Metabolic networks are the collections of all cellular activities taking place in a living cell and all the relationships among biological elements of the cell including genes, proteins, enzymes, metabolites, and reactions. They provide a better understanding of cellular mechanisms and phenotypic characteristics of the studied organism. In order to reconstruct a metabolic network, interactions among genes and their molecular attributes along with their functions must be known. Using this information, proteins are distributed among pathways as sub-networks of a greater metabolic network. Proteins which carry out various steps of a biological process operate in same pathway.<p>The metabolic network of <i>Caenorhabditis elegans</i> was reconstructed based on current genomic information obtained from the KEGG database, and commonly found in SWISS-PROT and WormBase. Assuming proteins operating in a pathway are interacting proteins, currently available protein-protein interaction map of the studied organism was assembled. This map contains all known protein-protein interactions collected from various sources up to the time. Topology of the reconstructed network was briefly studied and the role of key enzymes in the interconnectivity of the network was analysed. The analysis showed that the shortest metabolic paths represent the most probable routes taken by the organism where endogenous sources of nutrient are available to the organism. Nonetheless, there are alternate paths to allow the organism to survive under extraneous variations. <p>Signature content information of proteins was utilized to reveal protein interactions upon a notion that when two proteins share signature(s) in their primary structures, the two proteins are more likely to interact. The signature content of proteins was used to measure the extent of similarity between pairs of proteins based on binary similarity score. Pairs of proteins with a binary similarity score greater than a threshold corresponding to confidence level 95% were predicted as interacting proteins. The reliability of predicted pairs was statistically analyzed. The sensitivity and specificity analysis showed that the proposed approach outperformed maximum likelihood estimation (MLE) approach with a 22% increase in area under curve of receiving operator characteristic (ROC) when they were applied to the same datasets. When proteins containing one and two known signatures were removed from the protein dataset, the area under curve (AUC) increased from 0.549 to 0.584 and 0.655, respectively. Increase in the AUC indicates that proteins with one or two known signatures do not provide sufficient information to predict robust protein-protein interactions. Moreover, it demonstrates that when proteins with more known signatures are used in signature profiling methods the overlap with experimental findings will increase resulting in higher true positive rate and eventually greater AUC. <p>Despite the accuracy of protein-protein interaction methods proposed here and elsewhere, they often predict true positive interactions along with numerous false positive interactions. A global algorithm was also proposed to reduce the number of false positive predicted protein interacting pairs. This algorithm relies on gene ontology (GO) annotations of proteins involved in predicted interactions. A dataset of experimentally confirmed protein pair interactions and their GO annotations was used as a training set to train keywords which were able to recover both their source interactions (training set) and predicted interactions in other datasets (test sets). These keywords along with the cellular component annotation of proteins were employed to set a pair of rules that were to be satisfied by any predicted pair of interacting proteins. When this algorithm was applied to four predicted datasets obtained using phylogenetic profiles, gene expression patterns, chance co-occurrence distribution coefficient, and maximum likelihood estimation for S. cerevisiae and <i>C. elegans</i>, the improvement in true positive fractions of the datasets was observed in a magnitude of 2-fold to 10-fold depending on the computational method used to create the dataset and the available information on the organism of interest. <p>The predicted protein-protein interactions were incorporated into the prior reconstructed metabolic network of <i>C. elegans</i>, resulting in 1024 new interactions among 94 metabolic pathways. In each of 1024 new interactions one unknown protein was interacting with a known partner found in the reconstructed metabolic network. Unknown proteins were characterized based on the involvement of their known partners. Based on the binary similarity scores, the function of an uncharacterized protein in an interacting pair was defined according to its known counterpart whose function was already specified. With the incorporation of new predicted interactions to the metabolic network, an expanded version of that network was resulted with 27% increase in the number of known proteins involved in metabolism. Connectivity of proteins in protein-protein interaction map changed from 42 to 34 due to the increase in the number of characterized proteins in the network.

