Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

Nathan E. Lewis, Harish Nagarajan, Bernhard O. Palsson
2012 Nature Reviews Microbiology  
The genotype -phenotype relationship is fundamental to biology. For decades this relationship has been subjected to mostly argument, speculation and qualitative analysis. However, our ability to fundamentally understand the genotype-phenotype relationship began to change in the mid 1990s, on completion of the first bacterial genome-sequencing projects. Full genome sequences provide comprehensive, albeit not yet complete, information about the genetic elements that create an organism. A detailed
more » ... understanding of some cellular processes, such as metabolism, has resulted in structured knowledge bases that can be mathematically represented 1-3 . This mathematical representation enables the computation of phenotypic states 4-7 based on genetic and environmental parameters. Remarkably, this provides a mechanistic representation of the microbial metabolic genotype-phenotype relationship. Constraint-based models of genome-scale metabolic networks capture the genotype-phenotype relationship by simultaneously accounting for constraints that are imposed on phenotype by physicochemical laws and genetics. The realization that these quantitative genotype-phenotype relationships could be constructed from a genome has driven the emergence of this area of research, and the flood of increasingly rich high-throughput data has accelerated the evolution of constraint-based reconstruction and analysis (COBRA) methods from a set of basic tools for metabolic network analysis into a powerful analytical framework that is increasingly used. Here, we describe basic features of the COBRA framework, the 'phylogeny' of evolving COBRA methods and the COBRA 'ecology' (that is, how COBRA methods complement each other in answering larger questions in biology). Constraint-based modelling defined The COBRA approach is based on a few fundamental concepts. These concepts include the imposition of physicochemical constraints that limit computable phenotypes (FIG. 1a-d) , the identification and mathematical description of evolutionary selective pressures (FIG. 1e) , and a genome-scale perspective of cell metabolism that accounts for all metabolic gene products in a cell (FIG. 1d,f) . These fundamental concepts are briefly described below. Constraints on reaction networks. Metabolism is a complex network of biochemical reactions. The reaction occurrence is limited by three primary constraints: substrate and enzyme availability, mass and charge conservation, and thermodynamics. For metabolic reactions, substrates must be present in the microenvironment of the cells or produced from other reactions, and enzymes must be available. Mass conservation further limits the possible reaction products and their stoichiometry, and thermodynamics constrains reaction directionality. For a given organism, this information can be obtained Abstract | Reconstructed microbial metabolic networks facilitate a mechanistic description of the genotype-phenotype relationship through the deployment of constraint-based reconstruction and analysis (COBRA) methods. As reconstructed networks leverage genomic data for insight and phenotype prediction, the development of COBRA methods has accelerated following the advent of whole-genome sequencing. Here, we describe a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods. These methods have enabled genome-scale analysis of microbial metabolism for numerous basic and applied uses, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour. www.nature.com/reviews/micro
doi:10.1038/nrmicro2737 pmid:22367118 pmcid:PMC3536058 fatcat:ybk5wpy67fbcpnbg5azcu4rrse