The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Remnants of an ancient metabolism without phosphate

Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a "metabolic fossil" of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system. PAPERCLIP

Doctor of Philosophy

dissertationRecent breakthroughs in silicon photonics technology are enabling the integration of optical devices into silicon-based semiconductor processes. Photonics technology enables high-speed, high-bandwidth, and high-fidelity communications on the chip-scale-an important development in an increasingly communications-oriented semiconductor world. Significant developments in silicon photonic manufacturing and integration are also enabling investigations into applications beyond that of traditional telecom: sensing, filtering, signal processing, quantum technology-and even optical computing. In effect, we are now seeing a convergence of communications and computation, where the traditional roles of optics and microelectronics are becoming blurred. As the applications for opto-electronic integrated circuits (OEICs) are developed, and manufacturing capabilities expand, design support is necessary to fully exploit the potential of this optics technology. Such design support for moving beyond custom-design to automated synthesis and optimization is not well developed. Scalability requires abstractions, which in turn enables and requires the use of optimization algorithms and design methodology flows. Design automation represents an opportunity to take OEIC design to a larger scale, facilitating design-space exploration, and laying the foundation for current and future optical applications-thus fully realizing the potential of this technology. This dissertation proposes design automation for integrated optic system design. Using a buildingblock model for optical devices, we provide an EDA-inspired design flow and methodologies for optical design automation. Underlying these flows and methodologies are new supporting techniques in behavioral and physical synthesis, as well as device-resynthesis techniques for thermal-aware system integration. We also provide modeling for optical devices and determine optimization and constraint parameters that guide the automation techniques. Our techniques and methodologies are then applied to the design and optimization of optical circuits and devices. Experimental results are analyzed to evaluate their efficacy. We conclude with discussions on the contributions and limitations of the approaches in the context of optical design automation, and describe the tremendous opportunities for future research in design automation for integrated optics

In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction

BACKGROUND: Sinorhizobium meliloti is a soil bacterium, known for its capability to establish symbiotic nitrogen fixation (SNF) with leguminous plants such as alfalfa. S. meliloti 1021 is the most extensively studied strain to understand the mechanism of SNF and further to study the legume-microbe interaction. In order to provide insight into the metabolic characteristics underlying the SNF mechanism of S. meliloti 1021, there is an increasing demand to reconstruct a metabolic network for the stage of SNF in S. meliloti 1021. RESULTS: Through an iterative reconstruction process, a metabolic network during the stage of SNF in S. meliloti 1021 was presented, named as iHZ565, which accounts for 565 genes, 503 internal reactions, and 522 metabolites. Subjected to a novelly defined objective function, the in silico predicted flux distribution was highly consistent with the in vivo evidences reported previously, which proves the robustness of the model. Based on the model, refinement of genome annotation of S. meliloti 1021 was performed and 15 genes were re-annotated properly. There were 19.8% (112) of the 565 metabolic genes included in iHZ565 predicted to be essential for efficient SNF in bacteroids under the in silico microaerobic and nutrient sharing condition. CONCLUSIONS: As the first metabolic network during the stage of SNF in S. meliloti 1021, the manually curated model iHZ565 provides an overview of the major metabolic properties of the SNF bioprocess in S. meliloti 1021. The predicted SNF-required essential genes will facilitate understanding of the key functions in SNF and help identify key genes and design experiments for further validation. The model iHZ565 can be used as a knowledge-based framework for better understanding the symbiotic relationship between rhizobia and legumes, ultimately, uncovering the mechanism of nitrogen fixation in bacteroids and providing new strategies to efficiently improve biological nitrogen fixation

