Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

Ishtiyaq Ahmed; Jeanette Hahn; Amy Henrickson; Faisal Tarique Khaja; Borries Demeler; David Dubnau; Matthew B. Neiditch

doi:10.1038/s41467-022-35129-0

Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

Ishtiyaq Ahmed
, Jeanette Hahn
, Amy Henrickson
, Faisal Tarique Khaja
, Borries Demeler
, David Dubnau
, Matthew B. Neiditch

Chemistry and Biochemistry

Research output: Contribution to journal › Article › peer-review

19 Scopus citations

Abstract

An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

Original language	English
Article number	7724
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-35129-0
State	Published - Dec 2022

Funding

X-ray diffraction data were collected at the Stanford Synchrotron Radiation Light Source. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS, NIAID, or NIH. Support for this work was provided by National Institutes of Health Grant R01 GM057720 (M.B.N. and D.D.). Analytical ultracentrifugation experiments were supported by the Canada 150 Research Chairs program (C150-2017-00015, BD), the Canada Foundation for Innovation (CFI-37589, BD), the National Institutes of Health (1R01GM120600, BD) and the Canadian Natural Science and Engineering Research Council (DG-RGPIN-2019-05637, BD). UltraScan supercomputer calculations were supported through NSF/XSEDE grant TG-MCB070039N (BD), and University of Texas grant TG457201 (BD). The Canadian Natural Science and Engineering Research Council supports AH through a scholarship grant. X-ray diffraction data were collected at the Stanford Synchrotron Radiation Light Source. Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P41GM103393). The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS, NIAID, or NIH. Support for this work was provided by National Institutes of Health Grant R01 GM057720 (M.B.N. and D.D.). Analytical ultracentrifugation experiments were supported by the Canada 150 Research Chairs program (C150-2017-00015, BD), the Canada Foundation for Innovation (CFI-37589, BD), the National Institutes of Health (1R01GM120600, BD) and the Canadian Natural Science and Engineering Research Council (DG-RGPIN-2019-05637, BD). UltraScan supercomputer calculations were supported through NSF/XSEDE grant TG-MCB070039N (BD), and University of Texas grant TG457201 (BD). The Canadian Natural Science and Engineering Research Council supports AH through a scholarship grant.

Funders	Funder number
TG457201
TG-MCB070039N
R01 GM057720, P41GM103393, R01GM120600, C150-2017-00015
DE-AC02-76SF00515
Biological and Environmental Research
DG-RGPIN-2019-05637
Canada Foundation for Innovation	1R01GM120600, CFI-37589

Access to Document

10.1038/s41467-022-35129-0

Cite this

@article{587caedbe5e44462a53ae32caed74d2c,

title = "Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria",

abstract = "An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.",

author = "Ishtiyaq Ahmed and Jeanette Hahn and Amy Henrickson and Khaja, \{Faisal Tarique\} and Borries Demeler and David Dubnau and Neiditch, \{Matthew B.\}",

note = "Publisher Copyright: {\textcopyright} 2022, The Author(s).",

year = "2022",

month = dec,

doi = "10.1038/s41467-022-35129-0",

language = "English",

volume = "13",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

TY - JOUR

T1 - Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

AU - Ahmed, Ishtiyaq

AU - Hahn, Jeanette

AU - Henrickson, Amy

AU - Khaja, Faisal Tarique

AU - Demeler, Borries

AU - Dubnau, David

AU - Neiditch, Matthew B.

PY - 2022/12

Y1 - 2022/12

N2 - An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

AB - An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.

UR - https://www.scopus.com/pages/publications/85144113347

U2 - 10.1038/s41467-022-35129-0

DO - 10.1038/s41467-022-35129-0

M3 - Article

C2 - 36513643

AN - SCOPUS:85144113347

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 7724

ER -

Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria

Abstract

Funding

Access to Document

Other files and links

Fingerprint

Cite this