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Ciaco S, Aronne R, Fiabane M, Mori M. The Rise of Bacterial G-Quadruplexes in Current Antimicrobial Discovery. ACS OMEGA 2024; 9:24163-24180. [PMID: 38882119 PMCID: PMC11170735 DOI: 10.1021/acsomega.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024]
Abstract
Antimicrobial resistance (AMR) is a silent critical issue that poses several challenges to health systems. While the discovery of novel antibiotics is currently stalled and prevalently focused on chemical variations of the scaffolds of available drugs, novel targets and innovative strategies are urgently needed to face this global threat. In this context, bacterial G-quadruplexes (G4s) are emerging as timely and profitable targets for the design and development of antimicrobial agents. Indeed, they are expressed in regulatory regions of bacterial genomes, and their modulation has been observed to provide antimicrobial effects with translational perspectives in the context of AMR. In this work, we review the current knowledge of bacterial G4s as well as their modulation by small molecules, including tools and techniques suitable for these investigations. Finally, we critically analyze the needs and future directions in the field, with a focus on the development of small molecules as bacterial G4s modulators endowed with remarkable drug-likeness.
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Affiliation(s)
- Stefano Ciaco
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Rossella Aronne
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Martina Fiabane
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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Janečková K, Roos C, Fedrová P, Tom N, Čejková D, Lueert S, Keyyu JD, Chuma IS, Knauf S, Šmajs D. The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct. PLoS Negl Trop Dis 2023; 17:e0011602. [PMID: 37703251 PMCID: PMC10499264 DOI: 10.1371/journal.pntd.0011602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes. METHODOLOGY/PRINCIPAL FINDINGS In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes. CONCLUSION/SIGNIFICANCE Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans.
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Affiliation(s)
- Klára Janečková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Christian Roos
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
| | - Pavla Fedrová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Simone Lueert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - Julius D. Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Idrissa S. Chuma
- Department of Veterinary Medicine and Public Health, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Deutsches Primatenzentrum GmbH, Leibniz-Institute for Primate Research, Göttingen, Germany
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald—Insel Riems, Germany
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Jain N, Shankar U, Singh A, Sharma TK, Kumar A. G-quadruplex motifs in Neisseria gonorrhoeae as anti-gonococcal targets. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12646-6. [PMID: 37410137 DOI: 10.1007/s00253-023-12646-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023]
Abstract
Neisseria gonorrhoeae is an obligate human pathogen that causes gonorrhea and has shown a vast emergence of multidrug resistance in recent times. It is necessary to develop novel therapeutic strategies to combat this multidrug-resistant pathogen. The non-canonical stable secondary structures of nucleic acids, G-quadruplexes (GQs), are reported to regulate gene expressions in viruses, prokaryotes, and eukaryotes. Herein, we explored the whole genome of N. gonorrhoeae to mine evolutionary conserved GQ motifs. The Ng-GQs were highly enriched in the genes involved in various important biological and molecular processes of N. gonorrhoeae. Five of these GQ motifs were characterized using biophysical and biomolecular techniques. The GQ-specific ligand, BRACO-19, showed a high affinity towards these GQ motifs and stabilized them in both in vitro and in vivo conditions. The ligand showed potent anti-gonococcal activity and modulated the gene expression of the GQ-harboring genes. Strikingly, BRACO-19 also altered the biofilm formation in N. gonorrhoeae and its adhesion and invasion of the human cervical epithelial cells. In summary, the present study showed a significant role of GQ motifs in N. gonorrhoeae biology and put forward a step closer towards the search for therapeutic measures in combating the emerging antimicrobial resistance in the pathogen. KEY POINTS: •Neisseria gonorrhoeae genome is enriched in non-canonical nucleic acid structures-G-quadruplexes. •These G-quadruplexes might regulate bacterial growth, virulence, and pathogenesis. •G-quadruplex ligands inhibit biofilm formation, adhesion, and invasion of the gonococcus bacterium.
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Affiliation(s)
- Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | - Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India
| | | | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore-IIT Indore, Khandwa Road, Simrol, Indore, Madhya Pradesh, 453 552, India.
