1
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Nien YC, Vanek A, Axtell MJ. Trans-Species Mobility of RNA Interference between Plants and Associated Organisms. PLANT & CELL PHYSIOLOGY 2024; 65:694-703. [PMID: 38288670 DOI: 10.1093/pcp/pcae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 05/31/2024]
Abstract
Trans-species RNA interference (RNAi) occurs naturally when small RNAs (sRNAs) silence genes in species different from their origin. This phenomenon has been observed between plants and various organisms including fungi, animals and other plant species. Understanding the mechanisms used in natural cases of trans-species RNAi, such as sRNA processing and movement, will enable more effective development of crop protection methods using host-induced gene silencing (HIGS). Recent progress has been made in understanding the mechanisms of cell-to-cell and long-distance movement of sRNAs within individual plants. This increased understanding of endogenous plant sRNA movement may be translatable to trans-species sRNA movement. Here, we review diverse cases of natural trans-species RNAi focusing on current theories regarding intercellular and long-distance sRNA movement. We also touch on trans-species sRNA evolution, highlighting its research potential and its role in improving the efficacy of HIGS.
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Affiliation(s)
- Ya-Chi Nien
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Allison Vanek
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael J Axtell
- Plant Biology Intercollege Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Bioinformatics and Genomics Ph.D. Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Liang D, Jiang Y, Zhang Y, Mao C, Ma T, Zhang C. The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families of Botryosphaeria dothidea Related to Pathogenicity on Chinese Hickory Tree. J Fungi (Basel) 2024; 10:299. [PMID: 38667970 PMCID: PMC11051394 DOI: 10.3390/jof10040299] [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: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea's pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea's pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea's genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea's pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.
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Affiliation(s)
| | | | | | | | - Tianlin Ma
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
| | - Chuanqing Zhang
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
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3
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Singh R, Caseys C, Kliebenstein DJ. Genetic and molecular landscapes of the generalist phytopathogen Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2024; 25:e13404. [PMID: 38037862 PMCID: PMC10788480 DOI: 10.1111/mpp.13404] [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: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Botrytis cinerea Pers. Fr. (teleomorph: Botryotinia fuckeliana) is a necrotrophic fungal pathogen that attacks a wide range of plants. This updated pathogen profile explores the extensive genetic diversity of B. cinerea, highlights the progress in genome sequencing, and provides current knowledge of genetic and molecular mechanisms employed by the fungus to attack its hosts. In addition, we also discuss recent innovative strategies to combat B. cinerea. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, subphylum: Pezizomycotina, class: Leotiomycetes, order: Helotiales, family: Sclerotiniaceae, genus: Botrytis, species: cinerea. HOST RANGE B. cinerea infects almost all of the plant groups (angiosperms, gymnosperms, pteridophytes, and bryophytes). To date, 1606 plant species have been identified as hosts of B. cinerea. GENETIC DIVERSITY This polyphagous necrotroph has extensive genetic diversity at all population levels shaped by climate, geography, and plant host variation. PATHOGENICITY Genetic architecture of virulence and host specificity is polygenic using multiple weapons to target hosts, including secretory proteins, complex signal transduction pathways, metabolites, and mobile small RNA. DISEASE CONTROL STRATEGIES Efforts to control B. cinerea, being a high-diversity generalist pathogen, are complicated. However, integrated disease management strategies that combine cultural practices, chemical and biological controls, and the use of appropriate crop varieties will lessen yield losses. Recently, studies conducted worldwide have explored the potential of small RNA as an efficient and environmentally friendly approach for combating grey mould. However, additional research is necessary, especially on risk assessment and regulatory frameworks, to fully harness the potential of this technology.
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Affiliation(s)
- Ritu Singh
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
| | - Celine Caseys
- Department of Plant ScienceUniversity of CaliforniaDavisCaliforniaUSA
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4
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Cheng AP, Lederer B, Oberkofler L, Huang L, Johnson NR, Platten F, Dunker F, Tisserant C, Weiberg A. A fungal RNA-dependent RNA polymerase is a novel player in plant infection and cross-kingdom RNA interference. PLoS Pathog 2023; 19:e1011885. [PMID: 38117848 PMCID: PMC10766185 DOI: 10.1371/journal.ppat.1011885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/04/2024] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Small RNAs act as fungal pathogen effectors that silence host target genes to promote infection, a virulence mechanism termed cross-kingdom RNA interference (RNAi). The essential pathogen factors of cross-kingdom small RNA production are largely unknown. We here characterized the RNA-dependent RNA polymerase (RDR)1 in the fungal plant pathogen Botrytis cinerea that is required for pathogenicity and cross-kingdom RNAi. B. cinerea bcrdr1 knockout (ko) mutants exhibited reduced pathogenicity and loss of cross-kingdom small RNAs. We developed a "switch-on" GFP reporter to study cross-kingdom RNAi in real-time within the living plant tissue which highlighted that bcrdr1 ko mutants were compromised in cross-kingdom RNAi. Moreover, blocking seven pathogen cross-kingdom small RNAs by expressing a short-tandem target mimic RNA in transgenic Arabidopsis thaliana led to reduced infection levels of the fungal pathogen B. cinerea and the oomycete pathogen Hyaloperonospora arabidopsidis. These results demonstrate that cross-kingdom RNAi is significant to promote host infection and making pathogen small RNAs an effective target for crop protection.
