DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport

Abstract

ATP-binding cassette (ABC) transporters constitute a large family of proteins present in all domains of life. They are powered by dynamic ATPases that harness energy from binding and hydrolyzing ATP through a cycle that involves the closing and reopening of their two ATP-binding domains. The LptB2FGC exporter is an essential ABC transporter that assembles lipopolysaccharides (LPS) on the surface of Gram-negative bacteria to form a permeability barrier against many antibiotics. LptB2FGC extracts newly synthesized LPS molecules from the inner membrane and powers their transport across the periplasm and through the outer membrane. How LptB2FGC functions remains poorly understood. Here, we show that the C-terminal domain of the dimeric LptB ATPase is essential for LPS transport in Escherichia coli. Specific changes in the C-terminal domain of LptB cause LPS transport defects that can be repaired by intragenic suppressors altering the ATP-binding domains. Surprisingly, we found that each of two lethal changes in the ATP-binding and C-terminal domains of LptB, when present in combined form, suppressed the defects associated with the other to restore LPS transport to wild-type levels both in vivo and in vitro. We present biochemical evidence explaining the effect that each of these mutations has on LptB function andmore » how the observed cosuppression results from the opposing lethal effects these changes have on the dimerization state of the LptB ATPase. We therefore propose that these sites modulate the closing and reopening of the LptB dimer, providing insight into how the LptB2FGC transporter cycles to export LPS to the cell surface and how to inhibit this essential envelope biogenesis process.« less

Authors:
 [1];  [2];  [2];  [3];  [3];  [4]; ORCiD logo [3]
  1. The Ohio State Univ., Columbus, OH (United States); Univ. of Georgia, Athens, GA (United States)
  2. Harvard Univ., Cambridge, MA (United States)
  3. The Ohio State Univ., Columbus, OH (United States)
  4. Harvard Univ., Cambridge, MA (United States); Harvard Medical School, Boston, MA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1569912
Grant/Contract Number:  
R01-GM100951; R01-GM066174; R0-AI081059
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 4; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; ABC transporters; ATPase; cell envelope; lipopolysaccharide; outer membrane

Citation Formats

Simpson, Brent W., Pahil, Karanbir S., Owens, Tristan W., Lundstedt, Emily A., Davis, Rebecca M., Kahne, Daniel, and Ruiz, Natividad. Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. United States: N. p., 2019. Web. doi:10.1128/mbio.01931-19.
Simpson, Brent W., Pahil, Karanbir S., Owens, Tristan W., Lundstedt, Emily A., Davis, Rebecca M., Kahne, Daniel, & Ruiz, Natividad. Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport. United States. https://doi.org/10.1128/mbio.01931-19
Simpson, Brent W., Pahil, Karanbir S., Owens, Tristan W., Lundstedt, Emily A., Davis, Rebecca M., Kahne, Daniel, and Ruiz, Natividad. Tue . "Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport". United States. https://doi.org/10.1128/mbio.01931-19. https://www.osti.gov/servlets/purl/1569912.
@article{osti_1569912,
title = {Combining Mutations That Inhibit Two Distinct Steps of the ATP Hydrolysis Cycle Restores Wild-Type Function in the Lipopolysaccharide Transporter and Shows that ATP Binding Triggers Transport},
author = {Simpson, Brent W. and Pahil, Karanbir S. and Owens, Tristan W. and Lundstedt, Emily A. and Davis, Rebecca M. and Kahne, Daniel and Ruiz, Natividad},
abstractNote = {ATP-binding cassette (ABC) transporters constitute a large family of proteins present in all domains of life. They are powered by dynamic ATPases that harness energy from binding and hydrolyzing ATP through a cycle that involves the closing and reopening of their two ATP-binding domains. The LptB2FGC exporter is an essential ABC transporter that assembles lipopolysaccharides (LPS) on the surface of Gram-negative bacteria to form a permeability barrier against many antibiotics. LptB2FGC extracts newly synthesized LPS molecules from the inner membrane and powers their transport across the periplasm and through the outer membrane. How LptB2FGC functions remains poorly understood. Here, we show that the C-terminal domain of the dimeric LptB ATPase is essential for LPS transport in Escherichia coli. Specific changes in the C-terminal domain of LptB cause LPS transport defects that can be repaired by intragenic suppressors altering the ATP-binding domains. Surprisingly, we found that each of two lethal changes in the ATP-binding and C-terminal domains of LptB, when present in combined form, suppressed the defects associated with the other to restore LPS transport to wild-type levels both in vivo and in vitro. We present biochemical evidence explaining the effect that each of these mutations has on LptB function and how the observed cosuppression results from the opposing lethal effects these changes have on the dimerization state of the LptB ATPase. We therefore propose that these sites modulate the closing and reopening of the LptB dimer, providing insight into how the LptB2FGC transporter cycles to export LPS to the cell surface and how to inhibit this essential envelope biogenesis process.},
doi = {10.1128/mbio.01931-19},
journal = {mBio (Online)},
number = 4,
volume = 10,
place = {United States},
year = {Tue Aug 20 00:00:00 EDT 2019},
month = {Tue Aug 20 00:00:00 EDT 2019}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 11 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Molecular Basis of Bacterial Outer Membrane Permeability Revisited
journal, December 2003


Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

The Pfam protein families database
journal, December 2007

  • Finn, R. D.; Tate, J.; Mistry, J.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm960

Mechanistic diversity in ATP-binding cassette (ABC) transporters
journal, June 2016

  • Locher, Kaspar P.
  • Nature Structural & Molecular Biology, Vol. 23, Issue 6
  • DOI: 10.1038/nsmb.3216

Characterization of the human multidrug resistance protein containing mutations in the ATP-binding cassette signature region
journal, May 1997

  • Bakos, Éva; Klein, Izabella; Welker, Ervin
  • Biochemical Journal, Vol. 323, Issue 3
  • DOI: 10.1042/bj3230777

Expanding the paradigm for the outer membrane: Acinetobacter baumannii in the absence of endotoxin
journal, November 2017

  • Powers, Matthew Joseph; Trent, M. Stephen
  • Molecular Microbiology, Vol. 107, Issue 1
  • DOI: 10.1111/mmi.13872

Collaboration gets the most out of software
journal, September 2013


Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging
journal, October 2014

  • Yaginuma, Hideyuki; Kawai, Shinnosuke; Tabata, Kazuhito V.
  • Scientific Reports, Vol. 4, Issue 1
  • DOI: 10.1038/srep06522

Structural basis of unidirectional export of lipopolysaccharide to the cell surface
journal, March 2019


Probing the Barrier Function of the Outer Membrane with Chemical Conditionality
journal, July 2006

  • Ruiz, Natividad; Wu, Tao; Kahne, Daniel
  • ACS Chemical Biology, Vol. 1, Issue 6
  • DOI: 10.1021/cb600128v

Characterization of lptA and lptB, Two Essential Genes Implicated in Lipopolysaccharide Transport to the Outer Membrane of Escherichia coli
journal, October 2006

  • Sperandeo, P.; Cescutti, R.; Villa, R.
  • Journal of Bacteriology, Vol. 189, Issue 1
  • DOI: 10.1128/JB.01126-06

On the essentiality of lipopolysaccharide to Gram-negative bacteria
journal, December 2013

  • Zhang, Ge; Meredith, Timothy C.; Kahne, Daniel
  • Current Opinion in Microbiology, Vol. 16, Issue 6
  • DOI: 10.1016/j.mib.2013.09.007

Structure and mechanism of ATP-binding cassette transporters
journal, October 2008

  • Locher, Kaspar P.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 364, Issue 1514
  • DOI: 10.1098/rstb.2008.0125

How good are my data and what is the resolution?
journal, June 2013

  • Evans, Philip R.; Murshudov, Garib N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7
  • DOI: 10.1107/S0907444913000061

Functional consequences of mutations in the conserved 'signature sequence' of the ATP-binding-cassette protein MalK
journal, December 1999


Function and Biogenesis of Lipopolysaccharides
journal, February 2018


Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport
journal, March 2014

  • Sherman, David J.; Lazarus, Michael B.; Murphy, Lea
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 13
  • DOI: 10.1073/pnas.1323516111

The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport
journal, November 2017

  • May, Janine M.; Owens, Tristan W.; Mandler, Michael D.
  • Journal of the American Chemical Society, Vol. 139, Issue 48
  • DOI: 10.1021/jacs.7b07736

Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter
journal, November 2014

  • Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6419

XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

Synthetic antibodies against BRIL as universal fiducial marks for single−particle cryoEM structure determination of membrane proteins
journal, March 2020

  • Mukherjee, Somnath; Erramilli, Satchal K.; Ammirati, Mark
  • Nature Communications, Vol. 11, Issue 1
  • DOI: 10.1038/s41467-020-15363-0

Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG
journal, August 2017


Multifaceted structures and mechanisms of ABC transport systems in health and disease
journal, August 2018


Lipopolysaccharide is transported to the cell surface by a membrane-to-membrane protein bridge
journal, February 2018


Structural basis of lipopolysaccharide extraction by the LptB2FGC complex
journal, March 2019


PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome
journal, December 2019


Lipopolysaccharide transport and assembly at the outer membrane: the PEZ model
journal, March 2016

