title: Unraveling the target genes of RIN transcription factor during tomato fruit ripening and softening.
abstract: BACKGROUND
  The RIN transcription factor is one of the MADS box family members and predominantly controls fruit ripening. In this study, effort was made to demonstrate the regulation network of RIN transcription factor during tomato fruit ripening and softening. Novel RIN target genes were identified by proteomics, electrophoresis mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) analysis.
  
  
  RESULTS
  Over 700 protein spots were achieved by two-dimensional gel electrophoresis, and 42 proteins were successfully identified. Among them, 1-aminocyclopropane-1-carboxylate oxidase (LeACO4, ethylene synthesis, spot 3) and α-galactosidase-like isoform 2 (α-Gal, cell wall metabolism, spot 26) exhibited varied expression levels in different tomato fruits. Particularly high expression levels of LeACO4 and α-Gal were observed in wild type but not in the rin mutant. Additionally, CArG box, a RIN-binding site, was discovered in the promoter regions of both LeACO4 and α-Gal genes, suggesting that RIN possibly directly regulates their transcriptions, and this assumption was further confirmed by EMSA and ChIP assay.
  
  
  CONCLUSIONS
  Functional annotations of RIN target genes demonstrated the specific role of RIN in the process of fruit ripening and softening, especially in cell wall degradation and ethylene biosynthesis. This study will further illuminate the mechanism of tomato ripening and softening. © 2016 Society of Chemical Industry.
authors.affiliation: College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China.|Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Li
authors.affiliation: Institute of Microbiology Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
authors.forename: Xiaoguang
authors.initials: X
authors.lastname: Wang
authors.affiliation: School of Agricultural Engineering & Food Science, Shandong University of Technology, No. 266 Xincun West Road, Zibo, 255049, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China.|Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China.
authors.forename: Mei
authors.initials: M
authors.lastname: Guo
authors.affiliation: College of Food Science and Biotechnology, Tianjin Agricultural University, No. 22 Jinjing Road, Tianjin, 300384, China.|Tianjin Engineering Research Center of Agricultural Products Processing, No. 22 Jinjing Road, Tianjin, 300384, China.
authors.forename: Tieling
authors.initials: T
authors.lastname: Liu
mesh_terms: D000594:Amino Acid Oxidoreductases / Q000235:genetics / Q000378:metabolism*; D002473:Cell Wall / Q000378:metabolism; D055598:Chemical Phenomena; D047369:Chromatin Immunoprecipitation; D015180:Electrophoresis, Gel, Two-Dimensional; D024202:Electrophoretic Mobility Shift Assay; D005030:Ethylenes / Q000096:biosynthesis; D063427:Food Quality; D005638:Fruit / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D018551:Solanum lycopersicum / Q000737:chemistry / Q000254:growth & development / Q000378:metabolism*; D026161:MADS Domain Proteins / Q000235:genetics / Q000378:metabolism*; D055595:Mechanical Phenomena; D009154:Mutation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D040901:Proteomics / Q000379:methods; D020218:Response Elements; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D057825:Two-Dimensional Difference Gel Electrophoresis; D000519:alpha-Galactosidase / Q000235:genetics / Q000378:metabolism*
chemical_list: D005030:Ethylenes; D007527:Isoenzymes; D026161:MADS Domain Proteins; D010940:Plant Proteins; D014157:Transcription Factors; C036216:ethylene; D000594:Amino Acid Oxidoreductases; C059460:1-aminocyclopropane-1-carboxylic acid oxidase; D000519:alpha-Galactosidase
keywords: LeACO4; RIN transcription factor; fruit ripening; tomato; α-Gal