Arabidopsis C-Terminal Domain Phosphatase-Like 1 Functions in miRNA Accumulation and DNA Methylation

Abstract

Arabidopsis CTD-PHOSPHATASE-LIKE 1 (CPL1) is a protein phosphatase that can dephosphorylate RNA polymerase II C-terminal domain (CTD). Unlike typical CTD-phosphatases, CPL1 contains a double-stranded (ds) RNA-binding motif (dsRBM) and has been implicated for gene regulation mediated by dsRNA-dependent pathways. We investigated the role of CPL1 and its dsRBMs in various gene silencing pathways. Genetic interaction analyses revealed that cpl1 was able to partially suppress transcriptional gene silencing and DNA hypermethylation phenotype of ros1 suggesting CPL1 is involved in the RNA-directed DNA methylation pathway without reducing siRNA production. By contrast, cpl1 reduced some miRNA levels at the level of processing. Indeed, CPL1 protein interacted with proteins important for miRNA biogenesis, suggesting that CPL1 regulates miRNA processing. These results suggest that CPL1 regulates DNA methylation via a miRNA-dependent pathway.

KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

“…S7B), consistent with a partly redundant function of CPL1 and CPL2 (3). This interaction was not seen in another study (27), which, different from our experiments, did not use the full-length CPL2 protein. The interaction of RCF3 with CPL1/CPL2, together with the overaccumulation of miRNA* molecules in rcf3 and cpl1 mutants, suggested that RCF3 acts in the miRNA pathway through CPL1/2.…”

“…5B and Fig. S7A); this interaction has been previously reported (21,22,27) and confirmed in planta by bimolecular fluorescence complementation (Fig. S7B).…”

C-terminal domain (CTD) phosphatase links Rho GTPase signaling to Pol II CTD phosphorylation in Arabidopsis and yeast

“…1C). This gene was first identified as CPL1 or FRY2, which encodes a Pol II CTD phosphatase involved in stress responses and acting as a regulator of gene expression (18,19,(22)(23)(24)(25). The cae2-1 mutation resulted in three types of splicing products of CPL1 mRNA in cae2-1 CA1-1, and sequencing of the three cDNA molecules showed all of which differed from the WT CPL1 transcript ( Fig.…”

“…In Arabidopsis, there are several members of CTD phosphatases with sequence homology to yeast Fcp1 phosphatase (18)(19)(20)(21). Among these members, CPL1 has been extensively studied in stress response and gene expression regulation (18,19,(22)(23)(24)(25). CPL1 has been demonstrated to act as a Ser5 phosphatase in vitro, but its upstream regulatory pathway remains to be revealed.…”

A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function

“…In addition to this function, HWS has also been reported to affect general plant and organ growth (González-Carranza et al, 2007;Yu et al, 2015). Further, it is reminiscent of relatively weak, pleiotropic defects in other miRNA factors like CPL1 (Manavella et al, 2012;Jeong et al, 2013;Cui et al, 2016) and suggests that HWS may affect growth processes via the miRNA pathway, either through direct involvement in miRNA function, stability or even degradation, or upstream of miRNA-related processes.…”