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Affiliation(s)
- An-Po Cheng
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Bernhard Lederer
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Lorenz Oberkofler
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Lihong Huang
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Nathan R. Johnson
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, Santiago, Chile
- ANID-Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Fabian Platten
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Florian Dunker
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Constance Tisserant
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Arne Weiberg
- Institute of Genetics, Faculty of Biology, Ludwig Maximilian University of Munich, Martinsried, Germany
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5
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Cheng AP, Kwon S, Adeshara T, Göhre V, Feldbrügge M, Weiberg A. Extracellular RNAs released by plant-associated fungi: from fundamental mechanisms to biotechnological applications. Appl Microbiol Biotechnol 2023; 107:5935-5945. [PMID: 37572124 PMCID: PMC10485130 DOI: 10.1007/s00253-023-12718-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Extracellular RNAs are an emerging research topic in fungal-plant interactions. Fungal plant pathogens and symbionts release small RNAs that enter host cells to manipulate plant physiology and immunity. This communication via extracellular RNAs between fungi and plants is bidirectional. On the one hand, plants release RNAs encapsulated inside extracellular vesicles as a defense response as well as for intercellular and inter-organismal communication. On the other hand, recent reports suggest that also full-length mRNAs are transported within fungal EVs into plants, and these fungal mRNAs might get translated inside host cells. In this review article, we summarize the current views and fundamental concepts of extracellular RNAs released by plant-associated fungi, and we discuss new strategies to apply extracellular RNAs in crop protection against fungal pathogens. KEY POINTS: • Extracellular RNAs are an emerging topic in plant-fungal communication. • Fungi utilize RNAs to manipulate host plants for colonization. • Extracellular RNAs can be engineered to protect plants against fungal pathogens.
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Affiliation(s)
- An-Po Cheng
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany
| | - Seomun Kwon
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Trusha Adeshara
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Arne Weiberg
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany.
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6
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Derbyshire MC, Raffaele S. Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors. Nat Commun 2023; 14:5244. [PMID: 37640704 PMCID: PMC10462633 DOI: 10.1038/s41467-023-40949-9] [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: 01/10/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Sylvain Raffaele
- Laboratoire des Interactions Plantes Micro-organismes Environnement (LIPME), INRAE, CNRS, Université de Toulouse, 31326, Castanet-Tolosan, France.
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7
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You Y, Astudillo-Estévez I, Essenstam B, Qin S, van Kan JAL. Leaf resistance to Botrytis cinerea in wild tomato Solanum habrochaites depends on inoculum composition. FRONTIERS IN PLANT SCIENCE 2023; 14:1156804. [PMID: 37600190 PMCID: PMC10433766 DOI: 10.3389/fpls.2023.1156804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023]
Abstract
Tomato (Solanum lycopersicum) cv. Moneymaker (MM) is very susceptible to the grey mould Botrytis cinerea, while quantitative resistance in the wild species Solanum habrochaites (accession LYC4) has been reported. In leaf inoculation assays, an effect of nutrient and spore concentration on disease incidence was observed. Resistance in LYC4 leaves was manifested as a high incidence of tiny black, dispersed spots which did not expand ("incompatible interaction") and was pronounced when B. cinerea was inoculated at high spore density (1000 spores/µL) in medium with 10 mM sucrose and 10 mM phosphate buffer. Under the same condition, a high frequency of expanding lesions was observed on MM leaves ("compatible interaction"). Remarkably, inoculation of LYC4 with a high spore density in medium with higher concentrations of sucrose and/or phosphate as well as lower spore density (30 spores/µL) in medium with low sucrose and phosphate, all resulted in a higher percentage of expanding lesions. The lesion sizes at 3 days post inoculation differed markedly between all these inoculation conditions. This inoculation method provides a convenient tool to study mechanisms that determine the distinction between compatible and incompatible interactions between B. cinerea and a host plant.
