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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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2
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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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3
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Oliveira-Garcia E, Yan X, Oses-Ruiz M, de Paula S, Talbot NJ. Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae. THE NEW PHYTOLOGIST 2024; 241:1007-1020. [PMID: 38073141 DOI: 10.1111/nph.19446] [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: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024]
Abstract
Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Miriam Oses-Ruiz
- IMAB, Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Navarra, Spain
| | - Samuel de Paula
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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4
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Aggarwal B, Karlowski WM, Nuc P, Jarmolowski A, Szweykowska-Kulinska Z, Pietrykowska H. MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function. RNA Biol 2024; 21:1-12. [PMID: 38303117 PMCID: PMC10841014 DOI: 10.1080/15476286.2024.2303555] [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] [Accepted: 01/05/2024] [Indexed: 02/03/2024] Open
Abstract
MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.
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Affiliation(s)
- Bharti Aggarwal
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wojciech Maciej Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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5
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Rumyantsev SD, Veselova SV, Burkhanova GF, Alekseev VY, Maksimov IV. Bacillus subtilis 26D Triggers Induced Systemic Resistance against Rhopalosiphum padi L. by Regulating the Expression of Genes AGO, DCL and microRNA in Bread Spring Wheat. Microorganisms 2023; 11:2983. [PMID: 38138127 PMCID: PMC10745712 DOI: 10.3390/microorganisms11122983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is a serious pest that causes significant damage to crops throughout the world. However, the function of plant miRNAs in the response to aphid infestation remains unclear. The results of this work showed that B. subtilis 26D stimulated aphid resistance in wheat plants, inducing the expression of genes of hormonal signaling pathways ICS, WRKY13, PR1, ACS, EIN3, PR3, and ABI5. In addition, B. subtilis 26D activated the RNAi mechanism and regulated the expression of nine conserved miRNAs through activation of the ethylene, salicylic acid (SA), and abscisic acid (ABA) signaling pathways, which was demonstrated by using treatments with phytohormones. Treatment of plants with SA, ethylene, and ABA acted in a similar manner to B. subtilis 26D on induction of the expression of the AGO4, AGO5 and DCL2, DCL4 genes, as well as the expression of nine conserved miRNAs. Different patterns of miRNA expression were found in aphid-infested plants and in plants treated with B. subtilis 26D or SA, ethylene, and ABA and infested by aphids, suggesting that miRNAs play multiple roles in the plant response to phloem-feeding insects, associated with effects on hormonal signaling pathways, redox metabolism, and the synthesis of secondary metabolites. Our study provides new data to further elucidate the fine mechanisms of bacterial-induced priming. However, further extensive work is needed to fully unravel these mechanisms.
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Affiliation(s)
| | - Svetlana V. Veselova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (S.D.R.); (G.F.B.); (V.Y.A.); (I.V.M.)
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6
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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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7
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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: 0] [Impact Index Per Article: 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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8
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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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9
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Bauer I, Sarikaya Bayram Ö, Bayram Ö. The use of immunoaffinity purification approaches coupled with LC-MS/MS offers a powerful strategy to identify protein complexes in filamentous fungi. Essays Biochem 2023; 67:877-892. [PMID: 37681641 DOI: 10.1042/ebc20220253] [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: 05/19/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023]
Abstract
Fungi are a diverse group of organisms that can be both beneficial and harmful to mankind. They have advantages such as producing food processing enzymes and antibiotics, but they can also be pathogens and produce mycotoxins that contaminate food. Over the past two decades, there have been significant advancements in methods for studying fungal molecular biology. These advancements have led to important discoveries in fungal development, physiology, pathogenicity, biotechnology, and natural product research. Protein complexes and protein-protein interactions (PPIs) play crucial roles in fungal biology. Various methods, including yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC), are used to investigate PPIs. However, affinity-based PPI methods like co-immunoprecipitation (Co-IP) are highly preferred because they represent the natural conditions of PPIs. In recent years, the integration of liquid chromatography coupled with mass spectrometry (LC-MS/MS) has been used to analyse Co-IPs, leading to the discovery of important protein complexes in filamentous fungi. In this review, we discuss the tandem affinity purification (TAP) method and single affinity purification methods such as GFP, HA, FLAG, and MYC tag purifications. These techniques are used to identify PPIs and protein complexes in filamentous fungi. Additionally, we compare the efficiency, time requirements, and material usage of Sepharose™ and magnetic-based purification systems. Overall, the advancements in fungal molecular biology techniques have provided valuable insights into the complex interactions and functions of proteins in fungi. The methods discussed in this review offer powerful tools for studying fungal biology and will contribute to further discoveries in this field.
