Tandem affinity purification (TAP) is a generic two-step affinity purification protocol that enables the isolation of protein complexes under close-to-physiological conditions for subsequent analysis by mass spectrometry. Although TAP was instrumental in elucidating the yeast cellular machinery, in mammalian cells the method suffers from a low overall yield. We designed several dual-affinity tags optimized for use in mammalian cells and compared the efficiency of each tag to the conventional TAP tag. A tag based on protein G and the streptavidin-binding peptide (GS-TAP) resulted in a tenfold increase in protein-complex yield and improved the specificity of the procedure. This allows purification of protein complexes that were hitherto not amenable to TAP and use of less starting material, leading to higher success rates and enabling systematic interaction proteomics projects. Using the well-characterized Ku70-Ku80 protein complex as an example, we identified both core elements as well as new candidate effectors.

Cells that are taken from the nucleus pulposus (NP) and that are allowed to proliferate in monolayer cultures often exhibit changes in their cell morphology and matrix-protein synthesis. However, whether concomitant alterations occur with respect to their mRNA levels for collagen I (CI), collagen II (CII) and aggrecan (AGG) is unclear. In this study, human NP cells from seven individuals were cultured in monolayers and specific mRNAs for CI, CII and AGG were quantified by real-time polymerase chain reaction in fresh NP tissue and during four passages of NP-cell culture. In addition, the presence of CI, CII and AGG protein was determined by immunofluorescence staining of NP cells. We found a significant reduction of CI, CII and AGG mRNA after the initiation of culture in DMEM compared with mRNA levels in fresh NP tissue. During passages 2--4, no further reduction of mRNA levels for CII and AGG was observed. The mRNA level for CI was reduced significantly with duration of culture. Immunofluorescence staining of cultured NP cells revealed expression of CI, CII and AGG protein during the whole culture period. Our data thus demonstrate a reduction of specific mRNA for matrix proteins during the initiation of NP-cell culture but the stable expression of the key matrix proteins, CII and AGG, during further expansion of the cells in monolayers, suggesting no functional changes occur in cultured NP cells.

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