The nuclear run-on technique was used to measure the rate of transcription of flagellar genes during the differentiation of Naegleria gruberi amebae into flagellates. Synthesis of mRNAs for the axonemal proteins aand l-tubulin and flagellar calmodulin, as wel as a coordinately regulated poly(A)+ RNA that codes for an unidentified protein, showed transient increases averaging 22-fold. The rate of synthesis of two poly(A)+ RNAs common to amebae and flagellates was low until the transcription of the flagellar genes began to decline, at which time synthesis of the RNAs found in amebae increased 3-to 10-fold. The observed changes in the rate of transcription can account quantitatively for the 20-fold increase in flagellar mRNA concentration during the differentiation. The data for the flageilar calmodulin gene demonstrate transcriptional regulation for a nontubulin axonemal protein. The data also demonstrate at least two programs of transcriptional regulation during the differentiation and raise the intriguing possibility that some significant fraction of the nearly 200 different proteins of the flagellar axoneme is transcriptionally regulated during the 1 h it takes N. grubeni amebae to form visible flagella.Axonemes of eucaryotic flagella are composed of nearly 200 different proteins (28). Thus, neglecting proteins associated with basal bodies and the various rootlet structures found in most cells, the formation of cilia or flagella requires the synthesis and assembly of a minimum of 200 gene products. This complexity is particularly notable because some cells can assemble flagella quite rapidly.The best-studied example of flagellum formation is the biflagellated green alga Chlamydomonas reinhardtii. Most studies of flagellum formation in C. reinhardtii have taken advantage of the fact that the cells are readily deflagellated to examine the regeneration of flagella (e.g., see references 27, 32, 33, and 39). Regeneration involves both the assembly of preexisting flagellar proteins, which can produce about 50% of the original flagellar length, and the synthesis of new protein (33). Transient increases in a number of mRNAs coding for flagellar proteins have been documented during C. reinhardi flagellar regeneration (34), but changes in only two of these RNAs have been studied at the transcriptional level. Changes in the level of mRNAs for the a and ,B subunits of tubulin were found to be due, in part, to changes in the rate of their synthesis and, in part, to changes in tubulin mRNA stability (2,19). No data are available to suggest how proteins that are exclusively flagellar are regulated (C. reinhardtii contains only one form of ,-tubulin which presumably must be used in cytoplasmic and mitotic microtubules as well as flagella) (40). It is also of interest to ask whether the regulatory mechanisms governing regeneration of flagella in a normally flagellated cell would apply to a cell forming flagella de novo.The amebo-flagellate Naegleria gruberi provides an opportunity to examine this question. In contrast to C. rei...