CIPK9 regulates ammonium-dependent root growth in rice

Amino acids, the building blocks of proteins, use ammonium (NH₄⁺) ions that a plant gathers from the soil. Previously a gene called INDETERMINATE DOMAIN 10 (IDD10) has been identified as activating the expression of a large number of NH₄⁺-responsive genes including AMMONIUM TRANSPORTER 1;2 (AMT1;2). Yuan Hu Xuan and colleagues have published a new report identifying a further element in the genetic chain responding to ammonium: CBL-INTERACTING PROTEIN KINASE 9 regulates ammonium-dependent root growth downstream of IDD10 in rice (Oryza sativa)

“Nitrate (NO₃^–) and ammonium (NH₄⁺) are the major forms of nitrogen (N) in higher plants,” write the authors in their paper. “Nitrogen is an important macro-element required for the synthesis of cellular molecules such as amino acids and nucleotides. Reduction of NO₃^– to NH₄⁺ consumes 12–26 % of photosynthetically generated reductant, which makes NH₄⁺ an energetically favourable N source. At high concentrations, however, NH₄⁺ is toxic to many plant species.”

The team used quantitative reverse transcription–PCR to analyse NH₄⁺– and IDD10-dependent expression of CIPK genes. They identified IDD10-regulated CIPK target genes by using electrophoretic mobility shift assays, chromatin immunoprecipitation and transient transcription assays. The scientists then measured root growth rate, ammonium content and 15N uptake of cipk mutants to determine their sensitivity to NH4+ and to compare these phenotypes with those of idd10. The authors investigated the genetic relationship between CIPK9 OX and idd10 by crosses between the CIPK9 and IDD10 lines.

“The most notable finding was that disrupting CIPK9, a direct target of IDD10, produced almost identical root phenotypes to disruption of IDD10,” say Xuan and colleagues in their paper. “Moreover, roots of cipk9 and idd10 mutants showed the same response to MSX; NH₄⁺-dependent retardation of root elongation could be rescued in both mutants by MSX treatment.”

The study has moved on understanding of ammonium uptake in rice, Xuan and colleagues said. “This study demonstrated that CIPK9 is a regulator of NH₄⁺-dependent root growth in rice. Extensive analyses of transcriptomes and metabolomes are required to understand the molecular and physiological roles of IDD10 and CIPK9 in regulating root growth in response to NH₄⁺. These results provide an important foundation for a more extensive understanding of the regulatory basis of NH₄⁺ signalling in rice plants.”