1
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Hong SF, Wei WL, Pan ZJ, Yu JZ, Cheng S, Hung YL, Tjita V, Wang HC, Komatsu A, Nishihama R, Kohchi T, Chen HM, Chen WC, Lo JC, Chiu YH, Yang HC, Lu MY, Liu LYD, Lin SS. Molecular Insights into MpAGO1 and Its Regulatory miRNA, miR11707, in the High-Temperature Acclimation of Marchantia polymorpha. PLANT & CELL PHYSIOLOGY 2024; 65:1414-1433. [PMID: 38988198 DOI: 10.1093/pcp/pcae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 07/12/2024]
Abstract
As a model plant for bryophytes, Marchantia polymorpha offers insights into the role of RNA silencing in aiding early land plants navigate the challenges posed by high-temperature environments. Genomic analysis revealed unique ARGONAUTE1 ortholog gene (MpAGO1) in M. polymorpha, which is regulated by two species-specific microRNAs (miRNAs), miR11707.1 and miR11707.2. Comparative studies of small RNA profiles from M. polymorpha cellular and MpAGO1 immunoprecipitation (MpAGO1-IP) profiles at various temperatures, along with analyses of Arabidopsis AGO1 (AtAGO1), revealed that MpAGO1 has a low selectivity for a diverse range of small RNA species than AtAGO1. Protein structural comparisons revealed no discernible differences in the guide strand small RNA recognition middle domain, MID domain, of MpAGO1 and AtAGO1, suggesting the complexity of miRNA species specificity and necessitating further exploration. Small RNA profiling and size exclusion chromatography have pinpointed a subset of M. polymorpha miRNAs, notably miR11707, that remain in free form within the cell at 22°C but are loaded into MpAGO1 at 28°C to engage in RNA silencing. Investigations into the mir11707 gene editing (mir11707ge) mutants provided evidence of the regulation of miR11707 in MpAGO1. Notably, while MpAGO1 mRNA expression decreases at 28°C, the stability of the MpAGO1 protein and its associated miRNAs is essential for enhancing the RNA-inducing silencing complex (RISC) activity, revealing the importance of RNA silencing in enabling M. polymorpha to survive thermal stress. This study advances our understanding of RNA silencing in bryophytes and provides groundbreaking insights into the evolutionary resilience of land plants to climatic adversities.
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Affiliation(s)
- Syuan-Fei Hong
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Wei-Lun Wei
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Zhao-Jun Pan
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Jia-Zhen Yu
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Shiuan Cheng
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Yu-Ling Hung
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Veny Tjita
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
| | - Hao-Ching Wang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, No. 250 Wu-Xing St., Taipei 11031, Taiwan, ROC
| | - Aino Komatsu
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan, ROC
| | - Wan-Chieh Chen
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan, ROC
| | - Jing-Chi Lo
- Department of Horticulture and Biotechnology, Chinese Culture University, No. 55, Huagang Rd., Shilin Dist., Taipei 11114, Taiwan, ROC
| | - Yen-Hsin Chiu
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
- Taiwan Seed Improvement and Propagation Station, MOA, No.46, Xingzhong St., Xinshe Dist., Taichung 426015, Taiwan, ROC
| | - Ho-Chun Yang
- NGS High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, No. 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan, ROC
| | - Mei-Yeh Lu
- NGS High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, No. 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan, ROC
| | - Li-Yu Daisy Liu
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taipei 106319, Taiwan, ROC
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, No.1, Sec. 4, Roosevelt Rd., Taipei 106319, Taiwan, ROC
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd., Sec. 2, Nankang, Taipei 11529, Taiwan, ROC
- Center of Biotechnology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, Taipei 106319, Taiwan, ROC
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2
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Martín-Merchán A, Lavatelli A, Engler C, González-Miguel V, Moro B, Rosano G, Bologna N. Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications. Nucleic Acids Res 2024; 52:8466-8482. [PMID: 38769059 PMCID: PMC11317149 DOI: 10.1093/nar/gkae387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Plant ARGONAUTE (AGO) proteins play pivotal roles regulating gene expression through small RNA (sRNA) -guided mechanisms. Among the 10 AGO proteins in Arabidopsis thaliana, AGO1 stands out as the main effector of post-transcriptional gene silencing. Intriguingly, a specific region of AGO1, its N-terminal extension (NTE), has garnered attention in recent studies due to its involvement in diverse regulatory functions, including subcellular localization, sRNA loading and interactions with regulatory factors. In the field of post-translational modifications (PTMs), little is known about arginine methylation in Arabidopsis AGOs. In this study, we show that NTE of AGO1 (NTEAGO1) undergoes symmetric arginine dimethylation at specific residues. Moreover, NTEAGO1 interacts with the methyltransferase PRMT5, which catalyzes its methylation. Notably, we observed that the lack of symmetric dimethylarginine has no discernible impact on AGO1's subcellular localization or miRNA loading capabilities. However, the absence of PRMT5 significantly alters the loading of a subgroup of sRNAs into AGO1 and reshapes the NTEAGO1 interactome. Importantly, our research shows that symmetric arginine dimethylation of NTEs is a common process among Arabidopsis AGOs, with AGO1, AGO2, AGO3 and AGO5 undergoing this PTM. Overall, this work deepens our understanding of PTMs in the intricate landscape of RNA-associated gene regulation.
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Affiliation(s)
- Andrea Martín-Merchán
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Antonela Lavatelli
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Camila Engler
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Víctor M González-Miguel
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Belén Moro
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
| | - Germán L Rosano
- Institute of Molecular and Cellular Biology of Rosario, Rosario, Argentina
| | - Nicolas G Bologna
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona 08193, Spain
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3
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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Silanskas A, Rutkauskas D, Jankunec M, Zagorskaitė E, Jurgelaitis E, Grybauskas A, Venclovas Č, Zaremba M. The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein. Nucleic Acids Res 2024; 52:2530-2545. [PMID: 38197228 PMCID: PMC10954474 DOI: 10.1093/nar/gkad1241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
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Affiliation(s)
- Elena Manakova
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Arunas Silanskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Danielis Rutkauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, LT-02300, Vilnius, Lithuania
| | - Marija Jankunec
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Evelina Zagorskaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Edvinas Jurgelaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Česlovas Venclovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania
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5
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Miloro F, Kis A, Havelda Z, Dalmadi Á. Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation. PLANT CELL REPORTS 2024; 43:96. [PMID: 38480545 PMCID: PMC10937801 DOI: 10.1007/s00299-024-03177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
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Affiliation(s)
- Fabio Miloro
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary.
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6
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Fujimoto Y, Iwakawa HO. Mechanisms that regulate the production of secondary siRNAs in plants. J Biochem 2023; 174:491-499. [PMID: 37757447 DOI: 10.1093/jb/mvad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Many organisms produce secondary small interfering RNAs (siRNAs) that are triggered by primary small RNAs to regulate various biological processes. Plants have evolved several types of secondary siRNA biogenesis pathways that play important roles in development, stress responses and defense against viruses and transposons. The critical step of these pathways is the production of double-stranded RNAs by RNA-dependent RNA polymerases. This step is normally tightly regulated, but when its control is released, secondary siRNA production is initiated. In this article, we will review the recent advances in secondary siRNA production triggered by microRNAs encoded in the genome and siRNAs derived from invasive nucleic acids. In particular, we will focus on the factors, events, and RNA/DNA elements that promote or inhibit the early steps of secondary siRNA biogenesis.
