Dissecting the plant transcriptome and the regulatory responses to phosphate deprivation

Abstract

Inorganic phosphate (Pi) is an essential nutrient for plants, and the low bioavailability of Pi in soils is often a limitation to growth and development. Consequently, plants have evolved a range of regulatory mechanisms to adapt to phosphorus-starvation in order to optimise uptake and assimilation of Pi. Recently, significant progress has been made in elucidating these mechanisms. The coordinated expression of a large number of genes is important for many of these adaptations. Several global expression studies using microarray analysis have been conducted in Arabidopsis thaliana. These studies provide a valuable basis for the identification of new regulatory genes and promoter elements to further the understanding of Pi-dependent gene regulation. With focus on the Arabidopsis transcriptome, we extract common findings that point to new groups of putative regulators, including the NAC, MYB, ethylene response factor/APETALA2, zinc-finger, WRKY and CCAAT-binding families. With a number of new discoveries of regulatory elements, a complex regulatory network is emerging. Some regulatory elements, e.g. the transcription factor PHR1 and the microRNA (miRNA) miR399 and associated factors are well documented, yet not fully understood, whereas other suggested components need further characterisation. Here, we evaluate the contribution of the regulatory elements to the P-responses and present a model comprising factors directly or indirectly involved in transcriptional regulation and the role of miRNAs as regulators and long-distance signals. A striking feature is a series of feedback loops and parallel mechanisms that can modify and attenuate responses. We suggest that these mechanisms are instrumental in providing an accurate response and in keeping P-homeostasis.

A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1

“…Therefore, further experiments with multiple knockouts are required to completely understand the function of this transcription factor family under phosphate deficiency. Additionally, other transcription factors were suggested to be involved in the lowphosphate response (Nilsson et al, 2010;Yang and Finnegan, 2010;Jain et al, 2012).…”

“…Upon phosphate starvation, plants induce a number of genes that function in recycling and mobilization of phosphate such as phosphate transporters, acid phosphatases, and nucleases (Nilsson et al, 2010;Plaxton and Tran, 2011). Furthermore, expression of genes coding for enzymes involved in galactolipid and sulfolipid biosynthesis is induced.…”

“…In addition, other transcription factors such as AtMYB62, ZINC FINGER OF ARABIDOPSIS THALIANA6, BASIC HELIX-LOOP-HELIX32, and AtWRKY75, posttranslational regulatory factors (e.g. belonging to the SYG1/Pho81/XPR1 [SPX] domain family), and microRNA399 are associated with signal transduction under phosphate starvation (Nilsson et al, 2010;Yang and Finnegan, 2010;Jain et al, 2012).…”

Differential responses of oat cultivars to phosphate deprivation: plant growth and acid phosphatase activities

“…Whole roots of plants hydroponically cultured for 1 week in phosphate-sufficient (?P) or phosphate-deficient (-P) nutrient medium (a); root crosssections of plants cultured for 1 week in ?P or -P nutrient media (b); selected fragments of root cross-sections from Szakal variety grown for 3 weeks in ?P or -P nutrient media (c) alterations of adequate genes expression (Fang et al 2009;Nilsson et al 2010;Lin et al 2011). Several studies have addressed the role of transcription factors like WRKY75, PHR1, MYB62 and ZAT6 in plant growth responses to Pi starvation (Fang et al 2009;Nilsson et al 2010;Yang and Finnegan 2010 and papers cited therein). Recently, clusters of genes were predicted, functioning in Pi deficiency signaling; analysis of mutants defective in genes expression from ''root hair cluster'' revealed eight novel genes involved in Pi deficiency-induced root hair elongation (Lin et al 2011).…”

“…Plants have developed many strategies to liberate phosphorus, including organic acid exudation from roots or secretion of enzymes, e.g., acid phosphatases (Schachtman et al 1998;Guame et al 2001;Vance et al 2003;Nilsson et al 2010). Pi absorption might be facilitated by expression of Pi transporters or via modifications of root system, strictly controlled and regulated at the molecular level ( _ Zebrowska and Ciereszko 2007;Desnos 2008;Fang et al 2009;Yang and Finnegan 2010).…”