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Kim DS, Li Y, Ahn HK, Woods-Tör A, Cevik V, Furzer OJ, Ma W, Tör M, Jones JDG. ATR2 C ala2 from Arabidopsis-infecting downy mildew requires 4 TIR-NLR immune receptors for full recognition. THE NEW PHYTOLOGIST 2024; 243:330-344. [PMID: 38742296 DOI: 10.1111/nph.19790] [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: 03/11/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Arabidopsis Col-0 RPP2A and RPP2B confer recognition of Arabidopsis downy mildew (Hyaloperonospora arabidopsidis [Hpa]) isolate Cala2, but the identity of the recognized ATR2Cala2 effector was unknown. To reveal ATR2Cala2, an F2 population was generated from a cross between Hpa-Cala2 and Hpa-Noks1. We identified ATR2Cala2 as a non-canonical RxLR-type effector that carries a signal peptide, a dEER motif, and WY domains but no RxLR motif. Recognition of ATR2Cala2 and its effector function were verified by biolistic bombardment, ectopic expression and Hpa infection. ATR2Cala2 is recognized in accession Col-0 but not in Ler-0 in which RPP2A and RPP2B are absent. In ATR2Emoy2 and ATR2Noks1 alleles, a frameshift results in an early stop codon. RPP2A and RPP2B are essential for the recognition of ATR2Cala2. Stable and transient expression of ATR2Cala2 under 35S promoter in Arabidopsis and Nicotiana benthamiana enhances disease susceptibility. Two additional Col-0 TIR-NLR (TNL) genes (RPP2C and RPP2D) adjacent to RPP2A and RPP2B are quantitatively required for full resistance to Hpa-Cala2. We compared RPP2 haplotypes in multiple Arabidopsis accessions and showed that all four genes are present in all ATR2Cala2-recognizing accessions.
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Affiliation(s)
- Dae Sung Kim
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan, 430062, China
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Yufei Li
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hee-Kyung Ahn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison Woods-Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
| | - Volkan Cevik
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, BA2 7AY, UK
| | - Oliver J Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mahmut Tör
- Department of Biological Sciences, School of Science and the Environment, University of Worcester, Worcester, WR2 6AJ, UK
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2
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Outram MA, Chen J, Broderick S, Li Z, Aditya S, Tasneem N, Arndell T, Blundell C, Ericsson DJ, Figueroa M, Sperschneider J, Dodds PN, Williams SJ. AvrSr27 is a zinc-bound effector with a modular structure important for immune recognition. THE NEW PHYTOLOGIST 2024; 243:314-329. [PMID: 38730532 DOI: 10.1111/nph.19801] [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: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Effector proteins are central to the success of plant pathogens, while immunity in host plants is driven by receptor-mediated recognition of these effectors. Understanding the molecular details of effector-receptor interactions is key for the engineering of novel immune receptors. Here, we experimentally determined the crystal structure of the Puccinia graminis f. sp. tritici (Pgt) effector AvrSr27, which was not accurately predicted using AlphaFold2. We characterised the role of the conserved cysteine residues in AvrSr27 using in vitro biochemical assays and examined Sr27-mediated recognition using transient expression in Nicotiana spp. and wheat protoplasts. The AvrSr27 structure contains a novel β-strand rich modular fold consisting of two structurally similar domains that bind to Zn2+ ions. The N-terminal domain of AvrSr27 is sufficient for interaction with Sr27 and triggering cell death. We identified two Pgt proteins structurally related to AvrSr27 but with low sequence identity that can also associate with Sr27, albeit more weakly. Though only the full-length proteins, trigger Sr27-dependent cell death in transient expression systems. Collectively, our findings have important implications for utilising protein prediction platforms for effector proteins, and those embarking on bespoke engineering of immunity receptors as solutions to plant disease.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Sean Broderick
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Zhao Li
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Shouvik Aditya
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nuren Tasneem
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Taj Arndell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Cheryl Blundell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3186, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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3
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Liu L, Li J, Wang Z, Zhou H, Wang Y, Qin W, Duan H, Zhao H, Ge X. Suppression of plant immunity by Verticillium dahliae effector Vd6317 through AtNAC53 association. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38924284 DOI: 10.1111/tpj.16883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Verticillium dahliae, a soil-borne fungal pathogen, compromises host innate immunity by secreting a plethora of effectors, thereby facilitating host colonization and causing substantial yield and quality losses. The mechanisms underlying the modulation of cotton immunity by V. dahliae effectors are predominantly unexplored. In this study, we identified that the V. dahliae effector Vd6317 inhibits plant cell death triggered by Vd424Y and enhances PVX viral infection in Nicotiana benthamiana. Attenuation of Vd6317 significantly decreased the virulence of V. dahliae, whereas ectopic expression of Vd6317 in Arabidopsis and cotton enhanced susceptibility to V. dahliae infection, underscoring Vd6317's critical role in pathogenicity. We observed that Vd6317 targeted the Arabidopsis immune regulator AtNAC53, thereby impeding its transcriptional activity on the defense-associated gene AtUGT74E2. Arabidopsis nac53 and ugt74e2 mutants exhibited heightened sensitivity to V. dahliae compared to wild-type plants. A mutation at the conserved residue 193L of Vd6317 abrogated its interaction with AtNAC53 and reduced the virulence of V. dahliae, which was partially attributable to a reduction in Vd6317 protein stability. Our findings unveil a hitherto unrecognized regulatory mechanism by which the V. dahliae effector Vd6317 directly inhibits the plant transcription factor AtNAC53 activity to suppress the expression of AtUGT74E2 and plant defense.
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Affiliation(s)
- Lisen Liu
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jianing Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaohan Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Haodan Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenqiang Qin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Hongying Duan
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
| | - Hang Zhao
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xiaoyang Ge
- Henan Normal University Research Base of National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Xinxiang, 453000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
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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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5
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Padilla-Padilla EA, De la Rosa C, Aragón W, Ávila-Sandoval AK, Torres M, Dorantes-Acosta AE, Arteaga-Vázquez MA, Formey D, Serrano M. Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction. PLoS One 2024; 19:e0304790. [PMID: 38875250 PMCID: PMC11178217 DOI: 10.1371/journal.pone.0304790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/19/2024] [Indexed: 06/16/2024] Open
Abstract
In plants, small RNAs (sRNAs), mainly microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been described as key regulators of plant development, growth, and abiotic and biotic responses. Despite reports indicating the involvement of certain sRNAs in regulating the interaction between Botrytis cinerea (a major necrotrophic fungal phytopathogen) and host plants, there remains a lack of analysis regarding the potential regulatory roles of plant sRNAs during early stages of the interaction despite early immune responses observed then during infection. We present the first transcriptome-wide analysis of small RNA expression on the early interaction between the necrotrophic fungus Botrytis cinerea and the model plant Arabidopsis thaliana. We found that evolutionary conserved A. thaliana miRNAs were the sRNAs that accumulated the most in the presence of B. cinerea. The upregulation of miR167, miR159 and miR319 was of particular interest because these, together with their target transcripts, are involved in the fine regulation of the plant hormone signaling pathways. We also describe that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 loci, as well as secondary siRNAs derived from these loci, is upregulated in response to B. cinerea. Thus, at an early stage of the interaction there are transcriptional changes of sRNA-guided silencing pathway genes and of a subset of sRNAs that targeted genes from the PPR gene superfamily, and these may be important mechanisms regulating the interaction between A. thaliana and B. cinerea. This work provides the basis for a better understanding of the regulation mediated by sRNAs during early B. cinerea-plant interaction and may help in the development of more effective strategies for its control.
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Affiliation(s)
- Emir Alejandro Padilla-Padilla
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Ciudad Universitaria, Coyoacán, Ciudad de México
| | - Carlos De la Rosa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Wendy Aragón
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Instituto de Biociencias, Universidad Autónoma de Chiapas, Chiapas, México
| | - Ana Karen Ávila-Sandoval
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Torres
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ana Elena Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Mario A Arteaga-Vázquez
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Veracruz, México
| | - Damien Formey
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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6
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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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7
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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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8
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Ledford WC, Silvestri A, Fiorilli V, Roth R, Rubio-Somoza I, Lanfranco L. A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2024; 242:1534-1544. [PMID: 37985403 DOI: 10.1111/nph.19394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.
