A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile
Abstract
AbstractTreatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival inmore »
- Authors:
-
- Univ. of South Florida, Tampa, FL (United States)
- Univ. of South Florida, Tampa, FL (United States). College of Public Health
- Univ. of Arizona, Tucson, AZ (United States)
- Rutgers Univ., Piscataway, NJ (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1879695
- Alternate Identifier(s):
- OSTI ID: 1900634
- Grant/Contract Number:
- AC02-06CH11357; S10_RR25528; S10_RR028976; R21 AI147654; R01 AI161762; R01 AI132711; R35 GM128624; R35 GM133617; T32 GM008804
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 13; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; antimicrobial resistance; bacteriology; pathogens; x-ray crystallography
Citation Formats
Sacco, Michael D., Wang, Shaohui, Adapa, Swamy R., Zhang, Xiujun, Lewandowski, Eric M., Gongora, Maura V., Keramisanou, Dimitra, Atlas, Zachary D., Townsend, Julia A., Gatdula, Jean R., Morgan, Ryan T., Hammond, Lauren R., Marty, Michael T., Wang, Jun, Eswara, Prahathees J., Gelis, Ioannis, Jiang, Rays H. Y., Sun, Xingmin, and Chen, Yu. A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. United States: N. p., 2022.
Web. doi:10.1038/s41467-022-32086-6.
Sacco, Michael D., Wang, Shaohui, Adapa, Swamy R., Zhang, Xiujun, Lewandowski, Eric M., Gongora, Maura V., Keramisanou, Dimitra, Atlas, Zachary D., Townsend, Julia A., Gatdula, Jean R., Morgan, Ryan T., Hammond, Lauren R., Marty, Michael T., Wang, Jun, Eswara, Prahathees J., Gelis, Ioannis, Jiang, Rays H. Y., Sun, Xingmin, & Chen, Yu. A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. United States. https://doi.org/10.1038/s41467-022-32086-6
Sacco, Michael D., Wang, Shaohui, Adapa, Swamy R., Zhang, Xiujun, Lewandowski, Eric M., Gongora, Maura V., Keramisanou, Dimitra, Atlas, Zachary D., Townsend, Julia A., Gatdula, Jean R., Morgan, Ryan T., Hammond, Lauren R., Marty, Michael T., Wang, Jun, Eswara, Prahathees J., Gelis, Ioannis, Jiang, Rays H. Y., Sun, Xingmin, and Chen, Yu. Thu .
"A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile". United States. https://doi.org/10.1038/s41467-022-32086-6. https://www.osti.gov/servlets/purl/1879695.
@article{osti_1879695,
title = {A unique class of Zn2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile},
author = {Sacco, Michael D. and Wang, Shaohui and Adapa, Swamy R. and Zhang, Xiujun and Lewandowski, Eric M. and Gongora, Maura V. and Keramisanou, Dimitra and Atlas, Zachary D. and Townsend, Julia A. and Gatdula, Jean R. and Morgan, Ryan T. and Hammond, Lauren R. and Marty, Michael T. and Wang, Jun and Eswara, Prahathees J. and Gelis, Ioannis and Jiang, Rays H. Y. and Sun, Xingmin and Chen, Yu},
abstractNote = {AbstractTreatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.},
doi = {10.1038/s41467-022-32086-6},
journal = {Nature Communications},
number = 1,
volume = 13,
place = {United States},
year = {Thu Jul 28 00:00:00 EDT 2022},
month = {Thu Jul 28 00:00:00 EDT 2022}
}
Works referenced in this record:
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
Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials
journal, February 2016
- Sauvage, Eric; Terrak, Mohammed
- Antibiotics, Vol. 5, Issue 1
Structural coordination of polymerization and crosslinking by a SEDS–bPBP peptidoglycan synthase complex
journal, March 2020
- Sjodt, Megan; Rohs, Patricia D. A.; Gilman, Morgan S. A.
- Nature Microbiology, Vol. 5, Issue 6
Rational design of a new antibiotic class for drug-resistant infections
journal, September 2021
- Durand-Reville, Thomas F.; Miller, Alita A.; O’Donnell, John P.
- Nature, Vol. 597, Issue 7878
Antibiotics and hospital-acquired Clostridium difficile infection: update of systematic review and meta-analysis
journal, December 2013
- Slimings, Claudia; Riley, Thomas V.
- Journal of Antimicrobial Chemotherapy, Vol. 69, Issue 4
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
Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 Å resolution
journal, September 1982
- Dideberg, O.; Charlier, P.; Dive, G.
- Nature, Vol. 299, Issue 5882
Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium
journal, January 2009
- Stabler, Richard A.; He, Miao; Dawson, Lisa
- Genome Biology, Vol. 10, Issue 9
Peptidoglycan Cross-Linking Activity of L,D-Transpeptidases from Clostridium difficile and Inactivation of These Enzymes by β-Lactams
journal, October 2017
- Sütterlin, Laetitia; Edoo, Zainab; Hugonnet, Jean-Emmanuel
- Antimicrobial Agents and Chemotherapy, Vol. 62, Issue 1
ImageJ2: ImageJ for the next generation of scientific image data
journal, November 2017
- Rueden, Curtis T.; Schindelin, Johannes; Hiner, Mark C.
