NITRATE-INDUCED GENES IN TOMATO ROOTS: ARRAY ANALYSIS REVEALS NOVEL GENES THAT MAY PLAY A ROLE IN NITROGEN NUTRITION

Authors: WANG, YI-HONG - CORNELL UNIVERSITY; Garvin, David; Kochian, Leon

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2001
Publication Date: 9/1/2001
Citation: WANG, Y., GARVIN, D.F., KOCHIAN, L.V. NITRATE-INDUCED GENES IN TOMATO ROOTS: ARRAY ANALYSIS REVEALS NOVEL GENES THAT MAY PLAY A ROLE IN NITROGEN NUTRITION. PLANT PHYSIOLOGY. 2001.

Interpretive Summary: Nitrogen (N) is the essential mineral element required in the greatest amount in plants (1.5-2% of plant dry matter). Because of the high N requirements for crop plants, N fertilization is a major worldwide agricultural investment, with 80 million metric tons of N fertilizers applied annually. There are also negative environmental consequences for the extensive use of N fertilizers in crop production, as N fertilizer not absorbed by crop plants can subsequently leach into & contaminate water supplies. Therefore, it is desirable to develop strategies to reduce N input while simultaneously maintaining productivity. A more complete understanding of the molecular & physiological basis of N uptake & metabolism in plants may reveal strategies for accomplishing these goals. In most agricultural soils, nitrate is the most important source of N. As it has been well documented that root exposure to nitrate turns on the biochemical machinery for nitrate assimilation in plants, we employed genomic approaches arraying root genes on nylon membranes to study those genes turned on in tomato roots by nitrate exposure. Using this approach, we identified a series of novel genes that exhibit nitrate inducibility, including stress response genes, mineral nutrient & water transport genes, & genes involved in the regulation of other genes. The identification of these genes is providing new avenues of research into the molecular basis of plant mineral nutrition, including the possible linkages & networking between regulation of N, P, and K nutrition, as well as processes & mechanisms by which plants sense & respond to changes in plant mineral status, & the connections between mineral ion transporters & plant metabolic pathways.

Technical Abstract: A subtractive tomato root cDNA library enriched in genes up-regulated by changes in plant mineral status was screened with labeled mRNA from roots of both nitrate-induced and mineral nutrient deficient (-N, -P, -K, -S, -Mg, -Ca, -Fe, -Zn, -Cu) tomato plants. A subset of cDNAs selected from this library based on mineral nutrient-related changes in expression as well as cDNAs selected from a second tomato root library based on homology to known genes yielded a set of 1280 mineral nutrition-related cDNAs that were arrayed on nylon membranes for further analysis. These high density arrays were hybridized with mRNA from tomato plants exposed to nitrate at different time points after nitrogen was withheld for 48 hrs. One hundred nineteen genes were found to be up-regulated by nitrate resupply. Among these genes were several previously identified as nitrate responsive, including those encoding nitrate transporters, nitrate and nitrate reductase, and metabolic enzymes such as transaldolase, transketolase, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase. We also identified sixteen novel nitrate-inducible genes, including 1) water channels, 2) root Pi and K+ transporters, 3) genes potentially involved in signaling and transcriptional regulation, 4) stress response genes, and 5) ribosomal protein genes. Time courses of nitrate-inducible expression for several of the most interesting genes were analyzed using RNA gel blots, and revealed a range of different induction patterns. The identification of these novel nitrate-inducible genes provides new insights into the molecular basis of plant nitrogen nutrition, as well as possible networking between the regulation of N, P, and K nutrition.