1
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Liu A, Giacani L, Hawley KL, Cameron CE, Seña A, Konda K, Radolf JD, Klausner JD. New Pathways in Syphilis Vaccine Development. Sex Transm Dis 2024; 51:e49-e53. [PMID: 39037061 PMCID: PMC11560727 DOI: 10.1097/olq.0000000000002050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
ABSTRACT The New Pathways in Syphilis Vaccine Development meeting was held before the start of the STI & HIV 2023 World Congress as a pre-meeting symposium to highlight recent advances in the development of an effective syphilis vaccine and discuss the challenges still faced by investigators. Internationally renowned public health officials, clinical investigators, and basic researchers from academia, government, and community-based organizations met on July 24, 2023, in Chicago, Illinois. Four speakers discussed key research findings in syphilis vaccine development, which included antigen selection, identification of epitopes associated with protective immunity, and delivery platforms, with great emphasis on development of chimeric antigens. Significant progress was also shown on the elucidation of Treponema pallidum genomes from virtually all continents to assess the diversity in vaccine candidates of the syphilis spirochete.
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Affiliation(s)
- Andy Liu
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Lorenzo Giacani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Kelly L. Hawley
- Division of Infectious Diseases, Connecticut Children’s, Hartford, CT, USA
- Department of Pediatrics, UConn Health, Farmington CT USA
| | - Caroline E. Cameron
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Arlene Seña
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kelika Konda
- Center for Interdisciplinary Studies in Sexuality, AIDS and Society, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Jeffrey D. Klausner
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
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2
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Grillová L, Romeis E, Lieberman NAP, Tantalo LC, Xu LH, Molini B, Trejos AT, Lacey G, Goulding D, Thomson NR, Greninger AL, Giacani L. Bright New Resources for Syphilis Research: Genetically Encoded Fluorescent Tags for Treponema pallidum and Sf1Ep Cells. Mol Microbiol 2024; 122:455-464. [PMID: 39115038 PMCID: PMC11479824 DOI: 10.1111/mmi.15304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/18/2024] [Accepted: 07/20/2024] [Indexed: 10/17/2024]
Abstract
The recently discovered methodologies to cultivate and genetically manipulate Treponema pallidum subsp. pallidum (T. pallidum) have significantly helped syphilis research, allowing the in vitro evaluation of antibiotic efficacy, performance of controlled studies to assess differential treponemal gene expression, and generation of loss-of-function mutants to evaluate the contribution of specific genetic loci to T. pallidum virulence. Building on this progress, we engineered the T. pallidum SS14 strain to express a red-shifted green fluorescent protein (GFP) and Sf1Ep cells to express mCherry and blue fluorescent protein (BFP) for enhanced visualization. These new resources improve microscopy- and cell sorting-based applications for T. pallidum, better capturing the physical interaction between the host and pathogen, among other possibilities. Continued efforts to develop and share new tools and resources are required to help our overall knowledge of T. pallidum biology and syphilis pathogenesis reach that of other bacterial pathogens, including spirochetes.
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Affiliation(s)
- Linda Grillová
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Emily Romeis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicole A P Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Lauren C Tantalo
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Linda H Xu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Barbara Molini
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Aldo T Trejos
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - George Lacey
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - David Goulding
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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3
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Houston S, Gomez A, Geppert A, Goodyear MC, Cameron CE. In-Depth Proteome Coverage of In Vitro-Cultured Treponema pallidum and Quantitative Comparison Analyses with In Vivo-Grown Treponemes. J Proteome Res 2024; 23:1725-1743. [PMID: 38636938 PMCID: PMC11077495 DOI: 10.1021/acs.jproteome.3c00891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024]
Abstract
Previous mass spectrometry (MS)-based global proteomics studies have detected a combined total of 86% of all Treponema pallidum proteins under infection conditions (in vivo-grown T. pallidum). Recently, a method was developed for the long-term culture of T. pallidum under in vitro conditions (in vitro-cultured T. pallidum). Herein, we used our previously reported optimized MS-based proteomics approach to characterize the T. pallidum global protein expression profile under in vitro culture conditions. These analyses provided a proteome coverage of 94%, which extends the combined T. pallidum proteome coverage from the previously reported 86% to a new combined total of 95%. This study provides a more complete understanding of the protein repertoire of T. pallidum. Further, comparison of the in vitro-expressed proteome with the previously determined in vivo-expressed proteome identifies only a few proteomic changes between the two growth conditions, reinforcing the suitability of in vitro-cultured T. pallidum as an alternative to rabbit-based treponemal growth. The MS proteomics data have been deposited in the MassIVE repository with the data set identifier MSV000093603 (ProteomeXchange identifier PXD047625).
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Affiliation(s)
- Simon Houston
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Alloysius Gomez
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Andrew Geppert
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Mara C. Goodyear
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Caroline E. Cameron
- Department
of Biochemistry and Microbiology, University
of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department
of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington 98195, United States
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4
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Houston S, Gomez A, Geppert A, Eshghi A, Smith DS, Waugh S, Hardie DB, Goodlett DR, Cameron CE. Deep proteome coverage advances knowledge of Treponema pallidum protein expression profiles during infection. Sci Rep 2023; 13:18259. [PMID: 37880309 PMCID: PMC10600179 DOI: 10.1038/s41598-023-45219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
Comprehensive proteome-wide analysis of the syphilis spirochete, Treponema pallidum ssp. pallidum, is technically challenging due to high sample complexity, difficulties with obtaining sufficient quantities of bacteria for analysis, and the inherent fragility of the T. pallidum cell envelope which further complicates proteomic identification of rare T. pallidum outer membrane proteins (OMPs). The main aim of the present study was to gain a deeper understanding of the T. pallidum global proteome expression profile under infection conditions. This will corroborate and extend genome annotations, identify protein modifications that are unable to be predicted at the genomic or transcriptomic levels, and provide a foundational knowledge of the T. pallidum protein expression repertoire. Here we describe the optimization of a T. pallidum-specific sample preparation workflow and mass spectrometry-based proteomics pipeline which allowed for the detection of 77% of the T. pallidum protein repertoire under infection conditions. When combined with prior studies, this brings the overall coverage of the T. pallidum proteome to almost 90%. These investigations identified 27 known/predicted OMPs, including potential vaccine candidates, and detected expression of 11 potential OMPs under infection conditions for the first time. The optimized pipeline provides a robust and reproducible workflow for investigating T. pallidum protein expression during infection. Importantly, the combined results provide the deepest coverage of the T. pallidum proteome to date.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Alloysius Gomez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Andrew Geppert
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Azad Eshghi
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Derek S Smith
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sean Waugh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - David R Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.
