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Liu X, Tachiyama S, Zhou X, Mathias RA, Bonny SQ, Khan MF, Xin Y, Roujeinikova A, Liu J, Ottemann KM. Bacterial flagella hijack type IV pili proteins to control motility. Proc Natl Acad Sci U S A 2024; 121:e2317452121. [PMID: 38236729 PMCID: PMC10823254 DOI: 10.1073/pnas.2317452121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/27/2023] [Indexed: 01/23/2024] Open
Abstract
Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in common. Here, we report that TFP and some flagella share proteins PilO, PilN, and PilM, which we identified as part of the Helicobacter pylori flagellar motor. H. pylori mutants lacking PilO or PilN migrated better than wild type in semisolid agar because they continued swimming rather than aggregated into microcolonies, mimicking the TFP-regulated surface response. Like their TFP homologs, flagellar PilO/PilN heterodimers formed a peripheral cage that encircled the flagellar motor. These results indicate that PilO and PilN act similarly in flagella and TFP by differentially regulating motility and microcolony formation when bacteria encounter surfaces.
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Affiliation(s)
- Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA95064
| | - Shoichi Tachiyama
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
- Microbial Sciences Institute, Yale University, West Haven, CT06516
| | - Xiaotian Zhou
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Rommel A. Mathias
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC3800, Australia
| | - Sharmin Q. Bonny
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Mohammad F. Khan
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Yue Xin
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC3800, Australia
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
- Microbial Sciences Institute, Yale University, West Haven, CT06516
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA95064
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2
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Botting JM, Tachiyama S, Gibson KH, Liu J, Starai VJ, Hoover TR. FlgV forms a flagellar motor ring that is required for optimal motility of Helicobacter pylori. PLoS One 2023; 18:e0287514. [PMID: 37976320 PMCID: PMC10655999 DOI: 10.1371/journal.pone.0287514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 11/19/2023] Open
Abstract
Flagella-driven motility is essential for Helicobacter pylori to colonize the human stomach, where it causes a variety of diseases, including chronic gastritis, peptic ulcer disease, and gastric cancer. H. pylori has evolved a high-torque-generating flagellar motor that possesses several accessories not found in the archetypical Escherichia coli motor. FlgV was one of the first flagellar accessory proteins identified in Campylobacter jejuni, but its structure and function remain poorly understood. Here, we confirm that deletion of flgV in H. pylori B128 and a highly motile variant of H. pylori G27 (G27M) results in reduced motility in soft agar medium. Comparative analyses of in-situ flagellar motor structures of wild-type, ΔflgV, and a strain expressing FlgV-YFP showed that FlgV forms a ring-like structure closely associated with the junction of two highly conserved flagellar components: the MS and C rings. The results of our studies suggest that the FlgV ring has adapted specifically in Campylobacterota to support the assembly and efficient function of the high-torque-generating motors.
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Affiliation(s)
- Jack M. Botting
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Shoichi Tachiyama
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Katherine H. Gibson
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Vincent J. Starai
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
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3
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Krypotou E, Townsend GE, Gao X, Tachiyama S, Liu J, Pokorzynski ND, Goodman AL, Groisman EA. Bacteria require phase separation for fitness in the mammalian gut. Science 2023; 379:1149-1156. [PMID: 36927025 PMCID: PMC10148683 DOI: 10.1126/science.abn7229] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Therapeutic manipulation of the gut microbiota holds great potential for human health. The mechanisms bacteria use to colonize the gut therefore present valuable targets for clinical intervention. We now report that bacteria use phase separation to enhance fitness in the mammalian gut. We establish that the intrinsically disordered region (IDR) of the broadly and highly conserved transcription termination factor Rho is necessary and sufficient for phase separation in vivo and in vitro in the human commensal Bacteroides thetaiotaomicron. Phase separation increases transcription termination by Rho in an IDR-dependent manner. Moreover, the IDR is critical for gene regulation in the gut. Our findings expose phase separation as vital for host-commensal bacteria interactions and relevant for novel clinical applications.
