Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites

Abstract

The Highly ABA-Induced 1 (HAI1) protein phosphatase is a central component of drought-related signaling. A screen for HAI1-interacting proteins identified HAI1-Interactor 1 (HIN1), a nuclear protein of unknown function which could be dephosphorylated by HAI1 in vitro. HIN1 colocalization and interaction with serine-arginine rich (SR) splicing factors and appearance of nuclear speckle-localized HIN1 during low water potential (ψw) stress suggested a pre-mRNA splicing-related function. RNA sequencing of Arabidopsis Col-0 wild type identified more than 500 introns where moderate severity low ψw altered intron retention (IR) frequency. Surprisingly, nearly 90% of these had increased splicing efficiency (decreased IR) during stress. For one-third of these introns, ectopic HIN1 expression (35S:HIN1) in unstressed plants mimicked the increased splicing efficiency seen in stress-treated wild type. HIN1 bound to a GAA-repeat, Exonic Splicing Enhancer-like RNA motif enriched in flanking sequence around HIN1-regulated introns. Genes with stress and HIN1-affected splicing efficiency were enriched for abiotic stress and signaling-related functions. The 35S:HIN1 plants had enhanced growth maintenance during low ψw, while hin1 mutants had reduced growth, further indicating the role of HIN1 in drought response. HIN1 is annotated as an MYB/SANT domain protein but has limited homology to other MYB/SANT proteins and is not related to known yeast or metazoan RNA-binding proteins or splicing regulators. Together these data identify HIN1 as a plant-specific RNA-binding protein, show a specific effect of drought acclimation to promote splicing efficiency of IR-prone introns, and also discover HAI1–HIN1 interaction and dephosphorylation that connects stress signaling to splicing regulation.

Plant-Specific AtS40.4 Acts as a Negative Regulator in Abscisic Acid Signaling During Seed Germination and Seedling Growth in Arabidopsis

“…To investigated whether or not the localization changes of AtS40.4 is caused by the stress response from ABA application, we used PEG-6000 to treatment the seedling root as described previously ( Chong et al, 2019 ). The fluorescent of GFP-particles was rarely detected in the root cells after PEG-induced moderate drought severity (-0.75 MPa, 24% PEG-6000) for 1 day ( Figures 4C,D and Supplementary Figure 4D ).…”

“…To test the effects of ABA on the subcellular localization of AtS40.4, the roots of 7-day-old seedlings were treated with 0.5 × MS liquid medium containing 100 μM ABA for 2 or 4 h ( Xu et al, 2019 ). PEG-induced moderate severity (-0.75 MPa) was used to simulate drought stress to roots ( Verslues et al, 2006 ; Chong et al, 2019 ).…”

DRT111/SFPS Splicing Factor Controls Abscisic Acid Sensitivity during Seed Development and Germination

“…Other splicing effectors and regulators affecting stress responses regulate these two AS classes. An increased splicing efficiency of IR-prone introns was shown to be important for acclimation to drought stress and splicing regulator HIN1 is involved in this process (Chong et al, 2019). Similarly, SAD1 splicing factor increased A3SS usage under salt stress conditions (Xing et al, 2015).…”

First Come, First Served: Sui Generis Features of the First Intron

“…Sessile plants have adopted sophisticated mechanisms to adjust to the varying environment, and the regulation of AS appears to play a more pivotal role than previously assumed. Splicing efficiency is regulated by stresses such as abiotic stress [ 116 ], drought [ 117 ], salt [ 118 ], cold [ 119 , 120 ], high temperature [ 34 , 121 ] phytochrome B signaling [ 122 , 123 ] thermo-priming [ 124 ], temperature-dependent regulation of circadian clock genes [ 125 ], and phosphate starvation [ 126 ]. Vernalization is, in part, regulated by AS of FLC , a central repressor in the flowering transition [ 37 ].…”