title: NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans.
abstract: The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.
authors.affiliation: ¶Genome Center.
authors.forename: Timothy W
authors.initials: TW
authors.lastname: Rhoads
authors.affiliation: ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706;
authors.forename: Aman
authors.initials: A
authors.lastname: Prasad
authors.affiliation: From the Departments of ‡Chemistry, ¶Genome Center.
authors.forename: Nicholas W
authors.initials: NW
authors.lastname: Kwiecien
authors.affiliation: ¶Genome Center.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Merrill
authors.affiliation: ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853.
authors.forename: Kelson
authors.initials: K
authors.lastname: Zawack
authors.affiliation: ¶Genome Center.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Westphall
authors.affiliation: ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853.
authors.forename: Frank C
authors.initials: FC
authors.lastname: Schroeder
authors.affiliation: ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706;
authors.forename: Judith
authors.initials: J
authors.lastname: Kimble
authors.affiliation: From the Departments of ‡Chemistry, §Biomolecular Chemistry, ¶Genome Center, jcoon@chem.wisc.edu.
authors.forename: Joshua J
authors.initials: JJ
authors.lastname: Coon
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D017173:Caenorhabditis elegans / Q000737:chemistry / Q000187:drug effects* / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry; D020387:Food Chain; D006017:Glycolipids / Q000494:pharmacology*; D007553:Isotope Labeling / Q000379:methods; D008239:Lysine / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D010675:Pheromones / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D010766:Phosphorylation; D025941:Protein Interaction Mapping; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D040901:Proteomics / Q000379:methods
chemical_list: D029742:Caenorhabditis elegans Proteins; D006017:Glycolipids; D010675:Pheromones; D010750:Phosphoproteins; D020543:Proteome; D008239:Lysine