  • Okuda, Suguru; Sherman, David J.; Silhavy, Thomas J.
  • Nature Reviews Microbiology, Vol. 14, Issue 6
  • DOI: 10.1038/nrmicro.2016.25

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021


Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG
journal, April 2017

  • Luo, Qingshan; Yang, Xu; Yu, Shan
  • Nature Structural & Molecular Biology, Vol. 24, Issue 5
  • DOI: 10.1038/nsmb.3399

Novobiocin Enhances Polymyxin Activity by Stimulating Lipopolysaccharide Transport
journal, April 2018

  • Mandler, Michael D.; Baidin, Vadim; Lee, James
  • Journal of the American Chemical Society, Vol. 140, Issue 22
  • DOI: 10.1021/jacs.8b02283

Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu
journal, July 1976


Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors
journal, May 2018

  • Zhang, Ge; Baidin, Vadim; Pahil, Karanbir S.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 26
  • DOI: 10.1073/pnas.1804670115

Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli
journal, March 2008

  • Ruiz, N.; Gronenberg, L. S.; Kahne, D.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 14
  • DOI: 10.1073/pnas.0801196105

Subunit interactions in ABC transporters: towards a functional architecture
journal, October 1999


A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli
journal, February 1989


Cytoplasmic ATP Hydrolysis Powers Transport of Lipopolysaccharide Across the Periplasm in E. coli
journal, November 2012


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

A Peptidomimetic Antibiotic Interacts with the Periplasmic Domain of LptD from Pseudomonas aeruginosa
journal, January 2018


Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli
journal, August 2012

  • Yao, Z.; Davis, R. M.; Kishony, R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
  • DOI: 10.1073/pnas.1209742109

Overview of the CCP4 suite and current developments.
text, January 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.52322

Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function
journal, October 2016

  • Simpson, Brent W.; Owens, Tristan W.; Orabella, Matthew J.
  • mBio, Vol. 7, Issue 5
  • DOI: 10.1128/mBio.01729-16

Peptidomimetic Antibiotics Target Outer-Membrane Biogenesis in Pseudomonas aeruginosa
journal, February 2010


Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems
journal, June 2008

  • Davidson, A. L.; Dassa, E.; Orelle, C.
  • Microbiology and Molecular Biology Reviews, Vol. 72, Issue 2
  • DOI: 10.1128/MMBR.00031-07

Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport
journal, September 2014

  • Wang, Zhongshan; Xiang, Quanju; Zhu, Xiaofeng
  • Biochemical and Biophysical Research Communications, Vol. 452, Issue 3
  • DOI: 10.1016/j.bbrc.2014.08.094

Comparison of mechanistic transport cycle models of ABC exporters
journal, April 2018

  • Szöllősi, Dániel; Rose-Sperling, Dania; Hellmich, Ute A.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1860, Issue 4
  • DOI: 10.1016/j.bbamem.2017.10.028

Validation of inhibitors of an ABC transporter required to transport lipopolysaccharide to the cell surface in Escherichia coli
journal, August 2013

  • Sherman, David J.; Okuda, Suguru; Denny, William A.
  • Bioorganic & Medicinal Chemistry, Vol. 21, Issue 16
  • DOI: 10.1016/j.bmc.2013.04.020

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Pushing the envelope: LPS modifications and their consequences
journal, May 2019


Structure-function analysis of the histidine permease and comparison with cystic fibrosis mutations.
journal, October 1991


A Peptidomimetic Antibiotic Interacts with the Periplasmic Domain of LptD from Pseudomonas aeruginosa
text, January 2018

  • Andolina, Gloria; Bencze, László-Csaba; Zerbe, Katja
  • American Chemical Society (ACS)
  • DOI: 10.5167/uzh-151164

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787

Peptidomimetic antibiotics target outer membrane biogenesis in Pseudomonas aeruginosa
text, January 2010

  • Srinivas, N.; Jetter, P.; Ueberbacher, B. J.
  • American Association for the Advancement of Science (AAAS)
  • DOI: 10.5167/uzh-32980

Getting In or Out: Early Segregation Between Importers and Exporters in the Evolution of ATP-Binding Cassette (ABC) Transporters
journal, January 1999

  • Saurin, William; Hofnung, Maurice; Dassa, Elie
  • Journal of Molecular Evolution, Vol. 48, Issue 1
  • DOI: 10.1007/pl00006442

A division inhibitor and a topological specificity factor coded for by the minicell locus determine proper placement of the division septum in E. coli
journal, February 1989


On the essentiality of lipopolysaccharide to Gram-negative bacteria
journal, December 2013

  • Zhang, Ge; Meredith, Timothy C.; Kahne, Daniel
  • Current Opinion in Microbiology, Vol. 16, Issue 6
  • DOI: 10.1016/j.mib.2013.09.007