The increasing prevalence of apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium represents a significant global healthcare burden. Treatment options are increasingly limited due to the emergence of new resistant strains. We postulate that parasites have evolved distinct metabolic strategies critical for growth and survival during human infections, and therefore susceptible to drug targeting using a systematic approach. I developed iCS306, a fully characterized metabolic network reconstruction of the model organism Toxoplasma gondii via extensive curation of available genomic and biochemical data. Using available microarray data, metabolic constraints for six different clinical strains of Toxoplasma were modeled. I conducted various in silico experiments using flux balance analysis in order to identify essential metabolic processes, and to illustrate the differences in metabolic behaviour across Toxoplasma strains. The results elucidate probable explanations for the underlying mechanisms which account for the similarities and differences among strains of Toxoplasma, and among species of Apicomplexa.

Metabolic networks are the collections of all cellular activities taking place in a living cell and all the relationships among biological elements of the cell including genes, proteins, enzymes, metabolites, and reactions. They provide a better understanding of cellular mechanisms and phenotypic characteristics of the studied organism. In order to reconstruct a metabolic network, interactions among genes and their molecular attributes along with their functions must be known. Using this information, proteins are distributed among pathways as sub-networks of a greater metabolic network. Proteins which carry out various steps of a biological process operate in same pathway.<p>The metabolic network of <i>Caenorhabditis elegans</i> was reconstructed based on current genomic information obtained from the KEGG database, and commonly found in SWISS-PROT and WormBase. Assuming proteins operating in a pathway are interacting proteins, currently available protein-protein interaction map of the studied organism was assembled. This map contains all known protein-protein interactions collected from various sources up to the time. Topology of the reconstructed network was briefly studied and the role of key enzymes in the interconnectivity of the network was analysed. The analysis showed that the shortest metabolic paths represent the most probable routes taken by the organism where endogenous sources of nutrient are available to the organism. Nonetheless, there are alternate paths to allow the organism to survive under extraneous variations. <p>Signature content information of proteins was utilized to reveal protein interactions upon a notion that when two proteins share signature(s) in their primary structures, the two proteins are more likely to interact. The signature content of proteins was used to measure the extent of similarity between pairs of proteins based on binary similarity score. Pairs of proteins with a binary similarity score greater than a threshold corresponding to confidence level 95% were predicted as interacting proteins. The reliability of predicted pairs was statistically analyzed. The sensitivity and specificity analysis showed that the proposed approach outperformed maximum likelihood estimation (MLE) approach with a 22% increase in area under curve of receiving operator characteristic (ROC) when they were applied to the same datasets. When proteins containing one and two known signatures were removed from the protein dataset, the area under curve (AUC) increased from 0.549 to 0.584 and 0.655, respectively. Increase in the AUC indicates that proteins with one or two known signatures do not provide sufficient information to predict robust protein-protein interactions. Moreover, it demonstrates that when proteins with more known signatures are used in signature profiling methods the overlap with experimental findings will increase resulting in higher true positive rate and eventually greater AUC. <p>Despite the accuracy of protein-protein interaction methods proposed here and elsewhere, they often predict true positive interactions along with numerous false positive interactions. A global algorithm was also proposed to reduce the number of false positive predicted protein interacting pairs. This algorithm relies on gene ontology (GO) annotations of proteins involved in predicted interactions. A dataset of experimentally confirmed protein pair interactions and their GO annotations was used as a training set to train keywords which were able to recover both their source interactions (training set) and predicted interactions in other datasets (test sets). These keywords along with the cellular component annotation of proteins were employed to set a pair of rules that were to be satisfied by any predicted pair of interacting proteins. When this algorithm was applied to four predicted datasets obtained using phylogenetic profiles, gene expression patterns, chance co-occurrence distribution coefficient, and maximum likelihood estimation for S. cerevisiae and <i>C. elegans</i>, the improvement in true positive fractions of the datasets was observed in a magnitude of 2-fold to 10-fold depending on the computational method used to create the dataset and the available information on the organism of interest. <p>The predicted protein-protein interactions were incorporated into the prior reconstructed metabolic network of <i>C. elegans</i>, resulting in 1024 new interactions among 94 metabolic pathways. In each of 1024 new interactions one unknown protein was interacting with a known partner found in the reconstructed metabolic network. Unknown proteins were characterized based on the involvement of their known partners. Based on the binary similarity scores, the function of an uncharacterized protein in an interacting pair was defined according to its known counterpart whose function was already specified. With the incorporation of new predicted interactions to the metabolic network, an expanded version of that network was resulted with 27% increase in the number of known proteins involved in metabolism. Connectivity of proteins in protein-protein interaction map changed from 42 to 34 due to the increase in the number of characterized proteins in the network.

