title: Tomato nuclear proteome reveals the involvement  of specific E2 ubiquitin-conjugating enzymes in  fruit ripening.
abstract: BACKGROUND
  Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits.
  
  
  RESULTS
  Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening.
  
  
  CONCLUSIONS
  Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
authors.forename: Yuying
authors.initials: Y
authors.lastname: Wang
authors.forename: Weihao
authors.initials: W
authors.lastname: Wang
authors.forename: Jianghua
authors.initials: J
authors.lastname: Cai
authors.forename: Yanrui
authors.initials: Y
authors.lastname: Zhang
authors.forename: Guozheng
authors.initials: G
authors.lastname: Qin
authors.forename: Shiping
authors.initials: S
authors.lastname: Tian
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000166:cytology / Q000502:physiology*; D005810:Multigene Family; D009154:Mutation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics; D044763:Ubiquitin-Conjugating Enzymes / Q000235:genetics / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D010940:Plant Proteins; D020543:Proteome; D044763:Ubiquitin-Conjugating Enzymes