Genomic Analysis of Carotenoid and Vitamin E Biosynthetic Pathways in the Extremophilic Red Alga Cyanidioschyzon merolae

<i>Cyanidioschyzon merolae</i>, an extremophilic unicellular red alga thriving in acidic hot springs at temperatures of 40-56 °C and pH 0.5-4.0, faces extreme oxidative stress conditions. This study presents a comprehensive genomic analysis of the carotenoid and vitamin E biosynthetic pathways, which are essential for antioxidant defense in this organism. Through comparative genomics using <i>Arabidopsis thaliana</i> sequences as queries, we identified and characterized genes encoding key enzymes involved in their metabolism. Our analysis reveals that <i>C. merolae</i> exclusively utilizes the methylerythritol-4-phosphate (MEP) pathway for isoprenoid biosynthesis and lacks a complete mevalonate (MVA) pathway. We identified eleven genes involved in terpenoid metabolism and seven genes specifically for carotenoid biosynthesis. Pigment analysis confirmed a streamlined carotenoid profile consisting solely of β-carotene, β-cryptoxanthin, and zeaxanthin, lacking the entire β,ε-branch and part of the β,β-branch. The complete tocopherol biosynthetic pathway produces exclusively α-tocopherol. The absence of the β,ε-carotenoid branch and the exclusive production of α-tocopherol demonstrate metabolic streamlining while maintaining antioxidant efficacy. These findings provide molecular blueprints for biotechnological applications, enabling targeted strategies to enhance antioxidant production through pathway optimization and metabolic engineering, while offering insights into developing stress-tolerant organisms and enhancing nutritional content in crops.