{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000394","ANALYSIS_ID":"AN000631","VERSION":"1","CREATED_ON":"May 10, 2016, 12:30 pm"},

"PROJECT":{"PROJECT_TITLE":"The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth","PROJECT_SUMMARY":"Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, and kaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","FUNDING_SOURCE":"NIH U24DK097154","PUBLICATIONS":"doi: 10.1073/pnas.1504576112"},

"STUDY":{"STUDY_TITLE":"The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth","STUDY_SUMMARY":"Cyanobacteria are increasingly being considered for use in large-scale outdoor production of fuels and industrial chemicals. Cyanobacteria can anticipate daily changes in light availability using an internal circadian clock and rapidly alter their metabolic processes in response to changes light availability. Understanding how signals from the internal circadian clock and external light availability are integrated to control metabolic shifts will be important for engineering cyanobacteria for production in natural outdoor environments. This study has assessed how “knowing” the correct time of day, via the circadian clock, affects metabolic changes when a cyanobacterium goes through a dark-to-light transition. Our data show that the circadian clock plays an important role in inhibiting activation of the oxidative pentose phosphate pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically tractable model cyanobacterium that has been engineered to produce industrially relevant biomolecules and is the best-studied model for a prokaryotic circadian clock. However, the organism is commonly grown in continuous light in the laboratory, and data on metabolic processes under diurnal conditions are lacking. Moreover, the influence of the circadian clock on diurnal metabolism has been investigated only briefly. Here, we demonstrate that the circadian oscillator influences rhythms of metabolism during diurnal growth, even though light–dark cycles can drive metabolic rhythms independently. Moreover, the phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Although RpaA activity is important for carbon degradation at night, KaiC is dispensable for those processes. Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning suppresses metabolic processes that normally are active at night, and kaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.","INSTITUTE":"University of California, Davis","DEPARTMENT":"Genome and Biomedical Sciences Facility","LABORATORY":"WCMC Metabolomics Core","LAST_NAME":"Fiehn","FIRST_NAME":"Oliver","ADDRESS":"1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616","EMAIL":"ofiehn@ucdavis.edu","PHONE":"(530) 754-8258","STUDY_COMMENTS":"The first 4 samples were a test run to see how efficient the analysis was and were run on a lipidomics platform. The next 12 samples were the used in the paper and were the same as the original 4 samples, but they were split into 3 biological replicates and run on the GC platform.","PUBLICATIONS":"doi: 10.1073/pnas.1504576112"},

"SUBJECT":{"SUBJECT_TYPE":"Cells","SUBJECT_SPECIES":"Synechococcus elongatus PCC7942 cells","TAXONOMY_ID":"1140"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"WT T0",
"Sample ID":"SDiamInj04_WT T0_CSH.d",
"Factors":{"Genotype":"WT","Time Point":"-"}
},
{
"Subject ID":"WT T4",
"Sample ID":"SDiamInj05_WT T4_CSH.d",
"Factors":{"Genotype":"WT","Time Point":"4"}
},
{
"Subject ID":"KaiC T0",
"Sample ID":"SDiamInj03_KaiC T0_CSH.d",
"Factors":{"Genotype":"KaiC mutant","Time Point":"-"}
},
{
"Subject ID":"KaiC T4",
"Sample ID":"SDiamInj02_KaiC T4_CSH.d",
"Factors":{"Genotype":"KaiC mutant","Time Point":"4"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Bacteria were grown in a turbidostat/bioreactor at equal cell density (measured by optical density at 750nm), under a 12:12h Light/Dark cycle. After collection samples were immediately placed on ice and then centrifuged at 5000RPM for 10min at ­4 degrees Celsius. After centrifugation supernatant was decanted and cell pellets were immediately frozen in liquid N2.","COLLECTION_PROTOCOL_FILENAME":"StudyDesign-SpencerDiamond-10814.pdf","SAMPLE_TYPE":"Cell","COLLECTION_TIME":"Samples were collected at T0 (beginning of day) and T4 (4h into day).","VOLUMEORAMOUNT_COLLECTED":"40ml of sample was collected at each time point","STORAGE_CONDITIONS":"Samples were put into a 50mL conical tube containing ice up to the 30ml mark."},

