1) includes central metabolism and biosynthetic routes for nucleotides, amino acids and cofactors. 2002, 4: 133-140. Aphids are sap-feeding insects infesting wide ranges of plant species. We have reconstructed and analysed the metabolic network of the γ-proteobacterium Buchnera aphidicola (symbiont of the pea aphid) as a model for using systems-level approaches to discover key traits of symbionts with small genomes. Verification of the phylogeny of Buchnera aphidicola was done by comparing the genome sequence with various species in the family called … the fluxes producing the metabolite and consuming it are equal), and flux is optimised to a desired output, also known as the objective function, usually biomass production. with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, et al. In this study, we have created a high quality manually constructed metabolic model for B. aphidicola that is more biologically realistic than previous studies [e.g. Some features of the site may not work correctly. Genome Biol. Google Scholar. 3B). Obligately intracellular bacteria with very small genomes (< 1 Mb) include important pathogens and required symbionts of parasites and disease vectors [1]. This condition is realistic because B. aphidicola lacks almost completely transcriptional regulation [10, 11] and sequence analysis of enzymes subject to feedback inhibition in E. coli suggests these features have been lost from B. aphidicola [12]. 2000, 182: 2967-2969. Appl Environ Microbiol. The reconstruction is also available in Buchnera Cyc http://www.buchneracyc.org a BioCyc genome/pathway database created and adopted for this project using the Pathologic software [22]. Article  B. aphidicola provide aphids with essential amino acids (EAAs), nutrients which the insect cannot synthesise de novo and which are in short supply in the diet of plant phloem sap [4]. The FBA model is, consequently, representative of a functional symbiotic bacterium; it is called the 5.21 model (Vgrowth is 5.21, see Additional File 3). A total of 214 genes were retained in all of the 500 simulations performed, comprising 148 (76%) of the 196 genes in iGT196 and a further 66 genes absent from iGT196 (Additional File 6). Visual inspection of the APS metabolic network revealed a particularly interesting feature, namely the proximal truncation of the purine biosynthesis pathway (Fig. Nature. 1) includes central metabolism and biosynthetic routes for … The analysis was performed as described previously [19] using the Fluxor software running on Orchestra (a 100-node cluster) and was repeated 500 times. This file contains additional methods for the construction and validation of the model and the flux correlation method with references. (2006) could replicate the proximal truncation of the purine biosynthetic pathway (Fig. The metabolic network of Buchnera aphidicola APS. In silico analyses provide valuable insight into the biology of obligately intracellular pathogens and symbionts with small genomes. 2000, 407: 651-654. Google Scholar. The in silico analysis reported here suggests that the supply of key precursors across the symbiosomal membrane may be sufficient to regulate EAA export from the bacteria. Additional file 1: Additional Methods. The construction and analysis of the model was performed by GHT, JZ, SJM, AS and IG. The limited number of metabolic pathways (Fig. For each pair of compound nodes in the reaction graph shortest path distance was calculated by breadth-first search. : Escherichia coli K-12: a cooperatively developed annotation snapshot – 2005. The model has been submitted in SBML to the BioModels database http://www.ebi.ac.uk/biomodels/ with accession number MODEL7434234848. Please consider upgrading,

An evidence describes the source of an annotation, e.g. Nature. The bacterial cells are restricted to a single insect cell type, the bacteriocyte, the sole function of which appears to be to house and maintain the bacteria; the cytoplasm of the bacteriocyte is packed with bacterial cells, each of which is enclosed by an insect membrane, known as the symbiosomal membrane [4]. Evidence for the establishment of aphid-eubacterium endosymbiosis in an ancestor of four aphid families. These metabolic traits underpin the sustained nutritional contribution of B. aphidicola to the host and, together with the impact of host-derived substrates on the profile of nutrients released from the bacteria, point to a dominant role of the host in controlling the symbiosis. For FBA analysis, all reactions in the network were permitted to be active simultaneously. Nat Protoc. Initial FBA analysis using iJR904 modified to have the biomass reaction from iGT196 did not produce a feasible solution because the biosynthetic pathways to biotin and thiamine diphosphate were incomplete. Identical data were also obtained by analysing the model using the COBRA software [13]. Nature. In an attempt to investigate the origin of the intracellular symbiont of the aphid (Buchnera), aphid gut aerobic bacteria were isolated, and their phylogenetic relations to other prokaryotes were examined based on nucleotide sequences of 16S rDNA. (2006) and this study. Article  1983, 1-25. 2005, 33: D334-D337.