Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis

The annotated full DNA sequence is becoming available for a growing number of organisms. This information along with additional biochemical and strain -specific data can be used to define metabolic genotypes and reconstruct ce llular metabolic networks. The first free-living organism for which the ent ire genomic sequence was established was Haemophilus influenzae. Its metabo lic network is reconstructed herein and contains 461 reactions operating on 367 intracellular and 84 extracellular metabolites. With the metabolic rea ction network established, it becomes necessary to determine its underlying pathway structure as defined by the set of extreme pathways. The H. influe nzae metabolic network was subdivided into six subsystems and the extreme p athways determined for each subsystem based on stoichiometric, thermodynami c, and systems-specific constraints. Positive linear combinations of these pathways can be taken to determine the extreme pathways for the complete sy stem. Since these pathways span the capabilities of the full system, they c ould be used to address a number of important physiological questions. Firs t, they were used to reconcile and curate the sequence annotation by identi fying reactions whose function was not supported in any of the extreme path ways. Second, they were used to predict gene products that should be co-reg ulated and perhaps co-expressed. Third, they were used to determine the com position of the minimal substrate requirements needed to support the produc tion of 51 required metabolic products such as amino acids, nucleotides, ph ospholipids, etc. Fourth, sets of critical gene deletions from core metabol ism were determined in the presence of the minimal substrate conditions and in more complete conditions reflecting the environmental niche of H. influ enzae in the human host. In the former case, 11 genes were determined to be critical while six remained critical under the latter conditions. This stu dy represents an important milestone in theoretical biology, namely the est ablishment of the first extreme pathway structure of a whole genome. (C) 20 00 Academic Press.