[PDF] Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels | Semantic Scholar (2024)

The proteomic and biochemical responses to different concentrations of CO 2 suggested multiple carbon metabolism strategies exist in P. tricornutum and might induce a mitochondrial-mediated C4-like CCM and the improvement of glycolysis, tricarboxylic acid cycle, photorespiration and ornithine–urea cycle activity contribute to the energy supply and carbon and nitrogen recapture in the HC environment.

This study indicated that breakdown of intracellular protein and soluble sugar provide C skeleton for lipid synthesis under high CO2 concentration, indicating that molecular regulation mechanisms of marine phytoplankton in response to ocean acidification should be selected for systematic study.

To date, marine microalgae are the first and most extensively studied marine organisms in terms of their functioning as coalescent molecular systems, and the richness of data, systematic integration, and predictive models therein set a new example for the broad new study of marine life at unprecedented detail and comparability.

A flexible metabolic network is suggested in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed.

Of great interest, under high light, the genes coding for the synthesis of aromatic amino acids and phenolic compounds were upregulated suggesting that the shikimate pathway was activated.

A synthetic ecosystem is assembled to assist the systems-level investigation of this biological association between diatom and heterotrophic bacteria and it is shown that, at high diatom/bacteria cell concentration ratio, stochastic fluctuations can lead to the extinction of bacteria from the co-culture, causing the explosion of diatom population.

ME-models significantly improve the quantitative prediction of gene expression and can predict the proteome investment in metabolism under any given condition, unlike M-models that can predict biological properties in only nutrient-limited condition.

This work used dynamic biomass composition data to predict changes in growth and reaction flux distributions using genome-scale metabolic models of five eukaryotic organisms and identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion.

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A genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum is performed and the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria is indicated.

It is shown how genome-enabled approaches are being leveraged to explore major phenomena of oceanographic and biogeochemical relevance, such as nutrient assimilation and life histories in diatoms.

Improved the molecular toolkit for diatoms and clarifies the role of urease in the urea cycle is clarified, suggesting a disruption of the cycle despite urea production.

It is shown that diatoms regulate ATP/NADPH through extensive energetic exchanges between plastids and mitochondria, and this interaction comprises the re-routing of reducing power generated in the plastid towards mitochondria and the import of mitochondrial ATP into thePlastid, and is mandatory for optimized carbon fixation and growth.

This work describes a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.

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