An objective function exploiting suboptimal solutions in metabolic networks

Background: Flux Balance Analysis is a theoretically elegant, computationally efficient, genome-scale approach to predicting biochemical reaction fluxes. Yet FBA models exhibit persistent mathematical degeneracy that generally limits their predictive power. Results: We propose a novel objective function for cellular metabolism that accounts for and exploits degeneracy in the metabolic network to improve flux predictions. In our model, regulation drives metabolism toward a region of flux space that allows nearly optimal growth. Metabolic mutants deviate minimally from this region, a function represented mathematically as a convex cone. Near-optimal flux configurations within this region are considered equally plausible and not subject to further optimizing regulation. Consistent with relaxed regulation near optimality, we find that the size of the near-optimal region predicts flux variability under experimental perturbation. Conclusion: Accounting for suboptimal solutions can improve the predictive power of metabolic FBA models. Because fluctuations of enzyme and metabolite levels are inevitable, tolerance for suboptimality may support a functionally robust metabolic network

A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism

<p>Abstract</p> <p>Background</p> <p>FeFe-hydrogenases are the most active class of H₂-producing enzymes known in nature and may have important applications in clean H₂energy production. Many potential uses are currently complicated by a crucial weakness: the active sites of all known FeFe-hydrogenases are irreversibly inactivated by O₂.</p> <p>Results</p> <p>We have developed a synthetic metabolic pathway in <it>E. coli </it>that links FeFe-hydrogenase activity to the production of the essential amino acid cysteine. Our design includes a complementary host strain whose endogenous redox pool is insulated from the synthetic metabolic pathway. Host viability on a selective medium requires hydrogenase expression, and moderate O₂levels eliminate growth. This pathway forms the basis for a genetic selection for O₂tolerance. Genetically selected hydrogenases did not show improved stability in O₂and in many cases had lost H₂production activity. The isolated mutations cluster significantly on charged surface residues, suggesting the evolution of binding surfaces that may accelerate hydrogenase electron transfer.</p> <p>Conclusions</p> <p>Rational design can optimize a fully heterologous three-component pathway to provide an essential metabolic flux while remaining insulated from the endogenous redox pool. We have developed a number of convenient <it>in vivo </it>assays to aid in the engineering of synthetic H₂metabolism. Our results also indicate a H₂-independent redox activity in three different FeFe-hydrogenases, with implications for the future directed evolution of H₂-activating catalysts.</p

Insulation of a synthetic hydrogen metabolism circuit in bacteria

<p>Abstract</p> <p>Background</p> <p>The engineering of metabolism holds tremendous promise for the production of desirable metabolites, particularly alternative fuels and other highly reduced molecules. Engineering approaches must redirect the transfer of chemical reducing equivalents, preventing these electrons from being lost to general cellular metabolism. This is especially the case for high energy electrons stored in iron-sulfur clusters within proteins, which are readily transferred when two such clusters are brought in close proximity. Iron sulfur proteins therefore require mechanisms to ensure interaction between proper partners, analogous to many signal transduction proteins. While there has been progress in the isolation of engineered metabolic pathways in recent years, the design of insulated electron metabolism circuits <it>in vivo </it>has not been pursued.</p> <p>Results</p> <p>Here we show that a synthetic hydrogen-producing electron transfer circuit in <it>Escherichia coli </it>can be insulated from existing cellular metabolism via multiple approaches, in many cases improving the function of the pathway. Our circuit is composed of heterologously expressed [Fe-Fe]-hydrogenase, ferredoxin, and pyruvate-ferredoxin oxidoreductase (PFOR), allowing the production of hydrogen gas to be coupled to the breakdown of glucose. We show that this synthetic pathway can be insulated through the deletion of competing reactions, rational engineering of protein interaction surfaces, direct protein fusion of interacting partners, and co-localization of pathway components on heterologous protein scaffolds.</p> <p>Conclusions</p> <p>Through the construction and characterization of a synthetic metabolic circuit <it>in vivo</it>, we demonstrate a novel system that allows for predictable engineering of an insulated electron transfer pathway. The development of this system demonstrates working principles for the optimization of engineered pathways for alternative energy production, as well as for understanding how electron transfer between proteins is controlled.</p

Dynamics in the mixed microbial concourse

Isolated, clonal populations of cells are rarely found in nature. The emergent properties of microbial consortia present a challenge for the systems approach to biology, as chances for competition, communication, or collaboration multiply with the number of interacting agents. This review focuses on recent work on intercourse within biofilms, among quorum-sensing populations, and between cross-feeding metabolic cooperators. New tools from synthetic biology allow microbial interactions to be designed and tightly controlled, creating valuable model systems. We address both natural and synthetic partnerships, with an emphasis on how system behaviors derive from the properties of their components. Essential features of microbial biology arose in the context of a very mixed culture and cannot be understood without unscrambling it

The smell of us – crowdsourcing human body odor evaluation

International audienceHuman body odor is produced when sweat-secreted compounds are metabolized by bacteria present on the skin. The resulting volatile mixture is often negatively perceived, motivating the use of personal cosmetic deodorants. Yet body odor may also be positively perceived in some contexts, and is proposed to play a role in sexual attraction, kin identification and social bonding. Because only human smellers can report the hedonic qualities of body odor, their persceptions are a valualbe complement to modern GC-MS-based quantitative chemical measurements. Here we present a crowdsourcing framework that engages volunteer smellers to characterize human sweat samples. Our approach seeks to reward both the sweat donor and the smeller with a web-based graphical interface that is informative, interesting, and fun. 300 samples from 87 individual donors were scored by 93 smellers for intensity, pleasantness, and a variety of odor descriptors. Body odor intensity and pleasantness were determined to vary with age, gender, and self-reported deodorant use. Counterintuitively, deodorant use showed no effect on the perceived intensity of body odor, and was associated with a decrease in the perceived pleasantness. From these data, we determine the precision and dynamic range of the volunteer nose as a body odor evaluation instrument and estimate the scale of crowdsourcing effort that would be required to precisely quantify the public perception of body odors