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Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2705-10. doi: 10.1073/pnas.1421567112. Epub 2015 Feb 17.

Cell-specific proteomic analysis in Caenorhabditis elegans.

Author information

1
Divisions of Chemistry and Chemical Engineering and.
2
Biology and Biological Engineering, Howard Hughes Medical Institute, and.
3
Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125; and.
4
Max Planck Institute for Brain Research, D-60528 Frankfurt am Main, Germany.
5
Divisions of Chemistry and Chemical Engineering and tirrell@caltech.edu.

Abstract

Proteomic analysis of rare cells in heterogeneous environments presents difficult challenges. Systematic methods are needed to enrich, identify, and quantify proteins expressed in specific cells in complex biological systems including multicellular plants and animals. Here, we have engineered a Caenorhabditis elegans phenylalanyl-tRNA synthetase capable of tagging proteins with the reactive noncanonical amino acid p-azido-L-phenylalanine. We achieved spatiotemporal selectivity in the labeling of C. elegans proteins by controlling expression of the mutant synthetase using cell-selective (body wall muscles, intestinal epithelial cells, neurons, and pharyngeal muscle) or state-selective (heat-shock) promoters in several transgenic lines. Tagged proteins are distinguished from the rest of the protein pool through bioorthogonal conjugation of the azide side chain to probes that permit visualization and isolation of labeled proteins. By coupling our methodology with stable-isotope labeling of amino acids in cell culture (SILAC), we successfully profiled proteins expressed in pharyngeal muscle cells, and in the process, identified proteins not previously known to be expressed in these cells. Our results show that tagging proteins with spatiotemporal selectivity can be achieved in C. elegans and illustrate a convenient and effective approach for unbiased discovery of proteins expressed in targeted subsets of cells.

KEYWORDS:

cell-specific protein expression; click chemistry; nematode pharyngeal muscle; protein engineering; proteomics

PMID:
25691744
PMCID:
PMC4352802
DOI:
10.1073/pnas.1421567112
[Indexed for MEDLINE]
Free PMC Article

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