The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport

May, Janine M.; Owens, Tristan W.; Mandler, Michael D.; Simpson, Brent W.; Lazarus, Michael B.; Sherman, David J.; Davis, Rebecca M.; Okuda, Suguru; Massefski, Walter; Ruiz, Natividad; Kahne, Daniel

doi:10.1021/jacs.7b07736

The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport

Journal Article · Tue Nov 14 00:00:00 EST 2017 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/jacs.7b07736· OSTI ID:1430332

May, Janine M. ^[1]; Owens, Tristan W. ^[1]; Mandler, Michael D. ^[1]; Simpson, Brent W. ^[2]; Lazarus, Michael B. ^[1]; Sherman, David J. ^[1]; Davis, Rebecca M. ^[2]; Okuda, Suguru ^[1]; Massefski, Walter ^[3]; Ruiz, Natividad ^[2]; ^[1]

Harvard Univ., Cambridge, MA (United States). Dept. of Chemistry and Chemical Biology
The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Chemistry

Novobiocin is an orally active antibiotic that inhibits DNA gyrase by binding the ATP-binding site in the ATPase subunit. Although effective against Gram-positive pathogens, novobiocin has limited activity against Gram-negative organisms due to the presence of the lipopolysaccharide-containing outer membrane, which acts as a permeability barrier. Using a novobiocin-sensitive Escherichia coli strain with a leaky outer membrane, we identified a mutant with increased resistance to novobiocin. Unexpectedly, the mutation that increases novobiocin resistance was not found to alter gyrase, but the ATPase that powers lipopolysaccharide (LPS) transport. Co-crystal structures, biochemical, and genetic evidence show novobiocin directly binds this ATPase. Novobiocin does not bind the ATP binding site but rather the interface between the ATPase subunits and the transmembrane subunits of the LPS transporter. This interaction increases the activity of the LPS transporter, which in turn alters the permeability of the outer membrane. We propose that novobiocin will be a useful tool for understanding how ATP hydrolysis is coupled to LPS transport.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1430332

Journal Information:: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Journal Issue: 48 Vol. 139; ISSN 0002-7863

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (34)

