Genome-Wide Analysis of the Arabidopsis Leaf Transcriptome Reveals Interaction of Phosphate and Sugar Metabolism

Abstract

Global gene expression was analyzed in Arabidopsis (Arabidopsis thaliana) by microarrays comprising 21,500 genes. Leaf segments derived from phosphorus (P)-starved and P-replenished plants were incubated with or without sucrose (Suc) to obtain tissues with contrasting combinations of P and carbohydrate levels. Transcript profiling revealed the influence of the two factors individually and the interactions between P-and sugar-dependent gene regulation. A large number of gene transcripts changed more than 2-fold: In response to P starvation, 171 genes were induced and 16 repressed, whereas Suc incubation resulted in 337 induced and 307 repressed genes. A number of new candidate genes involved in P acquisition were discovered. In addition, several putative transcription factors and signaling proteins of P sensing were disclosed. Several genes previously identified to be sugar responsive were also regulated by P starvation and known P-responsive genes were sugar inducible. Nearly 150 genes were synergistically or antagonistically regulated by the two factors. These genes exhibit more prominent or contrasting regulation in response to Suc and P in combination than expected from the effect of the two factors individually. The genes exhibiting interactions form three main clusters with different response patterns and functionality of genes. One cluster (cluster 1) most likely represents a regulatory program to support increased growth and development when both P and carbohydrates are ample. Another cluster (cluster 3) represents genes induced to alleviate P starvation and these are further induced by carbohydrate accumulation. Thus, interactions between P and Suc reveal two different signaling programs and novel interactions in gene regulation in response to environmental factors. cis-Regulatory elements were analyzed for each factor and for interaction clusters. PHR1 binding sites were more frequent in promoters of P-regulated genes as compared to the entire Arabidopsis genome, and E2F and PHR1 binding sites were more frequent in interaction clusters 1 and 3, respectively.

Genetic and Genomic Evidence That Sucrose Is a Global Regulator of Plant Responses to Phosphate Starvation in Arabidopsis

“…These synergistically induced genes could be the converging points for Suc and Pi signals to regulate multiple plant responses to Pi starvation. The synergistic interaction of Suc and low-Pi signals in regulating gene expression at the genomic level has also been observed in a previous study using exogenously applied Suc to Pi-starved excised leaves (Mü ller et al, 2007). Thus, Suc appears to act as a major regulator of the expression of genes that are involved in plant responses to Pi starvation.…”

“…In contrast, the Arabidopsis pho3 mutant carries a defective copy of the SUCROSE TRANSPORTER2 (SUC2) gene, leading to substantially reduced transport of Suc from shoot to root and the suppression of induction and secretion of APase on its root surface (Zakhleniuk et al, 2001;Lloyd and Zakhleniuk, 2004). In addition, earlier studies have revealed that the expression of many genes involved in the synthesis, translocation, and degradation of Suc was altered during Pi starvation (Hammond et al, 2003;Vance et al, 2003;Wu et al, 2003;Misson et al, 2005;Mü ller et al, 2007). Furthermore, an increase in Suc biosynthesis in Pi-starved leaves has been observed in a variety of plants, including Arabidopsis, bean, barley (Hordeum vulgare), spinach (Spinacia oleracea), and soybean (Glycine max; Hammond and White, 2008).…”

The Phosphate Fast-Responsive Genes PECP1 and PPsPase1 Affect Phosphocholine and Phosphoethanolamine Content

“…PPsPase1 and PECP1 are listed as strongly induced in several transcriptomics studies related to phosphate starvation (Misson et al, 2005; Bari et al, 2006;Müller et al, 2007;Thibaud et al, 2010;Hirsch et al, 2011). However, very little is known about their precise expression patterns.…”

“…Furthermore, their corresponding mutants exhibit altered gene induction and classical Pi starvation responses, including diminished effects on Pi content and lipid remobilization (Pant et al, 2015). Candidates for the systemic control of Pi starvation responses have been proposed, including substantial transport of mRNAs throughout the plant (as reviewed in Puga et al, 2017), and the direct sensing of Pi concentration (or Pi-containing metabolites) by SPX-type proteins (Wang et al, 2009;Puga et al, 2014;Wild et al, 2016).Two phosphatases belonging to the haloacid dehalogenase (HAD) superfamily were identified as some of the most strongly induced transcripts following Pi starvation (Bari et al, 2006;Müller et al, 2007;Thibaud et al, 2010). These enzymes were named PPsPase1 (for pyrophosphatase [PPi]-specific phosphatase1) and PECP1 (for phosphoethanolamine (PEth)/ phosphocholine [PCho] phosphatase1) on the basis of their in vitro activity, following their heterologous expression in bacteria and subsequent purification (May et al, 2011(May et al, , 2012.…”

“…Two phosphatases belonging to the haloacid dehalogenase (HAD) superfamily were identified as some of the most strongly induced transcripts following Pi starvation (Bari et al, 2006;Müller et al, 2007;Thibaud et al, 2010). These enzymes were named PPsPase1 (for pyrophosphatase [PPi]-specific phosphatase1) and PECP1 (for phosphoethanolamine (PEth)/ phosphocholine [PCho] phosphatase1) on the basis of their in vitro activity, following their heterologous expression in bacteria and subsequent purification (May et al, 2011(May et al, , 2012.…”