Letter | Published:

Global translational reprogramming is a fundamental layer of immune regulation in plants

Nature volume 545, pages 487490 (25 May 2017) | Download Citation

Abstract

In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood1,2. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting, here we perform global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern elf18. We find that during this pattern-triggered immunity, translation is tightly regulated and poorly correlated with transcription. Identification of genes with altered translational efficiency leads to the discovery of novel regulators of this immune response. Further investigation of these genes shows that messenger RNA sequence features are major determinants of the observed translational efficiency changes. In the 5′ leader sequences of transcripts with increased translational efficiency, we find a highly enriched messenger RNA consensus sequence, R-motif, consisting of mostly purines. We show that R-motif regulates translation in response to pattern-triggered immunity induction through interaction with poly(A)-binding proteins. Therefore, this study provides not only strong evidence, but also a molecular mechanism, for global translational reprogramming during pattern-triggered immunity in plants.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

References

  1. 1.

    et al. The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition. Curr. Biol. 22, 103–112 (2012)

  2. 2.

    , , & Growth-defense tradeoffs in plants: a balancing act to optimize fitness. Mol. Plant 7, 1267–1287 (2014)

  3. 3.

    & Regulation of pattern recognition receptor signalling in plants. Nature Rev. Immunol. 16, 537–552 (2016)

  4. 4.

    , & Microbial signature-triggered plant defense responses and early signaling mechanisms. Plant Sci. 228, 118–126 (2014)

  5. 5.

    , , , & C. elegans detects pathogen-induced translational inhibition to activate immune signaling. Cell Host Microbe 11, 375–386 (2012)

  6. 6.

    et al. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell 125, 749–760 (2006)

  7. 7.

    et al. Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress. Plant J. 84, 1206–1218 (2015)

  8. 8.

    et al. Gene-specific translation regulation mediated by the hormone-signaling molecule EIN2. Cell 163, 684–697 (2015)

  9. 9.

    et al. Translational landscape of photomorphogenic Arabidopsis. Plant Cell 25, 3699–3710 (2013)

  10. 10.

    , , & Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc. Natl Acad. Sci. USA 111, E203–E212 (2014)

  11. 11.

    , & Insights into the adaptive response of Arabidopsis thaliana to prolonged thermal stress by ribosomal profiling and RNA-seq. BMC Plant Biol. 16, 221 (2016)

  12. 12.

    , , & Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223 (2009)

  13. 13.

    Combined roles of ethylene and endogenous peptides in regulating plant immunity and growth. Proc. Natl Acad. Sci. USA 110, 5748–5749 (2013)

  14. 14.

    , & Regulation of plant translation by upstream open reading frames. Plant Sci. 214, 1–12 (2014)

  15. 15.

    , & Gene expression regulation by upstream open reading frames and human disease. PLoS Genet. 9, e1003529 (2013)

  16. 16.

    , & Translational control by 5′-untranslated regions of eukaryotic mRNAs. Science 352, 1413–1416 (2016)

  17. 17.

    , & The autoregulatory translational control element of poly(A)-binding protein mRNA forms a heteromeric ribonucleoprotein complex. Nucleic Acids Res. 33, 7074–7089 (2005)

  18. 18.

    , , & Arabidopsis thaliana class II poly(A)-binding proteins are required for efficient multiplication of turnip mosaic virus. J. Gen. Virol. 89, 2339–2348 (2008)

  19. 19.

    The role of the poly(A) binding protein in the assembly of the Cap-binding complex during translation initiation in plants. Translation 2, e959378 (2014)

  20. 20.

    Translational regulation of GCN4 and the general amino acid control of yeast. Annu. Rev. Microbiol. 59, 407–450 (2005)

  21. 21.

    , , & Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317, 1224–1227 (2007)

  22. 22.

    et al. Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. J. Biosci. Bioeng. 104, 34–41 (2007)

  23. 23.

