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.2020 Sep 1;117(35):21308-21318.
doi: 10.1073/pnas.2006429117. Epub 2020 Aug 17.

A cryptic tubulin-binding domain links MEKK1 to curved tubulin protomers

Affiliations

A cryptic tubulin-binding domain links MEKK1 to curved tubulin protomers

Pavel Filipčík et al. Proc Natl Acad Sci U S A..

Abstract

The MEKK1 protein is a pivotal kinase activator of responses to cellular stress. Activation of MEKK1 can trigger various responses, including mitogen-activated protein (MAP) kinases, NF-κB signaling, or cell migration. Notably, MEKK1 activity is triggered by microtubule-targeting chemotherapies, among other stressors. Here we show that MEKK1 contains a previously unidentified tumor overexpressed gene (TOG) domain. The MEKK1 TOG domain binds to tubulin heterodimers-a canonical function of TOG domains-but is unusual in that it appears alone rather than as part of a multi-TOG array, and has structural features distinct from previously characterized TOG domains. MEKK1 TOG demonstrates a clear preference for binding curved tubulin heterodimers, which exist in soluble tubulin and at sites of microtubule polymerization and depolymerization. Mutations disrupting tubulin binding decrease microtubule density at the leading edge of polarized cells, suggesting that tubulin binding may play a role in MEKK1 activity at the cellular periphery. We also show that MEKK1 mutations at the tubulin-binding interface of the TOG domain recur in patient-derived tumor sequences, suggesting selective enrichment of tumor cells with disrupted MEKK1-microtubule association. Together, these findings provide a direct link between the MEKK1 protein and tubulin, which is likely to be relevant to cancer cell migration and response to microtubule-modulating therapies.

Keywords: MAPK; MEKK1; kinase; tubulin.

Copyright © 2020 the Author(s). Published by PNAS.

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Conflict of interest statement

The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
Identification and structure of an uncharacterized domain of MEKK1. (A) Analysis of MEKK1 sequence conservation across species and predicted disorder.Top shows a schematic representation of known features of MEKK1, relative to sequence conservation (Middle) and predicted disorder (Bottom). (B) MEKK1(542 to 888) can be expressed and purified fromE. coli. S, I, FT, and E indicate soluble (S), insoluble (I), flow-through (FT), and eluate (E) fractions from lysis and Ni2+ affinity purification, as visualized using Coomassie staining. (C) MALLS analysis of MEKK1(542 to 888) indicates a monomeric species in solution. (D) The crystal structure of MEKK1(548 to 867), with termini and structural features labeled. Missing loops are denoted with L1, L3 and L4.
Fig. 2.
Fig. 2.
Comparison of TOG domains and their tubulin-binding modes: (A) MEKK1 TOG domain (blue, PDB ID code 6WHB) superimposed on Stu2p TOG1 domain (salmon, PDB ID code 4FFB) using secondary structure alignment across the whole structure. MEKK1 contains an additional structured helix on its N terminus (labeled in blue), while Stu2p TOG1’s C-terminal helix (labeled in salmon) is found in a different position. (B) Secondary structure superimposition of MEKK1 TOG and Stu2p TOG1, using only the N-terminal three HEAT repeats for alignment. This alignment showcases the difference in angle between HEAT 3 and HEAT 4 in Stu2p and MEKK1, leading to diverging orientation of the following HEAT repeats. (C) MEKK1 TOG domain (blue) superimposed on Msps TOG5 domain (orange, PDB ID code 5VJC) using secondary structure alignment across the whole structure. Msps TOG5 contains an additional HEAT 0 repeat (labeled in orange) on its N terminus. (D) Surface representations of MEKK1 TOG (blue), Stu2p TOG1 (salmon), and Msps TOG5 (orange) models shown inA andC in complex with (Top) curved tubulin (dark gray, PDB ID code 4FFB) and (Bottom) straight tubulin (light gray, PDB ID code 5SYF) showcases the differences in the extent and quality of contacts between the respective TOG domains and the α-tubulin subunit.
Fig. 3.
Fig. 3.
Tubulin binding and mutation analysis of MEKK1 TOG. (A) SEC trace of MEKK1 TOG (blue), tubulin (black), and their combination (red). Earlier elution of TOG and tubulin in combination suggests binding interaction. (B) SDS/PAGE analyses of SEC coelution experiments of MEKK1 TOG with tubulin. (C) SDS/PAGE analysis of SEC coelution assay with MEKK1 TOG and colchicine-treated tubulin. (D) The crystal structure of Stu2p TOG1−tubulin complex, used as the basis for mutant design. (E) A model of MEKK1 TOG interacting with tubulin, highlighting the conserved residues Trp-577 and Val-647, as well as the C-terminal Arg-851, tested in this work. (F) A detail of the β-tubulin interface, conserved between Stu2p TOG, and MEKK1. (G andH) Details of the C-terminal portions of Stu2p TOG and MEKK1 TOG, respectively, with tubulin surface colored by electrostatic potential. (I) SDS/PAGE analyses of SEC coelution experiments of MEKK1 TOG mutants with tubulin.
Fig. 4.
Fig. 4.
ITC comparison between MEKK1 TOG interacting with the free tubulin and paclitaxel-stabilized microtubules. (A) Thermograms (Top) and fitted isotherms (Bottom) from a global analysis of four experiments measuring MEKK1 TOG binding to tubulin in nonpolymerizing conditions, shown in maroon, orange, yellow, and blue. MEKK1 TOG dilution experiment and tubulin dilution experiment shown in cyan. (B) Thermograms (Top) and fitted isotherms (Bottom) from two experiments measuring MEKK1 TOG binding to stabilized microtubules, shown in maroon, and blue. Microtubule dilution experiment is shown in cyan. DP in the shown thermograms denotes differential power measured in the ITC experiment.
Fig. 5.
Fig. 5.
Analysis of mutant MEKK1 in COS-7 cells. (A) Distribution of WT (Top) and V647D/R851E (Bottom) MEKK1 and tubulin in COS-7 cells. MEKK1 signal is shown as magenta, tubulin as green, and DAPI blue. The arrows indicate MEKK1 enrichment at the leading edge and at centrosomes. (B) A detail of the leading edge of polarized cells expressing WT MEKK1 (Top) and MEKK1 V647D/R851E (Bottom). (C) An illustration of the quantification of leading-edge microtubule density. (D) Fraction of leading-edge area covered by microtubules in WT MEKK1-expressing cells (left, dark blue) and MEKK1 V647D/R851E-expressing cells (right, light blue). **P < 0.01. All scale bars are 10 μm.
Fig. 6.
Fig. 6.
MEKK1 TOG domain harbors mutations in human cancers. (A) Missense mutations in MEKK1 in a curated set of nonredundant human cancer sequence dataset. The TOG domain contains two of the top five mutation hot spots in the MEKK1 sequence. (B) A model of MEKK1 TOG−tubulin interaction, with MEKK1 TOG domain residues mutated three or more times colored orange and residues mutated 10 or more times colored red. Asp-806 and Arg-853 both lay on the interface with α-tubulin.
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