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Affiliation(s)
- William Conrad Ledford
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Alessandro Silvestri
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08001, Spain
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
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9
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Zeng B, Li Y, Xia J, Xiao Y, Khan N, Jiang B, Liang Y, Duan L. Micro Trojan horses: Engineering extracellular vesicles crossing biological barriers for drug delivery. Bioeng Transl Med 2024; 9:e10623. [PMID: 38435823 PMCID: PMC10905561 DOI: 10.1002/btm2.10623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 03/05/2024] Open
Abstract
The biological barriers of the body, such as the blood-brain, placental, intestinal, skin, and air-blood, protect against invading viruses and bacteria while providing necessary physical support. However, these barriers also hinder the delivery of drugs to target tissues, reducing their therapeutic efficacy. Extracellular vesicles (EVs), nanostructures with a diameter ranging from 30 nm to 10 μm secreted by cells, offer a potential solution to this challenge. These natural vesicles can effectively pass through various biological barriers, facilitating intercellular communication. As a result, artificially engineered EVs that mimic or are superior to the natural ones have emerged as a promising drug delivery vehicle, capable of delivering drugs to almost any body part to treat various diseases. This review first provides an overview of the formation and cross-species uptake of natural EVs from different organisms, including animals, plants, and bacteria. Later, it explores the current clinical applications, perspectives, and challenges associated with using engineered EVs as a drug delivery platform. Finally, it aims to inspire further research to help bioengineered EVs effectively cross biological barriers to treat diseases.
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Affiliation(s)
- Bin Zeng
- Graduate SchoolGuangxi University of Chinese MedicineNanningGuangxiChina
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Artificial Intelligence Biomedical Innovation Platform, Shenzhen Second People's Hospitalthe First Affiliated Hospital of Shenzhen UniversityShenzhenGuangdongChina
| | - Ying Li
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Artificial Intelligence Biomedical Innovation Platform, Shenzhen Second People's Hospitalthe First Affiliated Hospital of Shenzhen UniversityShenzhenGuangdongChina
| | - Jiang Xia
- Department of ChemistryThe Chinese University of Hong Kong, ShatinHong Kong SARChina
| | - Yin Xiao
- School of Medicine and Dentistry & Menzies Health Institute Queensland, SouthportGold CoastQueenslandAustralia
| | - Nawaz Khan
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Artificial Intelligence Biomedical Innovation Platform, Shenzhen Second People's Hospitalthe First Affiliated Hospital of Shenzhen UniversityShenzhenGuangdongChina
| | - Bin Jiang
- Graduate SchoolGuangxi University of Chinese MedicineNanningGuangxiChina
- R&D Division, Eureka Biotech Inc, PhiladelphiaPennsylvaniaUSA
| | - Yujie Liang
- Department of Child and Adolescent Psychiatry, Shenzhen Kangning HospitalShenzhen Mental Health Center, Shenzhen Key Laboratory for Psychological Healthcare and Shenzhen Institute of Mental HealthShenzhenGuangdongChina
| | - Li Duan
- Graduate SchoolGuangxi University of Chinese MedicineNanningGuangxiChina
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Artificial Intelligence Biomedical Innovation Platform, Shenzhen Second People's Hospitalthe First Affiliated Hospital of Shenzhen UniversityShenzhenGuangdongChina
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10
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Septiani P, Pramesti Y, Ningsih DU, Pancaningtyas S, Meitha K. Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease. Sci Rep 2024; 14:3272. [PMID: 38332251 PMCID: PMC10853554 DOI: 10.1038/s41598-024-53685-x] [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: 07/24/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defence genes. The objective of this study is to identify differentially expressed miRNAs in black pod-resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao's defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.
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Affiliation(s)
- Popi Septiani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Yonadita Pramesti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Devi Ulfa Ningsih
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Sulistyani Pancaningtyas
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jl. PB. Sudirman 90, Jember, 68118, Indonesia
| | - Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia.
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11
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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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12
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Imparato M, Maione A, Buonanno A, Gesuele R, Gallucci N, Corsaro MM, Paduano L, Casillo A, Guida M, Galdiero E, de Alteriis E. Extracellular Vesicles from a Biofilm of a Clinical Isolate of Candida albicans Negatively Impact on Klebsiella pneumoniae Adherence and Biofilm Formation. Antibiotics (Basel) 2024; 13:80. [PMID: 38247639 PMCID: PMC10812662 DOI: 10.3390/antibiotics13010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024] Open
Abstract
The opportunistic human fungal pathogen Candida albicans produces and releases into the surrounding medium extracellular vesicles (EVs), which are involved in some processes as communication between fungal cells and host-pathogen interactions during infection. Here, we have conducted the isolation of EVs produced by a clinical isolate of C. albicans during biofilm formation and proved their effect towards the ability of the Gram-negative bacterial pathogen Klebsiella pneumoniae to adhere to HaCaT cells and form a biofilm in vitro. The results represent the first evidence of an antagonistic action of fungal EVs against bacteria.
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Affiliation(s)
- Marianna Imparato
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
| | - Angela Maione
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
| | - Annalisa Buonanno
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
| | - Renato Gesuele
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
| | - Noemi Gallucci
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy; (N.G.); (M.M.C.); (L.P.); (A.C.)
| | - Maria Michela Corsaro
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy; (N.G.); (M.M.C.); (L.P.); (A.C.)
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy; (N.G.); (M.M.C.); (L.P.); (A.C.)
| | - Angela Casillo
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy; (N.G.); (M.M.C.); (L.P.); (A.C.)
| | - Marco Guida
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
- National Biodiversity Future Center (NBFC), 90133 Palermo, Italy
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), 80055 Portici, Italy
| | - Emilia Galdiero
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
- Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), 80055 Portici, Italy
| | - Elisabetta de Alteriis
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy; (M.I.); (A.M.); (A.B.); (R.G.); (M.G.); (E.d.A.)
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13
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Jian Y, Gong D, Wang Z, Liu L, He J, Han X, Tsuda K. How plants manage pathogen infection. EMBO Rep 2024; 25:31-44. [PMID: 38177909 PMCID: PMC10897293 DOI: 10.1038/s44319-023-00023-3] [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: 09/28/2023] [Revised: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
To combat microbial pathogens, plants have evolved specific immune responses that can be divided into three essential steps: microbial recognition by immune receptors, signal transduction within plant cells, and immune execution directly suppressing pathogens. During the past three decades, many plant immune receptors and signaling components and their mode of action have been revealed, markedly advancing our understanding of the first two steps. Activation of immune signaling results in physical and chemical actions that actually stop pathogen infection. Nevertheless, this third step of plant immunity is under explored. In addition to immune execution by plants, recent evidence suggests that the plant microbiota, which is considered an additional layer of the plant immune system, also plays a critical role in direct pathogen suppression. In this review, we summarize the current understanding of how plant immunity as well as microbiota control pathogen growth and behavior and highlight outstanding questions that need to be answered.
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Affiliation(s)
- Yinan Jian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhe Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Lijun Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Jingjing He
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Xiaowei Han
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Kenichi Tsuda
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
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14
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Ambrosone A, Barbulova A, Cappetta E, Cillo F, De Palma M, Ruocco M, Pocsfalvi G. Plant Extracellular Vesicles: Current Landscape and Future Directions. PLANTS (BASEL, SWITZERLAND) 2023; 12:4141. [PMID: 38140468 PMCID: PMC10747359 DOI: 10.3390/plants12244141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/24/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023]
Abstract
Plant cells secrete membrane-enclosed micrometer- and nanometer-sized vesicles that, similarly to the extracellular vesicles (EVs) released by mammalian or bacterial cells, carry a complex molecular cargo of proteins, nucleic acids, lipids, and primary and secondary metabolites. While it is technically complicated to isolate EVs from whole plants or their tissues, in vitro plant cell cultures provide excellent model systems for their study. Plant EVs have been isolated from the conditioned culture media of plant cell, pollen, hairy root, and protoplast cultures, and recent studies have gathered important structural and biological data that provide a framework to decipher their physiological roles and unveil previously unacknowledged links to their diverse biological functions. The primary function of plant EVs seems to be in the secretion that underlies cell growth and morphogenesis, cell wall composition, and cell-cell communication processes. Besides their physiological functions, plant EVs may participate in defence mechanisms against different plant pathogens, including fungi, viruses, and bacteria. Whereas edible and medicinal-plant-derived nanovesicles isolated from homogenised plant materials ex vivo are widely studied and exploited, today, plant EV research is still in its infancy. This review, for the first time, highlights the different in vitro sources that have been used to isolate plant EVs, together with the structural and biological studies that investigate the molecular cargo, and pinpoints the possible role of plant EVs as mediators in plant-pathogen interactions, which may contribute to opening up new scenarios for agricultural applications, biotechnology, and innovative strategies for plant disease management.
