Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence

  1. Florian Dunker
  2. Adriana Trutzenberg
  3. Jan S Rothenpieler
  4. Sarah Kuhn
  5. Reinhard Pröls
  6. Tom Schreiber
  7. Alain Tissier
  8. Ariane Kemen
  9. Eric Kemen
  10. Ralph Hückelhoven
  11. Arne Weiberg  Is a corresponding author
  1. Ludwig Maximilian University of Munich, Germany
  2. Technical University of Munich, Germany
  3. Leibniz Institute of Plant Biochemistry, Germany
  4. University of Tübingen, Germany

Abstract

The exchange of small RNAs (sRNAs) between hosts and pathogens can lead to gene silencing in the recipient organism, a mechanism termed cross-kingdom RNAi (ck-RNAi). While fungal sRNAs promoting virulence are established, the significance of ck-RNAi in distinct plant pathogens is not clear. Here, we describe that sRNAs of the pathogen Hyaloperonospora arabidopsidis, which represents the kingdom of oomycetes and is phylogenetically distant from fungi, employ the host plant's Argonaute (AGO)/RNA-induced silencing complex for virulence. To demonstrate H. arabidopsidis sRNA (HpasRNA) functionality in ck-RNAi, we designed a novel CRISPR endoribonuclease Csy4/GUS reporter that enabled in situ visualization of HpasRNA-induced target suppression in Arabidopsis. The significant role of HpasRNAs together with AtAGO1 in virulence was revealed in plant atago1 mutants and by transgenic Arabidopsis expressing a short-tandem-target-mimic to block HpasRNAs, that both exhibited enhanced resistance. HpasRNA-targeted plant genes contributed to host immunity, as Arabidopsis gene knockout mutants displayed quantitative enhanced susceptibility.

Data availability

Sequencing data have been deposited in NCBI SRA (PRJNA395139).

The following data sets were generated

Article and author information

Author details

  1. Florian Dunker

    Genetics, Ludwig Maximilian University of Munich, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  2. Adriana Trutzenberg

    Genetics, Ludwig Maximilian University of Munich, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  3. Jan S Rothenpieler

    Genetics, Ludwig Maximilian University of Munich, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8892-8230
  4. Sarah Kuhn

    Genetics, Ludwig Maximilian University of Munich, Martinsried, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Reinhard Pröls

    Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
    Competing interests
    The authors declare that no competing interests exist.
  6. Tom Schreiber

    Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Alain Tissier

    Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
    Competing interests
    The authors declare that no competing interests exist.
  8. Ariane Kemen

    Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Eric Kemen

    Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Ralph Hückelhoven

    Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
    Competing interests
    The authors declare that no competing interests exist.
  11. Arne Weiberg

    Genetics, Ludwig Maximilian University of Munich, Martinsried, Germany
    For correspondence
    a.weiberg@lmu.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4300-4864

Funding

Deutsche Forschungsgemeinschaft (WE 5707/1-1)

  • Arne Weiberg

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Axel A Brakhage, Hans Knöll Institute, Germany

Version history

  1. Received: February 17, 2020
  2. Accepted: May 21, 2020
  3. Accepted Manuscript published: May 22, 2020 (version 1)
  4. Accepted Manuscript updated: May 26, 2020 (version 2)
  5. Version of Record published: June 16, 2020 (version 3)

Copyright

© 2020, Dunker et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 6,168
    views
  • 892
    downloads
  • 87
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Florian Dunker
  2. Adriana Trutzenberg
  3. Jan S Rothenpieler
  4. Sarah Kuhn
  5. Reinhard Pröls
  6. Tom Schreiber
  7. Alain Tissier
  8. Ariane Kemen
  9. Eric Kemen
  10. Ralph Hückelhoven
  11. Arne Weiberg
(2020)
Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence
eLife 9:e56096.
https://doi.org/10.7554/eLife.56096

Share this article

https://doi.org/10.7554/eLife.56096

Further reading

    1. Microbiology and Infectious Disease
    Carolin Gerke, Liane Bauersfeld ... Anne Halenius
    Research Article

    Human leucocyte antigen class I (HLA-I) molecules play a central role for both NK and T-cell responses that prevent serious human cytomegalovirus (HCMV) disease. To create opportunities for viral spread, several HCMV-encoded immunoevasins employ diverse strategies to target HLA-I. Among these, the glycoprotein US10 is so far insufficiently studied. While it was reported that US10 interferes with HLA-G expression, its ability to manipulate classical HLA-I antigen presentation remains unknown. In this study, we demonstrate that US10 recognizes and binds to all HLA-I (HLA-A, -B, -C, -E, -G) heavy chains. Additionally, impaired recruitment of HLA-I to the peptide loading complex was observed. Notably, the associated effects varied significantly dependending on HLA-I genotype and allotype: (i) HLA-A molecules evaded downregulation by US10, (ii) tapasin-dependent HLA-B molecules showed impaired maturation and cell surface expression, and (iii) β2m-assembled HLA-C, in particular HLA-C*05:01 and -C*12:03, and HLA-G were strongly retained in complex with US10 in the endoplasmic reticulum. These genotype-specific effects on HLA-I were confirmed through unbiased HLA-I ligandome analyses. Furthermore, in HCMV-infected fibroblasts inhibition of overlapping US10 and US11 transcription had little effect on HLA-A, but induced HLA-B antigen presentation. Thus, the US10-mediated impact on HLA-I results in multiple geno- and allotypic effects in a so far unparalleled and multimodal manner.

    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease
    Ffion R Hammond, Amy Lewis ... Philip M Elks
    Research Article

    Tuberculosis is a major global health problem and is one of the top 10 causes of death worldwide. There is a pressing need for new treatments that circumvent emerging antibiotic resistance. Mycobacterium tuberculosis parasitises macrophages, reprogramming them to establish a niche in which to proliferate, therefore macrophage manipulation is a potential host-directed therapy if druggable molecular targets could be identified. The pseudokinase Tribbles1 (Trib1) regulates multiple innate immune processes and inflammatory profiles making it a potential drug target in infections. Trib1 controls macrophage function, cytokine production, and macrophage polarisation. Despite wide-ranging effects on leukocyte biology, data exploring the roles of Tribbles in infection in vivo are limited. Here, we identify that human Tribbles1 is expressed in monocytes and is upregulated at the transcript level after stimulation with mycobacterial antigen. To investigate the mechanistic roles of Tribbles in the host response to mycobacteria in vivo, we used a zebrafish Mycobacterium marinum (Mm) infection tuberculosis model. Zebrafish Tribbles family members were characterised and shown to have substantial mRNA and protein sequence homology to their human orthologues. trib1 overexpression was host-protective against Mm infection, reducing burden by approximately 50%. Conversely, trib1 knockdown/knockout exhibited increased infection. Mechanistically, trib1 overexpression significantly increased the levels of proinflammatory factors il-1β and nitric oxide. The host-protective effect of trib1 was found to be dependent on the E3 ubiquitin kinase Cop1. These findings highlight the importance of Trib1 and Cop1 as immune regulators during infection in vivo and suggest that enhancing macrophage TRIB1 levels may provide a tractable therapeutic intervention to improve bacterial infection outcomes in tuberculosis.