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Flavonoids are ubiquitous secondary metabolites in plants and possess a wide range of biological activities such as anti-oxidant, anti-microbial, and anti-cancer activities. As a food ingredient, flavonoids are also thought to have health-promoting and disease-preventing properties. Structural modifications of flavonoids can improve their biological activities. Methylation is a common flavonoid modification that is catalyzed by Omethyltransferases (OMTs). We isolated four putative OMTs from the miniature tomato cultivar Micro-Tom. One OMT (SlOMT3)was successfully expressed in E. coli and purified. Recombinant SlOMT3 was found to be a regiospecific flavonoid 3'/5'-Omethyltransferase. Biochemical parameters show that SlOMT3has higher binding affinity and catalytic efficiency for quercetin and luteolin than for eriodictyol. This suggests that flavonols and flavones are preferable substrates for SlOMT3. Biotransformation is considered a promising method to modify flavonoid structures. Transgenic E. coli expressing SlOMT3 was used to modify flavonoid substrates and was found to efficiently convert quercetin, luteolin, and eriodictyol to isorhamnetin, chrysoeriol and homoeriodictyol, respectively.