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Affiliation(s)
- Alfredo Ambrosone
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (A.A.); (E.C.)
| | - Ani Barbulova
- Institute of Biosciences and BioResources (IBBR), Research Division (R.D.) Naples, National Research Council of Italy (CNR), 80131 Naples, Italy;
| | - Elisa Cappetta
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy; (A.A.); (E.C.)
| | - Fabrizio Cillo
- Institute for Sustainable Plant Protection, Research Division (R.D.) Bari, National Research Council of Italy (CNR), 70126 Bari, Italy;
| | - Monica De Palma
- Institute of Biosciences and BioResources (IBBR), Research Division (R.D.) Portici, National Research Council of Italy (CNR), 80055 Portici, Italy;
| | - Michelina Ruocco
- Institute for Sustainable Plant Protection, Research Division (R.D.) Portici, National Research Council of Italy (CNR), 80055 Portici, Italy;
| | - Gabriella Pocsfalvi
- Institute of Biosciences and BioResources (IBBR), Research Division (R.D.) Naples, National Research Council of Italy (CNR), 80131 Naples, Italy;
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15
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Liu T, Xu LG, Duan CG. The trans-kingdom communication of noncoding RNAs in plant-environment interactions. THE PLANT GENOME 2023; 16:e20289. [PMID: 36444889 DOI: 10.1002/tpg2.20289] [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: 07/06/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
As conserved regulatory agents, noncoding RNAs (ncRNAs) have an important impact on many aspects of plant life, including growth, development, and environmental response. Noncoding RNAs can travel through not only plasmodesma and phloem but also intercellular barriers to regulate distinct processes. Increasing evidence shows that the intercellular trans-kingdom transmission of ncRNAs is able to modulate many important interactions between plants and other organisms, such as plant response to pathogen attack, the symbiosis between legume plants and rhizobia and the interactions with parasitic plants. In these interactions, plant ncRNAs are believed to be sorted into extracellular vesicles (EVs) or other nonvesicular vehicles to pass through cell barriers and trigger trans-kingdom RNA interference (RNAi) in recipient cells from different species. There is evidence that the features of extracellular RNAs and associated RNA-binding proteins (RBPs) play a role in defining the RNAs to retain in cell or secrete outside cells. Despite the few reports about RNA secretion pathway in plants, the export of extracellular ncRNAs is orchestrated by a series of pathways in plants. The identification and functional analysis of mobile small RNAs (sRNAs) are attracting increasing attention in recent years. In this review, we discuss recent advances in our understanding of the function, sorting, transport, and regulation of plant extracellular ncRNAs.
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Affiliation(s)
- Ting Liu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Univ. of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu-Gen Xu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Univ. of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Univ. of the Chinese Academy of Sciences, Beijing, 100049, China
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16
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Su C, Li Y, Liu S, Feng H, Wang J, Yan S. Star polymer soil delivery nanoplatform for applying biological agents in the field to control plant rhizosphere diseases. J Control Release 2023; 364:406-419. [PMID: 37924956 DOI: 10.1016/j.jconrel.2023.10.053] [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: 08/13/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
As the main cause of destructive plant diseases, pathogenic oomycete in plant rhizosphere brings about enormous losses to agricultural production. Although chemical pesticides are still one of the most important prevention and control methods for phytopathogens, the usage of chemical pesticides was limited by the 3R (resistance, residue, and rampant) problem. In the early stage of our research, analysis and comparison of the metabolome of resistance to Phytophthora nicotianae and common strain suggested that naringenin might be a highly efficient potential biogenic antimicrobial agent to prevent and control soil rhizosphere diseases. Unfortunately, the bioactivity and absorption capacity of active ingredients in the environment made it unsuitable for field application; thus, for efficient field application of naringenin, the 24 nm-sized naringenin-loaded nano-star-shaped polymerized (NSPs) were prepared with good loading efficiency 37.3% for naringenin. The soil mobility test indicated that NSPs could effectively reduce the adsorption of active ingredients and enhance the mobility of active ingredients in soil. The bacteriostatic test proved that these NSPs had better antimicrobial activity than the naringenin used alone and could efficiently induce the expression of plant resistance phenylpropanoid compounds. Finally, pot and field experiments showed improved control efficiency of NSPs 41% loaded with naringenin. Transcriptome analysis found that a large number of energy-related genes were downregulated in NSPs nematodes, suggesting that disturbed energy-related genes might lead to the disturbance of energy synthesis and metabolism. Naringenin-loaded nano-carriers were used to prevent and control plant disease-causing pathogens in the rhizosphere, which is of great significance to improve the prevention and control effect and reduce the environmental load of these anti-pathogenic agents.
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Affiliation(s)
- Chenyu Su
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yiting Li
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Shanshan Liu
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Hui Feng
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jie Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling & Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Shuo Yan
- College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
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17
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Tao Y, Li C, Liu Y, Xu C, Okabe S, Matsushita N, Lian C. Identification of microRNAs involved in ectomycorrhizal formation in Populus tomentosa. TREE PHYSIOLOGY 2023; 43:2012-2030. [PMID: 37777191 DOI: 10.1093/treephys/tpad102] [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: 01/29/2023] [Accepted: 08/17/2023] [Indexed: 10/02/2023]
Abstract
The majority of woody plants are able to form ectomycorrhizal (ECM) symbioses with fungi. During symbiotic development, plants undergo a complex re-programming process involving a series of physiological and morphological changes. MicroRNAs (miRNAs) are important components of the regulatory network underlying symbiotic development. To elucidate the mechanisms of miRNAs and miRNA-mediated mRNA cleavage during symbiotic development, we conducted high-throughput sequencing of small RNAs and degradome tags from roots of Populus tomentosa inoculated with Cenococcum geophilum. This process led to the annotation of 51 differentially expressed miRNAs between non-mycorrhizal and mycorrhizal roots of P. tomentosa, including 13 novel miRNAs. Increased or decreased accumulation of several novel and conserved miRNAs in ECM roots, including miR162, miR164, miR319, miR396, miR397, miR398, novel-miR44 and novel-miR47, suggests essential roles for these miRNAs in ECM formation. The degradome analysis identified root transcripts as miRNA-mediated mRNA cleavage targets, which was confirmed using real-time quantitative PCR. Several of the identified miRNAs and corresponding targets are involved in arbuscular mycorrhizal symbioses. In summary, increased or decreased accumulation of specific miRNAs and miRNA-mediated cleavage of symbiosis-related genes indicate that miRNAs play important roles in the regulatory network underlying symbiotic development.
