Identifying PTMs on PERIOD over a circadian day in Drosophila melanogaster
ABSTRACT: Circadian clocks coordinate time-of-day specific metabolic and physiological processes to maximize performance and fitness. In addition to light, which is considered the strongest time cue to entrain animal circadian clocks, metabolic input has emerged as an important signal for clock modulation and entrainment, especially in peripheral clocks. Circadian clock proteins have been to be substrates of O-GlcNAcylation, a nutrient sensitive post-translational modification (PTM), and the interplay between clock protein O-GlcNAcylation and other PTMs, like phosphorylation, is expected to facilitate the regulation of circadian physiology by metabolic signals. Here, we used mass spectrometry proteomics to identify PTMs on PERIOD, the key biochemical timer of the Drosophila clock, over the circadian cycle.
Project description:Differences in the selective pressures experienced by males and females are believed to be ubiquitous in dioecious organisms and are expected to result in the evolution of sexually antagonistic alleles, thereby driving the evolution of sexual dimorphism. Negative genetic correlation for fitness between the sexes has been documented, however, the identity, number and location of loci causing this relationship are unknown. Here we show that a large proportion of Drosophila melanogaster transcripts are associated with the interaction between genomic haplotype and gender and that at least 8% of loci in the fly genome are currently evolving under sexually antagonistic selection. Overall design: We measured gene expression of adult males and females of Drosophila melanogaster from 15 hemiclone lines, showing either high-male/low-female fitness, high-female/lowmale fitness or average fitness in both sexes. Data from four replicates for each sex/line are presented, giving a total of 120 arrays.
Project description:Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time. This data set contains the raw affymetrix gene expression data over three successive metabolic cycles. 12 time intervals per cycle, ~25 min per time interval.
Project description:Extracellular signaling and nutrient availability are major factors for cell fate decision. Responds to extracellular information requires metabolic alterations and differential gene expression. However, how cells integrate extracellular signals (e.g. hormones) and cellular metabolic status to coordinate transcriptional outcome is poorly understood. We hypothesized that fluctuations in nuclear nicotinamide adenine dinucleotide (NAD+) levels act as a signal to integrate cellular glucose metabolism and transcription program during adipocyte differentiation. To test this hypothesis, we performed RNA-seq on control, Nmnat1 and Parp1 knockdown 3T3-L1 cells during various time point of differentiation. Overall design: Using RNA-seq over a time course of DMI induced differention of 3T3-L1 preadipocytes expressing control or Nmnat1 or Parp1 shRNA.
Project description:Cancer cells utilize a unique form of aerobic glycolysis, called the Warburg effect, to efficiently produce the macromolecules required for proliferation. Here we show that a metabolic program related to the Warburg effect is used during normal Drosophila development and regulated by the fly ortholog of the Estrogen-Related Receptor (ERR) family of nuclear receptors. dERR null mutants die as second instar larvae with abnormally low ATP levels, diminished triacylglyceride stores, and elevated levels of circulating sugars. Metabolomic profiling revealed that the pathways affected in these mutants correspond to those used in the Warburg effect. The expression of active dERR protein in mid-embryogenesis triggers a coordinate switch in gene expression that drives a metabolic program supporting the dramatic growth that occurs during larval development. This study suggests that mammalian ERR family members may promote cancer by directing a metabolic state that supports proliferation. Overall design: Drosophila larvae were staged at a mid-second instar time point and hand sorted for developmental progression. Individual pools of isogenic animals were collected for each replicate. Three replcates were assayed for each genotype. The two genotypes assayed were a control wild type strain (w1118) and a transheteroallelic combination of err mutant alleles (err1/err2). Labled RNA was then hybridized onto Affymetrix microarrays.
Project description:Transcriptional profiling of Indy long lived flies and controls over the course of their entire lifespan. Mutations in the Indy gene extend life span in Drosophila melanogaster. This study investigates the changes in gene expression over time in Indy206 flies heterozygous over Canton-S (Indy206/CS) and compares them to genetically matched heterozygous controls (2216/CS). Samples from both fly strains were collected at age: 5, 10, 20, 30, 40, 50, 70 and 80. Overall design: mRNA samples were collected from the head and thorax of Indy206 and genetically matched control male adult flies at day 5, and every 10 days from day 10 to day 80 (day 60 excluded) and hybridized to two-color microarrays
Project description:The high physical activity/high aerobic fitness phenotype predicts low morbidity and mortality more strongly than any other known biological risk factor. Inherited and/or acquired properties of skeletal muscle seem to be linked with aerobic fitness and other cardio-metabolic risk factors3. However, physical activity-induced changes in muscle and fat tissue-related complex molecular networks and their links with cardio-metabolic disease risk are not comprehensively understood. Here we show that among the physically active members of twin pairs, as compared to their inactive co-twins, gene expression in musculus vastus lateralis tissue samples is chronically up-regulated for the central pathways or genes related to energy metabolism, including oxidative phosphorylation, lipid metabolism and supportive metabolic pathways. In addition to aerobic fitness, upregulation of these pathways is associated in particular with high HDL cholesterol levels. In fat tissue we found physical activity-induced increases in polyunsaturated fatty acid metabolism and in branched chain amino acid degradation, which increases were associated with decreased ‘high-risk’ ectopic body fat and low glucose levels. Consistent with other findings plasma lipidomics analyses showed up-regulation of the triacylglycerols containing the polyunsaturated fatty acids. The findings indicate the main pathways in skeletal muscle and fat tissue that mediate the chronic effects of physical activity on reduced cardio-metabolic disease risk, including the increase in aerobic fitness. Up-regulation of oxidative energy metabolism seems to be a common underlying mechanism. Overall design: Total RNA obtained from the biopsy samples of m. vastus lateralis from three mono- and seven dizygotic twin pairs that had been followed for their discordance for physical avtivity for 32 years.