- -

Argonaute PIWI domain and microRNA duplex structure contribute to small RNA sorting in Arabidopsis.

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Argonaute PIWI domain and microRNA duplex structure contribute to small RNA sorting in Arabidopsis.

Mostrar el registro completo del ítem

Zhang, X.; Niu, D.; Carbonell, A.; Wang, A.; Lee, A.; Tun, V.; Wang, Z.... (2014). Argonaute PIWI domain and microRNA duplex structure contribute to small RNA sorting in Arabidopsis. Nature Communications. 5:1-11. https://doi.org/10.1038/ncomms6468

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/161051

Ficheros en el ítem

Metadatos del ítem

Título: Argonaute PIWI domain and microRNA duplex structure contribute to small RNA sorting in Arabidopsis.
Autor: Zhang, Xiaoming Niu, DongDong CARBONELL, ALBERTO Wang, Airong Lee, Angel Tun, Vinnary Wang, Zonghua Carrington, James C. Chang, Chia-en A. Jin, Hailing
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Small RNAs (sRNAs) are loaded into ARGONAUTE (AGO) proteins to induce gene silencing. In plants, the 5¿-terminal nucleotide is important for sRNA sorting into different AGOs. Here we show that microRNA (miRNA) duplex ...[+]
Palabras clave: RNA silencing , Argonaute , Small RNA , MicroRNA
Derechos de uso: Reserva de todos los derechos
Fuente:
Nature Communications. (issn: 2041-1723 )
DOI: 10.1038/ncomms6468
Editorial:
Nature Publishing Group
Versión del editor: https://doi.org/10.1038/ncomms6468
Código del Proyecto:
info:eu-repo/grantAgreement/NSF//0956526/US/Function of Arabidopsis Small RNA-ARGONAUTE Complexes/
...[+]
info:eu-repo/grantAgreement/NSF//0956526/US/Function of Arabidopsis Small RNA-ARGONAUTE Complexes/
info:eu-repo/grantAgreement/NSF//0642843/US/CAREER:Genome-wide Analysis of Pathogen-induced Endogenous siRNAs in Plant Defense Responses in Arabidopsis/
info:eu-repo/grantAgreement/NIH//R01GM093008/
info:eu-repo/grantAgreement/NIH//AI043288/
info:eu-repo/grantAgreement/NSF//1257576/US/Investigate the role of small RNAs of a necrotrophic fungal pathogen B. cinerea in suppressing host Immunity/
info:eu-repo/grantAgreement/NSF//1231726/US/Function of Arabidopsis Small RNA-ARGONAUTE Complexes/
[-]
Agradecimientos:
We thank Yifan E. Lii, Patricia Springer and Hongwei Zhao for helpful comments; Yijun Qi, Xuemei Chen, David Baulcombe, Olivier Voinnet and Robert A. Martienssen for providing antibodies, constructs and seeds. This work ...[+]
Tipo: Artículo

References

Zamore, P. D. & Haley, B. Ribo-gnome: The big world of small RNAs. Science 309, 1519–1524 (2005).

Chapman, E. J. & Carrington, J. C. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8, 884–896 (2007).

Martínez de Alba, A. E., Elvira-Matelot, E. & Vaucheret, H. Gene silencing in plants: a diversity of pathways. Biochim. Biophys. Acta 1829, 1300–1308 (2013). [+]
Zamore, P. D. & Haley, B. Ribo-gnome: The big world of small RNAs. Science 309, 1519–1524 (2005).

Chapman, E. J. & Carrington, J. C. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8, 884–896 (2007).

Martínez de Alba, A. E., Elvira-Matelot, E. & Vaucheret, H. Gene silencing in plants: a diversity of pathways. Biochim. Biophys. Acta 1829, 1300–1308 (2013).

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).

Poulsen, C., Vaucheret, H. & Brodersen, P. Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures. Plant Cell 25, 22–37 (2013).

Wang, Y. et al. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456, 921–U72 (2008).

Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).

Elkayam, E. et al. The structure of human Argonaute-2 in complex with miR-20a. Cell 150, 100–110 (2012).

Boland, A., Huntzinger, E., Schmidt, S., Izaurralde, E. & Weichenrieder, O. Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein. Proc. Natl Acad. Sci. USA 108, 10466–10471 (2011).

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).

Nakanishi, K., Weinberg, D. E., Bartel, D. P. & Patel, D. J. Structure of yeast Argonaute with guide RNA. Nature 486, 368–374 (2012).