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Affiliation(s)
- Yuanxun Tao
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Chaofeng Li
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
- Maize Research Institute, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Ying Liu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei District, Chongqing, 400715 China
| | - Shin Okabe
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
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18
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Fu K, Wu Q, Jiang N, Hu S, Ye H, Hu Y, Li L, Li T, Sun Z. Identification and Expressional Analysis of siRNAs Responsive to Fusarium graminearum Infection in Wheat. Int J Mol Sci 2023; 24:16005. [PMID: 37958988 PMCID: PMC10650599 DOI: 10.3390/ijms242116005] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
The outbreak of Fusarium head blight (FHB) poses a serious threat to wheat production as it leads to both significant yield losses and accumulation of several mycotoxins including deoxynivalenol (DON) in the grains, which are harmful to human and livestock. To date, hundreds of FHB-resistance-related quantitative trait loci (QTLs) have been reported, but only a few of them have been cloned and used for breeding. Small interfering RNAs (siRNA) have been reported in plants to mediate host defense against pathogens, but they have rarely been reported in wheat-FHB interaction. In order to identify the key siRNAs that can potentially be used in the improvement of resistance to FHB, siRNAs from the spikes of an FHB-resistant variety Sumai 3 and an FHB-susceptible variety of Chinese Spring (CS) were sequenced after F. graminearum infection and mock inoculation, respectively. The expression patterns of the siRNAs of interest were analyzed. A total of 4019 siRNAs of high-confidence were identified, with 131 being CS-specific, 309 Sumai 3-specific and 3071 being common in both varieties. More than 87% of these siRNAs were 24 nt in length. An overall down-regulation trend was found for siRNAs in the spikes of both varieties after being infected with F. graminearum. The expression patterns for Triticum aestivum Dicer-like 3 (TaDCL3) that synthesizes 24 nt siRNAs were validated by qRT-PCR, which were positively correlated with those of the siRNAs. A total of 85% of the differentially expressed genes putatively targeted by the siRNAs were significantly up-regulated after infection, showing a negative correlation with the overall down-regulated expression of siRNAs. Interestingly, the majority of the up-regulated genes are annotated as disease resistance. These results suggested that the inhibition of siRNA by F. graminearum up-regulated the disease resistance genes, which were putatively suppressed by siRNAs through RNA-directed DNA methylation (RdDM). Consequently, the resistant capability to F. graminearum infection was enhanced. This study provides novel clues for investigating the function of siRNA in wheat-F. graminearum interaction.
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Affiliation(s)
- Kai Fu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qianhui Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Ning Jiang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Sijia Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Ye
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yi Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Lei Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tao Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zhengxi Sun
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou 225009, China; (K.F.); (Q.W.); (N.J.); (S.H.); (H.Y.); (Y.H.); (L.L.); (T.L.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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19
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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20
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Qiao SA, Gao Z, Roth R. A perspective on cross-kingdom RNA interference in mutualistic symbioses. THE NEW PHYTOLOGIST 2023; 240:68-79. [PMID: 37452489 PMCID: PMC10952549 DOI: 10.1111/nph.19122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/24/2023] [Indexed: 07/18/2023]
Abstract
RNA interference (RNAi) is arguably one of the more versatile mechanisms in cell biology, facilitating the fine regulation of gene expression and protection against mobile genomic elements, whilst also constituting a key aspect of induced plant immunity. More recently, the use of this mechanism to regulate gene expression in heterospecific partners - cross-kingdom RNAi (ckRNAi) - has been shown to form a critical part of bidirectional interactions between hosts and endosymbionts, regulating the interplay between microbial infection mechanisms and host immunity. Here, we review the current understanding of ckRNAi as it relates to interactions between plants and their pathogenic and mutualistic endosymbionts, with particular emphasis on evidence in support of ckRNAi in the arbuscular mycorrhizal symbiosis.
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Affiliation(s)
- Serena A Qiao
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Zongyu Gao
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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21
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Parperides E, El Mounadi K, Garcia‐Ruiz H. Induction and suppression of gene silencing in plants by nonviral microbes. MOLECULAR PLANT PATHOLOGY 2023; 24:1347-1356. [PMID: 37438989 PMCID: PMC10502822 DOI: 10.1111/mpp.13362] [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: 04/18/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 07/14/2023]
Abstract
Gene silencing is a conserved mechanism in eukaryotes that dynamically regulates gene expression. In plants, gene silencing is critical for development and for maintenance of genome integrity. Additionally, it is a critical component of antiviral defence in plants, nematodes, insects, and fungi. To overcome gene silencing, viruses encode effectors that suppress gene silencing. A growing body of evidence shows that gene silencing and suppression of silencing are also used by plants during their interaction with nonviral pathogens such as fungi, oomycetes, and bacteria. Plant-pathogen interactions involve trans-kingdom movement of small RNAs into the pathogens to alter the function of genes required for their development and virulence. In turn, plant-associated pathogenic and nonpathogenic microbes also produce small RNAs that move trans-kingdom into host plants to disrupt pathogen defence through silencing of plant genes. The mechanisms by which these small RNAs move from the microbe to the plant remain poorly understood. In this review, we examine the roles of trans-kingdom small RNAs and silencing suppressors produced by nonviral microbes in inducing and suppressing gene silencing in plants. The emerging model is that gene silencing and suppression of silencing play critical roles in the interactions between plants and their associated nonviral microbes.
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Affiliation(s)
- Eric Parperides
- Department of Plant Pathology and Nebraska Center for VirologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Kaoutar El Mounadi
- Department of BiologyKutztown University of PennsylvaniaKutztownPennsylvaniaUSA
| | - Hernan Garcia‐Ruiz
- Department of Plant Pathology and Nebraska Center for VirologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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22
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Andika IB, Tian M, Bian R, Cao X, Luo M, Kondo H, Sun L. Cross-Kingdom Interactions Between Plant and Fungal Viruses. Annu Rev Virol 2023; 10:119-138. [PMID: 37406341 DOI: 10.1146/annurev-virology-111821-122539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The large genetic and structural divergences between plants and fungi may hinder the transmission of viruses between these two kingdoms to some extent. However, recent accumulating evidence from virus phylogenetic analyses and the discovery of naturally occurring virus cross-infection suggest the occurrence of past and current transmissions of viruses between plants and plant-associated fungi. Moreover, artificial virus inoculation experiments showed that diverse plant viruses can multiply in fungi and vice versa. Thus, virus cross-infection between plants and fungi may play an important role in the spread, emergence, and evolution of both plant and fungal viruses and facilitate the interaction between them. In this review, we summarize current knowledge related to cross-kingdom virus infection in plants and fungi and further discuss the relevance of this new virological topic in the context of understanding virus spread and transmission in nature as well as developing control strategies for crop plant diseases.
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Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Mengyuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Ruiling Bian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Ming Luo
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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23
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Forte FP, Malinowska M, Nagy I, Schmid J, Dijkwel P, Hume DE, Johnson RD, Simpson WR, Asp T. Methylome changes in Lolium perenne associated with long-term colonisation by the endophytic fungus Epichloë sp. LpTG-3 strain AR37. FRONTIERS IN PLANT SCIENCE 2023; 14:1258100. [PMID: 37810388 PMCID: PMC10557135 DOI: 10.3389/fpls.2023.1258100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023]
Abstract
Epichloë spp. often form mutualistic interactions with cool-season grasses, such as Lolium perenne. However, the molecular mechanisms underlying this interaction remain poorly understood. In this study, we employed reduced representation bisulfite sequencing method (epiGBS) to investigate the impact of the Epichloë sp. LpTG-3 strain AR37 on the methylome of L. perenne across multiple grass generations and under drought stress conditions. Our results showed that the presence of the endophyte leads to a decrease in DNA methylation across genomic features, with differentially methylated regions primarily located in intergenic regions and CHH contexts. The presence of the endophyte was consistently associated with hypomethylation in plants across generations. This research sheds new light on the molecular mechanisms governing the mutualistic interaction between Epichloë sp. LpTG-3 strain AR37 and L. perenne. It underscores the role of methylation changes associated with endophyte infection and suggests that the observed global DNA hypomethylation in L. perenne may be influenced by factors such as the duration of the endophyte-plant association and the accumulation of genetic and epigenetic changes over time.
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Affiliation(s)
- Flavia Pilar Forte
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Marta Malinowska
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
| | - Jan Schmid
- Ferguson Street Laboratories, Palmerston North, New Zealand
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Paul Dijkwel
- Ferguson Street Laboratories, Palmerston North, New Zealand
| | - David E. Hume
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Wayne R. Simpson
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Torben Asp
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Aarhus, Denmark
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24
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Quesada-Ocampo LM, Parada-Rojas CH, Hansen Z, Vogel G, Smart C, Hausbeck MK, Carmo RM, Huitema E, Naegele RP, Kousik CS, Tandy P, Lamour K. Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:185-208. [PMID: 37257056 DOI: 10.1146/annurev-phyto-021622-103801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.