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Affiliation(s)
- Yuji Fujimoto
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | - Hiro-Oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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7
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Li Y, Kim EJ, Voshall A, Moriyama EN, Cerutti H. Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas. THE PLANT CELL 2023; 35:1868-1887. [PMID: 36945744 DOI: 10.1093/plcell/koad093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 05/30/2023]
Abstract
Small RNAs (sRNAs) associate with ARGONAUTE (AGO) proteins forming effector complexes with key roles in gene regulation and defense responses against molecular parasites. In multicellular eukaryotes, extensive duplication and diversification of RNA interference (RNAi) components have resulted in intricate pathways for epigenetic control of gene expression. The unicellular alga Chlamydomonas reinhardtii also has a complex RNAi machinery, including 3 AGOs and 3 DICER-like proteins. However, little is known about the biogenesis and function of most endogenous sRNAs. We demonstrate here that Chlamydomonas contains uncommonly long (>26 nt) sRNAs that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these >26 nt sRNAs are derived from moderately repetitive genomic clusters and their biogenesis is DICER-independent. Interestingly, the sequences generating these >26-nt sRNAs have been conserved and amplified in several Chlamydomonas species. Moreover, expression of these longer sRNAs increases substantially under nitrogen or sulfur deprivation, concurrently with the downregulation of predicted target transcripts. We hypothesize that the transposon-like sequences from which >26-nt sRNAs are produced might have been ancestrally targeted for silencing by the RNAi machinery but, during evolution, certain sRNAs might have fortuitously acquired endogenous target genes and become integrated into gene regulatory networks.
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Affiliation(s)
- Yingshan Li
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Eun-Jeong Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Adam Voshall
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Etsuko N Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Nebraska-Lincoln, NE 68588-0666, USA
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8
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Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Grybauskas A, Gražulis S, Zaremba M. Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein. Sci Rep 2023; 13:6123. [PMID: 37059709 PMCID: PMC10104839 DOI: 10.1038/s41598-023-32600-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos). Being the structural core of RNA interference machinery, they use guide RNA molecules for RNA targeting. Prokaryotic Argonautes (pAgos) are more diverse, both in terms of structure (there are eAgo-like 'long' and truncated 'short' pAgos) and mechanism, as many pAgos are specific for DNA, not RNA guide and/or target strands. Some long pAgos act as antiviral defence systems. Their defensive role was recently demonstrated for short pAgo-encoding systems SPARTA and GsSir2/Ago, but the function and action mechanisms of all other short pAgos remain unknown. In this work, we focus on the guide and target strand preferences of AfAgo, a truncated long-B Argonaute protein encoded by an archaeon Archaeoglobus fulgidus. We demonstrate that AfAgo associates with small RNA molecules carrying 5'-terminal AUU nucleotides in vivo, and characterize its affinity to various RNA and DNA guide/target strands in vitro. We also present X-ray structures of AfAgo bound to oligoduplex DNAs that provide atomic details for base-specific AfAgo interactions with both guide and target strands. Our findings broaden the range of currently known Argonaute-nucleic acid recognition mechanisms.
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Affiliation(s)
- Elena Manakova
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Edvardas Golovinas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Reda Pocevičiūtė
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Giedrius Sasnauskas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Algirdas Grybauskas
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Saulius Gražulis
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania
| | - Mindaugas Zaremba
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Sauletekio Av. 7, 10257, Vilnius, Lithuania.
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9
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Xu Y, Zhang Y, Li Z, Soloria AK, Potter S, Chen X. The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities. PLoS Genet 2023; 19:e1010450. [PMID: 36888599 PMCID: PMC9994745 DOI: 10.1371/journal.pgen.1010450] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
microRNAs (miRNAs) regulate target gene expression through their ARGONAUTE (AGO) effector protein, mainly AGO1 in Arabidopsis thaliana. In addition to the highly conserved N, PAZ, MID and PIWI domains with known roles in RNA silencing, AGO1 contains a long, unstructured N-terminal extension (NTE) of little-known function. Here, we show that the NTE is indispensable for the functions of Arabidopsis AGO1, as a lack of the NTE leads to seedling lethality. Within the NTE, the region containing amino acids (a.a.) 91 to 189 is essential for rescuing an ago1 null mutant. Through global analyses of small RNAs, AGO1-associated small RNAs, and miRNA target gene expression, we show that the region containing a.a. 91-189 is required for the loading of miRNAs into AGO1. Moreover, we show that reduced nuclear partitioning of AGO1 did not affect its profiles of miRNA and ta-siRNA association. Furthermore, we show that the 1-to-90a.a. and 91-to-189a.a. regions of the NTE redundantly promote the activities of AGO1 in the biogenesis of trans-acting siRNAs. Together, we report novel roles of the NTE of Arabidopsis AGO1.
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Affiliation(s)
- Ye Xu
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
| | - Yong Zhang
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Zhenfang Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Alyssa K. Soloria
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Savannah Potter
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
| | - Xuemei Chen
- Institute for Integrative Genome Biology, University of California, Riverside, California, United States of America
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States of America
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10
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Wang F, Huang HY, Huang J, Singh J, Pikaard CS. Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention. Genes Dev 2023; 37:103-118. [PMID: 36746605 PMCID: PMC10069450 DOI: 10.1101/gad.350240.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023]
Abstract
RNA-directed DNA methylation in plants is guided by 24-nt siRNAs generated in parallel with 23-nt RNAs of unknown function. We show that 23-nt RNAs function as passenger strands during 24-nt siRNA incorporation into AGO4. The 23-nt RNAs are then sliced into 11- and 12-nt fragments, with 12-nt fragments remaining associated with AGO4. Slicing recapitulated with recombinant AGO4 and synthetic RNAs reveals that siRNAs of 21-24 nt, with any 5'-terminal nucleotide, can guide slicing, with sliced RNAs then retained by AGO4. In vivo, RdDM target locus RNAs that copurify with AGO4 also display a sequence signature of slicing. Comparing plants expressing slicing-competent versus slicing-defective AGO4 shows that slicing elevates cytosine methylation levels at virtually all RdDM loci. We propose that siRNA passenger strand elimination and AGO4 tethering to sliced target RNAs are distinct modes by which AGO4 slicing enhances RNA-directed DNA methylation.