Faehnle, C. R., Elkayam, E., Haase, A. D., Hannon, G. J. & Joshua-Tor, L. The making of a slicer: activation of human argonaute-1. Cell Rep. 3, 1901–1909 (2013).

Nakanishi, K. et al. Eukaryote-specific insertion elements control human ARGONAUTE slicer activity. Cell Rep. 3, 1893–1900 (2013).

Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).

Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).

Tomari, Y., Du, T. & Zamore, P. D. Sorting of Drosophila small silencing RNAs. Cell 130, 299–308 (2007).

Ghildiyal, M. et al. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077–1081 (2008).

Ameres, S. L. et al. Target RNA–directed trimming and tailing of small silencing RNAs. Science 328, 1534–1539 (2010).

Kawamata, T., Seitz, H. & Tomari, Y. Structural determinants of miRNAs for RISC loading and slicer-independent unwinding. Nat. Struct. Mol. Biol. 16, 953–U77 (2009).

Czech, B. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–U7 (2008).

Czech, B. et al. Hierarchical rules for argonaute loading in Drosophila. Mol. Cell 36, 445–456 (2009).

Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. P. & Zamore, P. D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43–56 (2010).

Ameres, S. L., Hung, J.-H., Xu, J., Weng, Z. & Zamore, P. D. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17, 54–63 (2011).

Förstemann, K., Horwich, M. D., Wee, L., Tomari, Y. & Zamore, P. D. Drosophila microRNAs are sorted into functionally distinct argonaute complexes after production by Dicer-1. Cell 130, 287–297 (2007).

Steiner, F. A. et al. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat. Struct. Mol. Biol. 14, 927–933 (2007).

Frank, F., Sonenberg, N. & Nagar, B. Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818–822 (2010).

Czech, B. & Hannon, G. J. Small RNA sorting: matchmaking for Argonautes. Nat. Rev. Genet. 12, 19–31 (2010).

Meister, G. Argonaute proteins: functional insights and emerging roles. Nat. Rev. Genet. 14, 447–459 (2013).

Montgomery, T. A. et al. Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133, 128–141 (2008).

Mi, S. J. et al. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5 ' terminal nucleotide. Cell 133, 116–127 (2008).

Mallory, A. & Vaucheret, H. Form, function, and regulation of ARGONAUTE proteins. Plant Cell 22, 3879–3889 (2010).

Vaucheret, H. Plant ARGONAUTES. Trends Plant Sci. 13, 350–358 (2008).

Zhu, H. L. et al. Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell 145, 242–256 (2011).

Endo, Y., Iwakawa, H.-O. & Tomari, Y. Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly. EMBO Rep. 14, 652–658 (2013).

Maunoury, N. & Vaucheret, H. AGO1 and AGO2 act redundantly in miR408-mediated Plantacyanin regulation. PLoS ONE 6, e28729 (2011).

Zhang, X. M. et al. Arabidopsis Argonaute 2 regulates innate immunity via miRNA393*-mediated silencing of a golgi-localized SNARE gene, MEMB12. Mol. Cell 42, 356–366 (2011).

Okamura, K., Liu, N. & Lai, E. C. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol. Cell 36, 431–444 (2009).

Carbonell, A. et al. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. Plant Cell 24, 3613–3629 (2012).

Kidner, C. A. & Martienssen, R. A. Spatially restricted microRNA directs leaf polarity through ARGONAUTE1. Nature 428, 81–84 (2004).

McConnell, J. R. et al. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 411, 709–713 (2001).

Mallory, A. C. et al. MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region. EMBO J. 23, 3356–3364 (2004).

McConnell, J. R. & Barton, M. K. Leaf polarity and meristem formation in Arabidopsis. Development 125, 2935–2942 (1998).

Eamens, A. L., Smith, N. A., Curtin, S. J., Wang, M. B. & Waterhouse, P. M. The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA 15, 2219–2235 (2009).

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).

Li, S. B. et al. MicroRNAs inhibit the translation of target mRNAs on the endoplasmic reticulum in Arabidopsis. Cell 153, 562–574 (2013).

Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. Model. 14, 33–38 (1996).

Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).

Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22, 195–201 (2006).

Pedretti, A., Villa, L. & Vistoli, G. VEGA—An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J. Comput. Aided Mol. Des. 18, 167–173 (2004).

Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).

Phillips, J. C. et al. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005).

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem