Most enzymes in the central pathway of carotenoid biosynthesis in plants have been identified and studied at the molecular level. However, the specificity and role of cis-trans-isomerization of carotenoids, which occurs in vivo during carotene biosynthesis, remained unresolved. We have previously cloned from tomato (Solanum lycopersicum) the CrtISO gene, which encodes a carotene cis-trans-isomerase. To study the biochemical properties of the enzyme, we developed an enzymatic in vitro assay in which a purified tomato CRTISO polypeptide overexpressed in Escherichia coli cells is active in the presence of an E. coli lysate that includes membranes. We show that CRTISO is an authentic carotene isomerase. Its catalytic activity of cis-totrans isomerization requires redox-active components, suggesting that isomerization is achieved by a reversible redox reaction acting at specific double bonds. Our data demonstrate that CRTISO isomerizes adjacent cis-double bonds at C7 and C9 pairwise into the trans-configuration, but is incapable of isomerizing single cis-double bonds at C9 and C9#. We conclude that CRTISO functions in the carotenoid biosynthesis pathway in parallel with z-carotene desaturation, by converting 7,9,9#-tri-cisneurosporene to 9#-cis-neurosporene and 7#9#-di-cis-lycopene into all-trans-lycopene. These results establish that in plants carotene desaturation to lycopene proceeds via cis-carotene intermediates.Carotenoids comprise a large group of terpenoid pigments synthesized by all plants algae and cyanobacteria as well as by several nonphotosynthetic bacteria and fungi. Carotenoids fulfill indispensable functions in photosynthesis (Frank et al., 1999), and in plants they also provide colors to flowers and fruits. Dietary carotenoids are essential precursors to vitamin A, and they are implicated in reducing the occurrence of certain cancers and cardiovascular diseases, possibly by serving as antioxidants and free radical scavengers (for review, see Demmig-Adams and Adams, 2002; Fraser and Bramley, 2004).Our understanding of the carotenoid biosynthetic pathway in plants has been advanced greatly in the past decade, mainly due to cloning of many of the genes for enzymes involved in the pathway. The first carotenoid in the pathway is phytoene, a product of condensation of two geranylgeranyl diphosphate (GGDP) molecules. The colorless phytoene undergoes four consecutive dehydrogenation reactions that introduce four double bonds in conjugation, giving rise to the red polyene chromophore of lycopene, the precursor of a diverse group of cyclic carotenoids. In plants, two desaturases, phytoene desaturase (PDS) and z-carotene desaturase (ZDS), carry out these reactions, whereas in bacteria all four dehydrogenation reactions are carried out by a single gene product, named CRTI (for review, see Hirschberg, 2001). Most plant carotenoids carry trans-configured double bonds. However, specific cis-isomers do exist, for example, 9-cis-neoxanthin in the light-harvesting complex (Liu et al., 2004;Snyder et al., 2004) and 9-c...