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5
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Li S, Li W, Jin Y, Wu B, Wu Y. Advancements in the development of nucleic acid vaccines for syphilis prevention and control. Hum Vaccin Immunother 2023; 19:2234790. [PMID: 37538024 PMCID: PMC10405752 DOI: 10.1080/21645515.2023.2234790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/12/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
Syphilis, a chronic systemic sexually transmitted disease, is caused by the bacterium Treponema pallidum (T. pallidum). Currently, syphilis remains a widespread infectious disease with significant disease burden in many countries. Despite the absence of identified penicillin-resistant strains, challenges in syphilis treatment persist due to penicillin allergies, supply issues, and the emergence of macrolide-resistant strains. Vaccines represent the most cost-effective strategy to prevent and control the syphilis epidemic. In light of the ongoing global coronavirus disease 2019 (COVID-19) pandemic, nucleic acid vaccines have gained prominence in the field of vaccine research and development, owing to their superior efficiency compared to traditional vaccines. This review summarizes the current state of the syphilis epidemic and the preliminary findings in T. pallidum nucleic acid vaccine research, discusses the challenges associated with the development of T. pallidum nucleic acid vaccines, and proposes strategies and measures for future T. pallidum vaccine development.
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Affiliation(s)
- Sijia Li
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, Institution of Pathogenic Biology, University of South China, Hengyang, China
| | - Weiwei Li
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, Institution of Pathogenic Biology, University of South China, Hengyang, China
- Department of Clinical Laboratory, The Second People’s Hospital of Foshan, Foshan, China
| | - Yinqi Jin
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, Institution of Pathogenic Biology, University of South China, Hengyang, China
| | - Bin Wu
- First Affiliated Hospital, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Yimou Wu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical College, Institution of Pathogenic Biology, University of South China, Hengyang, China
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Ávila-Nieto C, Pedreño-López N, Mitjà O, Clotet B, Blanco J, Carrillo J. Syphilis vaccine: challenges, controversies and opportunities. Front Immunol 2023; 14:1126170. [PMID: 37090699 PMCID: PMC10118025 DOI: 10.3389/fimmu.2023.1126170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Syphilis is a sexually or vertically (mother to fetus) transmitted disease caused by the infection of Treponema pallidum subspecie pallidum (TPA). The incidence of syphilis has increased over the past years despite the fact that this bacterium is an obligate human pathogen, the infection route is well known, and the disease can be successfully treated with penicillin. As complementary measures to preventive campaigns and early treatment of infected individuals, development of a syphilis vaccine may be crucial for controlling disease spread and/or severity, particularly in countries where the effectiveness of the aforementioned measures is limited. In the last century, several vaccine prototypes have been tested in preclinical studies, mainly in rabbits. While none of them provided protection against infection, some prototypes prevented bacteria from disseminating to distal organs, attenuated lesion development, and accelerated their healing. In spite of these promising results, there is still some controversy regarding the identification of vaccine candidates and the characteristics of a syphilis-protective immune response. In this review, we describe what is known about TPA immune response, and the main mechanisms used by this pathogen to evade it. Moreover, we emphasize the importance of integrating this knowledge, in conjunction with the characterization of outer membrane proteins (OMPs), to expedite the development of a syphilis vaccine that can protect against TPA infection.
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Affiliation(s)
- Carlos Ávila-Nieto
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Autonomous University of Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | | | - Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Department, Germans Trias i Pujol Hospital, Badalona, Spain
- Fight Infections Foundation, Germans Trias i Pujol Hospital, Badalona, Catalonia, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Fight Infections Foundation, Germans Trias i Pujol Hospital, Badalona, Catalonia, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Catalonia, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- CIBERINFEC, Instituto de Salut Carlos III (ISCIII), Madrid, Spain
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7
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Edmondson DG, De Lay BD, Hanson BM, Kowis LE, Norris SJ. Clonal isolates of Treponema pallidum subsp. pallidum Nichols provide evidence for the occurrence of microevolution during experimental rabbit infection and in vitro culture. PLoS One 2023; 18:e0281187. [PMID: 36917571 PMCID: PMC10013896 DOI: 10.1371/journal.pone.0281187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/17/2023] [Indexed: 03/15/2023] Open
Abstract
The recent development of a system for long-term in vitro culture of the syphilis spirochete, Treponema pallidum subsp. pallidum, has introduced the possibility of detailed genetic analysis of this bacterium. In this study, the in vitro culture system was used to isolate and characterize clonal populations of T. pallidum subsp. pallidum Nichols, the most widely studied strain. In limiting dilutions experiments, it was possible to establish cultures with inocula as low as 0.5 T. pallidum per well despite the long generation time (~35 to 40 hours) of this organism. Six Nichols strain clones isolated by limiting dilution were characterized in detail. All clones exhibited indistinguishable morphology and motility, highly similar in vitro multiplication rates, and comparable infectivity in the rabbit model (ID50 ≤ 100 bacteria). Genomic sequencing revealed sequence heterogeneity in the form of insertions or deletions at 5 sites, single nucleotide variations at 20 sites, and polynucleotide (polyG/C) tract length differences at 22 locations. Genomic sequences of the uncloned Nichols strain preparations propagated in rabbits or in vitro cultures exhibited substantial heterogeneity at these locations, indicating coexistence of many varied 'clonotypes' within these populations. Nearly all genetic variations were specific for the Nichols strain and were not detected in the >280 T. pallidum genomic sequences that are currently available. We hypothesize that these Nichols strain-specific sequence variations arose independently either during human infection or within the 110 years since the strain's initial isolation, and thus represent examples of microevolution and divergence.
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Affiliation(s)
- Diane G. Edmondson
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Bridget D. De Lay
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Blake M. Hanson
- Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- Department of Epidemiology, Human Genetics & Environmental Sciences, Center for Infectious Diseases, School of Public Health, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lindsay E. Kowis
- Houston Methodist Research Institute, Infectious Disease, Houston, Texas, United States of America
| | - Steven J. Norris
- Department of Pathology & Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
- Department of Microbiology & Molecular Genetics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas, United States of America
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8
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Tang Y, Zhou Y, He B, Cao T, Zhou X, Ning L, Chen E, Li Y, Xie X, Peng B, Hu Y, Liu S. Investigation of the immune escape mechanism of Treponema pallidum. Infection 2022; 51:305-321. [PMID: 36260281 DOI: 10.1007/s15010-022-01939-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Syphilis is a chronic sexually transmitted disease caused by Treponema pallidum subspecies pallidum (T. pallidum), which is a public health problem that seriously affects human health worldwide. T. pallidum is characterized by early transmission and immune escape and is therefore termed an "invisible pathogen". METHODS This review systematically summarizes the host's innate and adaptive immune responses to T. pallidum infection as well as the escape mechanisms of T. pallidum. PURPOSE To lay the foundation for assessing the pathogenic mechanism and the systematic prevention and treatment of syphilis. CONCLUSION The immune escape mechanism of T. pallidum plays an important role in its survival. Exploring the occurrence and development of these mechanisms has laid the foundation for the development of syphilis vaccine.
