DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments

Abstract

The phosphatidylinositol (PI) metabolic pathway is considered critical in plant responses to many environmental factors, and previous studies have indicated the involvement of multiple PI-related gene families during cellular responses. Through a detailed analysis of the Arabidopsis thaliana genome, 82 polypeptides were identified as being involved in PI signaling. These could be grouped into different families including PI synthases (PIS), PI-phosphate kinases (PIPK), phospholipases (PL), inositol polyphosphate phosphatases (IPPase), inositol polyphosphate kinases (IPK), PI transfer proteins and putative inositol polyphosphate receptors. The presence of more than 10 isoforms of PIPK, PLC, PLD and IPPase suggested that these genes might be differentially expressed during plant cellular responses or growth and development. Accordingly, DNA chip technology was employed to study the expression patterns of various isoforms. In total, 79 mRNA clones were amplified and used for DNA chip generation. Expression profile analysis was performed using samples that represented multiple tissues or cellular responses. Tested samples included normal leaf, stem and flower tissues, and leaves from plants treated with various hormones (auxin, cytokinin, gibberellin, abscisic acid and brassinosteroid) or environmental factors (temperature, calcium, sodium, drought, salicylic acid and jasmonic acid). Results showed that many PI pathway-related genes were differentially expressed under these experimental conditions. In particular, the different isoforms of each family were specifically expressed in many cases, suggesting their involvement in tissue specificity and cellular responses to environmental conditions. This work provides a starting point for functional studies of the relevant PI-related proteins and may help shed light onto the role of PI pathways in development and cellular responses.

Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

“…Nitrilases are key enzymes in the biosynthesis of the plant hormone IAA (16), which belongs to the auxin class of plant growth regulators. The enzyme phosphatidylinositol 3-kinase, found in the signal transduction functional group, can also be related to this putative reduced IAA content because the phosphatidylinositol signaling pathway is also involved in plant responses to hormones, like auxins (17). We also found, in this experiment, a group of genes implicated in protein modifications whose altered transcription can be related to the hypothetical reduced IAA content.…”

“…This domain has been correlated with stress signaling (22). In the stable mutagenized line we found two signal transduction-associated proteins, both also already characterized as stress/defense associated (Table 1): a receptor-like kinase (9, 10) and a phosphatidylinositol 3-kinase (17). Finally, concerning the unstable mutagenized line (Table 1) we found, in this category, an apyrase (23), a S receptor kinase (9, 10), a putative serine/threonine kinase (24), and a protein tyrosine kinase (25).…”

Regulation of de novo phosphatidylinositol synthesis

“…In yeast, upregulation of the pis1 gene, which codes for PIS, has been shown to be consistent with an overall increase in PtdIns levels (35). Plants have also been shown to regulate the expression of pis1 (36). With respect to mammals, the pis1 gene has been identified in rats (37) and humans (13), but data pertinent to the regulation of its expression are lacking.…”

MORN motifs in plant PIPKs are involved in the regulation of subcellular localization and phospholipid binding

“…Now most phosphoinositide molecules presented in mammalian cells have been identified in plant cells, and plant genes encoding the PI metabolism enzymes have been cloned in succession, including those for PI synthase [16], PI 3-kinases [17,18], PI4K [19], PIPK [20], PI-PLCs [21,22], inositol polyphosphate phosphatases [23,24], inositol polyphosphate kinases [25,26], and others. In 1998, a cDNA of plant PIPK (AtPIP5K1) from Arabidopsis was cloned, which was the first report of plant PIPK [20].…”