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Nien YC, Vanek A, Axtell MJ. Trans-Species Mobility of RNA Interference between Plants and Associated Organisms. PLANT & CELL PHYSIOLOGY 2024; 65:694-703. [PMID: 38288670 DOI: 10.1093/pcp/pcae012] [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: 10/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 05/31/2024]
Abstract
Trans-species RNA interference (RNAi) occurs naturally when small RNAs (sRNAs) silence genes in species different from their origin. This phenomenon has been observed between plants and various organisms including fungi, animals and other plant species. Understanding the mechanisms used in natural cases of trans-species RNAi, such as sRNA processing and movement, will enable more effective development of crop protection methods using host-induced gene silencing (HIGS). Recent progress has been made in understanding the mechanisms of cell-to-cell and long-distance movement of sRNAs within individual plants. This increased understanding of endogenous plant sRNA movement may be translatable to trans-species sRNA movement. Here, we review diverse cases of natural trans-species RNAi focusing on current theories regarding intercellular and long-distance sRNA movement. We also touch on trans-species sRNA evolution, highlighting its research potential and its role in improving the efficacy of HIGS.
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Affiliation(s)
- Ya-Chi Nien
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Allison Vanek
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Silvestri A, Bansal C, Rubio-Somoza I. After silencing suppression: miRNA targets strike back. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00119-5. [PMID: 38811245 DOI: 10.1016/j.tplants.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/26/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]
Abstract
Within the continuous tug-of-war between plants and microbes, RNA silencing stands out as a key battleground. Pathogens, in their quest to colonize host plants, have evolved a diverse arsenal of silencing suppressors as a common strategy to undermine the host's RNA silencing-based defenses. When RNA silencing malfunctions in the host, genes that are usually targeted and silenced by microRNAs (miRNAs) become active and can contribute to the reprogramming of host cells, providing an additional defense mechanism. A growing body of evidence suggests that miRNAs may act as intracellular sensors to enable a rapid response to pathogen threats. Herein we review how plant miRNA targets play a crucial role in immune responses against different pathogens.
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Affiliation(s)
- Alessandro Silvestri
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain
| | - Chandni Bansal
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution Laboratory, Centre for Research in Agricultural Genomics, 08193 Barcelona, Spain; Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08001, Spain.
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3
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Zhou B, Yu H, Xue Y, Li M, Zhang C, Yu B. The spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis. Nat Commun 2024; 15:2399. [PMID: 38493158 PMCID: PMC10944506 DOI: 10.1038/s41467-024-46676-z] [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: 06/27/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
MicroRNAs (miRNAs) play a key role in regulating gene expression and their biogenesis is precisely controlled through modulating the activity of microprocessor. Here, we report that CWC15, a spliceosome-associated protein, acts as a positive regulator of miRNA biogenesis. CWC15 binds the promoters of genes encoding miRNAs (MIRs), promotes their activity, and increases the occupancy of DNA-dependent RNA polymerases at MIR promoters, suggesting that CWC15 positively regulates the transcription of primary miRNA transcripts (pri-miRNAs). In addition, CWC15 interacts with Serrate (SE) and HYL1, two key components of microprocessor, and is required for efficient pri-miRNA processing and the HYL1-pri-miRNA interaction. Moreover, CWC15 interacts with the 20 S proteasome and PRP4KA, facilitating SE phosphorylation by PRP4KA, and subsequent non-functional SE degradation by the 20 S proteasome. These data reveal that CWC15 ensures optimal miRNA biogenesis by maintaining proper SE levels and by modulating pri-miRNA levels. Taken together, this study uncovers the role of a conserved splicing-related protein in miRNA biogenesis.
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Affiliation(s)
- Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Yong Xue
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA.
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588-0118, USA.
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Zhong C, Smith NA, Zhang D, Gou X, Greaves IK, Millar AA, Walsh TK, Shan W, Wang MB. G-U base-paired hpRNA confers potent inhibition of small RNA function in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1206-1222. [PMID: 38038953 DOI: 10.1111/tpj.16555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
MicroRNA (miRNA) target mimicry technologies, utilizing naturally occurring miRNA decoy molecules, represent a potent tool for analyzing miRNA function. In this study, we present a highly efficient small RNA (sRNA) target mimicry design based on G-U base-paired hairpin RNA (hpG:U), which allows for the simultaneous targeting of multiple sRNAs. The hpG:U constructs consistently generate high amounts of intact, polyadenylated stem-loop (SL) RNA outside the nuclei, in contrast to traditional hairpin RNA designs with canonical base pairing (hpWT), which were predominantly processed resulting in a loop. By incorporating a 460-bp G-U base-paired double-stranded stem and a 312-576 nt loop carrying multiple miRNA target mimicry sites (GUMIC), the hpG:U construct displayed effective repression of three Arabidopsis miRNAs, namely miR165/166, miR157, and miR160, both individually and in combination. Additionally, a GUMIC construct targeting a prominent cluster of siRNAs derived from cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) effectively inhibited Y-Sat siRNA-directed silencing of the chlorophyll biosynthetic gene CHLI, thereby reducing the yellowing symptoms in infected Nicotiana plants. Therefore, the G-U base-paired hpRNA, characterized by differential processing compared to traditional hpRNA, acts as an efficient decoy for both miRNAs and siRNAs. This technology holds great potential for sRNA functional analysis and the management of sRNA-mediated diseases.
