Rewiring and regulation of cross-compartmentalized metabolism in protists

Abstract

Plastid acquisition, endosymbiotic associations, lateral gene transfer, organelle degeneracy or even organelle loss influence metabolic capabilities in many different protists. Thus, metabolic diversity is sculpted through the gain of new metabolic functions and moderation or loss of pathways that are often essential in the majority of eukaryotes. What is perhaps less apparent to the casual observer is that the sub-compartmentalization of ubiquitous pathways has been repeatedly remodelled during eukaryotic evolution, and the textbook pictures of intermediary metabolism established for animals, yeast and plants are not conserved in many protists. Moreover, metabolic remodelling can strongly influence the regulatory mechanisms that control carbon flux through the major metabolic pathways. Here, we provide an overview of how core metabolism has been reorganized in various unicellular eukaryotes, focusing in particular on one near universal catabolic pathway (glycolysis) and one ancient anabolic pathway (isoprenoid biosynthesis). For the example of isoprenoid biosynthesis, the compartmentalization of this process in protists often appears to have been influenced by plastid acquisition and loss, whereas for glycolysis several unexpected modes of compartmentalization have emerged. Significantly, the example of trypanosomatid glycolysis illustrates nicely how mathematical modelling and systems biology can be used to uncover or understand novel modes of pathway regulation.

Figure 1.

Simplified diagrams of compartmentalized glycolysis. (a) Dynamic association of a complex of glycolytic enzymes at the outer surface of the mitochondria as observed in plants. The fraction of enzymes associating with mitochondria is related to the respiratory activity and is thus probably determined by organellar demand for the glycolytic end-product, pyruvate. The major glycolytic activity is found in the cytosol and serves various purposes; intermediates are exchanged with other pathways in the cytosol and chloroplasts/plastids. Metabolite channelling in the multi-enzyme complex, however, restricts the exchange of glycolytic intermediates with the cytosol and thus favours the flux towards the mitochondria. (b) Glycolysis in diatoms and oomycetes. A fusion enzyme comprising TPI and GAPDH is mitochondrial. Genomic information also suggests that the downstream, but not the upstream, enzymes of the glycolytic pathway are present in mitochondria. Glycolytic enzymes are also found or predicted from genome analysis to be present in the cytosol and, in the case of diatoms, plastids. (c) Comparison of non-compartmentalized glycolysis as occurs in most cell types (i) compared with compartmentalized glycolysis in glycosomes as observed in bloodstream-form Trypanosoma brucei (ii) and procyclic, insect-stage trypanosomes and other kinetoplastid species (iii); for a full description, see the text. Arrows with full lines represent demonstrated reactions or fluxes; arrows with dashed lines inferred fluxes and arrows with stippled lines feedback regulation. Positive feedback is indicated by an encircled +, negative feedback by an encircled −. Question marks indicate inferred fluxes between compartments.

Figure 2.

Isoprenoid biosynthesis in eukaryotes. (a) Reactions required for classic MVA-dependent biosynthesis of IPP and DMAPP. Enzymes listed: 1. thiolase, 2. HMG-CoA synthase, 3. HMGR, 4. mevalonate kinase, 5. mevalonate phosphate dikinase, 6. diphosphomevalonate decarboxykinase, and 7. IPP isomerase. (b) The MEP pathway for isoprenoid biosynthesis; note how ispH catalyses synthesis of IPP and DMAPP.

Figure 3.

Distribution of MVA and MEP pathways in eukaryotes. Putative relationships between taxonomic groups are based on recent, but still equivocal views of eukaryotic evolution (Burki et al. 2008; Hampl et al. 2009; Roger & Simpson 2009).

Figure 4.

Compartmentalization of isoprenoid biosynthesis. (a) Textbook view of how the MVA pathway is compartmentalized in animals and yeast; 3. HMGR (enzyme 3 from figure 2). The localization of several enzymes from the pre-squalene stage of the MVA pathway in mammals has been debated: peroxisomal locations for all enzymes leading to farnesyl diphosphate have been reported, too (see main text). (b) Compartmentalization of sterol biosynthesis in trypanosomatid protists. (c) Compartmentalization of isoprenoid biosynthesis in apicomplexan parasites (other than Cryptosporidium species).