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HomeInternational Letters of Natural SciencesInternational Letters of Natural Sciences Vol. 61DCL and Associated Proteins of Arabidopsis...

DCL and Associated Proteins of Arabidopsis thaliana - An Interaction Study

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Abstract:

During RNA interference in plants, Dicer-like/DCL proteins process longer double-stranded RNA (dsRNA) precursors into small RNA molecules. In Arabidopsis thaliana there are four DCLs (DCL1, DCL2, DCL3, and DCL4) that interact with various associated proteins to carry out this processing. The lack of complete structural-functional information and characterization of DCLs and their associated proteins leads to this study where we have generated the structures by modelling, analysed the structures and studied the interactions of Arabidopsis thaliana DCLs with their associated proteins with the homology-derived models to screen the interacting residues. Structural analyses indicate existence of significant conserved domains that may play imperative roles during protein-protein interactions. The interaction study shows some key domain-domain (including multi-domains and inter-residue interactions) interfaces and specific residue biases (like arginine and leucine) that may help in augmenting the protein expression level during stress responses. Results point towards plausible stable associations to carry out RNA processing in a synchronised pattern by elucidating the structural properties and protein-protein interactions of DCLs that may hold significance for RNAi researchers.

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Periodical:

International Letters of Natural Sciences (Volume 61)

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85-94

DOI:

https://doi.org/10.56431/p-p7a5s1

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Online since:

January 2017

Authors:

Paushali Roy*, Abhijit Datta

Keywords:

DCL-Associated Proteins, Dicer-Like Protein, Domain-Domain Interactions, RNA Interference

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Creative Commons CC BY 4.0

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* - Corresponding Author

[1] B.L. Davidson, P.B. McCray Jr., Current prospects for RNA interference-based therapies, Nature Reviews Genetics. 12 (2011) 329-340.

DOI: 10.1038/nrg2968

[2] E.J. Finnegan, M.A. Matzke, The small RNA world, Journal of Cell Science. 116(23) (2003) 4689-4693.

DOI: 10.1242/jcs.00838

[3] Q. Liu, Y. Feng, Z. Zhu, Dicer-like (DCL) proteins in plants, Funct. Integr. Genomics. 9(3) (2009) 277-286.

DOI: 10.1007/s10142-009-0111-5

[4] A.F. Fusaro et al., RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway, EMBO reports. 7(11) (2006) 1168–1175.

DOI: 10.1038/sj.embor.7400837

[5] X. Chen, microRNA biogenesis and function in plants, FEBS Letters. 579(26) (2005) 5923-5931.

DOI: 10.1016/j.febslet.2005.07.071

[6] N.S. Mishra, S.K. Mukherjee, A Peep into the Plant miRNA World, The Open Plant Science Journal. 12 (2007) 1-9.

[7] A.L. Eamens et al., DRB2 Is Required for MicroRNA Biogenesis in Arabidopsis thaliana, PLoS ONE. 7(4) (2012) 1-15.

DOI: 10.1371/journal.pone.0035933

[8] Y. Kurihara, Y. Takashi, Y. Watanabe, The interaction between DCL1 and HYL1 is important for efficient and precise processing of pri-miRNA in plant microRNA biogenesis, RNA. 12 (2006) 206-212.

DOI: 10.1261/rna.2146906

[9] B. Yu et al., The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in human's act in small RNA biogenesis, Proceedings of the National Academy of Sciences. 105(29) (2008) 10073–10078.

DOI: 10.1073/pnas.0804218105

[10] Y. Fang, D.L. Spector, Identification of Nuclear Dicing Bodies Containing Proteins for MicroRNA Biogenesis in Living Arabidopsis Plants, Curr. Biol. 17(9) (2007) 818–823.

DOI: 10.1016/j.cub.2007.04.005

[11] A. Hiraguri et al., Specific interactions between Dicer-like proteins and HYL1/DRB-family dsRNA-binding proteins in Arabidopsis thaliana, Plant Mol. Biol. 57(2) (2005) 173-188.

DOI: 10.1007/s11103-004-6853-5

[12] A. Eamens et al., RNA Silencing in Plants: Yesterday, Today, and Tomorrow, Plant Physiology. 147 (2008) 456–468.

DOI: 10.1104/pp.108.117275

[13] H. Qin et al., Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction, RNA. 16(3) (2010) 474–481.

DOI: 10.1261/rna.1965310

[14] F. Vazquez et al., Arabidopsis endogenous small RNAs: highways and byways, Trends in Plant Science. 11(9) (2006) 460-468.

DOI: 10.1016/j.tplants.2006.07.006

[15] Z. Xie et al., Genetic and functional diversification of small RNA pathways in plants, PLoS Biol. 2(5) (2004) 642-652.

[16] F. Qu et al., Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1, Proceedings of the National Academy of Sciences. 105(38) (2008) 14732-14737.

DOI: 10.1073/pnas.0805760105

[17] Y. Nakazawa et al., The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway, Plant Mol. Biol. 63(6) (2007) 777-785.

DOI: 10.1007/s11103-006-9125-8

[18] A. Fukudome et al., Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4, RNA. 17(4) (2011) 750-760.

DOI: 10.1261/rna.2455411

[19] A. Mallory, H. Vaucheret, Form, Function, and Regulation of ARGONAUTE Proteins, The Plant Cell. 22 (2010) 3879–3889.

DOI: 10.1105/tpc.110.080671

[20] P. Benkert et al., QMEAN: A comprehensive scoring function for model quality assessment, Proteins: Structure, Function, and Bioinformatics. 71(1) (2008) 261-277.

DOI: 10.1002/prot.21715

[21] P. Benkert, et al., QMEAN Server for Protein Model Quality Estimation, Nucleic Acids Res. 37(1) (2009) 1-5.

DOI: 10.1093/nar/gkp322

[22] P. Benkert et.al., Toward the estimation of the absolute quality of individual protein structure models, Bioinformatics. 27(3) (2011) 343-350.

DOI: 10.1093/bioinformatics/btq662

[23] S.R. Comeau et al., ClusPro: an automated docking and discrimination method for the prediction of protein complexes, Bioinformatics. 20(1) (2004) 45-50.

DOI: 10.1093/bioinformatics/btg371

[24] S.R. Comeau et al., ClusPro: a fully automated algorithm for protein-protein docking, Nucleic Acids Research. 32(2) (2004) 96-99.

DOI: 10.1093/nar/gkh354

[25] D. Kozakov et al., PIPER: An FFT-based protein docking program with pairwise potentials, Proteins. 65(2) (2006) 392-406.

DOI: 10.1002/prot.21117

[26] D. Kozakov et al., How good is automated protein docking? Proteins. 81(12) (2013) 2159-2166.

DOI: 10.1002/prot.24403