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Karanfilian KM, Almohssen AA, Kapila R, Schwartz RA. Malignant syphilis: a new and revised definition. Int J Dermatol 2023; 62:369-375. [PMID: 36250867 DOI: 10.1111/ijd.16444] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/07/2022] [Accepted: 09/22/2022] [Indexed: 12/01/2022]
Abstract
Malignant syphilis is a rare, severe variant of secondary syphilis that primarily affects immunocompromised patients. Historically, the clinical presentation included a prodrome of constitutional symptoms followed by the development of characteristic skin lesions. The definition of malignant syphilis has not been updated since it was first described as only a cutaneous manifestation. In recent years, syphilis has reemerged as a major public health issue, particularly in men who have sex with men (MSM) and patients with HIV. With increasing rates of syphilis in the HIV-positive population, the systemic manifestations of malignant syphilis have become more apparent. We propose a revised definition and elucidate why the term malignant syphilis should be expanded to include systemic manifestations, stressing musculoskeletal, central nervous system, ocular, ear, cardiovascular, rectal, liver, lung, and renal involvement. This updated definition is dramatically expanded to reflect its systemic manifestations. Recognition of these manifestations may prevent devastating long-term effects.
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Affiliation(s)
| | | | - Rajendra Kapila
- Infectious Disease, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Robert A Schwartz
- Dermatology and Pathology, Rutgers New Jersey Medical School, Newark, NJ, USA
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Romeis E, Lieberman NAP, Molini B, Tantalo LC, Chung B, Phung Q, Avendaño C, Vorobieva A, Greninger AL, Giacani L. Treponema pallidum subsp. pallidum with an Artificially impaired TprK antigenic variation system is attenuated in the Rabbit model of syphilis. PLoS Pathog 2023; 19:e1011259. [PMID: 36940224 PMCID: PMC10063172 DOI: 10.1371/journal.ppat.1011259] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/30/2023] [Accepted: 03/01/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND The TprK protein of the syphilis agent, Treponema pallidum subsp. pallidum (T. pallidum), undergoes antigenic variation in seven discrete variable (V) regions via non-reciprocal segmental gene conversion. These recombination events transfer information from a repertoire of 53 silent chromosomal donor cassettes (DCs) into the single tprK expression site to continually generate TprK variants. Several lines of research developed over the last two decades support the theory that this mechanism is central to T. pallidum's ability for immune avoidance and persistence in the host. Structural and modeling data, for example, identify TprK as an integral outer membrane porin with the V regions exposed on the pathogen's surface. Furthermore, infection-induced antibodies preferentially target the V regions rather than the predicted β-barrel scaffolding, and sequence variation abrogates the binding of antibodies elicited by antigenically different V regions. Here, we engineered a T. pallidum strain to impair its ability to vary TprK and assessed its virulence in the rabbit model of syphilis. PRINCIPAL FINDINGS A suicide vector was transformed into the wild-type (WT) SS14 T. pallidum isolate to eliminate 96% of its tprK DCs. The resulting SS14-DCKO strain exhibited an in vitro growth rate identical to the untransformed strain, supporting that the elimination of the DCs did not affect strain viability in absence of immune pressure. In rabbits injected intradermally with the SS14-DCKO strain, generation of new TprK sequences was impaired, and the animals developed attenuated lesions with a significantly reduced treponemal burden compared to control animals. During infection, clearance of V region variants originally in the inoculum mirrored the generation of antibodies to these variants, although no new variants were generated in the SS14-DCKO strain to overcome immune pressure. Naïve rabbits that received lymph node extracts from animals infected with the SS14-DCKO strain remained uninfected. CONCLUSION These data further support the critical role of TprK in T. pallidum virulence and persistence during infection.
