SE141:/S1/M2/D1

Sample Set Information

ID	TSE1242
Title	Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination.
Description	In higher plants, the circadian clock controls a wide range of cellular processes such as photosynthesis and stress responses. Understanding metabolic changes in arrhythmic plants and determining output-related function of clock genes would help in elucidating circadian-clock mechanisms underlying plant growth and development. In this work, we investigated physiological relevance of PSEUDO-RESPONSE REGULATORS (PRR 9, 7, and 5) in Arabidopsis thaliana by transcriptomic and metabolomic analyses. Metabolite profiling using gas chromatography-time-of-flight mass spectrometry demonstrated well-differentiated metabolite phenotypes of seven mutants, including two arrhythmic plants with similar morphology, a PRR 9, 7, and 5 triple mutant and a CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1)-overexpressor line. Despite different light and time conditions, the triple mutant exhibited a dramatic increase in intermediates in the tricarboxylic acid cycle. This suggests that proteins PRR 9, 7, and 5 are involved in maintaining mitochondrial homeostasis. Integrated analysis of transcriptomics and metabolomics revealed that PRR 9, 7, and 5 negatively regulate the biosynthetic pathways of chlorophyll, carotenoid and abscisic acid, and alpha-tocopherol, highlighting them as additional outputs of pseudo-response regulators. These findings indicated that mitochondrial functions are coupled with the circadian system in plants.
Authors	Fukushima A, Kusano M, Nakamichi N, Kobayashi M, Hayashi N, Sakakibara H, Mizuno T, Saito K.
Reference	Proc Natl Acad Sci U S A. 2009 Apr 28;106(17):7251-6. doi: 10.1073/pnas.0900952106. Epub 2009 Apr 9. Erratum in: Proc Natl Acad Sci U S A. 2009 May 26;106(21):8791.
Comment

PubMed

Sample Information

ID	S1
Title	Plant Materials and Growth Conditions
Organism - Scientific Name	Arabidopsis thaliana
Organism - ID	NCBI taxonomy 3702
Compound - ID
Compound - Source
Preparation	A. thaliana accession Columbia (Col-0) was used as a WT plant source. Triple-knockout Arabidopsis mutant prr9-10/prr7-11/prr5-11 has been described in ref. 9. Seedling were grown on Murashige and Skoog (392-00591;Wako) with 0.3% gellan gumand 2% sucrose at pH 5.7 under continuous light (LL) or 12-h light/12-h dark (LD) cycles at 22 °C for 18 days. Whole plants were sampled during days 18–19 to reduce possible developmental effects.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M2
Title	Design 2
Method Details ID	MS1
Sample Amount	167 μg fresh weight of the derivatized extract
Comment

Analytical Method Details Information

ID	MS1
Title	GC-TOF MS
Instrument	GC:Agilent 6890N MS:LECO Pegasus 4D MS system
Instrument Type
Ionization	EI
Ion Mode	Positive
Description	Each sample was extracted, derivatized, and analyzed by using gas chromatography–time-of-flight (GC-TOF/MS) as described in ref. 48. See also SI Methods(http://www.pnas.org/cgi/data/0900952106/DCSupplemental/Supplemental_PDF#nameddest=STXT). All the derivatization steps were performed in the vacuum glove box VSC-100 (Sanplatec, Japan) filled with 99.9995% (G3 grade) of dry nitrogen. The analysis of metabolites by GC-TOF/MS was performed as described previously.
Comment_of_details

PubMed

Data Analysis Information

ID	D1
Title	Data Processing
Data Analysis Details ID	DS1
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS1
Title	Data processing
Description	Nonprocessed raw data were treated by using a custom script described by Jonsson et al. to perform baseline correction, alignment, and peak deconvolution. Metabolites were identified by comparing their mass spectrum and retention time index (RI) with those generated for authentic compounds analyzed on our instrumentation as well as those in the MS and RI libraries in the Golm Metabolome Database.
Comment_of_details