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Affiliation(s)
- Feng Wang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
| | - Hsiao-Yun Huang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Jie Huang
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Jasleen Singh
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
| | - Craig S Pikaard
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA
- Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
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11
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Liu W, Shoji K, Naganuma M, Tomari Y, Iwakawa HO. The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation. Nucleic Acids Res 2022; 50:12997-13010. [PMID: 36477368 PMCID: PMC9825178 DOI: 10.1093/nar/gkac1135] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
The model plant Arabidopsis thaliana encodes as many as ten Argonaute proteins (AGO1-10) with different functions. Each AGO selectively loads a set of small RNAs by recognizing their length and 5' nucleotide identity to properly regulate target genes. Previous studies showed that AGO4 and AGO6, key factors in DNA methylation, incorporate 24-nt small-interfering RNAs with 5' adenine (24A siRNAs). However, it has been unclear how these AGOs specifically load 24A siRNAs. Here, we biochemically investigated the siRNA preference of AGO4, AGO6 and their chimeric mutants. We found that AGO4 and AGO6 use distinct mechanisms to preferentially load 24A siRNAs. Moreover, we showed that the 5' A specificity of AGO4 and AGO6 is not determined by the previously known nucleotide specificity loop in the MID domain but rather by the coordination of the MID and PIWI domains. These findings advance our mechanistic understanding of how small RNAs are accurately sorted into different AGO proteins in plants.
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Affiliation(s)
- Wei Liu
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Keisuke Shoji
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masahiro Naganuma
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihide Tomari
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiro-oki Iwakawa
- Department of Life Science, College of Science, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
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12
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Xiao Y, MacRae IJ. The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10. Nucleic Acids Res 2022; 50:10041-10052. [PMID: 35801914 PMCID: PMC9508841 DOI: 10.1093/nar/gkac571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/31/2022] [Accepted: 07/04/2022] [Indexed: 11/12/2022] Open
Abstract
Small RNAs (sRNAs), including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are essential gene regulators for plant and animal development. The loading of sRNA duplexes into the proper ARGONAUTE (AGO) protein is a key step to forming a functional silencing complex. In Arabidopsis thaliana, the specific loading of miR166/165 into AGO10 (AtAGO10) is critical for the maintenance of the shoot apical meristem, the source of all shoot organs, but the mechanism by which AtAGO10 distinguishes miR166/165 from other cellular miRNAs is not known. Here, we show purified AtAGO10 alone lacks loading selectivity towards miR166/165 duplexes. However, phosphate and HSP chaperone systems reshape the selectivity of AtAGO10 to its physiological substrates. A loop in the AtAGO10 central cleft is essential for recognizing specific mismatches opposite the guide strand 3' region in miR166/165 duplexes. Replacing this loop with the equivalent loop from Homo sapiens AGO2 (HsAGO2) changes AtAGO10 miRNA loading behavior such that 3' region mismatches are ignored and mismatches opposite the guide 5' end instead drive loading, as in HsAGO2. Thus, this study uncovers the molecular mechanism underlying the miR166/165 selectivity of AtAGO10, essential for plant development, and provides new insights into how miRNA duplex structures are recognized for sRNA sorting.
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Affiliation(s)
- Yao Xiao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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13
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Li Z, Li W, Guo M, Liu S, Liu L, Yu Y, Mo B, Chen X, Gao L. Origin, evolution and diversification of plant ARGONAUTE proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1086-1097. [PMID: 34845788 PMCID: PMC9208301 DOI: 10.1111/tpj.15615] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/13/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Argonaute (AGO) proteins are central players in RNA interference in eukaryotes. They associate with small RNAs (sRNA) and lead to transcriptional or posttranscriptional silencing of targets, thereby regulating diverse biological processes. The molecular and biological functions of AGO proteins have been extensively characterized, particularly in a few angiosperm species, leading to the recognition that the AGO family has expanded to accommodate diverse sRNAs thereby performing diverse biological functions. However, understanding of the expansion of AGO proteins in plants is still limited, due to a dearth of knowledge of AGO proteins in green algal groups. Here, we identified more than 2900 AGO proteins from 244 plant species, including green algae, and performed a large-scale phylogenetic analysis. The phylogeny shows that the plant AGO family gave rise to four clades after the emergence of hydrobiontic algae and prior to the emergence of land plants. Subsequent parallel expansion in ferns and angiosperms resulted in eight main clades in angiosperms: AGO2, AGO7, AGO6, AGO4, AGO1, AGO10a, AGO10b and AGO5. On the basis of this phylogeny, we identified two novel AGO4 orthologs that Arabidopsis does not have, and redefined AGO10, which is composed of AGO10a and AGO10b. Finally, we propose a hypothetical evolutionary model of AGO proteins in plants. Our studies provide a deeper understanding of the phylogenetic relationships of AGO family members in the green lineage, which would help to further reveal their roles as RNAi effectors.
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Affiliation(s)
- Zancong Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Wenqi Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Mingxi Guo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Simu Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - 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
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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14
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Yang P, Havecker E, Bauer M, Diehl C, Hendrix B, Hoffer P, Boyle T, Bradley J, Caruano-Yzermans A, Deikman J. Beyond identity: Understanding the contribution of the 5' nucleotide of the antisense strand to RNAi activity. PLoS One 2021; 16:e0256863. [PMID: 34492058 PMCID: PMC8423273 DOI: 10.1371/journal.pone.0256863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/18/2021] [Indexed: 11/19/2022] Open
Abstract
In both the pharmaceutical and agricultural fields, RNA-based products have capitalized upon the mechanism of RNA interference for targeted reduction of gene expression to improve phenotypes and traits. Reduction in gene expression by RNAi is the result of a small interfering RNA (siRNA) molecule binding to an ARGONAUTE (AGO) protein and directing the effector complex to a homologous region of a target gene's mRNA. siRNAs properties that govern RNA-AGO association have been studied in detail. The siRNA 5' nucleotide (nt) identity has been demonstrated in plants to be an important property responsible for directing association of endogenous small RNAs with different AGO effector proteins. However, it has not been investigated whether the 5' nt identity is an efficacious determinant for topically-applied chemically synthesized siRNAs. In this study, we employed a sandpaper abrasion method to study the silencing efficacies of topically-applied 21 base-pair siRNA duplexes. The MAGNESIUM CHELATASE and GREEN FLUORESCENT PROTEIN genes were selected as endogenous and transgenic gene targets, respectively, to assess the molecular and phenotypic effects of gene silencing. Collections of siRNA variants with different 5' nt identities and different pairing states between the 5' antisense nt and its match in the sense strand of the siRNA duplex were tested for their silencing efficacy. Our results suggest a flexibility in the 5' nt requirement for topically applied siRNA duplexes in planta and highlight the similarity of 5' thermodynamic rules governing topical siRNA efficacy across plants and animals.