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Affiliation(s)
- Chengcheng Zhong
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Neil A Smith
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Daai Zhang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Xiuhong Gou
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ian K Greaves
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, 2601, ACT, Australia
| | - Tom K Walsh
- CSIRO Environment, Canberra, 2601, ACT, Australia
| | - Weixing Shan
- Stake Key Laboratory for Crop Stress Resistance and High-Efficiency Production and College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming-Bo Wang
- CSIRO Agriculture and Food, Canberra, 2601, ACT, Australia
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Othman SMIS, Mustaffa AF, Mohd Zahid NII, Che-Othman MH, Samad AFA, Goh HH, Ismail I. Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108387. [PMID: 38266565 DOI: 10.1016/j.plaphy.2024.108387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/02/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.
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Affiliation(s)
- Syed Muhammad Iqbal Syed Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Arif Faisal Mustaffa
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Nur Irdina Izzatie Mohd Zahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - M Hafiz Che-Othman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Abdul Fatah A Samad
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru, 81310, Johor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia
| | - Ismanizan Ismail
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia; Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi, 43600, Selangor, Malaysia.
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6
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Li M, Yu H, Zhou B, Gan L, Li S, Zhang C, Yu B. JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2024; 52:420-430. [PMID: 37994727 PMCID: PMC10783502 DOI: 10.1093/nar/gkad1105] [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: 06/30/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.
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Affiliation(s)
- Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Lu Gan
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shangdong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
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7
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Cheng AP, Kwon S, Adeshara T, Göhre V, Feldbrügge M, Weiberg A. Extracellular RNAs released by plant-associated fungi: from fundamental mechanisms to biotechnological applications. Appl Microbiol Biotechnol 2023; 107:5935-5945. [PMID: 37572124 PMCID: PMC10485130 DOI: 10.1007/s00253-023-12718-7] [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: 05/31/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Extracellular RNAs are an emerging research topic in fungal-plant interactions. Fungal plant pathogens and symbionts release small RNAs that enter host cells to manipulate plant physiology and immunity. This communication via extracellular RNAs between fungi and plants is bidirectional. On the one hand, plants release RNAs encapsulated inside extracellular vesicles as a defense response as well as for intercellular and inter-organismal communication. On the other hand, recent reports suggest that also full-length mRNAs are transported within fungal EVs into plants, and these fungal mRNAs might get translated inside host cells. In this review article, we summarize the current views and fundamental concepts of extracellular RNAs released by plant-associated fungi, and we discuss new strategies to apply extracellular RNAs in crop protection against fungal pathogens. KEY POINTS: • Extracellular RNAs are an emerging topic in plant-fungal communication. • Fungi utilize RNAs to manipulate host plants for colonization. • Extracellular RNAs can be engineered to protect plants against fungal pathogens.
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Affiliation(s)
- An-Po Cheng
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany
| | - Seomun Kwon
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Trusha Adeshara
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Arne Weiberg
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany.
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Hudzik C, Maguire S, Guan S, Held J, Axtell MJ. Trans-species microRNA loci in the parasitic plant Cuscuta campestris have a U6-like snRNA promoter. THE PLANT CELL 2023; 35:1834-1847. [PMID: 36896651 PMCID: PMC10226579 DOI: 10.1093/plcell/koad076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/09/2023] [Accepted: 02/12/2023] [Indexed: 05/30/2023]
Abstract
Small regulatory RNAs can move between organisms and regulate gene expression in the recipient. Whether the trans-species small RNAs being exported are distinguished from the normal endogenous small RNAs of the source organism is not known. The parasitic plant Cuscuta campestris (dodder) produces many microRNAs that specifically accumulate at the host-parasite interface, several of which have trans-species activity. We found that induction of C. campestris interface-induced microRNAs is similar regardless of host species and occurs in C. campestris haustoria produced in the absence of any host. The loci-encoding C. campestris interface-induced microRNAs are distinguished by a common cis-regulatory element. This element is identical to a conserved upstream sequence element (USE) used by plant small nuclear RNA loci. The properties of the interface-induced microRNA primary transcripts strongly suggest that they are produced via U6-like transcription by RNA polymerase III. The USE promotes accumulation of interface-induced miRNAs (IIMs) in a heterologous system. This promoter element distinguishes C. campestris IIM loci from other plant small RNAs. Our data suggest that C. campestris IIMs are produced in a manner distinct from canonical miRNAs. All confirmed C. campestris microRNAs with documented trans-species activity are interface-induced and possess these features. We speculate that RNA polymerase III transcription of IIMs may allow these miRNAs to be exported to hosts.
