Conformational ensembles in Klebsiella pneumoniae FimH impact uropathogenesis
Edited by Kim Orth, The University of Texas Southwestern Medical Center Department of Molecular Biology, Dallas, TX; received May 14, 2024; accepted August 1, 2024
Significance
Klebsiella pneumoniae is recognized by the CDC as a pathogen of urgent concern, due to the increase of multidrug-resistant strains. K. pneumoniae use type 1 pili tipped with the two-domain FimH adhesin to cause urinary tract infections (UTIs). FimH interdomain interactions result in a conformational equilibrium between low-affinity and high-affinity forms. We found that the K. pneumoniae FimH conformational equilibrium is skewed toward a low-affinity state. Analysis of K. pneumoniae isolates from catheterized patients revealed carriage of variant residues that shift FimH into a more high-affinity state, favoring persistence in the urinary tract. These results provide evidence for the necessity of a fine-tuned FimH conformational equilibrium in uropathogenesis and implicate FimH as a therapeutic target to neutralize K. pneumoniae UTIs.
Abstract
Klebsiella pneumoniae is an important pathogen causing difficult-to-treat urinary tract infections (UTIs). Over 1.5 million women per year suffer from recurrent UTI, reducing quality of life and causing substantial morbidity and mortality, especially in the hospital setting. Uropathogenic E. coli (UPEC) is the most prevalent cause of UTI. Like UPEC, K. pneumoniae relies on type 1 pili, tipped with the mannose-binding adhesin FimH, to cause cystitis. However, K. pneumoniae FimH is a poor binder of mannose, despite a mannose-binding pocket identical to UPEC FimH. FimH is composed of two domains that are in an equilibrium between tense (low-affinity) and relaxed (high-affinity) conformations. Substantial interdomain interactions in the tense conformation yield a low-affinity, deformed mannose-binding pocket, while domain–domain interactions are broken in the relaxed state, resulting in a high-affinity binding pocket. Using crystallography, we identified the structural basis by which domain–domain interactions direct the conformational equilibrium of K. pneumoniae FimH, which is strongly shifted toward the low-affinity tense state. Removal of the pilin domain restores mannose binding to the lectin domain, thus showing that poor mannose binding by K. pneumoniae FimH is not an inherent feature of the mannose-binding pocket. Phylogenetic analyses of K. pneumoniae genomes found that FimH sequences are highly conserved. However, we surveyed a collection of K. pneumoniae isolates from patients with long-term indwelling catheters and identified isolates that possessed relaxed higher-binding FimH variants, which increased K. pneumoniae fitness in bladder infection models, suggesting that long-term residence within the urinary tract may select for higher-binding FimH variants.
Data, Materials, and Software Availability
Structure of biological macromolecule data have been deposited in Protein Data Bank (9AT9) (59). All study data are included in the article and/or SI Appendix.
Acknowledgments
We acknowledge the members of the Hultgren and Kau labs for their support of this research, including Jesús Santiago-Borges for creation of the J96 fimChis plasmid. We also thank Dr. David Rosen and Casey Goltz for technical assistance and insights regarding working with K. pneumoniae. We thank Dr. Wandy Beatty for assistance with electron microscopy and Dr. Matthew Chapman for his feedback on the manuscript. We thank Dr. Thomas Hooton for the TOP52 strain. We acknowledge the crystallography assistance of Jay Nix and the ALS 4.2.2 beamline (P30 GM124169-07). This work was funded by NIH grants R01 AI029549 (S.J.H.), R37 AI048689 (S.J.H.), R01 DK051406 (S.J.H.), U19 AI157797 (S.J.H. and J.W.J.), and R01 AI158418 (D.A.H.).
Author contributions
E.D.B.L., J.S.P., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., N.C.G., K.W.D., J.W.J., D.A.H., and S.J.H. designed research; E.D.B.L., J.S.P., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., and N.C.G. performed research; J.W.J. contributed new reagents/analytic tools; E.D.B.L., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., K.W.D., J.W.J., D.A.H., and S.J.H. analyzed data; and E.D.B.L., K.W.D., J.W.J., D.A.H., and S.J.H. wrote the paper.
