Specific association of mRNAs with the eIF3e and eIF3m complexes. (A) The eIF3 complexes shown were affinity-purified as described in the Methods section, and separated by SDS-PAGE followed by staining with Coomassie Brilliant Blue. The labeled bands were identified by LC-MS/MS. eIF3f* refers to a band in the eIF3m complex that was not identified by mass spectrometry in this experiment, and is therefore assigned based on its comigration with eIF3f identified in the eIF3e complex (right lane). eIF3f was positively identified by MALDI-TOF mass spectrometry as a subunit of the eIF3m complex in Fig. 1B. (B) The indicated eIF3e- and eIF3m-associated mRNAs were extracted from the purified complexes and employed in RT-PCR reactions using primers specific for each mRNA (see Table 3). PCR products obtained with total S. pombe RNA are shown for reference in the left panel. The factor of enrichment of each mRNA in the respective eIF3 complex and the enrichment rank (out of all 106 mRNAs enriched in either complex) are indicated below the gels.