Metris et al. BMC Genomics 2011, 12:535 http://www.biomedcentral.com/1471-2164/12/535 glycolate is degraded further through glyoxylate metabo- lism [16,18]. Alternatively glycolate can diffuse out of the cell in the case of E. coli [16]. Since a glyoxylate oxi- dase (Cj1213c) has been annotated [23] and since glyox- ylate has been shown to be degraded via a malate synthase in H. pylori [29], we assumed a malate synthase in our model despite the genome lacking the corre- sponding annotation as in H. pylori [30,31]. Amino acid metabolism The reactions for the amino acid metabolism have been mainly drawn from the genome annotation. Contrarily to H. pylori, C. jejuni seems to have the capacity to synthesize all the amino acids and vitamins it requires. This was shown experimentally with BIOLOG pheno- type microarrays, where respiration was detected on growth medium containing salts and a carbon source only [32]. From the genome sequence, complete path- ways for the synthesis of isoleucine, leucine and valine, are present in C. jejuni, whereas these pathways are incomplete or absent in H. pylori. In addition to the amino acids required by H. pylori, a complete pathway to synthesize histidine was found in C. jejuni (cj0317, cj1315c, cj1597-99, cj1600-01, cj1603-04) while orthologs of these genes are absent in the H. pylori genome. The gene for the last step of methionine synthesis is pre- dicted to be present in C. jejuni (cj1201), so no demand reaction was included in the model to artificially con- sume S-adenosylmethione. In common with H. pylori, only one gene of the methionine salvage pathway was found to be present in C. jejuni (cj0117). In the iIT341 GSM/GPR H. pylori model, the pathway was neverthe- less included to ensure the recycling of 5-methylthioade- nosine, a by-product of spermidine biosynthesis, to methionine, based on the assumption that the pathways vary from one micro-organism to another. However it has recently been suggested that the last steps of sper- midine biosynthesis in C. jejuni differ from the pathway proposed for H. pylori [33] eliminating the necessity for recycling 5-methylthioadenosine, so the methionine sal- vage pathway was not included in this model. Nucleotide metabolism The reactions for the nucleotide metabolism have been almost exclusively derived from the genome annota- tion. The pathway for the synthesis of IMP is more similar to that of E. coli, rather than that of H. pylori. Only a few genes have been annotated at the level of nucleotide inter-conversions such as cj0293 which has been predicted to encode for a nucleotidase [23]. How- ever most of the products of the reactions catalysed by this enzyme are not reutilised in the metabolic net- work, they are dead-ends. So either cj0293 is incor- rectly annotated, or genes encoding enzymes to utilize the products of the nucleotidase have not been annotated. Page 3 of 14 Vitamin and cofactor metabolism In the H. pylori model iIT341 GSM/GPR, it was assumed that pimelate diffuses into the cell and that the first step of the synthesis of biotin is catalysed by pime- lyl-CoA synthetase although no locus was found for such a gene [18]. Having no better alternative, we kept the assumption of the H. pylori model. C. jejuni does not contain ubiquinone, but uses menaquinone 6 and a methyl-substituted menaquinone [34]. It has been shown that for Streptomyces coelicolor, H. pylori, C. jejuni and Thermus thermophilus, the pathway for menaquinone synthesis diverges from the one from E. coli with futalosine as an intermediate [35]. However the pathway is not completely elucidated so in this model, the equations of the pathway of E. coli were kept as in the model iIT341 GSM/GPR. As for the ubiquinone, the same three gene orthologs of the genes present in H. pylori have been predicted to be present in C. jejuni. Thiamine is essential for the growth of some strains of Campylobacter [36] but not for the strain NCTC11168 [32]. According to the genome annotation, the pathway for its synthesis is complete. Cell wall metabolism There is little evidence about the composition of the cell wall of C. jejuni in the literature, and the genome anno- tation suggests that the pathways are neither those of E. coli nor those of H. pylori. For instance, only 2 genes are annotated as part of the fucose biosynthesis pathway in C. jejuni (cj1407c and cj1428c), while 6 such genes are annotated in H. pylori. However in the absence of better data, the pathways for the cell wall metabolism were copied from the model iIT341 GSM/GPR. It has been shown that the fatty acid composition of C. jejuni changes with the environmental conditions and/or the growth rate [37,38] but the predominant fatty acid have been reported to be the saturated hexadecanoic acid, the unsaturated octodec-1l-enoic acid and to a lesser extent cyclopropane in C19 and tetradecanoic acid which increased with stress [37-40]. These are the same fatty acids that are included in the model iIT341 GSM/GPR. Other It is not clear from the genome sequence nor from the literature how C. jejuni assimilates sulphur, and hence we have used the assumptions used for H. pylori [18]. Transport reactions were mainly drawn from circum- stantial evidence. Three “sink reactions” were added to the model because the pathways for the degradation of the corresponding products are unknown, and the ones used are the same as the ones introduced in E. coli [16] and H. pylori [18]. Exploration of the predicted metabolism of C. jejuni To test the model, the production of biomass from dif- ferent carbon sources was simulated and the results are