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Affiliation(s)
- L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - C H Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - Z Hansen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Vogel
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - C Smart
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - M K Hausbeck
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - R M Carmo
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
| | - E Huitema
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - R P Naegele
- Sugarbeet and Bean Research Unit, USDA, ARS, East Lansing, Michigan, USA
| | - C S Kousik
- US Vegetable Laboratory, USDA, ARS, Charleston, South Carolina, USA
| | - P Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
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25
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Singh S, Hu X, Dixelius C. Dynamics of nucleic acid mobility. Genetics 2023; 225:iyad132. [PMID: 37491977 PMCID: PMC10471207 DOI: 10.1093/genetics/iyad132] [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: 04/18/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023] Open
Abstract
Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species.
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Affiliation(s)
- Shailja Singh
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Xinyi Hu
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnéan Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, SE-75007, Sweden
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26
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Zhu J, Qiao Q, Sun Y, Xu Y, Shu H, Zhang Z, Liu F, Wang H, Ye W, Dong S, Wang Y, Ma Z, Wang Y. Divergent sequences of tetraspanins enable plants to specifically recognize microbe-derived extracellular vesicles. Nat Commun 2023; 14:4877. [PMID: 37573360 PMCID: PMC10423219 DOI: 10.1038/s41467-023-40623-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 08/03/2023] [Indexed: 08/14/2023] Open
Abstract
Extracellular vesicles (EVs) are important for cell-to-cell communication in animals. EVs also play important roles in plant-microbe interactions, but the underlying mechanisms remain elusive. Here, proteomic analyses of EVs from the soybean (Glycine max) root rot pathogen Phytophthora sojae identify the tetraspanin family proteins PsTET1 and PsTET3, which are recognized by Nicotiana benthamiana to trigger plant immune responses. Both proteins are required for the full virulence of P. sojae. The large extracellular loop (EC2) of PsTET3 is the key region recognized by N. benthamiana and soybean cells in a plant receptor-like kinase NbSERK3a/b dependent manner. TET proteins from oomycete and fungal plant pathogens are recognized by N. benthamiana thus inducing immune responses, whereas plant-derived TET proteins are not due to the sequence divergence of sixteen amino acids at the C-terminal of EC2. This feature allows plants to distinguish self and non-self EVs to trigger active defense responses against pathogenic eukaryotes.
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Affiliation(s)
- Jinyi Zhu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qian Qiao
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yujing Sun
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yuanpeng Xu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Haidong Shu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Fan Liu
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Haonan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhenchuan Ma
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, 210095, Nanjing, China.
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), 210095, Nanjing, China.
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, 210095, Nanjing, China.
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27
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Jiang C, Li Z, Zheng L, Yu Y, Niu D. Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions. MOLECULAR PLANT PATHOLOGY 2023; 24:999-1013. [PMID: 37026481 PMCID: PMC10346379 DOI: 10.1111/mpp.13329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
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Affiliation(s)
- Chun‐Hao Jiang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zi‐Jie Li
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Li‐Yu Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Yi‐Yang Yu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dong‐Dong Niu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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28
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Li H, Wang J, Kuan TA, Tang B, Feng L, Wang J, Cheng Z, Skłenar J, Derbyshire P, Hulin M, Li Y, Zhai Y, Hou Y, Menke FLH, Wang Y, Ma W. Pathogen protein modularity enables elaborate mimicry of a host phosphatase. Cell 2023:S0092-8674(23)00640-2. [PMID: 37369204 DOI: 10.1016/j.cell.2023.05.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/18/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023]
Abstract
Pathogens produce diverse effector proteins to manipulate host cellular processes. However, how functional diversity is generated in an effector repertoire is poorly understood. Many effectors in the devastating plant pathogen Phytophthora contain tandem repeats of the "(L)WY" motif, which are structurally conserved but variable in sequences. Here, we discovered a functional module formed by a specific (L)WY-LWY combination in multiple Phytophthora effectors, which efficiently recruits the serine/threonine protein phosphatase 2A (PP2A) core enzyme in plant hosts. Crystal structure of an effector-PP2A complex shows that the (L)WY-LWY module enables hijacking of the host PP2A core enzyme to form functional holoenzymes. While sharing the PP2A-interacting module at the amino terminus, these effectors possess divergent C-terminal LWY units and regulate distinct sets of phosphoproteins in the host. Our results highlight the appropriation of an essential host phosphatase through molecular mimicry by pathogens and diversification promoted by protein modularity in an effector repertoire.
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Affiliation(s)
- Hui Li
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jinlong Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tung Ariel Kuan
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Bozeng Tang
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Li Feng
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jiuyu Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi Cheng
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jan Skłenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul Derbyshire
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Michelle Hulin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yufei Li
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yi Zhai
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Yingnan Hou
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; School of Agriculture & Biology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Yanli Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenbo Ma
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.
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Kusch S, Singh M, Thieron H, Spanu PD, Panstruga R. Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction. MOLECULAR PLANT PATHOLOGY 2023; 24:570-587. [PMID: 36917011 DOI: 10.1111/mpp.13324] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 05/18/2023]
Abstract
The establishment of host-microbe interactions requires molecular communication between both partners, which may involve the mutual transfer of noncoding small RNAs. Previous evidence suggests that this is also true for powdery mildew disease in barley, which is caused by the fungal pathogen Blumeria hordei. However, previous studies lacked spatial resolution regarding the accumulation of small RNAs upon host infection by B. hordei. Here, we analysed site-specific small RNA repertoires in the context of the barley-B. hordei interaction. To this end, we dissected infected leaves into separate fractions representing different sites that are key to the pathogenic process: epiphytic fungal mycelium, infected plant epidermis, isolated haustoria, a vesicle-enriched fraction from infected epidermis, and extracellular vesicles. Unexpectedly, we discovered enrichment of specific 31-33-base 5'-terminal fragments of barley 5.8S ribosomal RNA in extracellular vesicles and infected epidermis, as well as particular B. hordei transfer RNA fragments in haustoria. We describe canonical small RNAs from both the plant host and the fungal pathogen that may confer cross-kingdom RNA interference activity. Interestingly, we found first evidence of phased small interfering RNAs in B. hordei, a feature usually attributed to plants, which may be associated with the posttranscriptional control of fungal coding genes, pseudogenes, and transposable elements. Our data suggest a key and possibly site-specific role for cross-kingdom RNA interference and noncoding RNA fragments in the host-pathogen communication between B. hordei and its host barley.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Mansi Singh
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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30
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Cai Q, Halilovic L, Shi T, Chen A, He B, Wu H, Jin H. Extracellular vesicles: cross-organismal RNA trafficking in plants, microbes, and mammalian cells. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2023; 4:262-282. [PMID: 37575974 PMCID: PMC10419970 DOI: 10.20517/evcna.2023.10] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed nanometer-scale particles that transport biological materials such as RNAs, proteins, and metabolites. EVs have been discovered in nearly all kingdoms of life as a form of cellular communication across different cells and between interacting organisms. EV research has primarily focused on EV-mediated intra-organismal transport in mammals, which has led to the characterization of a plethora of EV contents from diverse cell types with distinct and impactful physiological effects. In contrast, research into EV-mediated transport in plants has focused on inter-organismal interactions between plants and interacting microbes. However, the overall molecular content and functions of plant and microbial EVs remain largely unknown. Recent studies into the plant-pathogen interface have demonstrated that plants produce and secrete EVs that transport small RNAs into pathogen cells to silence virulence-related genes. Plant-interacting microbes such as bacteria and fungi also secrete EVs which transport proteins, metabolites, and potentially RNAs into plant cells to enhance their virulence. This review will focus on recent advances in EV-mediated communications in plant-pathogen interactions compared to the current state of knowledge of mammalian EV capabilities and highlight the role of EVs in cross-kingdom RNA interference.
