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Metabolic pathways

Last update on the 30th of April, 2018

A metabolic pathway of carotenoid biosynthesis is studied in KEGG database.

Basic information about the pathway

The carotenoid biosynthesis pathway is stored in KEGG DB under map00906 accession and shown in figure 1. Carotenoids are plant isoprenoid pigments possessing extended conjugated polyene bonds. Main functions are photoprotection and light collection in chloroplasts. The initial compound is geranyl-geranyl diphosphate (GGPP) that is synthesized from isopentenyl diphosphate and dimethylallyl diphosphate in terpenoid backbone biosynthesis.

Fig. 1. Reference pathway of carotenoid biosynthesis.
Hub compounds are circled, significant output compounds are starred. The reaction (see below) is coloured with red. Links with other pathways are placed in rectangles.

The information about significant output compounds is provided in table 1.

Table 1. Significant output compounds.
Compound Function
Beta-carotene Energy transmission from chlorophyll
Antioxidant
Abscisic acid Plant hormone
Stress and pathogen response
Lutein Absorbtion of additional light
Photoprotection
Antioxidant
Astaxanthin Antioxidant

This pathway is connected with terpenoid backbone synthesis at its start and with retinol metabolism in animals at beta-carotene.

The pathway in life domains

Three organisms from distinct domains were chosen (table 2) to study the carotenoid biosynthesis pathway.

Table 2. Organisms implementing the pathway
Domain Species Lineage
Archaea Sulfolobus solfactricus SULA Crenarchaeota
Bacteria Streptomyces glaucescens Actinobacteria
Eukaryota Arabidopsis thaliana Plantae, Angiospermae
Fig. 2. Reactions of carotenoid biosynthesis pathwat implemented in A. thaliana.
Participating enzymes are coloured green, consequtive reactions are linked with red lines.
Fig. 3. Reactions of carotenoid biosynthesis pathwat implemented in S. glaucescens.
Participating enzymes are coloured green, consequtive reactions are linked with red lines.
Fig. 4. Reactions of carotenoid biosynthesis pathwat implemented in S. solfactaricus SULA.
Participating enzymes are coloured green, consequtive reactions are linked with red lines.

Reactions specific to chosen organisms are shown in figures 2-4. All three organisms are able to synthesize lycopene from GGPP. The archaeon and the bacterium are unable to synthesize abscisic acid (as they do not need it) and have no direct connection from lycopene to lutein. The bacterium and the plant can synthesize beta-carotene and 7,8-dihydro-beta-carotene as well as the plant and the archaeon can synthesize astaxanthin. So, these organisms are able to execute some finished parts of the reference pathway.

Neurosporene desaturation in KEGG DB

The neurosporene desaturation (R04800) is the last step in lycopene biosynthesis (fig. 1) and carried out by zeta-carotene desaturase (EC1.3.5.6). The sceme of the reaction is provided in figure 5.

Fig. 5. Reaction of neurosporene desaturation (R04800).
The acceptor is not provided in KEGG; it is probably quinone. The changing bond is circled.