Comparative genomics and evolutionary insights into zeaxanthin biosynthesis in two novel Flavobacterium species

During the screening of pigment-producing microbes from domestic sources, 102 yellow- or orange-pigmented bacteria were isolated. Among these, two novel Flavobacterium strains, F. sedimentum SUN046^T and F. fluvius SUN052^T, were identified as zeaxanthin producers. A polyphasic taxonomic characterization, combined with comparative genomic analysis of 45 Flavobacterium species, was conducted to determine their taxonomic positions and explore potential evolutionary relationships in zeaxanthin biosynthesis.

Both strains utilized the mevalonic acid (MVA) pathway and possessed the crt gene cluster (crtB, crtI, crtY/crtY_cd, and crtZ). Strain SUN046^T exhibited unique features in the carotenoid biosynthesis pathway, notably the absence of HMG-CoA synthase (HMGCS) in the upper MVA pathway and the presence of the rare lycopene β-cyclase crtY_cd, which is uncommon among bacteria. The CrtY_cd in SUN046^T possessed a single active site and direct lycopene-binding modes. Conversely, CrtY in SUN052^T exhibited multiple active sites, which is flavin adenine dinucleotide (FAD) dependent. These structural differences has impacted catalytic efficiencies, as evidenced by zeaxanthin yields of 6.49 µg/mL in SUN046^T and 13.23 µg/mL in SUN052^T. Variations in carotenoid biosynthetic pathway among other Flavobacterium species were also observed.

These findings suggest that both strains represent valuable new resources for zeaxanthin production and provide foundational insights for biotechnological applications involving the genus Flavobacterium, highlighting the genetic and evolutionary complexity of microbial carotenoid biosynthesis.