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GNPS - Microbial and host compensation in a model of leucine breakdown deficiency

ABSTRACT: Representative MS/MS data for WT and mccc-1 mutant C. elegans reared on Comamonas aquatica. Data in both positive and negative ionization mode, as indicated in the files names. The worm bodies (endo-metabolome) and conditioned media (exo-metabolome) were harvested, extracted, and analyzed separately.

INSTRUMENT(S): Q Exactive HF, Q Exactive

ORGANISM(S): Caenorhabditis Elegans (ncbitaxon:6239)

SUBMITTER: Frank Schroeder A.J. Marian Walhout

PROVIDER: MSV000093813 | GNPS | Wed Jan 10 12:46:00 GMT 2024

REPOSITORIES: GNPS

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Publications

Host-microbe interactions rewire metabolism in a C. elegans model of leucine breakdown deficiency.

Lee Yong-Uk YU Fox Bennett W BW Guo Rui R Curtis Brian J BJ Yu Jingfang J Kim Sookyung S Nanda Shivani S Baumann Victor V Yilmaz L Safak LS Haynes Cole M CM Schroeder Frank C FC Walhout Albertha J M AJM

Nature metabolism 20240808 8

In humans, defects in leucine catabolism cause a variety of inborn errors in metabolism. Here, we use Caenorhabditis elegans to investigate the impact of mutations in mccc-1, an enzyme that functions in leucine breakdown. Through untargeted metabolomic and transcriptomic analyses we find extensive metabolic rewiring that helps to detoxify leucine breakdown intermediates via conversion into previously undescribed metabolites and to synthesize mevalonate, an essential metabolite. We also find that ...[more]

PMID: 39117959

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Microbial and host compensation in a model of leucine breakdown deficiency

Project description:Representative MS/MS data for WT and mccc-1 mutant C. elegans reared on Comamonas aquatica. Data in both positive and negative ionization mode, as indicated in the files names. The worm bodies (endo-metabolome) and conditioned media (exo-metabolome) were harvested, extracted, and analyzed separately.

2024-01-10 | MSV000093813 | MassIVE

Parallel host and microbial pathways regulate lipid desaturation

Project description:4 datasets, each in their own subfolder. 1) acdh-11 comparative metabolomics. 4 genotypes (N2, fcmt-1, WT FAT-7::GFP, and acdh-11;FAT-7::GFP) grown at 3 temperatures (15, 20, 25). Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately. 2) acdh-11 comparative metabolomics re: diet. 2 genotypes (WT FAT-7::GFP, and acdh-11;FAT-7::GFP) and 2 diets (WT E. coli, BW25113, and cyclopropane-deficient E. Coli, JW1653-1). The cyclopropane-deficient strain was additionally supplemented with cyclopropane fatty acids lactobacillic acid (LBA) or dihydrosterculic acid (DHSA) at 20 uM. 3) fcmt-1 comparative metabolomics. 4 genotypes (N2, fcmt-1(gk155709), fcmt-1(tm2382), hacl-1(tm6725)) grown at 20C. Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately. 4) vaccenic acid isotope labeling. 2 genotypes (N2 and hacl-1(tm6725)) grown at 20C. Each genotype was supplemented with vehicle, cis-vaccenic acid (cis-VA), stable isotope labeled D13-cis-VA, trans-vaccenic acid (trans-VA), and stable isotope labeled D13-trans-VA. Conditioned media (exo-metabolome) and worm pellet (endo-metabolome) isolated and extracted separately.

2023-08-20 | MSV000092700 | MassIVE

GNPS - Parallel host and microbial pathways regulate lipid desaturation

2023-08-20 | MSV000092700 | GNPS

untargeted metabolomics analysis of WT vs ACOT-15 exo-metabolome (C. elegans)

Project description:This study focuses on the untargeted analysis of the exo-metabolome of both WT and acot-15 mutant C. elegans worms.

2023-08-08 | MSV000092618 | MassIVE

Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila

Project description:In Drosophila, siRNAs are classified as endo- or exo-siRNAs based on their origin. Both are processed from double-stranded RNA precursors by Dcr-2, then loaded into the Argonaute protein Ago2. While exo-siRNAs serve to defend the cell against viruses, endo-siRNAs restrict the spread of selfish DNA in somatic cells, analogous to piRNAs in the germ line. Endo- and exo-siRNAs display a differential requirement for double-stranded RNA binding domain proteins (dsRBPs): R2D2 is needed to load exo-siRNAs into Ago2 while the PD isoform of Loquacious (Loqs-PD) stimulates Dcr-2 during the nucleolytic processing of hairpin-derived endo-siRNAs. In cell culture assays, R2D2 antagonizes Loqs-PD in endo-siRNA silencing and Loqs-PD is an inhibitor of RNA interference. Loqs-PD can interact via the C-terminus unique to this isoform with the DExH/D-helicase domain of Drosophila Dcr-2, where binding of R2D2 has also been localized. Separation of the two pathways is not complete; rather, the dicing and Ago2-loading steps appear uncoupled, analogous to the corresponding steps in miRNA biogenesis. Analysis of deep sequencing data further demonstrates that in r2d2 mutant flies, siRNAs can be loaded into Ago2 but not all siRNA classes are equally proficient for this. Thus, the canonical Ago2-RISC loading complex can be bypassed under certain circumstances. Examination of small RNAs from two different mutant strains as well as the corresponding heterozygous controls

2011-02-10 | E-GEOD-26230 | biostudies-arrayexpress

Untargeted comparative metabolomics of WT vs ACOT-15 endo-metabolome in C. elegans

Project description:This study focuses on the untargeted comparative metabolomics analysis of the endo-metabolome of both WT and acot-15 mutant C. elegans worms. Hydroxylamine was used to treat certain samples to capture the reactive electrophilic metabolites.

2023-08-08 | MSV000092620 | MassIVE

Loqs-PD and R2D2 define independent pathways for RISC generation in Drosophila

2011-02-10 | GSE26230 | GEO

Multi-omics analysis of BCG macrophage activation

Project description:THP-1-derived macrophages were infected with M. bovis BCG. Separately, proteomic analysis was performed on histones (file names containing IKP) and the total proteome (file names containing JMI).

2024-10-08 | PXD051187 | Pride

GNPS - untargeted metabolomics analysis of WT vs ACOT-15 exo-metabolome (C. elegans)

Project description:This study focuses on the untargeted analysis of the exo-metabolome of both WT and acot-15 mutant C. elegans worms.

2023-08-08 | MSV000092618 | GNPS

Endogenous siRNAs promote proteostasis and longevity in germline-less Caenorhabditis elegans

Project description:How lifespan and the rate of aging are set is a key problem in biology. Small RNAs are conserved molecules that impact diverse biological processes through the control of gene expression. However, in contrast to miRNAs, the role of endo-siRNAs in aging remains unexplored. Here, by combining deep sequencing and genomic and genetic approaches in C.CaenorhabditisC. elegans elegans, we reveal an unprecedented role for endo-siRNA molecules in the maintenance of proteostasis and lifespan extension in germline-less animals. Furthermore, we identify an endo-siRNA-regulated tyrosine phosphatase, which limits the longevity of germline-less animals by restricting the activity of the heat shock transcription factor HSF-1. Altogether, our findings point to endo-siRNAs as a link between germline removal and the HSF-1 proteostasis and longevity-promoting somatic pathway. This establishes a role for endo siRNAs in the aging process and identifies downstream genes and physiological processes that are regulated by the endo siRNAs to affect longevity.

2020-04-03 | GSE128935 | GEO

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