Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation

Lei Shi, Andrea Cavagnino, Jean-Luc Rabefiraisana, Noureddine Lazar, Inés Li de la Sierra-Gallay, Francoise Ochsenbein, Marie Valerio-Lepiniec, Agathe Urvoas, Philippe Minard, Ivan Mijakovic*, Sylvie Nessler

*Corresponding author for this work

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Abstract

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 essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. 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. In comparison with its closest structural homolog, 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.
Original languageEnglish
Article number3014
JournalFrontiers in Microbiology
Volume9
Number of pages12
ISSN1664-302X
DOIs
Publication statusPublished - 2019

Keywords

  • Autophosphorylation
  • Dimerization
  • Regulatory mechanism
  • Crystallization chaperone
  • Spore development

Cite this

Shi, L., Cavagnino, A., Rabefiraisana, J-L., Lazar, N., Li de la Sierra-Gallay, I., Ochsenbein, F., ... Nessler, S. (2019). Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation. Frontiers in Microbiology, 9, [3014]. https://doi.org/10.3389/fmicb.2018.03014
Shi, Lei ; Cavagnino, Andrea ; Rabefiraisana, Jean-Luc ; Lazar, Noureddine ; Li de la Sierra-Gallay, Inés ; Ochsenbein, Francoise ; Valerio-Lepiniec, Marie ; Urvoas, Agathe ; Minard, Philippe ; Mijakovic, Ivan ; Nessler, Sylvie. / Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation. In: Frontiers in Microbiology. 2019 ; Vol. 9.
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title = "Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation",
abstract = "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 essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. 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. In comparison with its closest structural homolog, 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",
author = "Lei Shi and Andrea Cavagnino and Jean-Luc Rabefiraisana and Noureddine Lazar and {Li de la Sierra-Gallay}, In{\'e}s and Francoise Ochsenbein and Marie Valerio-Lepiniec and Agathe Urvoas and Philippe Minard and Ivan Mijakovic and Sylvie Nessler",
year = "2019",
doi = "10.3389/fmicb.2018.03014",
language = "English",
volume = "9",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S.A.",

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Shi, L, Cavagnino, A, Rabefiraisana, J-L, Lazar, N, Li de la Sierra-Gallay, I, Ochsenbein, F, Valerio-Lepiniec, M, Urvoas, A, Minard, P, Mijakovic, I & Nessler, S 2019, 'Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation', Frontiers in Microbiology, vol. 9, 3014. https://doi.org/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. / Shi, Lei; Cavagnino, Andrea; Rabefiraisana, Jean-Luc; Lazar, Noureddine; Li de la Sierra-Gallay, Inés; Ochsenbein, Francoise; Valerio-Lepiniec, Marie; Urvoas, Agathe; Minard, Philippe; Mijakovic, Ivan; Nessler, Sylvie.

In: Frontiers in Microbiology, Vol. 9, 3014, 2019.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation

AU - Shi, Lei

AU - Cavagnino, Andrea

AU - Rabefiraisana, Jean-Luc

AU - Lazar, Noureddine

AU - Li de la Sierra-Gallay, Inés

AU - Ochsenbein, Francoise

AU - Valerio-Lepiniec, Marie

AU - Urvoas, Agathe

AU - Minard, Philippe

AU - Mijakovic, Ivan

AU - Nessler, Sylvie

PY - 2019

Y1 - 2019

N2 - 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 essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. 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. In comparison with its closest structural homolog, 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.

AB - 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 essential proteins involved in genome maintenance, such as RecA, SsbA, and YabA. YabT has also been shown to phosphorylate proteins involved in protein synthesis, such as AbrB and Ef-Tu, suggesting a possible regulatory role in the progressive metabolic quiescence of the forespore. Finally, cross phosphorylations with other protein kinases implicate YabT in the regulation of numerous other cellular processes. 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. In comparison with its closest structural homolog, 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.

KW - Autophosphorylation

KW - Dimerization

KW - Regulatory mechanism

KW - Crystallization chaperone

KW - Spore development

U2 - 10.3389/fmicb.2018.03014

DO - 10.3389/fmicb.2018.03014

M3 - Journal article

VL - 9

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

M1 - 3014

ER -