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Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.

Frank F, Hauver J, Sonenberg N, Nagar B
EMBO J 31 3588-95 (2012)
Related entries: 4g0m, 4g0o, 4g0p, 4g0q, 4g0x, 4g0z

Cited: 62 times
EuropePMC logo PMID: 22850669

Abstract

The 5'-nucleotide of small RNAs associates directly with the MID domain of Argonaute (AGO) proteins. In humans, the identity of the 5'-base is sensed by the MID domain nucleotide specificity loop and regulates the integrity of miRNAs. In Arabidopsis thaliana, the 5'-nucleotide also controls sorting of small RNAs into the appropriate member of the AGO family; however, the structural basis for this mechanism is unknown. Here, we present crystal structures of the MID domain from three Arabidopsis AGOs, AtAGO1, AtAGO2 and AtAGO5, and characterize their interactions with nucleoside monophosphates (NMPs). In AtAGOs, the nucleotide specificity loop also senses the identity of the 5'-nucleotide but uses more diverse modes of recognition owing to the greater complexity of small RNAs found in plants. Binding analyses of these interactions reveal a strong correlation between their affinities and evolutionary conservation.

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  1. Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs. Frank F, Hauver J, Sonenberg N, Nagar B. EMBO J 31 3588-3595 (2012)


Reviews citing this publication (18)

  1. Argonaute proteins: functional insights and emerging roles. Meister G. Nat Rev Genet 14 447-459 (2013)
  2. The expanding world of small RNAs in plants. Borges F, Martienssen RA. Nat Rev Mol Cell Biol 16 727-741 (2015)
  3. The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Bologna NG, Voinnet O. Annu Rev Plant Biol 65 473-503 (2014)
  4. The evolutionary journey of Argonaute proteins. Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin EV, Patel DJ, van der Oost J. Nat Struct Mol Biol 21 743-753 (2014)
  5. RNAi in Plants: An Argonaute-Centered View. Fang X, Qi Y. Plant Cell 28 272-285 (2016)
  6. From guide to target: molecular insights into eukaryotic RNA-interference machinery. Ipsaro JJ, Joshua-Tor L. Nat Struct Mol Biol 22 20-28 (2015)
  7. Structural Foundations of RNA Silencing by Argonaute. Sheu-Gruttadauria J, MacRae IJ. J Mol Biol 429 2619-2639 (2017)
  8. Eukaryotic Argonautes come into focus. Kuhn CD, Joshua-Tor L. Trends Biochem Sci 38 263-271 (2013)
  9. To be or not to be a piRNA: genomic origin and processing of piRNAs. Le Thomas A, Tóth KF, Aravin AA. Genome Biol 15 204 (2014)
  10. siRNA Specificity: RNAi Mechanisms and Strategies to Reduce Off-Target Effects. Neumeier J, Meister G. Front Plant Sci 11 526455 (2020)
  11. DNA silencing by prokaryotic Argonaute proteins adds a new layer of defense against invading nucleic acids. Willkomm S, Makarova KS, Grohmann D. FEMS Microbiol Rev 42 376-387 (2018)
  12. The AGO proteins: an overview. Niaz S. Biol Chem 399 525-547 (2018)
  13. A prokaryotic twist on argonaute function. Willkomm S, Zander A, Gust A, Grohmann D. Life (Basel) 5 538-553 (2015)
  14. microRNA biogenesis and turnover in plants. Rogers K, Chen X. Cold Spring Harb Symp Quant Biol 77 183-194 (2012)
  15. Messages on small RNA duplexes in plants. Iki T. J Plant Res 130 7-16 (2017)
  16. Argonaute proteins: structures and their endonuclease activity. Jin S, Zhan J, Zhou Y. Mol Biol Rep 48 4837-4849 (2021)
  17. Conformational Dynamics of Ago-Mediated Silencing Processes. Willkomm S, Restle T. Int J Mol Sci 16 14769-14785 (2015)
  18. Structural insights into the arms race between host and virus along RNA silencing pathways in Arabidopsis thaliana. Guo W, Liew JY, Yuan YA. Biol Rev Camb Philos Soc 89 337-355 (2014)

Articles citing this publication (43)