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Affiliation(s)
- Emily Romeis
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Barbara Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Lauren C. Tantalo
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Chung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Carlos Avendaño
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Anastassia Vorobieva
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - 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
| | - 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
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Romeis E, Lieberman NAP, Molini B, Tantalo LC, Chung B, Phung Q, Avendaño C, Vorobieva A, Greninger AL, Giacani L. Treponema pallidum subsp. pallidum with an Artificially Impaired TprK Antigenic Variation System is Attenuated in the Rabbit Model of Syphilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524629. [PMID: 36711914 PMCID: PMC9882362 DOI: 10.1101/2023.01.18.524629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background The TprK protein of the syphilis agent, Treponema pallidum subsp. pallidum ( T. pallidum ), undergoes antigenic variation in seven discrete variable (V) regions via non-reciprocal segmental gene conversion. These recombination events transfer information from a repertoire of 53 silent chromosomal donor cassettes (DCs) into the single tprK expression site to continually generate TprK variants. Several lines of research developed over the last two decades support the theory that this mechanism is central to T. pallidum 's ability for immune avoidance and persistence in the host. Structural and modeling data, for example, identify TprK as an integral outer membrane porin with the V regions exposed on the pathogen's surface. Furthermore, infection-induced antibodies preferentially target the V regions rather than the predicted β-barrel scaffolding, and sequence variation abrogates the binding of antibodies elicited by antigenically different V regions. Here, we engineered a T. pallidum strain to impair its ability to vary TprK and assessed its virulence in the rabbit model of syphilis. Principal findings A suicide vector was transformed into the wild-type (WT) SS14 T. pallidum isolate to eliminate 96% of its tprK DCs. The resulting SS14-DC KO strain exhibited an in vitro growth rate identical to the untransformed strain, supporting that the elimination of the DCs did not affect strain viability in absence of immune pressure. In rabbits injected intradermally with the SS14-DC KO strain, generation of new TprK sequences was impaired, and the animals developed attenuated lesions with a significantly reduced treponemal burden compared to control animals. During infection, clearance of V region variants originally in the inoculum mirrored the generation of antibodies to these variants, although no new variants were generated in the SS14-DC KO strain to overcome immune pressure. Naïve rabbits that received lymph node extracts from animals infected with the SS14-DC KO strain remained uninfected. Conclusion These data further support the critical role of TprK in T. pallidum virulence and persistence during infection. Author Summary Syphilis is still endemic in low- and middle-income countries, and it has been resurgent in high-income nations, including the U.S., for years. In endemic areas, there is still significant morbidity and mortality associated with this disease, particularly when its causative agent, the spirochete Treponema pallidum subsp . pallidum ( T. pallidum ) infects the fetus during pregnancy. Improving our understanding of syphilis pathogenesis and T. pallidum biology could help investigators devise better control strategies for this serious infection. Now that tools to genetically manipulate this pathogen are available, we can engineer T. pallidum strains lacking specific genes or genomic regions known (or believed) to be associated with virulence. This approach can shed light on the role of the ablated genes or sequences in disease development using loss-of-function strains. Here, we derived a knockout (KO) T. pallidum mutant (SS14-DC KO ) impaired in its ability to undergo antigenic variation of TprK, a protein that has long been hypothesized to be central in evasion of the host immune response and pathogen persistence during infection. When compared to the WT isolate, which is still capable of antigenic variation, the SS14-DC KO strain is significantly attenuated in its ability to proliferate and to induce early disease manifestations in infected rabbits. Our results further support the importance of TprK antigenic variation in syphilis pathogenesis and pathogen persistence.
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. G-Quadruplex Structures in Bacteria: Functional Properties and Prospects for Use as Biotargets. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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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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Cueny RR, McMillan SD, Keck JL. G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures. Crit Rev Biochem Mol Biol 2022; 57:539-561. [PMID: 36999585 PMCID: PMC10336854 DOI: 10.1080/10409238.2023.2181310] [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: 08/04/2022] [Revised: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that depend upon their positions within genomes or transcripts. These include potential roles as impediments to genome replication, transcription, and translation or, in other contexts, as activators of genome stability, transcription, and recombination. This duality suggests that G4 sequences can aid cellular processes but that their presence can also be problematic. Despite their documented importance in bacterial species, G4s remain understudied in bacteria relative to eukaryotes. In this review, we highlight the roles of bacterial G4s by discussing their prevalence in bacterial genomes, the proteins that bind and unwind G4s in bacteria, and the processes regulated by bacterial G4s. We identify limitations in our current understanding of the functions of G4s in bacteria and describe new avenues for studying these remarkable nucleic acid structures.
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Affiliation(s)
- Rachel R. Cueny
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Sarah D. McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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10
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Shitikov EA, Bespiatykh DA, Bodoev IN, Zaychikova MV. [G-quadruplex structures in bacteria: functional properties and prospects for use as biotargets]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:93-103. [PMID: 35485483 DOI: 10.18097/pbmc20226802093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
G-quadruplexes (G4), non-canonical secondary DNA structures, are intensively investigated for a long time. In eukaryotic organisms they play an important role in the regulation of gene expression and DNA repair. G4 have also been found in the genomes of numerous bacteria and archaea, but their functional role has not yet been fully explored. Nevertheless, their participation in the formation of antigenic variability, pathogenicity, antibiotic resistance and survival in extreme conditions has been established. Currently, many tools have been developed to detect potential G4 sequences and confirm their formation ability. Since the controlled formation and resolution of the quadruplex are significant means for the regulation of genes critical for survival, a promising direction is the search for ligands - compounds that can have a stabilizing effect on the quadruplex structure and thereby alter gene expression. Currently, a number of ligands are already known, their use stops the growth of pathogenic microorganisms. G4 ligands are of interest as potential antibiotics, which are extremely relevant due to the wide spread of drug resistant pathogens.
