The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression

Abstract

The phosphorylation state of the C-terminal domain (CTD) of the RNA polymerase II plays crucial roles in transcription and mRNA processing. Previous studies showed that the plant CTD phosphatase-like 1 (CPL1) dephosphorylates Ser-5-specific CTD and regulates abiotic stress response in Arabidopsis. Here, we report the identification of a K-homology domain-containing protein named SHINY1 (SHI1) that interacts with CPL1 to modulate gene expression. The shi1 mutant was isolated from a forward genetic screening for mutants showing elevated expression of the luciferase reporter gene driven by a salt-inducible promoter. The shi1 mutant is more sensitive to cold treatment during vegetative growth and insensitive to abscisic acid in seed germination, resembling the phenotypes of shi4 that is allelic to the cpl1 mutant. Both SHI1 and SHI4/CPL1 are nuclear-localized proteins. SHI1 interacts with SHI4/CPL1 in vitro and in vivo. Loss-of-function mutations in shi1 and shi4 resulted in similar changes in the expression of some stress-inducible genes. Moreover, both shi1 and shi4 mutants display higher mRNA capping efficiency and altered polyadenylation site selection for some of the stress-inducible genes, when compared with wild type. We propose that the SHI1-SHI4/CPL1 complex inhibits transcription by preventing mRNA capping and transition from transcription initiation to elongation.

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.…”

“…Given the role of CTD Ser5 phosphorylation in the Pol II control of gene expression (18,19,(22)(23)(24), we performed transcriptome analysis to determine whether ROP2 and CPL1 affected expression of a similar set of downstream genes. RNAsequencing analysis revealed that 1,333 genes were differentially expressed (with a twofold cutoff) in cae2-1, CA1-1, or cae2-1 CA1-1 compared with WT (SI Appendix, 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.…”

Salt Stress Reveals a New Role for ARGONAUTE1 in miRNA Biogenesis at the Transcriptional and Posttranscriptional Levels

“…Interestingly, CPL1 was originally described as a phosphatase that is important for dephosphorylation of the RNAPII C-terminal domain (CTD) at Ser-5 (Koiwa et al, 2004;Jiang et al, 2013). This phosphorylation of CTD is required for cap formation, the transition from the initiation to the elongation phase and proper poly(A) site selection (Jiang et al, 2013). It has been suggested that the phosphorylation of Figure 8.…”

The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis

“…Recently, we found that FRY2 contributes to the regulation of pre-mRNA splicing via interacting with the KH-domain RNA binding protein HOS5 and two splicing factor proteins, RS40 and RS41 (Chen et al, 2013). In addition, FRY2 has been suggested to inhibit transcription by preventing mRNA capping and the transition from transcription initiation to elongation (Jiang et al, 2013). These studies suggest that FRY2 plays important regulatory roles in many aspects of RNA metabolism in Arabidopsis.…”