Localization of proteins in their natural habitat

J. Simpson, R. Pepperkok (EMBL), S. Wiemann, S. Bechtel, A. Poustka (DKFZ)

Among the greatest challenges facing biology today is the exploitation of huge amounts of genomic data, and their conversion into functional information about the proteins encoded. The German cDNA Consortium is providing a sequence validated ORF resource, encoding novel proteins of completely unknown function. This consortium clones ORFs into vectors allowing to express N- and C-terminal fusions with the green fluorescent protein (GFP).

As a first step towards the characterization of proteins we examine their subcellular localizations in living cells (Wiemann et al., 2004, Simpson et al., 2000). This data allow us  to classify the proteins into subcellular groups, determining the next steps towards a detailed functional characterization.  We have thus far localized over 1,000 different proteins in living cells, employing 4,000 different expression constructs. The localization data in many cases are the first functional information for these proteins, helping to identify targets to be funnelled into high throughput functional assay projects of SMP-Cell.

An ORF and protein-tracking database was developed, which has been expanded to the LIFEdb web-database where bioinformatic and functional (e.g. localization, cellular assays) data are made public.

Further reading (http://www.smp-cell.org/Files/Reports/SMP-Cell_Localization.pdf)