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Affiliation(s)
- E A Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D A Bespiatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I N Bodoev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - M V Zaychikova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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11
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Pla-Díaz M, Sánchez-Busó L, Giacani L, Šmajs D, Bosshard PP, Bagheri HC, Schuenemann VJ, Nieselt K, Arora N, González-Candelas F. Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum. Mol Biol Evol 2021; 39:6427636. [PMID: 34791386 PMCID: PMC8789261 DOI: 10.1093/molbev/msab318] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diversity and differentiation acting during the evolution of T. pallidum subspecies. Using a custom-tailored procedure, named phylogenetic incongruence method, with 75 complete genome sequences, we found strong evidence for recombination among the T. pallidum subspecies, involving 12 genes and 21 events. In most cases, only one recombination event per gene was detected and all but one event corresponded to intersubspecies transfers, from TPE/TEN to TPA. We found a clear signal of natural selection acting on the recombinant genes, which is more intense in their recombinant regions. The phylogenetic location of the recombination events detected and the functional role of the genes with signals of positive selection suggest that these evolutionary processes had a key role in the evolution and recent expansion of the syphilis bacteria and significant implications for the selection of vaccine candidates and the design of a broadly protective syphilis vaccine.
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Affiliation(s)
- Marta Pla-Díaz
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, and Department of Global Health, University of Washington, Seattle, WA, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Czech Republic
| | - Philipp P Bosshard
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | | | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Germany
| | - Natasha Arora
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.,Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universidad de Valencia-I2SysBio, Spain.,CIBER in Epidemiology and Public Health, Spain.,Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain
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Lin MJ, Haynes AM, Addetia A, Lieberman NAP, Phung Q, Xie H, Nguyen TV, Molini BJ, Lukehart SA, Giacani L, Greninger AL. Longitudinal TprK profiling of in vivo and in vitro-propagated Treponema pallidum subsp. pallidum reveals accumulation of antigenic variants in absence of immune pressure. PLoS Negl Trop Dis 2021; 15:e0009753. [PMID: 34492041 PMCID: PMC8480903 DOI: 10.1371/journal.pntd.0009753] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/29/2021] [Accepted: 08/23/2021] [Indexed: 11/25/2022] Open
Abstract
Immune evasion by Treponema pallidum subspecies pallidum (T. pallidum) has been attributed to antigenic variation of its putative outer-membrane protein TprK. In TprK, amino acid diversity is confined to seven variable (V) regions, and generation of sequence diversity within the V regions occurs via a non-reciprocal segmental gene conversion mechanism where donor cassettes recombine into the tprK expression site. Although previous studies have shown the significant role of immune selection in driving accumulation of TprK variants, the contribution of baseline gene conversion activity to variant diversity is less clear. Here, combining longitudinal tprK deep sequencing of near clonal Chicago C from immunocompetent and immunosuppressed rabbits along with the newly developed in vitro cultivation system for T. pallidum, we directly characterized TprK alleles in the presence and absence of immune selection. Our data confirm significantly greater sequence diversity over time within the V6 region during syphilis infection in immunocompetent rabbits compared to immunosuppressed rabbits, consistent with previous studies on the role of TprK in evasion of the host immune response. Compared to strains grown in immunocompetent rabbits, strains passaged in vitro displayed low level changes in allele frequencies of TprK variable region sequences similar to that of strains passaged in immunosuppressed rabbits. Notably, we found significantly increased rates of V6 allele generation relative to other variable regions in in vitro cultivated T, pallidum strains, illustrating that the diversity within these hypervariable regions occurs in the complete absence of immune selection. Together, our results demonstrate antigenic variation in T. pallidum can be studied in vitro and occurs even in the complete absence of immune pressure, allowing the T. pallidum population to continuously evade the immune system of the infected host.