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Affiliation(s)
- Peizhen Yang
- Bayer Crop Science, St. Louis, Missouri, United States of America
| | - Ericka Havecker
- Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Matthew Bauer
- Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - Carl Diehl
- Bayer Crop Science, St. Louis, Missouri, United States of America
| | - Bill Hendrix
- Bayer Crop Science, Woodland, California, United States of America
| | - Paul Hoffer
- Bayer Crop Science, Woodland, California, United States of America
| | - Timothy Boyle
- Bayer Crop Science, Chesterfield, Missouri, United States of America
| | - John Bradley
- Bayer Crop Science, Chesterfield, Missouri, United States of America
| | | | - Jill Deikman
- Bayer Crop Science, Woodland, California, United States of America
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15
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Guo X, Sun Y, Chen L, Huang F, Liu Q, Feng Y. A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern. Front Microbiol 2021; 12:654345. [PMID: 34220743 PMCID: PMC8248672 DOI: 10.3389/fmicb.2021.654345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022] Open
Abstract
Argonaute proteins (Agos) from thermophilic archaea are involved in several important processes, such as host defense and DNA replication. The catalytic mechanism of Ago from different microbes with great diversity and genome editing potential is attracting increasing attention. Here, we describe an Argonaute from hyperthermophilic Ferroglobus placidus (FpAgo), with a typical DNA-guided DNA endonuclease activity but adopted with only a short guide 15–20 nt length rather than a broad guide selectivity for reported Agos. FpAgo performed the precise cleavage of phosphodiester bonds between 10 and 11 nt on the target strand (counting from the guide strand) guided strictly by 5′-phosphorylated DNA at temperatures ranging from 75 to 99°C. The cleavage activity was regulated by the divalent cations Mn2+, Mg2+, Co2+, and Ni2+. In addition, FpAgo possesses guide/target mismatch tolerance in the seed region but is sensitive to mismatches in the 3′-guide region. Notably, the EMSA assay revealed that the FpAgo-guide-target ternary complex exhibited a stronger binding affinity for short 15 and 16 nt guide DNAs than longer guides. Moreover, we performed structural modeling analyses that implied the unique PAZ domain of FpAgo for 3′-guide recognition and binding to affect guide length specificity. This study broadens our understanding of thermophilic Agos and paves the way for their use in DNA manipulation.
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Affiliation(s)
- Xiang Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liuqing Chen
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fei Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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16
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Jin S, Zhan J, Zhou Y. Argonaute proteins: structures and their endonuclease activity. Mol Biol Rep 2021; 48:4837-4849. [PMID: 34117606 DOI: 10.1007/s11033-021-06476-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/05/2021] [Indexed: 01/12/2023]
Abstract
Argonaute proteins are highly conserved and widely expressed in almost all organisms. They not only play a critical role in the biogenesis of small RNAs but also defend against invading nucleic acids via small RNA or DNA-mediated gene silencing pathways. One functional mechanism of Argonaute proteins is acting as a nucleic-acid-guided endonuclease, which can cleave targets complementary to DNA or RNA guides. The cleavage then leads to translational silencing directly or indirectly by recruiting additional silencing proteins. Here, we summarized the latest research progress in structural and biological studies of Argonaute proteins and pointed out their potential applications in the field of gene editing.
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Affiliation(s)
- Shujuan Jin
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jian Zhan
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Yaoqi Zhou
- Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Institute for Glycomics, Griffith University, Brisbane, QLD, Australia.
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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17
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Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Sci Rep 2021; 11:4518. [PMID: 33633170 PMCID: PMC7907199 DOI: 10.1038/s41598-021-83889-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/09/2021] [Indexed: 11/23/2022] Open
Abstract
Argonaute (Ago) proteins are found in all three domains of life. The best-characterized group is eukaryotic Argonautes (eAgos), which are the core of RNA interference. The best understood prokaryotic Ago (pAgo) proteins are full-length pAgos. They are composed of four major structural/functional domains (N, PAZ, MID, and PIWI) and thereby closely resemble eAgos. It was demonstrated that full-length pAgos function as prokaryotic antiviral systems, with the PIWI domain performing cleavage of invading nucleic acids. However, the majority of identified pAgos are shorter and catalytically inactive (encode just MID and inactive PIWI domains), thus their action mechanism and function remain unknown. In this work we focus on AfAgo, a short pAgo protein encoded by an archaeon Archaeoglobus fulgidus. We find that in all previously solved AfAgo structures, its two monomers form substantial dimerization interfaces involving the C-terminal β-sheets. Led by this finding, we have employed various biochemical and biophysical assays, including SEC-MALS, SAXS, single-molecule FRET, and AFM, to show that AfAgo is indeed a homodimer in solution, which is capable of simultaneous interaction with two DNA molecules. This finding underscores the diversity of prokaryotic Agos and broadens the range of currently known Argonaute-nucleic acid interaction mechanisms.
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18
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Neumeier J, Meister G. siRNA Specificity: RNAi Mechanisms and Strategies to Reduce Off-Target Effects. FRONTIERS IN PLANT SCIENCE 2021; 11:526455. [PMID: 33584737 PMCID: PMC7876455 DOI: 10.3389/fpls.2020.526455] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 12/15/2020] [Indexed: 05/04/2023]
Abstract
Short interfering RNAs (siRNAs) are processed from long double-stranded RNA (dsRNA), and a guide strand is selected and incorporated into the RNA-induced silencing complex (RISC). Within RISC, a member of the Argonaute protein family directly binds the guide strand and the siRNA guides RISC to fully complementary sites on-target RNAs, which are then sequence-specifically cleaved by the Argonaute protein-a process commonly referred to as RNA interference (RNAi). In animals, endogenous microRNAs (miRNAs) function similarly but do not lead to direct cleavage of the target RNA but to translational inhibition followed by exonucleolytic decay. This is due to only partial complementarity between the miRNA and the target RNA. SiRNAs, however, can function as miRNAs, and partial complementarity can lead to miRNA-like off-target effects in RNAi applications. Since siRNAs are widely used not only for screening but also for therapeutics as well as crop protection purposes, such miRNA-like off-target effects need to be minimized. Strategies such as RNA modifications or pooling of siRNAs have been developed and are used to reduce off-target effects.
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Affiliation(s)
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
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19
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Genome-wide identification of Argonautes in Solanaceae with emphasis on potato. Sci Rep 2020; 10:20577. [PMID: 33239724 PMCID: PMC7689493 DOI: 10.1038/s41598-020-77593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/03/2020] [Indexed: 12/17/2022] Open
Abstract
Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.
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20
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Silva-Martins G, Bolaji A, Moffett P. What does it take to be antiviral? An Argonaute-centered perspective on plant antiviral defense. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6197-6210. [PMID: 32835379 DOI: 10.1093/jxb/eraa377] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
RNA silencing is a major mechanism of constitutive antiviral defense in plants, mediated by a number of proteins, including the Dicer-like (DCL) and Argonaute (AGO) endoribonucleases. Both DCL and AGO protein families comprise multiple members. In particular, the AGO protein family has expanded considerably in different plant lineages, with different family members having specialized functions. Although the general mode of action of AGO proteins is well established, the properties that make different AGO proteins more or less efficient at targeting viruses are less well understood. In this report, we review methodologies used to study AGO antiviral activity and current knowledge about which AGO family members are involved in antiviral defense. In addition, we discuss what is known about the different properties of AGO proteins thought to be associated with this function.