"TREATMENT":{"TREATMENT_SUMMARY":"2: WT bacteria and KaiC mutant The phenotype associated with loss of the core oscillator protein, KaiC, is distinct from that caused by absence of the circadian output transcriptional regulator, RpaA (regulator of phycobilisome-associated A). Untargeted metabolomics analysis and glycogen kinetics suggest that functional KaiC is important for metabolite partitioning in the morning. Additionally, output from the oscillator functions to inhibit RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active output state, phenocopies a ΔrpaA strain. KaiC-null strains show indications of oxidative pentose phosphate pathway activation as well as increased abundance of primary metabolites. Inhibitory clock output may serve to allow secondary metabolite biosynthesis in the morning, and some metabolites resulting from these processes may feed back to reinforce clock timing.","TREATMENT_PROTOCOL_FILENAME":"StudyDesign-SpencerDiamond-10814.pdf"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells, transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250 rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh 2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine with supernatant collected in step 5. Total volume of extracted sample will be approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube for GC-TOF analysis. 9. Store backups in -20 or -80C.","SAMPLEPREP_PROTOCOL_FILENAME":"SOP_Extraction_of_Yeast_Cells.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6550","COLUMN_NAME":"Waters Acquity CSH C18 (100 x 2.1mm, 1.7um) 1.7um Pre-Column","FLOW_GRADIENT":"15% B to 99%B","FLOW_RATE":"0.6 mL/min","COLUMN_TEMPERATURE":"65 C","METHODS_FILENAME":"Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf","SOLVENT_A":"60:40 Acetonitrile:Water +10mM Ammonium Acetate +10mM Acetic Acid","SOLVENT_B":"9:1 Isopropanol:Acetonitrile +10mM Ammonium Acetate +10mM Acetic Acid","COLUMN_PRESSURE":"450-850 bar","INTERNAL_STANDARD":"See data dictionary","RETENTION_TIME":"See data dictionary","SAMPLE_INJECTION":"5 uL","ANALYTICAL_TIME":"13 min","CAPILLARY_VOLTAGE":"3500 V","TIME_PROGRAM":"15 min","WEAK_WASH_SOLVENT_NAME":"Isopropanol","STRONG_WASH_SOLVENT_NAME":"Isopropanol","TARGET_SAMPLE_TEMPERATURE":"Autosampler temp 4 C","RANDOMIZATION_ORDER":"Excel generated"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"WCMC Metabolomics Core","SOFTWARE_VERSION":"MassHunter","DATA_FORMAT":".d"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","CAPILLARY_VOLTAGE":"3500 V","COLLISION_GAS":"Nitrogen","DRY_GAS_FLOW":"13 L/min","DRY_GAS_TEMP":"200 C","FRAGMENT_VOLTAGE":"175 V","FRAGMENTATION_METHOD":"Auto MS/MS","ION_SOURCE_TEMPERATURE":"325 C","ION_SPRAY_VOLTAGE":"1000 V","IONIZATION":"Neg","PRECURSOR_TYPE":"Intact Molecule","REAGENT_GAS":"Nitrogen","SOURCE_TEMPERATURE":"325 C","DATAFORMAT":".d","DESOLVATION_GAS_FLOW":"11 L/min","DESOLVATION_TEMPERATURE":"350 C","NEBULIZER":"35 psig","OCTPOLE_VOLTAGE":"750 V","RESOLUTION_SETTING":"extended dynamic range","SCAN_RANGE_MOVERZ":"60-1700 Da","SCANNING_CYCLE":"2 Hz","SCANNING_RANGE":"60-1700 Da","SKIMMER_VOLTAGE":"65 V"},

"MS_METABOLITE_DATA":{
"Units":"counts",

"Data":[{"Metabolite":"6.36_600.51 _6.55_610.54","SDiamInj04_WT T0_CSH.d":"1168","SDiamInj05_WT T4_CSH.d":"1696","SDiamInj03_KaiC T0_CSH.d":"138","SDiamInj02_KaiC T4_CSH.d":"166"},{"Metabolite":"7.06_628.54","SDiamInj04_WT T0_CSH.d":"482","SDiamInj05_WT T4_CSH.d":"1400","SDiamInj03_KaiC T0_CSH.d":"511","SDiamInj02_KaiC T4_CSH.d":"1899"},{"Metabolite":"7.74_656.58 _7.91_666.6","SDiamInj04_WT T0_CSH.d":"683","SDiamInj05_WT T4_CSH.d":"2919","SDiamInj03_KaiC T0_CSH.d":"290","SDiamInj02_KaiC T4_CSH.d":"411"},{"Metabolite":"7.08_654.56","SDiamInj04_WT T0_CSH.d":"26944","SDiamInj05_WT T4_CSH.d":"28181","SDiamInj03_KaiC T0_CSH.d":"12103","SDiamInj02_KaiC T4_CSH.d":"26095"},{"Metabolite":"8.59_686.62 _8.59_696.65","SDiamInj04_WT T0_CSH.d":"627","SDiamInj05_WT T4_CSH.d":"281","SDiamInj03_KaiC T0_CSH.d":"548","SDiamInj02_KaiC T4_CSH.d":"592"},{"Metabolite":"8.37_684.61 _8.52_694.64","SDiamInj04_WT T0_CSH.d":"507","SDiamInj05_WT T4_CSH.d":"413","SDiamInj03_KaiC T0_CSH.d":"567","SDiamInj02_KaiC 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