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Affiliation(s)
- Michelle J. Lin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Austin M. Haynes
- Pathobiology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Amin Addetia
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Quynh Phung
- 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
| | - Tien V. Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Barbara J. Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, 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
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, 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
- * E-mail:
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13
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G-Quadruplex Structures in Bacteria: Biological Relevance and Potential as an Antimicrobial Target. J Bacteriol 2021; 203:e0057720. [PMID: 33649149 DOI: 10.1128/jb.00577-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA strands consisting of multiple runs of guanines can adopt a noncanonical, four-stranded DNA secondary structure known as G-quadruplex or G4 DNA. G4 DNA is thought to play an important role in transcriptional and translational regulation of genes, DNA replication, genome stability, and oncogene expression in eukaryotic genomes. In other organisms, including several bacterial pathogens and some plant species, the biological roles of G4 DNA and G4 RNA are starting to be explored. Recent investigations showed that G4 DNA and G4 RNA are generally conserved across plant species. In silico analyses of several bacterial genomes identified putative guanine-rich, G4 DNA-forming sequences in promoter regions. The sequences were particularly abundant in certain gene classes, suggesting that these highly diverse structures can be employed to regulate the expression of genes involved in secondary metabolite synthesis and signal transduction. Furthermore, in the pathogen Mycobacterium tuberculosis, the distribution of G4 motifs and their potential role in the regulation of gene transcription advocate for the use of G4 ligands to develop novel antitubercular therapies. In this review, we discuss the various roles of G4 structures in bacterial DNA and the application of G4 DNA as inhibitors or therapeutic agents to address bacterial pathogens.
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Dey U, Sarkar S, Teronpi V, Yella VR, Kumar A. G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation. Biochimie 2021; 184:40-51. [PMID: 33548392 DOI: 10.1016/j.biochi.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The role of G-quadruplexes in the cellular physiology of human pathogenesis is an intriguing area of research. Nonetheless, their functional roles and evolutionary conservation have not been compared comprehensively in pathogenic forms of various bacterial genera and species. In the current in silico study, we addressed the role of G-quadruplex-forming sequences (G4 motifs) in the context of cis-regulation, expression variation, regulatory networks, gene orthology and ontology. Genome-wide screening across seven pathogenic genomes using the G4Hunter tool revealed the significant prevalence of G4 motifs in cis-regulatory regions compared to the intragenic regions. Significant conservation of G4 motifs was observed in the regulatory region of 300 orthologous genes. Further analysis of published ChIP-Seq data (Minch et al., 2015) of 91 DNA-binding proteins of the M. tuberculosis genome revealed significant links between G4 motifs and target sites of transcriptional regulators. Interestingly, the transcription factors entangled with virulence, in specific, CsoR, Rv0081, DevR/DosR, and TetR family are found to have G4 motifs in their target regulatory regions. Overall the current study applies positional-functional relationship computation to delve into the cis-regulation of G-quadruplex structures in the context of gene orthology in pathogenic bacteria.
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Affiliation(s)
- Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, 784184, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522502, Andhra Pradesh, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
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15
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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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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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Shankar U, Jain N, Majee P, Kodgire P, Sharma TK, Kumar A. Exploring Computational and Biophysical Tools to Study the Presence of G-Quadruplex Structures: A Promising Therapeutic Solution for Drug-Resistant Vibrio cholerae. Front Genet 2020; 11:935. [PMID: 33101360 PMCID: PMC7545536 DOI: 10.3389/fgene.2020.00935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Vibrio cholerae, a gram-negative bacterium that causes cholera, has already caused seven major pandemics across the world and infects roughly 1.3–4 million people every year. Cholera treatment primarily involves oral rehydration therapy supplemented with antibiotics. But recently, multidrug-resistant strains of V. cholerae have emerged. High genomic plasticity further enhances the pathogenesis of this human pathogen. Guanines in DNA or RNA assemble to form G-quadruplex (GQ) structures which have begun to be seen as potential drug targeting sites for different pathogenic bacteria and viruses. In this perspective, we carried out a genome-wide hunt in V. cholerae using a bio-informatics approach and observed ∼85 G-quadruplex forming motifs (VC-PGQs) in chromosome I and ∼45 putative G-quadruplexs (PGQs) in chromosome II. Ten putative G-quadruplex forming motifs (VC-PGQs) were selected on the basis of conservation throughout the genus and functional analysis displayed their location in the essential genes encoding bacterial proteins, for example, methyl-accepting chemotaxis protein, orotate phosphoribosyl transferase protein, amidase proteins, etc. The predicted VC-PGQs were validated using different bio-physical techniques, including Nuclear Magnetic Resonance spectroscopy, Circular Dichroism spectroscopy, and electrophoretic mobility shift assay, which demonstrated the formation of highly stable GQ structures in the bacteria. The interaction of these VC-PGQs with the known specific GQ ligand, TMPyP4, was analyzed using ITC and molecular dynamics studies that displayed the stabilization of the VC-PGQs by the GQ ligands and thus represents a potential therapeutic strategy against this enteric pathogen by inhibiting the PGQ harboring gene expression, thereby inhibiting the bacterial growth and virulence. In summary, this study reveals the presence of conserved GQ forming motifs in the V. cholerae genome that has the potential to be used to treat the multi-drug resistance problem of the notorious enteric pathogen.
