Abstract
In this issue of Developmental Cell, Skopelitis et al. (2017) demonstrate that sharp boundaries of gene expression can be created by threshold-based readout of mobile small RNA gradients. Support for this hypothesis comes from manipulation of small RNAs involved in top-bottom leaf patterning and from a novel synthetic biology approach.
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Affiliation(s)
- Dana O Robinson
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY, USA.
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Mach J. Making Connections: MAC Function in Splicing and MicroRNA Biogenesis. THE PLANT CELL 2017; 29:2316-2317. [PMID: 28986393 PMCID: PMC5774566 DOI: 10.1105/tpc.17.00786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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40
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Jia T, Zhang B, You C, Zhang Y, Zeng L, Li S, Johnson KCM, Yu B, Li X, Chen X. The Arabidopsis MOS4-Associated Complex Promotes MicroRNA Biogenesis and Precursor Messenger RNA Splicing. THE PLANT CELL 2017; 29:2626-2643. [PMID: 28947490 PMCID: PMC5774577 DOI: 10.1105/tpc.17.00370] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/07/2017] [Accepted: 09/25/2017] [Indexed: 05/18/2023]
Abstract
In Arabidopsis thaliana, the MOS4-ASSOCIATED COMPLEX (MAC) is required for defense and development. The evolutionarily conserved, putative RNA helicase MAC7 is a component of the Arabidopsis MAC, and the human MAC7 homolog, Aquarius, is implicated in pre-mRNA splicing. Here, we show that mac7-1, a partial loss-of-function mutant in MAC7, and two other MAC subunit mutants, mac3a mac3b and prl1 prl2 (pleiotropic regulatory locus), exhibit reduced microRNA (miRNA) levels, indicating that MAC promotes miRNA biogenesis. The mac7-1 mutant shows reduced primary miRNA (pri-miRNA) levels without affecting miRNA gene (MIR) promoter activity or the half-life of pri-miRNA transcripts. As a nuclear protein, MAC7 is not concentrated in dicing bodies, but it affects the localization of HYPONASTIC LEAVES1 (HYL1), a key protein in pri-miRNA processing, to dicing bodies. Immunoprecipitation of HYL1 retrieved 11 known MAC subunits, including MAC7, indicating association between HYL1 and MAC. We propose that MAC7 links MIR transcription to pri-miRNA processing. RNA-seq analysis showed that downregulated genes in MAC subunit mutants are mostly involved in plant defense and stimulus responses, confirming a role of MAC in biotic and abiotic stress responses. We also discovered global intron retention defects in mutants in three subunits of MAC, thus linking MAC function to splicing in Arabidopsis.
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Affiliation(s)
- Tianran Jia
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Bailong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Liping Zeng
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
| | - Shengjun Li
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Kaeli C M Johnson
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Bin Yu
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Howard Hughes Medical Institute, University of California, Riverside, California 92521
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41
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de Felippes FF, Marchais A, Sarazin A, Oberlin S, Voinnet O. A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis. Nucleic Acids Res 2017; 45:5539-5554. [PMID: 28334969 PMCID: PMC5435969 DOI: 10.1093/nar/gkx119] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023] Open
Abstract
In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called ‘two-hit’ process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. Interestingly, features for TAS3 tasiRNA production differ in other plant species and we show here that such features also enable TAS3 tasiRNA biogenesis in Arabidopsis, and that a single miR390 targeting event is, in fact, sufficient for this process, suggesting that the ‘one-hit’ model underpins all the necessary rudiments of secondary siRNA biogenesis from plant TAS transcripts. Further results suggest that the two-hit configuration likely enhances the fidelity of tasiRNA production and, hence, the accuracy of downstream gene regulation. Finally, we show that a ‘non-cleavable one-hit’ process allows tasiRNA production from both TAS1 and TAS3 transcripts, indicating that RDR6 recruitment does not require miRNA cleavage, nor does the recruitment, as we further show, of SUPRRESSOR-OF-GENE-SILENCING-3, indispensable for tasiRNA generation.