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Affiliation(s)
- Yun Tang
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Yingjie Zhou
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Bisha He
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Ting Cao
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Xiangping Zhou
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Lichang Ning
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - En Chen
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Yumeng Li
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Xiaoping Xie
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Binfeng Peng
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Yibao Hu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China
| | - Shuangquan Liu
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, The First Affiliated Hospital, University of South China, No. 69, Chuanshan Road, Hengyang City, 421000, Hunan, China.
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9
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Lieberman NAP, Armstrong TD, Chung B, Pfalmer D, Hennelly CM, Haynes A, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Conte ID, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitja O, Rompalo A, Mulcahy F, Hook EW, Hoffman IF, Matoga MM, Zheng H, Yang B, Lopez-Medina E, Ramirez LG, Radolf JD, Hawley KL, Salazar JC, Lukehart SA, Seña AC, Parr JB, Giacani L, Greninger AL. High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny. Front Microbiol 2022; 13:1007056. [PMID: 36204625 PMCID: PMC9531955 DOI: 10.3389/fmicb.2022.1007056] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Sequencing of most Treponema pallidum genomes excludes repeat regions in tp0470 and the tp0433 gene, encoding the acidic repeat protein (arp). As a first step to understanding the evolution and function of these genes and the proteins they encode, we developed a protocol to nanopore sequence tp0470 and arp genes from 212 clinical samples collected from ten countries on six continents. Both tp0470 and arp repeat structures recapitulate the whole genome phylogeny, with subclade-specific patterns emerging. The number of tp0470 repeats is on average appears to be higher in Nichols-like clade strains than in SS14-like clade strains. Consistent with previous studies, we found that 14-repeat arp sequences predominate across both major clades, but the combination and order of repeat type varies among subclades, with many arp sequence variants limited to a single subclade. Although strains that were closely related by whole genome sequencing frequently had the same arp repeat length, this was not always the case. Structural modeling of TP0470 suggested that the eight residue repeats form an extended α-helix, predicted to be periplasmic. Modeling of the ARP revealed a C-terminal sporulation-related repeat (SPOR) domain, predicted to bind denuded peptidoglycan, with repeat regions possibly incorporated into a highly charged β-sheet. Outside of the repeats, all TP0470 and ARP amino acid sequences were identical. Together, our data, along with functional considerations, suggests that both TP0470 and ARP proteins may be involved in T. pallidum cell envelope remodeling and homeostasis, with their highly plastic repeat regions playing as-yet-undetermined roles.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Thaddeus D. Armstrong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Benjamin Chung
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Christopher M. Hennelly
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Austin Haynes
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Emily Romeis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- Sexual Health Center, Department of Prevention, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Section of Dermatology, Department of Health Sciences, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development, Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Oriol Mitja
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre, International SOS, Londolovit, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, MD, United States
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St. James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Irving F. Hoffman
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Mitch M. Matoga
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Project-Malawi, Lilongwe, Malawi
| | - Heping Zheng
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Bin Yang
- Dermatology Hospital of Southern Medical University, Guangzhou, China
- Institute for Global Health and Sexually Transmitted Infections, Guangzhou, China
| | - Eduardo Lopez-Medina
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Centro de Estudios en Infectología Pediátrica (CEIP), Cali, Colombia
| | - Lady G. Ramirez
- Centro Internacional de Entrenamiento e Investigaciones Medicas (CIDEIM), Cali, Colombia
- Universidad ICESI, Cali, Colombia
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, United States
| | - Kelly L. Hawley
- Department of Medicine, UConn Health, Farmington, CT, United States
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Juan C. Salazar
- Department of Pediatrics, UConn Health, Farmington, CT, United States
- Department of Immunology, UConn Health, Farmington, CT, United States
- Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Sheila A. Lukehart
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Arlene C. Seña
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jonathan B. Parr
- Division of Infectious Diseases, Institute for Global Health and Infectious Diseases, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lorenzo Giacani
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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10
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Kojima N, Konda KA, Klausner JD. Notes on syphilis vaccine development. Front Immunol 2022; 13:952284. [PMID: 35967432 PMCID: PMC9365935 DOI: 10.3389/fimmu.2022.952284] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The quest for a syphilis vaccine to provide protection from infection or disease began not long after the isolation of the first Treponema pallidum subspecies pallidum (T. pallidum) strain in 1912. Yet, a practical and effective vaccine formulation continues to elude scientists. Over the last few years, however, efforts toward developing a syphilis vaccine have increased thanks to an improved understanding of the repertoire of T. pallidum outer membrane proteins (OMPs), which are the most likely syphilis vaccine candidates. More has been also learned about the molecular mechanisms behind pathogen persistence and immune evasion. Published vaccine formulations based on a subset of the pathogen's OMPs have conferred only partial protection upon challenge of immunized laboratory animals, primarily rabbits. Nonetheless, those experiments have improved our approach to the choice of immunization regimens, adjuvants, and vaccine target selection, although significant knowledge gaps remain. Herein, we provide a brief overview on current technologies and approaches employed in syphilis vaccinology, and possible future directions to develop a vaccine that could be pivotal to future syphilis control and elimination initiatives.
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Affiliation(s)
- Noah Kojima
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Kelika A. Konda
- Department of Medicine, University of California Los Angeles, Los Angeles, CA, United States
- Centro de Investigación Interdisciplinaria en Sexualidad Sida y Sociedad, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Departments of Medicine and Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, CA, United States
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11
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Chen J, Huang J, Liu Z, Xie Y. Treponema pallidum outer membrane proteins: current status and prospects. Pathog Dis 2022; 80:6649208. [PMID: 35869970 DOI: 10.1093/femspd/ftac023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
The outer membrane proteins (OMPs) of Treponema pallidum subsp. Pallidum (T. pallidum), the etiological agent of the sexually transmitted disease syphilis, has long been a hot research topic. Despite many hurdles to studying the pathogen, especially the inability to manipulate T. pallidum in vitro genetically1, considerable progress has been made in elucidating the structure, pathogenesis, and functions of T. pallidum OMPs. In this review, we integrate this information to garner fresh insights into the role of OMPs in the diagnosis, pathogenicity, and vaccine development of T. pallidum. Collectively, the essential scientific discussions herein should provide a framework for understanding the current status and prospects of T. pallidum OMPs.