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Affiliation(s)
- Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prativa Majee
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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18
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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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Addetia A, Tantalo LC, Lin MJ, Xie H, Huang ML, Marra CM, Greninger AL. Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection. PLoS Negl Trop Dis 2020; 14:e0007921. [PMID: 32251462 PMCID: PMC7162541 DOI: 10.1371/journal.pntd.0007921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 04/16/2020] [Accepted: 02/08/2020] [Indexed: 12/25/2022] Open
Abstract
Developing a vaccine against Treponema pallidum subspecies pallidum, the causative agent of syphilis, remains a public health priority. Syphilis vaccine design efforts have been complicated by lack of an in vitro T. pallidum culture system, prolific antigenic variation in outer membrane protein TprK, and lack of functional annotation for nearly half of the genes. Understanding the genetic basis of T. pallidum reinfection can provide insights into variation among strains that escape cross-protective immunity. Here, we present comparative genomic sequencing and deep, full-length tprK profiling of two T. pallidum isolates from blood from the same patient that were collected six years apart. Notably, this patient was diagnosed with syphilis four times, with two of these episodes meeting the definition of neurosyphilis, during this interval. Outside of the highly variable tprK gene, we identified 14 coding changes in 13 genes. Nine of these genes putatively localized to the periplasmic or outer membrane spaces, consistent with a potential role in serological immunoevasion. Using a newly developed full-length tprK deep sequencing protocol, we profiled the diversity of this gene that far outpaces the rest of the genome. Intriguingly, we found that the reinfecting isolate demonstrated less diversity across each tprK variable region compared to the isolate from the first infection. Notably, the two isolates did not share any full-length TprK sequences. Our results are consistent with an immunodominant-evasion model in which the diversity of TprK explains the ability of T. pallidum to successfully reinfect individuals, even when they have been infected with the organism multiple times.
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Affiliation(s)
- Amin Addetia
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lauren C. Tantalo
- Department of Neurology, University of Washington, Seattle, Washington, United States of America
| | - Michelle J. Lin
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Christina M. Marra
- Department of Neurology, University of Washington, Seattle, Washington, United States of America
| | - Alexander L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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20
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Mikalová L, Janečková K, Nováková M, Strouhal M, Čejková D, Harper KN, Šmajs D. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains. PLoS One 2020; 15:e0230926. [PMID: 32236138 PMCID: PMC7112178 DOI: 10.1371/journal.pone.0230926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/11/2020] [Indexed: 11/25/2022] Open
Abstract
Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). Until now, only a single TEN strain, Bosnia A, has been completely sequenced. The only other laboratory TEN strain available, Iraq B, was isolated in Iraq in 1951 by researchers from the US Centers for Disease Control and Prevention. In this study, the complete genome of the Iraq B strain was amplified as overlapping PCR products and sequenced using the pooled segment genome sequencing method and Illumina sequencing. Total average genome sequencing coverage reached 3469×, with a total genome size of 1,137,653 bp. Compared to the genome sequence of Bosnia A, a set of 37 single nucleotide differences, 4 indels, 2 differences in the number of tandem repetitions, and 18 differences in the length of homopolymeric regions were found in the Iraq B genome. Moreover, the tprF and tprG genes that were previously found deleted in the genome of the TEN Bosnia A strain (spanning 2.3 kb in length) were present in a subpopulation of TEN Iraq B and Bosnia A microbes, and their sequence was highly similar to those found in T. p. subsp. pertenue strains, which cause the disease yaws. The genome sequence of TEN Iraq B revealed close genetic relatedness between both available bejel-causing laboratory strains (i.e., Iraq B and Bosnia A) and also genetic variability within the bejel treponemes comparable to that found within yaws- or syphilis-causing strains. In addition, genetic relatedness to TPE strains was demonstrated by the sequence of the tprF and tprG genes found in subpopulations of both TEN Iraq B and Bosnia A. The loss of the tprF and tprG genes in most TEN microbes suggest that TEN genomes have been evolving via the loss of genomic regions, a phenomenon previously found among the treponemes causing both syphilis and rabbit syphilis.