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Affiliation(s)
- Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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10
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Chen YY, Zhu C, Zhao JH, Liu T, Gao F, Zhang YC, Duan CG. DNA methylation-dependent epigenetic regulation of Verticillium dahliae virulence in plants. ABIOTECH 2023; 4:185-201. [PMID: 37970467 PMCID: PMC10638132 DOI: 10.1007/s42994-023-00117-5] [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: 05/15/2023] [Accepted: 08/31/2023] [Indexed: 11/17/2023]
Abstract
As a conserved epigenetic mark, DNA cytosine methylation, at the 5' position (5-mC), plays important roles in multiple biological processes, including plant immunity. However, the involvement of DNA methylation in the determinants of virulence of phytopathogenic fungi remains elusive. In this study, we profiled the DNA methylation patterns of the phytopathogenic fungus Verticillium dahliae, one of the major causal pathogens of Verticillium wilt disease that causes great losses in many crops, and explored its contribution in fungal pathogenicity. We reveal that DNA methylation modification is present in V. dahliae and is required for its full virulence in host plants. The major enzymes responsible for the establishment of DNA methylation in V. dahliae were identified. We provided evidence that DNA methyltransferase-mediated establishment of DNA methylation pattern positively regulates fungal virulence, mainly through repressing a conserved protein kinase VdRim15-mediated Ca2+ signaling and ROS production, which is essential for the penetration activity of V. dahliae. In addition, we further demonstrated that histone H3 lysine 9 trimethylation (H3K9me3), another heterochromatin marker that is closely associated with 5-mC in eukaryotes, also participates in the regulation of V. dahliae pathogenicity, through a similar mechanism. More importantly, DNA methyltransferase genes VdRid, VdDnmt5, as well as H3K9me3 methyltransferase genes, were greatly induced during the early infection phase, implying that a dynamic regulation of 5-mC and H3K9me3 homeostasis is required for an efficient infection. Collectively, our findings uncover an epigenetic mechanism in the regulation of phytopathogenic fungal virulence. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-023-00117-5.
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Affiliation(s)
- Yun-Ya Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 200032 China
- College of Life Sciences, Anhui Normal University, Wuhu, 241000 China
| | - Jian-Hua Zhao
- University of Chinese Academy of Sciences, Beijing, 100049 China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ting Liu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Feng Gao
- Qilu Zhongke Academy of Modern Microbiology Technology, Jinan, 250000 China
| | - Ying-Chao Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 200032 China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai, 200032 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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11
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Harris W, Kim S, Vӧlz R, Lee YH. Nuclear effectors of plant pathogens: Distinct strategies to be one step ahead. MOLECULAR PLANT PATHOLOGY 2023; 24:637-650. [PMID: 36942744 DOI: 10.1111/mpp.13315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 02/08/2023] [Indexed: 05/18/2023]
Abstract
Nuclear effector proteins released by bacteria, oomycete, nematode, and fungi burden the global environment and crop yield. Microbial effectors are key weapons in the evolutionary arms race between plants and pathogens, vital in determining the success of pathogenic colonization. Secreted effectors undermine a multitude of host cellular processes depending on their target destination. Effectors are classified by their localization as either extracellular (apoplastic) or intracellular. Intracellular effectors can be further subclassified by their compartment such as the nucleus, cytoplasm or chloroplast. Nuclear effectors bring into question the role of the plant nucleus' intrinsic defence strategies and their vulnerability to effector-based manipulation. Nuclear effectors interfere with multiple nuclear processes including the epigenetic regulation of the host chromatin, the impairment of the trans-kingdom antifungal RNAi machinery, and diverse classes of immunity-associated host proteins. These effector-targeted pathways are widely conserved among different hosts and regulate a broad array of plant cellular processes. Thus, these nuclear sites constitute meaningful targets for effectors to subvert the plant defence system and acquire resources for pathogenic propagation. This review provides an extensive and comparative compilation of diverse plant microbe nuclear effector libraries, thereby highlighting the distinct and conserved mechanisms these effectors employ to modulate plant cellular processes for the pathogen's profit.
