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Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
PLoS Comput Biol, 7 (3): e1001116+ (31.03.2011)
DOI: 10.1371/journal.pcbi.1001116
Аннотация
In the past decade, over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms. These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism, leading to greater understanding of observed phenotypes. These methods have been sparsely applied to comparisons between multiple organisms, however, due mainly to the existence of differences between reconstructions that are inherited from the respective reconstruction processes of the organisms to be compared. To circumvent this obstacle, we developed a novel process, termed metabolic network reconciliation, whereby non-biological differences are removed from genome-scale reconstructions while keeping the reconstructions as true as possible to the underlying biological data on which they are based. This process was applied to two organisms of great importance to disease and biotechnological applications, Pseudomonas aeruginosa and Pseudomonas putida, respectively. The result is a pair of revised genome-scale reconstructions for these organisms that can be analyzed at a systems level with confidence that differences are indicative of true biological differences (to the degree that is currently known), rather than artifacts of the reconstruction process. The reconstructions were re-validated with various experimental data after reconciliation. With the reconciled and validated reconstructions, we performed a genome-wide comparison of metabolic flexibility between P. aeruginosa and P. putida that generated significant new insight into the underlying biology of these important organisms. Through this work, we provide a novel methodology for reconciling models, present new genome-scale reconstructions of P. aeruginosa and P. putida that can be directly compared at a network level, and perform a network-wide comparison of the two species. These reconstructions provide fresh insights into the metabolic similarities and differences between these important Pseudomonads, and pave the way towards full comparative analysis of genome-scale metabolic reconstructions of multiple species. Over the past decade, the increasing availability of fully sequenced genomes, functional genomics databases, and a broad existing scientific literature on metabolism have been leveraged towards the generation of genome-scale metabolic reconstructions for a wide variety of organisms. A major hurdle in the field, however, is the lack of standardization in this 'metabolic reconstruction' process, which makes it difficult to compare reconstructions of multiple species with each other. Notably, it is difficult to determine if differences seen between the models are of biological origin, or if they reflect noise from the respective reconstruction processes. To address this problem, we have developed a novel method, termed metabolic network reconciliation, in which genome-scale models of two well-studied and phylogenetically related bacteria (P. aeruginosa and P. putida) were compared such that differences between the models not upheld by biological evidence were eliminated. These reconciled models were re-validated with experimental data, and used to explore differences in the biology of these organisms and to gain insight into the reconstruction process itself.
