Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins.

Masakazu Satou,Atsushi Fukushima,Kazunori Saito,Kazuo Shinozaki,Masatomo Kobayashi,Fumiyoshi Myouga,Hitoshi Sakakibara,Takushi Hachiya,Akira Oikawa,Miyako Kusano,Daisaku Ohta,Kazuki Saito,Noriko Nagata,Harumi Enoki,Reiko Motohashi

doi:10.1007/s11103-014-0194-9

Abstract

We used four mutants having albino or pale green phenotypes with disrupted nuclear-encoded chloroplast proteins to analyze the regulatory system of metabolites in chloroplast. We performed an integrated analyses of transcriptomes and metabolomes of the four mutants. Transcriptome analysis was carried out using the Agilent Arabidopsis 2 Oligo Microarray, and metabolome analysis with two mass spectrometers; a direct-infusion Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR/MS) and a gas chromatograph-time of flight mass spectrometer. Among approximately 200 known metabolites detected by the FT-ICR/MS, 71 metabolites showed significant changes in the mutants when compared with controls (Ds donor plants). Significant accumulation of several amino acids (glutamine, glutamate and asparagine) was observed in the albino and pale green mutants. Transcriptome analysis revealed altered expressions of genes in several metabolic pathways. For example, genes involved in the tricarboxylic acid cycle, the oxidative pentose phosphate pathway, and the de novo purine nucleotide biosynthetic pathway were up-regulated. These results suggest that nitrogen assimilation is constitutively promoted in the albino and pale green mutants. The accumulation of ammonium ions in the albino and pale green mutants was consistently higher than in Ds donor lines. Furthermore, genes related to pyridoxin accumulation and the de novo purine nucleotide biosynthetic pathway were up-regulated, which may have occurred as a result of the accumulation of glutamine in the albino and pale green mutants. The difference in metabolic profiles seems to be correlated with the disruption of chloroplast internal membrane structures in the mutants. In albino mutants, the alteration of metabolites accumulation and genes expression is stronger than pale green mutants.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-014-0194-9) contains supplementary material, which is available to authorized users.

Highlights

In the post genome-sequencing era, functional analyses of identified genes have been performed systematically by using various mutant collections
The apg3 mutant is disrupted in a gene homologous to a eukaryotic ribosome release factor (RF1) and APG3 operates as a ribosome release factor in chloroplast (Motohashi et al 2007)
The mutation in the ch42 mutant is in the protoporphyrin IX chelatase subunit CHLI1 that functions in chlorophyll biosynthesis (Rissler et al 2002)

Summary

Introduction

In the post genome-sequencing era, functional analyses of identified genes have been performed systematically by using various mutant collections. Transcriptome analyses have provided us systematic characterization of gene expression profiles in various tissues and organs and under various growth conditions. Proteome analyses have revealed various novel proteins in various tissues and organelle and under various environmental conditions. Technology development in mass spectrometry has improved its reliability, sensitivity of detection and measurement speed in comprehensive analyses of whole metabolites (Sumner et al 2003; Villas-Bôas et al 2005; Hall 2006) and whole proteins (proteome) (Kersten et al 2002; Baginsky and Gruissem 2006; Giacomelli et al 2006). Tools have been developed for the joined visualization of transcriptomics and metabolomics (Wägele et al 2012)

Methods

Results

Discussion

Conclusion