The increasing prevalence of apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium represents a significant global healthcare burden. Treatment options are increasingly limited due to the emergence of new resistant strains. We postulate that parasites have evolved distinct metabolic strategies critical for growth and survival during human infections, and therefore susceptible to drug targeting using a systematic approach. I developed iCS306, a fully characterized metabolic network reconstruction of the model organism Toxoplasma gondii via extensive curation of available genomic and biochemical data. Using available microarray data, metabolic constraints for six different clinical strains of Toxoplasma were modeled. I conducted various in silico experiments using flux balance analysis in order to identify essential metabolic processes, and to illustrate the differences in metabolic behaviour across Toxoplasma strains. The results elucidate probable explanations for the underlying mechanisms which account for the similarities and differences among strains of Toxoplasma, and among species of Apicomplexa.

The current investigation is aimed at the reconstruction and analysis of genome-scale metabolic models. Specifically, it is focused on the use of mathematical-computational simulations to predict the cellular metabolism behavior towards bio-products production. The photosynthetic cyanobacterium Synechococcus elongatus PCC7942 was studied as biological system. This prokaryotic has been used in several studies as a biological platform for the synthesis of several substances for industrial interest. These studies are based on the advantage of autotrophic systems, which basically requires light and CO2 for growth. The main objective of this thesis is the integration of different types of biological information, whose interaction can be extract applicable knowledge for economic interests. To this end, our study was addressed to the use of methods for modeling, analyzing and predicting the behavior of metabolic phenotypes of cyanobacterium. The work has been divided into chapters organized sequentially, where the starting point was the in silico metabolic reconstruction network. This process intent to join in a metabolic model of all chemical reactions codified in genome. The stoichiometric coefficients of each reactions, can be arranged into a sparse matrix (stoichiometric matrix), where the columns corresponds to reactions and rows to metabolites. As a result of this process the first model was obtained (iSyf646) than later was updated to another (iSyf714). Both were generated from data ¿omics published in databases, scientific reviews as well as textbooks. To validate them, each one of the stoichiometric matrix together with relevant constraints were used by simulation techniques based on linear programming. These reconstructions have to be flexible enough to allow autotrophic growth under which the organism grows in nature. Once the reconstructions were validated, environmental variations can be simulated and we were able to study its effects through changes in outline system parameters. Subsequently, synthetic capabilities were evaluated from the in silico models in order to design metabolic engineering strategies. To do this a genetic variation was simulated in reactions network, where the disturbed stoichiometric matrix was the object of the quadratic optimization methods. As a results sets of optimal solutions were generated to enhanced production of various metabolites of energetic interest such as: ethanol, n-butanol isomers, lipids and hydrogen, as well as lactic acid as the compound which is an interest to the industry. Furthermore, functionally coupled reactions have been studied and have been weighted to the importance in the production of metabolites. Finally, genome-scale metabolic models allow us to establish criteria to integrate different types of data to help of find important points of regulation that may be subject to genetic modification. These regulatory centers have been investigated under drastic changes of illumination and have been inferred operational principles of cyanobacterium metabolism. In general, this thesis presents the metabolic capabilities of photosynthetic cyanobacterium Synechococcus elongatus PCC7942 to produce substances of interest, being a potential biological platform for clean and sustainable production. / Triana Dopico, J. (2014). Model-based analysis and metabolic design of a cyanobacterium for bio-products synthesis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/39351 / TESIS