Structure of precursor microRNA’s terminal loop regulates human Dicer’s dicing activity by switching DExH/D domain

Abstract

Almost all pre-miRNAs in eukaryotic cytoplasm are recognized and processed into double-stranded microRNAs by the endonuclease Dicer protein comprising of multiple domains. As a key player in the small RNA induced gene silencing pathway, the major domains of Dicer are conserved among different species with the exception of the N-terminal components. Human Dicer’s N-terminal domain has been shown to play an autoinhibitory function of the protein’s dicing activity. Such an auto-inhibition can be released when the human Dicer protein dimerizes with its partner protein, such as TRBP, PACT through the N-terminal DExH/D (ATPase-helicase) domain. The typical feature of a pre-miRNA contains a terminal loop and a stem duplex, which bind to human Dicer’s DExH/D (ATPase-helicase) domain and PAZ domain respectively during the dicing reaction. Here, we show that pre-miRNA’s terminal loop can regulate human Dicer’s enzymatic activity by interacting with the DExH/D (ATPase-helicase) domain. We found that various editing products of pre-miR-151 by the ADAR1P110 protein, an A-to-I editing enzyme that modifies pre-miRNAs sequence, have different terminal loop structures and different activity regulatory effects on human Dicer. Single particle electron microscopy reconstruction revealed that pre-miRNAs with different terminal loop structures induce human Dicer’s DExH/D (ATPase-helicase) domain into different conformational states, in correlation with their activity regulatory effects.

Keywords

human Dicer / DExH/D (ATPase-helicase) domain / pre-miRNA-151 / A-to-I editing / single particle electron microscopy

References

[1] Ando Y, Maida Y, Morinaga A, Burroughs AM, Kimura R, Chiba J, Suzuki H, Masutomi K, Hayashizaki Y (2011) Two-step cleavage of hairpin RNA with 5’ overhangs by human DICER. BMC Mol Biol12: 6

[2] Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR (2006) RNA editing of human microRNAs. Genome Biol7: R27

[3] Brennicke A, Marchfelder A, Binder S (1999) RNA editing. FEMS Microbiol Rev23: 297-316

[4] Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell136: 642-655

[5] Castilla-Llorente V, Nicastro G, Ramos A (2013) Terminal loopmediated regulation of miRNA biogenesis: selectivity and mechanisms. Biochem Soc Trans41: 861-865

[6] Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R (2005) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature436: 740-744

[7] Das AK, Carmichael GG (2007) ADAR editing wobbles the microRNA world. ACS Chem Biol2: 217-220

[8] Grifflths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res36: D154-D158

[9] Gu S, Jin L, Zhang Y, Huang Y, Zhang F, Valdmanis PN, Kay MA (2012) The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell151: 900-911

[10] He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet5: 522-531

[11] Heo I, Joo C, Cho J, Ha M, Han J, Kim VN (2008) Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell32: 276-284

[12] Heo I, Ha M, Lim J, Yoon MJ, Park JE, Kwon SC, Chang H, Kim VN (2012) Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell151: 521-532

[13] Kawahara Y, Zinshteyn B, Chendrimada TP, Shiekhattar R, Nishikura K (2007a) RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep8: 763-769

[14] Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K (2007b) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science315: 1137-1140

[15] Lau P-W, Guiley KZ, De N, Potter CS, Carragher B, MacRae IJ (2012) The molecular architecture of human Dicer. Nat Struct Mol Biol19: 436-440

[16] Lee Y, Hur I, Park S-Y, Kim Y-K, Suh MR, Kim AVN (2006) The role of PACT in the RNA silencing pathway. EMBO J25: 522-532

[17] Ma E, MacRae IJ, Kirsch JF, Doudna JA (2008) Autoinhibition of human dicer by its internal helicase domain. J Mol Biol380: 237-243

[18] MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA (2008) In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci USA105(2): 512-517

[19] Nishikura K (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem79: 321-349

[20] Ota H, Sakurai M, Gupta R, Valente L, Wulff BE, Ariyoshi K, Iizasa H, Davuluri RV, Nishikura K (2013) ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing. Cell153: 575-589

[21] Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN (2011) Dicer recognizes the 5′ end of RNA for efficient and accurate processing. Nature475: 201-205

[22] Scheres SHW (2012) RELION: implementationofaBayesianapproach to cryo-EM structure determination. J Struct Biol180: 519-530

[23] Schraml E, Grillari J (2012) From cellular senescence to age associated diseases: the miRNA connection. Longev Heal1: 1-15

[24] Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J (2008) SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc3: 1941-1974

[25] Su AAH, Randau L (2011) A-to-I and C-to-U editing within transfer RNAs. Biochemistry76: 932-937

[26] Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol157: 38-46

[27] Taylor DW, Ma E, Shigematsu H, Cianfrocco MA, Noland CL, Nagayama K, Nogales E, Doudna JA, Wang H-W (2013) Substrate-speciflc structural rearrangements of human Dicer. Nat Struct Mol Biol: 662-670

[28] Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y (2011) Recognition of the pre-miRNA structure by Drosophila Dicer-1. Nat Struct Mol Biol18: 1153-1158

[29] van Heel M, Harauz G, Orlova EV, Schmidt R, Schatz M (1996) A new generation of the IMAGIC image processing system. J Struct Biol116: 17-24

[30] Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, Felderer K, Doudna JA, Nogales E (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol16: 1148-1153

[31] Xie M, Li M, Vilborg A, Lee N, Shu MD, Yartseva V, Sestan N, Steitz JA (2013) Mammalian 5′-capped microRNA precursors that generate a single microRNA. Cell155: 1568-1580

[32] Yang W, Chendrimada TP, Wang Q, Higuchi M, Seeburg PH, Shiekhattar R, Nishikura K (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol13: 13-21

[33] Zhang X, Zeng Y (2010) The terminal loop region controls microRNA processing by Drosha and Dicer. Nucleic Acids Res38: 7689-7697

[34] Zhang H, Kolb FA, Vincent Brondani EBA, Filipowicz W (2002) Human Dicer preferentially cleaves dsRNAs at their termini without ATP. EMBO J21: 5875-5885

[35] Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase III. Cell118: 57-68

[36] Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res31: 3406-3415

RIGHTS & PERMISSIONS

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.