Biochemical characterization of an ABC transporter LptBFGC complex required for the outer membrane sorting of lipopolysaccharides Narita, Shin-ichiro; Tokuda, Hajime FEBS Letters, Vol. 583, Issue 13 https://doi.org/10.1016/j.febslet.2009.05.051	journal	June 2009
Novel Structure of the Conserved Gram-Negative Lipopolysaccharide Transport Protein A and Mutagenesis Analysis Suits, Michael D. L.; Sperandeo, Paola; Dehò, Gianni Journal of Molecular Biology, Vol. 380, Issue 3 https://doi.org/10.1016/j.jmb.2008.04.045	journal	July 2008
Non-essential KDO biosynthesis and new essential cell envelope biogenesis genes in the Escherichia coli yrbG–yhbG locus Sperandeo, Paola; Pozzi, Clarissa; Dehò, Gianni Research in Microbiology, Vol. 157, Issue 6 https://doi.org/10.1016/j.resmic.2005.11.014	journal	July 2006
Structure and mechanism of ABC transporter proteins Hollenstein, Kaspar; Dawson, Roger JP; Locher, Kaspar P. Current Opinion in Structural Biology, Vol. 17, Issue 4 https://doi.org/10.1016/j.sbi.2007.07.003	journal	August 2007
Proteins Required for Lipopolysaccharide Assembly in Escherichia coli Form a Transenvelope Complex Chng, Shu-Sin; Gronenberg, Luisa S.; Kahne, Daniel Biochemistry, Vol. 49, Issue 22 https://doi.org/10.1021/bi100493e	journal	June 2010
Regulated Assembly of the Transenvelope Protein Complex Required for Lipopolysaccharide Export Freinkman, Elizaveta; Okuda, Suguru; Ruiz, Natividad Biochemistry, Vol. 51, Issue 24 https://doi.org/10.1021/bi300592c	journal	June 2012
Probing the Barrier Function of the Outer Membrane with Chemical Conditionality Ruiz, Natividad; Wu, Tao; Kahne, Daniel ACS Chemical Biology, Vol. 1, Issue 6 https://doi.org/10.1021/cb600128v	journal	July 2006
A New-Class Antibacterial—Almost. Lessons in Drug Discovery and Development: A Critical Analysis of More than 50 Years of Effort toward ATPase Inhibitors of DNA Gyrase and Topoisomerase IV Bisacchi, Gregory S.; Manchester, John I. ACS Infectious Diseases, Vol. 1, Issue 1 https://doi.org/10.1021/id500013t	journal	December 2014
Structural basis for outer membrane lipopolysaccharide insertion Dong, Haohao; Xiang, Quanju; Gu, Yinghong Nature, Vol. 511, Issue 7507 https://doi.org/10.1038/nature13464	journal	June 2014
Structural basis for lipopolysaccharide insertion in the bacterial outer membrane Qiao, Shuai; Luo, Qingshan; Zhao, Yan Nature, Vol. 511, Issue 7507 https://doi.org/10.1038/nature13484	journal	June 2014
Lipopolysaccharide transport and assembly at the outer membrane: the PEZ model Okuda, Suguru; Sherman, David J.; Silhavy, Thomas J. Nature Reviews Microbiology, Vol. 14, Issue 6 https://doi.org/10.1038/nrmicro.2016.25	journal	March 2016
Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG Luo, Qingshan; Yang, Xu; Yu, Shan Nature Structural & Molecular Biology, Vol. 24, Issue 5 https://doi.org/10.1038/nsmb.3399	journal	April 2017
Imp/OstA is required for cell envelope biogenesis in Escherichia coli: Imp/OstA and envelope biogenesis Braun, Martin; Silhavy, Thomas J. Molecular Microbiology, Vol. 45, Issue 5 https://doi.org/10.1046/j.1365-2958.2002.03091.x	journal	September 2002
Identification of an outer membrane protein required for the transport of lipopolysaccharide to the bacterial cell surface Bos, M. P.; Tefsen, B.; Geurtsen, J. Proceedings of the National Academy of Sciences, Vol. 101, Issue 25 https://doi.org/10.1073/pnas.0402340101	journal	June 2004
Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli Wu, T.; McCandlish, A. C.; Gronenberg, L. S. Proceedings of the National Academy of Sciences, Vol. 103, Issue 31 https://doi.org/10.1073/pnas.0604744103	journal	July 2006
Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli Ruiz, N.; Gronenberg, L. S.; Kahne, D. Proceedings of the National Academy of Sciences, Vol. 105, Issue 14 https://doi.org/10.1073/pnas.0801196105	journal	March 2008
Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane Chng, S. -S.; Ruiz, N.; Chimalakonda, G. Proceedings of the National Academy of Sciences, Vol. 107, Issue 12 https://doi.org/10.1073/pnas.0912872107	journal	March 2010
The complex that inserts lipopolysaccharide into the bacterial outer membrane forms a two-protein plug-and-barrel Freinkman, E.; Chng, S. -S.; Kahne, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 6 https://doi.org/10.1073/pnas.1015617108	journal	January 2011
Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli Yao, Z.; Davis, R. M.; Kishony, R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 38 https://doi.org/10.1073/pnas.1209742109	journal	August 2012
Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport Sherman, David J.; Lazarus, Michael B.; Murphy, Lea Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1323516111	journal	March 2014
Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. Gellert, M.; O'Dea, M. H.; Itoh, T. Proceedings of the National Academy of Sciences, Vol. 73, Issue 12 https://doi.org/10.1073/pnas.73.12.4474	journal	December 1976
Nalidixic acid resistance: A second genetic character involved in DNA gyrase activity Gellert, M.; Mizuuchi, K.; O'Dea, M. H. Proceedings of the National Academy of Sciences, Vol. 74, Issue 11 https://doi.org/10.1073/pnas.74.11.4772	journal	November 1977
Structure and Functional Analysis of LptC, a Conserved Membrane Protein Involved in the Lipopolysaccharide Export Pathway in Escherichia coli Tran, An X.; Dong, Changjiang; Whitfield, Chris Journal of Biological Chemistry, Vol. 285, Issue 43 https://doi.org/10.1074/jbc.M110.144709	journal	August 2010
The LptA Protein of Escherichia coli Is a Periplasmic Lipid A-binding Protein Involved in the Lipopolysaccharide Export Pathway Tran, An X.; Trent, M. Stephen; Whitfield, Chris Journal of Biological Chemistry, Vol. 283, Issue 29 https://doi.org/10.1074/jbc.M802503200	journal	July 2008
The Bacterial Cell Envelope Silhavy, T. J.; Kahne, D.; Walker, S. Cold Spring Harbor Perspectives in Biology, Vol. 2, Issue 5 https://doi.org/10.1101/cshperspect.a000414	journal	April 2010
Cytoplasmic ATP Hydrolysis Powers Transport of Lipopolysaccharide Across the Periplasm in E. coli Okuda, S.; Freinkman, E.; Kahne, D. Science, Vol. 338, Issue 6111 https://doi.org/10.1126/science.1228984	journal	November 2012
Functional Analysis of the Protein Machinery Required for Transport of Lipopolysaccharide to the Outer Membrane of Escherichia coli Sperandeo, P.; Lau, F. K.; Carpentieri, A. Journal of Bacteriology, Vol. 190, Issue 13 https://doi.org/10.1128/JB.00270-08	journal	April 2008
New Insights into the Lpt Machinery for Lipopolysaccharide Transport to the Cell Surface: LptA-LptC Interaction and LptA Stability as Sensors of a Properly Assembled Transenvelope Complex Sperandeo, P.; Villa, R.; Martorana, A. M. Journal of Bacteriology, Vol. 193, Issue 5 https://doi.org/10.1128/JB.01037-10	journal	December 2010
Characterization of lptA and lptB, Two Essential Genes Implicated in Lipopolysaccharide Transport to the Outer Membrane of Escherichia coli Sperandeo, P.; Cescutti, R.; Villa, R. Journal of Bacteriology, Vol. 189, Issue 1 https://doi.org/10.1128/JB.01126-06	journal	October 2006
Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems Davidson, A. L.; Dassa, E.; Orelle, C. Microbiology and Molecular Biology Reviews, Vol. 72, Issue 2 https://doi.org/10.1128/MMBR.00031-07	journal	June 2008
Molecular Basis of Bacterial Outer Membrane Permeability Revisited Nikaido, H. Microbiology and Molecular Biology Reviews, Vol. 67, Issue 4 https://doi.org/10.1128/MMBR.67.4.593-656.2003	journal	December 2003
Identification of Residues in the Lipopolysaccharide ABC Transporter That Coordinate ATPase Activity with Extractor Function Simpson, Brent W.; Owens, Tristan W.; Orabella, Matthew J. mBio, Vol. 7, Issue 5 https://doi.org/10.1128/mBio.01729-16	journal	October 2016
Lipopolysaccharide Endotoxins Raetz, Christian R. H.; Whitfield, Chris Annual Review of Biochemistry, Vol. 71, Issue 1 https://doi.org/10.1146/annurev.biochem.71.110601.135414	journal	June 2002
Multidrug Resistance in Bacteria Nikaido, Hiroshi Annual Review of Biochemistry, Vol. 78, Issue 1 https://doi.org/10.1146/annurev.biochem.78.082907.145923	journal	June 2009

