Matrix-assisted laser desorption/ionization time-offlight mass spectrometry was used to determine the state of N-terminal acetylation of 68 ribosomal proteins from a normal strain of Saccharomyces cerevisiae and from the ard1-⌬, nat3-⌬, and mak3-⌬ mutants (4), each lacking a catalytic subunit of three different N-terminal acetyltransferases. A total 30 of the of 68 ribosomal proteins were N-terminal-acetylated, and 24 of these (80%) were NatA substrates, unacetylated in solely the ard1-⌬ mutant and having mainly Ac-Ser-termini and a few with Ac-Ala-or Ac-Thr-termini. Only 4 (13%) were NatB substrates, unacetylated in solely the nat3-⌬ mutant, and having Ac-Met-Asp-or Ac-Met-Glu-termini. No NatC substrates were uncovered, e.g. unacetylated in solely mak3-⌬ mutants, consistent with finding that none of the ribosomal proteins had Ac-Met-Ile-, Ac-Met-Leu-, or Ac-Met-Phe-termini. Interestingly, two new types of the unusual NatD substrates were uncovered, having either Ac-Ser-Asp-Phe-or Ac-Ser-Asp-Ala-termini that were unacetylated in the ard1-⌬ mutant, and only partially acetylated in the mak3-⌬ mutant and, for one case, also only partially in the nat3-⌬ mutant. We suggest that the acetylation of NatD substrates requires not only Ard1p and Nat1p, but also auxiliary factors that are acetylated by the Mak3p and Nat3p N-terminal acetyltransferases.Cleavage of N-terminal 1 methionine residues and N-terminal acetylation are the most common modifications, occurring cotranslationally on the vast majority of eukaryotic proteins. Methionine is cleaved from penultimate residues having radii of gyration of 1.29 Å or less, resulting in N-terminal residues of glycine, alanine, serine, cysteine, threonine, proline, and valine (1-3). Subsequently, N-terminal acetylation occurs on some but not all proteins containing N-terminal residues of methionine, serine, alanine, glycine, or threonine. We are determining the amino acid sequence requirements for N-terminal acetylation and the NATs (N-terminal acetyltransferases) responsible for this modification in the yeast Saccharomyces cerevisiae. Polevoda et al. (4) have investigated Ard1p, Nat3p, and Mak3p, which are related to each other by amino acid sequence, and which are believed to be the catalytic subunits of three different NATs, each acting on different sets of proteins having different N-terminal regions. Certain proteins, which are normally N-terminal acetylated, lack this modification in mutants deleted in one or an other of these NAT genes. Subclasses of proteins with Ser-, Ala-, Gly-or Thr-termini are not acetylated in ard1-⌬ mutants (NatA substrates) (4); proteins with Met-Glu-or Met-Asp-termini and subclasses of proteins with Met-Asn-termini are not acetylated in nat3-⌬ mutants (NatB substrates) (4); and subclasses of proteins with Met-Ile-, Met-Leu-, Met-Trp-, or Met-Phe-termini are not acetylated in mak3-⌬ mutants (NatC substrates) 1 (4, 6, 7). In addition, a special subclass of substrates with Ser-Glu-Phe-, Ala-Glu-Phe-, or Gly-Glu-Phe-termini are not acetylated in mutan...