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Affiliation(s)
- Felipe Fenselau de Felippes
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Antonin Marchais
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Alexis Sarazin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Stefan Oberlin
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
| | - Olivier Voinnet
- Department of Biology, Chair of RNA biology, Swiss Federal Institute of Technology Zurich (ETH-Z), Zürich CH-8092, Switzerland
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42
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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43
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Regulation of miR163 and its targets in defense against Pseudomonas syringae in Arabidopsis thaliana. Sci Rep 2017; 7:46433. [PMID: 28401908 PMCID: PMC5388894 DOI: 10.1038/srep46433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/20/2017] [Indexed: 02/07/2023] Open
Abstract
Small RNAs are important regulators for a variety of biological processes, including leaf development, flowering-time, embryogenesis and defense responses. miR163 is a non-conserved miRNA and its locus has evolved recently through inverted duplication of its target genes to which they belong to the SABATH family of related small-molecule methyltransferases (MTs). In Arabidopsis thaliana, previous study demonstrated that miR163 accumulation was induced by alamethicin treatment, suggesting its roles in defense response pathways. Enhanced resistance against Pseudomonas syringae pv. tomato (Pst) was observed in the mir163 mutant, whereas transgenic lines overexpressing miR163 showed increase sensitivity to Pst, suggesting that miR163 is a negative regulator of defense response. Elevated level of miR163 and its targets in A. thaliana were observed upon Pst treatment, suggesting a modulating relationship between miR163 and its targets. In addition, miR163 and histone deacetylase were found to act cooperatively in mediating defense against Pst. Transgenic plants overexpressing miR163-resistant targets suggested their different contributions in defense. Results from this study revealed that the stress-inducible miR163 and its targets act in concert to modulate defense responses against bacterial pathogen in A. thaliana.
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44
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Li S, Le B, Ma X, Li S, You C, Yu Y, Zhang B, Liu L, Gao L, Shi T, Zhao Y, Mo B, Cao X, Chen X. Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife 2016; 5:e22750. [PMID: 27938667 PMCID: PMC5207768 DOI: 10.7554/elife.22750] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs - production of phased siRNAs (phasiRNAs) from select target RNAs. The phasiRNA precursor RNAs, thought to be noncoding, are on MBPs and are occupied by ribosomes in a manner that supports miRNA-triggered phasiRNA production, suggesting that ribosomes on the rough ER impact siRNA biogenesis. This study reveals global patterns of cytoplasmic partitioning of small RNAs and expands the known functions of ribosomes and ER.
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Affiliation(s)
- Shengben Li
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Brandon Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Xuan Ma
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Beijing, China
| | - Shaofang Li
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yu Yu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Bailong Zhang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Lin Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Lei Gao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ting Shi
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yonghui Zhao
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Beijing, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, United States
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Howard Hughes Medical Institute, University of California, Riverside, Riverside, United States
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45
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Affiliation(s)
- Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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46
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Mermigka G, Verret F, Kalantidis K. RNA silencing movement in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:328-42. [PMID: 26297506 DOI: 10.1111/jipb.12423] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/20/2015] [Indexed: 05/21/2023]
Abstract
Multicellular organisms, like higher plants, need to coordinate their growth and development and to cope with environmental cues. To achieve this, various signal molecules are transported between neighboring cells and distant organs to control the fate of the recipient cells and organs. RNA silencing produces cell non-autonomous signal molecules that can move over short or long distances leading to the sequence specific silencing of a target gene in a well defined area of cells or throughout the entire plant, respectively. The nature of these signal molecules, the route of silencing spread, and the genes involved in their production, movement and reception are discussed in this review. Additionally, a short section on features of silencing spread in animal models is presented at the end of this review.
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Affiliation(s)
- Glykeria Mermigka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Frédéric Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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47
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Martínez G, Panda K, Köhler C, Slotkin RK. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. NATURE PLANTS 2016; 2:16030. [PMID: 27249563 DOI: 10.1038/nplants.2016.30] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 02/04/2016] [Indexed: 05/23/2023]
Abstract
Plant small interfering RNAs (siRNAs) communicate from cell to cell and travel long distances through the vasculature. However, siRNA movement into germ cells has remained controversial, and has gained interest because the terminally differentiated pollen vegetative nurse cell surrounding the sperm cells undergoes a programmed heterochromatin decondensation and transcriptional reactivation of transposable elements (TEs). Transcription of TEs leads to their post-transcriptional degradation into siRNAs, and it has been proposed that the purpose of this TE reactivation is to generate and load TE siRNAs into the sperm cells. Here, we identify the molecular pathway of TE siRNA production in the pollen grain and demonstrate that siRNAs produced from pollen vegetative cell transcripts can silence TE reporters in the sperm cells. Our data demonstrates that TE siRNAs act non-cell-autonomously, inhibiting TE activity in the germ cells and potentially the next generation.
