GNPS - Escherichia coli metabolic test
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Escherichia Coli (ncbitaxon:562)
SUBMITTER: 
Daniel Petras
PROVIDER: MSV000090833 | GNPS | Mon Dec 05 07:05:00 GMT 2022
REPOSITORIES: GNPS
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2022-12-05 | MSV000090833 | MassIVE
Project description:We utilize ribosome profiling to directly monitor translation in E. coli at 30 °C and investigate how this changes after 10-20 minutes of heat shock at 42 °C. Translation is controlled by the interplay of several RNA hybridization processes, which are expected to be temperature sensitive. We observe that translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat shock response transcriptional program at 30 °C.
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Project description:We have shown the quorum-sensing signals acylhomoserine lactones (AHLs), autoinducer-2 (AI-2), and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, i.e., temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30°C (186 genes) than at 37°C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25°C and 30°C than at 37°C, and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30°C compared to 37°C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD pyrF, and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30°C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37°C, indole more significantly decreased flagella-related qseB, flhD, and fliA promoter activity, enhanced antibiotic resistance, and inhibited cell division at 30°C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37°C (63 genes) than at 30°C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37°C (but not at 30°C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37°C but not at 30°C. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined.
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Project description:Escherichia coli Genome sequencing, proteomics and metabolomics
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Project description:Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli.
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Project description:Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli. The experimental design involves measuring transcriptome in three strains (in triplicates) of E. coli during mid-exponential phase of growth on MOPS media supplemented with glucose. The three strains are: 1. REF: MG1655/pAK80 (MG1655 transformed with a plasmid with no insert) 2. NOX: MG1655/pAC06 (MG1655 transformed with a plasmid containing NADH oxidase) 3. ATPase: MG1655/pCP41 (MG1655 transformed with a plasmid containing soluble ATPase) RNA was extracted using Qiagen RNeasy kit and processes according to Affymetrix® guidelines. The quality of RNA was verified using BioAnalyzer (Agilent BioSystems) and the electropherograms are shown in the file âRNA quality.pdfâ. Samples 1-3 are REF, Samples 4-6 are NOX and Samples 7-9 are ATPase. The fragmented cRNA was hybridized to E. coli Genome 2.0 chips.
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