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Nonsense-mediated mRNA decay modulates FLM-dependent thermosensory flowering response in Arabidopsis

Abstract

Increasing global temperatures have an impact on flowering, and the underlying mechanisms are just beginning to be unravelled1,2. Elevated temperatures can induce flowering, and different mechanisms that involve either activation or de-repression of FLOWERING LOCUS T (FT) by transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) or the FLOWERING LOCUS M (FLM)–SHORT VEGETATIVE PHASE (SVP) complex, respectively, have been suggested to be involved36. Thermosensitivity in flowering has been mapped to FLM5, which encodes a floral repressor7,8. FLM undergoes alternative splicing8 and it has been suggested that temperature-dependent alternative splicing leads to differential accumulation of the FLM-β and FLM-δ transcripts, encoding proteins with antagonistic effects, and that their ratio determines floral transition4. Here we show that high temperatures downregulate FLM expression by alternative splicing coupled with nonsense-mediated mRNA decay (AS-NMD). We identify thermosensitive splice sites in FLM and show that the primary effect of temperature is explained by an increase in NMD target transcripts. We also show that flm is epistatic to pif4, which suggests that most of the PIF4 effects are FLM dependent. Our findings suggest a model in which the loss of the floral repressor FLM occurs through mRNA degradation in response to elevated temperatures, signifying a role for AS-NMD in conferring environmental responses in plants.

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Figure 1: Higher temperatures lead to downregulation of FLM expression by modulating alternative splicing.
Figure 2: Temperature affects the efficiency of specific splice sites, resulting in production of transcripts that undergo NMD.
Figure 3: Overexpression of the potential NMD target transcripts can interfere with floral repression.
Figure 4: Thermal induction of floral transition in short days.

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Acknowledgements

We thank C.A. Kraupner-Taylor for technical support, the Arabidopsis Biological Resource Centre (ABRC) and C. Fankhauser for seeds, H. Eimer and W. Zhu for providing some of the DNA and RNA samples used in this study, and J. Bowman, R. Burke, R. Clark, D. Smyth and W. Zhu for critical reading of the manuscript. This work is supported by Australian Research Council Discovery Projects DP110100964 and DP0987835 to S.S. and S.B., respectively, an ARC-Discovery Early Career Researcher Award (DE130100320) to C.T., an ARC Future Fellowship (FT100100377) to S.B. and funds from the Larkins Fellowship programme at Monash University to S.B.

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Authors

Contributions

S.S. and S.B. designed the study. S.S. carried out most of the experiments. S.S., C.D., A.S., C.T. and S.B. analysed the data. S.S., C.D. and S.B. wrote the manuscript with input from all authors. S.B. supervised the study.

Corresponding author

Correspondence to Sureshkumar Balasubramanian.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information (PDF 1068 kb)

Supplementary Table 1

Different splice forms identified through Sanger sequencing. (XLSX 41 kb)

Supplementary Table 2

Effect of temperature on splicing at the FLM locus in Col-0. (XLSX 32 kb)

Supplementary Table 3

Actual counts and normalized counts from RNA-Seq. (XLSX 57 kb)

Supplementary Table 4

Flowering time measured as total leaf number in accessions that are potential knockouts for FLM-δ. (XLSX 48 kb)

Supplementary Table 5

Primers used in this study. (XLSX 39 kb)

Supplementary Table 6

NMD target genes, whose expression is analysed in Col-0 and upf 1-5 mutants. (XLSX 42 kb)

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Sureshkumar, S., Dent, C., Seleznev, A. et al. Nonsense-mediated mRNA decay modulates FLM-dependent thermosensory flowering response in Arabidopsis. Nature Plants 2, 16055 (2016). https://doi.org/10.1038/nplants.2016.55

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