Decades ago, researchers postulated that the poor surface antigenicity of T. pallidum is the basis for its ability to cause persistent infection. Still, they believed that the mysterious properties of T. pallidum should not be attributed to the presence of the outer membrane proteins (OMPs). Subsequent studies revealed that the OM, which lacks integral membrane proteins, prevents antibody binding2. Since the advent of recombinant DNA technology, the fragility of the OM, low protein content, and the lack of sequence relatedness between T. pallidum and Gram-negative OMPs have complicated efforts to characterize molecules residing at the host-pathogen interface. These hurdles have been overcome by using the genomic sequence with computational tools to identify proteins predicted to form beta barrels, the hallmark conformation of OMPs in many organisms. Diverse methodologies have also confirmed that some candidate OMPs from amphiphilic β-barrels are surface-exposed in T. pallidum. These studies have led to a structural homology model for BamA and established the bipartite topology of the T. pallidum repeat (Tpr) family of proteins. Recent bioinformatics has identified several structural orthologs for well-characterized Gram-negative OMPs, suggesting that the T. pallidum OMPs are more Gram-negative-like than previously supposed. Lipoprotein adhesins and proteases on the spirochete surface also may contribute to disease pathogenesis and protective immunity.
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Affiliation(s)
- Jinlin Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China , Hengyang 421001 , China
| | - Jielite Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China , Hengyang 421001 , China
| | - Zhuoran Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China , Hengyang 421001 , China
| | - Yafeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of University of South China , Hengyang 421001 , China
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12
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Lieberman NAP, Lin MJ, Xie H, Shrestha L, Nguyen T, Huang ML, Haynes AM, Romeis E, Wang QQ, Zhang RL, Kou CX, Ciccarese G, Dal Conte I, Cusini M, Drago F, Nakayama SI, Lee K, Ohnishi M, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Mitjà O, Rompalo A, Mulcahy F, Hook EW, Lukehart SA, Casto AM, Roychoudhury P, DiMaio F, Giacani L, Greninger AL. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis 2021; 15:e0010063. [PMID: 34936652 PMCID: PMC8735616 DOI: 10.1371/journal.pntd.0010063] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/06/2022] [Accepted: 12/06/2021] [Indexed: 11/19/2022] Open
Abstract
In spite of its immutable susceptibility to penicillin, Treponema pallidum (T. pallidum) subsp. pallidum continues to cause millions of cases of syphilis each year worldwide, resulting in significant morbidity and mortality and underscoring the urgency of developing an effective vaccine to curtail the spread of the infection. Several technical challenges, including absence of an in vitro culture system until very recently, have hampered efforts to catalog the diversity of strains collected worldwide. Here, we provide near-complete genomes from 196 T. pallidum strains-including 191 T. pallidum subsp. pallidum-sequenced directly from patient samples collected from 8 countries and 6 continents. Maximum likelihood phylogeny revealed that samples from most sites were predominantly SS14 clade. However, 99% (84/85) of the samples from Madagascar formed two of the five distinct Nichols subclades. Although recombination was uncommon in the evolution of modern circulating strains, we found multiple putative recombination events between T. pallidum subsp. pallidum and subsp. endemicum, shaping the genomes of several subclades. Temporal analysis dated the most recent common ancestor of Nichols and SS14 clades to 1717 (95% HPD: 1543-1869), in agreement with other recent studies. Rates of SNP accumulation varied significantly among subclades, particularly among different Nichols subclades, and was associated in the Nichols A subclade with a C394F substitution in TP0380, a ERCC3-like DNA repair helicase. Our data highlight the role played by variation in genes encoding putative surface-exposed outer membrane proteins in defining separate lineages, and provide a critical resource for the design of broadly protective syphilis vaccines targeting surface antigens.
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Affiliation(s)
- Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Lasata Shrestha
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Tien Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Qian-Qiu Wang
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Rui-Li Zhang
- Department of Dermatology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Cai-Xia Kou
- Institute of Dermatology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- National Center for STD Control, China Centers for Disease Control and Prevention, Nanjing, China
| | - Giulia Ciccarese
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Ivano Dal Conte
- STI Clinic, Infectious Diseases Unit, University of Turin, Turin, Italy
| | - Marco Cusini
- Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Drago
- Health Sciences Department, Section of Dermatology, San Martino University Hospital, Genoa, Italy
| | - Shu-ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Anne Rompalo
- Department of Infectious Diseases, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Fiona Mulcahy
- Department of Genito Urinary Medicine and Infectious Diseases, St James’s Hospital, Dublin, Ireland
| | - Edward W. Hook
- Department of Medicine, University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Amanda M. Casto
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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13
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Hawley KL, Montezuma-Rusca JM, Delgado KN, Singh N, Uversky VN, Caimano MJ, Radolf JD, Luthra A. Structural Modeling of the Treponema pallidum Outer Membrane Protein Repertoire: a Road Map for Deconvolution of Syphilis Pathogenesis and Development of a Syphilis Vaccine. J Bacteriol 2021; 203:e0008221. [PMID: 33972353 PMCID: PMC8407342 DOI: 10.1128/jb.00082-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
Treponema pallidum, an obligate human pathogen, has an outer membrane (OM) whose physical properties, ultrastructure, and composition differ markedly from those of phylogenetically distant Gram-negative bacteria. We developed structural models for the outer membrane protein (OMP) repertoire (OMPeome) of T. pallidum Nichols using solved Gram-negative structures, computational tools, and small-angle X-ray scattering (SAXS) of selected recombinant periplasmic domains. The T. pallidum "OMPeome" harbors two "stand-alone" proteins (BamA and LptD) involved in OM biogenesis and four paralogous families involved in the influx/efflux of small molecules: 8-stranded β-barrels, long-chain-fatty-acid transporters (FadLs), OM factors (OMFs) for efflux pumps, and T. pallidum repeat proteins (Tprs). BamA (TP0326), the central component of a β-barrel assembly machine (BAM)/translocation and assembly module (TAM) hybrid, possesses a highly flexible polypeptide-transport-associated (POTRA) 1-5 arm predicted to interact with TamB (TP0325). TP0515, an LptD ortholog, contains a novel, unstructured C-terminal domain that models inside the β-barrel. T. pallidum has four 8-stranded β-barrels, each containing positively charged extracellular loops that could contribute to pathogenesis. Three of five FadL-like orthologs have a novel α-helical, presumptively periplasmic C-terminal extension. SAXS and structural modeling further supported the bipartite membrane topology and tridomain architecture of full-length members of the Tpr family. T. pallidum's two efflux pumps presumably extrude noxious small molecules via four coexpressed OMFs with variably charged tunnels. For BamA, LptD, and OMFs, we modeled the molecular machines that deliver their substrates into the OM or external milieu. The spirochete's extended families of OM transporters collectively confer a broad capacity for nutrient uptake. The models also furnish a structural road map for vaccine development. IMPORTANCE The unusual outer membrane (OM) of T. pallidum, the syphilis spirochete, is the ultrastructural basis for its well-recognized capacity for invasiveness, immune evasion, and persistence. In recent years, we have made considerable progress in identifying T. pallidum's repertoire of OMPs. Here, we developed three-dimensional (3D) models for the T. pallidum Nichols OMPeome using structural modeling, bioinformatics, and solution scattering. The OM contains three families of OMP transporters, an OMP family involved in the extrusion of noxious molecules, and two "stand-alone" proteins involved in OM biogenesis. This work represents a major advance toward elucidating host-pathogen interactions during syphilis; understanding how T. pallidum, an extreme auxotroph, obtains a wide array of biomolecules from its obligate human host; and developing a vaccine with global efficacy.
