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Title: Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells

Abstract

Chronic bacterial infections are difficult to eradicate, though they are caused primarily by drug-susceptible pathogens. Antibiotic-tolerant persisters largely account for this paradox. In spite of their significance in the recalcitrance of chronic infections, the mechanism of persister formation is poorly understood. We previously reported that a decrease in ATP levels leads to drug tolerance inEscherichia coli,Pseudomonas aeruginosa, andStaphylococcus aureus. We reasoned that stochastic fluctuation in the expression of tricarboxylic acid (TCA) cycle enzymes can produce cells with low energy levels.S. aureusknockouts in glutamate dehydrogenase, 2-oxoketoglutarate dehydrogenase, succinyl coenzyme A (CoA) synthetase, and fumarase have low ATP levels and exhibit increased tolerance of fluoroquinolone, aminoglycoside, and β-lactam antibiotics. Fluorescence-activated cell sorter (FACS) analysis of TCA genes shows a broad Gaussian distribution in a population, with differences of over 3 orders of magnitude in the levels of expression between individual cells. Sorted cells with low levels of TCA enzyme expression have an increased tolerance of antibiotic treatment. Here, these findings suggest that fluctuations in the levels of expression of energy-generating components serve as a mechanism of persister formation. Persister cells are rare phenotypic variants that are able to survive antibiotic treatment. Unlike resistant bacteria, which have specific mechanisms to prevent antibiotics frommore » binding to their targets, persisters evade antibiotic killing by entering a tolerant nongrowing state. Persisters have been implicated in chronic infections in multiple species, and growing evidence suggests that persister cells are responsible for many cases of antibiotic treatment failure. New antibiotic treatment strategies aim to kill tolerant persister cells more effectively, but the mechanism of tolerance has remained unclear until now.« less

Authors:
 [1];  [2];  [1]; ORCiD logo [3];  [4];  [4]; ORCiD logo [3]; ORCiD logo [1]
  1. Northeastern Univ., Boston, MA (United States)
  2. Northeastern Univ., Boston, MA (United States); Univ. of Nebraska at Kearney, Kearney, NE (United States)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  4. North Carolina School of Medicine, Chapel Hill, NC (United States)
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1573351
Report Number(s):
PNNL-SA-147078
Journal ID: ISSN 2150-7511
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 10; Journal Issue: 5; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zalis, Eliza A., Nuxoll, Austin S., Manuse, Sylvie, Clair, Geremy, Radlinski, Lauren C., Conlon, Brian P., Adkins, Joshua N., and Lewis, Kim. Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. United States: N. p., 2019. Web. doi:10.1128/mBio.01930-19.
Zalis, Eliza A., Nuxoll, Austin S., Manuse, Sylvie, Clair, Geremy, Radlinski, Lauren C., Conlon, Brian P., Adkins, Joshua N., & Lewis, Kim. Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells. United States. doi:10.1128/mBio.01930-19.
Zalis, Eliza A., Nuxoll, Austin S., Manuse, Sylvie, Clair, Geremy, Radlinski, Lauren C., Conlon, Brian P., Adkins, Joshua N., and Lewis, Kim. Tue . "Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells". United States. doi:10.1128/mBio.01930-19. https://www.osti.gov/servlets/purl/1573351.
@article{osti_1573351,
title = {Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells},
author = {Zalis, Eliza A. and Nuxoll, Austin S. and Manuse, Sylvie and Clair, Geremy and Radlinski, Lauren C. and Conlon, Brian P. and Adkins, Joshua N. and Lewis, Kim},
abstractNote = {Chronic bacterial infections are difficult to eradicate, though they are caused primarily by drug-susceptible pathogens. Antibiotic-tolerant persisters largely account for this paradox. In spite of their significance in the recalcitrance of chronic infections, the mechanism of persister formation is poorly understood. We previously reported that a decrease in ATP levels leads to drug tolerance inEscherichia coli,Pseudomonas aeruginosa, andStaphylococcus aureus. We reasoned that stochastic fluctuation in the expression of tricarboxylic acid (TCA) cycle enzymes can produce cells with low energy levels.S. aureusknockouts in glutamate dehydrogenase, 2-oxoketoglutarate dehydrogenase, succinyl coenzyme A (CoA) synthetase, and fumarase have low ATP levels and exhibit increased tolerance of fluoroquinolone, aminoglycoside, and β-lactam antibiotics. Fluorescence-activated cell sorter (FACS) analysis of TCA genes shows a broad Gaussian distribution in a population, with differences of over 3 orders of magnitude in the levels of expression between individual cells. Sorted cells with low levels of TCA enzyme expression have an increased tolerance of antibiotic treatment. Here, these findings suggest that fluctuations in the levels of expression of energy-generating components serve as a mechanism of persister formation. Persister cells are rare phenotypic variants that are able to survive antibiotic treatment. Unlike resistant bacteria, which have specific mechanisms to prevent antibiotics from binding to their targets, persisters evade antibiotic killing by entering a tolerant nongrowing state. Persisters have been implicated in chronic infections in multiple species, and growing evidence suggests that persister cells are responsible for many cases of antibiotic treatment failure. New antibiotic treatment strategies aim to kill tolerant persister cells more effectively, but the mechanism of tolerance has remained unclear until now.},
doi = {10.1128/mBio.01930-19},
journal = {mBio (Online)},
number = 5,
volume = 10,
place = {United States},
year = {2019},
month = {9}
}