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Affiliation(s)
- Emilia Krypotou
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
| | - Guy E Townsend
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, 700 HMC Crescent Road, Hershey, PA 17033, USA
| | - Xiaohui Gao
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Shoichi Tachiyama
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
| | - Nick D Pokorzynski
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
- Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA
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4
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Tachiyama S, Skaar R, Chang Y, Carroll BL, Muthuramalingam M, Whittier SK, Barta ML, Picking WL, Liu J, Picking WD. Composition and Biophysical Properties of the Sorting Platform Pods in the Shigella Type III Secretion System. Front Cell Infect Microbiol 2021; 11:682635. [PMID: 34150677 PMCID: PMC8211105 DOI: 10.3389/fcimb.2021.682635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 01/28/2023] Open
Abstract
Shigella flexneri, causative agent of bacillary dysentery (shigellosis), uses a type III secretion system (T3SS) as its primary virulence factor. The T3SS injectisome delivers effector proteins into host cells to promote entry and create an important intracellular niche. The injectisome's cytoplasmic sorting platform (SP) is a critical assembly that contributes to substrate selection and energizing secretion. The SP consists of oligomeric Spa33 "pods" that associate with the basal body via MxiK and connect to the Spa47 ATPase via MxiN. The pods contain heterotrimers of Spa33 with one full-length copy associated with two copies of a C-terminal domain (Spa33C). The structure of Spa33C is known, but the precise makeup and structure of the pods in situ remains elusive. We show here that recombinant wild-type Spa33 can be prepared as a heterotrimer that forms distinct stable complexes with MxiK and MxiN. In two-hybrid analyses, association of the Spa33 complex with these proteins occurs via the full-length Spa33 component. Furthermore, these complexes each have distinct biophysical properties. Based on these properties, new high-resolution cryo-electron tomography data and architectural similarities between the Spa33 and flagellar FliM-FliN complexes, we provide a preliminary model of the Spa33 heterotrimers within the SP pods. From these findings and evolving models of SP interfaces and dynamics in the Yersinia and Salmonella T3SS, we suggest a model for SP function in which two distinct complexes come together within the context of the SP to contribute to form the complete pod structures during the recruitment of T3SS secretion substrates.
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Affiliation(s)
- Shoichi Tachiyama
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - Ryan Skaar
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - Brittany L. Carroll
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | | | - Sean K. Whittier
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Michael L. Barta
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Wendy L. Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, United States,Microbial Sciences Institute, Yale University, West Haven, CT, United States
| | - William D. Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States,*Correspondence: William D. Picking,
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5
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Muthuramalingam M, Whittier SK, Lovell S, Battaile KP, Tachiyama S, Johnson DK, Picking WL, Picking WD. The Structures of SctK and SctD from Pseudomonas aeruginosa Reveal the Interface of the Type III Secretion System Basal Body and Sorting Platform. J Mol Biol 2020; 432:166693. [PMID: 33122003 PMCID: PMC10550303 DOI: 10.1016/j.jmb.2020.10.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Many Gram-negative bacterial pathogens use type III secretion systems (T3SS) to inject proteins into eukaryotic cells to subvert normal cellular functions. The T3SS apparatus (injectisome) shares a common architecture in all systems studied thus far, comprising three major components - the cytoplasmic sorting platform, envelope-spanning basal body and external needle with tip complex. The sorting platform consists of an ATPase (SctN) connected to "pods" (SctQ) having six-fold symmetry via radial spokes (SctL). These pods interface with the 24-fold symmetric SctD inner membrane ring (IR) via an adaptor protein (SctK). Here we report the first high-resolution structure of a SctK protein family member, PscK from Pseudomonas aeruginosa, as well as the structure of its interacting partner, the cytoplasmic domain of PscD (SctD). The cytoplasmic domain of PscD forms a forkhead-associated (FHA) fold, like that of its homologues from other T3SS. PscK, on the other hand, forms a helix-rich structure that does not resemble any known protein fold. Based on these structural findings, we present the first model for an interaction between proteins from the sorting platform and the IR. We also test the importance of the PscD residues predicted to mediate this electrostatic interaction using a two-hybrid analysis. The functional need for these residues in vivo was then confirmed by monitoring secretion of the effector ExoU. These structures will contribute to the development of atomic-resolution models of the entire sorting platform and to our understanding of the mechanistic interface between the sorting platform and the basal body of the injectisome.
