Microarray analysis for transcriptional profiling of potato cells under abrupt or gradual-adaptive exposure to water stress

To distinguish transcriptome changes as generalized response to water stress from those involved in adaptation/tolerance, potato cells were abruptly exposed or gradually acclimated to grow at low water potential created by addition of increasing concentrations of polyethylene glycol (PEG) to the nutrient medium. Physiological and biochemical analysis has revealed that gradual acclimation allows active growth by means of a set of metabolic changes, including proline accumulation, de novo protein synthesis, changes in membrane lipid composition, not observed in PEG-shocked cells (Leone et al, 1994, Plant Physiol, 106: 703-712; Leone et al, 1996, Plant, Cell & Environ 19: 1103-1109). TIGR 10K potato cDNA slides (www.tigr.org) were hybrized, at least in six replicates, including dye swap, with labeled Cy3-dUTP and Cy5-dUTP retro-transcribed total RNA from control vs PEG-shocked cells or control vs PEG-adapted cells. Although up-regulated genes (>2.0 fold increase) belonging to different functional categories (including transcription factors, stress-proteins, amino-acid, protein and carbohydrate metabolism, cell wall synthesis and others) were identified in both PEG-shocked and adapted potato cells, only 13 cDNAs were common to both treatments. Similarly, a limited number of common down-regulated genes were identified in the two cell populations. Altogether these data confirm that different gene networks are mediating the short- and long-term cellular response to water stress. The contribution of specific functional gene classes in the adaptation or in the abrupt response to water stress will be discussed on the basis of the microarray results as well as the differential expression validation by RT-PCR or Real-time RT-PCR.