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Affiliation(s)
- Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430072, Hubei, China
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Ting Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Hubei Hongshan Laboratory, Wuhan 430072, Hubei, China
| | - Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Baoye He
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Huaitong Wu
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92507, United States
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31
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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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32
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Wei X, Li X, Zhang Y, Wang J, Shen S. Advances in the Therapeutic Applications of Plant-Derived Exosomes in the Treatment of Inflammatory Diseases. Biomedicines 2023; 11:1554. [PMID: 37371649 DOI: 10.3390/biomedicines11061554] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/14/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Plant-derived exosomes (PLDEs) are small extracellular vesicles that encapsulate proteins, nucleic acids and lipids, and they are usually involved in intercellular communication and molecular transport in plants. PLDEs are widely used in the therapy of diseases due to their abundance and easy availability. The diverse roles of PLDEs, which include transportation of drugs, acting as biomarkers for diagnosis of diseases and their roles in different therapies, suggest that there is a need to fully understand all the mechanisms involved in order to provide the optimum conditions for their therapeutic use. This review summarizes the biogenesis, components and functions of PLDEs and focuses on their use as therapeutic agents in the treatment of inflammatory diseases. It also explores new ideas for novel approaches in which PLDEs could potentially help patients with inflammatory diseases in the future.
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Affiliation(s)
- Xiaofang Wei
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiuyu Li
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangyuan Academy of Agricultural Sciences, Guangyuan 628017, China
| | - Yuejun Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jian Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shuibao Shen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
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33
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Borniego ML, Innes RW. Extracellular RNA: mechanisms of secretion and potential functions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2389-2404. [PMID: 36609873 PMCID: PMC10082932 DOI: 10.1093/jxb/erac512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/21/2022] [Indexed: 06/06/2023]
Abstract
Extracellular RNA (exRNA) has long been considered as cellular waste that plants can degrade and utilize to recycle nutrients. However, recent findings highlight the need to reconsider the biological significance of RNAs found outside of plant cells. A handful of studies suggest that the exRNA repertoire, which turns out to be an extremely heterogenous group of non-coding RNAs, comprises species as small as a dozen nucleotides to hundreds of nucleotides long. They are found mostly in free form or associated with RNA-binding proteins, while very few are found inside extracellular vesicles (EVs). Despite their low abundance, small RNAs associated with EVs have been a focus of exRNA research due to their putative role in mediating trans-kingdom RNAi. Therefore, non-vesicular exRNAs have remained completely under the radar until very recently. Here we summarize our current knowledge of the RNA species that constitute the extracellular RNAome and discuss mechanisms that could explain the diversity of exRNAs, focusing not only on the potential mechanisms involved in RNA secretion but also on post-release processing of exRNAs. We will also share our thoughts on the putative roles of vesicular and extravesicular exRNAs in plant-pathogen interactions, intercellular communication, and other physiological processes in plants.
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Affiliation(s)
- M Lucía Borniego
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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34
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Holland S, Roth R. Extracellular Vesicles in the Arbuscular Mycorrhizal Symbiosis: Current Understanding and Future Perspectives. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:235-244. [PMID: 36867731 DOI: 10.1094/mpmi-09-22-0189-fi] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The arbuscular mycorrhizal (AM) symbiosis is an ancient and highly conserved mutualism between plant and fungal symbionts, in which a highly specialized membrane-delimited fungal arbuscule acts as the symbiotic interface for nutrient exchange and signaling. As a ubiquitous means of biomolecule transport and intercellular communication, extracellular vesicles (EVs) are likely to play a role in this intimate cross-kingdom symbiosis, yet, there is a lack of research investigating the importance of EVs in AM symbiosis despite known roles in microbial interactions in both animal and plant pathosystems. Clarifying the current understanding of EVs in this symbiosis in light of recent ultrastructural observations is paramount to guiding future investigations in the field, and, to this end, this review summarizes recent research investigating these areas. Namely, this review discusses the available knowledge regarding biogenesis pathways and marker proteins associated with the various plant EV subclasses, EV trafficking pathways during symbiosis, and the endocytic mechanisms implicated in the uptake of these EVs. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Samuel Holland
- Department of Biology, University of Oxford, Oxford OX1 3RB, U.K
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford OX1 3RB, U.K
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35
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Zhu X, Guo L, Zhu R, Zhou X, Zhang J, Li D, He S, Qiao Y. Phytophthora sojae effector PsAvh113 associates with the soybean transcription factor GmDPB to inhibit catalase-mediated immunity. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 36972124 DOI: 10.1111/pbi.14043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Phytophthora species are the most destructive plant pathogens worldwide and the main threat to agricultural and natural ecosystems; however, their pathogenic mechanism remains largely unknown. Here, we show that Avh113 effector is required for the virulence of Phytophthora sojae and is important for development of Phytophthora root and stem rot (PRSR) in soybean (Glycine max). Ectopic expression of PsAvh113 enhanced viral and Phytophthora infection in Nicotiana benthamiana. PsAvh113 directly associated with the soybean transcription factor GmDPB, inducing its degradation by the 26S proteasome. The internal repeat 2 (IR2) motif of PsAvh113 was important for its virulence and interaction with GmDPB, while silencing and overexpression of GmDPB in soybean hairy roots altered the resistance to P. sojae. Upon binding to GmDPB, PsAvh113 decreased the transcription of the downstream gene GmCAT1, which acts as a positive regulator of plant immunity. Furthermore, we revealed that PsAvh113 suppressed the GmCAT1-induced cell death by associating with GmDPB, thereby enhancing plant susceptibility to Phytophthora. Together, our findings reveal a vital role of PsAvh113 in inducing PRSR in soybean and offer a novel insight into the interplay between defence and counter-defence during the P. sojae infection of soybean.
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Affiliation(s)
- Xiaoguo Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ruiqing Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoyi Zhou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianing Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shidan He
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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36
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Qin S, Veloso J, Puccetti G, van Kan JAL. Molecular characterization of cross-kingdom RNA interference in Botrytis cinerea by tomato small RNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1107888. [PMID: 36968352 PMCID: PMC10031073 DOI: 10.3389/fpls.2023.1107888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Previous studies have suggested that plants can modulate gene expression in pathogenic fungi by producing small RNAs (sRNAs) that can be translocated into the fungus and mediate gene silencing, which may interfere with the infection mechanism of the intruder. We sequenced sRNAs and mRNAs in early phases of the Solanum lycopersicum (tomato)-Botrytis cinerea interaction and examined the potential of plant sRNAs to silence their predicted mRNA targets in the fungus. Almost a million unique plant sRNAs were identified that could potentially target 97% of all fungal genes. We selected three fungal genes for detailed RT-qPCR analysis of the correlation between the abundance of specific plant sRNAs and their target mRNAs in the fungus. The fungal Bcspl1 gene, which had been reported to be important for the fungal virulence, showed transient down-regulation around 20 hours post inoculation and contained a unique target site for a single plant sRNA that was present at high levels. In order to study the functionality of this plant sRNA in reducing the Bcspl1 transcript level, we generated a fungal mutant that contained a 5-nucleotide substitution that would abolish the interaction between the transcript and the sRNA without changing the encoded protein sequence. The level of the mutant Bcspl1 transcript showed a transient decrease similar to wild type transcript, indicating that the tomato sRNA was not responsible for the downregulation of the Bcspl1 transcript. The virulence of the Bcspl1 target site mutant was identical to the wild type fungus.
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Affiliation(s)
- Si Qin
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Departamento de Biología Funcional, Escuela Politécnica Superior de Ingeniería, Universidad de Santiago de Compostela, Lugo, Spain
| | - Guido Puccetti
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
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37
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Alternative biological sources for extracellular vesicles production and purification strategies for process scale-up. Biotechnol Adv 2023; 63:108092. [PMID: 36608746 DOI: 10.1016/j.biotechadv.2022.108092] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023]
Abstract
Extracellular vesicles (EVs) are phospholipidic bi-layer enclosed nanoparticles secreted naturally by all cell types. They are attracting increasing attention in the fields of nanomedicine, nutraceutics and cosmetics as biocompatible carriers for drug delivery, with intrinsic properties beneficial to human health. Scientific work now focuses on developing techniques for isolating EVs that can translate into industrial-scale production and meet rigorous clinical requirements. The science of EVs is ongoing, and many pitfalls must be addressed, such as the requirement for standard, reproducible, inexpensive, and Good Manufacturing Practices (GMP) adherent EV processing techniques. Researchers are exploring the use of alternative sources to EVs derived from mammalian cultures, such as plant EVs, as well as the use of bacteria, algae and milk. Regarding the downstream processing of EVs, many alternative techniques to the ultracentrifugation (UC) protocols most commonly used in the laboratory are emerging. In the context of process scale-up, membrane-based processes for isolation and purification of EVs are the most promising, either as stand-alone processes or in combination with chromatographic techniques. This review discusses current trends on EVs source selection and EVs downstream processing techniques, with a focus on plant-derived EVs and membrane-based techniques for EVs enrichment.