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Affiliation(s)
- Collin Hudzik
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sean Maguire
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Jeremy Held
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Matsumura EE, Kormelink R. Small Talk: On the Possible Role of Trans-Kingdom Small RNAs during Plant-Virus-Vector Tritrophic Communication. PLANTS (BASEL, SWITZERLAND) 2023; 12:1411. [PMID: 36987098 PMCID: PMC10059270 DOI: 10.3390/plants12061411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Small RNAs (sRNAs) are the hallmark and main effectors of RNA silencing and therefore are involved in major biological processes in plants, such as regulation of gene expression, antiviral defense, and plant genome integrity. The mechanisms of sRNA amplification as well as their mobile nature and rapid generation suggest sRNAs as potential key modulators of intercellular and interspecies communication in plant-pathogen-pest interactions. Plant endogenous sRNAs can act in cis to regulate plant innate immunity against pathogens, or in trans to silence pathogens' messenger RNAs (mRNAs) and impair virulence. Likewise, pathogen-derived sRNAs can act in cis to regulate expression of their own genes and increase virulence towards a plant host, or in trans to silence plant mRNAs and interfere with host defense. In plant viral diseases, virus infection alters the composition and abundance of sRNAs in plant cells, not only by triggering and interfering with the plant RNA silencing antiviral response, which accumulates virus-derived small interfering RNAs (vsiRNAs), but also by modulating plant endogenous sRNAs. Here, we review the current knowledge on the nature and activity of virus-responsive sRNAs during virus-plant interactions and discuss their role in trans-kingdom modulation of virus vectors for the benefit of virus dissemination.
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:jof9010004. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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11
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Lang C, Lin HT, Wu C, Alavi M. In Silico analysis of the sequence and structure of plant microRNAs packaged in extracellular vesicles. Comput Biol Chem 2022; 101:107771. [DOI: 10.1016/j.compbiolchem.2022.107771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
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12
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Kong X, Yang M, Le BH, He W, Hou Y. The master role of siRNAs in plant immunity. MOLECULAR PLANT PATHOLOGY 2022; 23:1565-1574. [PMID: 35869407 PMCID: PMC9452763 DOI: 10.1111/mpp.13250] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 06/01/2023]
Abstract
Gene silencing mediated by small noncoding RNAs (sRNAs) is a fundamental gene regulation mechanism in eukaryotes that broadly governs cellular processes. It has been established that sRNAs are critical regulators of plant growth, development, and antiviral defence, while accumulating studies support positive roles of sRNAs in plant defence against bacteria and eukaryotic pathogens such as fungi and oomycetes. Emerging evidence suggests that plant sRNAs move between species and function as antimicrobial agents against nonviral parasites. Multiple plant pathosystems have been shown to involve a similar exchange of small RNAs between species. Recent analysis about extracellular sRNAs shed light on the understanding of the selection and transportation of sRNAs moving from plant to parasites. In this review, we summarize current advances regarding the function and regulatory mechanism of plant endogenous small interfering RNAs (siRNAs) in mediating plant defence against pathogen intruders including viruses, bacteria, fungi, oomycetes, and parasitic plants. Beyond that, we propose potential mechanisms behind the sorting of sRNAs moving between species and the idea that engineering siRNA-producing loci could be a useful strategy to improve disease resistance of crops.
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Affiliation(s)
- Xiuzhen Kong
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Meng Yang
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Brandon H. Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome BiologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Wenrong He
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCaliforniaUSA
| | - Yingnan Hou
- Shanghai Collaborative Innovation Center of Agri‐Seeds/School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
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13
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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14
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Mansour A, Mannaa M, Hewedy O, Ali MG, Jung H, Seo YS. Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions. THE PLANT PATHOLOGY JOURNAL 2022; 38:432-448. [PMID: 36221916 PMCID: PMC9561162 DOI: 10.5423/ppj.rw.07.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 06/16/2023]
Abstract
Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.
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Affiliation(s)
- Abdelaziz Mansour
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza 12613,
Egypt
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
- Department of Plant Pathology, Cairo University, Giza 12613,
Egypt
| | - Omar Hewedy
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1,
Canada
- Department of Genetics, Faculty of Agriculture, Menoufia University, Shibin El-Kom 32514,
Egypt
| | - Mostafa G. Ali
- Department of Botany and Microbiology, Faculty of Science, Benha University, Benha 13518,
Egypt
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241,
Korea
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15
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Robles-Fort A, Pescador-Dionisio S, García-Robles I, Sentandreu V, Martínez-Ramírez AC, Real MD, Rausell C. Unveiling gene expression regulation of the Bacillus thuringiensis Cry3Aa toxin receptor ADAM10 by the potato dietary miR171c in Colorado potato beetle. PEST MANAGEMENT SCIENCE 2022; 78:3760-3768. [PMID: 34846789 DOI: 10.1002/ps.6743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The Colorado potato beetle (CPB) is a worldwide devastating pest of potato plants and other Solanaceae characterized by its remarkable ability to evolve resistance to insecticides. Bacillus thuringiensis (Bt) Cry3Aa toxin represents an environmentally safe alternative for CPB control but larvae susceptibility to this toxin has been reported to vary depending on the host plant on which larvae feed. To gain more insight into how nutrition mediates Bt tolerance through effects on gene expression, here we explored the post-transcriptional regulation by microRNAs (miRNAs) of the CPB-ADAM10 gene encoding the Cry3Aa toxin functional receptor ADAM10. RESULTS The lower CPB-ADAM10 gene expression in CPB larvae fed on potato plants cv. Vivaldi than those fed on potato cv. Monalisa or tomato plants was inversely related to Cry3Aa toxicity. By high-throughput sequencing we identified seven CPB miRNAs and one potato miRNA predicted to base pair with the CPB-ADAM10 messenger RNA. No differential expression of the endogenous lde-miR1175-5p was found in larvae feeding on any of the two potato plant varieties. However, statistically significant increased amounts of potato stu-miR171c-5p were detected in CPB larvae fed on potato cv. Vivaldi compared to larvae fed on potato cv. Monalisa. CONCLUSION Our results support a role for dietary miRNAs in Bt toxicity by regulating the CPB-ADAM10 gene encoding the Cry3Aa toxin receptor ADAM10 in CPB larvae and opening up the possibility of exploiting plant natural variation in miRNAs to provide more sustainable potato crop protection against CPB. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Aida Robles-Fort