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Affiliation(s)
- Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Klára Janečková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Markéta Nováková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - Kristin N. Harper
- Department of Population Biology, Ecology, and Evolution, Emory University, Atlanta, Georgia, United States of America
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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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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Prister LL, Ozer EA, Cahoon LA, Seifert HS. Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae. Mol Microbiol 2019; 112:1219-1234. [PMID: 31338863 PMCID: PMC6800796 DOI: 10.1111/mmi.14356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2019] [Indexed: 02/06/2023]
Abstract
Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis-acting sRNA (G4-sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal Av frequencies. Using chromatin immunoprecipitation (ChIP) assays, we show that cellular G4s are less abundant when sRNA transcription is lower. In addition, using ChIP, we demonstrate that the G4-sRNA forms a stable RNA:DNA hybrid (R-loop) with its template strand. However, modulating R-loop levels by controlling RNase HI expression does not alter G4 abundance quantified through ChIP. Since pilin Av frequencies were not altered when modulating R-loop levels by controlling RNase HI expression, we conclude that transcription of the sRNA is necessary, but stable R-loops are not required to promote pilin Av.
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Affiliation(s)
- Lauren L Prister
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - Egon A Ozer
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
- Department of Medicine, Division of Infectious DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - Laty A Cahoon
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
| | - H Steven Seifert
- Department of Microbiology-Immunology, DiseaseNorthwestern University Feinberg School of Medicine, Chicago, IL US
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Maděránková D, Mikalová L, Strouhal M, Vadják Š, Kuklová I, Pospíšilová P, Krbková L, Koščová P, Provazník I, Šmajs D. Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution. PLoS Negl Trop Dis 2019; 13:e0007463. [PMID: 31216284 PMCID: PMC6602244 DOI: 10.1371/journal.pntd.0007463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 07/01/2019] [Accepted: 05/14/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Pathogenic treponemes related to Treponema pallidum are both human (causing syphilis, yaws, bejel) and animal pathogens (infections of primates, venereal spirochetosis in rabbits). A set of 11 treponemal genome sequences including those of five Treponema pallidum ssp. pallidum (TPA) strains (Nichols, DAL-1, Mexico A, SS14, Chicago), four T. p. ssp. pertenue (TPE) strains (CDC-2, Gauthier, Samoa D, Fribourg-Blanc), one T. p. ssp. endemicum (TEN) strain (Bosnia A) and one strain (Cuniculi A) of Treponema paraluisleporidarum ecovar Cuniculus (TPeC) were tested for the presence of positively selected genes. METHODOLOGY/PRINCIPAL FINDINGS A total of 1068 orthologous genes annotated in all 11 genomes were tested for the presence of positively selected genes using both site and branch-site models with CODEML (PAML package). Subsequent analyses with sequences obtained from 62 treponemal draft genomes were used for the identification of positively selected amino acid positions. Synthetic biotinylated peptides were designed to cover positively selected protein regions and these peptides were tested for reactivity with the patient's syphilis sera. Altogether, 22 positively selected genes were identified in the TP genomes and TPA sets of positively selected genes differed from TPE genes. While genetic variability among TPA strains was predominantly present in a number of genetic loci, genetic variability within TPE and TEN strains was distributed more equally along the chromosome. Several syphilitic sera were shown to react with some peptides derived from the protein sequences evolving under positive selection. CONCLUSIONS/SIGNIFICANCE The syphilis-, yaws-, and bejel-causing strains differed relative to sets of positively selected genes. Most of the positively selected chromosomal loci were identified among the TPA treponemes. The local accumulation of genetic variability suggests that the diversification of TPA strains took place predominantly in a limited number of genomic regions compared to the more dispersed genetic diversity differentiating TPE and TEN strains. The identification of positively selected sites in tpr genes and genes encoding outer membrane proteins suggests their role during infection of human and animal hosts. The driving force for adaptive evolution at these loci thus appears to be the host immune response as supported by observed reactivity of syphilitic sera with some peptides derived from protein sequences showing adaptive evolution.
