Integrated metabolite and gene expression profiling revealing phytochrome A regulation of polyamine biosynthesis of Arabidopsis thaliana

Abstract

In this study, metabolite profiling was demonstrated as a useful tool to plot a specific metabolic pathway, which is regulated by phytochrome A (phyA). Etiolated Arabidopsis wild-type (WT) and phyA mutant seedlings were irradiated with either far-red light (FR) or white light (W). Primary metabolites of the irradiated seedlings were profiled by gas chromatography time-of-flight mass spectrometry (GC/TOF-MS) to obtain new insights on phyA-regulated metabolic pathways. Comparison of metabolite profiles in phyA and WT seedlings grown under FR revealed a number of metabolites that contribute to the differences between phyA and the WT. Several metabolites, including some amino acids, organic acids, and major sugars, as well as putrescine, were found in smaller amounts in WT compared with the content in phyA seedlings grown under FR. There were also significant differences between metabolite profiles of WT and phyA seedlings during de-etiolation under W. The polyamine biosynthetic pathway was investigated further, because putrescine, one of the polyamines existing in a wide variety of living organisms, was found to be present in lower amounts in WT than in phyA under both light conditions. The expression levels of polyamine biosynthesis-related genes were investigated by quantitative real-time RT-PCR. The gene expression profiles revealed that the arginine decarboxylase 2 (ADC2) gene was transcribed less in the WT than in phyA seedlings under both light conditions. This finding suggests that ADC2 is negatively regulated by phyA during photomorphogenesis. In addition, S-adenosylmethionine decarboxylase 2 and 4 (SAMDC2 and SAMDC4) were found to be regulated by phyA but in a different manner from the regulation of ADC2.

Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity

“…B, Lack of phytochrome signaling leads to enhanced levels of several organic acids, sugars, and amino acids in most studies. The heat map visualizes fold changes in soluble metabolite content in phytochrome mutants and the prr975 mutant compared with wild-type (WT) controls, or in response to low R-FR ratio, as seen in gas chromatography-mass spectrometry (GC-MS) data sets (Jumtee et al, 2008(Jumtee et al, , 2009Fukushima et al, 2009;Yang et al, 2016; extent as in seedlings (Hu et al, 2013;Patel et al, 2013;Yang et al, 2016). In tomato (Solanum lycopersicum), phy effects on chlorophyll levels also are quite evident in adult plants (Kharshiing and Sinha, 2016).…”

“…Fold changes were calculated by dividing the metabolite content of the mutant (or low R-FR ratio-treated plants) by that of the wild type (or high R-FR-treated plants). For Jumtee et al (2008), values at 24 h after the start of FR or white light treatment were first normalized by the respective dark control of each genotype at the same time point, and then fold change of phyA over the wild type was determined from these values. Experimental setup, samples, and conditions for each study are indicated above the heat map.…”

“…Evidence is emerging that phy signaling has sizable effects on the majority of such primary carbon metabolic pathways and a subset of secondary metabolites. Studies published over the last 11 years reported metabolomics experiments comparing phy mutants with wild-type controls in Arabidopsis and rice (Oryza sativa; Ghassemian et al, 2006;Jumtee et al, 2008Jumtee et al, , 2009Patel et al, 2013;Yang et al, 2016;Han et al, 2017). One of these studies analyzed metabolic changes during the first 24 h of FR-or white-light induced deetiolation of dark-germinated wild-type and phyA seedlings (Jumtee et al, 2008), while Ghassemian et al (2006) investigated changes due to deetiolation in R light.…”

“…Studies published over the last 11 years reported metabolomics experiments comparing phy mutants with wild-type controls in Arabidopsis and rice (Oryza sativa; Ghassemian et al, 2006;Jumtee et al, 2008Jumtee et al, , 2009Patel et al, 2013;Yang et al, 2016;Han et al, 2017). One of these studies analyzed metabolic changes during the first 24 h of FR-or white-light induced deetiolation of dark-germinated wild-type and phyA seedlings (Jumtee et al, 2008), while Ghassemian et al (2006) investigated changes due to deetiolation in R light. The other reports (Patel et al, 2013;Yang et al, 2016;Han et al, 2017) focused on metabolic changes in low R-FR ratio or phy single and multiallele mutant whole rosettes (more than 2.5 weeks old), while the rice study distinguished between young and mature leaves (Jumtee et al, 2009).…”

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

“…It is well known that light plays a critical role in the regulation of anthocyanin and flavonoid biosynthesis (Koes et al, 2005;Grotewold, 2006). In addition, through an integrated analysis of gene expression and metabolite profiling, Jumtee et al (2008) found that the photoreceptor phytochrome A regulated the biosynthesis of polyamines, including spermidine and spermine. However, no previous reports that we are aware of have described the possible participation of light involvement in stachyose biosynthesis.…”