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38
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Sun L, Wu X, Diao J, Zhang J. Pathogenesis mechanisms of phytopathogen effectors. WIREs Mech Dis 2023; 15:e1592. [PMID: 36593734 DOI: 10.1002/wsbm.1592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 01/04/2023]
Abstract
Plants commonly face the threat of invasion by a wide variety of pathogens and have developed sophisticated immune mechanisms to defend against infectious diseases. However, successful pathogens have evolved diverse mechanisms to overcome host immunity and cause diseases. Different cell structures and unique cellular organelles carried by plant cells endow plant-specific defense mechanisms, in addition to the common framework of innate immune system shared by both plants and animals. Effectors serve as crucial virulence weapons employed by phytopathogens to disarm the plant immune system and promote infection. Here we summarized the many diverse strategies by which phytopathogen effectors overcome plant defense and prospected future perspectives. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyun Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Diao
- Northeast Forestry University, College of Forestry, Harbin, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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39
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Qin S, Veloso J, Baak M, Boogmans B, Bosman T, Puccetti G, Shi‐Kunne X, Smit S, Grant‐Downton R, Leisen T, Hahn M, van Kan JAL. Molecular characterization reveals no functional evidence for naturally occurring cross-kingdom RNA interference in the early stages of Botrytis cinerea-tomato interaction. MOLECULAR PLANT PATHOLOGY 2023; 24:3-15. [PMID: 36168919 PMCID: PMC9742496 DOI: 10.1111/mpp.13269] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 05/14/2023]
Abstract
Plant immune responses are triggered during the interaction with pathogens. The fungus Botrytis cinerea has previously been reported to use small RNAs (sRNAs) as effector molecules capable of interfering with the host immune response. Conversely, a host plant produces sRNAs that may interfere with the infection mechanism of an intruder. We used high-throughput sequencing to identify sRNAs produced by B. cinerea and Solanum lycopersicum (tomato) during early phases of interaction and to examine the expression of their predicted mRNA targets in the other organism. A total of 7042 B. cinerea sRNAs were predicted to target 3185 mRNAs in tomato. Of the predicted tomato target genes, 163 were indeed transcriptionally down-regulated during the early phase of infection. Several experiments were performed to study a causal relation between the production of B. cinerea sRNAs and the down-regulation of predicted target genes in tomato. We generated B. cinerea mutants in which a transposon region was deleted that is the source of c.10% of the fungal sRNAs. Furthermore, mutants were generated in which both Dicer-like genes (Bcdcl1 and Bcdcl2) were deleted and these displayed a >99% reduction of transposon-derived sRNA production. Neither of these mutants was significantly reduced in virulence on any plant species tested. Our results reveal no evidence for any detectable role of B. cinerea sRNAs in the virulence of the fungus.
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Affiliation(s)
- Si Qin
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Javier Veloso
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- FISAPLANTUniversity of A CoruñaA CoruñaSpain
| | - Mirna Baak
- Bioinformatics GroupWageningen UniversityWageningenNetherlands
| | - Britt Boogmans
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Tim Bosman
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | - Guido Puccetti
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
| | | | - Sandra Smit
- Bioinformatics GroupWageningen UniversityWageningenNetherlands
| | | | - Thomas Leisen
- Department of BiologyUniversity of KaiserslauternKaiserslauternGermany
| | - Matthias Hahn
- Department of BiologyUniversity of KaiserslauternKaiserslauternGermany
| | - Jan A. L. van Kan
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
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40
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Abstract
Time is an often-neglected variable in biological research. Plants respond to biotic and abiotic stressors with a range of chemical signals, but as plants are non-equilibrium systems, single-point measurements often cannot provide sufficient temporal resolution to capture these time-dependent signals. In this article, we critically review the advances in continuous monitoring of chemical signals in living plants under stress. We discuss methods for sustained measurement of the most important chemical species, including ions, organic molecules, inorganic molecules and radicals. We examine analytical and modelling approaches currently used to identify and predict stress in plants. We also explore how the methods discussed can be used for applications beyond a research laboratory, in agricultural settings. Finally, we present the current challenges and future perspectives for the continuous monitoring of chemical signals in plants.
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41
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Maksimov IV, Shein MY, Burkhanova GF. RNA Interference in Plant Protection from Fungal and Oomycete Infection. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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42
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Sun M, Li L, Wang C, Wang L, Lu D, Shen D, Wang J, Jiang C, Cheng L, Pan X, Yang A, Wang Y, Zhu X, Li B, Li Y, Zhang F. Naringenin confers defence against Phytophthora nicotianae through antimicrobial activity and induction of pathogen resistance in tobacco. MOLECULAR PLANT PATHOLOGY 2022; 23:1737-1750. [PMID: 36094814 PMCID: PMC9644278 DOI: 10.1111/mpp.13255] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Tobacco black shank caused by Phytophthora nicotianae is a serious disease in tobacco cultivation. We found that naringenin is a key factor that causes different sensitivity to P. nicotianae between resistant and susceptible tobacco. The level of basal flavonoids in resistant tobacco was distinct from that in susceptible tobacco. Of all flavonoids with different content, naringenin showed the best antimicrobial activity against mycelial growth and sporangia production of P. nicotianae in vitro. However, naringenin showed very low or no antimicrobial activity to other plant pathogens. We found that naringenin induced not only the accumulation of reactive oxygen species, but also the expression of salicylic acid biosynthesis-related genes. Naringenin induced the expression of the basal pathogen resistance gene PR1 and the SAR8.2 gene that contributes to plant resistance to P. nicotianae. We then interfered with the expression of the chalcone synthase (NtCHS) gene, the key gene of the naringenin synthesis pathway, to inhibit naringenin biosynthesis. NtCHS-RNAi rendered tobacco highly sensitive to P. nicotianae, but there was no change in susceptibility to another plant pathogen, Ralstonia solanacearum. Finally, exogenous application of naringenin on susceptible tobacco enhanced resistance to P. nicotianae and naringenin was very stable in this environment. Our findings revealed that naringenin plays a core role in the defence against P. nicotianae and expanded the possibilities for the application of plant secondary metabolites in the control of P. nicotianae.
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Affiliation(s)
- Mingming Sun
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
- China Tobacco Shandong Industrial Co., Ltd.JinanChina
| | - Lei Li
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Chengdong Wang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Luanming Wang
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Di Lu
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Danyu Shen
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Jie Wang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Caihong Jiang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Lirui Cheng
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Xuhao Pan
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Aiguo Yang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Yuanying Wang
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | | | - Bin Li
- Sichuan Tobacco CorporationChengduChina
| | - Yiting Li
- Key Laboratory of Tobacco Genetic Improvement and Biotechnology, Tobacco Research InstituteChinese Academy of Agricultural SciencesQingdaoChina
| | - Feng Zhang
- College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
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43
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Yan Y. Insights into Mobile Small-RNAs Mediated Signaling in Plants. PLANTS (BASEL, SWITZERLAND) 2022; 11:3155. [PMID: 36432884 PMCID: PMC9698838 DOI: 10.3390/plants11223155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In higher plants, small RNA (sRNA)-mediated RNA interfering (RNAi) is involved in a broad range of biological processes. Growing evidence supports the model that sRNAs are mobile signaling agents that move intercellularly, systemically and cross-species. Recently, considerable progress has been made in terms of characterization of the mobile sRNAs population and their function. In this review, recent progress in identification of new mobile sRNAs is assessed. Here, critical questions related to the function of these mobile sRNAs in coordinating developmental, physiological and defense-related processes is discussed. The forms of mobile sRNAs and the underlying mechanisms mediating sRNA trafficking are discussed next. A concerted effort has been made to integrate these new findings into a comprehensive overview of mobile sRNAs signaling in plants. Finally, potential important areas for both basic science and potential applications are highlighted for future research.
