Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism

Abstract

Plant metabolomics developed as a powerful tool to examine gene functions and to gain deeper insight into the physiology of the plant cell. In this study, we screened Arabidopsis lines overexpressing rice full-length (FL) cDNAs (rice FOX Arabidopsis lines) using a gas chromatography-time-of-flight mass spectrometry (GC-TOF/MS)-based technique to identify rice genes that caused metabolic changes. This screening system allows fast and reliable identification of candidate lines showing altered metabolite profiles. We performed metabolomic and transcriptomic analysis of a rice FOX Arabidopsis line that harbored the FL cDNA of the rice ortholog of the Lateral Organ Boundaries (LOB) Domain (LBD)/Asymmetric Leaves2-like (ASL) gene of Arabidopsis, At-LBD37/ASL39. The investigated rice FOX Arabidopsis line showed prominent changes in the levels of metabolites related to nitrogen metabolism. The transcriptomic data as well as the results from the metabolite analysis of the Arabidopsis At-LBD37/ASL39-overexpressor plants were consistent with these findings. Furthermore, the metabolomic and transcriptomic analysis of the Os-LBD37/ASL39-overexpressing rice plants indicated that Os-LBD37/ASL39 is associated with processes related to nitrogen metabolism in rice. Thus, the combination of a metabolomics-based screening method and a gain-of-function approach is useful for rapid characterization of novel genes in both Arabidopsis and rice.

Ubiquitin ligase EL5 maintains the viability of root meristems by influencing cytokinin-mediated nitrogen effects in rice

“…These results strongly suggest that reduction of EL5 function causes activation of nitrogen signalling despite the absence of a nitrogen source. Recently, transcription factors that regulate nitrogen signalling have been identified in rice and Arabidopsis (LOB, Rubin et al , 2009; Albinsky et al , 2010; NIGT1, Sawaki et al , 2013; NLP6 and NLP7, Castaings et al , 2009; Konishi and Yanagisawa, 2013; Marchive et al , 2013). Expression of genes in the same family as these transcription factor genes was induced in rice roots after nitrite treatment, but in mEL5 their expression levels were elevated prior to nitrite treatment (Fig.…”

LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration

“…Rice CROWN ROOTLESS1 and maize ROOTLESS CON-CERNING CROWN AND SEMINAL ROOTS, two close homologues of Arabidopsis LBD29, regulate the formation of monocot-specific crown roots [29][30][31]. Recent studies also indicate that some of LBD members, such as Arabidopsis LBD37, LBD38, LBD39 and rice LBD37, are involved in the regulation of anthocyanin and nitrogen metabolism [32,33].…”

Moving Toward a Comprehensive Map of Central Plant Metabolism

“…Most do rely on the 35S promoter, with all the advantages and disadvantages described above. These approaches are also amenable to combination with metabolomic screens, a technique that has revealed new regulatory mechanisms of plant nitrogen metabolism (2,95).…”