Cyanobacteria FBA Model

From FreeBio

Media:Shastri_FBA_of_Phototrophic_Metabolism_Biotechnol_Progress_2005.pdf Media:Cyanobacteria-FBA-model.pdf Attached is a recently published FBA model for Synechocystis. It contains 70 fluxes, and it has several important experimentally determined/empirically calculated parameters that seem directly transferable to other cyanobacterial FBA models, like Prochlorococcus:

• Stoichiometric equations to represent Photosystem I and II
• Experimentally measured growth rates under specific carbon dioxide and light levels at a given pH.
• Photosynthetic photon flux density (PPFD) expressed as moles of photosynthetically active radiation (PAR) per area per second.
• Cell surface area empirically calculated as a function of biomass.
• Empirically determined maximum uptake rates for glucose, carbon dioxide, and light flux.
• ATP maintenance requirements empirically calculated.
• Reformulation of objective function. When Synechocystis grows autotrophically, it does not produce any overflow products. Carbon dioxide is the only carbon input and biomass is the only carbon output, so the biomass yield is fixed with respect to carbon dioxide uptake. Therefore, the pertinent question is how to minimize the amount of light energy necessary to produce a unit of biomass. They formulate the objective as two-step optimization. First they fix CO2/h uptake to 100 moles, allow photon flux to be a free parameter, and maximize growth rate. Then, they use that growth rate as a constraint, and minimize the photon flux. The result is an energy-minimizing Synechocystis that grows as quickly as a growth-optimized Synechocystis.
• Experimental measurements of Biomass under autotrophic, heterotrophic, and mixotrophic conditions
  • protein concentration measured spectrophotometrically using Pierce BCA protein assay kit standard.
  • amino acid composition from GC-MS data of proteins
  • carbohydrate percentage by spectrophotometer using the phenol-sulfuric acid method
  • lipids measured by chloroform-methanol extraction
  • nucleic acids calculated as the balance
  • elemental composition of dry mass also calculated

Using these measurements, they predicted different growth yields and flux distributions under each growth condition:

• Autotrophic conditions using only carbon dioxide and light as nutrients.
• Heterotrophic growth conditions using only glucose and no light as nutrients.
• Mixotrophic growth conditions using glucose and varying levels of light and carbon dioxide as nutrients.

They also investigated the role of the glyoxylate shunt to produce succinyl CoA and succinate, the role of transhydrogenase to produce NADPH, and the optimal ratio of cyclic to noncyclic photophosphorylation to produce the correct ATP/NADPH ratio.

Finally, they investigate the effect of enzyme deletions and additions on growth rate and the TCA cycle.

Hopefully, these experimental measurements will make it significantly easier to construct our family of Prochlorococcus FBA models. However, Shastri felt that a more detailed model of electron transport organization in the thylakoid and cytoplasmic membranes would need to be added to capture the interactions between components of the respiratory and photosynthetic transport chains. He also pointed out that including efficiencies of light transmission, harvesting, and photochemical energy transduction will be necessary for model validation. Finally, he felt the model should be extended to include the metabolic reactions leading to the formation of various components and storage compounds.

--JeremyZucker 01:52, 1 July 2006 (EDT)

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