### Isoprenoids
#### 2.1.1 Biosynthesis of Isoprenoids
\begin{table}
\begin{tabular}{c c c} \hline \hline
**Genes** & **Enzyme and Its Alternative Names in Arabidopsis** & **Functions** \\ \hline _At5g16440_ & & Enzymes with dimethyl allyl diphosphate isomerase activity. It is involved in the biosynthesis of IPP, isopentenyl diphosphate. IPP \\ _At3g02780_ & IPPI, isopentenyl diphosphate isomerases & is a subject for further condensation reactions to form intermediates in the synthesis of plastic and mitochondrial isoprenoids (carotenoids, tocopherools, PQ, plastochromanol, UQ) \\ \hline _At4g19010_ & AT4G & \\  & 19010 & Peroxisomal 4-comarate CoA ligases & 4-HBA (hydroxybenzoic acid) biosynthesis from phenylalanine in peroxisomes for further UQ biosynthesis [16; 17] \\ \hline _At5g38120_ & 4 CL8 & \\ \hline _At5g47770_ & FPPS1 & Farnesyl diphosphate & Isoprenoid farnesyl diphosphate (FPP) biosynthesis for further \\ \hline _At4g17190_ & FPPS2 & synthases & UQ biosynthesis [18; 19] \\ \hline _At2g34630_ & CoQ1, SPS3, solanesyl diphosphate synthase & Isoprene polymerization for further UQ biosynthesis [20] \\ \hline _At4g23660_ & Coq2, PPT1, 4-hydroxybenzoate polytprenyl diphosphate transferase & Rate-limiting enzyme in UQ biosynthesis. Catalysis of benzoquinone ring of 4-HB condensation with polyisoprenoid side chain of polytprenyl pyrophosphate to form 3-polyphenyl-4-hydroxybenzoate [21] \\ \hline _At3g24200_ & Coq6 & Flavin-dependent monooxygenases \\ \hline _At1g24340_ & CoqF & Aromatic hydroxylation of C-H in different positions in UQ biosynthesis \\ \hline _At2g30920_ & Coq3 & S-adenosylyl-l-methionine (SAM)-dependent methyl & \\ \hline _At5g57300_ & Coq5 & Transfares \\ \hline _At2g03690_ & Coq4 & Presumably a scaffold protein, which is responsible for organization of UQ biosynthetic complex [22] \\ \hline _At5g17230_ & PSY, phytoene synthase & Condensation of two molecules of GGDP to produce phytoene for further carotenoid biosynthesis \\ \hline _At4g14210_ & PDS, phytoene desaturase & Desaturation of phytoene to \(\zeta\)-carotene by introduction of four double bonds into phytoene for further carotenoid biosynthesis \\ \hline _At3g04870_ & ZDS, \(\zeta\)-carotene desaturase & Reduction of \(\zeta\)-carotene to lycopene by introduction of four double bonds for further carotenoid biosynthesis \\ \hline \hline \end{tabular}
\end{table} 
Table 1: _Arabidopsis thaliana_ genes encoding the key enzymes involved in synthesis of isoprenoid antioxidants. The transformation of IPP to DMAPP occurs both in the stroma of chloroplasts and in the matrix of mitochondria with the involvement of polyprenyl diphosphate synthase (PPS), such as geranyl diphosphate synthase (GPPS), farnesyl diphosphate synthase (FPPS), and geranylgeranyl diphosphate synthase (GGPPS) [38; 39]. These diphosphate synthases catalyze the formation of polyprenyl diphosphates with various chain lengths, making them the key enzymes in the biosynthesis of many isoprenoid compounds, such as PQ and UQ, vitamin E, carotenoids, and others [40]. \begin{table}
\begin{tabular}{c c c} \hline \hline
**Genes** & **Enzyme and Its Alternative Names in Arabidopsis** & **Functions** \\ \hline \multirow{4}{*}{_At1g06820_} & & \multirow{4}{*}{Catalyzzes cis–trans isomerization of poly-cis-carotenoids to all-trans-lycopene. Together with PDS and ZDS, CRTiso is required to complete the synthesis of lycopene from phytoene for further carotenoid biosynthesis [23; 24] \\  & & \\ \cline{2-3} \cline{2-3  
Ubiquinone Synthesis  
For the synthesis of UQ, IPP is transported to mitochondria, where further stages of UQ synthesis are carried out. In plants, the isoprene subunits for the UQ side chain are generated through the mevalonate (MVA) pathway, which takes place both in cytoplasm and peroxis (Figure 2). The produced precursors are further used for the biosynthesis of sesquiterpenes, triterpenes, sterols, and brassinosteroids [41; 42].