Comparative Proteomics Reveals Timely Transport into Cilia of Regulators or Effectors as a Mechanism Underlying Ciliary Disassembly

J Proteome Res. 2017 Jul 7;16(7):2410-2418. doi: 10.1021/acs.jproteome.6b01048. Epub 2017 Jun 2.


Primary cilia are assembled and disassembled during cell cycle progression. During ciliary disassembly, ciliary axonemal microtubules (MTs) are depolymerized accompanied by extensive posttranslational protein modifications of ciliary proteins including protein phosphorylation, methylation, and ubiquitination. These events are hypothesized to involve transport of effectors or regulators into cilia at the time of ciliary disassembly from the cell body. To prove this hypothesis and identify new proteins involved in ciliary disassembly, we analyzed disassembling flagella in Chlamydomonas using comparative proteomics with TMT labeling. Ninety-one proteins were found to increase more than 1.4-fold in four replicates. The proteins of the IFT machinery not only increase but also exhibit stoichiometric changes. The other proteins that increase include signaling molecules, chaperones, and proteins involved in microtubule dynamics or stability. In particular, we have identified a ciliopathy protein C21orf2, the AAA-ATPase CDC48, that is involved in segregating polypeptides from large assemblies or cellular structures, FAP203 and FAP236, which are homologous to stabilizers of axonemal microtubules. Our data demonstrate that ciliary transport of effectors or regulators is one of the mechanisms underlying ciliary disassembly. Further characterization of the proteins identified will provide new insights into our understanding of ciliary disassembly and likely ciliopathy.

Keywords: Chlamydomonas; cilia and flagella; ciliary disassembly; comparative proteomics; intraflagellar transport (IFT).

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATPases Associated with Diverse Cellular Activities / genetics
  • ATPases Associated with Diverse Cellular Activities / metabolism
  • Algal Proteins / genetics*
  • Algal Proteins / metabolism
  • Biological Transport
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cell Division
  • Chlamydomonas reinhardtii / genetics
  • Chlamydomonas reinhardtii / metabolism*
  • Chlamydomonas reinhardtii / ultrastructure
  • Cilia / genetics
  • Cilia / metabolism*
  • Cilia / ultrastructure
  • Flagella / genetics
  • Flagella / metabolism*
  • Flagella / ultrastructure
  • Microscopy, Interference
  • Microtubule-Associated Proteins / genetics
  • Microtubule-Associated Proteins / metabolism
  • Microtubules / genetics
  • Microtubules / metabolism*
  • Microtubules / ultrastructure
  • Protein Processing, Post-Translational*
  • Proteomics / methods
  • Signal Transduction


  • Algal Proteins
  • Cell Cycle Proteins
  • Microtubule-Associated Proteins
  • ATPases Associated with Diverse Cellular Activities