skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae

Abstract

Aerobactin, a citryl-hydroxamate siderophore, is produced by a number of pathogenic Gram-negative bacteria to aid in iron assimilation. Interest in this well-known siderophore was reignited by recent investigations suggesting that it plays a key role in mediating the enhanced virulence of a hypervirulent pathotype of Klebsiella pneumoniae (hvKP). In contrast to classical opportunistic strains of K. pneumoniae, hvKP causes serious life-threatening infections in previously healthy individuals in the community. Multiple contemporary reports have confirmed fears that the convergence of multidrug-resistant and hvKP pathotypes has led to the evolution of a highly transmissible, drug-resistant, and virulent “super bug.” Despite hvKP harboring four distinct siderophore operons, knocking out production of only aerobactin led to a significant attenuation of virulence. Herein, we continue our structural and functional studies on the biosynthesis of this crucial virulence factor. In vivo heterologous production and in vitro reconstitution of aerobactin biosynthesis from hvKP was carried out in this work, demonstrating the specificity, stereoselectivity, and kinetic throughput of the complete pathway. Additionally, we present a steady-state kinetic analysis and the X-ray crystal structure of the second aerobactin synthetase IucC, as well as describe a surface entropy reduction strategy that was employed for structure determination. Finally, we show solutionmore » X-ray scattering data that support a unique dimeric quaternary structure for IucC. These new insights into aerobactin assembly will help inform potential antivirulence strategies and advance our understanding of siderophore biosynthesis.« less

Authors:
 [1];  [2];  [3];  [1];  [1];  [2]; ORCiD logo [1]
  1. State Univ. of New York (SUNY), Buffalo, NY (United States); Hauptman-Woodward Medical Research Inst., Buffalo, NY (United States)
  2. Univ. of Minnesota, Minneapolis, MN (United States)
  3. Hauptman-Woodward Medical Research Inst., Buffalo, NY (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); The Buffalo Clinical and Translational Research Center; Richard W. and Mae Stone Goode Foundation; National Cancer Institute (NCI); National Institute of General Medical Sciences (NIGMS); USDOE
OSTI Identifier:
1439640
Grant/Contract Number:  
AI116998; UL1TR001412; ACB-12002; AGM-12006; AC02-06CH11357; 1S10OD012289-01A1; T32-AI007614
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 293; Journal Issue: 20; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; siderophore; natural product biosynthesis; structural biology; enzyme structure; Klebsiella pneumonia; protein structure; X-ray crystallography; Aerobactin; Surface Entropy Reduction

Citation Formats

Bailey, Daniel C., Alexander, Evan, Rice, Matthew R., Drake, Eric J., Mydy, Lisa S., Aldrich, Courtney C., and Gulick, Andrew M. Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae. United States: N. p., 2018. Web. doi:10.1074/jbc.RA118.002798.
Bailey, Daniel C., Alexander, Evan, Rice, Matthew R., Drake, Eric J., Mydy, Lisa S., Aldrich, Courtney C., & Gulick, Andrew M. Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae. United States. doi:10.1074/jbc.RA118.002798.
Bailey, Daniel C., Alexander, Evan, Rice, Matthew R., Drake, Eric J., Mydy, Lisa S., Aldrich, Courtney C., and Gulick, Andrew M. Wed . "Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae". United States. doi:10.1074/jbc.RA118.002798. https://www.osti.gov/servlets/purl/1439640.
@article{osti_1439640,
title = {Structural and functional delineation of aerobactin biosynthesis in hypervirulent Klebsiella pneumoniae},
author = {Bailey, Daniel C. and Alexander, Evan and Rice, Matthew R. and Drake, Eric J. and Mydy, Lisa S. and Aldrich, Courtney C. and Gulick, Andrew M.},
abstractNote = {Aerobactin, a citryl-hydroxamate siderophore, is produced by a number of pathogenic Gram-negative bacteria to aid in iron assimilation. Interest in this well-known siderophore was reignited by recent investigations suggesting that it plays a key role in mediating the enhanced virulence of a hypervirulent pathotype of Klebsiella pneumoniae (hvKP). In contrast to classical opportunistic strains of K. pneumoniae, hvKP causes serious life-threatening infections in previously healthy individuals in the community. Multiple contemporary reports have confirmed fears that the convergence of multidrug-resistant and hvKP pathotypes has led to the evolution of a highly transmissible, drug-resistant, and virulent “super bug.” Despite hvKP harboring four distinct siderophore operons, knocking out production of only aerobactin led to a significant attenuation of virulence. Herein, we continue our structural and functional studies on the biosynthesis of this crucial virulence factor. In vivo heterologous production and in vitro reconstitution of aerobactin biosynthesis from hvKP was carried out in this work, demonstrating the specificity, stereoselectivity, and kinetic throughput of the complete pathway. Additionally, we present a steady-state kinetic analysis and the X-ray crystal structure of the second aerobactin synthetase IucC, as well as describe a surface entropy reduction strategy that was employed for structure determination. Finally, we show solution X-ray scattering data that support a unique dimeric quaternary structure for IucC. These new insights into aerobactin assembly will help inform potential antivirulence strategies and advance our understanding of siderophore biosynthesis.},
doi = {10.1074/jbc.RA118.002798},
journal = {Journal of Biological Chemistry},
issn = {0021-9258},
number = 20,
volume = 293,
place = {United States},
year = {2018},
month = {4}
}

