Structural basis for piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 3, 2011, Pages 903-910

  Tian, Yuan ^a,b   Simanshu, Dhirendra K ^a   Ma, Jin Biao ^a,c   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HILI PROTEIN; HIWI1 PROTEIN; HIWI2 PROTEIN; HIWI3 PROTEIN; PIWI INTERACTING RNA; PIWI PROTEIN; UNCLASSIFIED DRUG; EIF2C1 PROTEIN, HUMAN; INITIATION FACTOR; PIWIL1 PROTEIN, HUMAN; PRIMER DNA; PROTEIN; SMALL INTERFERING RNA;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN METHYLATION; RNA STRUCTURE; BINDING SITE; CHEMICAL STRUCTURE; CRYSTALLOGRAPHY; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; RNA INTERFERENCE; ULTRASTRUCTURE;

BINDING SITES; CRYSTALLOGRAPHY; DNA PRIMERS; EUKARYOTIC INITIATION FACTORS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 79551634514     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1017762108     Document Type: Article

References (42)

1. Kim VN, Han J, Siomi MC (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10:126-139.
2. Farazi TA, Juranek SA, Tuschl T (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135: 1201-1214.
3. Wang Y, et al. (2009) Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461:754-761.
4. Girard A, Hannon GJ (2008) Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol 18:136-148.
5. Siomi MC, Kuramochi-Miyagawa S (2009) RNA silencing in germlines - exquisite collaboration of Argonaute proteins with small RNAs for germline survival. Curr Opin Cell Biol 21:426-434.
6. Lingel A, Simon B, Izaurralde E, Sattler M (2003) Structure and nucleic-acid binding of the Drosophila Argonaute2 PAZ domain. Nature 426:465-469.
7. Song JJ, et al. (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol 10:1026-1032.
8. Yan KS, et al. (2003) Structure and conserved RNA binding of the PAZ domain. Nature 426:468-474.
9. Ma JB, Ye K, Patel DJ (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429:318-322.
10. Lingel A, Simon B, Izaurralde E, Sattler M (2004) Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain. Nat Struct Mol Biol 11:576-577. (Pubitemid 38691927)
11. Hock J, Meister G (2008) The Argonaute protein family. Genome Biol 9:210.1-210.8.
12. Hutvagner G, Simard MJ (2008) Argonaute proteins: Key players in RNA silencing. Nat Rev Mol Cell Biol 9:22-32.
13. Bartel DP (2009) MicroRNAs: Target recognition and regulatory functions. Cell 136:215-233.
14. Bernstein E, Caudy AA, Hammond SM, Hannon GJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-366.
15. Macrae IJ, et al. (2006) Structural basis for double-stranded RNA processing by Dicer. Science 311:195-198.
16. Dykxhoorn DM, Novina CD, Sharp PA (2003) Killing the messenger: Short RNAs that silence gene expression. Nat Rev Mol Cell Biol 4:457-467.
17. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343-349.
18. Filipowicz W (2005) RNAi: The nuts and bolts of the RISC machine. Cell 122:17-20.
19. Wang Y, Sheng G, Juranek S, Tuschl T, Patel DJ (2008) Structure of the guide-strand-containing argonaute silencing complex. Nature 456:209-213.
20. Parker JS (2010) How to slice: Snapshots of Argonaute in action. Silence 1:3.1-3.10.
21. Aravin A, et al. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203-207.
22. Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442:199-202.
23. Grivna ST, Beyret E, Wang Z, Lin H (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20:1709-1714.
24. Lau NC, et al. (2006) Characterization of the piRNA complex from rat testes. Science 313:363-367.
25. Watanabe T, et al. (2006) Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev 20:1732-1743.
26. Kirino Y, Mourelatos Z (2007) Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nat Struct Mol Biol 14:347-348. (Pubitemid 46608343)
27. Ohara T, Sakaguchi Y, Suzuki T, Ueda H, Miyauchi K (2007) The 3′ termini of mouse Piwi-interacting RNAs are 2′-O-methylated. Nat Struct Mol Biol 14:349-350.
28. Horwich MD, et al. (2007) The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr Biol 17:1265-1272.
29. Saito K, Sakaguchi Y, Suzuki T, Siomi H, Siomi MC (2007) Pimet, the Drosophila homolog of HEN1, mediates 2′-O-methylation of Piwi- interacting RNAs at their 3′ ends. Genes Dev 21:1603-1608.
30. Li J, Yang Z, Yu B, Liu J, Chen X (2005) Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr Biol 15:1501-1507. (Pubitemid 41187490)
31. Yu B, et al. (2005) Methylation as a crucial step in plant microRNA biogenesis. Science 307:932-935.
32. Aravin AA, Sachidanandam R, Girard A, Fejes-Toth K, Hannon GJ (2007) Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316: 744-747.
33. Gunawardane LS, et al. (2007) A slicer-mediated mechanism for repeat-associated siRNA 5′ end formation in Drosophila. Science 315:1587-1590.
34. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
35. Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W (2003) Generation, representation and flow of phase information in structure determination: Recent developments in and around SHARP 2.0. Acta Crystallogr, Sect D: Biol Crystallogr 59:2023-2030.
36. Abrahams JP, Leslie AG (1996) Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr, Sect D: Biol Crystallogr 52:30-42.
37. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr, Sect D: Biol Crystallogr 60:2126-2132.
38. Afonine PV, Grosse-Kunstleve RW, Adams PD (2005) The Phenix refinement framework. CCP4 Newsletter on Protein Crystallography 42. contribution 8.
39. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr, Sect D: Biol Crystallogr 53:240-255.
40. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck-a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283-291.
41. DeLano WL (2002) The PyMOL Molecular Graphics System (DeLano Scientific, Palo Alto, CA).
42. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31:3320-3323. (Pubitemid 37442149)