Competing interests
D.A.H. serves on the Board of Directors of BioVersys AG, Basel, Switzerland. S.J.H., J.W.J., and J.S.P. own company stock in Fimbrion Therapeutics, who has licensed the mannoside patents, and they may benefit if the company is successful in marketing mannosides, S.J.H., J.W.J. and J.S.P. are co-inventors on the issued patents US 10,273,260, US 9,957,289, and US 8,937,167 which cover the use of mannoside-based FimH ligand antagonists for the treatment of disease. J.W.J. is an inventor on the patent applications covering FIM1006, FIM1028, FIM1033, and FIM2065; WO2017156508 and US20200002303.
Supporting Information
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Cover image: Pictured are rescue tigers (Panthera tigris) at In-Sync Exotics Wildlife Rescue and Educational Center in Wylie, Texas. Ellie Armstrong, Jazlyn Mooney et al. explored the genomic diversity of the privately owned captive tiger population in the United States based on genomic sequencing of 138 individuals. The study population had ancestry from all six extant wild tiger subspecies and measures of genetic diversity and inbreeding that were comparable to wild tiger populations. The results could help inform tiger conservation efforts and illegal trafficking investigations. See the article by Armstrong, Mooney et al. e2402924121. Image credit: Keri Ostermann (In-Sync Exotics Wildlife Rescue and Educational Center, Wylie, TX).
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Copyright © 2024 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).
Data, Materials, and Software Availability
Structure of biological macromolecule data have been deposited in Protein Data Bank (9AT9) (59). All study data are included in the article and/or SI Appendix.
Submission history
Received: May 14, 2024
Accepted: August 1, 2024
Published online: September 17, 2024
Published in issue: September 24, 2024
Change history
October 2, 2024: The data availability statement and a reference have been updated. Previous version (September 17, 2024)
Keywords
Acknowledgments
We acknowledge the members of the Hultgren and Kau labs for their support of this research, including Jesús Santiago-Borges for creation of the J96 fimChis plasmid. We also thank Dr. David Rosen and Casey Goltz for technical assistance and insights regarding working with K. pneumoniae. We thank Dr. Wandy Beatty for assistance with electron microscopy and Dr. Matthew Chapman for his feedback on the manuscript. We thank Dr. Thomas Hooton for the TOP52 strain. We acknowledge the crystallography assistance of Jay Nix and the ALS 4.2.2 beamline (P30 GM124169-07). This work was funded by NIH grants R01 AI029549 (S.J.H.), R37 AI048689 (S.J.H.), R01 DK051406 (S.J.H.), U19 AI157797 (S.J.H. and J.W.J.), and R01 AI158418 (D.A.H.).
Author Contributions
E.D.B.L., J.S.P., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., N.C.G., K.W.D., J.W.J., D.A.H., and S.J.H. designed research; E.D.B.L., J.S.P., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., and N.C.G. performed research; J.W.J. contributed new reagents/analytic tools; E.D.B.L., D.A.S., R.F.P., L.X.L., J.B.V., K.O.T., Y.Y., M.I.Z., K.W.D., J.W.J., D.A.H., and S.J.H. analyzed data; and E.D.B.L., K.W.D., J.W.J., D.A.H., and S.J.H. wrote the paper.
Competing Interests
D.A.H. serves on the Board of Directors of BioVersys AG, Basel, Switzerland. S.J.H., J.W.J., and J.S.P. own company stock in Fimbrion Therapeutics, who has licensed the mannoside patents, and they may benefit if the company is successful in marketing mannosides, S.J.H., J.W.J. and J.S.P. are co-inventors on the issued patents US 10,273,260, US 9,957,289, and US 8,937,167 which cover the use of mannoside-based FimH ligand antagonists for the treatment of disease. J.W.J. is an inventor on the patent applications covering FIM1006, FIM1028, FIM1033, and FIM2065; WO2017156508 and US20200002303.
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This article is a PNAS Direct Submission.
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