SE178:/S01/M02/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	M02
Title	Amino Acid Analysis with GC-MS
Method Details ID	MS02
Sample Amount	1 μl
Comment

Analytical Method Details Information

ID	MS02
Title	Amino Acid Analysis with GC-MS
Instrument	GCMS‐QP2010Plus (Shimadzu)
Instrument Type
Ionization	EI
Ion Mode	Positive
Description	Equal amounts of cells (50 mL of cell culture with A730 = 1) were harvested by rapid filtration using a previously described method (Osanai et al., 2014). In total, 300 μL of the upper phase was transferred to a new tube and vacuum dried. Samples were suspended in 500 μL of methanol with 1 μm nor-Val as an internal standard and derivatized using the EZ:faast kit (Phenomenex; Badawy et al., 2008). GC-MS was performed using a GCMS-QP2010Plus (Shimadzu) equipped with a 10-m × 0.25-mm ZB-AAA capillary gas chromatography column. The injection volume was 1 μL at a carrier gas flow of 1.17 mL min−1 helium with a split ratio of 1:15. The initial column oven temperature of 110°C was maintained for 1 min and raised to 300°C at 20°C min−1. The interface and ion source temperatures were 280°C and 240°C, respectively.
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