Deconvoluting the Engineering and Assembly Instructions for Complex Iii Activity

In respiratory systems, membrane-bound Complex III catalyzes the oxidation of ubiquinone and the reduction of a soluble cytochrome with the bioenergetic formation of a transmembrane proton gradient (∆μH+). Complex III turnover is initiated by a unique two electron oxidation of ubiquinone at the Qo site; one electron is delivered to a high potential chain containing an iron-sulfur cluster, cytochrome c1 and cytochrome c2, and a second electron is transferred to a low potential chain that terminates at the Qi site. All Complex III electron tunneling reactions are reversible, and a critical part of Complex III maintaining productive turnover is its suppression of energy-wasting reverse electron transfer reactions. The key to uncovering the controversial mechanism of Qo oxidation is determining how Complex III is regulated such that productive electron-transfer steps overwhelm unproductive steps. This thesis focuses on understanding the structural and biochemical tolerances of the redox cofactors in Complex III and applying that knowledge towards the design of a simple, but robust, amphiphilic maquette that is capable of transmembrane proton and electron transfer. In chapter two, kinetic studies of heme c1 mutants reveal that R. sphaeroides Complex III is engineered to withstand large changes in heme c1 active site residues while still preserving heme c1 midpoint potential and enzyme turnover. In chapter three, the maquette approach was applied toward developing a simple model protein (AP6) that retained the minimum engineering requirements for Complex III electron and proton transfer reactions but lacked the complexity found in the natural system. The AP6 peptide assembles as a four-α-helix bundle protein and can potentially bind up to six hemes tightly across a membrane interface. Chapter four demonstrates that AP6 successfully performs quinol-cytochrome c oxidoreductase activity in hundreds of milliseconds. AP6 is the first example of a synthetic enzyme capable of near-natural turnover rates. Chapter five focuses on defining the thermodynamic limit for maquette activity. This work supports the further development of simple model proteins to study aspects of Complex III mechanism

Network design and analysis for multi-enzyme biocatalysis

In vitro synthesis is a biotechnological alternative to classic chemical catalysts. However, the manual design of multi-step biosynthesis routes is very challenging, especially when enzymes from different organisms are involved. There is therefore a demand for in silico tools to guide the design of such synthesis routes using computational methods for the path-finding, as well as the reconstruction of suitable genome-scale metabolic networks that are able to harness the growing amount of biological data available. This work presents an algorithm for finding pathways from arbitrary metabolites to a target product of interest. The algorithm is based on a mixed-integer linear program (MILP) and combines graph topology and reaction stoichiometry. The pathway candidates are ranked using different ranking criteria to help finding the best suited synthesis pathway candidates. Additionally, a comprehensive workflow for the reconstruction of metabolic networks based on data of the Kyoto Encyclopedia of Genes and Genomes (KEGG) combined with thermodynamic data for the determination of reaction directions is presented. The workflow comprises a filtering scheme to remove unsuitable data. With this workflow, a panorganism network reconstruction as well as single organism network models are established. These models are analyzed with graph-theoretical methods. It is also discussed how the results can be used for the planning of biosynthetic production pathways.In vitro Synthese ist eine biotechnologische Alternative zu klassischen chemischen Katalysen. Der manuelle Entwurf von mehrstufigen Biosynthesewegen ist jedoch sehr anspruchsvoll, vor allem wenn Enzyme verschiedener Organismen beteiligt sind. Daher besteht ein Bedarf an Methoden, die helfen solche Synthesewege in silico zu entwerfen und die in der Lage sind große Mengen biologischer Daten zu bewältigen - insbesondere in Hinblick auf die Rekonstruktion genomskaliger metabolischer Netzwerkmodelle und die Pfadsuche in solchen Netzwerken. In dieser Arbeit wird ein Algorithmus zur Pfadsuche zu einem Zielprodukt ausgehend von beliebigen Substraten präsentiert. Der Algorithmus basiert auf einem gemischt-ganzzahligen linearen Programm, das Graphtopologie mit Reaktionsstöchiometrien kombiniert. Die Pfadkandidaten werden anhand verschiedener Kriterien geordnet, um die am besten geeigneten Kandidaten für die Synthese zu finden. Außerdem wird ein umfassender Workflow für die Rekonstruktion metabolischer Netzwerke basierend auf der Datenbank KEGG sowie thermodynamischen Daten vorgestellt. Dieser umfasst einen Filter, der anhand verschiedener Kriterien geeignete Reaktionen auswählt. Der Workflow wird zum Erstellen einer organismusübergreifenden Netzwerkrekonstruktion, sowie Netzwerken einzelner Organismen genutzt. Diese Modelle werden mit graphentheoretischen Methoden analysiert. Es wird diskutiert, wie die Ergebnisse für die Planung von biosynthetischen Produktionswegen genutzt werden können.BMBF; Initiative “Biotechnologie 2020+: Basistechnologien für eine nächste Generation biotechnologischer Verfahren”; Projekt MECA

Food is our medicine

The paper describes the role of foods and nutrition in the promotion of human health. The relationship between foods, metabolism, homeostasis and metabolic disorder are briefly described. The aim of the paper is to highlight a simple strategy based on biochemistry, process engineering, human physiology and foods to achieve cellular homeostasis and health