title: Transcriptional regulation of fruit ripening by tomato FRUITFULL homologs and associated MADS box proteins.
abstract: The tomato (Solanum lycopersicum) MADS box FRUITFULL homologs FUL1 and FUL2 act as key ripening regulators and interact with the master regulator MADS box protein RIPENING INHIBITOR (RIN). Here, we report the large-scale identification of direct targets of FUL1 and FUL2 by transcriptome analysis of FUL1/FUL2 suppressed fruits and chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip) targeting tomato gene promoters. The ChIP-chip and transcriptome analysis identified FUL1/FUL2 target genes that contain at least one genomic region bound by FUL1 or FUL2 (regions that occur mainly in their promoters) and exhibit FUL1/FUL2-dependent expression during ripening. These analyses identified 860 direct FUL1 targets and 878 direct FUL2 targets; this set of genes includes both direct targets of RIN and nontargets of RIN. Functional classification of the FUL1/FUL2 targets revealed that these FUL homologs function in many biological processes via the regulation of ripening-related gene expression, both in cooperation with and independent of RIN. Our in vitro assay showed that the FUL homologs, RIN, and tomato AGAMOUS-LIKE1 form DNA binding complexes, suggesting that tetramer complexes of these MADS box proteins are mainly responsible for the regulation of ripening.
authors.affiliation: National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan.
authors.forename: Masaki
authors.initials: M
authors.lastname: Fujisawa
authors.forename: Yoko
authors.initials: Y
authors.lastname: Shima
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Nakagawa
authors.forename: Mamiko
authors.initials: M
authors.lastname: Kitagawa
authors.forename: Junji
authors.initials: J
authors.lastname: Kimbara
authors.forename: Toshitsugu
authors.initials: T
authors.lastname: Nakano
authors.forename: Takafumi
authors.initials: T
authors.lastname: Kasumi
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Ito
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D005419:Flavonoids / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D026161:MADS Domain Proteins / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D017423:Sequence Analysis, RNA
chemical_list: D005419:Flavonoids; D026161:MADS Domain Proteins; D010940:Plant Proteins