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Affiliation(s)
| | - Ayooluwa Bolaji
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
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21
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Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley ( Hordeum vulgare L.). Biomolecules 2020; 10:biom10060929. [PMID: 32570964 PMCID: PMC7356095 DOI: 10.3390/biom10060929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Barley (Hordeum vulgare L.) is an economically important crop cultivated in temperate climates all over the world. Adverse environmental factors negatively affect its survival and productivity. RNA silencing is a conserved pathway involved in the regulation of growth, development and stress responses. The key components of RNA silencing are the Dicer-like proteins (DCLs), Argonautes (AGOs) and RNA-dependent RNA polymerases (RDRs). Despite its economic importance, there is no available comprehensive report on barley RNA silencing machinery and its regulation. In this study, we in silico identified five DCL (HvDCL), eleven AGO (HvAGO) and seven RDR (HvRDR) genes in the barley genome. Genomic localization, phylogenetic analysis, domain organization and functional/catalytic motif identification were also performed. To understand the regulation of RNA silencing, we experimentally analysed the transcriptional changes in response to moderate, persistent or gradient heat stress treatments: transcriptional accumulation of siRNA- but not miRNA-based silencing factor was consistently detected. These results suggest that RNA silencing is dynamically regulated and may be involved in the coordination of development and environmental adaptation in barley. In summary, our work provides information about barley RNA silencing components and will be a ground for the selection of candidate factors and in-depth functional/mechanistic analyses.
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22
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Abundant expression of maternal siRNAs is a conserved feature of seed development. Proc Natl Acad Sci U S A 2020; 117:15305-15315. [PMID: 32541052 DOI: 10.1073/pnas.2001332117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Small RNAs are abundant in plant reproductive tissues, especially 24-nucleotide (nt) small interfering RNAs (siRNAs). Most 24-nt siRNAs are dependent on RNA Pol IV and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and establish DNA methylation at thousands of genomic loci in a process called RNA-directed DNA methylation (RdDM). In Brassica rapa, RdDM is required in the maternal sporophyte for successful seed development. Here, we demonstrate that a small number of siRNA loci account for over 90% of siRNA expression during B. rapa seed development. These loci exhibit unique characteristics with regard to their copy number and association with genomic features, but they resemble canonical 24-nt siRNA loci in their dependence on RNA Pol IV/RDR2 and role in RdDM. These loci are expressed in ovules before fertilization and in the seed coat, embryo, and endosperm following fertilization. We observed a similar pattern of 24-nt siRNA expression in diverse angiosperms despite rapid sequence evolution at siren loci. In the endosperm, siren siRNAs show a marked maternal bias, and siren expression in maternal sporophytic tissues is required for siren siRNA accumulation. Together, these results demonstrate that seed development occurs under the influence of abundant maternal siRNAs that might be transported to, and function in, filial tissues.
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23
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Leclercq J, Wu S, Farinas B, Pointet S, Favreau B, Vignes H, Kuswanhadi K, Ortega-Abboud E, Dufayard JF, Gao S, Droc G, Hu S, Tang C, Montoro P. Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. PeerJ 2020; 8:e8932. [PMID: 32391199 PMCID: PMC7195832 DOI: 10.7717/peerj.8932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/17/2020] [Indexed: 11/20/2022] Open
Abstract
Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.
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Affiliation(s)
- Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shuangyang Wu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Benoît Farinas
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stéphanie Pointet
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bénédicte Favreau
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hélène Vignes
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Enrique Ortega-Abboud
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shenghan Gao
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Songnian Hu
- University of Chinese Academy of Sciences, CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Chaorong Tang
- Hainan University, College of Tropical Crops, Haikou, China
| | - Pascal Montoro
- CIRAD, UMR AGAP, Montpellier, France.,AGAP, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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24
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Sabbione A, Daurelio L, Vegetti A, Talón M, Tadeo F, Dotto M. Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis. BMC PLANT BIOLOGY 2019; 19:401. [PMID: 31510935 PMCID: PMC6739940 DOI: 10.1186/s12870-019-1998-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/29/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet. RESULTS Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis. CONCLUSIONS The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis.
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Affiliation(s)
- Agustín Sabbione
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucas Daurelio
- Laboratorio de Investigaciones en Fisiología y Biología Molecular Vegetal (LIFiBVe), Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Abelardo Vegetti
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Manuel Talón
- Centre de Genómica, Institut Valencià d’Investigacions Agràries (IVIA), Montcada, València, Spain
| | - Francisco Tadeo
- Centre de Genómica, Institut Valencià d’Investigacions Agràries (IVIA), Montcada, València, Spain
| | - Marcela Dotto
- Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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25
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Chung BYW, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC. Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Sci Rep 2019; 9:11091. [PMID: 31366981 PMCID: PMC6668577 DOI: 10.1038/s41598-019-47415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identified as the predominant miRNA with effects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom. .,Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom.
| | - Adrian Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.,Department of Plant Molecular Genetics, Spanish National Centre for Biotechnology, Madrid, 28049, Spain
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Francisco J Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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26
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Hegge JW, Swarts DC, Chandradoss SD, Cui T, Kneppers J, Jinek M, Joo C, van der Oost J. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Nucleic Acids Res 2019; 47:5809-5821. [PMID: 31069393 PMCID: PMC6582352 DOI: 10.1093/nar/gkz306] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/05/2019] [Accepted: 05/03/2019] [Indexed: 12/22/2022] Open
Abstract
Prokaryotic Argonaute proteins (pAgos) constitute a diverse group of endonucleases of which some mediate host defense by utilizing small interfering DNA guides (siDNA) to cleave complementary invading DNA. This activity can be repurposed for programmable DNA cleavage. However, currently characterized DNA-cleaving pAgos require elevated temperatures (≥65°C) for their activity, making them less suitable for applications that require moderate temperatures, such as genome editing. Here, we report the functional and structural characterization of the siDNA-guided DNA-targeting pAgo from the mesophilic bacterium Clostridium butyricum (CbAgo). CbAgo displays a preference for siDNAs that have a deoxyadenosine at the 5'-end and thymidines at nucleotides 2-4. Furthermore, CbAgo mediates DNA-guided DNA cleavage of AT-rich double stranded DNA at moderate temperatures (37°C). This study demonstrates that certain pAgos are capable of programmable DNA cleavage at moderate temperatures and thereby expands the scope of the potential pAgo-based applications.
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Affiliation(s)
- Jorrit W Hegge
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Daan C Swarts
- Laboratory of Biochemistry, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Tao Ju Cui
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Jeroen Kneppers
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
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27
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Abstract
Small RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.
