Structure of the <i>Arabidopsis thaliana</i> DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction

Qin, Haina; Chen, Fading; Huan, Xuelu; Machida, Satoru; Song, Jianxing; Yuan, Yunbin

doi:10.1261/rna.1965310

Cited by 90 publications

(96 citation statements)

References 40 publications

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“…This observation indicates that histidine at position 32 on the dsRBD1 is also involved in the interaction with DCL4 and facilitates its dsRNA-cleaving activity. Another report shows that DRB4 dsRBD1 specifically interacts with the DUF283 (domain of unknown function) of DCL4 (Qin et al 2010). It is possible that DRB4 dsRBD1 interacts with DCL4-DUF283, while dsRBD2 interacts with the C-terminal region of DCL4, and these two dsRBDs cooperatively facilitate the dsRNAcleaving activity of DCL4.…”

Section: Discussionmentioning

confidence: 99%

“…It is possible that DRB4 dsRBD1 interacts with DCL4-DUF283, while dsRBD2 interacts with the C-terminal region of DCL4, and these two dsRBDs cooperatively facilitate the dsRNAcleaving activity of DCL4. There may be functional specialization between dsRBD1 and dsRBD2 of DRB4; such specialization is common for many eukaryotic dsRBPs (Hiraguri et al 2005;Laraki et al 2008;Qin et al 2010).…”

Section: Discussionmentioning

confidence: 99%

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Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4

Fukudome¹,

Kanaya²,

Egami³

et al. 2011

RNA

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Arabidopsis thaliana Dicer-like 4 (DCL4) produces 21-nt small interfering RNAs from both endogenous and exogenous doublestranded RNAs (dsRNAs), and it interacts with DRB4, a dsRNA-binding protein, in vivo and in vitro. However, the role of DRB4 in DCL4 activity remains unclear because the dsRNA-cleaving activity of DCL4 has not been characterized biochemically. In this study, we biochemically characterize DCL4's Dicer activity and establish that DRB4 is required for this activity in vitro. Crude extracts from Arabidopsis seedlings cleave long dsRNAs into 21-nt small RNAs in a DCL4/DRB4-dependent manner. Immunoaffinity-purified DCL4 complexes produce 21-nt small RNAs from long dsRNA, and these complexes have biochemical properties similar to those of known Dicer family proteins. The DCL4 complexes purified from drb4-1 do not cleave dsRNA, and the addition of recombinant DRB4 to drb4-1 complexes specifically recovers the 21-nt small RNA generation. These results reveal that DCL4 requires DRB4 to cleave long dsRNA into 21-nt small RNAs in vitro. Amino acid substitutions in conserved dsRNA-binding domains (dsRBDs) of DRB4 impair three activities: binding to dsRNA, interacting with DCL4, and facilitating DCL4 activity. These observations indicate that the dsRBDs are critical for DRB4 function. Our biochemical approach and observations clearly show that DRB4 is specifically required for DCL4 activity in vitro.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4

Fukudome¹,

Kanaya²,

Egami³

et al. 2011

RNA

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“…DCL proteins contain several conserved domains, including a bipartite helicase domain, a DUF283 domain that was recently defined as a novel RNA binding motif (Qin et al, 2010), two RNase III domains (RNase IIIa and RNase IIIb), and two doublestranded RNA binding domains ( Figure 2B). The dcl1 locus corresponds to gene model GRMZM2G040762.…”

Section: Fzt Contains a Mutation In Dcl1mentioning

confidence: 99%

The dicer-like1 Homolog fuzzy tassel Is Required for the Regulation of Meristem Determinacy in the Inflorescence and Vegetative Growth in Maize

et al. 2014

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Plant architecture is determined by meristems that initiate leaves during vegetative development and flowers during reproductive development. Maize (Zea mays) inflorescences are patterned by a series of branching events, culminating in floral meristems that produce sexual organs. The maize fuzzy tassel (fzt) mutant has striking inflorescence defects with indeterminate meristems, fasciation, and alterations in sex determination. fzt plants have dramatically reduced plant height and shorter, narrower leaves with leaf polarity and phase change defects. We positionally cloned fzt and discovered that it contains a mutation in a dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. miRNAs are small noncoding RNAs that reduce target mRNA levels and are key regulators of plant development and physiology. Small RNA sequencing analysis showed that most miRNAs are moderately reduced in fzt plants and a few miRNAs are dramatically reduced. Some aspects of the fzt phenotype can be explained by reduced levels of known miRNAs, including miRNAs that influence meristem determinacy, phase change, and leaf polarity. miRNAs responsible for other aspects of the fzt phenotype are unknown and likely to be those miRNAs most severely reduced in fzt mutants. The fzt mutation provides a tool to link specific miRNAs and targets to discrete phenotypes and developmental roles.

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“…Dawdle (DDL) associates with DCL and helps in accumulation of sRNA molecules [9]. The DRB family proteins help in locating the small RNA target sequences [11,13,14,16,17,18]. RDR2 associates with DCL3 to stabilize DCL3 protein complex [15,19].…”

Section: Introductionmentioning

confidence: 99%

DCL and Associated Proteins of <i>Arabidopsis thaliana </i>- An Interaction Study

Roy

Datta²

2017

ILNS

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Abstract. During RNA interference in plants, Dicer-like/DCL proteins process longer doublestranded 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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Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein–protein interaction

Cited by 90 publications

References 40 publications

Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4

Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4

The dicer-like1 Homolog fuzzy tassel Is Required for the Regulation of Meristem Determinacy in the Inflorescence and Vegetative Growth in Maize

DCL and Associated Proteins of <i>Arabidopsis thaliana </i>- An Interaction Study

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