Fig 1.
Analysis outline and module structure.
A. The program logic flow chart for module completion algorithm is included. Data for module analysis is obtained by “Annotation and Quantification" (yellow box) to obtain data for module analysis. The 3 sections of analysis are illustrated with different colored boxes—Module completion; phylogenetic restriction / conservation of metabolic potential; Metabolic dynamics vs. development and parasitism. More detailed description of annotation, module completion and abundance algorithms are in the Methods section. B. Modules not containing a cycle can exhibit features such as multiple inputs (1 and 2) and forked network leading to multiple outputs (4 and 6). In general, more than 1 compound might be substrate-only (1 and 2 here), and hence needs to be treated as a ‘given’ compound for module completion determination. Rectangles are enzymes. Ovals are substrates/products. C. Network Reduction for simplifying completion algorithm. In this case with no reversible reactions, if none of the KOs representing reaction C is present in the organism, this leads to the following sequence of inferences. Reaction C absent = > no reaction has compound 4 as its product = > compound 4 is absent = > reaction B does not have 1 of its substrates = > compound 3 is absent = > reaction A does not have 1 of its substrates = > compound 2 is absent. This leaves the original network highly simplified and reduces it to just two nodes 1 and 5 (i.e. the original ‘given’ compounds) without any node connecting them.
Fig 2.
Enzyme annotation, module completion and phylogenetic distribution of metabolic potential.
A. Number of complete modules and distinct KOs mapped to them. B. Clustering based on module presence correlation. A version of the figure that includes the module names is presented as S5 Fig.
Fig 3.
Enzyme diversification between host and parasite.
A. Enzyme diversification between human and human hookworm Necator americanus. Reactions R01518 (2-Phospho-D-glycerate 2,3-phosphomutase) and R00200 (pyruvate kinase) are indispensable steps for the completion of M00001 (Glycolysis Embden-Meyerhof pathway). N. americanus, a human hookworm parasite, uses KO K15633 for R01518, which the human proteome lacks. Human proteome has genes mapping to K01837 and K01834 instead, which completes the same reaction. For R00200, both Human and N. americanus have K00873 available for completion, but only human have K12406 as an alternative for reaction completion. B. Enzyme diversification between plants and plant –parasitic nematodes. Plants have many more examples of exclusive KO usage between hosts and parasites. Module M00087 (beta-oxidation) is an interesting case where the last 2 reactions—R04727 and R03991—use different KOs for completion in all the 3 plants vs the 3 plant parasite nematodes. Different KOs are likely to be mapped to genes that are not orthologous to each other, providing an opportunity to target the parasite-specific activity.
Table 1.
Examples of exclusive enzyme usage by parasite and host.
Fig 4.
Developmental stage based metabolic profiles for Caenorhabditis elegans and Brugia malayi.
The clusters are based on similarity between abundance profiles across developmental stages (see S12 Fig). The black line (green bounds) represents the mean (standard deviation) of the Z-score of abundances for that developmental stage of all modules in the cluster. The Z-score is a measure of relative over- of under-abundance of the module in that developmental stage compared to its mean over all stages. EE: Early Embryo; LE: Late Embryo; IM: Immature Microfilariae; MM: Mature Microfilariae; YA: Young Adult; AM: Adult Male; AF: Adult Female.
Fig 5.
Combined analysis of differentially abundant enzymes in Caenorhabditis elegans and Necator americanus.
Infective L3 stage in N. americanus is developmentally analogous to the Dauer stage of C. elegans. KOs that are overabundant in the parasitic Adult stage in the hookworm, as compared to the infective L3 stage are likely to be enriched from parasitism related enzymes, but this result is confounded by the development related KOs needed in the adult stage. We obtain a highly enriched subset of parasitism related KOs by only compiling those KOs that are underabundant in the Adult stage of C. elegans, hence, less likely to be important for the worms’ adult stage for any non-parasitism related function. The shaded region represents KOs that are among the top 25 percentile in abundance rank differential between the Dauer stage and the adult stage in C. elegans and among the bottom 25 percentile in abundance rank differential between the infective L3 stage and the adult stage in N. americanus. A total of 133 KOs lie in this region, and hence are putative parasitism-relevant KOs.
Table 2.
Parasitism related KEGG categories.