Summary of Study ST003340
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 PR002071. The data can be accessed directly via it's Project DOI: 10.21228/M8X835 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST003340 |
| Study Title | Effect of feeding and the mTORC1 activity on metabolism in Caenorhabditis elegans |
| Study Summary | Cellular growth and organismal development are remarkably complex processes that require the nutrient-responsive kinase mTORC1. Anticipating that important mTORC1 functions remained to be identified, we employed genetic and bioinformatic screening in C. elegans to uncover mechanisms of mTORC1 action. Here we show that during larval growth nutrients induce an extensive reprogramming of gene expression and alternative mRNA splicing by acting through mTORC1. mTORC1 regulates mRNA splicing and production of protein-coding mRNA isoforms largely independently of its target p70S6K, by increasing the activity of the serine/arginine-rich (SR) protein RSP-6 (SRSF3/7) and other splicing factors. mTORC1-mediated mRNA splicing regulation is critical for growth, mediates nutrient control of mechanisms that include energy, nucleotide, amino acid, and other metabolic pathways, and may be conserved in humans. Although mTORC1 inhibition delays aging, mTORC1-induced mRNA splicing promotes longevity, suggesting that when mTORC1 is inhibited enhancement of this splicing might provide additional anti-aging benefits. |
| Institute | Hiroshima University |
| Last Name | Ogawa |
| First Name | Takafumi |
| Address | 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan |
| takafumi-ogawa@hiroshima-u.ac.jp | |
| Phone | +81-80-9790-5278 |
| Submit Date | 2024-07-17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002071 |
| Project DOI: | doi: 10.21228/M8X835 |
| Project Title: | Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing |
| Project Summary: | Steady-state non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) was carried out on Caenorhabditis elegans that overexpress RSP-6 and were treated with Empty Vector (EV) or raga-1 RNAi at the L1 larval stage. |
| Institute: | Hiroshima University |
| Last Name: | Ogawa |
| First Name: | Takafumi |
| Address: | 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima, 739-8530, Japan |
| Email: | takafumi-ogawa@hiroshima-u.ac.jp |
| Phone: | +81-80-9790-5278 |
Subject:
| Subject ID: | SU003461 |
| Subject Type: | Invertebrate |
| Subject Species: | Caenorhabditis elegans |
| Taxonomy ID: | 6239 |
| Age Or Age Range: | L1 larva stage |
Factors:
Subject type: Invertebrate; Subject species: Caenorhabditis elegans (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment | Treatment2 |
|---|---|---|---|---|
| SA364562 | WT_EV_Fed_1 | worms | empty vector | feeding |
| SA364563 | WT_EV_Fed_2 | worms | empty vector | feeding |
| SA364564 | WT_EV_Fed_3 | worms | empty vector | feeding |
| SA364565 | WT_EV_Stv_1 | worms | empty vector | starvation |
| SA364566 | WT_EV_Stv_2 | worms | empty vector | starvation |
| SA364567 | WT_EV_Stv_3 | worms | empty vector | starvation |
| SA364568 | WT_raga1_Fed_1 | worms | raga-1 | feeding |
| SA364569 | WT_raga1_Fed_2 | worms | raga-1 | feeding |
| SA364570 | WT_raga1_Fed_3 | worms | raga-1 | feeding |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003454 |
| Collection Summary: | Animals were collected and washed 3 times with M9 buffer and once quickly with HPLC-grade water quickly and flash-frozen in liquid nitrogen. Metabolites were extracted using 800µL of 40:40:20 acetonitrile:methanol:water solvent at -20ºC, vortexed for 10 sec, and further lysed with a TissueLyser LT (Qiagen) with stainless steel beads. |
| Sample Type: | Worms |
Treatment:
| Treatment ID: | TR003470 |
| Treatment Summary: | All worms were passaged on NGM with OP50 bacteria for at least two generations before the assay. 25,000 second generation L1 animals treated with RNAi against EV or raga-1 were incubated on NGM with the corresponding food source for 4 hours. |
Sample Preparation:
| Sampleprep ID: | SP003468 |
| Sampleprep Summary: | The samples were then centrifuged at 16,000g for 15 minutes at 4ºC, and the supernatant was passed through an Ultrafree-MC VV Centrifugal Filter, 0.1 µm (Millipore) by centrifuging at 9100g. The filtrate was concentrated and dried using a Speedvac (Thermo Scientific), and resuspended in 50:50 acetonitrile:water for LC-MS analysis. Metabolites were resolved on a Vanquish U-HPLC system coupled to a Q Exactive HF-X hybrid quadrupole-orbitrap mass spectrometer (ThermoFisher) with a HESI source operating in negative ion mode. |
Combined analysis:
| Analysis ID | AN005474 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | iHILIC®-(P) Classic HILIC Column PEEK (150 x 2.1mm, 5µm) Cat.# W 160.152.0520 |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF-X Orbitrap |
| Ion Mode | NEGATIVE |
| Units | peak areas |
Chromatography:
| Chromatography ID: | CH004158 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | iHILIC®-(P) Classic HILIC Column PEEK (150 x 2.1mm, 5µm) Cat.# W 160.152.0520 |
| Column Temperature: | 30ºC |
| Flow Gradient: | 0-23 min linear gradient from 95% B to 5% B; 23-25 min hold at 5% B |
| Flow Rate: | 0.150 mL/min |
| Solvent A: | 100% Water; 20 mM ammonium carbonate, 0.1% ammonium hydroxide |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005200 |
| Analysis ID: | AN005474 |
| Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS data acquisition and targeted feature extraction and quantification were performed using TraceFinder 5.1 or open-source EL-MAVEN software. Peak area integration and metabolite identification were done using accurate mass and retention time curated with in-house standard library compounds. Three biological replicates were used for each condition. |
| Ion Mode: | NEGATIVE |
