Cilia and flagella are dynamic organelles that are assembled and disassembled during cell differentiation, during stress, and during the cell cycle. Although intraflagellar transport (IFT) is well documented to be responsible for transport of ciliary/flagellar precursors from the cell body to the flagella, little is known about the molecular mechanisms for mobilizing the cell body-localized precursors to make them available for transport during organelle assembly or for disassembling the microtubule-based axoneme during shortening. Here, we show that Chlamydomonas kinesin-13 (CrKinesin-13), a member of the kinesin-13 family of microtubule depolymerizing kinesins best known for their roles in the cell cycle, functions in flagellar disassembly and flagellar assembly. Activation of a cell to generate new flagella induces rapid phosphorylation of CrKinesin-13, and activation of flagellar shortening induces the immediate transport of CrKinesin-13 via intraflagellar transport from the cell body into the flagella. Cells depleted of CrKinesin-13 by RNAi assemble flagella after cell division but are incapable of the rapid assembly of flagella that normally occurs after flagellar detachment. Furthermore, they are inhibited in flagellar shortening. Thus, CrKinesin-13 is dynamically regulated during flagellar assembly and disassembly in Chlamydomonas and functions in each.cilia ͉ flagella ͉ intraflagellar transport ͉ Kinesin-13

Flagella and cilia are structurally polarized organelles whose lengths are precisely defined, and alterations in length are related to several human disorders [1, 2]. Intraflagellar transport (IFT) and protein signaling molecules are implicated in specifying flagellar/ciliary length [3–6], but evidence has been lacking for a flagellum/cilium length sensor that could participate in active length control or establishment of structural polarity. Previously, we showed that the phosphorylation state of the aurora-like protein kinase CALK in Chlamydomonas is a marker of the absence of flagella. Here, we show that CALK phosphorylation state also is a marker for flagellar length. CALK is phosphorylated in cells without flagella, and during flagellar assembly it becomes desphosphorylated. Dephosphorylation is not simply a consequence of initiation of flagellar assembly or of time after experimentally-induced flagellar loss, but requires flagellar assembly to a threshold length. Analysis of cells with flagella of varying lengths shows that the threshold length for CALK dephosphorylation is ~6 µm (half-length). Studies with short and long flagellar mutants indicate that cells detect absolute rather than relative flagellar length. Our results demonstrate that cells possess a mechanism for translating flagellar length into a posttranslational modification of a known flagellar regulatory protein.

Research funding is provided by the Ministry of Science and Technology of China [2012CB944704; 2012CB966702], the National Natural Science Foundation of China [Grant number: 31171429] and Beijing Advanced Innovation Center for Structural Biology. The authors declare no conflict of interest.

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