title: Proteomics and transcriptomics analyses of Arabidopsis floral buds uncover important functions of ARABIDOPSIS SKP1-LIKE1.
abstract: BACKGROUND
  The ARABIDOPSIS SKP1-LIKE1 (ASK1) protein functions as a subunit of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligases. Previous genetic studies showed that ASK1 plays important roles in Arabidopsis flower development and male meiosis. However, the molecular impact of ASK1-containing SCF E3 ubiquitin ligases (ASK1-E3s) on the floral proteome and transcriptome is unknown.
  
  
  RESULTS
  Here we identified proteins that are potentially regulated by ASK1-E3s by comparing floral bud proteomes of wild-type and the ask1 mutant plants. More than 200 proteins were detected in the ask1 mutant but not in wild-type and >300 were detected at higher levels in the ask1 mutant than in wild-type, but their RNA levels were not significantly different between wild-type and ask1 floral buds as shown by transcriptomics analysis, suggesting that they are likely regulated at the protein level by ASK1-E3s. Integrated analyses of floral proteomics and transcriptomics of ask1 and wild-type uncovered several potential aspects of ASK1-E3 functions, including regulation of transcription regulators, kinases, peptidases, and ribosomal proteins, with implications on possible mechanisms of ASK1-E3 functions in floral development.
  
  
  CONCLUSIONS
  Our results suggested that ASK1-E3s play important roles in Arabidopsis protein degradation during flower development. This study opens up new possibilities for further functional studies of these candidate E3 substrates.
authors.affiliation: Intercollege Graduate Degree Program in Plant Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, PA, 16802, USA. ludihong123@gmail.com.
authors.forename: Dihong
authors.initials: D
authors.lastname: Lu
authors.affiliation: Department of Biology, the Pennsylvania State University, University Park, PA, 16802, USA. wzb1@berkeley.edu.|Current address: Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA. wzb1@berkeley.edu.
authors.forename: Weimin
authors.initials: W
authors.lastname: Ni
authors.affiliation: Section of Research Resources, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. bstanley@psu.edu.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Stanley
authors.affiliation: State Key Laboratory of Genetic Engineering and Institute of Plant Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China. hongma@fudan.edu.cn.
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000502:physiology*; D035264:Flowers / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D009154:Mutation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D055550:Protein Stability; D040901:Proteomics; D012269:Ribosomal Proteins / Q000378:metabolism; D059467:Transcriptome; D044767:Ubiquitin-Protein Ligases / Q000378:metabolism
chemical_list: C120363:ASK1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D010940:Plant Proteins; D012269:Ribosomal Proteins; D044767:Ubiquitin-Protein Ligases