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Works referenced in this record:

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
journal, June 2014

  • Cox, Jürgen; Hein, Marco Y.; Luber, Christian A.
  • Molecular & Cellular Proteomics, Vol. 13, Issue 9
  • DOI: 10.1074/mcp.M113.031591

Two regulatory RNA elements affect TisB-dependent depolarization and persister formation: RNA-based regulation of depolarization and persistence
journal, January 2017

  • Berghoff, Bork A.; Hoekzema, Mirthe; Aulbach, Lena
  • Molecular Microbiology, Vol. 103, Issue 6
  • DOI: 10.1111/mmi.13607

Persister Cells
journal, October 2010


Persister-promoting bacterial toxin TisB produces anion-selective pores in planar lipid bilayers
journal, June 2012


Inactivation of TCA cycle enhances Staphylococcus aureus persister cell formation in stationary phase
journal, July 2018

  • Wang, Ying; Bojer, Martin Saxtorph; George, Shilpa Elizabeth
  • Scientific Reports, Vol. 8, Issue 1
  • DOI: 10.1038/s41598-018-29123-0

HipBA–promoter structures reveal the basis of heritable multidrug tolerance
journal, July 2015

  • Schumacher, Maria A.; Balani, Pooja; Min, Jungki
  • Nature, Vol. 524, Issue 7563
  • DOI: 10.1038/nature14662

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

Kinase Activity of Overexpressed HipA Is Required for Growth Arrest and Multidrug Tolerance in Escherichia coli
journal, October 2006

  • Correia, F. F.; D'Onofrio, A.; Rejtar, T.
  • Journal of Bacteriology, Vol. 188, Issue 24, p. 8360-8367
  • DOI: 10.1128/JB.01237-06

ATP-Dependent Persister Formation in Escherichia coli
journal, February 2017


Staphylococcus aureus Aconitase Inactivation Unexpectedly Inhibits Post-Exponential-Phase Growth and Enhances Stationary-Phase Survival
journal, November 2002


Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression
journal, February 2017


HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase
journal, December 2013

  • Kaspy, Ilana; Rotem, Eitan; Weiss, Noga
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms4001

Molecular Mechanism of Bacterial Persistence by HipA
journal, October 2013


Fiji: an open-source platform for biological-image analysis
journal, June 2012

  • Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin
  • Nature Methods, Vol. 9, Issue 7
  • DOI: 10.1038/nmeth.2019

A Genetic Resource for Rapid and Comprehensive Phenotype Screening of Nonessential Staphylococcus aureus Genes
journal, February 2013

  • Fey, Paul D.; Endres, Jennifer L.; Yajjala, Vijaya Kumar
  • mBio, Vol. 4, Issue 1
  • DOI: 10.1128/mBio.00537-12

Simple method for correct enumeration of Staphylococcus aureus
journal, June 2016


A genome-wide strategy for the identification of essential genes in Staphylococcus aureus
journal, March 2002


Prophages and Growth Dynamics Confound Experimental Results with Antibiotic-Tolerant Persister Cells
journal, December 2017


Reassessing the Role of Type II Toxin-Antitoxin Systems in Formation of Escherichia coli Type II Persister Cells
journal, June 2018

  • Goormaghtigh, Frédéric; Fraikin, Nathan; Putrinš, Marta
  • mBio, Vol. 9, Issue 3
  • DOI: 10.1128/mBio.00640-18

Molecular Mechanisms Underlying Bacterial Persisters
journal, April 2014


JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
journal, July 2005

  • Grote, A.; Hiller, K.; Scheer, M.
  • Nucleic Acids Research, Vol. 33, Issue Web Server
  • DOI: 10.1093/nar/gki376

Treatment of Staphylococcal Infections with Penicillin by Intermittent Sterilisation
journal, October 1944


The Persistence-Inducing Toxin HokB Forms Dynamic Pores That Cause ATP Leakage
journal, August 2018

  • Wilmaerts, Dorien; Bayoumi, Mariam; Dewachter, Liselot
  • mBio, Vol. 9, Issue 4
  • DOI: 10.1128/mBio.00744-18

Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli
journal, February 2010


Persister formation in Staphylococcus aureus is associated with ATP depletion
journal, April 2016


A Genetic Determinant of Persister Cell Formation in Bacterial Pathogens
journal, June 2018

  • Cameron, David R.; Shan, Yue; Zalis, Eliza A.
  • Journal of Bacteriology, Vol. 200, Issue 17
  • DOI: 10.1128/JB.00303-18

A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation
journal, January 2011

  • Liebeke, Manuel; Dörries, Kirsten; Zühlke, Daniela
  • Molecular BioSystems, Vol. 7, Issue 4
  • DOI: 10.1039/c0mb00315h

Cell type-resolved human lung lipidome reveals cellular cooperation in lung function
journal, September 2018