SE178:/S01/M01/D01

Sample Set Information

ID	TSE1336
Title	Pathway-level acceleration of glycogen catabolism by a response regulator in the cyanobacterium Synechocystis species PCC 6803.
Description	Response regulators of two-component systems play pivotal roles in the transcriptional regulation of responses to environmental signals in bacteria. Rre37, an OmpR-type response regulator, is induced by nitrogen depletion in the unicellular cyanobacterium Synechocystis species PCC 6803. Microarray and quantitative real-time polymerase chain reaction analyses revealed that genes related to sugar catabolism and nitrogen metabolism were up-regulated by rre37 overexpression. Protein levels of GlgP(slr1367), one of the two glycogen phosphorylases, in the rre37-overexpressing strain were higher than those of the parental wild-type strain under both nitrogen-replete and nitrogen-depleted conditions. Glycogen amounts decreased to less than one-tenth by rre37 overexpression under nitrogen-replete conditions. Metabolome analysis revealed that metabolites of the sugar catabolic pathway and amino acids were altered in the rre37-overexpressing strain after nitrogen depletion. These results demonstrate that Rre37 is a pathway-level regulator that activates the metabolic flow from glycogen to polyhydroxybutyrate and the hybrid tricarboxylic acid and ornithine cycle, unraveling the mechanism of the transcriptional regulation of primary metabolism in this unicellular cyanobacterium.
Authors	Osanai, T., Oikawa, A., Numata, K., Kuwahara, A., Iijima, H., Doi, Y., Saito, K. and Hirai, M.Y.
Reference	Plant Physiol. 2014 Apr;164(4):1831-41. doi: 10.1104/pp.113.232025.
Comment

PubMed

Sample Information

ID	S01
Title	Synechocystis sp. PCC 6803
Organism - Scientific Name	Synechocystis sp. PCC 6803 substr. GT-I
Organism - ID	NCBI:txid1080228
Compound - ID
Compound - Source
Preparation	Among the GT strains of Synechocystis sp. PCC 6803 (isolated by Williams [1988]), the GT-I strain was used in this study (Kanesaki et al., 2012). The cells were grown in modified BG-11 medium (Rippka, 1988), which is BG-110 liquid medium containing 5 mm NH4Cl (buffered with 20 mm HEPES-KOH, pH 7.8). Liquid cultures were bubbled with 1% (v/v) CO2 in air at 30°C under continuous white light (approximately 50–70 μmol photons m–2 s–1). Growth and cell densities were measured at A730 using the Hitachi U-3310 spectrophotometer.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M01
Title	CE-MS analysis
Method Details ID	MS01
Sample Amount	20 μl
Comment

Analytical Method Details Information

ID	MS01
Title	CE-MS Analysis
Instrument	CE:Agilent CE capillary electrophoresis system (Agilent Technologies) TOF-MS:Agilent G3250AA LC/MSD TOF system (Agilent Technologies) CE-MS:Agilent G1603A
Instrument Type
Ionization	ESI
Ion Mode	positive and negative
Description	Cells were collected by centrifugation at 9,800g for 2 min, followed by freezing in liquid nitrogen. Cells (50–100 mg fresh weight) were suspended in 600 μL of a mixture containing 60% (v/v) methanol and 200 μm each 10-camphorsulfonic acid and trimesic acid as internal standards, and it was mixed using an MT-200 microtube mixer (Tomy) for 20 min at room temperature, followed by centrifugation at 20,500g for 5 min at 4°C. A 300-μL aliquot of the supernatant was centrifuged through a Millipore 5-kD cutoff filter at 10,000g for 90 min. A 250-μL aliquot of the filtrate was dried in a centrifugal concentrator (drying time, 120 min). The residue was dissolved in 20 μL of water and subjected to CE-MS analysis. The CE-MS system and conditions were as described previously (Oikawa et al., 2011).
Comment_of_details

PubMed

Data Analysis Information

ID	D01
Title	Statistical analysis
Data Analysis Details ID	DS01
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS01
Title	Statistical Analyses
Description	Statistical analyses were performed using StatPlus:macLE software for MacOSX (Analyst Soft) or Microsoft Excel version 14.3.2 (Microsoft). P values were determined using paired two-tailed Student’s t tests. A 95% confidence interval was used to determine significance.
Comment_of_details