Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

Abstract

Recent advances allow tracking the levels and locations of a thousand proteins in individual living human cells over time using a library of annotated reporter cell clones (LARC). This library was created by Cohen et al. to study the proteome dynamics of a human lung carcinoma cell-line treated with an anti-cancer drug. Here, we report the Dynamic Proteomics database for the proteins studied by Cohen et al. Each cell-line clone in LARC has a protein tagged with yellow fluorescent protein, expressed from its endogenous chromosomal location, under its natural regulation. The Dynamic Proteomics interface facilitates searches for genes of interest, downloads of protein fluorescent movies and alignments of dynamics following drug addition. Each protein in the database is displayed with its annotation, cDNA sequence, fluorescent images and movies obtained by the time-lapse microscopy. The protein dynamics in the database represents a quantitative trace of the protein fluorescence levels in nucleus and cytoplasm produced by image analysis of movies over time. Furthermore, a sequence analysis provides a search and comparison of up to 50 input DNA sequences with all cDNAs in the library. The raw movies may be useful as a benchmark for developing image analysis tools for individual-cell dynamic-proteomics. The database is available at http://www.dynamicproteomics.net/.

Figure 1.

Tagged proteins in the LARC library are found across all cellular localizations. The localization distribution is similar to that of all known proteins. Represented are distributions of cellular localizations for: (A) all proteins in the Dynamic Proteomics database with published localizations; (B) all proteins in the GO database; (C) uncharacterized proteins in the database based on manual inspection. These proteins have no available published localization.

Figure 2.

Example of the database entry page with a detailed protein annotation for LMNA (Lamin A/C isoform 2). The protein is localized in nucleus as it can be seen on the fluorescent image (white ‘beans’). This entry includes links to four microscopy movies. In addition, the clone ID, the published and image localizations, the protein description and annotation, the eYFP insertion point, the protein dynamics following drug addition, and links to other public databases are shown on the database entry page.

Figure 3.

The alignment of protein dynamics for ACTN4 (actinin, alpha 4), GARS (glycyl-tRNA synthetase) and TOP1 (DNA topoisomerase I). (A) The dynamics is presented for the individual proteins normalized to the total fluorescence at time t = 0. (B) The alignment of protein dynamics in cytoplasm, nucleus and total protein dynamics are presented for all three proteins together.