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Affiliation(s)
- Saife Niaz
- Department of Biotechnology, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
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28
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Seo M, Lei L, Egli M. Label-Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein-RNA Complexes. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2019; 76:e70. [PMID: 30461222 PMCID: PMC6391183 DOI: 10.1002/cpnc.70] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The electrophoretic mobility shift assay (EMSA) is a well-established method to detect formation of complexes between proteins and nucleic acids and to determine, among other parameters, equilibrium constants for the interaction. Mixtures of protein and nucleic acid solutions of various ratios are analyzed via polyacrylamide gel electrophoresis (PAGE) under native conditions. In general, protein-nucleic acid complexes will migrate more slowly than the free nucleic acid. From the distributions of the nucleic acid components in the observed bands in individual gel lanes, quantitative parameters such as the dissociation constant (Kd ) of the interaction can be measured. This article describes a simple and rapid EMSA that relies either on precast commercial or handcast polyacrylamide gels and uses unlabeled protein and nucleic acid. Nucleic acids are instead detected with SYBR Gold stain and band intensities established with a standard gel imaging system. We used this protocol specifically to determine Kd values for complexes between the PAZ domain of Argonaute 2 (Ago2) enzyme and native and chemically modified RNA oligonucleotides. EMSA-based equilibrium constants are compared to those determined with isothermal titration calorimetry (ITC). Advantages and limitations of this simple EMSA are discussed by comparing it to other techniques used for determination of equilibrium constants of protein-RNA interactions, and a troubleshooting guide is provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Minguk Seo
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
| | - Li Lei
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University,
Nashville TN 37232
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29
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Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Nat Commun 2019; 10:828. [PMID: 30783109 PMCID: PMC6381166 DOI: 10.1038/s41467-019-08803-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are at the center of a small RNA-based immune system that defends genomes against the deleterious action of mobile genetic elements (transposons). PiRNAs are highly variable in sequence with extensive targeting potential. Their diversity is restricted by their preference to start with a Uridine (U) at the 5' most position (1U-bias), a bias that remains poorly understood. Here we uncover that the 1U-bias of Piwi-piRNAs is established by consecutive discrimination against all nucleotides but U, first during piRNA biogenesis and then upon interaction with Piwi's specificity loop. Sequence preferences during piRNA processing also restrict U across the piRNA body with the potential to directly impact target recognition. Overall, the uncovered signatures could modulate specificity and efficacy of piRNA-mediated transposon restriction, and provide a substrate for purifying selection in the ongoing arms race between genomes and their mobile parasites.
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Affiliation(s)
- Chad B Stein
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sanga Mitra
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexandra R Elchert
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jonathan J Ipsaro
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leif Benner
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sushil Sobti
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun Su
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, 11724, USA.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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30
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Šečić E, Zanini S, Kogel KH. Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2019; 10:1332. [PMID: 31708948 PMCID: PMC6822278 DOI: 10.3389/fpls.2019.01332] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 09/25/2019] [Indexed: 05/08/2023]
Abstract
RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.
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31
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Willkomm S, Makarova KS, Grohmann D. DNA silencing by prokaryotic Argonaute proteins adds a new layer of defense against invading nucleic acids. FEMS Microbiol Rev 2018; 42:376-387. [PMID: 29579258 PMCID: PMC5995195 DOI: 10.1093/femsre/fuy010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/19/2018] [Indexed: 01/05/2023] Open
Abstract
Argonaute (Ago) proteins are encoded in all three domains of life and are responsible for the regulation of intracellular nucleic acid levels. Whereas some Ago variants are able to cleave target nucleic acids by their endonucleolytic activity, others only bind to their target nucleic acids while target cleavage is mediated by other effector proteins. Although all Ago proteins show a high degree of overall structural homology, the nature of the nucleic acid binding partners differs significantly. Recent structural and functional data have provided intriguing new insights into the mechanisms of archaeal and bacterial Ago variants demonstrating the mechanistic diversity within the prokaryotic Ago family with astonishing differences in nucleic acid selection and nuclease specificity. In this review, we provide an overview of the structural organisation of archaeal Ago variants and discuss the current understanding of their biological functions that differ significantly from their eukaryotic counterparts.
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Affiliation(s)
- Sarah Willkomm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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32
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Bollmann SR, Press CM, Tyler BM, Grünwald NJ. Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora. Front Microbiol 2018; 9:2841. [PMID: 30555430 PMCID: PMC6284064 DOI: 10.3389/fmicb.2018.02841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/05/2018] [Indexed: 01/17/2023] Open
Abstract
Modulation of gene expression through RNA interference is well conserved in eukaryotes and is involved in many cellular processes. In the oomycete Phytophthora, research on the small RNA machinery and function has started to reveal potential roles in the pathogen, but much is still unknown. We examined Argonaute (AGO) homologs within oomycete genome sequences, especially among Phytophthora species, to gain a clearer understanding of the evolution of this well-conserved protein family. We identified AGO homologs across many representative oomycete and stramenopile species, and annotated representative homologs in P. sojae. Furthermore, we demonstrate variable transcript levels of all identified AGO homologs in comparison to previously identified Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) homologs. Our phylogenetic analysis further refines the relationship of the AGO homologs in oomycetes and identifies a conserved tandem duplication of AGO homologs in a subset of Phytophthora species.
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Affiliation(s)
- Stephanie R Bollmann
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Caroline M Press
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
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33
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Dayeh DM, Cantara WA, Kitzrow JP, Musier-Forsyth K, Nakanishi K. Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA. Nucleic Acids Res 2018; 46:e98. [PMID: 29897478 PMCID: PMC6144825 DOI: 10.1093/nar/gky496] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/20/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.
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Affiliation(s)
- Daniel M Dayeh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Jonathan P Kitzrow
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Frank F, Nagar B. Structural and Functional Characterization of Plant ARGONAUTE MID Domains. Methods Mol Biol 2018; 1640:227-239. [PMID: 28608347 DOI: 10.1007/978-1-4939-7165-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The interaction of small silencing RNA 5' nucleotides with the MID domain of ARGONAUTE (AGO) proteins provides an anchor point that contributes to strong binding between RNA and protein. The following protocols describe the necessary procedures to characterize the structure of AGO MID domains using X-ray crystallography as well as their interaction with nucleotides that mimic the 5' end of small silencing RNAs using two-dimensional NMR spectroscopy.
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Affiliation(s)
- Filipp Frank
- Department of Biochemistry, Emory University, 1510 Clifton Rd. NE, Atlanta, GA, 30322, USA.
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA, 30322, USA.
| | - Bhushan Nagar
- Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, Canada, H3F 0B1
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35
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Structural Foundations of RNA Silencing by Argonaute. J Mol Biol 2017; 429:2619-2639. [PMID: 28757069 DOI: 10.1016/j.jmb.2017.07.018] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
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36
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Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Nat Microbiol 2017; 2:17035. [PMID: 28319084 DOI: 10.1038/nmicrobiol.2017.35] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 02/10/2017] [Indexed: 12/17/2022]
Abstract
Argonaute (Ago) proteins in eukaryotes are known as key players in post-transcriptional gene silencing1, while recent studies on prokaryotic Agos hint at their role in the protection against invading DNA2,3. Here, we present crystal structures of the apo enzyme and a binary Ago-guide complex of the archaeal Methanocaldococcus jannaschii (Mj) Ago. Binding of a guide DNA leads to large structural rearrangements. This includes the structural transformation of a hinge region containing a switch helix, which has been shown for human Ago2 to be critical for the dynamic target search process4-6. To identify key residues crucial for MjAgo function, we analysed the effect of several MjAgo mutants. We observe that the nature of the 3' and 5' nucleotides in particular, as well as the switch helix, appear to impact MjAgo cleavage activity. In summary, we provide insights into the molecular mechanisms that drive DNA-guided DNA silencing by an archaeal Ago.
