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Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′-3′ exoribonuclease activity

Nature Structural & Molecular Biology volume 19, pages 1011–1017 (2012)Cite this article

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Abstract

Recent studies showed that Rai1 is a crucial component of the mRNA 5′-end-capping quality-control mechanism in yeast. The yeast genome encodes a weak homolog of Rai1, Ydr370C, but little is known about this protein. Here we report the crystal structures of Ydr370C from Kluyveromyces lactis and the first biochemical and functional studies on this protein. The overall structure of Ydr370C is similar to Rai1. Ydr370C has robust decapping activity on RNAs with unmethylated caps, but it has no detectable pyrophosphohydrolase activity. Unexpectedly, Ydr370C also possesses distributive, 5′-3′ exoRNase activity, and we propose the name Dxo1 for this new eukaryotic enzyme with both decapping and exonuclease activities. Studies of yeast in which both Dxo1 and Rai1 are disrupted reveal that mRNAs with incomplete caps are produced even under normal growth conditions, in sharp contrast to current understanding of the capping process.

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Figure 1: Sequence conservation among Ydr370C (Dxo1), Rai1 and Dom3Z.
Figure 2: Crystal structures of Ydr370C (Dxo1).
Figure 3: Remote structural similarity to D-(D/E)XK nucleases.
Figure 4: Ydr370C (Dxo1) has strong decapping activity but no PPH activity.
Figure 5: Ydr370C (Dxo1) has distributive 5′-3′ exoRNase activity.
Figure 6: Dxo1 is involved in mRNA 5′-end capping quality control.

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Acknowledgements

We thank T.G. Kinzy (University of Medicine and Dentistry of New Jersey, Piscataway , New Jersey, USA) for the TAP-tagged Ydr370C strain; N. Whalen, S. Myers and H. Robinson for setting up the X29A beamline at the National Synchrotron Light Source . This research was supported by grants from the US National Institutes of Health to L.T. (GM090059) and M.K. (GM67005).

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  1. Jeong Ho Chang and Xinfu Jiao: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biological Sciences, Columbia University, New York, New York, USA

    Jeong Ho Chang, Kunitoshi Chiba & Liang Tong

  2. Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA

    Xinfu Jiao, ChanSeok Oh, Charles E Martin & Megerditch Kiledjian

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  1. Jeong Ho Chang
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Contributions

J.H.C. and K.C. performed protein expression, purification and crystallization experiments. J.H.C. carried out crystallographic data collection, structure determination and refinement, as well as mutagenesis and exonuclease assays. X.J. carried out decapping assays and all the studies in yeast cells. C.O. and C.E.M. generated the Rai1 and Dxo1 deletion strains. All authors commented on the manuscript. L.T. and M.K. designed experiments, analyzed data, supervised the project and wrote the paper.

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Correspondence to Megerditch Kiledjian or Liang Tong.

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Chang, J., Jiao, X., Chiba, K. et al. Dxo1 is a new type of eukaryotic enzyme with both decapping and 5′-3′ exoribonuclease activity. Nat Struct Mol Biol 19, 1011–1017 (2012). https://doi.org/10.1038/nsmb.2381

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