Two types of polymeric post-translational modifications of ␣/-tubulin, glycylation and glutamylation, occur widely in cilia and flagella. Their respective cellular functions are poorly understood. Mass spectrometry and immunoblotting showed that two closely related species, the ciliates Tetrahymena and Paramecium, have dramatically different compositions of tubulin post-translational modifications in structurally identical axonemes. Whereas the axonemal tubulin of Paramecium is highly glycylated and has a very low glutamylation content, the axonemal tubulin of Tetrahymena is glycylated and extensively glutamylated. In addition, only the ␣-tubulin of Tetrahymena undergoes detyrosination. Mutations of the known glycylation sites in Tetrahymena tubulin affected the level of each polymeric modification type in both the mutated and nonmutated subunits, revealing cross-talk between ␣-and -tubulin. Ultrastructural analyses of glycylation site mutants uncovered defects in the doublet B-subfiber of axonemes and revealed an accumulation of dense material in the ciliary matrix, reminiscent of intraflagellar transport particles seen by others in Chlamydomonas. We propose that polyglycylation and/or polyglutamylation stabilize the B-subfiber of outer doublets and regulate the intraflagellar transport.Microtubules are subject to a set of post-translational modifications (PTMs) 1 whose significance has emerged only recently (1-4). Among PTMs, two polymeric modifications, glutamylation and glycylation, substantially increase the heterogeneity of the ␣/-tubulin heterodimer. These tubulin modifications, referred to as polyglutamylation and polyglycylation, correspond to the addition of a peptide polymer consisting of several glutamates (5) or glycines (6) onto the ␥-carboxyl group of a glutamate of the primary sequence of tubulin. These two PTMs will be referred to as "polymodifications" throughout this report. Polymodifications generate peptide branches of variable lengths distributed on several glutamate acceptor sites in the C-terminal tails of ␣-and -tubulin (7-9). Both polymodification types are enriched in flagella and cilia of protists and metazoan cells (4) and were implicated in axoneme motility (10, 11). Whereas polyglycylation is restricted to axonemes in the ciliated and flagellated metazoan cells, polyglutamylation occurs in both axonemes and basal bodies (12-15). In ciliates, both polymodification types are not only present in cilia and basal bodies (15-18), but also occur on the more dynamic intracytoplasmic microtubules (17,19,20). Ciliates assemble up to 17 types of distinct microtubular arrays in a single cell (19,(21)(22)(23). In these highly differentiated cells, the microtubular networks are involved in nuclear divisions, intracellular transport, organelle positioning, and are associated with specialized organelles that function in osmotic regulation, feeding, excretion, and locomotion. The ␣-and -tubulins of ciliates are biochemically heterogeneous (17,20,24), suggesting that structural differences amon...