Assessment of the Metabolic Capabilities of Haemophilus influenzae Rd through a Genome-scale Pathway Analysis
✍ Scribed by CHRISTOPHE H. SCHILLING; BERNHARD Ø. PALSSON
- Publisher
- Elsevier Science
- Year
- 2000
- Tongue
- English
- Weight
- 564 KB
- Volume
- 203
- Category
- Article
- ISSN
- 0022-5193
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✦ Synopsis
The annotated full DNA sequence is becoming available for a growing number of organisms. This information along with additional biochemical and strain-speci"c data can be used to de"ne metabolic genotypes and reconstruct cellular metabolic networks. The "rst free-living organism for which the entire genomic sequence was established was Haemophilus in-uenzae. Its metabolic network is reconstructed herein and contains 461 reactions operating on 367 intracellular and 84 extracellular metabolites. With the metabolic reaction network established, it becomes necessary to determine its underlying pathway structure as de"ned by the set of extreme pathways. The H. in-uenzae metabolic network was subdivided into six subsystems and the extreme pathways determined for each subsystem based on stoichiometric, thermodynamic, and systems-speci"c constraints. Positive linear combinations of these pathways can be taken to determine the extreme pathways for the complete system. Since these pathways span the capabilities of the full system, they could be used to address a number of important physiological questions. First, they were used to reconcile and curate the sequence annotation by identifying reactions whose function was not supported in any of the extreme pathways. Second, they were used to predict gene products that should be co-regulated and perhaps co-expressed. Third, they were used to determine the composition of the minimal substrate requirements needed to support the production of 51 required metabolic products such as amino acids, nucleotides, phospholipids, etc. Fourth, sets of critical gene deletions from core metabolism were determined in the presence of the minimal substrate conditions and in more complete conditions re#ecting the environmental niche of H. in-uenzae in the human host. In the former case, 11 genes were determined to be critical while six remained critical under the latter conditions. This study represents an important milestone in theoretical biology, namely the establishment of the "rst extreme pathway structure of a whole genome.