DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis

Zhang, Shuxin; Dou, Yongchao; Li, Shengjun; Ren, Guodong; Chevalier, David; Zhang, Chi; Yu, Bin

doi:10.1104/pp.18.00354

Cited by 26 publications

(12 citation statements)

References 50 publications

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“…For example, nine outliers in the altitude transect were significant based on the null- W test in the latitude transect, including Potri.011G136100 (DAWDLE; DDL), which was associated with AHM, MSP, PAS, and SHM. This gene encodes a protein similar to DAWDLE, and its ortholog in Arabidopsis is involved in biogenesis of miRNAs (Zhang et al. 2018).…”

Section: Resultsmentioning

confidence: 99%

Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa

Zhang

Suren

Holliday

2019

Genome Biology and Evolution

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Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.

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Section: Resultsmentioning

confidence: 99%

Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa

Zhang

Suren

Holliday

2019

Genome Biology and Evolution

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“…Post‐translational modifications have emerged as a key regulatory component of the core miRNA‐biogenesis machinery (regulatory processes are discussed further in the next section). In this sense, the phosphorylation of DCL1 was shown to be a requirement for its interaction with DAWDLE (Machida and Yuan, ), which in turn is necessary for proper DCL1 activity (Zhang et al ., ). HYL1 activity, essential for DCL1 accurate processing, is also controlled by its phosphorylation state.…”

Section: Environmental Regulation Of the Mirna Biogenesis Machinerymentioning

confidence: 97%

Keep calm and carry on: miRNA biogenesis under stress

2019

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Summary MicroRNAs (miRNAs) are major post‐transcriptional regulators of gene expression. Their biogenesis relies on the cleavage of longer precursors by a nuclear localized processing machinery. The evolutionary preference of plant miRNAs to silence transcription factors turned these small molecules into key actors during growth and adaptive responses. Furthermore, during their life cycle plants are subject to changes in the environmental conditions surrounding them. In order to face these changes, plants display unique adaptive capacities based on an enormous developmental plasticity, where miRNAs play central roles. Many individual miRNAs have been shown to modulate the plant response to different environmental cues and stresses. In the last few years, increasing evidence has shown that not only individual genes encoding miRNAs but also the miRNA pathway as a whole is subject to regulation in response to external stimulus. In this review, we discuss the current knowledge about the miRNA pathway. We dissect the pathway to analyze the events leading to the generation of these small RNAs and emphasize the regulation of core components of the miRNA biogenesis machinery.

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“…Interestingly, our results show that AtBUD13 is also required for splicing genes involved in miRNA processing. For example, AGO1/DCL1‐ and AGO10 / ZLL ‐encoded proteins are members of the AGO family and acts as effective slicers for processing of pre‐miRNA in plants (Shao et al ., ; Zhang et al ., ). A similar scenario has been demonstrated for hBUD13, which is involved in miRNA metabolism by stabilizing miR‐144 and suppressing expression and processing of miR‐210 (Nussbacher and Yeo, ).…”

Section: Discussionmentioning

confidence: 97%

AtBUD13 affects pre‐mRNA splicing and is essential for embryo development in Arabidopsis

Xiong

Ren

et al. 2019

The Plant Journal

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Pre-mRNA splicing is an important step for gene expression regulation. Yeast Bud13p (bud-site selection protein 13) regulates the budding pattern and pre-mRNA splicing in yeast cells; however, no Bud13p homologs have been identified in plants. Here, we isolated two mutants that carry T-DNA insertions at the At1g31870 locus and shows early embryo lethality and seed abortion. At1g31870 encodes an Arabidopsis homolog of yeast Bud13p, AtBUD13. Although AtBUD13 homologs are widely distributed in eukaryotic organisms, phylogenetic analysis revealed that their protein domain organization is more complex in multicellular species. AtBUD13 is expressed throughout plant development including embryogenesis and AtBUD13 proteins is localized in the nucleus in Arabidopsis. RNA-seq analysis revealed that AtBUD13 mutation predominantly results in the intron retention, especially for shorter introns (≤100 bases). Within this group of genes, we identified 52 genes involved in embryogenesis, out of which 22 are involved in nucleic acid metabolism. Our results demonstrate that AtBUD13 plays critical roles in early embryo development by effecting pre-mRNA splicing.

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DAWDLE Interacts with DICER-LIKE Proteins to Mediate Small RNA Biogenesis

Cited by 26 publications

References 50 publications

Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa

Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa

Keep calm and carry on: miRNA biogenesis under stress

AtBUD13 affects pre‐mRNA splicing and is essential for embryo development in Arabidopsis

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