- Department of Genetics, University of Valencia, Burjassot, Spain
| | | | | | - Vicente Sentandreu
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, Burjassot, Spain
| | - Amparo C Martínez-Ramírez
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, Burjassot, Spain
| | - M Dolores Real
- Department of Genetics, University of Valencia, Burjassot, Spain
| | - Carolina Rausell
- Department of Genetics, University of Valencia, Burjassot, Spain
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16
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Van den Brande S, Gijbels M, Wynant N, Peeters P, Gansemans Y, Van Nieuwerburgh F, Santos D, Vanden Broeck J. Identification and profiling of stable microRNAs in hemolymph of young and old Locusta migratoria fifth instars. CURRENT RESEARCH IN INSECT SCIENCE 2022; 2:100041. [PMID: 36003267 PMCID: PMC9387440 DOI: 10.1016/j.cris.2022.100041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Since the discovery of the first microRNA (miRNA) in the nematode Caenorhabditis elegans, numerous novel miRNAs have been identified which can regulate presumably every biological process in a wide range of metazoan species. In accordance, several insect miRNAs have been identified and functionally characterized. While regulatory RNA pathways are traditionally described at an intracellular level, studies reporting on the presence and potential role of extracellular (small) sRNAs have been emerging in the last decade, mainly in mammalian systems. Interestingly, evidence in several species indicates the functional transfer of extracellular RNAs between donor and recipient cells, illustrating RNA-based intercellular communication. In insects, however, reports on extracellular small RNAs are emerging but the number of detailed studies is still very limited. Here, we demonstrate the presence of stable sRNAs in the hemolymph of the migratory locust, Locusta migratoria. Moreover, the levels of several extracellular miRNAs (ex-miRNAs) present in locust hemolymph differed significantly between young and old fifth nymphal instars. In addition, we performed a 'proof of principle' experiment which suggested that extracellularly delivered miRNA molecules are capable of affecting the locusts' development.
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Affiliation(s)
- Stijn Van den Brande
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Marijke Gijbels
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Niels Wynant
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Paulien Peeters
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dulce Santos
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
| | - Jozef Vanden Broeck
- Research group of Molecular Developmental Physiology and Signal Transduction, KU Leuven, Zoological Institute, Naamsestraat 59 box 2465, 3000 Leuven, Belgium
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17
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Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems. Nat Rev Mol Cell Biol 2022; 23:645-662. [PMID: 35710830 DOI: 10.1038/s41580-022-00496-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
RNA silencing is a well-established antiviral immunity system in plants, in which small RNAs guide Argonaute proteins to targets in viral RNA or DNA, resulting in virus repression. Virus-encoded suppressors of silencing counteract this defence system. In this Review, we discuss recent findings about antiviral RNA silencing, including the movement of RNA through plasmodesmata and the differentiation between plant self and viral RNAs. We also discuss the emerging role of RNA silencing in plant immunity against non-viral pathogens. This immunity is mediated by transkingdom movement of RNA into and out of the infected plant cells in vesicles or as extracellular nucleoproteins and, like antiviral immunity, is influenced by the silencing suppressors encoded in the pathogens' genomes. Another effect of RNA silencing on general immunity involves host-encoded small RNAs, including microRNAs, that regulate NOD-like receptors and defence signalling pathways in the innate immunity system of plants. These RNA silencing pathways form a network of processes with both positive and negative effects on the immune systems of plants.
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18
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Rabuma T, Gupta OP, Chhokar V. Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant's disease response. RNA Biol 2022; 19:519-532. [PMID: 35442163 PMCID: PMC9037536 DOI: 10.1080/15476286.2022.2062172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the recent past, cross-kingdom movement of miRNAs, small (20–25 bases), and endogenous regulatory RNA molecules has emerged as one of the major research areas to understand the potential implications in modulating the plant’s biotic stress response. The current review discussed the recent developments in the mechanism of cross-kingdom movement (long and short distance) and critical cross-talk between host’s miRNAs in regulating gene function in bacteria, fungi, viruses, insects, and nematodes, and vice-versa during host-pathogen interaction and their potential implications in crop protection. Moreover, cross-kingdom movement during symbiotic interaction, the emerging role of plant’s miRNAs in modulating animal’s gene function, and feasibility of spray-induced gene silencing (SIGS) in combating biotic stresses in plants are also critically evaluated. The current review article analysed the horizontal transfer of miRNAs among plants, animals, and microbes that regulates gene expression in the host or pathogenic organisms, contributing to crop protection. Further, it highlighted the challenges and opportunities to harness the full potential of this emerging approach to mitigate biotic stress efficiently.