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Affiliation(s)
- William Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Ronny Vӧlz
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
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12
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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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13
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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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14
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Aparicio Chacón MV, Van Dingenen J, Goormachtig S. Characterization of Arbuscular Mycorrhizal Effector Proteins. Int J Mol Sci 2023; 24:ijms24119125. [PMID: 37298075 DOI: 10.3390/ijms24119125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.
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Affiliation(s)
- María V Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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15
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Zhang Y, Zhang Y, Ge X, Yuan Y, Jin Y, Wang Y, Zhao L, Han X, Hu W, Yang L, Gao C, Wei X, Li F, Yang Z. Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton. Genome Biol 2023; 24:111. [PMID: 37165460 PMCID: PMC10170703 DOI: 10.1186/s13059-023-02950-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown. RESULTS By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae. CONCLUSIONS We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.
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Affiliation(s)
- Yihao Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yaning Zhang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xiaoyang Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuan Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuying Jin
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ye Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lihong Zhao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao Han
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China
| | - Xi Wei
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, Xinjiang, China.
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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16
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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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17
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Xie SS, Zhang YZ, Peng L, Yu DT, Zhu G, Zhao Q, Wang CH, Xie Q, Duan CG. JMJ28 guides sequence-specific targeting of ATX1/2-containing COMPASS-like complex in Arabidopsis. Cell Rep 2023; 42:112163. [PMID: 36827182 DOI: 10.1016/j.celrep.2023.112163] [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: 01/30/2022] [Revised: 09/21/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Despite extensive investigations in mammals and yeasts, the importance and specificity of COMPASS-like complex, which catalyzes histone 3 lysine 4 methylation (H3K4me), are not fully understood in plants. Here, we report that JMJ28, a Jumonji C domain-containing protein in Arabidopsis, recognizes specific DNA motifs through a plant-specific WRC domain and acts as an interacting factor to guide the chromatin targeting of ATX1/2-containing COMPASS-like complex. JMJ28 associates with COMPASS-like complex in vivo via direct interaction with RBL. The DNA-binding activity of JMJ28 is essential for both the targeting specificity of ATX1/2-COMPASS and the deposition of H3K4me at specific loci but exhibit functional redundancy with alternative COMPASS-like complexes at other loci. Finally, we demonstrate that JMJ28 is a negative regulator of plant immunity. In summary, our findings reveal a plant-specific recruitment mechanism of COMPASS-like complex. These findings help to gain deeper insights into the regulatory mechanism of COMPASS-like complex in plants.
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Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Zhe Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ding-Tian Yu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qingzhen Zhao
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Chun-Han Wang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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18
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Hu X, Yin G, Zhang Y, Zhu L, Huang H, Lv K. Recent advances in the functional explorations of nuclear microRNAs. Front Immunol 2023; 14:1097491. [PMID: 36911728 PMCID: PMC9992549 DOI: 10.3389/fimmu.2023.1097491] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Approximately 22 nucleotide-long non-coding small RNAs (ncRNAs) play crucial roles in physiological and pathological activities, including microRNAs (miRNAs). Long ncRNAs often stay in the cytoplasm, modulating post-transcriptional gene expression. Briefly, miRNA binds with the target mRNA and builds a miRNA-induced silencing complex to silence the transcripts or prevent their translation. Interestingly, data from recent animal and plant studies suggested that mature miRNAs are present in the nucleus, where they regulate transcriptionally whether genes are activated or silenced. This significantly broadens the functional range of miRNAs. Here, we reviewed and summarized studies on the functions of nuclear miRNAs to better understand the modulatory networks associated with nuclear miRNAs.
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Affiliation(s)
- Xiaozhu Hu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Guoquan Yin
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Yuan Zhang
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Liangyu Zhu
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Haoyu Huang
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
| | - Kun Lv
- Central Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu, China.,Key Laboratory of Non-Coding RNA Transformation Research of Anhui Higher Education Institutes (Wannan Medical College), Wuhu, China
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19
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Zhu Y, Zhao M, Li T, Wang L, Liao C, Liu D, Zhang H, Zhao Y, Liu L, Ge X, Li B. Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt. FRONTIERS IN PLANT SCIENCE 2023; 14:1174281. [PMID: 37152175 PMCID: PMC10161258 DOI: 10.3389/fpls.2023.1174281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca2+ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.