- BMC Bioinformatics, Vol. 18, Issue 1
High-Throughput Analysis of Gene Essentiality and Sporulation in Clostridium difficile
journal, May 2015
- Dembek, Marcin; Barquist, Lars; Boinett, Christine J.
- mBio, Vol. 6, Issue 2
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
journal, October 2019
- Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L.
- Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10
The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis
journal, March 2008
- Sauvage, Eric; Kerff, Frédéric; Terrak, Mohammed
- FEMS Microbiology Reviews, Vol. 32, Issue 2
Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa
journal, December 2010
- Han, S.; Zaniewski, R. P.; Marr, E. S.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 51
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
How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function
journal, October 2013
- Otero, L. H.; Rojas-Altuve, A.; Llarrull, L. I.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 42
The Immune Protein Calprotectin Impacts Clostridioides difficile Metabolism through Zinc Limitation
journal, December 2019
- Lopez, Christopher A.; Beavers, William N.; Weiss, Andy
- mBio, Vol. 10, Issue 6
Susceptibilities of clinical Clostridium difficile isolates to antimicrobials: a systematic review and meta-analysis of studies since 1970
journal, February 2018
- Khanafer, N.; Daneman, N.; Greene, T.
- Clinical Microbiology and Infection, Vol. 24, Issue 2
Interactions of zinc- and redox-signaling pathways
journal, May 2021
- Hübner, Christopher; Haase, Hajo
- Redox Biology, Vol. 41
Sequencing and functional analysis of the genome of Bacillus subtilis strain 168
journal, June 1996
- Harwood, Colin R.; Wipat, Anil
- FEBS Letters, Vol. 389, Issue 1
MoRDa , an automatic molecular replacement pipeline
journal, August 2015
- Vagin, Alexey; Lebedev, Andrey
- Acta Crystallographica Section A Foundations and Advances, Vol. 71, Issue a1
Zinc Level and Its Role in Recurrent Clostridium difficile Infection: A Case Report and Literature Review
journal, January 2020
- Parvataneni, Swetha; Dasari, Avinash R.
- Journal of Investigative Medicine High Impact Case Reports, Vol. 8
Reversible inactivation of a peptidoglycan transpeptidase by a β-lactam antibiotic mediated by β-lactam-ring recyclization in the enzyme active site
journal, August 2017
- Edoo, Zainab; Arthur, Michel; Hugonnet, Jean-Emmanuel
- Scientific Reports, Vol. 7, Issue 1
Clostridium difficile Has an Original Peptidoglycan Structure with a High Level of N-Acetylglucosamine Deacetylation and Mainly 3-3 Cross-links
journal, August 2011
- Peltier, Johann; Courtin, Pascal; El Meouche, Imane
- Journal of Biological Chemistry, Vol. 286, Issue 33
Clostridium difficile Infection
journal, April 2015
- Leffler, Daniel A.; Lamont, J. Thomas
- New England Journal of Medicine, Vol. 372, Issue 16
Dietary zinc alters the microbiota and decreases resistance to Clostridium difficile infection
journal, September 2016
- Zackular, Joseph P.; Moore, Jessica L.; Jordan, Ashley T.
- Nature Medicine, Vol. 22, Issue 11
iMOSFLM : a new graphical interface for diffraction-image processing with MOSFLM
journal, March 2011
- Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Metallo‐β‐Lactamases: A Class Apart
journal, August 1998
- Bush, Karen
- Clinical Infectious Diseases, Vol. 27, Issue s1
SEDS proteins are a widespread family of bacterial cell wall polymerases
journal, August 2016
- Meeske, Alexander J.; Riley, Eammon P.; Robins, William P.
- Nature, Vol. 537, Issue 7622
Heliobacterium modesticaldum, sp. nov., a thermophilic heliobacterium of hot springs and volcanic soils
journal, April 1995
- Kimble, Linda K.; Mandelco, Linda; Woese, Carl R.
- Archives of Microbiology, Vol. 163, Issue 4
Determination of the in vitro Sporulation Frequency of Clostridium difficile
journal, January 2017
- Edwards, Adrianne; McBride, Shonna
- BIO-PROTOCOL, Vol. 7, Issue 3
The PSIPRED protein structure prediction server
journal, April 2000
- McGuffin, L. J.; Bryson, K.; Jones, D. T.
- Bioinformatics, Vol. 16, Issue 4
Zinc finger proteins: new insights into structural and functional diversity
journal, February 2001
- Laity, John H.; Lee, Brian M.; Wright, Peter E.
- Current Opinion in Structural Biology, Vol. 11, Issue 1
Bis‐Cyclic Guanidines as a Novel Class of Compounds Potent against Clostridium difficile
journal, June 2018
- Li, Chunhui; Teng, Peng; Peng, Zhong
- ChemMedChem, Vol. 13, Issue 14
Elimination of a good leaving group from the 3'-position of a cephalosporin need not be concerted with .beta.-lactam ring opening: TEM-2 .beta.-lactamase-catalyzed hydrolysis of pyridine-2-azo-4'-(N',N'-dimethylaniline) cephalosporin (PADAC) and of cephaloridine
journal, March 1984
- Faraci, W. Stephen; Pratt, R. F.
