SE178:/S01/M01/D01

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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.
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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
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Analytical Method Information

ID M01
Title CE-MS analysis
Method Details ID MS01
Sample Amount 20 μl
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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).
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Data Analysis Information

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