SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis

Abstract

Light signals regulate plant growth and development by controlling a plethora of gene expression changes. Posttranscriptional regulation, especially pre-mRNA processing, is a key modulator of gene expression; however, the molecular mechanisms linking pre-mRNA processing and light signaling are not well understood. Here we report a protein related to the human splicing factor 45 (SPF45) named splicing factor for phytochrome signaling (SFPS), which directly interacts with the photoreceptor phytochrome B (phyB). In response to light, SFPS-RFP (red fluorescent protein) colocalizes with phyB-GFP in photobodies. loss-of-function plants are hyposensitive to red, far-red, and blue light, and flower precociously. SFPS colocalizes with U2 small nuclear ribonucleoprotein-associated factors including U2AF65B, U2A', and U2AF35A in nuclear speckles, suggesting SFPS might be involved in the 3' splice site determination. SFPS regulates pre-mRNA splicing of a large number of genes, of which many are involved in regulating light signaling, photosynthesis, and the circadian clock under both dark and light conditions. In vivo RNA immunoprecipitation (RIP) assays revealed that SFPS associates with () mRNA, a critical link between light signaling and the circadian clock. Moreover, PHYTOCHROME INTERACTING FACTORS () transcription factor genes act downstream of SFPS, as the quadruple mutant suppresses defects of mutants. Taken together, these data strongly suggest SFPS modulates light-regulated developmental processes by controlling pre-mRNA splicing of light signaling and circadian clock genes.

DRT111/SFPS splicing factor controls ABA sensitivity in Arabidopsis seed development and germination

“…3A), while lack of DRT111 expression resulted in early flowering, as previously reported (Fig. S3D, Xin et al, 2017).…”

“…BQ510509, corresponding to PGSC0003DMT400054608, Potato genome sequencing consortium, 2011), up-regulated in adapted cells (Ambrosone et al, 2017). The protein deduced from PGSC0003DMT400054608 shared 64% sequence identity with Arabidopsis At1g30480, encoding a predicted splicing factor (also referred to as DRT111/ RSN2/SFPS, SPF45-related, Pang et al, 1993; Xin et al, 2017; Zhang et al, 2014, Supplemental Figure S1).…”

“…DRT111/SFPS encodes a nuclear-localized potential orthologue of human splicing factor RBM17/SPF45 (Supplemental Figure S2, Xin et al, 2017), shown to interact with Splicing factor 1 (SF1), a protein involved in early pre-spliceosome assembly (Crisci et al, 2015; Hegele et al, 2012). Therefore, we verified if this interaction is conserved in Arabidopsis.…”

“…In this study we show that the splicing factor DNA-DAMAGE REPAIR/TOLERATION PROTEIN 111 (DRT111), previously characterized in the control of pre-mRNA splicing in light-regulated developmental processes (Xin et al, 2017), is involved in ABA response mechanisms. Manipulation of DRT111 expression results in a modified sensitivity to ABA of stomatal movements and during seed germination.…”

PhyB induces intron retention and uORF-mediated translational inhibition of PIF3

“…Light causes wide-spread alternative splicing (AS) in plant transcriptome (Shikata et al, 2014; Hartmann et al, 2016; Xin et al, 2017; Godoy Herz et al, 2019). Although PIF3 has not been experimentally demonstrated to undergo light regulated AS, based on the information from Araport (Arabidopsis Information Portal: www.araport.org), transcripts with alternative splicing patterns at an intron of approximately 500 bp in PIF3 5’ untranslated region (UTR) have been found in the database (Figure 2A).…”