title: Proteomic Analysis of the Ubiquitin Landscape in the Drosophila Embryonic Nervous System and the Adult Photoreceptor Cells.
abstract: BACKGROUND
  Ubiquitination is known to regulate physiological neuronal functions as well as to be involved in a number of neuronal diseases. Several ubiquitin proteomic approaches have been developed during the last decade but, as they have been mostly applied to non-neuronal cell culture, very little is yet known about neuronal ubiquitination pathways in vivo.
  
  
  RESULTS
  Using an in vivo biotinylation strategy we have isolated and identified the ubiquitinated proteome in neurons both for the developing embryonic brain and for the adult eye of Drosophila melanogaster. Bioinformatic comparison of both datasets indicates a significant difference on the ubiquitin substrates, which logically correlates with the processes that are most active at each of the developmental stages. Detection within the isolated material of two ubiquitin E3 ligases, Parkin and Ube3a, indicates their ubiquitinating activity on the studied tissues. Further identification of the proteins that do accumulate upon interference with the proteasomal degradative pathway provides an indication of the proteins that are targeted for clearance in neurons. Last, we report the proof-of-principle validation of two lysine residues required for nSyb ubiquitination.
  
  
  CONCLUSIONS
  These data cast light on the differential and common ubiquitination pathways between the embryonic and adult neurons, and hence will contribute to the understanding of the mechanisms by which neuronal function is regulated. The in vivo biotinylation methodology described here complements other approaches for ubiquitome study and offers unique advantages, and is poised to provide further insight into disease mechanisms related to the ubiquitin proteasome system.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Functional Genomics Unit, CIC bioGUNE, Derio, Spain.
authors.forename: Juanma
authors.initials: J
authors.lastname: Ramirez
authors.affiliation: Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Functional Genomics Unit, CIC bioGUNE, Derio, Spain; Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Aitor
authors.initials: A
authors.lastname: Martinez
authors.affiliation: Functional Genomics Unit, CIC bioGUNE, Derio, Spain; Mollecular Cell Biology, Turku Centre for Biotechnology, Turku, Finland.
authors.forename: Benoit
authors.initials: B
authors.lastname: Lectez
authors.affiliation: Functional Genomics Unit, CIC bioGUNE, Derio, Spain.
authors.forename: So Young
authors.initials: SY
authors.lastname: Lee
authors.affiliation: Functional Genomics Unit, CIC bioGUNE, Derio, Spain; Developmental Neurobiology, Institute of Neurosciences, CSIC/UMH, Sant Joan d'Alacant, Alicante, Spain.
authors.forename: Maribel
authors.initials: M
authors.lastname: Franco
authors.affiliation: Functional Genomics Unit, CIC bioGUNE, Derio, Spain.
authors.forename: Rosa
authors.initials: R
authors.lastname: Barrio
authors.affiliation: Max Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Dittmar
authors.affiliation: Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Leioa, Bizkaia, Spain; Functional Genomics Unit, CIC bioGUNE, Derio, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Bizkaia, Spain.
authors.forename: Ugo
authors.initials: U
authors.lastname: Mayor
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019921:Biotinylation; D015153:Blotting, Western; D002460:Cell Line; D029721:Drosophila Proteins / Q000737:chemistry / Q000378:metabolism; D004331:Drosophila melanogaster / Q000166:cytology / Q000196:embryology* / Q000378:metabolism*; D004625:Embryo, Nonmammalian / Q000378:metabolism*; D049452:Green Fluorescent Proteins / Q000378:metabolism; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D009420:Nervous System / Q000196:embryology* / Q000378:metabolism; D009474:Neurons / Q000378:metabolism; D017956:Photoreceptor Cells, Invertebrate / Q000166:cytology / Q000378:metabolism*; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D025801:Ubiquitin / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D029721:Drosophila Proteins; D025801:Ubiquitin; D049452:Green Fluorescent Proteins; D046988:Proteasome Endopeptidase Complex