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Affiliation(s)
- Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases and Immunology, Connecticut Children’s, Hartford, Connecticut, USA
| | - Jairo M. Montezuma-Rusca
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Division of Infectious Diseases, UConn Health, Farmington, Connecticut, USA
| | | | - Navreeta Singh
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Melissa J. Caimano
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Justin D. Radolf
- Department of Pediatrics, UConn Health, Farmington, Connecticut, USA
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA
- Department of Immunology, UConn Health, Farmington, Connecticut, USA
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
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14
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Haynes AM, Fernandez M, Romeis E, Mitjà O, Konda KA, Vargas SK, Eguiluz M, Caceres CF, Klausner JD, Giacani L. Transcriptional and immunological analysis of the putative outer membrane protein and vaccine candidate TprL of Treponema pallidum. PLoS Negl Trop Dis 2021; 15:e0008812. [PMID: 33497377 PMCID: PMC7864442 DOI: 10.1371/journal.pntd.0008812] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 02/05/2021] [Accepted: 01/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background An effective syphilis vaccine should elicit antibodies to Treponema pallidum subsp. pallidum (T. p. pallidum) surface antigens to induce pathogen clearance through opsonophagocytosis. Although the combination of bioinformatics, structural, and functional analyses of T. p. pallidum genes to identify putative outer membrane proteins (OMPs) resulted in a list of potential vaccine candidates, still very little is known about whether and how transcription of these genes is regulated during infection. This knowledge gap is a limitation to vaccine design, as immunity generated to an antigen that can be down-regulated or even silenced at the transcriptional level without affecting virulence would not induce clearance of the pathogen, hence allowing disease progression. Principal findings We report here that tp1031, the T. p. pallidum gene encoding the putative OMP and vaccine candidate TprL is differentially expressed in several T. p. pallidum strains, suggesting transcriptional regulation. Experimental identification of the tprL transcriptional start site revealed that a homopolymeric G sequence of varying length resides within the tprL promoter and that its length affects promoter activity compatible with phase variation. Conversely, in the closely related pathogen T. p. subsp. pertenue, the agent of yaws, where a naturally-occurring deletion has eliminated the tprL promoter region, elements necessary for protein synthesis, and part of the gene ORF, tprL transcription level are negligible compared to T. p. pallidum strains. Accordingly, the humoral response to TprL is absent in yaws-infected laboratory animals and patients compared to syphilis-infected subjects. Conclusion The ability of T. p. pallidum to stochastically vary tprL expression should be considered in any vaccine development effort that includes this antigen. The role of phase variation in contributing to T. p. pallidum antigenic diversity should be further studied. Syphilis is still an endemic disease in many low- and middle-income countries and has been resurgent in high-income nations for almost two decades now. In endemic areas, syphilis still causes significant morbidity and mortality in patients, particularly when its causative agent, the bacterium Treponema pallidum subsp. pallidum is transmitted to the fetus during pregnancy. Although there are significant ongoing efforts to identify an effective syphilis vaccine to bring into clinical trials within the decade in the U.S., such efforts are partially hindered by the lack of knowledge on transcriptional regulation of many genes encoding vaccine candidates. Here, we start addressing this knowledge gap for the putative outer membrane protein (OMP) and vaccine candidates TprL, encoded by the tp1031 gene. As we previously reported for other putative OMP-encoding genes of the syphilis agent, tprL transcription level appears to be affected by the length of a homopolymeric sequence of guanosines (Gs) located within the gene promoter. This is a mechanism known as phase variation and often involved in altering the surface antigenic profile of a bacterial pathogen to facilitate immune evasion and/or adaptation to the host milieu.
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Affiliation(s)
- Austin M. Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Mark Fernandez
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Oriol Mitjà
- Fight Aids and Infectious Diseases Foundation, Hospital Germans Trias I Pujol, Badalona, Barcelona, Spain
- Lihir Medical Centre-International SOS, Newcrest Mining, Lihir Island, Papua New Guinea
| | - Kelika A. Konda
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Silver K. Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
- School of Public Health and Administration “Carlos Vidal Layseca”, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Maria Eguiluz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Carlos F. Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano-Heredia, Lima, Peru
| | - Jeffrey D. Klausner
- David Geffen School of Medicine, Division of Infectious Diseases, University of California Los Angeles, Los Angeles, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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15
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Liu D, Tong ML, Liu LL, Lin LR, Zhang HL, Yang TC. Characterisation of the novel clinical isolate X-4 containing a new tp0548 sequence-type. Sex Transm Infect 2020; 97:120-125. [PMID: 33214321 DOI: 10.1136/sextrans-2020-054687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/10/2020] [Accepted: 10/25/2020] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES A novel tp0548 sequence-type was identified in one clinical isolate (X-4) from a patient diagnosed with primary syphilis in Xiamen, China. To precisely define and characterise a new clinical isolate, we performed further genome-scale molecular analysis. METHODS The pooled segment genome sequencing method followed by Illumina sequencing was performed. RESULTS This novel sequence-type contained a unique nucleotide substitution 'T' at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was closely related to the SS14 strain, with 42 single-nucleotide variations and 12 insertions/deletions. In addition, high intrastrain heterogeneity in the length of the poly G/C tracts was found in the TPAChi_0347 locus, which might indicate that this gene of the X-4 isolate is likely involved in phase variation events. The length heterogeneity of the poly A/T tracts was lower than the genetic variability of the poly G/C tracts, and all the observed intrastrain variations fell within coding regions. CONCLUSION The novel tp0548 sequence-type was determined to belong to a new TPA isolate, X-4. The identification of variable length in homopolymetic tracts (G/C and A/T) could provide a snapshot of the genes that potentially involved in genotype-phenotype variations. These findings provide an unequivocal characterisation for better understanding the molecular variation of this emerging isolate.
