Summary of Study ST000394
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000308. The data can be accessed directly via it's Project DOI: 10.21228/M82P59 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST000394 |
Study Title | The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth (part I) |
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 |
ofiehn@ucdavis.edu | |
Phone | (530) 754-8258 |
Submit Date | 2016-05-04 |
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 |
Raw Data Available | Yes |
Raw Data File Type(s) | d |
Analysis Type Detail | LC-MS |
Release Date | 2016-06-18 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
Analysis ID | AN000630 | AN000631 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Agilent 6530 | Agilent 6550 |
Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | QTOF | QTOF |
MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
Ion Mode | POSITIVE | NEGATIVE |
Units | counts | counts |
MS:
MS ID: | MS000563 |
Analysis ID: | AN000630 |
Instrument Name: | Agilent 6530 QTOF |
Instrument Type: | QTOF |
MS Type: | ESI |
Ion Mode: | POSITIVE |
Capillary Voltage: | 3500 V |
Collision Gas: | Nitrogen |
Dry Gas Flow: | 8 L/min |
Dry Gas Temp: | 325 C |
Fragment Voltage: | 120 V |
Fragmentation Method: | Auto MS/MS |
Ion Source Temperature: | 325 C |
Ion Spray Voltage: | 1000 V |
Ionization: | Pos |
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 ID: | MS000564 |
Analysis ID: | AN000631 |
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 |