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Front. Microbiol. | doi: 10.3389/fmicb.2018.03014

Structural analysis of the Hanks-type Protein Kinase YabT from Bacillus subtilis provides new insights in its DNA-Dependent Activation

 Lei Shi1, Andrea Cavagnino2, Jean-Luc Rabefiraisana2,  Noureddine Lazar2,  Ines Li de la Sierra-Gallay2,  Françoise Ochsenbein2, Marie Valerio-Lepiniec2,  Agathe Urvoas2, Philippe Minard2, 3,  Ivan Mijakovic1 and  Sylvie Nessler2, 4*
  • 1Chalmers University of Technology, Sweden
  • 2UMR9198 Institut de Biologie Intégrative de la Cellule (I2BC), France
  • 3The Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain), Denmark
  • 4Université Paris-Sud, France

YabT is a serine/threonine kinase of the Hanks family from Bacillus subtilis, which lacks the canonical extracellular signal receptor domain but is anchored to the membrane through a C-terminal transmembrane helix. A previous study demonstrated that a basic juxtamembrane region corresponds to a DNA-binding motif essential for the activation of YabT trans-autophosphorylation. YabT is expressed during spore development and localizes to the asymmetric septum where it specifically phosphorylates the DNA-recombinase RecA, thus ensuring chromosome integrity during sporulation. The function of YabT is thus reminiscent of the human kinase C-Abl, which binds DNA and phosphorylates the RecA homologue Rad51 involved in DNA repair. Using an artificial protein scaffold as crystallization helper, we determined the first crystal structure of this DNA-dependent bacterial protein kinase. This allowed us to trap the active conformation of the kinase domain of YabT. Using NMR, we showed that the basic juxtamembrane region of YabT is disordered in the absence of DNA in solution, just like it is in the crystal, and that it is stabilized upon DNA binding. Comparison with its closest structural homologue, the mycobacterial kinase PknB, allowed us to discuss the dimerization mode of YabT. Together with phosphorylation assays and DNA-binding experiments, this structural analysis helped us to gain new insights into the regulatory activation mechanism of YabT.

Keywords: Autophosphorylation, dimerization, Regulatory mechanism, Crystallization chaperone, Spore development

Received: 28 Aug 2018; Accepted: 21 Nov 2018.

Edited by:

Biswarup Mukhopadhyay, Virginia Tech, United States

Reviewed by:

Philippe H. Noirot, Argonne National Laboratory (DOE), United States
Andaleeb Sajid, National Institutes of Health (NIH), United States  

Copyright: © 2018 Shi, Cavagnino, Rabefiraisana, Lazar, Li de la Sierra-Gallay, Ochsenbein, Valerio-Lepiniec, Urvoas, Minard, Mijakovic and Nessler. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Sylvie Nessler, Université Paris-Sud, Orsay, France, sylvie.nessler@u-psud.fr