Acetylation of α-tubulin at the lysine 40 residue (αK40) by the ATAT1/MEC-17 acetyltransferase influences the properties of microtubules and is a widespread phenomenon in eukaryotic cells. Previous research indicates that microtubules that undergo acetylation at αK40 are more stable and resilient to damage. Notably, αK40 acetylation represents the sole identified post-translational modification site within the microtubule lumen, suggesting its role in regulating the lateral interactions among protofilaments within the microtubule structure. This investigation focuses on evaluating the impact of tubulin acetylation on doublet microtubules present in the cilia of Tetrahymena thermophila, employing mass spectrometry analysis. Cilia samples derived from Tetrahymena wild type, acetylation mutants (K40R and MEC17-Knockout), and non-acetylation mutants (RIB72B-Knockout and RIB72AB-Knockout) underwent comparative mass spectrometry analysis. The results from mass spectrometry revealed a correlation between αK40 acetylation and phosphorylation within the ciliary structures.

Purified axoneme from Tetrahymena cells underwent subsequent mass spectrometry examination. The axoneme solution was supplemented with Laemmli buffer at a 4X concentration (#1610747, Bio-Rad) to achieve a 1x concentration, and approximately 25-30 μg of protein was loaded onto an SDS‒PAGE gel. Electrophoresis was initiated but halted prior to the proteins traversing into the separation gel. Subsequently, a gel section containing all proteins within the sample was excised and subjected to in-gel digestion. The resulting peptides (~2 μg) were chromatographically separated utilizing a Dionex Ultimate 3000 UHPLC system. Initially, peptides were loaded onto a Thermo Acclaim Pepmap precolumn (Thermo, 75 μm ID × 2 cm with 3 μm C18 beads) and subsequently onto an Acclaim Pepmap Easyspray analytical column (Thermo, 75 μm × 25 cm with 2 μm C18 beads), with separation achieved at a flow rate of 200 nl/min employing a gradient of 2-35% solvent (acetonitrile containing 0.1% formic acid) over 2 hours. Peptides possessing a charge of 2+ or higher were detected utilizing a Thermo Orbitrap Fusion mass spectrometer operating at a resolution of 120,000 (FWHM in MS1, 15,000 for MS/MS). The acquired data were interrogated against the Tetrahymena thermophila protein dataset sourced from UniProt (https://www.uniprot.org/).

The subsequent analysis of the mass spectrometry data was conducted using Scaffold_4.8.4 (Proteome Software Inc.). Proteins with a mean value of exclusive unique peptide count of 2 or greater in the wildtype mass spectrometry outcomes were selected for further analysis. Additionally, raw mass spectrometry data were normalized by the total spectra.