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Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA

Nature volume 451, pages 94–97 (2008)Cite this article

Abstract

The ‘RNA world’ hypothesis holds that during evolution the structural and enzymatic functions initially served by RNA were assumed by proteins, leading to the latter’s domination of biological catalysis. This progression can still be seen in modern biology, where ribozymes, such as the ribosome and RNase P, have evolved into protein-dependent RNA catalysts (‘RNPzymes’). Similarly, group I introns use RNA-catalysed splicing reactions, but many function as RNPzymes bound to proteins that stabilize their catalytically active RNA structure1,2. One such protein, the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (TyrRS; CYT-18), is bifunctional and both aminoacylates mitochondrial tRNATyr and promotes the splicing of mitochondrial group I introns3. Here we determine a 4.5-Å co-crystal structure of the Twort orf142-I2 group I intron ribozyme bound to splicing-active, carboxy-terminally truncated CYT-18. The structure shows that the group I intron binds across the two subunits of the homodimeric protein with a newly evolved RNA-binding surface distinct from that which binds tRNATyr. This RNA binding surface provides an extended scaffold for the phosphodiester backbone of the conserved catalytic core of the intron RNA, allowing the protein to promote the splicing of a wide variety of group I introns. The group I intron-binding surface includes three small insertions and additional structural adaptations relative to non-splicing bacterial TyrRSs, indicating a multistep adaptation for splicing function. The co-crystal structure provides insight into how CYT-18 promotes group I intron splicing, how it evolved to have this function, and how proteins could have incrementally replaced RNA structures during the transition from an RNA world to an RNP world.

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Figure 1: Co-crystal structure of the Twort orf 142-I2 group I intron ribozyme bound to CYT-18/Δ424–669.
Figure 2: CYT-18 binding to the P4–P6 domain.
Figure 3: CYT-18-specific insertions bridge the P4–P6 and P3–P9 domains.
Figure 4: CYT-18 and the P5abc peripheral RNA structure found in some group I introns interact similarly with the P4–P6 domain.

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Acknowledgements

We thank C. Correll, M. Hermodson, R. Russell and J. Tesmer for comments on the manuscript; T. Cech for discussions; the staff of SER-CAT and GM/CA-CAT, N. Sanishvili, D. Khare and M. Oldham for assistance with crystallographic data collection; and H. Kim for performing kinetic assays. Data were collected at GM/CA-CAT and SER-CAT beamlines at the Advanced Photon Source, Argonne National Laboratory. This work was supported by a grant from the National Institutes of Health to A.M.L.

Author Contributions P.J.P. and E.C. prepared materials for crystallization. E.C. crystallized the CYT-18–Twort RNA complex. J-H.C. collected and processed diffraction data. P.J.P. solved the structure. P.J.P., B.L.G. and A.M.L. interpreted data and wrote the paper.

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Author notes

  1. Alan M. Lambowitz and Barbara L. Golden: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712, USA,

    Paul J. Paukstelis & Alan M. Lambowitz

  2. Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA,

    Jui-Hui Chen, Elaine Chase & Barbara L. Golden

Authors
  1. Paul J. Paukstelis
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  3. Elaine Chase
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Corresponding authors

Correspondence to Alan M. Lambowitz or Barbara L. Golden.

Supplementary information

Supplementary Information

This file contains Supplementary Notes on structure validation, Supplementary Tables 1-3, Supplementary Figures 1-11 with Legends, and additional references. (PDF 2344 kb)

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Paukstelis, P., Chen, JH., Chase, E. et al. Structure of a tyrosyl-tRNA synthetase splicing factor bound to a group I intron RNA. Nature 451, 94–97 (2008). https://doi.org/10.1038/nature06413

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