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Affiliation(s)
- Sarah Willkomm
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Christine A Oellig
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Adrian Zander
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Ronan Keegan
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dina Grohmann
- Institute of Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
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Swarts DC, Szczepaniak M, Sheng G, Chandradoss SD, Zhu Y, Timmers EM, Zhang Y, Zhao H, Lou J, Wang Y, Joo C, van der Oost J. Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute. Mol Cell 2017; 65:985-998.e6. [PMID: 28262506 DOI: 10.1016/j.molcel.2017.01.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/09/2016] [Accepted: 01/27/2017] [Indexed: 01/20/2023]
Abstract
Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here, we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade double-stranded DNA (dsDNA), thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations, and structural studies, we show that TtAgo loads dsDNA molecules with a preference toward a deoxyguanosine on the passenger strand at the position opposite to the 5' end of the guide strand. This explains why in vivo TtAgo is preferentially loaded with guides with a 5' end deoxycytidine. Our data demonstrate that TtAgo can independently generate and selectively load functional DNA guides.
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Affiliation(s)
- Daan C Swarts
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Malwina Szczepaniak
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Gang Sheng
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Stanley D Chandradoss
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Yifan Zhu
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Elizabeth M Timmers
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Yong Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongtu Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chirlmin Joo
- Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, 2628 CD Delft, the Netherlands.
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, the Netherlands.
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Cock JM, Liu F, Duan D, Bourdareau S, Lipinska AP, Coelho SM, Tarver JE. Rapid Evolution of microRNA Loci in the Brown Algae. Genome Biol Evol 2017; 9:740-749. [PMID: 28338896 PMCID: PMC5381526 DOI: 10.1093/gbe/evx038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2017] [Indexed: 02/06/2023] Open
Abstract
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a single species, the filamentous brown alga Ectocarpus sp. Here, we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families. Surprisingly, none of the S. japonica miRNAs share significant sequence similarity with the Ectocarpus sp. miRNAs. However, the miRNA repertoires of the two species share a number of structural and genomic features indicating that they were generated by similar evolutionary processes and therefore probably evolved within the context of a common, ancestral miRNA system. This lack of sequence similarity suggests that miRNAs evolve rapidly in the brown algae (the two species are separated by ∼95 Myr of evolution). The sets of predicted targets of miRNAs in the two species were also very different suggesting that the divergence of the miRNAs may have had significant consequences for miRNA function.
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Affiliation(s)
- J. Mark Cock
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Fuli Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Delin Duan
- Key Lab of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Qingdao National Laboratory for Marine Science and Technology, Lab for Marine Biology and Biotechnology, Qingdao, China
| | - Simon Bourdareau
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Agnieszka P. Lipinska
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Susana M. Coelho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - James E. Tarver
- School of Earth Sciences, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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39
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Iki T. Messages on small RNA duplexes in plants. JOURNAL OF PLANT RESEARCH 2017; 130:7-16. [PMID: 27878651 DOI: 10.1007/s10265-016-0876-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/12/2016] [Indexed: 06/06/2023]
Abstract
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs. Based at the small RNA duplex-centered view, this review describes the recent advances in understanding the small RNA pathways in plants.
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Affiliation(s)
- Taichiro Iki
- Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Suita, Osaka, 565-0871, Japan.
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40
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Garg V, Agarwal G, Pazhamala LT, Nayak SN, Kudapa H, Khan AW, Doddamani D, Sharma M, Kavi Kishor PB, Varshney RK. Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:488. [PMID: 28487701 PMCID: PMC5404147 DOI: 10.3389/fpls.2017.00488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/21/2017] [Indexed: 05/09/2023]
Abstract
Biotic stress in legume crops is one of the major threats to crop yield and productivity. Being sessile organisms, plants have evolved a myriad of mechanisms to combat different stresses imposed on them. One such mechanism, deciphered in the last decade, is small RNA (sRNA) mediated defense in plants. Small RNAs (sRNAs) have emerged as one of the major players in gene expression regulation in plants during developmental stages and under stress conditions. They are known to act both at transcriptional and post-transcriptional levels. Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDR) constitute the major components of sRNA biogenesis machinery and are known to play a significant role in combating biotic and abiotic stresses. This study is, therefore, focused on identification and characterization of sRNA biogenesis proteins in three important legume crops, namely chickpea, pigeonpea, and groundnut. Phylogenetic analysis of these proteins between legume species classified them into distinct clades and suggests the evolutionary conservation of these genes across the members of Papillionidoids subfamily. Variable expression of sRNA biogenesis genes in response to the biotic stresses among the three legumes indicate the possible existence of specialized regulatory mechanisms in different legumes. This is the first ever study to understand the role of sRNA biogenesis genes in response to pathogen attacks in the studied legumes.
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Affiliation(s)
- Vanika Garg
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Department of Genetics, Osmania UniversityHyderabad, India
| | - Gaurav Agarwal
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Lekha T. Pazhamala
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Spurthi N. Nayak
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Himabindu Kudapa
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Aamir W. Khan
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Dadakhalandar Doddamani
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Mamta Sharma
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | | | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Agriculture and Environment, The University of Western AustraliaCrawley, WA, Australia
- *Correspondence: Rajeev K. Varshney
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41
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Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. BMC Genomics 2016; 17:853. [PMID: 27806710 PMCID: PMC5093975 DOI: 10.1186/s12864-016-3202-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/25/2016] [Indexed: 11/14/2022] Open
Abstract
Background Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages. Results Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs. Conclusion Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3202-4) contains supplementary material, which is available to authorized users.
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42
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Miyoshi T, Ito K, Murakami R, Uchiumi T. Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nat Commun 2016; 7:11846. [PMID: 27325485 PMCID: PMC4919518 DOI: 10.1038/ncomms11846] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/05/2016] [Indexed: 01/05/2023] Open
Abstract
Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson-Crick base-pairing even in the 3'-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5' base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.
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Affiliation(s)
- Tomohiro Miyoshi
- Center for Transdisciplinary Research, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Ryo Murakami
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
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43
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Fang X, Qi Y. RNAi in Plants: An Argonaute-Centered View. THE PLANT CELL 2016; 28:272-85. [PMID: 26869699 PMCID: PMC4790879 DOI: 10.1105/tpc.15.00920] [Citation(s) in RCA: 197] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/29/2015] [Accepted: 02/10/2016] [Indexed: 05/18/2023]
Abstract
Argonaute (AGO) family proteins are effectors of RNAi in eukaryotes. AGOs bind small RNAs and use them as guides to silence target genes or transposable elements at the transcriptional or posttranscriptional level. Eukaryotic AGO proteins share common structural and biochemical properties and function through conserved core mechanisms in RNAi pathways, yet plant AGOs have evolved specialized and diversified functions. This Review covers the general features of AGO proteins and highlights recent progress toward our understanding of the mechanisms and functions of plant AGOs.
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Affiliation(s)
- Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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Abstract
Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.
