Genomic analysis of a nutrient response in Arabidopsis reveals diverse expression patterns and novel metabolic and potential regulatory genes induced by nitrate.
Microarray and RNA gel blot analyses were performed to identify Arabidopsis genes that responded to nitrate at both low (250 microM) and high (5 to 10 mM) nitrate concentrations. Genes involved directly or indirectly with nitrite reduction were the most highly induced by nitrate. Most of the known nitrate-regulated genes (including those encoding nitrate reductase, the nitrate transporter NRT1, and glutamate synthase) appeared in the 40 most strongly nitrate-induced genes/clones on at least one of the microarrays of the 5524 genes/clones investigated. Novel nitrate-induced genes were also found, including those encoding (1) possible regulatory proteins, including an MYB transcription factor, a calcium antiporter, and putative protein kinases; (2) metabolic enzymes, including transaldolase and transketolase of the nonoxidative pentose pathway, malate dehydrogenase, asparagine synthetase, and histidine decarboxylase; and (3) proteins with unknown functions, including nonsymbiotic hemoglobin, a senescence-associated protein, and two methyltransferases. The primary pattern of induction observed for many of these genes was a transient increase in mRNA at low nitrate concentrations and a sustained increase when treated with high nitrate concentrations. Other patterns of induction observed included transient inductions after both low and high nitrate treatments and sustained or increasing amounts of mRNA after either treatment. Two genes, AMT1;1 encoding an ammonium transporter and ANR1 encoding a MADS-box factor, were repressed by nitrate. These findings indicate that nitrate induces not just one but many diverse responses at the mRNA level in Arabidopsis.
Wang
R
R
Division of Biology, University of California at San Diego, La Jolla, California 92093-0016, USA.
Guegler
K
K
LaBrie
S T
ST
Crawford
N M
NM
D020816:Amino Acid Motifs; D000641:Ammonia / Q000378:metabolism; D027321:Anion Transport Proteins; D017360:Arabidopsis / Q000187:drug effects / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D001217:Aspartate-Ammonia Ligase / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D002118:Calcium / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D002352:Carrier Proteins / Q000235:genetics; D005288:Ferredoxins / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D006601:Hexoses / Q000378:metabolism; D006640:Histidine Decarboxylase / Q000235:genetics; D007210:Indoleacetic Acids / Q000494:pharmacology; D008780:Methyltransferases / Q000235:genetics; D000091285:Nitrate Transporters; D009573:Nitrites / Q000378:metabolism / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D010088:Oxidoreductases / Q000235:genetics; D010427:Pentose Phosphate Pathway; D011494:Protein Kinases / Q000235:genetics; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D015854:Up-Regulation / Q000187:drug effects
D027321:Anion Transport Proteins; D001426:Bacterial Proteins; D002352:Carrier Proteins; D005288:Ferredoxins; D006601:Hexoses; D007210:Indoleacetic Acids; D000091285:Nitrate Transporters; D009573:Nitrites; D018749:RNA, Plant; D014157:Transcription Factors; D002244:Carbon; D000641:Ammonia; D010088:Oxidoreductases; D008780:Methyltransferases; D011494:Protein Kinases; D006640:Histidine Decarboxylase; D001217:Aspartate-Ammonia Ligase; D002118:Calcium