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A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs

Nature Structural & Molecular Biology volume 16, pages 541–549 (2009)Cite this article

Abstract

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with clear resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. As the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein–mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing.

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Figure 1: A conserved structured RNA element in plants resembles 5S rRNA.
Figure 2: The cassette exon containing the plant 5S rRNA mimic shows regulated alternative splicing and yields two splice products giving different gene expression.
Figure 3: Ribosomal protein L5 specifically increases TFIIIA gene expression by promoting splice product I formation.
Figure 4: GST-L5 fusion protein binds to P5SM RNA in vitro.
Figure 5: The P2 stem of P5SM RNA is critical for binding to GST-L5 in vitro, and disruption of L5 binding abolishes regulation of splicing in vivo.
Figure 6: The constitutive splicing patterns of deregulated mutants reveal that P5SM is involved in both exon definition and skipping, leading to a proposed model for regulation of TFIIIA pre-mRNA splicing.

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NCBI Reference Sequence

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Acknowledgements

We thank K. Corbino, K. Leppek and A. Westermann for technical assistance, Z. Weinberg for advice on bioinformatics, E. Puerta-Fernandez for advice on gel-shift assays and A. Roth for critical reading of the manuscript. M.C.H. is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund, and A.W. was supported by the German Research Foundation while in the Breaker laboratory. The research was supported by a grant from the US National Institutes of Health (GM068819). RNA science in the Breaker laboratory also is supported by the Howard Hughes Medical Institute.

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Author notes

  1. Andreas Wachter

    Present address: Present address: Center for Plant Molecular Biology (ZMBP), Department of General Genetics, University of Tuebingen, Tuebingen, Germany.,

Authors and Affiliations

  1. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA

    Ming C Hammond & Ronald R Breaker

  2. Heidelberg Institute of Plant Science, Heidelberg University, Heidelberg, Germany

    Andreas Wachter

  3. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA

    Ronald R Breaker

  4. Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA

    Ronald R Breaker

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  1. Ming C Hammond
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Contributions

M.C.H. conceived of and led project, performed bioinformatics analysis, designed and carried out in vitro structural probing and binding experiments, and wrote the manuscript. A.W. designed and carried out RT-PCR and qRT-PCR analyses and in vivo reporter assays, and edited the manuscript. R.R.B. advised on the project and edited the manuscript. All authors contributed to discussions regarding the data and their interpretation.

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Correspondence to Ronald R Breaker.

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Hammond, M., Wachter, A. & Breaker, R. A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs. Nat Struct Mol Biol 16, 541–549 (2009). https://doi.org/10.1038/nsmb.1588

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