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Deinococcus radiodurans strain R1 utilizes multiple antioxidants including a unique carotenoid, deinoxanthin, to fight again oxidative stress. Most of the enzymes involved in the deinoxanthin biosynthetic pathway have been identified. However, the enzyme catalysing the synthesis of geranylgeranyl diphosphate (GGPP), which is a precursor of carotenoid biosynthesis, has yet to be identified. Two putative isoprenyl diphosphate synthases (IPPS) homologues (DR1395 and DR932) were screened out by analysis of conserved amino acid regions, and their biochemical functions were investigated. Gene mutation, gene expression in Escherichia coli and analysis of carotenoid products were used to investigate the functions of these candidates. The results suggested that DR1395 encodes the protein for GGPP synthesis. Site-directed mutant analysis indicated that the amino acid composition of and around the first aspartate-rich motif is vital for GGPP synthase function.Deinococcus radiodurans strain R1 produces a unique carotenoid product, deinoxanthin, as an antioxidant. In this study, DR1395 was identified as the gene encoding geranylgeranyl diphosphate synthase (GGPPS) for entrance to deinoxanthin biosynthesis in D. radiodurans. Moreover, site-directed mutagenesis studies on DR1395 identified the effect of amino acid composition of the aspartate-rich motif on the production of this carotenoid. This study demonstrated the entrance step in the deinoxanthin biosynthetic pathway. These results can be useful in genetic engineering strategies for deinoxanthin production including enhancement of GGPPS gene expression in D. radiodurans.