title: Neofunctionalization of Chromoplast Specific Lycopene Beta Cyclase Gene (CYC-B) in Tomato Clade.
abstract: The ancestor of tomato underwent whole genome triplication ca. 71 Myr ago followed by widespread gene loss. However, few of the triplicated genes are retained in modern day tomato including lycopene beta cyclase that mediates conversion of lycopene to β-carotene. The fruit specific β-carotene formation is mediated by a chromoplast-specific paralog of lycopene beta cyclase (CYC-B) gene. Presently limited information is available about how the variations in CYC-B gene contributed to its neofunctionalization. CYC-B gene in tomato clade contained several SNPs and In-Dels in the coding sequence (33 haplotypes) and promoter region (44 haplotypes). The CYC-B gene coding sequence in tomato appeared to undergo purifying selection. The transit peptide sequence of CYC-B protein was predicted to have a stronger plastid targeting signal than its chloroplast specific paralog indicating a possible neofunctionalization. In promoter of two Bog (Beta old gold) mutants, a NUPT (nuclear plastid) DNA fragment of 256 bp, likely derived from a S. chilense accession, was present. In transient expression assay, this promoter was more efficient than the "Beta type" promoter. CARGATCONSENSUS box sequences are required for the binding of the MADS-box regulatory protein RIPENING INHIBITOR (RIN). The loss of CARGATCONSENSUS box sequence from CYC-B promoter in tomato may be related to attenuation of its efficiency to promote higher accumulation of β-carotene than lycopene during fruit ripening.
authors.affiliation: Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
authors.forename: Vijee
authors.initials: V
authors.lastname: Mohan
authors.affiliation: Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
authors.forename: Arun
authors.initials: A
authors.lastname: Pandey
authors.affiliation: Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
authors.forename: Yellamaraju
authors.initials: Y
authors.lastname: Sreelakshmi
authors.affiliation: Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
authors.forename: Rameshwar
authors.initials: R
authors.lastname: Sharma
mesh_terms: D001483:Base Sequence; D002338:Carotenoids / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics; D005638:Fruit / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D019753:Intramolecular Lyases / Q000235:genetics*; D000077276:Lycopene; D018551:Solanum lycopersicum / Q000235:genetics*; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics; D018087:Plastids / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics; D019207:beta Carotene / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D019207:beta Carotene; D002338:Carotenoids; D019753:Intramolecular Lyases; C070925:lycopene cyclase-isomerase; D000077276:Lycopene