The genome of Tetrahymena thermophila contains 39 loci encoding NIMA-related kinases (NRKs), an extraordinarily large number for a unicellular organism. Evolutionary analyses grouped these sequences into several subfamilies, some of which have orthologues in animals, whereas others are protist specific. When overproduced, NRKs of three subfamilies caused rapid shortening of cilia. Ultrastructural studies revealed that each NRK triggered ciliary resorption by a distinct mechanism that involved preferential depolymerization of a subset of axonemal microtubules, at either the distal or proximal end. Overexpression of a kinase-inactive variant caused lengthening of cilia, indicating that constitutive NRK-mediated resorption regulates the length of cilia. Each NRK preferentially resorbed a distinct subset of cilia, depending on the location along the anteroposterior axis. We also show that normal Tetrahymena cells maintain unequal length cilia. We propose that ciliates used a large number of NRK paralogues to differentially regulate the length of specific subsets of cilia in the same cell. INTRODUCTIONHow the size of organelles is determined is an important and largely unanswered question. Cilia have emerged as a model organelle to study the mechanism of size regulation (Marshall, 2002). The size of an organelle is determined by the balance between assembly pathways that deliver structural components and disassembly pathways that remove components. In cilia, the intraflagellar transport (IFT), a bidirectional motility system that operates inside cilia (Rosenbaum and Witman, 2002;Scholey, 2003), plays a key role in length regulation. The anterograde IFT supplies structural subunits during assembly (Piperno et al., 1996;Qin et al., 2005) and maintains the axoneme after assembly (Brown et al., 1999). The retrograde IFT recycles the IFT machinery (Signor et al., 1999) and removes ciliary structural components that turn over (Qin et al., 2004). This turnover is the basis of the disassembly pathway (Stephens, 1997;Marshall and Rosenbaum, 2001;Song and Dentler, 2001;Thazhath et al., 2004). Experimental data and mathematical modeling in Chlamydomonas reinhardtii indicate that the length of flagella is dependent on the rates of elongation (equivalent to the efficiency of anterograde IFT) and disassembly. As the flagellum grows, the rate of elongation decreases due to the limited supply of IFT components that need to travel longer distances to the tip (Marshall and Rosenbaum, 2001). According to the "balance point model," the steady-state length is achieved when the rate of elongation equals the rate of disassembly (Marshall and Rosenbaum, 2001;Marshall et al., 2005).The length of already assembled cilia can be reduced drastically using two mechanisms: autotomy or resorption (reviewed by Quarmby, 2004). During autotomy, the axoneme breaks off from the basal body, the cilium falls off, and the plasma membrane reseals over the basal body. Protists undergo autotomy in response to low pH (Lewin et al., 1982). It is unclear whether...