Cited By (9)

Cryo-EM structures of lipopolysaccharide transporter LptB2FGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism Tang, Xiaodi; Chang, Shenghai; Luo, Qinghua Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-11977-1	journal	September 2019
Structural basis of unidirectional export of lipopolysaccharide to the cell surface Owens, Tristan W.; Taylor, Rebecca J.; Pahil, Karanbir S. Nature, Vol. 567, Issue 7749 https://doi.org/10.1038/s41586-019-1039-0	journal	March 2019
Countering Gram-Negative Antibiotic Resistance: Recent Progress in Disrupting the Outer Membrane with Novel Therapeutics Lehman, Kelly M.; Grabowicz, Marcin Antibiotics, Vol. 8, Issue 4 https://doi.org/10.3390/antibiotics8040163	journal	September 2019
Structural Basis for the Lipopolysaccharide Export Activity of the Bacterial Lipopolysaccharide Transport System Hicks, Greg; Jia, Zongchao International Journal of Molecular Sciences, Vol. 19, Issue 9 https://doi.org/10.3390/ijms19092680	journal	September 2018
Constructing and deconstructing the bacterial cell wall Fisher, Jed F.; Mobashery, Shahriar Protein Science, Vol. 29, Issue 3 https://doi.org/10.1002/pro.3737	journal	November 2019
Pushing the envelope: LPS modifications and their consequences Simpson, Brent W.; Trent, M. Stephen Nature Reviews Microbiology, Vol. 17, Issue 7 https://doi.org/10.1038/s41579-019-0201-x	journal	May 2019
Structural and functional investigation of the Small Ribosomal Subunit Biogenesis GTP ase A (RsgA) from Pseudomonas aeruginosa Rocchio, Serena; Santorelli, Daniele; Rinaldo, Serena The FEBS Journal, Vol. 286, Issue 21 https://doi.org/10.1111/febs.14959	journal	July 2019
Creative targeting of the Gram‐negative outer membrane in antibiotic discovery MacNair, Craig R.; Tsai, Caressa N.; Brown, Eric D. Annals of the New York Academy of Sciences, Vol. 1459, Issue 1 https://doi.org/10.1111/nyas.14280	journal	September 2019
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 Simpson, Brent W.; Pahil, Karanbir S.; Owens, Tristan W. mBio, Vol. 10, Issue 4 https://doi.org/10.1128/mBio.01931-19	journal	August 2019

Similar Records

Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

Journal Article · Fri Sep 26 00:00:00 EDT 2014 · Biochemical and Biophysical Research Communications · OSTI ID:22416746

Modification of Salmonella Lipopolysaccharides Prevents the Outer Membrane Penetration of Novobiocin

Journal Article · Mon Nov 30 23:00:00 EST 2015 · Biophysical Journal · OSTI ID:1415464

Structural Basis for the Lipopolysaccharide Export Activity of the Bacterial Lipopolysaccharide Transport System

Journal Article · Sun Sep 09 20:00:00 EDT 2018 · International Journal of Molecular Sciences (Online) · OSTI ID:1600798

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
59 BASIC BIOLOGICAL SCIENCES
antimicrobial agents
defects
genetics
membranes
vesicles

The Antibiotic Novobiocin Binds and Activates the ATPase That Powers Lipopolysaccharide Transport

Citation Formats

References (34)

Cited By (9)

Similar Records

Related Subjects