Shoot nitrate status regulates Arabidopsis shoot growth and systemic transcriptional responses via shoot adenosine phosphate-isopentenyltransferase 3

Abstract Plants systemically regulate growth and gene expression according to their internal nitrate status. Our previous study reported that shoot nitrate accumulation increases shoot expression of adenosine phosphate-ISOPENTENYLTRANSFERASE 3 (IPT3) and shoot levels of N6-(Δ2-isopentenyl) adenine (iP)-type cytokinins (CKs). IPT3 expression is localized in the phloem, and iP-type CKs, which are synthesized by IPT3, are phloem-mobile. As CKs are a class of phytohormones that control growth and genome-wide gene expression, shoot-expressed IPT3 may mediate the systemic regulation of growth and transcriptomic responses to shoot nitrate status. To examine this, we developed a novel system to manipulate nitrate levels and IPT3 expression in a shoot-specific manner and performed growth analysis, CK determination, and RNA-sequencing. Our results demonstrated that shoot nitrate accumulation significantly promoted shoot growth and elevated shoot concentrations of iP ribotides, iP-7-N-glucoside, and iP-9-N-glucoside through the action of shoot IPT3. Transcriptomic responses to shoot nitrate accumulation were largely tuned by shoot IPT3, with opposite effects in shoots and roots. Shoot IPT3 amplified shoot responses of nitrate-inducible genes and immune response genes to shoot nitrate accumulation, while it dampened root responses of nitrate transport/assimilation genes. This transcriptomic modulation via shoot IPT3 was accompanied by coherent transcriptional changes in genes encoding mobile peptides and transcriptional repressors. Here we present a novel scheme integrating shoot nitrate status responses with CK signaling. Competing Interest Statement The authors have declared no competing interest. Footnotes Funding: This study was supported by JSPS KAKENHI [No. 20K05771 and 23K04978 to TH and No. JP24KJ1709 to KM], by JST SPRING [No. JPMJSP2155 to KM], and by the Sasakawa Scientific Research Grant from the Japan Science Society [No. 2022-4039 to KM]. According to the reviewers' comments, we revised the Introduction, Materials and Methods, Results and Discussion, and Figure legends. We also added Supplementary Table S10 and statistical analyses. In addition, we changed the title from "Shoot nitrate status regulates Arabidopsis shoot growth and systemic transcriptional responses via shoot adenylate isopentenyltransferase 3" to "Shoot nitrate status regulates Arabidopsis shoot growth and systemic transcriptional responses via shoot adenosine phosphate-isopentenyltransferase 3."