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Affiliation(s)
- Tilahun Rabuma
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA.,Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia
| | - Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, INDIA
| | - Vinod Chhokar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA
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19
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Aslam M, Fakher B, Qin Y. Big Role of Small RNAs in Female Gametophyte Development. Int J Mol Sci 2022; 23:ijms23041979. [PMID: 35216096 PMCID: PMC8878111 DOI: 10.3390/ijms23041979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
In living organisms, sexual reproduction relies on the successful development of the gametes. Flowering plants produce gametes in the specialized organs of the flower, the gametophytes. The female gametophyte (FG), a multicellular structure containing female gametes (egg cell and central cell), is often referred to as an embryo sac. Intriguingly, several protein complexes, molecular and genetic mechanisms participate and tightly regulate the female gametophyte development. Recent evidence indicates that small RNA (sRNA) mediated pathways play vital roles in female gametophyte development and specification. Here, we present an insight into our understanding and the recent updates on the molecular mechanism of different players of small RNA-directed regulatory pathways during ovule formation and growth.
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Affiliation(s)
- Mohammad Aslam
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Beenish Fakher
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yuan Qin
- Guangxi Key Lab of Sugarcane Biology, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China;
- Center for Genomics and Biotechnology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Correspondence:
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20
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Okeke C, Silas U, Nnodu O, Clementina O. HSC and miRNA Regulation with Implication for Foetal Haemoglobin Induction in Beta Haemoglobinopathies. Curr Stem Cell Res Ther 2022; 17:339-347. [PMID: 35189805 DOI: 10.2174/1574888x17666220221104711] [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: 09/02/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/22/2022]
Abstract
Sickle cell disease (SCD) is one of the most common haemoglobinopathies worldwide, with up to 70 % of global SCD annual births occurring in sub-Saharan Africa. Reports have shown that 50 to 80 % of affected children in these countries die annually. Efforts geared towards understanding and controlling HbF production in SCD patients could lead to strategies for effective control of globin gene expression and therapeutic approaches that could be beneficial to individuals with haemoglobinopathies. Hemopoietic stem cells (HSCs) are characterized by a specific miRNA signature in every state of differentiation. The role of miRNAs has become evident both in the maintenance of the "stemness" and in the early induction of differentiation by modulation of the expression of the master pluripotency genes and during early organogenesis. miRNAs are extra regulatory mechanisms in hematopoietic stem cells (HSCs) via influencing transcription profiles together with transcript stability. miRNAs have been reported to be used to reprogram primary somatic cells toward pluripotency. Their involvement in cell editing holds the potential for therapy for many genetic diseases. This review provides a snapshot of miRNA involvement in cell fate decisions, haemoglobin induction pathway, and their journey as some emerge prime targets for therapy in beta haemoglobinopathies.
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Affiliation(s)
- Chinwe Okeke
- Department of Medical Laboratory Science, Faculty of Health Science and Technology, University of Nigeria, Nsukka, Nigeria
| | - Ufele Silas
- Department of Medical Laboratory Science, Faculty of Health Science and Technology, University of Nigeria, Nsukka, Nigeria
| | - Obiageli Nnodu
- Department of Haematology, College of Medicine, University of Abuja, Abuja Nigeria
| | - Odoh Clementina
- Department of Medical Laboratory Science, Faculty of Health Science and Technology, University of Nigeria, Nsukka, Nigeria
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21
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Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C. Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease. THE NEW PHYTOLOGIST 2022; 233:443-457. [PMID: 34605025 DOI: 10.1111/nph.17758] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Phytophthora spp. cause serious damage to plants by exploiting a large number of effector proteins and small RNAs (sRNAs). Several reports have described modulation of host RNA biogenesis and defence gene expression. Here, we analysed Phytophthora infestans Argonaute (Ago) 1 associated small RNAs during potato leaf infection. Small RNAs were co-immunoprecipitated, deep sequenced and analysed against the P. infestans and potato genomes, followed by transcript analyses and transgenic assays on a predicted target. Extensive targeting of potato and pathogen-derived sRNAs to a range of mRNAs was observed, including 638 sequences coding for resistance (R) proteins in the host genome. The single miRNA encoded by P. infestans (miR8788) was found to target a potato alpha/beta hydrolase-type encoding gene (StABH1), a protein localized to the plasma membrane. Analyses of stable transgenic potato lines harbouring overexpressed StABH1 or artificial miRNA gene constructs demonstrated the importance of StABH1 during infection by P. infestans. miR8788 knock-down strains showed reduced growth on potato, and elevated StABH1 expression levels were observed when plants were inoculated with the two knock-down strains compared to the wild-type strain 88069. The findings of our study suggest that sRNA encoded by P. infestans can affect potato mRNA, thereby expanding our knowledge of the multifaceted strategies this species uses to facilitate infection.
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Affiliation(s)
- Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Kristian Persson Hodén
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Zhen Liao
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
| | - Anna Åsman
- Department of Molecular Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7015, S-75007, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, S-75007, Uppsala, Sweden
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22
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Qiao Y, Xia R, Zhai J, Hou Y, Feng L, Zhai Y, Ma W. Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:265-288. [PMID: 34077241 DOI: 10.1146/annurev-phyto-121520-023514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host-pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of trans-species gene silencing at the host-pathogen interface are discussed.