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Affiliation(s)
- Yan Yan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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44
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Todd JNA, Carreón-Anguiano KG, Islas-Flores I, Canto-Canché B. Fungal Effectoromics: A World in Constant Evolution. Int J Mol Sci 2022; 23:13433. [PMID: 36362218 PMCID: PMC9656242 DOI: 10.3390/ijms232113433] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 10/28/2023] Open
Abstract
Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.
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Affiliation(s)
- Jewel Nicole Anna Todd
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico
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45
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Černoša A, Gostinčar C, Lavrin T, Kostanjšek R, Lenassi M, Gunde-Cimerman N. Isolation and characterization of extracellular vesicles from biotechnologically important fungus Aureobasidium pullulans. Fungal Biol Biotechnol 2022; 9:16. [PMID: 36320088 PMCID: PMC9628041 DOI: 10.1186/s40694-022-00146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022] Open
Abstract
Extracellular vesicles (EVs) are increasingly recognized as an important mechanism for cell-cell interactions. Their role in fungi is still poorly understood and they have been isolated from only a handful of species. Here, we isolated and characterized EVs from Aureobasidium pullulans, a biotechnologically important black yeast-like fungus that is increasingly used for biocontrol of phytopathogenic fungi and bacteria. After optimization of the isolation protocol, characterization of EVs from A. pullulans by transmission electron microscopy (TEM) revealed a typical cup-shaped morphology and different subpopulations of EVs. These results were confirmed by nanoparticle tracking analysis (NTA), which revealed that A. pullulans produced 6.1 × 108 nanoparticles per milliliter of culture medium. Proteomic analysis of EVs detected 642 proteins. A small fraction of them had signal peptides for secretion and transmembrane domains. Proteins characteristic of different synthesis pathways were found, suggesting that EVs are synthesized by multiple pathways in A. pullulans. Enrichment analysis using Gene Ontology showed that most of the proteins found in the EVs were associated with primary metabolism. When sequencing the small RNA fraction of A. pullulans EVs, we found two hypothetical novel mil-RNAs. Finally, we tested the biocontrol potential of EVs from A. pullulans. The EVs did not inhibit the germination of spores of three important phytopathogenic fungi-Botrytis cinerea, Colletotrichum acutatum, and Penicillium expansum. However, exposure of grown cultures of C. acutatum and P. expansum to A. pullulans EVs resulted in visible changes in morphology of colonies. These preliminary results suggest that EVs may be part of the antagonistic activity of A. pullulans, which is so far only partially understood. Thus, the first isolation and characterization of EVs from A. pullulans provides a starting point for further studies of EVs in the biotechnologically important traits of the biocontrol black fungus A. pullulans in particular and in the biological role of fungal EVs in general.
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Affiliation(s)
- Anja Černoša
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Cene Gostinčar
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Teja Lavrin
- grid.8954.00000 0001 0721 6013Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Kostanjšek
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Metka Lenassi
- grid.8954.00000 0001 0721 6013Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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46
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Macquet J, Mounichetty S, Raffaele S. Genetic co-option into plant-filamentous pathogen interactions. TRENDS IN PLANT SCIENCE 2022; 27:1144-1158. [PMID: 35909010 DOI: 10.1016/j.tplants.2022.06.011] [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: 02/23/2022] [Revised: 06/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plants are engaged in a coevolutionary arms race with their pathogens that drives rapid diversification and specialization of genes involved in resistance and virulence. However, some major innovations in plant-pathogen interactions, such as molecular decoys, trans-kingdom RNA interference, two-speed genomes, and receptor networks, evolved through the expansion of the functional landscape of genes. This is a typical outcome of genetic co-option, the evolutionary process by which available genes are recruited into new biological functions. Co-option into plant-pathogen interactions emerges generally from (i) cis-regulatory variation, (ii) horizontal gene transfer (HGT), (iii) mutations altering molecular promiscuity, and (iv) rewiring of gene networks and protein complexes. Understanding these molecular mechanisms is key for the functional and predictive biology of plant-pathogen interactions.
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Affiliation(s)
- Joris Macquet
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Shantala Mounichetty
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France
| | - Sylvain Raffaele
- Laboratoire des Interactions Plante-Microbe-Environnement (LIPME), Université de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Castanet Tolosan, France.
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47
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Zhao Y, Yang B, Xu H, Wu J, Xu Z, Wang Y. The Phytophthora effector Avh94 manipulates host jasmonic acid signaling to promote infection. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2199-2210. [PMID: 36067028 DOI: 10.1111/jipb.13358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
The oomycete pathogen Phytophthora sojae is a causal agent of soybean root rot. Upon colonization of soybeans, P. sojae secretes various RXLR effectors to suppress host immune responses, supporting successful infection. Previous research has demonstrated that the RXLR effector Avh94 functions as a virulence effector, but the molecular mechanism underlying its role in virulence remains unknown. Here, we demonstrate that Avh94 overexpression in plants and pathogens promotes Phytophthora infection. Avh94 interacts with soybean JAZ1/2, which is a repressor of jasmonic acid (JA) signaling. Avh94 stabilizes JAZ1/2 to inhibit JA signaling and silencing of JAZ1/2 enhances soybean resistance against P. sojae. Moreover, P. sojae lines overexpressing Avh94 inhibit JA signaling. Furthermore, exogenous application of methyl jasmonate improves plant resistance to Phytophthora. Taken together, these findings suggest that P. sojae employs an RXLR effector to hijack JA signaling and thereby promote infection.
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Affiliation(s)
- Yao Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bo Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huawei Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinbin Wu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiyang Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
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48
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Mueth NA, Hulbert SH. Small RNAs target native and cross-kingdom transcripts on both sides of the wheat stripe rust interaction. Genomics 2022; 114:110526. [PMID: 36427746 DOI: 10.1016/j.ygeno.2022.110526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global wheat production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host and microbe causes cross-kingdom gene silencing, but few examples are known in rust fungi. This study combined sRNA, parallel analysis of RNA ends, and gene expression data to discover sRNA-target pairs on each side of the interaction. Specific wheat 24 nt sRNAs were suppressed, while particular 35 nt fragments were strongly induced upon infection. Wheat sRNAs cleaved fungal transcripts coding for a ribosomal protein and a glycosyl hydrolase effector. Fungal microRNA-like and phased 21 nt sRNAs originated from long inverted repeats near protein coding genes. Fungal sRNAs targeted native transcripts: transposons and kinases; and cross-kingdom transcripts: a wheat nucleotide-binding domain leucine-rich repeat receptor (NLR) and multiple defense-related transcription factor families. This work sheds light on host-microbe coevolution and delivers prospects for developing pathogen control biotechnology.
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Affiliation(s)
- Nicholas A Mueth
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA.
| | - Scot H Hulbert
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA; Department of Plant Pathology, Washington State University, Pullman, WA, USA
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49
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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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50
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Pradhan M, Requena N. Distinguishing friends from foes: Can smRNAs modulate plant interactions with beneficial and pathogenic organisms? CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102259. [PMID: 35841651 DOI: 10.1016/j.pbi.2022.102259] [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: 01/31/2022] [Revised: 05/25/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
In their agro-ecological habitats, plants are constantly challenged by fungal interactions that might be pathogenic or beneficial in nature, and thus, plants need to exhibit appropriate responses to discriminate between them. Such interactions involve sophisticated molecular mechanism of signal exchange, signal transduction and regulation of gene expression. Small RNAs (smRNAs), including the microRNAs (miRNAs), form an essential layer of regulation in plant developmental processes as well as in plant adaptation to environmental stresses, being key for the outcome during plant-microbial interactions. Further, smRNAs are mobile signals that can go across kingdoms from one interacting partner to the other and hence can be used as communication as well as regulatory tools not only by the host plant but also by the colonising fungus. Here, largely with a focus on plant-fungal interactions and miRNAs, we will discuss the role of smRNAs, and how they might help plants to discriminate between friends and foes.
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Affiliation(s)
- Maitree Pradhan
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany
| | - Natalia Requena
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, D-76131, Karlsruhe, Germany.
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