ABSTRACT: Metabolic model of Buchnera aphidicola, as presented in Gerlin et al., "Quantifying supply and demand in the pea aphid-Buchnera symbiosis reveals the metabolic Achilles’ heels of this interaction" (Metabolic Engineering, 2025).
Project description:The use of high levels of marine fish oil in aquafeeds is a non-sustainable practice. However, more sustainable oils sources from terrestrial plants do not contain long-chain polyunsaturated fatty acids (LC-PUFA). Consequently, feeds based on conventional vegetable oils reduce n-3 LC-PUFA levels in farmed fish. Therefore, the aquaculture industry desperately requires new, sustainable oil sources that contain high levels of n-3 LC-PUFA in order to supply the increasing demand for fish and seafood while maintaining the high nutritional quality of the farmed product. One approach to the renewable supply of n-3 LC-PUFA is metabolic engineering oilseed crops with the capacity to synthesize these essential fatty acids in seeds. In the present study, the oilseed Camelina sativa has been transformed with algal genes encoding the n-3 biosynthetic pathway and expression restricted to the seeds via seed-specific promoters to produce an oil containing > 20% eicosapentaenoic acid (EPA). This oil was investigated as a replacement for marine fish oil in feeds for post-smolt Atlantic salmon. In addition, this study with EPA-rich oil will contribute to our understanding of the biochemical and molecular mechanisms involved in the control and regulation of docosahexaenoic acid (DHA) production from EPA, and will thus better inform our understanding of this key part of the LC-PUFA biosynthetic pathway.
Project description:AMP-activated protein kinase (AMPK) is a major regulator of cellular energy homeostasis that coordinates metabolic pathways in order to balance nutrient supply with energy demand. AMPK elicits acute and diverse metabolic effects by directly phosphorylating various targets. AMPK activation also promotes metabolic reprogramming in longer term via effects on gene expression. The aim of this study is to elucidate molecular mechanism(s) by which AMPK activation modulates metabolic adaptation through its impact on gene regulation.
Project description:The metabolic bases of the interaction between the coral Acropora millepora and its dinoflagellate symbiont were investigated by comparing gene expression levels under light and dark conditions at the whole transcriptome level. Among the differentially expressed genes identified, a suite of genes involved in cholesterol transport was found to be up-regulated under light conditions, confirming the significance of this compound in the coral symbiosis. Although ion transporters likely to have roles in calcification were not differentially expressed in this study, expression levels of many genes associated with skeletal organic matrix composition and organization were higher in light conditions. This implies that the rate of organic matrix synthesis is one factor limiting calcification at night. Thus, LEC during the day is likely to be a consequence of increases in both matrix synthesis and the supply of precursor molecules as a result of photosynthetic activity. Branch tips from three adult colonies of Acropora millepora were sampled at midday and midnight
Project description:A transcriptome of Cluster II Frankia in nitrogen-fixing root-nodule symbiosis with the host plant, Datisca glomerata, was obtained by Illumina sequencing and mapping to the corresponding published genome (NCBI Bioproject PRJNA46257). Major metabolic pathways detected in Cluster II Frankia in symbiosis with Datisca glomerata were comparable to those described as up-regulated in the Frankia alni-Alnus glutinosa symbiosis (N Alloisio et al, MPMI 23(5):593-607, 2010): nitrogenase biosynthesis, tricarboxylic acid cycle, respiratory-chain related functions, oxidation protection, and terpenoid biosynthesis. These functions are consistent with the primary activities of Frankia in root nodules, e.g. to carry out the energetically-demanding fixation of atmospheric dinitrogen to ammonium, and to maintain internal reducing conditions. Expression of genes coding for amino-acid biosynthetic pathways, including arginine as reported previously (AM Berry et al. Funct Plant Biol 38, 645–652, 2011) was detected. A striking difference from other Frankia strains, revealed in the transcriptome of the Cluster II Frankia in symbiosis, was the expression of homologs of rhizobial nodulation genes, nodA, nodB and nodC.
