Phytochrome controls alternative splicing to mediate light responses in Arabidopsis

Abstract

Plants monitor the ambient light conditions using several informational photoreceptors, including red/far-red light absorbing phytochrome. Phytochrome is widely believed to regulate the transcription of light-responsive genes by modulating the activity of several transcription factors. Here we provide evidence that phytochrome significantly changes alternative splicing (AS) profiles at the genomic level in Arabidopsis, to approximately the same degree as it affects steady-state transcript levels. mRNA sequencing analysis revealed that 1,505 and 1,678 genes underwent changes in their AS and steady-state transcript level profiles, respectively, within 1 h of red light exposure in a phytochromedependent manner. Furthermore, we show that splicing factor genes were the main early targets of AS control by phytochrome, whereas transcription factor genes were the primary direct targets of phytochrome-mediated transcriptional regulation. We experimentally validated phytochrome-induced changes in the AS of genes that are involved in RNA splicing, phytochrome signaling, the circadian clock, and photosynthesis. Moreover, we show that phytochrome-induced AS changes of SPA1-RELATED 3, the negative regulator of light signaling, physiologically contributed to promoting photomorphogenesis. Finally, photophysiological experiments demonstrated that phytochrome transduces the signal from its photosensory domain to induce light-dependent AS alterations in the nucleus. Taking these data together, we show that phytochrome directly induces AS cascades in parallel with transcriptional cascades to mediate light responses in Arabidopsis.phytochrome | alternative splicing | light signaling | posttranscriptional regulation | photomorphogenesis

Evolutionarily Conserved Alternative Splicing Across Monocots

“…Both splice isoforms harbor premature termination codons resulting in truncated proteins that retain interaction with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COPI) but lose the ability to bind to DAMAGED DNA-BINDING PROTEIN 1 (DDB1). Evidence suggests that phytochrome could mediate the production of AS transcripts of SPA3 in response to some light conditions, thus promoting plant photomorphogenesis (Shikata et al 2014). Both IntronR and AltD events were identified in our analysis: the AltD event is conserved across all nine species examined and the IntronR event is conserved in four species: maize, foxtail millet, African oil palm, and Arabidopsis.…”

“…This event was also identified in all species examined in our study. Shikata et al (2014) previously characterized IntronR and AltD events within SPA3-a protein that plays a pivotal role in light signaling as a suppressor of photomorphogenesis (Laubinger and Hoecker 2003). Both splice isoforms harbor premature termination codons resulting in truncated proteins that retain interaction with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COPI) but lose the ability to bind to DAMAGED DNA-BINDING PROTEIN 1 (DDB1).…”

“…AS isoforms that are translated can influence proteome diversity, while others that are purposefully nonfunctional can act to post-transcriptionally modulate protein levels (Fu et al 2009;Hammond et al 2009). AS participates in many important processes during the lifecycle of plants (Staiger and Brown 2013), and AS occurs in response to many abiotic stresses (Mastrangelo et al 2012), for example red/ blue light (Shikata et al 2014;Wu et al 2014), salt stress , drought (Thatcher et al 2016), flooding (Syed et al 2015), and temperature (James et al 2012;Streitner et al 2013).…”

Diverse photoreceptors and light responses in plants

“…Phys are involved in germination, de-etiolation, shadeavoidance responses and so on. Recently, it was identified that phy also regulates alternative splicing (Shikata et al 2014). Cry also regulates transcription and mediates various blue light responses including inhibition of hypocotyl elongation, photoperiodic control of floral initiation, circadian rhythms, etc.…”

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts

“…A number of recent high-profile publications demonstrate the importance of AS and differential functions of AS variants in, for example, organ development (Zhang and Mount, 2009), flowering time control and the circadian clock (Sanchez et al, 2010;James et al, 2012;Posé et al, 2013;Li et al, 2015), light signaling (Shikata et al, 2014), dark-light retrograde signaling from chloroplast to nucleus (Petrillo et al, 2014), and zinc tolerance (Remy et al, 2014). AS of around 18% of Arabidopsis genes generates unproductive mRNA transcript isoforms that are degraded by NMD, which modulates transcript levels thereby regulating levels of protein produced from a gene Drechsel et al, 2013).…”