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:

“Nightmare” Bacteria on the Rise in US Hospitals, Long-term Care Facilities
journal, April 2013


Necrotizing fasciitis and psoas abscess caused by hypervirulent Klebsiella pneumoniae
journal, January 2013


AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis
journal, February 2009

  • Schmelz, Stefan; Kadi, Nadia; McMahon, Stephen A.
  • Nature Chemical Biology, Vol. 5, Issue 3
  • DOI: 10.1038/nchembio.145

Analysis of a DtxR-Regulated Iron Transport and Siderophore Biosynthesis Gene Cluster in Corynebacterium diphtheriae
journal, January 2005


Protein interface classification by evolutionary analysis
journal, January 2012

  • Duarte, Jose M.; Srebniak, Adam; Schärer, Martin A.
  • BMC Bioinformatics, Vol. 13, Issue 1
  • DOI: 10.1186/1471-2105-13-334

Primary osteomyelitis caused by hypervirulent Klebsiella pneumoniae
journal, September 2016


Yersiniabactin Synthetase
journal, March 2002


Aerobactin production by a planktonic marine Vibrio sp
journal, July 1993

  • Haygood, Margo G.; Holt, Pamela D.; Butler, Alison
  • Limnology and Oceanography, Vol. 38, Issue 5
  • DOI: 10.4319/lo.1993.38.5.1091

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
journal, December 2007

  • Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1
  • DOI: 10.1107/S090744490705024X

Optimization of protein purification and characterization using Thermofluor screens
journal, October 2013

  • Boivin, Stephane; Kozak, Sandra; Meijers, Rob
  • Protein Expression and Purification, Vol. 91, Issue 2
  • DOI: 10.1016/j.pep.2013.08.002

The isolation and characterization of a hydroxamic acid (aerobactin) formed by Aerobacter aerogenes 62-1
journal, November 1969


A Continuous Spectrophotometric Assay for the Aminoacylation of Transfer RNA by Alanyl-Transfer RNA Synthetase
journal, June 1993


Hypervirulent Klebsiella pneumoniae
journal, March 2014

  • Patel, P. K.; Russo, T. A.; Karchmer, A. W.
  • Open Forum Infectious Diseases, Vol. 1, Issue 1
  • DOI: 10.1093/ofid/ofu028

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

A New Method for the Synthesis ofN.epsilon.-Acetyl-N.epsilon.-hydroxy-L-lysine, the Iron-Binding Constituent of Several Important Siderophores
journal, August 1994

  • Hu, Jingdan; Miller, Marvin J.
  • The Journal of Organic Chemistry, Vol. 59, Issue 17
  • DOI: 10.1021/jo00096a030

Isolation and properties of N.epsilon.-hydroxylysine:acetyl coenzyme A N.epsilon.-transacetylase from Escherichia coli pABN11
journal, May 1986