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Affiliation(s)
- Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou 510640, China
| | - Jixian Zhai
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Li Feng
- School of Life Sciences, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yi Zhai
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK;
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23
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Exosome/Liposome-like Nanoparticles: New Carriers for CRISPR Genome Editing in Plants. Int J Mol Sci 2021; 22:ijms22147456. [PMID: 34299081 PMCID: PMC8304373 DOI: 10.3390/ijms22147456] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Rapid developments in the field of plant genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems necessitate more detailed consideration of the delivery of the CRISPR system into plants. Successful and safe editing of plant genomes is partly based on efficient delivery of the CRISPR system. Along with the use of plasmids and viral vectors as cargo material for genome editing, non-viral vectors have also been considered for delivery purposes. These non-viral vectors can be made of a variety of materials, including inorganic nanoparticles, carbon nanotubes, liposomes, and protein- and peptide-based nanoparticles, as well as nanoscale polymeric materials. They have a decreased immune response, an advantage over viral vectors, and offer additional flexibility in their design, allowing them to be functionalized and targeted to specific sites in a biological system with low cytotoxicity. This review is dedicated to describing the delivery methods of CRISPR system into plants with emphasis on the use of non-viral vectors.
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24
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Lyko P, Wicke S. Genomic reconfiguration in parasitic plants involves considerable gene losses alongside global genome size inflation and gene births. PLANT PHYSIOLOGY 2021; 186:1412-1423. [PMID: 33909907 PMCID: PMC8260112 DOI: 10.1093/plphys/kiab192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/13/2021] [Indexed: 05/02/2023]
Abstract
Parasitic plant genomes and transcriptomes reveal numerous genetic innovations, the functional-evolutionary relevance and roles of which open unprecedented research avenues.
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Affiliation(s)
- Peter Lyko
- Institute for Biology, Humboldt-University of Berlin, Germany
| | - Susann Wicke
- Institute for Biology, Humboldt-University of Berlin, Germany
- Author for communication:
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25
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Meitha K, Esyanti RR, Iriawati, Hanisia RH, Rohyani. Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA. Noncoding RNA Res 2021; 6:42-50. [PMID: 33778217 PMCID: PMC7970063 DOI: 10.1016/j.ncrna.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.
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Affiliation(s)
- Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rizkita Rachmi Esyanti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Iriawati
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Ristag Hamida Hanisia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
| | - Rohyani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, West Java, Indonesia
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26
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Díez-Sainz E, Lorente-Cebrián S, Aranaz P, Riezu-Boj JI, Martínez JA, Milagro FI. Potential Mechanisms Linking Food-Derived MicroRNAs, Gut Microbiota and Intestinal Barrier Functions in the Context of Nutrition and Human Health. Front Nutr 2021; 8:586564. [PMID: 33768107 PMCID: PMC7985180 DOI: 10.3389/fnut.2021.586564] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/15/2021] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules from 18 to 24 nucleotides that are produced by prokaryote and eukaryote organisms, which play a crucial role in regulating gene expression through binding to their mRNA targets. MiRNAs have acquired special attention for their potential in cross kingdom communication, notably food-derived microRNAs (xenomiRs), which could have an impact on microorganism and mammal physiology. In this review, we mainly aim to deal with new perspectives on: (1) The mechanism by which food-derived xenomiRs (mainly dietary plant xenomiRs) could be incorporated into humans through diet, in a free form, associated with proteins or encapsulated in exosome-like nanoparticles. (2) The impact of dietary plant-derived miRNAs in modulating gut microbiota composition, which in turn, could regulate intestinal barrier permeability and therefore, affect dietary metabolite, postbiotics or food-derived miRNAs uptake efficiency. Individual gut microbiota signature/composition could be also involved in xenomiR uptake efficiency through several mechanisms such us increasing the bioavailability of exosome-like nanoparticles miRNAs. (3) Gut microbiota dysbiosis has been proposed to contribute to disease development by affecting gut epithelial barrier permeability. For his reason, the availability and uptake of dietary plant xenomiRs might depend, among other factors, on this microbiota-related permeability of the intestine. We hypothesize and critically review that xenomiRs-microbiota interaction, which has been scarcely explored yet, could contribute to explain, at least in part, the current disparity of evidences found dealing with dietary miRNA uptake and function in humans. Furthermore, dietary plant xenomiRs could be involved in the establishment of the multiple gut microenvironments, in which microorganism would adapt in order to optimize the resources and thrive in them. Additionally, a particular xenomiR could preferentially accumulate in a specific region of the gastrointestinal tract and participate in the selection and functions of specific gut microbial communities.
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Affiliation(s)
- Ester Díez-Sainz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Silvia Lorente-Cebrián
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Paula Aranaz
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - José I. Riezu-Boj
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - J. Alfredo Martínez
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
| | - Fermín I. Milagro
- Department of Nutrition, Food Science and Physiology/Center for Nutrition Research, Faculty of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Madrid, Spain
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Santos D, Remans S, Van den Brande S, Vanden Broeck J. RNAs on the Go: Extracellular Transfer in Insects with Promising Prospects for Pest Management. PLANTS (BASEL, SWITZERLAND) 2021; 10:484. [PMID: 33806650 PMCID: PMC8001424 DOI: 10.3390/plants10030484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 01/16/2023]
Abstract
RNA-mediated pathways form an important regulatory layer of myriad biological processes. In the last decade, the potential of RNA molecules to contribute to the control of agricultural pests has not been disregarded, specifically via the RNA interference (RNAi) mechanism. In fact, several proofs-of-concept have been made in this scope. Furthermore, a novel research field regarding extracellular RNAs and RNA-based intercellular/interorganismal communication is booming. In this article, we review key discoveries concerning extracellular RNAs in insects, insect RNA-based cell-to-cell communication, and plant-insect transfer of RNA. In addition, we overview the molecular mechanisms implicated in this form of communication and discuss future biotechnological prospects, namely from the insect pest-control perspective.
