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