The branched-chain amino acids (BCAAs) leucine, isoleucine and valine are among nine essential amino acids that humans and other animals must obtain from their diets, and can be nutritionally limiting in plant foods. Rapid development of transcript profiling technologies has enabled research on plant metabolism that offers potential to improve crop nutritional quality by allowing researchers to apply correlative analysis in hypothesis generation followed by experimental validation. Despite genetic evidence of its importance in regulating seed amino acid levels, the full BCAA catabolic network is not completely understood in plants, and limited information is available regarding its regulation. In this study, a combination of transcript and mutant analyses was performed to study the pathway and regulation of BCAA catabolism in Arabidopsis thaliana. Transcript coexpression analyses revealed positive correlations among BCAA catabolic genes in stress, development, diurnal/circadian and light datasets. BCAA catabolism genes show coordinated oscillation in diurnal and circadian treatments, and their expression patterns are altered in clock and phytochrome B mutants, providing evidence for the regulation of BCAA catabolism by the circadian clock and light. Functional divergence is suggested by transcript profile comparison between four pairs of BCAA catabolic enzyme paralogs, and the paralogs do not increase their transcript levels upon the loss of their duplicated copies in the dark. In addition, mutants defective in putative branched-chain ketoacid dehydrogenase subunits accumulate higher levels of BCAAs in mature seeds, providing genetic evidence for their function in BCAA catabolism. BCAA catabolism genes are highly expressed during the night on a diel cycle and during prolonged darkness, and mutants undergo senescence early and over-accumulate leaf BCAAs during prolonged darkness. These results extend the previous evidence that BCAAs can be catabolized and serve as respiratory substrates at multiple steps. Furthermore, comparison of amino acid profiles between mature seeds and dark-treated leaves revealed differences in amino acid accumulation when BCAA catabolism is perturbed. Together, these results demonstrate the consequences of blocking BCAA catabolism during both normal growth conditions and under energy-limited conditions.
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