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Affiliation(s)
- Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; (S.R.); (S.V.d.B.); (J.V.B.)
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28
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Dunker F, Oberkofler L, Lederer B, Trutzenberg A, Weiberg A. An Arabidopsis downy mildew non-RxLR effector suppresses induced plant cell death to promote biotroph infection. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:718-732. [PMID: 33063828 PMCID: PMC7853606 DOI: 10.1093/jxb/eraa472] [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: 07/06/2020] [Accepted: 10/13/2020] [Indexed: 05/11/2023]
Abstract
Our understanding of obligate biotrophic pathogens is limited by lack of knowledge concerning the molecular function of virulence factors. We established Arabidopsis host-induced gene silencing (HIGS) to explore gene functions of Hyaloperonospora arabidopsidis, including CYSTEINE-RICH PROTEIN (HaCR)1, a potential secreted effector gene of this obligate biotrophic pathogen. HaCR1 HIGS resulted in H. arabidopsidis-induced local plant cell death and reduced pathogen reproduction. We functionally characterized HaCR1 by ectopic expression in Nicotiana benthamiana. HaCR1 was capable of inhibiting effector-triggered plant cell death. Consistent with this, HaCR1 expression in N. benthamiana led to stronger disease symptoms caused by the hemibiotrophic oomycete pathogen Phytophthora capsici, but reduced disease symptoms caused by the necrotrophic fungal pathogen Botrytis cinerea. Expressing HaCR1 in transgenic Arabidopsis confirmed higher susceptibility to H. arabidopsidis and to the bacterial hemibiotrophic pathogen Pseudomonas syringae. Increased H. arabidopsidis infection was in accordance with reduced PATHOGENESIS RELATED (PR)1 induction. Expression of full-length HaCR1 was required for its function, which was lost if the signal peptide was deleted, suggesting its site of action in the plant apoplast. This study provides phytopathological and molecular evidence for the importance of this widespread, but largely unexplored class of non-RxLR effectors in biotrophic oomycetes.
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Affiliation(s)
- Florian Dunker
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Lorenz Oberkofler
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Bernhard Lederer
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Adriana Trutzenberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
| | - Arne Weiberg
- Faculty of Biology, Genetics, Biocenter Martinsried, LMU Munich, Planegg-Martinsried, Germany
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29
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Sanan-Mishra N, Abdul Kader Jailani A, Mandal B, Mukherjee SK. Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology. FRONTIERS IN PLANT SCIENCE 2021; 12:610283. [PMID: 33737942 PMCID: PMC7960677 DOI: 10.3389/fpls.2021.610283] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/18/2021] [Indexed: 05/13/2023]
Abstract
The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant-virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.
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Affiliation(s)
- Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - A. Abdul Kader Jailani
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Bikash Mandal
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sunil K. Mukherjee
- Advanced Center for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sunil K. Mukherjee,
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30
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Abstract
Plant diseases caused by a variety of pathogens can have severe effects on crop plants and even plants in natural ecosystems. Despite many effective conventional approaches to control plant diseases, new, efficacious, environmentally sound and cost-effective approaches are needed, particularly with our increasing human population and the effects on crop production and plant health caused by climate change. RNA interference (RNAi) is a gene regulation and antiviral response mechanism in eukaryotes; transgenic and non transgenic plant-based RNAi approaches have shown great effectiveness and potential to target specific plant pathogens and help control plant diseases, especially when no alternatives are available. Here we discuss ways in which RNAi has been used against different plant pathogens, and some new potential applications for plant disease control.
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31
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C. elegans interprets bacterial non-coding RNAs to learn pathogenic avoidance. Nature 2020; 586:445-451. [PMID: 32908307 PMCID: PMC8547118 DOI: 10.1038/s41586-020-2699-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/16/2020] [Indexed: 11/24/2022]
Abstract
C. elegans must distinguish pathogenic from nutritious bacterial food sources among the many bacteria it is exposed to in its environment1. Here we show that a single exposure to purified small RNAs isolated from pathogenic Pseudomonas aeruginosa (PA14) is sufficient to induce pathogen avoidance, both in the treated animals and in four subsequent generations of progeny. The RNA interference and piRNA pathways, the germline, and the ASI neuron are required for bacterial small RNA-induced avoidance behavior and transgenerational inheritance. A single P. aeruginosa non-coding RNA, P11, is both necessary and sufficient to convey learned avoidance of PA14, and its C. elegans target, maco-1, is required for avoidance. Our results suggest that this ncRNA-dependent mechanism evolved to survey the worm’s microbial environment, use this information to make appropriate behavioral decisions, and pass this information on to its progeny.