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Affiliation(s)
- Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
| | - Mei Zhao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Taotao Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Lianzhe Wang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Chunli Liao
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Dongxiao Liu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Huamin Zhang
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
| | - Yanpeng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bingbing Li
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, China
- *Correspondence: Yutao Zhu, ; Bingbing Li,
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20
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:jof9010004. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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21
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De Mandal S, Jeon J. Nuclear Effectors in Plant Pathogenic Fungi. MYCOBIOLOGY 2022; 50:259-268. [PMID: 36404902 PMCID: PMC9645283 DOI: 10.1080/12298093.2022.2118928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 05/29/2023]
Abstract
The nuclear import of proteins is a fundamental process in the eukaryotes including plant. It has become evident that such basic process is exploited by nuclear effectors that contain nuclear localization signal (NLS) and are secreted into host cells by fungal pathogens of plants. However, only a handful of nuclear effectors have been known and characterized to date. Here, we first summarize the types of NLSs and prediction tools available, and then delineate examples of fungal nuclear effectors and their roles in pathogenesis. Based on the knowledge on NLSs and what has been gleaned from the known nuclear effectors, we point out the gaps in our understanding of fungal nuclear effectors that need to be filled in the future researches.
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Affiliation(s)
- Surajit De Mandal
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Korea
| | - Junhyun Jeon
- Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
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22
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Fick A, Swart V, van den Berg N. The Ups and Downs of Plant NLR Expression During Pathogen Infection. FRONTIERS IN PLANT SCIENCE 2022; 13:921148. [PMID: 35720583 PMCID: PMC9201817 DOI: 10.3389/fpls.2022.921148] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Plant Nucleotide binding-Leucine rich repeat (NLR) proteins play a significant role in pathogen detection and the activation of effector-triggered immunity. NLR regulation has mainly been studied at a protein level, with large knowledge gaps remaining regarding the transcriptional control of NLR genes. The mis-regulation of NLR gene expression may lead to the inability of plants to recognize pathogen infection, lower levels of immune response activation, and ultimately plant susceptibility. This highlights the importance of understanding all aspects of NLR regulation. Three main mechanisms have been shown to control NLR expression: epigenetic modifications, cis elements which bind transcription factors, and post-transcriptional modifications. In this review, we aim to provide an overview of these mechanisms known to control NLR expression, and those which contribute toward successful immune responses. Furthermore, we discuss how pathogens can interfere with NLR expression to increase pathogen virulence. Understanding how these molecular mechanisms control NLR expression would contribute significantly toward building a complete picture of how plant immune responses are activated during pathogen infection-knowledge which can be applied during crop breeding programs aimed to increase resistance toward numerous plant pathogens.
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Affiliation(s)
- Alicia Fick
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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23
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Lai Y, Wang L, Zheng W, Wang S. Regulatory Roles of Histone Modifications in Filamentous Fungal Pathogens. J Fungi (Basel) 2022; 8:jof8060565. [PMID: 35736048 PMCID: PMC9224773 DOI: 10.3390/jof8060565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungal pathogens have evolved diverse strategies to infect a variety of hosts including plants and insects. The dynamic infection process requires rapid and fine-tuning regulation of fungal gene expression programs in response to the changing host environment and defenses. Therefore, transcriptional reprogramming of fungal pathogens is critical for fungal development and pathogenicity. Histone post-translational modification, one of the main mechanisms of epigenetic regulation, has been shown to play an important role in the regulation of gene expressions, and is involved in, e.g., fungal development, infection-related morphogenesis, environmental stress responses, biosynthesis of secondary metabolites, and pathogenicity. This review highlights recent findings and insights into regulatory mechanisms of histone methylation and acetylation in fungal development and pathogenicity, as well as their roles in modulating pathogenic fungi–host interactions.
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Affiliation(s)
- Yiling Lai
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
| | - Lili Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weilu Zheng
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), Shanghai 200032, China; (L.W.); (W.Z.)
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (Y.L.); (S.W.)
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The Non-Coding RNA Journal Club: Highlights on Recent Papers—11. Noncoding RNA 2022; 8:ncrna8030031. [PMID: 35645338 PMCID: PMC9149905 DOI: 10.3390/ncrna8030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
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