Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
Fig 5
Tisochrysis lutea metabolic model exploration: Origin of reactions according to the reconstruction pipeline.
(A) Comparison of the numbers of EC numbers introduced in the network either by the annotation pipeline or by the orthology-based analysis 898 enzymes were identified via annotation-based information and 790 enzymes through orthology-based data, among which 524 were already identified via annotation information. (B) Number of T-Iso ortholog enzymes according to their origin in template models. For each of the 790 T-Iso ortholog enzymes, the figure depicts in which of the four template models an ortholog of the enzyme had been identified. The four templates used were: A. thaliana, C. reinhardtii, E. siliculosus and Synechocystis sp. PCC 6803 to decipher ortholog enzymes in T. lutea. (C) T-Iso carnosine biosynthesis. Reconstruction of T-Iso carnosine synthesis pathway was performed using three sources of data (i) T-Iso genome annotations (cyan star); (ii) template metabolic models (stars) of four organisms: A. thaliana (blue), C. reinhardtii (green), E. siliculosus (red), and Synechocystis sp. (yellow) with orthology-based information; (iii) complete proteomes of the four organisms (squares) with sequence alignment information (best reciprocal hit in blasts). All reactions of the T-Iso carnosine biosynthesis are common to the four organisms except for three of them: ASPDECARBOX-RXN, HISTIDPHOS-RXN, and CARNOSINE-SYNTHASE-RXN. The first seems to belong to an alternative pathway to produce β-alanine, also found in C. reinhardtii, Synechocystis sp and Candidatus Phaeomarinobacter ectocarpi, a symbiotic bacterium to E. siliculosus. HISTIDPHOS-RXN was not found in E. siliculosus but was identified in its symbiotic bacterium Candidatus Phaeomarinobacter ectocarpi. CARNOSINE-SYNTHASE-RXN was only identified in algae (C. reinhardtii, E. siliculosus and T. lutea).