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32
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White R, Kumar S, Chow FWN, Robertson E, Hayes KS, Grencis RK, Duque-Correa MA, Buck AH. Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host. Int J Parasitol 2020; 50:719-729. [PMID: 32659276 PMCID: PMC7435682 DOI: 10.1016/j.ijpara.2020.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/07/2023]
Abstract
Extracellular vesicles (EVs) have emerged as a ubiquitous component of helminth excretory-secretory products that can deliver parasite molecules to host cells to elicit immunomodulatory effects. RNAs are one type of cargo molecule that can underpin EV functions, hence there is extensive interest in characterising the RNAs that are present in EVs from different helminth species. Here we outline methods for identifying all of the small RNAs (sRNA) in helminth EVs and address how different methodologies may influence the sRNAs detected. We show that different EV purification methods introduce relatively little variation in the sRNAs that are detected, and that different RNA library preparation methods yielded larger differences. We compared the EV sRNAs in the gastrointestinal nematode Heligmosomoides bakeri with those in EVs from the distantly related gastrointestinal nematode Trichuris muris, and found that many of the sRNAs in both organisms derive from repetitive elements or intergenic regions. However, only in H. bakeri do these RNAs contain a 5' triphosphate, and Guanine (G) starting nucleotide, consistent with their biogenesis by RNA-dependent RNA polymerases (RdRPs). Distinct microRNA (miRNA) families are carried in EVs from each parasite, with H. bakeri EVs specific for miR-71, miR-49, miR-63, miR-259 and miR-240 gene families, and T. muris EVs specific for miR-1, miR-1822 and miR-252, and enriched for miR-59, miR-72 and miR-44 families, with the miR-9, miR-10, miR-80 and let-7 families abundant in both. We found a larger proportion of miRNA reads derive from the mouse host in T. muris EVs, compared with H. bakeri EVs. Our report underscores potential biases in the sRNAs sequenced based on library preparation methods, suggests specific nematode lineages have evolved distinct sRNA synthesis/export pathways, and highlights specific differences in EV miRNAs from H. bakeri and T. muris that may underpin functional adaptation to their host niches.
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Affiliation(s)
- Ruby White
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sujai Kumar
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Franklin Wang-Ngai Chow
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Elaine Robertson
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kelly S Hayes
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research and Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Amy H Buck
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
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Summanwar A, Basu U, Rahman H, Kav NNV. Non-coding RNAs as emerging targets for crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 297:110521. [PMID: 32563460 DOI: 10.1016/j.plantsci.2020.110521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/30/2020] [Accepted: 05/03/2020] [Indexed: 05/23/2023]
Abstract
Food security is affected by climate change, population growth, as well as abiotic and biotic stresses. Conventional and molecular marker assisted breeding and genetic engineering techniques have been employed extensively for improving resistance to biotic stress in crop plants. Advances in next-generation sequencing technologies have permitted the exploration and identification of parts of the genome that extend beyond the regions with protein coding potential. These non-coding regions of the genome are transcribed to generate many types of non-coding RNAs (ncRNAs). These ncRNAs are involved in the regulation of growth, development, and response to stresses at transcriptional and translational levels. ncRNAs, including long ncRNAs (lncRNAs), small RNAs and circular RNAs have been recognized as important regulators of gene expression in plants and have been suggested to play important roles in plant immunity and adaptation to abiotic and biotic stresses. In this article, we have reviewed the current state of knowledge with respect to lncRNAs and their mechanism(s) of action as well as their regulatory functions, specifically within the context of biotic stresses. Additionally, we have provided insights into how our increased knowledge about lncRNAs may be used to improve crop tolerance to these devastating biotic stresses.
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Affiliation(s)
- Aarohi Summanwar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Urmila Basu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
| | - Nat N V Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
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Leung J, Gaudin V. Who Rules the Cell? An Epi-Tale of Histone, DNA, RNA, and the Metabolic Deep State. FRONTIERS IN PLANT SCIENCE 2020; 11:181. [PMID: 32194593 PMCID: PMC7066317 DOI: 10.3389/fpls.2020.00181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/06/2020] [Indexed: 05/23/2023]
Abstract
Epigenetics refers to the mode of inheritance independent of mutational changes in the DNA. Early evidence has revealed methylation, acetylation, and phosphorylation of histones, as well as methylation of DNA as part of the underlying mechanisms. The recent awareness that many human diseases have in fact an epigenetic basis, due to unbalanced diets, has led to a resurgence of interest in how epigenetics might be connected with, or even controlled by, metabolism. The Next-Generation genomic technologies have now unleashed torrents of results exposing a wondrous array of metabolites that are covalently attached to selective sites on histones, DNA and RNA. Metabolites are often cofactors or targets of chromatin-modifying enzymes. Many metabolites themselves can be acetylated or methylated. This indicates that the acetylome and methylome can actually be deep and pervasive networks to ensure the nuclear activities are coordinated with the metabolic status of the cell. The discovery of novel histone marks also raises the question on the types of pathways by which their corresponding metabolites are replenished, how they are corralled to the specific histone residues and how they are recognized. Further, atypical cytosines and uracil have also been found in eukaryotic genomes. Although these new and extensive connections between metabolism and epigenetics have been established mostly in animal models, parallels must exist in plants, inasmuch as many of the basic components of chromatin and its modifying enzymes are conserved. Plants are chemical factories constantly responding to stress. Plants, therefore, should lend themselves readily for identifying new endogenous metabolites that are also modulators of nuclear activities in adapting to stress.
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Affiliation(s)
- Jeffrey Leung
- Institut Jean-Pierre Bourgin, ERL3559 CNRS, INRAE, Versailles, France
| | - Valérie Gaudin
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Université Paris-Saclay, Versailles, France
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Bailey-Serres J, Zhai J, Seki M. The Dynamic Kaleidoscope of RNA Biology in Plants. PLANT PHYSIOLOGY 2020; 182:1-9. [PMID: 31908318 PMCID: PMC6945830 DOI: 10.1104/pp.19.01558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Julia Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jixian Zhai
- Department of Biology and Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
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