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Affiliation(s)
- Yaohua You
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | | | - Bert Essenstam
- Wageningen University & Research, Unifarm, Wageningen, Netherlands
| | - Si Qin
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
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8
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Chen T, Zhang Z, Chen Y, Li B, Tian S. Botrytis cinerea. Curr Biol 2023; 33:R460-R462. [PMID: 37279671 DOI: 10.1016/j.cub.2023.01.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chen, Zhang et al. introduce the necrotrophic fungal plant pathogen Botrytis cinerea more commonly known as gray mold.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Sun B, Kim H, Mello CC, Priess JR. The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods. PLoS Genet 2023; 19:e1010804. [PMID: 37384599 PMCID: PMC10309623 DOI: 10.1371/journal.pgen.1010804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL polyproteins. Because gRNA often includes splice acceptor and donor sequences used to splice viral mRNAs, retroelements must overcome host mechanisms that retain intron-containing RNAs in the nucleus. Here we examine gRNA expression in Cer1, an LTR retrotransposon in C. elegans which somehow avoids silencing and is highly expressed in germ cells. Newly exported Cer1 gRNA associates rapidly with the Cer1 GAG protein, which has structural similarity with retroviral GAG proteins. gRNA export requires CERV (C. elegans regulator of viral expression), a novel protein encoded by a spliced Cer1 mRNA. CERV phosphorylation at S214 is essential for gRNA export, and phosphorylated CERV colocalizes with nuclear gRNA at presumptive sites of transcription. By electron microscopy, tagged CERV proteins surround clusters of distinct, linear fibrils that likely represent gRNA molecules. Single fibrils, or groups of aligned fibrils, also localize near nuclear pores. During the C. elegans self-fertile period, when hermaphrodites fertilize oocytes with their own sperm, CERV concentrates in two nuclear foci that are coincident with gRNA. However, as hermaphrodites cease self-fertilization, and can only produce cross-progeny, CERV undergoes a remarkable transition to form giant nuclear rods or cylinders that can be up to 5 microns in length. We propose a novel mechanism of rod formation, in which stage-specific changes in the nucleolus induce CERV to localize to the nucleolar periphery in flattened streaks of protein and gRNA; these streaks then roll up into cylinders. The rods are a widespread feature of Cer1 in wild strains of C. elegans, but their function is not known and might be limited to cross-progeny. We speculate that the adaptive strategy Cer1 uses for the identical self-progeny of a host hermaphrodite might differ for heterozygous cross-progeny sired by males. For example, mating introduces male chromosomes which can have different, or no, Cer1 elements.
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Affiliation(s)
- Bing Sun
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Haram Kim
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Craig C. Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester,United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - James R. Priess
- Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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10
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Urquhart AS, Vogan AA, Gardiner DM, Idnurm A. Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases. Proc Natl Acad Sci U S A 2023; 120:e2214521120. [PMID: 37023132 PMCID: PMC10104507 DOI: 10.1073/pnas.2214521120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/04/2023] [Indexed: 04/07/2023] Open
Abstract
Transposable elements in eukaryotic organisms have historically been considered "selfish," at best conferring indirect benefits to their host organisms. The Starships are a recently discovered feature in fungal genomes that are, in some cases, predicted to confer beneficial traits to their hosts and also have hallmarks of being transposable elements. Here, we provide experimental evidence that Starships are indeed autonomous transposons, using the model Paecilomyces variotii, and identify the HhpA "Captain" tyrosine recombinase as essential for their mobilization into genomic sites with a specific target site consensus sequence. Furthermore, we identify multiple recent horizontal gene transfers of Starships, implying that they jump between species. Fungal genomes have mechanisms to defend against mobile elements, which are frequently detrimental to the host. We discover that Starships are also vulnerable to repeat-induced point mutation defense, thereby having implications on the evolutionary stability of such elements.
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Affiliation(s)
- Andrew S. Urquhart
- Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD4067, Australia
- Applied Biosciences, Macquarie University, Macquarie Park, NSW2109, Australia
| | - Aaron A. Vogan
- Department of Organismal Biology, Uppsala University, 752 36Uppsala, Sweden
| | - Donald M. Gardiner
- Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD4067, Australia
- University of Queensland, St Lucia, QLD4067, Australia
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Parkville, VIC3010, Australia
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11
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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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12
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Papolu PK, Ramakrishnan M, Mullasseri S, Kalendar R, Wei Q, Zou L, Ahmad Z, Vinod KK, Yang P, Zhou M. Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1064847. [PMID: 36570931 PMCID: PMC9780303 DOI: 10.3389/fpls.2022.1064847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their "copy-out and paste-in" life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copia and Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
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Affiliation(s)
- Pradeep K. Papolu
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Long−Hai Zou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | | | - Ping Yang
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
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13
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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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14
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Janjic A, Wange LE, Bagnoli JW, Geuder J, Nguyen P, Richter D, Vieth B, Vick B, Jeremias I, Ziegenhain C, Hellmann I, Enard W. Prime-seq, efficient and powerful bulk RNA sequencing. Genome Biol 2022; 23:88. [PMID: 35361256 PMCID: PMC8969310 DOI: 10.1186/s13059-022-02660-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022] Open
Abstract
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard bulk RNA-seq method, but is fourfold more cost-efficient due to almost 50-fold cheaper library costs. We also validate a direct RNA isolation step, show that intronic reads are derived from RNA, and compare cost-efficiencies of available protocols. We conclude that prime-seq is currently one of the best options to set up an early barcoding bulk RNA-seq protocol from which many labs would profit.
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Affiliation(s)
- Aleksandar Janjic
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.,Graduate School of Systemic Neurosciences, Faculty of Biology, Ludwig-Maximilians University, Martinsried, Germany
| | - Lucas E Wange
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Johanna Geuder
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Phong Nguyen
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Daniel Richter
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Beate Vieth
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Christoph Ziegenhain
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ines Hellmann
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Anthropology & Human Genomics, Faculty of Biology, Ludwig-Maximilians University, Großhaderner Str. 2, 82152, Martinsried, Germany.
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