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Affiliation(s)
| | - Sean K Whittier
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, United States
| | - Kevin P Battaile
- IMCA-CAT, Hauptman Woodward Medical Research Institute, Argonne, IL 60439, United States
| | - Shoichi Tachiyama
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - David K Johnson
- Computational Chemical Biology Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS 66047, United States
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States
| | - William D Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, United States.
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6
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Tachiyama S, Chang Y, Muthuramalingam M, Hu B, Barta ML, Picking WL, Liu J, Picking WD. The cytoplasmic domain of MxiG interacts with MxiK and directs assembly of the sorting platform in the Shigella type III secretion system. J Biol Chem 2019; 294:19184-19196. [PMID: 31699894 DOI: 10.1074/jbc.ra119.009125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/25/2019] [Indexed: 01/23/2023] Open
Abstract
Many Gram-negative bacteria use type III secretion systems (T3SSs) to inject virulence effector proteins into eukaryotic cells. The T3SS apparatus (T3SA) is structurally conserved among diverse bacterial pathogens and consists of a cytoplasmic sorting platform, an envelope-spanning basal body, and an extracellular needle with tip complex. The sorting platform is essential for effector recognition and powering secretion. Studies using bacterial "minicells" have revealed an unprecedented level of structural detail of the sorting platform; however, many of the structure-function relationships within this complex remain enigmatic. Here, we report on improved cryo-electron tomographic approaches to enhance the resolution of the Shigella T3SA sorting platform (at ≤2 nm resolution) done in concert with biochemical and genetic methods to define the sorting platform interactome and interactions with the T3SA inner membrane ring (IR). We observed that the sorting platform consists of "pods" with 6-fold symmetry that interact with the Spa47 ATPase via radial extensions comprising MxiN. Most importantly, MxiK maintained an interaction with the IR via specific interactions with the cytoplasmic domain of the IR protein MxiG (MxiGC), which is a noncanonical forkhead-associated domain, and MxiK has an elongated structure that interacts with the IR via MxiGC T4 lysozyme-mediated insertional mutagenesis of MxiK revealed its orientation within the sorting platform and enabled disruption of interactions with its binding partners, which abolished sorting platform assembly. Finally, a comparison with the homologous interactions in the Salmonella T3SS sorting platform revealed clear differences in their IR-sorting platform interfaces that have possible mechanistic implications.
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Affiliation(s)
- Shoichi Tachiyama
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Yunjie Chang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06516.,Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516
| | | | - Bo Hu
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, Texas 77030
| | - Michael L Barta
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06516 .,Microbial Sciences Institute, Yale University, West Haven, Connecticut 06516
| | - William D Picking
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 .,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047
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7
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Barta ML, Tachiyama S, Muthuramalingam M, Arizmendi O, Villanueva CE, Ramyar KX, Geisbrecht BV, Lovell S, Battaile KP, Picking WL, Picking WD. Using disruptive insertional mutagenesis to identify the in situ structure-function landscape of the Shigella translocator protein IpaB. Protein Sci 2018; 27:1392-1406. [PMID: 29672980 DOI: 10.1002/pro.3428] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/11/2022]
Abstract
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction. We employed disruptive insertional mutagenesis, using bacteriophage T4 lysozyme (T4L), within predicted IpaB loops to show how topological features affect TC functions (secretion control, translocon formation and effector secretion). Insertions within the N-terminal half of IpaB were most likely to result in a loss of steady-state secretion control, however, all but the two that were not recognized by the T3SA retained nearly wild-type hemolysis (translocon formation) and invasiveness levels (effector secretion). In contrast, all but one insertion in the C-terminal half of IpaB maintained secretion control but were impaired for hemolysis and invasion. These nature of the data suggest the latter mutants are defective in a post-secretion event, most likely due to impaired interactions with the second translocator protein IpaC. Intriguingly, only two insertion mutants displayed readily detectable T4L on the bacterial surface. The data create a picture in which the makeup and structure of a functional T3SA TC is highly amenable to physical perturbation, indicating that the tertiary structure of IpaB within the TC is more plastic than previously realized.
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Affiliation(s)
- Michael L Barta
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Shoichi Tachiyama
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | | | - Olivia Arizmendi
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047
| | - Cecilia E Villanueva
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045
| | - Kasra X Ramyar
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Brian V Geisbrecht
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045
| | - Kevin P Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439
| | - Wendy L Picking
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
| | - William D Picking
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047
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