  1. DNA-guided DNA interference by a prokaryotic Argonaute. Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J. Nature 507 258-261 (2014)
  2. Bacterial argonaute samples the transcriptome to identify foreign DNA. Olovnikov I, Chan K, Sachidanandam R, Newman DK, Aravin AA. Mol Cell 51 594-605 (2013)
  3. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Swarts DC, Hegge JW, Hinojo I, Shiimori M, Ellis MA, Dumrongkulraksa J, Terns RM, Terns MP, van der Oost J. Nucleic Acids Res 43 5120-5129 (2015)
  4. Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures. Poulsen C, Vaucheret H, Brodersen P. Plant Cell 25 22-37 (2013)
  5. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD. Mol Cell 56 708-716 (2014)
  6. DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute. Hegge JW, Swarts DC, Chandradoss SD, Cui TJ, Kneppers J, Jinek M, Joo C, van der Oost J. Nucleic Acids Res 47 5809-5821 (2019)
  7. Structural and mechanistic insights into an archaeal DNA-guided Argonaute protein. Willkomm S, Oellig CA, Zander A, Restle T, Keegan R, Grohmann D, Schneider S. Nat Microbiol 2 17035 (2017)
  8. Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Miyoshi T, Ito K, Murakami R, Uchiumi T. Nat Commun 7 11846 (2016)
  9. The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. Cora E, Pandey RR, Xiol J, Taylor J, Sachidanandam R, McCarthy AA, Pillai RS. RNA 20 773-781 (2014)
  10. Small-RNA asymmetry is directly driven by mammalian Argonautes. Suzuki HI, Katsura A, Yasuda T, Ueno T, Mano H, Sugimoto K, Miyazono K. Nat Struct Mol Biol 22 512-521 (2015)
  11. Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute. Swarts DC, Szczepaniak M, Sheng G, Chandradoss SD, Zhu Y, Timmers EM, Zhang Y, Zhao H, Lou J, Wang Y, Joo C, van der Oost J. Mol Cell 65 985-998.e6 (2017)
  12. Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. Endo Y, Iwakawa HO, Tomari Y. EMBO Rep 14 652-658 (2013)
  13. Decoding the 5' nucleotide bias of PIWI-interacting RNAs. Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Nat Commun 10 828 (2019)
  14. Molecular evolution and diversification of the Argonaute family of proteins in plants. Singh RK, Gase K, Baldwin IT, Pandey SP. BMC Plant Biol 15 23 (2015)
  15. Abundant expression of maternal siRNAs is a conserved feature of seed development. Grover JW, Burgess D, Kendall T, Baten A, Pokhrel S, King GJ, Meyers BC, Freeling M, Mosher RA. Proc Natl Acad Sci U S A 117 15305-15315 (2020)
  16. FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts. Harris CJ, Molnar A, Müller SY, Baulcombe DC. Nucleic Acids Res 43 7590-7599 (2015)
  17. Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Voshall A, Kim EJ, Ma X, Moriyama EN, Cerutti H. Genetics 200 105-121 (2015)
  18. Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis. Sabbione A, Daurelio L, Vegetti A, Talón M, Tadeo F, Dotto M. BMC Plant Biol 19 401 (2019)
  19. 08B1-1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source. Fodje M, Grochulski P, Janzen K, Labiuk S, Gorin J, Berg R. J Synchrotron Radiat 21 633-637 (2014)
  20. Origin, evolution and diversification of plant ARGONAUTE proteins. Li Z, Li W, Guo M, Liu S, Liu L, Yu Y, Mo B, Chen X, Gao L. Plant J 109 1086-1097 (2022)
  21. Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA. Dayeh DM, Cantara WA, Kitzrow JP, Musier-Forsyth K, Nakanishi K. Nucleic Acids Res 46 e98 (2018)
  22. Give It AGO: The Search for miRNA-Argonaute Sorting Signals in Arabidopsis thaliana Indicates a Relevance of Sequence Positions Other than the 5'-Position Alone. Thieme CJ, Schudoma C, May P, Walther D. Front Plant Sci 3 272 (2012)
  23. Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Chung BY, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC. Sci Rep 9 11091 (2019)
