Letter

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs

  • Nature volume 553, pages 8285 (04 January 2018)
  • doi:10.1038/nature25027
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Abstract

Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bidirectional movement of viruses, proteins and mRNAs between host and parasite1, but the functional effects of these movements are not known. Here we show that Cuscuta campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana. Many of these miRNAs are 22 nucleotides in length. Plant miRNAs of this length are uncommon, and are associated with amplification of target silencing through secondary short interfering RNA (siRNA) production2. Several A. thaliana mRNAs are targeted by 22-nucleotide C. campestris miRNAs during parasitism, resulting in mRNA cleavage, secondary siRNA production, and decreased mRNA accumulation. Hosts with mutations in two of the loci that encode target mRNAs supported significantly higher growth of C. campestris. The same miRNAs that are expressed and active when C. campestris parasitizes A. thaliana are also expressed and active when it infects Nicotiana benthamiana. Homologues of target mRNAs from many other plant species also contain the predicted target sites for the induced C. campestris miRNAs. These data show that C. campestris miRNAs act as trans-species regulators of host-gene expression, and suggest that they may act as virulence factors during parasitism.

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Acknowledgements

This research was supported in part by awards from the US National Science Foundation (1238057 to J.H.W. and C.W.D.; 1339207 to M.J.A.) and the US National Institute of Food and Agriculture (135997 to J.H.W.).

Author information

Author notes

    • Feng Wang
    •  & Ceyda Coruh

    Present addresses: Department of Biology, Indiana University, Bloomington, Indiana 47405, USA (F.W.); Salk Institute for Biological Studies, La Jolla, California 92037, USA (C.C.).

Affiliations

  1. Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

    • Saima Shahid
    • , Nathan R. Johnson
    • , Feng Wang
    • , Ceyda Coruh
    • , Claude W. dePamphilis
    •  & Michael J. Axtell
  2. Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

    • Saima Shahid
    • , Nathan R. Johnson
    • , Eric Wafula
    • , Feng Wang
    • , Ceyda Coruh
    • , Claude W. dePamphilis
    •  & Michael J. Axtell
  3. Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA

    • Gunjune Kim
    • , Vivian Bernal-Galeano
    •  & James H. Westwood
  4. Knox College, Galesburg, Illinois 61401, USA

    • Tamia Phifer

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Contributions

S.S. and M.J.A. did the bioinformatics analysis. S.S., M.J.A. and N.R.J. prepared figures and tables. G.K., J.H.W., N.R.J., S.S., T.P. and M.J.A. cultivated and harvested plant specimens. E.W., G.K., C.W.D. and J.H.W. performed genome and transcriptome sequencing and assemblies. F.W., S.S. and N.R.J. did RNA blotting. S.S. and M.J.A. performed 5′-RLM-RACE and qRT–PCR. C.C. and T.P. constructed small-RNA-seq libraries. N.R.J. and V.B.-G. performed growth assays. M.J.A. and J.H.W. conceived the project. M.J.A. wrote and revised the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael J. Axtell.

Reviewer Information Nature thanks M. Albert, F. Tang and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Data 4

    This file contains images showing C. campestris hairpins overlaid with color-codes representing total read-depth (all six 'original' C. campestris x A. thaliana small RNA libraries). (pdf, 43 pages).

  3. 3.

    Supplementary Fig. 1

    This file contains uncropped gel figures.

Excel files

  1. 1.

    Supplementary Data 1

    This file contains A. thaliana and C. campestris small RNA loci. Output from ShortStack 3.8.3 (https://github.com/MikeAxtell/ShortStack) showing all small RNA loci identified in this study. (.xlsx format)

  2. 2.

    Supplementary Data 2

    This file contains mature miRNAs and miRNA*s fromC. campestris Interface-induced MIRNA loci. (.xlsx format)

  3. 3.

    Supplementary Data 6

    This file contains oligonucleotide sequences. Excel (.xlsx) format.

Text files

  1. 1.

    Supplementary Data 3

    This file contains details ofC. campestris MIRNA loci: Text-based sequences, predicted secondary structures, and aligned small RNA reads (all six libraries). Lower-case letters indicate small RNA bases that are mismatched to the genomic sequence. Plain-text (ASCII) format.

  2. 2.

    Supplementary Data 5

    This file contains alignments of mature miRNAs and miRNA*s (from Supplementary Data 2 -- the induced C. campestris miRNAs) against the A. thaliana genome. Note that most have three or more mismatches. (SAM format).

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