- Journal of the American Chemical Society, Vol. 106, Issue 5
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
REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011
- Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Crystal Structure of Penicillin-Binding Protein 3 (PBP3) from Escherichia coli
journal, May 2014
- Sauvage, Eric; Derouaux, Adeline; Fraipont, Claudine
- PLoS ONE, Vol. 9, Issue 5
Penicillin-binding protein SpoVD disulphide is a target for StoA in Bacillus subtilis forespores
journal, January 2010
- Liu, Yiming; Carlsson Möller, Mirja; Petersen, Lise
- Molecular Microbiology, Vol. 75, Issue 1
Molecular architecture of the PBP2–MreC core bacterial cell wall synthesis complex
journal, October 2017
- Contreras-Martel, Carlos; Martins, Alexandre; Ecobichon, Chantal
- Nature Communications, Vol. 8, Issue 1
Strain-Dependent RstA Regulation of Clostridioides difficile Toxin Production and Sporulation
journal, January 2020
- Edwards, Adrianne N.; Krall, Ellen G.; McBride, Shonna M.
- Journal of Bacteriology, Vol. 202, Issue 2
Role of the Intestinal Microbiota in Resistance to Colonization by Clostridium difficile
journal, May 2014
- Britton, Robert A.; Young, Vincent B.
- Gastroenterology, Vol. 146, Issue 6
Historical Perspectives on Studies of Clostridium difficile and C. difficile Infection
journal, January 2008
- Bartlett, John G.
- Clinical Infectious Diseases, Vol. 46, Issue s1
Automatic generation of protein structure cartoons with Pro-origami
journal, October 2011
- Stivala, A.; Wybrow, M.; Wirth, A.
- Bioinformatics, Vol. 27, Issue 23
Overview of Zinc Absorption and Excretion in the Human Gastrointestinal Tract
journal, May 2000
- Krebs, Nancy F.
- The Journal of Nutrition, Vol. 130, Issue 5
Cephamycins inhibit pathogen sporulation and effectively treat recurrent Clostridioides difficile infection
journal, August 2019
- Srikhanta, Yogitha N.; Hutton, Melanie L.; Awad, Milena M.
- Nature Microbiology, Vol. 4, Issue 12
Metal and Redox Modulation of Cysteine Protein Function
journal, August 2003
- Giles, Niroshini M.; Watts, Aaron B.; Giles, Gregory I.
- Chemistry & Biology, Vol. 10, Issue 8
HMMER web server: interactive sequence similarity searching
journal, May 2011
- Finn, R. D.; Clements, J.; Eddy, S. R.
- Nucleic Acids Research, Vol. 39, Issue suppl
Penicillin Binding Proteins: key players in bacterial cell cycle and drug resistance processes
journal, September 2006
- Macheboeuf, Pauline; Contreras-Martel, Carlos; Job, Viviana
- FEMS Microbiology Reviews, Vol. 30, Issue 5
When anaerobes encounter oxygen: mechanisms of oxygen toxicity, tolerance and defence
journal, June 2021
- Lu, Zheng; Imlay, James A.
- Nature Reviews Microbiology, Vol. 19, Issue 12
A novel regulator controls C lostridium difficile sporulation, motility and toxin production: A novel regulator of C. difficile physiology
journal, March 2016
- Edwards, Adrianne N.; Tamayo, Rita; McBride, Shonna M.
- Molecular Microbiology, Vol. 100, Issue 6
Antistaphylococcal Activity of Ceftobiprole, a New Broad-Spectrum Cephalosporin
journal, October 2005
- Bogdanovich, Tatiana; Ednie, Lois M.; Shapiro, Stuart
- Antimicrobial Agents and Chemotherapy, Vol. 49, Issue 10
The Role of Reactive Oxygen Species in Antibiotic-Mediated Killing of Bacteria
journal, June 2017
- Van Acker, Heleen; Coenye, Tom
- Trends in Microbiology, Vol. 25, Issue 6
Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay
journal, June 2021
- Ma, Chunlong; Sacco, Michael Dominic; Xia, Zilei
- ACS Central Science, Vol. 7, Issue 7
Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection
journal, December 2015
- Spigaglia, Patrizia
- Therapeutic Advances in Infectious Disease, Vol. 3, Issue 1
Structural Insight into the Transglycosylation Step of Bacterial Cell-Wall Biosynthesis
journal, March 2007
- Lovering, A. L.; de Castro, L. H.; Lim, D.
- Science, Vol. 315, Issue 5817
Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles
journal, April 2015
- Marty, Michael T.; Baldwin, Andrew J.; Marklund, Erik G.
- Analytical Chemistry, Vol. 87, Issue 8
Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov.
journal, October 2018
- Zhang, Xue; Tu, Bo; Dai, Li-rong
- International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 10