Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

Nature

Volumn 465, Issue 7299, 2010, Pages 818-822

  Frank, Filipp ^a,b,c   Sonenberg, Nahum ^a,b   Nagar, Bhushan ^a,c  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c Groupe de Recherche Axé sur la Structure des Protéines   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE PHOSPHATE; ARGONAUTE 2 PROTEIN; CYCLIC AMP; DNA BASE; GUANOSINE PHOSPHATE; GUIDE RNA; MICRORNA; URIDINE PHOSPHATE;

CRYSTAL STRUCTURE; EUKARYOTE; EXPERIMENTAL STUDY; GENETIC ANALYSIS; PHOSPHATE; PROKARYOTE; PROTEIN; RNA;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE;

5'-GUANYLIC ACID; ADENOSINE MONOPHOSPHATE; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; CYTIDINE MONOPHOSPHATE; EUKARYOTIC INITIATION FACTOR-2; HUMANS; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; RNA, GUIDE; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; THERMODYNAMICS; URIDINE MONOPHOSPHATE;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 77953479619     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09039     Document Type: Article

References (30)

1. Hutvagner, G. & Simard, M. J. Argonaute proteins: key players in RNA silencing. Nature Rev. Mol. Cell Biol. 9, 22-32 (2008).
2. Ma, J.-B. et al. Structural basis for 59-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666-670 (2005).
3. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663-666 (2005).
4. Ghildiyal, M. et al. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077-1081 (2008).
5. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43-56 (2009).
6. Hu, H. Y. et al. Sequence features associated with microRNA strand selection in humans and flies. BMC Genomics 10, doi:10.1186/1471-2164-10-413 (2009).
7. Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862 (2001).
8. Ghildiyal, M. & Zamore, P. D. Small silencing RNAs: an expanding universe. Nature Rev. Genet. 10, 94-108 (2009).
9. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102-114 (2008).
10. Seitz, H., Ghildiyal, M. & Zamore, P. D. Argonaute loading improves the 59 precision of both microRNAs and their miRNA strands in flies. Curr. Biol. 18, 147-151 (2008).
11. Mi, S. et al. Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 59 terminal nucleotide. Cell 133, 116-127 (2008).
12. Montgomery, T. A. et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133, 128-141 (2008).
13. Takeda, A., Iwasaki, S., Watanabe, T., Utsumi, M. & Watanabe, Y. The mechanism selecting the guide strand from small RNA duplexes is different among Argonaute proteins. Plant Cell Physiol. 49, 493-500 (2008).
14. Ma, J.-B., Ye, K. & Patel, D. J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318-322 (2004).
15. Wang, Y. et al. Structure of an Argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921-926 (2008).
16. Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754-761 (2009).
17. Wang, Y., Sheng, G., Juranek, S., Tuschl, T. & Patel, D. J. Structure of the guide-strand-containing Argonaute silencing complex. Nature 456, 209-213 (2008).
18. Parker, J. S., Parizotto, E. A., Wang, M., Roe, S. M. & Barford, D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol. Cell 33, 204-214 (2009).
19. Song, J.-J., Smith, S. K., Hannon, G. J. & Joshua-Tor, L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305, 1434-1437 (2004).
20. Wahl, M. C. & Sundaralingam, M. C-HO hydrogen bonding in biology. Trends Biochem. Sci. 22, 97-102 (1997).
21. Felice, K. M., Salzman, D. W., Shubert-Coleman, J., Jensen, K. P. & Furneaux, H. M. The 59 terminal uracil of let-7a is critical for the recruitment of mRNA to Argonaute2. Biochem. J. 422, 329-341 (2009).
22. Wu, L. et al. Rice microRNA effector complexes and targets. Plant Cell 21, 3421-3435 (2009).
23. Czech, B. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798-802 (2008).
24. Kiriakidou, M. et al. An mRNA m7G cap binding-like motif within human Ago2 represses translation. Cell 129, 1141-1151 (2007).
25. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037-10041 (2001).
26. Mossessova, E. & Lima, C. D. Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast. Mol. Cell 5, 865-876 (2000).
27. Otwinowski, Z. Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276, 307-326 (1997).
28. Terwilliger, T. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D 59, 38-44 (2002).
29. Langer, G., Cohen, S. X., Lamzin, V. S. & Perrakis, A. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nature Protoc. 3, 1171-1179 (2008).
30. Adams, P., Grosse-Kunstleve, R. & Hung, L. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948-1954 (2002).