  • Coy, Mark; Paw, Barry H.; Bindereif, Albrecht
  • Biochemistry, Vol. 25, Issue 9
  • DOI: 10.1021/bi00357a030

Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12.
journal, February 1986


Photoreactivity of Iron(III)−Aerobactin:  Photoproduct Structure and Iron(III) Coordination
journal, July 2006

  • Küpper, Frithjof C.; Carrano, Carl J.; Kuhn, Jens-Uwe
  • Inorganic Chemistry, Vol. 45, Issue 15
  • DOI: 10.1021/ic0604967

Protein crystallization by surface entropy reduction: optimization of the SER strategy
journal, April 2007

  • Cooper, David R.; Boczek, Tomasz; Grelewska, Katarzyna
  • Acta Crystallographica Section D Biological Crystallography, Vol. 63, Issue 5
  • DOI: 10.1107/S0907444907010931

Inference of Macromolecular Assemblies from Crystalline State
journal, September 2007


Universal chemical assay for the detection and determination of siderophores
journal, January 1987


A fatal outbreak of ST11 carbapenem-resistant hypervirulent Klebsiella pneumoniae in a Chinese hospital: a molecular epidemiological study
journal, January 2018


Functional and Structural Analysis of the Siderophore Synthetase AsbB through Reconstitution of the Petrobactin Biosynthetic Pathway from Bacillus anthracis
journal, March 2012

  • Nusca, Tyler D.; Kim, Youngchang; Maltseva, Natalia
  • Journal of Biological Chemistry, Vol. 287, Issue 19
  • DOI: 10.1074/jbc.M112.359349

Klebsiella pneumoniae Antimicrobial Drug Resistance, United States, 1998–2010
journal, January 2013

  • Sanchez, Guillermo V.; Master, Ronald N.; Clark, Richard B.
  • Emerging Infectious Diseases, Vol. 19, Issue 1
  • DOI: 10.3201/eid1901.120310

Klebsiella pneumoniae liver abscess in an immunocompetent child
journal, January 2013


The changing face of Klebsiella pneumoniae infections in the community
journal, November 2007


Structural and Functional Characterization of Aerobactin Synthetase IucA from a Hypervirulent Pathotype of Klebsiella pneumoniae
journal, June 2016


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Klebsiella spp. as Nosocomial Pathogens: Epidemiology, Taxonomy, Typing Methods, and Pathogenicity Factors
journal, October 1998

  • Podschun, R.; Ullmann, U.
  • Clinical Microbiology Reviews, Vol. 11, Issue 4
  • DOI: 10.1128/CMR.11.4.589

Resolution of a citric acid derivative: synthesis of (R)-(−)-homocitric acid-γ-lactone
journal, October 1997


Molecular pathogenesis of Klebsiella pneumoniae
journal, September 2014

  • Li, Bei; Zhao, Yuling; Liu, Changting
  • Future Microbiology, Vol. 9, Issue 9
  • DOI: 10.2217/fmb.14.48

Thermofluor-based high-throughput stability optimization of proteins for structural studies
journal, October 2006

  • Ericsson, Ulrika B.; Hallberg, B. Martin; DeTitta, George T.
  • Analytical Biochemistry, Vol. 357, Issue 2
  • DOI: 10.1016/j.ab.2006.07.027

How pathogenic bacteria evade mammalian sabotage in the battle for iron
journal, February 2006

  • Fischbach, Michael A.; Lin, Hening; Liu, David R.
  • Nature Chemical Biology, Vol. 2, Issue 3
  • DOI: 10.1038/nchembio771

New developments in the ATSAS program package for small-angle scattering data analysis
journal, March 2012

  • Petoukhov, Maxim V.; Franke, Daniel; Shkumatov, Alexander V.
  • Journal of Applied Crystallography, Vol. 45, Issue 2
  • DOI: 10.1107/S0021889812007662

The emergence of Klebsiella pneumoniae endogenous endophthalmitis in the USA: basic and clinical advances
journal, January 2013

  • Kashani, Amir H.; Eliott, Dean
  • Journal of Ophthalmic Inflammation and Infection, Vol. 3, Issue 1
  • DOI: 10.1186/1869-5760-3-28