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Affiliation(s)
- Dan Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Man-Li Tong
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China.,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Li Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Hui-Lin Zhang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China .,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Tian-Ci Yang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China .,Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
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16
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Abstract
Syphilis continues to be a significant public health issue in both low- and high-income countries, including the United States where the rate of syphilis infection has increased over the past 5 years. Treponema pallidum subsp. pallidum, the causative agent of syphilis, carries the outer membrane protein TprK that undergoes segmental gene conversion to constantly create new sequences. We performed full-length deep sequencing of TprK to examine TprK diversity in clinical T. pallidum subsp. pallidum strains. We then combined our results with data from all samples for which TprK deep sequencing results were available. We found almost no overlap in TprK sequences between different patients. Moreover, our data allowed us to estimate the total number of TprK variants that T. pallidum subsp. pallidum can potentially generate. Our results support how the T. pallidum subsp. pallidum TprK antigenic variation system is an equal adversary of the human immune system leading to pathogen persistence in the host. Immune evasion and disease progression of Treponema pallidum subsp. pallidum are associated with sequence diversity in the hypervariable outer membrane protein TprK. Previous attempts to study variation within TprK have sequenced at depths insufficient to fully appreciate the hypervariable nature of the protein, failed to establish linkage between the protein’s seven variable regions, or were conducted on isolates passed through rabbits. As a consequence, a complete profile of tprK during infection in the human host is still lacking. Furthermore, prior studies examining how T. pallidum subsp. pallidum uses its repertoire of genomic donor sites to generate diversity within the variable regions of the tprK have yielded a partial understanding of this process due to the limited number of tprK alleles examined. In this study, we used short- and long-read deep sequencing to directly characterize full-length tprK alleles from T. pallidum subsp. pallidum collected from early lesions of patients attending two sexually transmitted infection clinics in Italy. We demonstrate that strains collected from cases of secondary syphilis contain significantly more unique variable region sequences and full-length TprK sequences than those from cases of primary syphilis. Our data, combined with recent data available on Chinese T. pallidum subsp. pallidum specimens, show the near-complete absence of overlap in TprK sequences among the 41 specimens profiled to date. We further estimate that the potential antigenic variability carried by TprK rivals that of current estimates of the human adaptive immune system. These data underscore the immunoevasive ability of TprK that allows T. pallidum subsp. pallidum to establish lifelong infection.
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17
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Osias E, Hung P, Giacani L, Stafylis C, Konda KA, Vargas SK, Reyes-Díaz EM, Comulada WS, Haake DA, Haynes AM, Caceres CF, Klausner JD. Investigation of syphilis immunology and Treponema pallidum subsp. pallidum biology to improve clinical management and design a broadly protective vaccine: study protocol. BMC Infect Dis 2020; 20:444. [PMID: 32576149 PMCID: PMC7309211 DOI: 10.1186/s12879-020-05141-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/08/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The syphilis epidemic continues to cause substantial morbidity and mortality worldwide, particularly in low- and middle-income countries, despite several recent disease control initiatives. Though our understanding of the pathogenesis of this disease and the biology of the syphilis agent, Treponema pallidum subsp. pallidum has improved over the last two decades, further research is necessary to improve clinical diagnosis and disease management protocols. Additionally, such research efforts could contribute to the identification of possible targets for the development of an effective vaccine to stem syphilis spread. METHODS This study will recruit two cohorts of participants with active syphilis infection, one with de novo infection, one with repeat infection. Whole blood specimens will be collected from each study participant at baseline, 4, 12, 24, 36, and 48 weeks, to track specific markers of their immunological response, as well as to compare humoral reactivity to Treponema pallidum antigens between the two groups. Additionally, we will use serum specimens to look for unique cytokine patterns in participants with early syphilis. Oral and blood samples, as well as samples from any syphilitic lesions present, will also be collected to sequence any Treponema pallidum DNA found. DISCUSSION By furthering our understanding of syphilis pathogenesis and human host immune response to Treponema pallidum, we will provide important data that will help in development of new point-of-care tests that could better identify active infection, leading to improved syphilis diagnosis and management. Findings could also contribute to vaccine development efforts.
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Affiliation(s)
- Ethan Osias
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA.
| | - Phoebe Hung
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, University of Washington, Seattle, WA, USA
| | - Chrysovalantis Stafylis
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA
| | - Kelika A Konda
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA.,Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Silver K Vargas
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - E Michael Reyes-Díaz
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - W Scott Comulada
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA
| | - David A Haake
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA.,Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Austin M Haynes
- Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, University of Washington, Seattle, WA, USA
| | - Carlos F Caceres
- Unit of Health, Sexuality and Human Development and Laboratory of Sexual Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jeffrey D Klausner
- Division of Infectious Diseases, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Ave, Los Angeles, CA, 90095, USA
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18
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Fernandez MC, Giacani L. Molecular and Immunological Strategies Against Treponema pallidum Infections. Sex Transm Infect 2020. [DOI: 10.1007/978-3-030-02200-6_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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19
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Evaluation of the Protective Ability of the Treponema pallidum subsp. pallidum Tp0126 OmpW Homolog in the Rabbit Model of Syphilis. Infect Immun 2019; 87:IAI.00323-19. [PMID: 31182617 DOI: 10.1128/iai.00323-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
In silico analyses of Treponema pallidum subsp. pallidum genomes and predicted proteomes to search for homologs of known bacterial outer membrane proteins (OMPs) led to the identification of tp0126 as a gene encoding a putative member of the OmpW family of porins/virulence factors. Our previous investigations on the role of Tp0126 in T. pallidum biology and syphilis pathogenesis showed that Tp0126 is fully conserved among T. pallidum strains and that transcription of tp0126 is driven by σ70 These initial results pointed to a housekeeping function for this protein. We also demonstrated that a guanosine homopolymer of various lengths located between the -10 and -35 consensus sequences in the tp0126 promoter modulates transcription consistently with phase variation, a mechanism that we also previously described for other T. pallidum genes encoding putative OMPs/virulence factors and that is often employed as a strategy for immune evasion. Circular dichroism spectra of recombinant Tp0126 also supported its structural homology with OmpW. Here we further investigated the humoral and cellular responses to Tp0126 during experimental and natural syphilis and the ability of Tp0126 to confer protection against syphilis in immunized rabbits. B-cell epitope mapping showed that compared to sera from experimentally infected animals, immunizations enhanced humoral immunity to sequences located in the putative Tp0126 surface-exposed loops, while phagocytosis assays showed that postimmunization sera opsonized T. pallidum Despite such promising results, no significant protection was seen following infectious challenge in immunized animals versus controls. Functional redundancy and phase variation might explain the lack of effectiveness of this vaccine candidate and/or design.
