title: Systems biology of tomato fruit development: combined transcript, protein, and metabolite analysis of tomato transcription factor (nor, rin) and ethylene receptor (Nr) mutants reveals novel regulatory interactions.
abstract: Tomato (Solanum lycopersicum) is an established model to study fleshy fruit development and ripening. Tomato ripening is regulated independently and cooperatively by ethylene and transcription factors, including nonripening (NOR) and ripening-inhibitor (RIN). Mutations of NOR, RIN, and the ethylene receptor Never-ripe (Nr), which block ethylene perception and inhibit ripening, have proven to be great tools for advancing our understanding of the developmental programs regulating ripening. In this study, we present systems analysis of nor, rin, and Nr at the transcriptomic, proteomic, and metabolomic levels during development and ripening. Metabolic profiling marked shifts in the abundance of metabolites of primary metabolism, which lead to decreases in metabolic activity during ripening. When combined with transcriptomic and proteomic data, several aspects of the regulation of metabolism during ripening were revealed. First, correlations between the expression levels of a transcript and the abundance of its corresponding protein were infrequently observed during early ripening, suggesting that posttranscriptional regulatory mechanisms play an important role in these stages; however, this correlation was much greater in later stages. Second, we observed very strong correlation between ripening-associated transcripts and specific metabolite groups, such as organic acids, sugars, and cell wall-related metabolites, underlining the importance of these metabolic pathways during fruit ripening. These results further revealed multiple ethylene-associated events during tomato ripening, providing new insights into the molecular biology of ethylene-mediated ripening regulatory networks.
authors.affiliation: Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany.
authors.forename: Sonia
authors.initials: S
authors.lastname: Osorio
authors.forename: Rob
authors.initials: R
authors.lastname: Alba
authors.forename: Cynthia M B
authors.initials: CM
authors.lastname: Damasceno
authors.forename: Gloria
authors.initials: G
authors.lastname: Lopez-Casado
authors.forename: Marc
authors.initials: M
authors.lastname: Lohse
authors.forename: Maria Inés
authors.initials: MI
authors.lastname: Zanor
authors.forename: Takayuki
authors.initials: T
authors.lastname: Tohge
authors.forename: Björn
authors.initials: B
authors.lastname: Usadel
authors.forename: Jocelyn K C
authors.initials: JK
authors.lastname: Rose
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.forename: Alisdair R
authors.initials: AR
authors.lastname: Fernie
mesh_terms: D002473:Cell Wall / Q000378:metabolism; D005030:Ethylenes / Q000378:metabolism*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018551:Solanum lycopersicum / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D055442:Metabolome; D010940:Plant Proteins / Q000378:metabolism*; D020543:Proteome; D012333:RNA, Messenger / Q000378:metabolism*; D049490:Systems Biology; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D005030:Ethylenes; D010940:Plant Proteins; D020543:Proteome; D012333:RNA, Messenger; D014157:Transcription Factors; C036216:ethylene