Analysis of gene expression between monomethyl branched-chain fatty acid deficient (elo-5) and wild type N2 C. elegans L1 larvae hatched on food-free NGM plates
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE64973 | GEO | 2016/01/14
SECONDARY ACCESSION(S): PRJNA272614
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expresssion is not globally shut down in elo-5 as compared to N2 Many changes in metabolic and regulatory gene expression were detected between elo-5 and N2 L1 larvae. RNA samples for hybridization with the C. elegans Affymetrix Gene Chips were prepared as follows. elo-5(gk208) and N2 control animals were grown from eggs for one generation on NGM plates spotted with 300µl OP50 overnight liquid culture supplemented with 1mM C17ISO in DMSO at 20°C. Gravid adults were washed off the plates with M9 and bleached. Eggs were plated on OP50/NGM plates supplemented with 1mM of either C13ISO or C17ISO and maintained at 20°C to obtain gravid adults. Adults were washed off the plates and bleached, and eggs were then plated on food-free NGM or OP50/NGM plates at 20°C. Twenty-four hours later, L1s from food-free plates were collected for RNA isolation with Trizol and Qiagenâ??s RNAse Easy Kit, according to the manufacturersâ?? protocols. On the following days, animals on OP50/NGM were checked for phenotypes to confirm C17ISO-deficiency in elo-5(gk208) grown with C13ISO supplement. Two biological replicates were prepared for each condition; elo-5(gk208) with C13ISO and C17ISO supplements and a control N2 with C13ISO supplement. Data analysis was performed with dChip analytical software (Li and Wong, 2001).
2016-01-14 | E-GEOD-64973 | biostudies-arrayexpress
Project description:Branched-chain ?-ketoacid dehydrogenase (BCKDH) catalyzes the critical step in the branched-chain amino acid (BCAA) catabolic pathway and has been the focus of extensive studies. Mutations in the complex disrupt many fundamental metabolic pathways and cause multiple human diseases including maple syrup urine disease (MSUD), autism, and other related neurological disorders. BCKDH may also be required for the synthesis of monomethyl branched-chain fatty acids (mmBCFAs) from BCAAs. The pathology of MSUD has been attributed mainly to BCAA accumulation, but the role of mmBCFA has not been evaluated. Here we show that disrupting BCKDH in Caenorhabditis elegans causes mmBCFA deficiency, in addition to BCAA accumulation. Worms with deficiency in BCKDH function manifest larval arrest and embryonic lethal phenotypes, and mmBCFA supplementation suppressed both without correcting BCAA levels. The majority of developmental defects caused by BCKDH deficiency may thus be attributed to lacking mmBCFAs in worms. Tissue-specific analysis shows that restoration of BCKDH function in multiple tissues can rescue the defects, but is especially effective in neurons. Taken together, we conclude that mmBCFA deficiency is largely responsible for the developmental defects in the worm and conceivably might also be a critical contributor to the pathology of human MSUD.
| S-EPMC4742758 | biostudies-literature
Project description:Monomethyl branched-chain fatty acids (mmBCFAs) are commonly found in many organisms from bacteria to mammals. In humans, they have been detected in skin, brain, blood, and cancer cells. Despite a broad distribution, mmBCFAs remain exotic in eukaryotes, where their origin and physiological roles are not understood. Here we report our study of the function and regulation of mmBCFAs in Caenorhabditis elegans, combining genetics, gas chromatography, and DNA microarray analysis. We show that C. elegans synthesizes mmBCFAs de novo and utilizes the long-chain fatty acid elongation enzymes ELO-5 and ELO-6 to produce two mmBCFAs, C15ISO and C17ISO. These mmBCFAs are essential for C. elegans growth and development, as suppression of their biosynthesis results in a growth arrest at the first larval stage. The arrest is reversible and can be overcome by feeding the arrested animals with mmBCFA supplements. We show not only that the levels of C15ISO and C17ISO affect the expression of several genes, but also that the activities of some of these genes affect biosynthesis of mmBCFAs, suggesting a potential feedback regulation. One of the genes, lpd-1, encodes a homolog of a mammalian sterol regulatory element-binding protein (SREBP 1c). We present results suggesting that elo-5 and elo-6 may be transcriptional targets of LPD-1. This study exposes unexpected and crucial physiological functions of C15ISO and C17ISO in C. elegans and suggests a potentially important role for mmBCFAs in other eukaryotes.
| S-EPMC514883 | biostudies-literature
Project description:An increase in circulating branched-chain amino acids (BCAA) is associated with insulin resistance. Adipose tissue is a potentially important site for BCAA metabolism. It was evaluated whether monomethyl branched-chain fatty acids (mmBCFA) in adipose tissue, which are likely derived from BCAA catabolism, are associated with insulin sensitivity.Insulin-stimulated glucose disposal was determined by using the hyperinsulinemic-euglycemic clamp procedure with stable isotope glucose tracer infusion in nine lean and nine obese subjects, and in a separate group of nine obese subjects before and 1 year after Roux-en-Y gastric bypass (RYGB) surgery (38% weight loss). Adipose tissue mmBCFA content was measured in tissue biopsies taken in the basal state.Total adipose tissue mmBCFA content was ?30% lower in obese than lean subjects (P=0.02) and increased by ?65% after weight loss in the RYGB group (P=0.01). Adipose tissue mmBCFA content correlated positively with skeletal muscle insulin sensitivity (R(2) =35%, P=0.01, n=18).These results demonstrate a novel association between adipose tissue mmBCFA content and obesity-related insulin resistance. Additional studies are needed to determine whether the association between adipose tissue mmBCFA and muscle insulin sensitivity is causal or a simple association.