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20
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Abstract
The outer membrane (OM) of Treponema pallidum, the uncultivatable agent of venereal syphilis, has long been the subject of misconceptions and controversy. Decades ago, researchers postulated that T. pallidum's poor surface antigenicity is the basis for its ability to cause persistent infection, but they mistakenly attributed this enigmatic property to the presence of a protective outer coat of serum proteins and mucopolysaccharides. Subsequent studies revealed that the OM is the barrier to antibody binding, that it contains a paucity of integral membrane proteins, and that the preponderance of the spirochete's immunogenic lipoproteins is periplasmic. Since the advent of recombinant DNA technology, the fragility of the OM, its low protein content, and the lack of sequence relatedness between T. pallidum and Gram-negative outer membrane proteins (OMPs) have complicated efforts to characterize molecules residing at the host-pathogen interface. We have overcome these hurdles using the genomic sequence in concert with computational tools to identify proteins predicted to form β-barrels, the hallmark conformation of OMPs in double-membrane organisms and evolutionarily related eukaryotic organelles. We also have employed diverse methodologies to confirm that some candidate OMPs do, in fact, form amphiphilic β-barrels and are surface-exposed in T. pallidum. These studies have led to a structural homology model for BamA and established the bipartite topology of the T. pallidum repeat (Tpr) family of proteins. Recent bioinformatics has identified several structural orthologs for well-characterized Gram-negative OMPs, suggesting that the T. pallidum OMP repertoire is more Gram-negative-like than previously supposed. Lipoprotein adhesins and proteases on the spirochete surface also may contribute to disease pathogenesis and protective immunity.
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Affiliation(s)
- Justin D Radolf
- Departments of Medicine, Pediatrics, Molecular Biology and Biophysics, Genetics and Genomic Sciences, and Immunology, UConn Health, Farmington, CT 06030-3715, USA.
| | - Sanjiv Kumar
- Department of Medicine, UConn Health, Farmington, CT 06030-3715, USA
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21
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Houston S, Lithgow KV, Osbak KK, Kenyon CR, Cameron CE. Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis. BMC STRUCTURAL BIOLOGY 2018; 18:7. [PMID: 29769048 PMCID: PMC5956850 DOI: 10.1186/s12900-018-0086-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/27/2018] [Indexed: 12/21/2022]
Abstract
Background Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens. In fact, approximately 30% of its predicted protein-coding genes have no known orthologs or assigned functions. Here we employed a structural bioinformatics approach using Phyre2-based tertiary structure modeling to improve our understanding of T. pallidum protein function on a proteome-wide scale. Results Phyre2-based tertiary structure modeling generated high-confidence predictions for 80% of the T. pallidum proteome (780/978 predicted proteins). Tertiary structure modeling also inferred the same function as primary structure-based annotations from genome sequencing pipelines for 525/605 proteins (87%), which represents 54% (525/978) of all T. pallidum proteins. Of the 175 T. pallidum proteins modeled with high confidence that were not assigned functions in the previously annotated published proteome, 167 (95%) were able to be assigned predicted functions. Twenty-one of the 175 hypothetical proteins modeled with high confidence were also predicted to exhibit significant structural similarity with proteins experimentally confirmed to be required for virulence in other pathogens. Conclusions Phyre2-based structural modeling is a powerful bioinformatics tool that has provided insight into the potential structure and function of the majority of T. pallidum proteins and helped validate the primary structure-based annotation of more than 50% of all T. pallidum proteins with high confidence. This work represents the first T. pallidum proteome-wide structural modeling study and is one of few studies to apply this approach for the functional annotation of a whole proteome. Electronic supplementary material The online version of this article (10.1186/s12900-018-0086-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karen Vivien Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | | | - Chris Richard Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
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Mycoplasma genitalium Nonadherent Phase Variants Arise by Multiple Mechanisms and Escape Antibody-Dependent Growth Inhibition. Infect Immun 2018; 86:IAI.00866-17. [PMID: 29358335 DOI: 10.1128/iai.00866-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
Antigenic variation of the immunodominant MgpB and MgpC proteins has been suggested to be a mechanism of immune evasion of the human pathogen Mycoplasma genitalium, a cause of several reproductive tract disease syndromes. Phase variation resulting in the loss of adherence has also been documented, but the molecular mechanisms underlying this process and its role in pathogenesis are still poorly understood. In this study, we isolated and characterized 40 spontaneous, nonadherent phase variants from in vitro-passaged M. genitalium cultures. In all cases, nonadherence was associated with the loss of MgpBC protein expression, attributable to sequence changes in the mgpBC expression site. Phase variants were grouped into seven classes on the basis of the nature of the mutation. Consistent with the established role of RecA in phase variation, 31 (79.5%) variants arose via recombination with MgPa repeat regions that contain mgpBC variable sequences. The remaining mutants arose via nonsense or frameshift mutations. As expected, revertants were obtained for phase variants that were predicted to be reversible but not for those that arose via an irreversible mechanism. Furthermore, phase variants were enriched in M. genitalium cultures exposed to antibodies reacting to the extracellular, conserved C terminus of MgpB but not in cultures exposed to antibodies reacting to an intracellular domain of MgpB or the cytoplasmic HU protein. Genetic characterization of the antibody-selected phase variants confirmed that they arose via reversible and irreversible recombination and point mutations within mgpBC These phase variants resisted antibody-mediated growth inhibition, suggesting that phase variation promotes immune evasion.
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23
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Šmajs D, Strouhal M, Knauf S. Genetics of human and animal uncultivable treponemal pathogens. INFECTION GENETICS AND EVOLUTION 2018; 61:92-107. [PMID: 29578082 DOI: 10.1016/j.meegid.2018.03.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
Abstract
Treponema pallidum is an uncultivable bacterium and the causative agent of syphilis (subsp. pallidum [TPA]), human yaws (subsp. pertenue [TPE]), and bejel (subsp. endemicum). Several species of nonhuman primates in Africa are infected by treponemes genetically undistinguishable from known human TPE strains. Besides Treponema pallidum, the equally uncultivable Treponema carateum causes pinta in humans. In lagomorphs, Treponema paraluisleporidarum ecovar Cuniculus and ecovar Lepus are the causative agents of rabbit and hare syphilis, respectively. All uncultivable pathogenic treponemes harbor a relatively small chromosome (1.1334-1.1405 Mbp) and show gene synteny with minimal genetic differences (>98% identity at the DNA level) between subspecies and species. While uncultivable pathogenic treponemes contain a highly conserved core genome, there are a number of highly variable and/or recombinant chromosomal loci. This is also reflected in the occurrence of intrastrain heterogeneity (genetic diversity within an infecting bacterial population). Molecular differences at several different chromosomal loci identified among TPA strains or isolates have been used for molecular typing and the epidemiological characterization of syphilis isolates. This review summarizes genome structure of uncultivable pathogenic treponemes including genetically variable regions.