  24. Rapid Evolution of microRNA Loci in the Brown Algae. Cock JM, Liu F, Duan D, Bourdareau S, Lipinska AP, Coelho SM, Tarver JE. Genome Biol Evol 9 740-749 (2017)
  25. Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants. Dueck A, Evers M, Henz SR, Unger K, Eichner N, Merkl R, Berezikov E, Engelmann JC, Weigel D, Wenzl S, Meister G. BMC Genomics 17 853 (2016)
  26. Genome-Wide Identification, Characterization, and Expression Analysis of Small RNA Biogenesis Purveyors Reveal Their Role in Regulation of Biotic Stress Responses in Three Legume Crops. Garg V, Agarwal G, Pazhamala LT, Nayak SN, Kudapa H, Khan AW, Doddamani D, Sharma M, Kavi Kishor PB, Varshney RK. Front Plant Sci 8 488 (2017)
  27. Evolution of structural and functional diversification among plant Argonautes. Singh RK, Pandey SP. Plant Signal Behav 10 e1069455 (2015)
  28. Label-Free Electrophoretic Mobility Shift Assay (EMSA) for Measuring Dissociation Constants of Protein-RNA Complexes. Seo M, Lei L, Egli M. Curr Protoc Nucleic Acid Chem 76 e70 (2019)
  29. A Hyperthermophilic Argonaute From Ferroglobus placidus With Specificity on Guide Binding Pattern. Guo X, Sun Y, Chen L, Huang F, Liu Q, Feng Y. Front Microbiol 12 654345 (2021)
  30. Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.). Hamar É, Szaker HM, Kis A, Dalmadi Á, Miloro F, Szittya G, Taller J, Gyula P, Csorba T, Havelda Z, Havelda Z. Biomolecules 10 E929 (2020)
  31. Genome-wide identification of Argonautes in Solanaceae with emphasis on potato. Liao Z, Hodén KP, Singh RK, Dixelius C. Sci Rep 10 20577 (2020)
  32. Enzymatic reactions of AGO4 in RNA-directed DNA methylation: siRNA duplex loading, passenger strand elimination, target RNA slicing, and sliced target retention. Wang F, Huang HY, Huang J, Singh J, Pikaard CS. Genes Dev 37 103-118 (2023)
  33. Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon. Šečić E, Zanini S, Kogel KH. Front Plant Sci 10 1332 (2019)
  34. The mechanisms of siRNA selection by plant Argonaute proteins triggering DNA methylation. Liu W, Shoji K, Naganuma M, Tomari Y, Iwakawa HO. Nucleic Acids Res 50 12997-13010 (2022)
  35. The molecular mechanism of microRNA duplex selectivity of Arabidopsis ARGONAUTE10. Xiao Y, MacRae IJ. Nucleic Acids Res 50 10041-10052 (2022)
  36. Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora. Bollmann SR, Press CM, Tyler BM, Grünwald NJ. Front Microbiol 9 2841 (2018)
  37. Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis. Leclercq J, Wu S, Farinas B, Pointet S, Favreau B, Vignes H, Kuswanhadi K, Ortega-Abboud E, Dufayard JF, Gao S, Droc G, Hu S, Tang C, Montoro P. PeerJ 8 e8932 (2020)
  38. Prokaryotic Argonaute from Archaeoglobus fulgidus interacts with DNA as a homodimer. Golovinas E, Rutkauskas D, Manakova E, Jankunec M, Silanskas A, Sasnauskas G, Zaremba M. Sci Rep 11 4518 (2021)
  39. A computational model for non-conserved mature miRNAs from the rice genome. Kumar SP, Pandya HA, Jasrai YT. SAR QSAR Environ Res 25 205-220 (2014)
  40. Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas. Li Y, Kim EJ, Voshall A, Moriyama EN, Cerutti H. Plant Cell 35 1868-1887 (2023)
  41. Beyond identity: Understanding the contribution of the 5' nucleotide of the antisense strand to RNAi activity. Yang P, Havecker E, Bauer M, Diehl C, Hendrix B, Hoffer P, Boyle T, Bradley J, Caruano-Yzermans A, Deikman J. PLoS One 16 e0256863 (2021)
  42. Structural basis for sequence-specific recognition of guide and target strands by the Archaeoglobus fulgidus Argonaute protein. Manakova E, Golovinas E, Pocevičiūtė R, Sasnauskas G, Grybauskas A, Gražulis S, Zaremba M. Sci Rep 13 6123 (2023)
  43. The N-terminal extension of Arabidopsis ARGONAUTE 1 is essential for microRNA activities. Xu Y, Zhang Y, Li Z, Soloria AK, Potter S, Chen X. PLoS Genet 19 e1010450 (2023)


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