CK2 phosphorylates a wide variety of substrates, including translation initiation factors. A mass spectrometric approach was used to identify residues phosphorylated by CK2, which may regulate the activity of initiation factors during the translation initiation process in plants. CK2 in vitro phosphorylation sites were identified in wheat and Arabidopsis thaliana eIF2␣, eIF2, eIF5, and wheat eIF3c. Native wheat eIF5 and eIF2␣ were found to have phosphorylation sites that corresponded to some of the in vitro CK2 phosphorylation sites. A large number of the CK2 sites identified in this study are in conserved binding domains that have been implicated in the yeast multifactor complex (eIF1-eIF3-eIF5-eIF2-GTP-Met-tRNA i Met ). This is the first study to demonstrate that plant initiation factors are capable of forming a multifactor complex in vitro. In addition, the interaction of factors within these complexes was enhanced both in vitro and in native extracts by phosphorylation of one or more initiation factors by CK2. The importance of CK2 phosphorylation of eIF5 was evaluated by site-directed mutagenesis of eIF5 to remove CK2 phosphorylation sites. Removal of CK2 phosphorylation sites from eIF5 inhibits the CK2-mediated increase in eIF5 interaction with eIF1 and eIF3c in pulldown assays and reduces the eIF5-mediated stimulation of translation initiation in vitro. These results suggest a functional role for CK2 phosphorylation in the initiation of plant translation.Translation initiation is a critical, rate-limiting step in eukaryotic gene expression, with a key step early in the pathway being the assembly of the 43 S preinitiation complex (1, 2). This 43 S preinitiation complex is composed of the small 40 S ribosomal subunit, eIF1, eIF1A, the eIF2-GTP-Met-tRNA i Met ternary complex, eIF3, and eIF5. Biochemical data from yeast suggest that a multifactor complex (MFC) 2 consisting of eIF3-eIF1-eIF5-eIF2-GTP-Met-tRNA i Met exists free of the ribosome allowing these factors to be simultaneously loaded onto the 40 S ribosomal subunit (3). Mutations that disrupt the interaction of factors within this complex result in substantial reductions in translation initiation (3, 4). Using a variety of in vitro binding assays, two-hybrid analysis, and in vivo purification of affinity-tagged subunits, an extensive analysis of the subunit interactions within the yeast MFC has resulted in a provisional model of the yeast MFC (5). The yeast eIF3c (NIP1) N-terminal domain plays a particularly important role in binding to other initiation factors in the context of the multifactor complex (6). The NIP1 N-terminal domain was found to bind directly to both eIF1 and eIF5 (7,8), and it is suspected that this binding coordinates the interaction between eIF1 and eIF5 that is responsible for the inhibition of GTP hydrolysis at non-AUG codons (6). The C-terminal domain (CTD) of yeast eIF5 simultaneously binds to both the N terminus of eIF3c, the N-terminal K-boxes of eIF2, and eIF1 (3, 9). This creates an indirect link between eIF3c and eIF2,...