Nitrate-induced genes in tomato roots. Array analysis reveals novel genes that may play a role in nitrogen nutrition

A subtractive tomato (Lycopersicon esculentum) root cDNA library enriched i n genes up-regulated by changes in plant mineral status was screened with l abeled mRNA from roots of both nitrate-induced and mineral nutrient-deficie nt (-nitrogen [N], -phosphorus, -potassium [K], -sulfur, -magnesium, -calci um, -iron, -zinc, and -copper) tomato plants. A subset of cDNAs was selecte d from this library based on mineral nutrient-related changes in expression . Additional cDNAs were selected from a second mineral-deficient tomato roo t library based on sequence homology to known genes. These selection proces ses yielded a set of 1,280 mineral nutrition-related cDNAs that were arraye d on nylon membranes for further analysis. These high-density arrays were h ybridized with mRNA from tomato plants exposed to nitrate at different time points after N was withheld for 48 h, for plants that were grown on nitrat e/ammonium for 5 weeks prior to the withholding of N. One hundred-fifteen g enes were found to be up-regulated by nitrate resupply. Among these genes w ere several previously identified as nitrate responsive, including nitrate transporters, nitrate and nitrite reductase, and metabolic enzymes such as transaldolase, transketolase, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase. We also identified 14 novel nitrate-inducible genes, including: (a) water channels, (b) root phosphate and K+ transporter s, (c) genes potentially involved in transcriptional regulation, (d) stress response genes, and (e) ribosomal protein genes. In addition, both familie s of nitrate transporters were also found to be inducible by phosphate, K, and iron deficiencies. The identification of these novel nitrate-inducible genes is providing avenues of research that will yield new insights into th e molecular basis of plant N nutrition, as well as possible networking betw een the regulation of N, phosphorus, and K nutrition.