Ly active under different nutritional perturbations in E. coli [28]. T…

Ly active under different nutritional perturbations in E. coli [28]. The second group contains reactions involved in amino acid metabolism, a process crucial for protein synthesis. Those reactions include acetylornithine transaminase, adenylsuccinate lyase, aspartate kinase, and L-serine transport. Another group contains reactions involved in nucleotides biosynthesis and degradation, processes essential for transcription and replication, including: purine-nucleoside phosphorylase (guanosine), pyrimidine-nucleoside phosphorylase (uracil), and thymidine phosphorylase, Staurosporine as well as thymidine kinase (ATP:thymidine). This group extends to three reactions involved in amino- and nucleotide-sugar metabolism, namely, UDP-N-acetylglucosamine 2-epimerase, UTP-glucose-1-phosphate uridylyltransferase, and UDPglucose-hexose-1-phosphate uridylyltransferase. Finally, we observe constant utilization of glutathione reductase and trimethylamine N-oxide reductase. The first can be understood by the fact that the ratio of reduced to oxidized glutathione in E. coli is kept on a high ratio, ensuring proper maintenance of reduced thiol groups, protection against oxidative damage, and formation of deoxyribonucleotide precursors for DNA synthesis [29]. The second is a part of the electron transport chain. The results of the functional enrichment analysis and biological interpretation of the metabolic role of indispensable reactions, showing flat profiles of fractional appearance, supports our assumption that these reactions constitute the most crucial part of the metabolic network.Fluctuating patterns capture condition-specific temporal responseNext we investigate reactions whose temporal appearance in EFMs changes as a result of the applied stress. The number of reactions showing such behavior is smaller compared to that of reactions which are constantly used. There are 35 reactions for cold stress and 29 for heat stress.?Topfer et al. BMC Systems Biology 2012, 6:148 http://www.biomedcentral.com/1752-0509/6/Page 8 ofOver-representation analysis of biological processes reveals that under cold stress cluster 2 is enriched for catabolic processes, in particular, of amino acids, organic acids, and coenzymes, followed by acetyl-CoA biosynthetic process from pyruvate, and glycolysis. The reactions in this cluster are excluded from the networks at 10 min and peak with respect to their fractional appearances at 30 min. A prominent representative in this group of reactions is the glycine cleavage system, which has been found to be slightly affected by cold stress [30]. Cluster 3 is enriched for biosynthesis of the aspartate PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/16989806 family of amino acids (i.e., homoserine and threonine), carbohydrate (glucose) catabolic process, and pentosephosphate shunt, among other more general GO terms. The fractional appearance profiles for the included reactions remain unchanged up to 30 min, after which the reactions are excluded from the time-specific networks to be reintroduced 50 min after application of the stress. This cluster includes the reactions: L-threonine dehydrogenase, threonine synthase, and aspartate-semialdehyde dehydrogenase. This suggest that even some prominent pathways, such as amino acid synthesis, are not constantly kept at high level throughout adaptation to the stress. Moreover, transaldolase appears to undergo the same transition in fractional appearance, which is due to the observation that, unlike in exponential growth, cells facing cold stress transiently use thi.