Telomere mutants have been well studied with respect to telomerase and the role of telomere binding proteins, but they have not been used to explore how a downstream morphogenic event is related to the mutated telomeric DNA. We report that alterations at the telomeres can have profound consequences on organellar morphogenesis. Specifically, a telomerase RNA mutation termed ter1-43AA results in the loss of germ line micronuclear telomeres in the binucleate protozoan Tetrahymena thermophila. These cells also display a micronuclear mitotic arrest, characterized by an extreme delay in anaphase with an elongated, condensed chromatin and a mitotic spindle apparatus. This anaphase defect suggests telomere fusions and consequently a spindle rather than a DNA damage checkpoint. Most surprisingly, these mutants exhibit unique, dramatic defects in the formation of the cell's oral apparatus. We suggest that micronuclear telomere loss leads to a "dynamic pause" in the program of cortical development, which may reveal an unusual cell cycle checkpoint.Telomeres have been implicated in a number of diverse cellular processes. Normal telomeres serve as the means by which chromosomes can be replicated completely, and they function as a cap, thereby protecting the natural ends from inappropriate fusion. Telomeric mutants can be generated by making predictable changes in the RNA template of the enzyme telomerase, which synthesizes telomeres, such that the corresponding complementary mutation is made at the telomeres. Although these types of telomeric DNA mutants in complex eukaryotes are poorly studied, particularly with respect to the downstream developmental consequences, those in simplified yeasts and the ciliated protozoa are better understood.Ciliated protozoa, such as Tetrahymena thermophila, provide excellent model systems for studying telomerase, telomeric DNA mutants, and the downstream developmental consequences to changing the telomeric repeat sequence. This is because the components of telomeres and telomerase have been exceptionally well documented (5) and the cells are large enough (roughly 60 to 70 m) to allow a glimpse of their unique developmental processes.Interestingly, T. thermophila, like other ciliates, bears two nuclei distinct in function and mode of division (reviewed in reference 25). The micronucleus represents the germ line nucleus and is transcriptionally silent, whereas the macronucleus serves as the vegetative nucleus of the cell. The micronucleus contains five pairs of chromosomes, which are passed on through mitosis and meiosis. In contrast, the macronucleus contains many subchromosomal fragments, each of which is amplified to ϳ45 copies, excluding the ribosomal DNA, which has thousands of copies. The macronuclear chromosomes are not faithfully inherited, as the macronucleus divides amitotically.The telomeres of the two T. thermophila nuclei are dramatically different. The macronuclear telomeres, present at a copy number of roughly 40,000 per cell, contain about 0.3 to 0.5 kb of G4T2 repeats (3). Mic...