Multifaceted structures and mechanisms of ABC transport systems in health and disease
journal, August 2018


Cystic fibrosis-type mutational analysis in the ATP-binding cassette transporter signature of human P-glycoprotein MDR1.
journal, August 1994


A Peptidomimetic Antibiotic Interacts with the Periplasmic Domain of LptD from Pseudomonas aeruginosa
journal, January 2018


Probing the Barrier Function of the Outer Membrane with Chemical Conditionality
journal, July 2006

  • Ruiz, Natividad; Wu, Tao; Kahne, Daniel
  • ACS Chemical Biology, Vol. 1, Issue 6
  • DOI: 10.1021/cb600128v

Novobiocin Enhances Polymyxin Activity by Stimulating Lipopolysaccharide Transport
journal, April 2018

  • Mandler, Michael D.; Baidin, Vadim; Lee, James
  • Journal of the American Chemical Society, Vol. 140, Issue 22
  • DOI: 10.1021/jacs.8b02283

Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter
journal, November 2014

  • Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6419

Lipopolysaccharide transport and assembly at the outer membrane: the PEZ model
journal, March 2016

  • Okuda, Suguru; Sherman, David J.; Silhavy, Thomas J.
  • Nature Reviews Microbiology, Vol. 14, Issue 6
  • DOI: 10.1038/nrmicro.2016.25

Mechanistic diversity in ATP-binding cassette (ABC) transporters
journal, June 2016

  • Locher, Kaspar P.
  • Nature Structural & Molecular Biology, Vol. 23, Issue 6
  • DOI: 10.1038/nsmb.3216

Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG
journal, August 2017


Pushing the envelope: LPS modifications and their consequences
journal, May 2019


Structural basis of unidirectional export of lipopolysaccharide to the cell surface
journal, March 2019


Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging
journal, October 2014

  • Yaginuma, Hideyuki; Kawai, Shinnosuke; Tabata, Kazuhito V.
  • Scientific Reports, Vol. 4, Issue 1
  • DOI: 10.1038/srep06522

Characterization of the human multidrug resistance protein containing mutations in the ATP-binding cassette signature region
journal, May 1997

  • Bakos, Éva; Klein, Izabella; Welker, Ervin
  • Biochemical Journal, Vol. 323, Issue 3
  • DOI: 10.1042/bj3230777

Functional consequences of mutations in the conserved 'signature sequence' of the ATP-binding-cassette protein MalK
journal, December 1999


Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli
journal, August 2012

  • Yao, Z.; Davis, R. M.; Kishony, R.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 38
  • DOI: 10.1073/pnas.1209742109

Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport
journal, March 2014

  • Sherman, David J.; Lazarus, Michael B.; Murphy, Lea
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 13
  • DOI: 10.1073/pnas.1323516111

Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors
journal, May 2018

  • Zhang, Ge; Baidin, Vadim; Pahil, Karanbir S.
  • Proceedings of the National Academy of Sciences, Vol. 115, Issue 26
  • DOI: 10.1073/pnas.1804670115

ATP Induces Conformational Changes of Periplasmic Loop Regions of the Maltose ATP-binding Cassette Transporter
journal, January 2006


The Pfam protein families database
journal, December 2007

  • Finn, R. D.; Tate, J.; Mistry, J.
  • Nucleic Acids Research, Vol. 36, Issue Database
  • DOI: 10.1093/nar/gkm960

Structure and mechanism of ATP-binding cassette transporters
journal, October 2008

  • Locher, Kaspar P.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 364, Issue 1514
  • DOI: 10.1098/rstb.2008.0125

Subunit interactions in ABC transporters: towards a functional architecture
journal, October 1999


Expanding the paradigm for the outer membrane: Acinetobacter baumannii in the absence of endotoxin
journal, November 2017

  • Powers, Matthew Joseph; Trent, M. Stephen
  • Molecular Microbiology, Vol. 107, Issue 1
  • DOI: 10.1111/mmi.13872

Peptidomimetic Antibiotics Target Outer-Membrane Biogenesis in Pseudomonas aeruginosa
journal, February 2010


Lipopolysaccharide is transported to the cell surface by a membrane-to-membrane protein bridge
journal, February 2018


Functional Analysis of the Protein Machinery Required for Transport of Lipopolysaccharide to the Outer Membrane of Escherichia coli
journal, April 2008

  • Sperandeo, P.; Lau, F. K.; Carpentieri, A.
  • Journal of Bacteriology, Vol. 190, Issue 13
  • DOI: 10.1128/jb.00270-08

Molecular Basis of Bacterial Outer Membrane Permeability Revisited
journal, December 2003