RESUMO
In this work we apply a bioinformatics approach to determine the most important enzymes of the metabolic network of mycoplasmas. The genomes of several mycoplasmas shared predicted important enzymes. Our method allows us to determine both enzymes that are isolated from the metabolic network of the organism and those that are redundant. We also compare the similarities of the mycoplasmas metabolic networks with the phylogenetic relationships predicted from their 16s rRNA sequences.
Assuntos
Biologia Computacional/métodos , Mycoplasma/metabolismo , Simulação por Computador , Deleção de Genes , Genoma Bacteriano , Fases de Leitura Aberta , Fenótipo , Filogenia , RNA Bacteriano , RNA Ribossômico 16S/metabolismoRESUMO
We present the MOlecular NETwork (MONET) ontology as a model to integrate data from different networks that govern cell function. To achieve this, different existing ontologies were analyzed and an integrated ontology was built in a way to make it possible to share and reuse knowledge, support interoperability between systems, and also allow the formulation of hypotheses through inferences. By studying the cell as an entity of a myriad of elements and networks of interactions, we aim to offer a means to understand the large-scale characteristics responsible for the behavior of the cell and to enable new biological insights.
Assuntos
Algoritmos , Fenômenos Fisiológicos Celulares , Modelos Biológicos , Animais , Simulação por Computador , Bases de Dados como Assunto/organização & administração , Humanos , Análise em Microsséries/métodosRESUMO
Understanding the architecture of physiological functions from annotated genome sequences is a major task for postgenomic biology. From the annotated genome sequence of the microbe Escherichia coli, we propose a general quantitative definition of enzyme importance in a metabolic network. Using a graph analysis of its metabolism, we relate the extent of the topological damage generated in the metabolic network by the deletion of an enzyme to the experimentally determined viability of the organism in the absence of that enzyme. We show that the network is robust and that the extent of the damage relates to enzyme importance. We predict that a large fraction (91%) of enzymes causes little damage when removed, while a small group (9%) can cause serious damage. Experimental results confirm that this group contains the majority of essential enzymes. The results may reveal a universal property of metabolic networks.
Assuntos
Enzimas/química , Enzimas/metabolismo , Escherichia coli/enzimologia , Metabolismo/fisiologia , Modelos Biológicos , Complexos Multienzimáticos/química , Complexos Multienzimáticos/metabolismo , Simulação por Computador , Ativação Enzimática , Estabilidade Enzimática , Enzimas/classificação , Enzimas/deficiência , Complexos Multienzimáticos/classificação , Complexos Multienzimáticos/deficiência , Mutação , Relação Estrutura-AtividadeRESUMO
In this work we apply a bioinformatics approach to determine the most important enzymes of the metabolic network of Eucalyptus to determine the coverage of the genome in the FORESTS library. We conclude that the library does not cover completely the metabolism of the organism. However, some important pathways could be analyzed, especially the lignin synthesis. We found that four of the most important enzymes predicted are involved in this pathway