Project description:dNTP supply and demand model in which maintaining dNTP homeostasis is essential in preventing replication catastrophe in response to CDK-induced replication stress
Project description:Abstract Ocean warming elevates metabolic rates in marine ectotherms but often constrains energetic resources, causing an imbalance between supply and demand. Transient hypoxia is near-ubiquitous across the world’s coral reefs and may exacerbate this imbalance, yet its effects on the energetics of reef fishes remain poorly understood. In this study, we assess the metabolic costs incurred by a cryptobenthic reef fish exposed to oxygen fluxes measured on the world’s hottest coral reefs in the Arabian/Persian Gulf. Hypoxia-exposure induced an 8.67% increase in aerobic metabolic rate over the six hours following reoxygenation, and resulted in an estimated 2.87% increase in total daily metabolic rate (mg O2 kg -1 day-1). This energetic cost did not coincide with detectable changes in anaerobic metabolism but was accompanied by increased activity during reoxygenation and a strong, acute transcriptomic response in genes related to oxygen-sensing. Oxygen availability on the reefs declined below the threshold for inducing such energetic costs on over half (56.04%) of the days throughout the summer, potentially leading to substantial cumulative costs. Such energetic costs represent an additional and previously under-appreciated consequence of hypoxia in coral reef environments that may exacerbate the temperature-induced mismatches between energy supply and demand, a key balance affecting growth and fitness.
Project description:A codon usage consonant with the cellular tRNA pool is important for efficient translation. However, Mimivirus, a giant DNA virus, relies on the host translation system of amoeba yet exhibits a codon usage distinct from its host. How this virus copes with the mismatch between the demand and supply of tRNAs remains unknown. Here, we found that the virus generates a subcellular compartment to translate virus mRNAs efficiently. The combination of genome-wide Ribo-Seq and RNA-Seq reveals that ribosomes traversed along viral mRNAs without pausing, despite the codon usage incompatibility with the host mRNAs. Although the virus encodes tRNA genes in the genome, mim-tRNA-Seq shows that the expression does not impact the composition of the cellular tRNA pool during infection. Instead, we observed that through in situ labeling of newly synthesized proteins, viral protein synthesis locally occurs around the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation shapes viral replication overcoming the mismatch of tRNA supply and codon demand.
Project description:A codon usage consonant with the cellular tRNA pool is important for efficient translation. However, Mimivirus, a giant DNA virus, relies on the host translation system of amoeba yet exhibits a codon usage distinct from its host. How this virus copes with the mismatch between the demand and supply of tRNAs remains unknown. Here, we found that the virus generates a subcellular compartment to translate virus mRNAs efficiently. The combination of genome-wide Ribo-Seq and RNA-Seq reveals that ribosomes traversed along viral mRNAs without pausing, despite the codon usage incompatibility with the host mRNAs. Although the virus encodes tRNA genes in the genome, mim-tRNA-Seq shows that the expression does not impact the composition of the cellular tRNA pool during infection. Instead, we observed that through in situ labeling of newly synthesized proteins, viral protein synthesis locally occurs around the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation shapes viral replication overcoming the mismatch of tRNA supply and codon demand.
Project description:A codon usage consonant with the cellular tRNA pool is important for efficient translation. However, Mimivirus, a giant DNA virus, relies on the host translation system of amoeba yet exhibits a codon usage distinct from its host. How this virus copes with the mismatch between the demand and supply of tRNAs remains unknown. Here, we found that the virus generates a subcellular compartment to translate virus mRNAs efficiently. The combination of genome-wide Ribo-Seq and RNA-Seq reveals that ribosomes traversed along viral mRNAs without pausing, despite the codon usage incompatibility with the host mRNAs. Although the virus encodes tRNA genes in the genome, mim-tRNA-Seq shows that the expression does not impact the composition of the cellular tRNA pool during infection. Instead, we observed that through in situ labeling of newly synthesized proteins, viral protein synthesis locally occurs around the periphery region of the viral factory, likely creating a unique environment to facilitate viral translation. Our data provide a perspective on how local translation shapes viral replication overcoming the mismatch of tRNA supply and codon demand.
Project description:The MYC oncogene is a potent driver of growth and proliferation but also sensitises cells to apoptosis, which limits its oncogenic potential. MYC induces several biosynthetic programmes and primary cells overexpressing MYC are highly sensitive to glutamine withdrawal suggesting that MYC-induced sensitisation to apoptosis may be due to an imbalance of metabolic/energetic supply and demand. Here we show that MYC elevates global transcription and translation, even in the absence of glutamine, revealing metabolic demand without corresponding supply. Glutamine withdrawal from MRC-5 fibroblasts depleted key TCA cycle metabolites and, in combination with MYC activation, led to AMP accumulation and nucleotide catabolism indicative of energetic stress. Further analyses revealed that glutamine supports viability through TCA cycle energetics rather than asparagine biosynthesis and that TCA cycle inhibition confers tumour suppression on MYC- driven lymphoma in vivo. In summary, glutamine supports the viability of MYC- overexpressing cells through an energetic rather than a biosynthetic mechanism.