The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 Stability

Abstract

The ability to sense and respond to sugar signals allows plants to cope with environmental and metabolic changes by adjusting growth and development accordingly. We previously reported that the SR45 splicing factor negatively regulates glucose signaling during early seedling development in Arabidopsis thaliana. Here, we show that under glucose-fed conditions, the Arabidopsis sr45-1 loss-of-function mutant contains higher amounts of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) despite unaffected SnRK1 transcript levels. In agreement, marker genes for SnRK1 activity are upregulated in sr45-1 plants, and the glucose hypersensitivity of sr45-1 is attenuated by disruption of the SnRK1 gene. Using a high-resolution RT-PCR panel, we found that the sr45-1 mutation broadly targets alternative splicing in vivo, including that of the SR45 pre-mRNA itself. Importantly, the enhanced SnRK1 levels in sr45-1 are suppressed by a proteasome inhibitor, indicating that SR45 promotes targeting of the SnRK1 protein for proteasomal destruction. Finally, we demonstrate that SR45 regulates alternative splicing of the Arabidopsis 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase previously shown to interact with and regulate the stability of SnRK1 in vitro, thus providing a mechanistic link between SR45 function and the modulation of degradation of the SnRK1 energy sensor in response to sugars.

Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

“…Two differential splicing genes— Solyc05g013750 and Solyc12g005340 —are likely involved in plant adaptation to light quality because they share high similarity with the respective Arabidopsis homologs Mitogen-activated protein kinase phosphatase 1 ( MKP1 ) and phytochrome A signal transduction 1 ( PAT1 ), which play roles in plant response to UV-B and far-red light mediated by phytochrome A ( PHY A ) [49,50,51,52]. Previous studies have shown that many splicing factors were regulated by AS [28,30,39,53,54,55,56,57]; we also found that there are three splicing factors including serine/arginine rich protein SR30 (Solyc01g099810), LHP1-interacting factor 2 (LIF2, Solyc02g088720) and a C1D family protein (Solyc07g008750), whose pre-mRNA were regulated by AS. Interestingly, we detected three differential splicing genes involved in the brassinosteroids (BR) signaling pathway; they all encode protein kinases similar to Arabidopsis BIR1 (Solyc07g006480), HERK1 (Solyc05g013300) and BSK2 (Solyc01g080880).…”

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

“…Notably, a role of AS in sugar responses is also supported by the findings that the splicing factor SR45 negatively regulates glucose signaling (Carvalho et al, 2010) and modulates SnRK1 protein stability in A. thaliana (Carvalho et al, 2016). SnRK1-mediated metabolic adjustment has been described to involve direct phosphorylation of key enzymes in metabolism (Sugden et al, 1999;Harthill et al, 2006) and differential transcriptional programs (Polge and Thomas, 2007;Baena-Gonzalez and Sheen, 2008;Mair et al, 2015).…”

Alternative Splicing of Barley Clock Genes in Response to Low Temperature

“…AS is an important level of regulation in plant gene expression and is involved in a wide range of environmental responses and developmental control [4–7,11]. The functional importance of AS has been demonstrated in sugar signalling [12], development [13], flowering time control [14], light responses [15], dark-light retrograde signalling from chloroplast to nucleus [16], and the circadian clock [17–19]. …”