    & A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462–469 (2003)

  24. 24.

    et al. One-step, zero-background ligation-independent cloning intron-containing hairpin RNA constructs for RNAi in plants. New Phytol. 187, 240–250 (2010)

  25. 25.

    et al. Modification of vectors for functional genomic analysis in plants. Genet. Mol. Res. 13, 7815–7825 (2014)

  26. 26.

    et al. Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis. Proc. Natl Acad. Sci. USA 100, 2992–2997 (2003)

  27. 27.

    et al. EIN4 and ERS2 are members of the putative ethylene receptor gene family in Arabidopsis. Plant Cell 10, 1321–1332 (1998)

  28. 28.

    , , & A link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Plant Cell 17, 2230–2242 (2005)

  29. 29.

    et al. Calmodulin-binding transcription activator 1 mediates auxin signaling and responds to stresses in Arabidopsis. Planta 232, 165–178 (2010)

  30. 30.

    & Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998)

  31. 31.

    , , , & The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols 7, 1534–1550 (2012)

  32. 32.

    , & Isolation of plant polysomal mRNA by differential centrifugation and ribosome immunopurification methods. Methods Mol. Biol. 553, 109–126 (2009)

  33. 33.

    & Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357–359 (2012)

  34. 34.

    , & HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015)

  35. 35.

    , & Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014)

  36. 36.

    et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–8 (2009)

  37. 37.

    , , , & The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730–2731 (2009)

  38. 38.

    & Modified ribosome profiling reveals high abundance of ribosome protected mRNA fragments derived from 3′ untranslated regions. Nucleic Acids Res. 43, 1019–1034 (2015)

Download references

Acknowledgements

This study was supported by grants from National Institutes of Health 5R01 GM069594-11 and the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (through grant GBMF3032) to X. Dong. We thank J. M. Alonso for ein4-1, wei7-4, and ers1-10 seeds; T. Girke, M. Hummel, and J. Bailey-Serres for providing the Ribo-Seq workflow package for data analyses; W. Wang, P. Y. Hsu, and P. N. Benfey for discussing the protocol; R. Zavaliev for the callose staining method; and the Arabidopsis Information Resource for gcn2, erf7, eicbp.b, pab2/4, and pab2/8 seeds. We thank P. Zwack and S. Zebell for comments on the manuscript.

Author information

Author notes

    • Guoyong Xu
    • , George H. Greene
    •  & Heejin Yoo

    These authors contributed equally to this work.

Affiliations

  1. Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Department of Biology, Duke University, Durham, North Carolina 27708, USA

    • Guoyong Xu
    • , George H. Greene
    • , Heejin Yoo
    • , Lijing Liu
    • , Jorge Marqués
    • , Jonathan Motley
    •  & Xinnian Dong

Authors

  1. Search for Guoyong Xu in:

  2. Search for George H. Greene in:

  3. Search for Heejin Yoo in:

  4. Search for Lijing Liu in:

  5. Search for Jorge Marqués in:

  6. Search for Jonathan Motley in:

  7. Search for Xinnian Dong in:

Contributions

G.X. and X.D. designed the research. G.X., H.Y. and J. Marqués optimized the footprinting protocol. H.Y. and G.X. performed ethylene-related and polysome profiling experiments. L.L. and G.X. generated the reporter lines. G.X. and J. Motley performed eIF2α phosphorylation assay. G.X. performed the rest of the experiments. G.G. and G.X. performed the bioinformatic analyses and prepared the figures. G.X. and X.D. wrote the manuscript with input from all authors.

Competing interests

A patent based on this study has been filed by Duke University with G.X., G.G. and X.D. as inventors.

Corresponding author

Correspondence to Xinnian Dong.

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.

    Supplementary Information

    This file contains Supplementary Results and a Supplementary Figure showing the uncropped immunoblots.

Excel files

  1. 1.

    Supplementary Table 1

    This table shows RSfc, RFfc and TEfc upon elf18 treatment.

  2. 2.

    Supplementary Table 2

    This table contains GO terms for TE-altered genes upon elf18 treatment.

  3. 3.

    Supplementary Table 3

    This table contains information regarding the genes involved in the elf18-ethylene-Peps signalling pathway.

  4. 4.

    Supplementary Table 4

    This table shows uORF-containing genes.

  5. 5.

    Supplementary Table 5

    This table shows R-motif-containing genes in Arabidopsis, Drosophila, mouse and humans.

  6. 6.

    Supplementary Table 6

    This table contains the plasmids, primers and antibodies used in this study.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature22371

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.