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Isomerization of 9,15,9′-tri- cis -ζ-carotene mediated by 15- cis -ζ-carotene isomerase Z-ISO is a critical step in the biosynthesis of carotenoids, which define fruit color. The tomato clade ( Solanum  section Lycopersicon) comprises the cultivated tomato ( Solanum lycopersicum ) and 12 related wild species differing in fruit color and, thus, represents a good model for studying carotenogenesis in fleshy fruit. In this study, we identified homologous  Z-ISO  genes, including 5′-UTRs and promoter regions, in 12  S. lycopersicum  cultivars and 5 wild tomato species (red-fruited  Solanum pimpinellifolium , yellow-fruited  Solanum cheesmaniae , and green-fruited  Solanum chilense ,  Solanum habrochaites , and  Solanum pennellii ).  Z-ISO  homologs had a highly conserved structure, suggesting that Z-ISO performs a similar function in tomato species despite the difference in their fruit color.  Z-ISO  transcription levels positively correlated with the carotenoid content in ripe fruit of the tomatoes. An analysis of the  Z-ISO  promoter and 5′-UTR sequences revealed over 130  cis -regulatory elements involved in response to light, stresses, and hormones, and in the binding of transcription factors. Green- and red/yellow-fruited  Solanum  species differed in the number and position of  cis -elements, indicating changes in the transcriptional regulation of  Z-ISO  expression during tomato evolution, which likely contribute to the difference in fruit color.

Characterization of 15-cis-ζ-Carotene Isomerase Z-ISO in Cultivated and Wild Tomato Species Differing in Ripe Fruit Pigmentation