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45
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Harris CJ, Molnar A, Müller SY, Baulcombe DC. FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts. Nucleic Acids Res 2015; 43:7590-9. [PMID: 26071954 PMCID: PMC4551911 DOI: 10.1093/nar/gkv604] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 12/16/2022] Open
Abstract
Small RNAs, between 18nt and 30nt in length, are a diverse class of non-coding RNAs that mediate a range of cellular processes, from gene regulation to pathogen defense. They guide ribonucleoprotein complexes to their target nucleic acids by Watson-Crick base pairing. We report here that current techniques for small RNA detection and library generation are biased by formation of RNA duplexes. To address this problem, we established FDF-PAGE (fully-denaturing formaldehyde polyacrylamide gel electrophoresis) to prevent annealing of sRNAs to their complement. By applying FDF-PAGE, we provide evidence that both strands of viral small RNA are present in near equimolar ratios, indicating that the predominant precursor is a long double-stranded RNA. Comparing non-denaturing conditions to FDF-PAGE uncovered extensive sequestration of miRNAs in model organisms and allowed us to identify candidate small RNAs under the control of competing endogenous RNAs (ceRNAs). By revealing the full repertoire of small RNAs, we can begin to create a better understanding of small RNA mediated interactions.
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Affiliation(s)
- C Jake Harris
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK
| | - Attila Molnar
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK School of Biological Sciences, Edinburgh University, Edinburgh, EH9 3JH, UK
| | | | - David C Baulcombe
- Plant Sciences Department, Cambridge University, Cambridge, CB2 3EA, UK
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46
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Conformational Dynamics of Ago-Mediated Silencing Processes. Int J Mol Sci 2015; 16:14769-85. [PMID: 26140373 PMCID: PMC4519871 DOI: 10.3390/ijms160714769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/10/2015] [Accepted: 06/17/2015] [Indexed: 12/15/2022] Open
Abstract
Argonaute (Ago) proteins are key players of nucleic acid-based interference mechanisms. Their domains and structural organization are widely conserved in all three domains of life. However, different Ago proteins display various substrate preferences. While some Ago proteins are able to use several substrates, others are limited to a single one. Thereby, they were demonstrated to act specifically on their preferred substrates. Here, we discuss mechanisms of Ago-mediated silencing in relation to structural and biochemical insights. The combination of biochemical and structural information enables detailed analyses of the complex dynamic interplay between Ago proteins and their substrates. Especially, transient binding data allow precise investigations of structural transitions taking place upon Ago-mediated guide and target binding.
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47
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Suzuki HI, Katsura A, Yasuda T, Ueno T, Mano H, Sugimoto K, Miyazono K. Small-RNA asymmetry is directly driven by mammalian Argonautes. Nat Struct Mol Biol 2015; 22:512-21. [PMID: 26098316 DOI: 10.1038/nsmb.3050] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/26/2015] [Indexed: 12/17/2022]
Abstract
Asymmetric selection of single-stranded guide RNAs from double-stranded RNA precursors is crucial in RNA silencing-mediated gene regulation. However, the precise mechanisms of small-RNA asymmetry are unclear, especially because asymmetric selection can still occur when the putative asymmetry sensors Drosophila R2D2 and mammalian Dicer are depleted. Here we report a direct contribution of mammalian Argonaute 2 (Ago2) to microRNA (miRNA) asymmetry. Ago2 selects strands with 5'-uridine or 5'-adenosine and thermodynamically unstable 5' ends in parallel through its two sensor regions, which contact the 5' nucleobases and 5'-phosphates of prospective guide strands. Hence, miRNA asymmetry shows superposed patterns reflecting 5'-end nucleotide identity ('digital' pattern) and thermodynamic stability ('analog' pattern). Furthermore, we demonstrate that cancer-associated miRNA variations reprogram asymmetric selection. Finally, our study presents a model of this universal principle, to aid in comprehensive understanding of miRNA function and development of new RNA-silencing therapies in precision medicine.
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Affiliation(s)
- Hiroshi I Suzuki
- 1] David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akihiro Katsura
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiko Yasuda
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihide Ueno
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koichi Sugimoto
- Department of Hematology and Oncology, JR Tokyo General Hospital, Tokyo, Japan
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Swarts DC, Hegge JW, Hinojo I, Shiimori M, Ellis MA, Dumrongkulraksa J, Terns RM, Terns MP, van der Oost J. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Res 2015; 43:5120-9. [PMID: 25925567 PMCID: PMC4446448 DOI: 10.1093/nar/gkv415] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/16/2015] [Indexed: 11/13/2022] Open
Abstract
Functions of prokaryotic Argonautes (pAgo) have long remained elusive. Recently, Argonautes of the bacteria Rhodobacter sphaeroides and Thermus thermophilus were demonstrated to be involved in host defense. The Argonaute of the archaeon Pyrococcus furiosus (PfAgo) belongs to a different branch in the phylogenetic tree, which is most closely related to that of RNA interference-mediating eukaryotic Argonautes. Here we describe a functional and mechanistic characterization of PfAgo. Like the bacterial counterparts, archaeal PfAgo contributes to host defense by interfering with the uptake of plasmid DNA. PfAgo utilizes small 5′-phosphorylated DNA guides to cleave both single stranded and double stranded DNA targets, and does not utilize RNA as guide or target. Thus, with respect to function and specificity, the archaeal PfAgo resembles bacterial Argonautes much more than eukaryotic Argonautes. These findings demonstrate that the role of Argonautes is conserved through the bacterial and archaeal domains of life and suggests that eukaryotic Argonautes are derived from DNA-guided DNA-interfering host defense systems.
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Affiliation(s)
- Daan C Swarts
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands
| | - Jorrit W Hegge
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands
| | - Ismael Hinojo
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands
| | - Masami Shiimori
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael A Ellis
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Justin Dumrongkulraksa
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Rebecca M Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Michael P Terns
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands
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Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Genetics 2015; 200:105-21. [PMID: 25769981 DOI: 10.1534/genetics.115.174797] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/11/2015] [Indexed: 11/18/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii harbors many types of small RNAs (sRNAs) but little is known about their role(s) in the regulation of endogenous genes and cellular processes. To define functional microRNAs (miRNAs) in Chlamydomonas, we characterized sRNAs associated with an argonaute protein, AGO3, by affinity purification and deep sequencing. Using a stringent set of criteria for canonical miRNA annotation, we identified 39 precursor miRNAs, which produce 45 unique, AGO3-associated miRNA sequences including 13 previously reported miRNAs and 32 novel ones. Potential miRNA targets were identified based on the complementarity of miRNAs with candidate binding sites on transcripts and classified, depending on the extent of complementarity, as being likely to be regulated through cleavage or translational repression. The search for cleavage targets identified 74 transcripts. However, only 6 of them showed an increase in messenger RNA (mRNA) levels in a mutant strain almost devoid of sRNAs. The search for translational repression targets, which used complementarity criteria more stringent than those empirically required for a reduction in target protein levels, identified 488 transcripts. However, unlike observations in metazoans, most predicted translation repression targets did not show appreciable changes in transcript abundance in the absence of sRNAs. Additionally, of three candidate targets examined at the protein level, only one showed a moderate variation in polypeptide amount in the mutant strain. Our results emphasize the difficulty in identifying genuine miRNA targets in Chlamydomonas and suggest that miRNAs, under standard laboratory conditions, might have mainly a modulatory role in endogenous gene regulation in this alga.
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Abstract
Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology.
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