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Affiliation(s)
- Germán Martínez
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Kaushik Panda
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
| | - Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, SE-750 07 Uppsala, Sweden
| | - R Keith Slotkin
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, 500 Aronoff Laboratory, 318 West 12th Avenue, Columbus, Ohio 43210, USA
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48
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Wang HLV, Chekanova JA. Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:356-81. [PMID: 26924473 DOI: 10.1002/wrna.1340] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 12/18/2022]
Abstract
Eukaryotic genomes produce thousands of diverse small RNAs (smRNAs), which play vital roles in regulating gene expression in all conditions, including in survival of biotic and abiotic environmental stresses. SmRNA pathways intersect with most of the pathways regulating different steps in the life of a messenger RNA (mRNA), starting from transcription and ending at mRNA decay. SmRNAs function in both nuclear and cytoplasmic compartments; the regulation of mRNA stability and translation in the cytoplasm and the epigenetic regulation of gene expression in the nucleus are the main and best-known modes of smRNA action. However, recent evidence from animal systems indicates that smRNAs and RNA interference (RNAi) also participate in the regulation of alternative pre-mRNA splicing, one of the most crucial steps in the fast, efficient global reprogramming of gene expression required for survival under stress. Emerging evidence from bioinformatics studies indicates that a specific class of plant smRNAs, induced by various abiotic stresses, the sutr-siRNAs, has the potential to target regulatory regions within introns and thus may act in the regulation of splicing in response to stresses. This review summarizes the major types of plant smRNAs in the context of their mechanisms of action and also provides examples of their involvement in regulation of gene expression in response to environmental cues and developmental stresses. In addition, we describe current advances in our understanding of how smRNAs function in the regulation of pre-mRNA splicing. WIREs RNA 2016, 7:356-381. doi: 10.1002/wrna.1340 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hsiao-Lin V Wang
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Julia A Chekanova
- School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO, USA
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49
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Flores-Sandoval E, Dierschke T, Fisher TJ, Bowman JL. Efficient and Inducible Use of Artificial MicroRNAs in Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2016; 57:281-90. [PMID: 25971256 DOI: 10.1093/pcp/pcv068] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/07/2015] [Indexed: 05/07/2023]
Abstract
We describe the efficient use of artificial microRNAs (amiRs) in Marchantia polymorpha using both endogenous and heterologous primary microRNA (pri-miR) hairpin backbones. Targeting of two transcription factor genes, MpARF1 and MpRR-B, mediating different hormonal responses, demonstrated that amiRs can create specific and reproducible physiological and morphological defects, facilitating interpretation of gene function. A third amiR was designed to target a gene encoding a component of the Polycomb recessive complex 2, MpE(z), and constitutive expression of this amiR results in sporeling lethality. Adaptation of an estrogen-inducible system allowed analysis of the phenotypic effects of induction of this amiR during other stages of the life cycle. We discuss the advantages and challenges of the use of amiRs as a tool for reverse genetic analysis in M. polymorpha.
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Affiliation(s)
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Victoria 3800, Australia Department of Plant Biology, UC Davis, Davis, CA 95616, USA
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50
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Jacobs TB, Lawler NJ, LaFayette PR, Vodkin LO, Parrott WA. Simple gene silencing using the trans-acting siRNA pathway. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:117-27. [PMID: 25816689 DOI: 10.1111/pbi.12362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 05/27/2023]
Abstract
In plants, particular micro-RNAs (miRNAs) induce the production of a class of small interfering RNAs (siRNA) called trans-acting siRNA (ta-siRNA) that lead to gene silencing. A single miRNA target is sufficient for the production of ta-siRNAs, which target can be incorporated into a vector to induce the production of siRNAs, and ultimately gene silencing. The term miRNA-induced gene silencing (MIGS) has been used to describe such vector systems in Arabidopsis. Several ta-siRNA loci have been identified in soybean, but, prior to this work, few of the inducing miRNAs have been experimentally validated, much less used to silence genes. Nine ta-siRNA loci and their respective miRNA targets were identified, and the abundance of the inducing miRNAs varies dramatically in different tissues. The miRNA targets were experimentally verified by silencing a transgenic GFP gene and two endogenous genes in hairy roots and transgenic plants. Small RNAs were produced in patterns consistent with the utilization of the ta-siRNA pathway. A side-by-side experiment demonstrated that MIGS is as effective at inducing gene silencing as traditional hairpin vectors in soybean hairy roots. Soybean plants transformed with MIGS vectors produced siRNAs and silencing was observed in the T1 generation. These results complement previous reports in Arabidopsis by demonstrating that MIGS is an efficient way to produce siRNAs and induce gene silencing in other species, as shown with soybean. The miRNA targets identified here are simple to incorporate into silencing vectors and offer an effective and efficient alternative to other gene silencing strategies.
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Affiliation(s)
- Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Noah J Lawler
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Peter R LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
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