Convergence of carbapenem-resistance and hypervirulence in Klebsiella pneumoniae
journal, January 2018


Breaking a pathogen's iron will: Inhibiting siderophore production as an antimicrobial strategy
journal, August 2015


FAD and substrate analogs as probes for lysine N6-hydroxylase from Escherichia coli EN 222
journal, May 1993


Trends in Resistance to Carbapenems and Third-Generation Cephalosporins among Clinical Isolates of Klebsiella pneumoniae in the United States, 1999–2010
journal, March 2013

  • Braykov, Nikolay P.; Eber, Michael R.; Klein, Eili Y.
  • Infection Control & Hospital Epidemiology, Vol. 34, Issue 3
  • DOI: 10.1086/669523

Klebsiella pneumoniae Liver Abscess Associated With Septic Endophthalmitis
journal, October 1986


Mapping the Evolution of Hypervirulent Klebsiella pneumoniae
journal, July 2015


Biological small-angle X-ray scattering facility at the Stanford Synchrotron Radiation Laboratory
journal, April 2007

  • Smolsky, Igor L.; Liu, Ping; Niebuhr, Marc
  • Journal of Applied Crystallography, Vol. 40, Issue s1
  • DOI: 10.1107/S0021889807009624

Hypervirulent (hypermucoviscous) Klebsiella pneumoniae : A new and dangerous breed
journal, February 2013

  • Shon, Alyssa S.; Bajwa, Rajinder P. S.; Russo, Thomas A.
  • Virulence, Vol. 4, Issue 2
  • DOI: 10.4161/viru.22718

Purification and Structural Characterization of Siderophore (Corynebactin) from Corynebacterium diphtheriae
journal, April 2012


An integrated high-throughput data acquisition system for biological solution X-ray scattering studies
journal, March 2012

  • Martel, Anne; Liu, Ping; Weiss, Thomas M.
  • Journal of Synchrotron Radiation, Vol. 19, Issue 3
  • DOI: 10.1107/S0909049512008072

Necrotizing Fasciitis Caused by Hypermucoviscous Klebsiella pneumoniae in a Filipino Female in North America
journal, January 2015


Characterization of iucA and iucC genes of the aerobactin system of plasmid ColV-K30 in Escherichia coli.
journal, July 1986


Hypervirulent Klebsiella pneumoniae: the next superbug?
journal, June 2012

  • Shon, Alyssa S.; Russo, Thomas A.
  • Future Microbiology, Vol. 7, Issue 6
  • DOI: 10.2217/fmb.12.43

The accurate assessment of small-angle X-ray scattering data
journal, January 2015

  • Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 71, Issue 1
  • DOI: 10.1107/S1399004714010876

Novel Cord-like Structures on MRI in a Case of Hypervirulent <i>Klebsiella pneumoniae</i>
journal, January 2015


Enantioselective desymmetrisation of citric acid catalysed by the substrate-tolerant petrobactin biosynthetic enzyme AsbA
journal, January 2009

  • Oves-Costales, Daniel; Song, Lijiang; Challis, Gregory L.
  • Chemical Communications, Issue 11
  • DOI: 10.1039/b823147h

A deliberate approach to screening for initial crystallization conditions of biological macromolecules
journal, April 2003


Structural Basis for Acyl Acceptor Specificity in the Achromobactin Biosynthetic Enzyme AcsD
journal, September 2011

  • Schmelz, Stefan; Botting, Catherine H.; Song, Lijiang
  • Journal of Molecular Biology, Vol. 412, Issue 3
  • DOI: 10.1016/j.jmb.2011.07.059

Draft Genome Sequence of the Hypervirulent Klebsiella pneumoniae Strain hvKP1, Isolated in Buffalo, New York
journal, February 2013


The long-overlooked enzymology of a nonribosomal peptide synthetase-independent pathway for virulence-conferring siderophore biosynthesis
journal, January 2009

  • Oves-Costales, Daniel; Kadi, Nadia; Challis, Gregory L.
  • Chemical Communications, Issue 43
  • DOI: 10.1039/B913092F

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