## 3 Biosynthesis of Aromatic and Isoprenic Precursors of Prenylquinones in Parasitic Protozoa
### Isoprenic Side Chain Biosynthesis  
Isoprenoid biosynthesis occurs in almost all known living organisms [45]. In addition to prenylquinones, isoprenoids and isoprenylated compounds include diverse and important molecules such as isoprenylated proteins, sterols, isoprene compounds bound to RNA, dolichols and carotenoids [95]. There are two well-characterized pathways for isoprenoid biosynthesis: the mevalonate (MVA) pathway and the MEP pathway (Figure 3). The final result of both pathways is the formation of isoprenenyl pyrophosphate (IPP) or its isomer dimethylallyl pyrophosphate (DMAPP), both of which are considered to be simple isoprenic units required for the formation of differently sized chains [45; 95]. For both pathways, well-known specific inhibitors exist, such as fosmidomycin for the MEP pathway and statins for the MVA pathway. Most archaeal species use the MVA pathway, while most bacteria use the MEP pathway [96; 97; 98; 99]. However, there are several exceptions. For example, _Myxococcus fulvus_ uses the MVA pathway, and _Streptomyces_ spp. have both isoprenic biosynthetic pathways [96]. The MVA pathway is also used as the only source of isoprenic precursors by all known animals and fungi [97]. Higher plants have the two pathways compartmentalized in different subcellular spaces, and these pathways are used to provide isoprenic precursors for different biosynthetic processes. The MVA pathway is found in the cytosol for UQ biosynthesis among other compounds, and the MEP pathway is located in the chloroplast, providing isoprenic precursors for chlorophyll, PK or PQ. In algae and protists, there are a few pathways for biosynthesis of isoprenoids [68; 97; 98; 100; 101]. In _Leishmana_ and _Trypanosoma_ species, indicators of leucine dependent pathways were observed for isoprenoid biosynthesis [70; 71; 102]. These pathways can be independent of the MVA pathway or coupled to the MVA pathway with or without conversion of leucine to acetyl-CoA for 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) regeneration [70; 71; 102]. In the case of the MVA-coupled pathway without the conversion of leucine to acetyl-CoA, leucine can be reduced to HMG-CoA in _T. brucei_. Alternatively, the MVA pathway-independent incorporation of leucine into isoprenoids, an intermediate step in leucine breakdown (probably to dimethylcrotonyl-CoA), could be directly reduced to produce isopentenol in _Leishmana mexicana_[70]. The incorporation of leucine to isoprenic chains without the conversion of leucine to acetyl-CoA has also been demonstrated in other widely divergent organisms, such as halophilic archaea [78]. In _P. falciparum_, some authors suggested that alternative MVA/MEP pathways could be active. [PERSON] et al. [103] found intermediates of the MEP pathway in _P. falciparum_ but also observed a poor inhibitory effect of fosmidomycin on some isoprenylated final products in specific intraerythrocytic stages. [PERSON] et al. suggested that an as-yet-unknown isoprenic source could be present in the parasite [103]. The author cited a hypothetical pathway initiated by pentose phosphate cycle intermediates, for the existence of which there is only some evidence in cyanobacteria [104]. However, there remain many uncertainties associated with pentose phosphate cycle intermediates/leucine-dependent pathways that are not coupled to the MVA pathway as an isoprenic precursor source. For these reasons, the sections below focus on the MVA and MEP pathways. Figure 3: Scheme of isoprenoid biosynthesis up to isopentenyl pyrophosphate (IPP). The dotted, red arrow indicates the hypothetical IPP Biosynthesis Pathway previously mentioned in the text, starting from intermediate metabolites of the pentose phosphate pathway in _Synechocystis_ sp. and a possibility that has not been investigated to date in any pathogenic protozoan [70].