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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References
Lambowitz, A. M., Caprara, M. G., Zimmerly, S. & Perlman, P. S. in The RNA World, 2nd edn (eds Gesteland, R.F., Cech, T.R. & Atkins, J.F.) 451–485 (Cold Spring Harbor Press, New York, 1999)
Lambowitz, A. M. & Perlman, P. S. Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing. Trends Biochem. Sci. 15, 440–444 (1990)
Akins, R. A. & Lambowitz, A. M. A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof. Cell 50, 331–345 (1987)
Michel, F. & Westhof, E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585–610 (1990)
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J. & Strobel, S. A. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45–50 (2004)
Guo, F., Gooding, A. R. & Cech, T. R. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol. Cell 16, 351–362 (2004)
Golden, B. L., Kim, H. & Chase, E. Crystal structure of a phage Twort group I ribozyme–product complex. Nat. Struct. Mol. Biol. 12, 82–89 (2005)
Mohr, G., Zhang, A., Gianelos, J. A., Belfort, M. & Lambowitz, A. M. The Neurospora CYT-18 protein suppresses defects in the phage T4 td intron by stabilizing the catalytically active structure of the intron core. Cell 69, 483–494 (1992)
Guo, Q. & Lambowitz, A. M. A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core. Genes Dev. 6, 1357–1372 (1992)
Mohr, G., Caprara, M. G., Guo, Q. & Lambowitz, A. M. A tyrosyl-tRNA synthetase can function similarly to an RNA structure in the Tetrahymena ribozyme. Nature 370, 147–150 (1994)
Caprara, M. G., Lehnert, V., Lambowitz, A. M. & Westhof, E. A tyrosyl-tRNA synthetase recognizes a conserved tRNA-like structural motif in the group I intron catalytic core. Cell 87, 1135–1145 (1996)
Paukstelis, P. J. et al. A tyrosyl-tRNA synthetase adapted to function in group I intron splicing by acquiring a new RNA binding surface. Mol. Cell 17, 417–428 (2005)
Yaremchuk, A., Kriklivyi, I., Tukalo, M. & Cusack, S. Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J. 21, 3829–3840 (2002)
Kämper, U., Kück, U., Cherniack, A. D. & Lambowitz, A. M. The mitochondrial tyrosyl-tRNA synthetase of Podospora anserina is a bifunctional enzyme active in protein synthesis and RNA splicing. Mol. Cell. Biol. 12, 499–511 (1992)
Kleinjung, J. & Fraternali, F. POPSCOMP: an automated interaction analysis of biomolecular complexes. Nucleic Acids Res. 33, W342–6 (2005)
Chen, X., Gutell, R. R. & Lambowitz, A. M. Function of tyrosyl-tRNA synthetase in splicing group I introns: an induced-fit model for binding to the P4–P6 domain based on analysis of mutations at the junction of the P4–P6 stacked helices. J. Mol. Biol. 301, 265–283 (2000)
Caprara, M. G., Myers, C. A. & Lambowitz, A. M. Interaction of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) with the group I intron P4–P6 domain. Thermodynamic analysis and the role of metal ions. J. Mol. Biol. 308, 165–190 (2001)
Caprara, M. G., Mohr, G. & Lambowitz, A. M. A tyrosyl-tRNA synthetase protein induces tertiary folding of the group I intron catalytic core. J. Mol. Biol. 257, 512–531 (1996)
Webb, A. E., Rose, M. A., Westhof, E. & Weeks, K. M. Protein-dependent transition states for ribonucleoprotein assembly. J. Mol. Biol. 309, 1087–1100 (2001)
Myers, C. A. et al. A tyrosyl-tRNA synthetase suppresses structural defects in the two major helical domains of the group I intron catalytic core. J. Mol. Biol. 262, 87–104 (1996)
Waldsich, C., Grossberger, R. & Schroeder, R. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo . Genes Dev. 16, 2300–2312 (2002)
Weeks, K. M. & Cech, T. R. Assembly of a ribonucleoprotein catalyst by tertiary structure capture. Science 271, 345–348 (1996)
Cate, J. H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678–1685 (1996)
Chen, X., Mohr, G. & Lambowitz, A. M. The Neurospora crassa CYT-18 protein C-terminal RNA-binding domain helps stabilize interdomain tertiary interactions in group I introns. RNA 10, 634–644 (2004)
Mohr, G., Rennard, R., Cherniack, A. D., Stryker, J. & Lambowitz, A. M. Function of the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase in RNA splicing. Role of the idiosyncratic N-terminal extension and different modes of interaction with different group I introns. J. Mol. Biol. 307, 75–92 (2001)
Galagan, J. E., Henn, M. R., Ma, L. J., Cuomo, C. A. & Birren, B. Genomics of the fungal kingdom: insights into eukaryotic biology. Genome Res. 15, 1620–1631 (2005)
Selker, E. U. Premeiotic instability of repeated sequences in Neurospora crassa . Annu. Rev. Genet. 24, 579–613 (1990)
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)
McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D Biol. Crystallogr. 61, 458–464 (2005)
Brünger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998)
Landthaler, M. & Shub, D. A. Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proc. Natl Acad. Sci. USA 96, 7005–7010 (1999)
DeLaBarre, B. & Brünger, A. T. Considerations for the refinement of low-resolution crystal structures. Acta Crystallogr. D Biol. Crystallogr. 62, 923–932 (2006)
Vriend, G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph. 8, 52–56 (1990)
McRee, D. E. XtalView/Xfit—a versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125, 156–165 (1999)
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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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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DOI: https://doi.org/10.1038/nature06413
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