| S-EPMC4310778 | biostudies-literature
Project description:Bifidobacterium pseudocatenulatum strain:N2 | isolate:N2 Genome sequencing
| PRJNA718013 | ENA
Project description:The branched-chain amino acids (BCAA) leucine, valine, and isoleucine provide precursors for monomethyl branched-chain fatty acids (BCFA). Established reference ranges for BCFAs are lacking. In maple syrup urine disease (MSUD), a rare inborn error of BCAA metabolism, the endogen production is impaired and MSUD patients are treated with a low protein (low BCAA) diet. The protein restriction may affect the dietary intake of BCFA, depending on the dietary choices made. Patients with MSUD are prescribed a more or less protein-restricted diet depending on the severity of the disease. The combination of a protein-restricted diet and subsequent impaired endogenous synthesis may render MSUD patients sensitive to BCFA deficiency, with yet unknown implications. To investigate the possibility of lower circulatory BCFA levels in MSUD that favors dietary BCFA supplementation, we first established fasting-state reference ranges for selected BCFAs and saturated/unsaturated fatty acids in plasma. Then, the effect of fasting on BCFA levels was evaluated by comparing the distribution in a fasting versus a non-fasting cohort. To test the hypothesis that BCFA deficiency could contribute to MSUD pathophysiology, we recruited patients with intermittent, intermediate, and classical form of MSUD and analyzed the corresponding BCFA z-scores. None of the BCFA species had |z-scores| > 2 relative to the reference range. Our findings do not support the requirement of BCFA supplementation in MSUD patients. The origin of BCFAs is discussed. Impaired capacity to synthesize BCFA do not manifest as reduced plasma levels in MSUD, suggesting that endogenous synthesis is dispensable for plasma levels.
| S-EPMC10494493 | biostudies-literature
Project description:Streptococcus agalactiae strain:N2 | isolate:N2 Genome sequencing and assembly
| PRJNA759724 | ENA
Project description:While various mass spectrometric approaches have been applied to lipid analysis, unraveling the extensive structural diversity of lipids remains a significant challenge. Notably, these approaches often fail to differentiate between isomeric lipids─a challenge that is particularly acute for branched-chain fatty acids (FAs) that often share similar (or identical) mass spectra to their straight-chain isomers. Here, we utilize charge-switching strategies that combine ligated magnesium dications with deprotonated fatty acid anions. Subsequent activation of these charge inverted anions yields mass spectra that differentiate anteiso-branched- from straight-chain and iso-branched-chain FA isomers with the predictable fragmentation enabling de novo assignment of anteiso branch points. The application of these charge-inversion chemistries in both gas- and solution-phase modalities is demonstrated to assign the position of anteiso-methyl branch-points in FAs and, with the aid of liquid chromatography, can be extended to de novo assignment of additional branching sites via predictable fragmentation patterns as methyl branching site(s) move closer to the carboxyl carbon. The gas-phase approach is shown to be compatible with top-down structure elucidation of complex lipids such as phosphatidylcholines, while the integration of solution-phase charge-inversion with reversed phase liquid chromatography enables separation and unambiguous identification of FA structures within isomeric mixtures. Taken together, the presented charge-switching MS-based technique, in combination with liquid chromatography, enables the structural identification of branched-chain FA without the requirement of authentic methyl-branched FA reference standards.
| S-EPMC10173259 | biostudies-literature
Project description:N2-heptynyl-dG sequencing in HEK293T cells
2024-06-15 | GSE261442 | GEO
Project description:DNA alkylation at the N2 position of guanine (N2-dG) is a prevalent type of DNA minor-groove lesions arising from various exogenous environmental contaminants and endogenous cellular processes. These N2-alkyl-dG lesions can induce G → T mutations during transcription if left unrepaired. However, the repair pathways of N2-alkyl-dG lesions remain incompletely elucidated. In this study, we identified a series of potential N2-alkyl-dG-binding proteins utilizing an affinity pulldown coupled with quantitative proteomic approach. We investigated their roles in DNA damage response and repair of these lesions. High-mobility group protein B3 (HMGB3) and activated RNA polymerase II transcriptional coactivator P15 (SUB1) exhibited preferential binding toward N2-nBudG-containing duplex DNA in quantitative proteomics analysis and in vitro binding assay using recombinant proteins. The presence of HMGB3 and SUB1 protected cells against alkylating agents (e.g., BPDE). Both HMGB3 and SUB1 modulated the repair of N2-nBudG and trans-N2-BPDE-dG in genomic DNA, while HMGB3 wasn’t involved in the repair of cis-N2-BPDE-dG. Together, our findings provided new knowledge about the cellular sensing and repair of minor-groove N2-alkyl-dG lesions.
2024-08-02 | PXD051678 | Pride