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Affiliation(s)
- David Šmajs
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Michal Strouhal
- Department of Biology, Masaryk University, Kamenice 5, Building A6, 625 00 Brno, Czech Republic.
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany,.
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24
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Abstract
Treponema pallidum subspecies pallidum (T. pallidum) causes syphilis via sexual exposure or via vertical transmission during pregnancy. T. pallidum is renowned for its invasiveness and immune-evasiveness; its clinical manifestations result from local inflammatory responses to replicating spirochaetes and often imitate those of other diseases. The spirochaete has a long latent period during which individuals have no signs or symptoms but can remain infectious. Despite the availability of simple diagnostic tests and the effectiveness of treatment with a single dose of long-acting penicillin, syphilis is re-emerging as a global public health problem, particularly among men who have sex with men (MSM) in high-income and middle-income countries. Syphilis also causes several hundred thousand stillbirths and neonatal deaths every year in developing nations. Although several low-income countries have achieved WHO targets for the elimination of congenital syphilis, an alarming increase in the prevalence of syphilis in HIV-infected MSM serves as a strong reminder of the tenacity of T. pallidum as a pathogen. Strong advocacy and community involvement are needed to ensure that syphilis is given a high priority on the global health agenda. More investment is needed in research on the interaction between HIV and syphilis in MSM as well as into improved diagnostics, a better test of cure, intensified public health measures and, ultimately, a vaccine.
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Affiliation(s)
- Rosanna W Peeling
- London School of Hygiene &Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David Mabey
- London School of Hygiene &Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Mary L Kamb
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Xiang-Sheng Chen
- National Center for STD Control, Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Dermatology, Nanjing, China
| | - Justin D Radolf
- Department of Medicine, UConn Health, Farmington, Connecticut, USA
| | - Adele S Benzaken
- Department of Surveillance, Prevention and Control of STI, HIV/AIDS and Viral Hepatitis, Ministry of Health, Brasília, Brazil
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25
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Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation. Nat Microbiol 2016; 2:16190. [PMID: 27748767 DOI: 10.1038/nmicrobiol.2016.190] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 11/08/2022]
Abstract
Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK). TprK demonstrated remarkable variability and redundancy, intra- and interpatient, suggesting ongoing parallel adaptive diversification during human infection. Some bacterial functions (for example, flagella- and chemotaxis-associated) were systematically targeted by both inter- and intrastrain single nucleotide polymorphisms, as well as by ongoing within-patient phase variation events. Finally, patient-derived genomes possess mutations targeting a penicillin-binding protein coding gene (mrcA) that had never been reported, unveiling it as a candidate target to investigate the impact on the susceptibility to penicillin. Our findings decode the major genetic mechanisms by which T. pallidum promotes immune evasion and survival, and demonstrate the exceptional power of characterizing evolving pathogen subpopulations during human infection.
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26
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Osbak KK, Houston S, Lithgow KV, Meehan CJ, Strouhal M, Šmajs D, Cameron CE, Van Ostade X, Kenyon CR, Van Raemdonck GA. Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry. PLoS Negl Trop Dis 2016; 10:e0004988. [PMID: 27606673 PMCID: PMC5015957 DOI: 10.1371/journal.pntd.0004988] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/19/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection. METHODOLOGY/PRINCIPAL FINDINGS To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF) and electrospray ionization (ESI-LTQ-Orbitrap) tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26) was found between previous microarray signal data and protein abundance. CONCLUSIONS This is the most comprehensive description of the global T. pallidum proteome to date. These data provide valuable insights into in vivo T. pallidum protein expression, paving the way for improved understanding of the pathogenicity of this enigmatic organism.
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Affiliation(s)
- Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Karen V Lithgow
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signaling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, Belgium
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27
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Reddy BL, Saier MH. Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PLoS One 2016; 11:e0152733. [PMID: 27064789 PMCID: PMC4827864 DOI: 10.1371/journal.pone.0152733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications.
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Affiliation(s)
- Bhaskara L. Reddy
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
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28
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Čejková D, Strouhal M, Norris SJ, Weinstock GM, Šmajs D. A Retrospective Study on Genetic Heterogeneity within Treponema Strains: Subpopulations Are Genetically Distinct in a Limited Number of Positions. PLoS Negl Trop Dis 2015; 9:e0004110. [PMID: 26436423 PMCID: PMC4593590 DOI: 10.1371/journal.pntd.0004110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pathogenic uncultivable treponemes comprise human and animal pathogens including agents of syphilis, yaws, bejel, pinta, and venereal spirochetosis in rabbits and hares. A set of 10 treponemal genome sequences including those of 4 Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14), 4 T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), 1 T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPLC) were examined with respect to the presence of nucleotide intrastrain heterogeneous sites. METHODOLOGY/PRINCIPAL FINDINGS The number of identified intrastrain heterogeneous sites in individual genomes ranged between 0 and 7. Altogether, 23 intrastrain heterogeneous sites (in 17 genes) were found in 5 out of 10 investigated treponemal genomes including TPA strains Nichols (n = 5), DAL-1 (n = 4), and SS14 (n = 7), TPE strain Samoa D (n = 1), and TEN strain Bosnia A (n = 5). Although only one heterogeneous site was identified among 4 tested TPE strains, 16 such sites were identified among 4 TPA strains. Heterogeneous sites were mostly strain-specific and were identified in four tpr genes (tprC, GI, I, K), in genes involved in bacterial motility and chemotaxis (fliI, cheC-fliY), in genes involved in cell structure (murC), translation (prfA), general and DNA metabolism (putative SAM dependent methyltransferase, topA), and in seven hypothetical genes. CONCLUSIONS/SIGNIFICANCE Heterogeneous sites likely represent both the selection of adaptive changes during infection of the host as well as an ongoing diversifying evolutionary process.
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Affiliation(s)
- Darina Čejková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Steven J. Norris
- Pathology & Laboratory Medicine, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - George M. Weinstock
- The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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