Previous studies have demonstrated that the a subunit of eukaryotic initiation factor 2 (eIF-2a), encoded by the SUI2 gene in the yeast Saccharomyces cerevisiae, is phosphorylated at Ser-51 by the GCN2 kinase in response to general amino acid control. Here we describe that yeast eIF-2a is a constitutively phosphorylated protein species that is multiply phosphorylated by a GCN2-independent mechanism. 32p; labeling and isoelectric focusing analysis of a SUI2+ Agcn2 strain identifies eIF-2ot as radiolabeled and a single isoelectric protein species. Treatment of SUI2+ Agcn2 strain extracts with phosphatase results in the identification of three additional isoelectric forms of eIF-2a that correspond to the stepwise removal of three phosphates from the protein. These data strongly support the conclusion that casein kinase II directly phosphorylates eIF-2oa at one or all of these Ser amino acids in vivo. Although substitution of SUI2 genes mutated at these sites for the wild-type gene have no obvious effect on cell growth, one test that we have used appears to demonstrate that the inability to phosphorylate these sites has a physiological consequence on eIF-2 function in S. cerevisiae. Haploid strains constructed to contain Ser-to-Ala mutations at the consensus casein kinase II sequences in SUI2 in combination with a mutated allele of either the GCN2, GCN3, or GCD7 gene have synthetic growth defects. These genetic data appear to indicate that the modifications that we describe at the carboxyl end of the eIF-2a protein are required for optimal eIF-2 function in S. cerevisiae.Eukaryotic translation initiation factor 2 (eIF-2) has been extensively characterized at the biochemical and genetic levels. Biochemical studies have established eIF-2 to be composed of three nonidentical subunits, cx, 1, and y, that function during the early steps of translation initiation by forming a ternary complex with GTP and the initiator tRNA (reviewed in references 29 and 39). This complex then binds the 40S ribosomal subunit, which in turn binds the 5' end of mRNA. According to the scanning model, this preinitiation complex scans the leader region until the first AUG codon is reached, whereupon translation begins (reviewed in references 33 and 34). Genetic studies from our laboratory have implicated eIF-2 to also play a role in ribosomal recognition of an AUG start codon. By reverting his4-initiator codon mutants, three unlinked genes, suil, sui2, and SUI3, were identified that when mutated act in trans to restore his4 expression (12). Characterization of the SUI2 and SUI3 genes showed that they encoded the a and a subunits of eIF-2, which are 42 and 58% identical in amino acid sequence to the human eIF-2oa and -13 proteins, respectively (17,25). Further analysis demonstrated that suppressor mutations in these genes conferred the ability to the ribosome to initiate translation at a UUG codon in the early his4 coding region by allowing a mismatched base pair interaction between the UUG codon and the initiator tRNA (17,25,63). The mutations ...