Position of fusion proteins in the gel is indicated with stars. Chosen clones obtained after integrations of the cassettes were monitored by western blot to confirm the presence of the fusion proteins (Figure  1B). Additionally it was verified that C-terminal TAP tag fusion does not affect RNase R induction after temperature downshift (Figure  1C). The first purifications were performed according

to the standard TAP tag procedures [15]. We detected sufficient amounts of target proteins in the final elutions in the case of both fusion proteins (Figure  1D). Analysis of Coomassie-stained SDS-PAGE gels showed almost no background on the RNase R GFP fusion purification this website which proved specificity of the method used. In the case of the RpoC TAP fusion we saw enrichment on other RNAP subunits in the final elutions. One of the bands was extracted and mass spectrometry analysis proved that it corresponded to the RNAP subunit RpoA. In the RNase R-TAP fusion purification we mainly detected our Selleckchem GDC-0994 target protein in the final

elution, although there was some background enrichment compared to RNase R-GFP preparation. This result suggests that RNase R does not form stable complexes and that eventual interactions are rather transient. Similar results were obtained in several independent experiments using cells grown under different conditions (cold shock, exponential or stationary phase), and varying the amount of the background signal between the experiments (data not shown). Even though stable complexes formed by RNase R were not detected, some bands were found to be enriched in the RNase R-TAP preparation in relation to RNase R-GFP and RpoC-TAP. One of these bands was extracted from the gel and subjected to mass spectrometry analysis;

which resulted in the detection of three ribosomal proteins: RpsD, RpsC and RplC (Figure  1D). RNase R does not form stable complexes but it does co-purify with ribosomal proteins In order to obtain more comprehensive information about the transient interactions caused by RNase R we subjected the whole elution fraction to mass spectrometry analysis. For this analysis we chose the material obtained from cells subjected to cold shock treatment, since in this condition purification 17-DMAG (Alvespimycin) HCl was the most efficient, probably due to increased levels of cellular RNase R [6]. We detected 212 proteins in the RNase R-TAP elution and 65 proteins in the control RpoC-TAP elution. Mass-spectrometry data were subsequently subjected to the label free quantification using MaxQuant software [18], which allowed relative values to be obtained that corresponded to the amount of each protein in the sample (intensity values). In the graphical representation of the results the intensity values of the proteins identified in RNase R and RpoC samples were plotted against the specificity value of the protein in the samples.