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Background  Glutamine is a major amino donor for the synthesis of amino acids, nucleotides, and other nitrogen-containing compounds in all organisms. In addition to its role in nutrition and metabolism, glutamine can also function as a signaling molecule in bacteria, yeast, and humans. By contrast, the functions of glutamine in nutrition and as a signaling molecule remain unclear in plants.    Results  We demonstrated that glutamine could effectively support the growth of rice seedlings. In glutamine-treated rice roots, the glutamine contents increased dramatically, whereas levels of glutamate remained relatively constant. Transcriptome analysis of rice roots revealed that glutamine induced the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses within 30 min. Interestingly, 10 of the 35 early glutamine responsive genes encode putative transcription factors, including two  LBD37 - like  genes that are involved in the regulation of nitrogen metabolism. Glutamine also rapidly induced the expression of the  DREB1A ,  IRO2 , and  NAC5  transcription factor genes, which are involved in the regulation of stress responses.    Conclusions  In addition to its role as a metabolic fuel, glutamine may also function as a signaling molecule to regulate gene expression in plants. The rapid induction of transcription factor genes suggests that glutamine may efficiently amplify its signal and interact with the other signal transduction pathways to regulate plant growth and stress responses. Thus, glutamine is a functional amino acid that plays important roles in plant nutrition and signal transduction.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1892-7) contains supplementary material, which is available to authorized users.

Glutamine rapidly induces the expression of key transcription factor genes involved in nitrogen and stress responses in rice roots