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Affiliation(s)
- Denisa Maděránková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Šimon Vadják
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivana Kuklová
- Department of Dermatology, 1st Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Krbková
- Department of Children's Infectious Diseases, Faculty of Medicine and University Hospital, Masaryk University, Brno, Czech Republic
| | - Pavlína Koščová
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - Ivo Provazník
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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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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Saranathan N, Biswas B, Patra A, Vivekanandan P. G-quadruplexes may determine the landscape of recombination in HSV-1. BMC Genomics 2019; 20:382. [PMID: 31096907 PMCID: PMC6524338 DOI: 10.1186/s12864-019-5731-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Several lines of evidence suggest that recombination plays a central role in replication and evolution of herpes simplex virus-1 (HSV-1). G-quadruplex (G4)-motifs have been linked to recombination events in human and microbial genomes, but their role in recombination has not been studied in DNA viruses. Results The availability of near full-length sequences from 40 HSV-1 recombinant strains with exact position of the recombination breakpoints provided us with a unique opportunity to investigate the role of G4-motifs in recombination among herpes viruses. We mapped the G4-motifs in the parental and all the 40 recombinant strains. Interestingly, the genome-wide distribution of breakpoints closely mirrors the G4 densities in the HSV-1 genome; regions of the genome with higher G4 densities had higher number of recombination breakpoints. Biophysical characterization of oligonucleotides from a subset of predicted G4-motifs confirmed the formation of G-quadruplex structures. Our analysis also reveals that G4-motifs are enriched in regions flanking the recombination breakpoints. Interestingly, about 11% of breakpoints lie within a G4-motif, making these DNA secondary structures hotspots for recombination in the HSV-1 genome. Breakpoints within G4-motifs predominantly lie within G4-clusters rather than individual G4-motifs. Of note, we identified the terminal guanosine of G4-clusters at the boundaries of the UL (unique long) region on either side of the OriL (origin of replication within UL) represented the commonest breakpoint among the HSV-1 recombinants. Conclusion Our findings suggest a correlation between the HSV-1 recombination landscape and the distribution of G4-motifs and G4-clusters, with possible implications for the evolution of DNA viruses. Electronic supplementary material The online version of this article (10.1186/s12864-019-5731-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anupam Patra
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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Mishra SK, Shankar U, Jain N, Sikri K, Tyagi JS, Sharma TK, Mergny JL, Kumar A. Characterization of G-Quadruplex Motifs in espB, espK, and cyp51 Genes of Mycobacterium tuberculosis as Potential Drug Targets. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:698-706. [PMID: 31128421 PMCID: PMC6531831 DOI: 10.1016/j.omtn.2019.04.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 01/31/2023]
Abstract
G-quadruplex structure forming motifs are among the most studied evolutionarily conserved drug targets that are present throughout the genome of different organisms and susceptible to influencing various biological processes. Here we report highly conserved potential G-quadruplex motifs (PGQs) in three essential genes (espK, espB, and cyp51) among 160 strains of the Mycobacterium tuberculosis genome. Products of these genes are involved in pathways that are responsible for virulence determination of bacteria inside the host cell and its survival by maintaining membrane fluidity. The espK and espB genes are essential players that prevent the formation of mature phagolysosome and antigen presentation by host macrophages. The cyp51 is another PGQ-possessing gene involved in sterol biosynthesis pathway and membrane formation. In the present study, we revealed the formation of stable intramolecular parallel G-quadruplex structures by Mycobacterium PGQs using a combination of techniques (NMR, circular dichroism [CD], and gel electrophoresis). Next, isothermal titration calorimetry (ITC) and CD melting analysis demonstrated that a well-known G-quadruplex ligand, TMPyP4, binds to and stabilizes these PGQ motifs. Finally, polymerase inhibition and qRT-PCR assays highlight the biological relevance of PGQ-possessing genes in this pathogen and demonstrate that G-quadruplexes are potential drug targets for the development of effective anti-tuberculosis therapeutics.
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Affiliation(s)
- Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Kriti Sikri
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tarun Kumar Sharma
- Centre for Bio-design and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Jean-Louis Mergny
- ARNA Laboratory, INSERM U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
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Liu D, Tong ML, Luo X, Liu LL, Lin LR, Zhang HL, Lin Y, Niu JJ, Yang TC. Profile of the tprK gene in primary syphilis patients based on next-generation sequencing. PLoS Negl Trop Dis 2019; 13:e0006855. [PMID: 30789907 PMCID: PMC6400401 DOI: 10.1371/journal.pntd.0006855] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 03/05/2019] [Accepted: 12/07/2018] [Indexed: 12/04/2022] Open
Abstract
Background The highly variable tprK gene of Treponema pallidum has been acknowledged to be one of the mechanisms that causes persistent infection. Previous studies have mainly focused on the heterogeneity in tprK in propagated strains using a clone-based Sanger approach. Few studies have investigated tprK directly from clinical samples using deep sequencing. Methods/Principal findings We conducted a comprehensive analysis of 14 primary syphilis clinical isolates of T. pallidum via next-generation sequencing to gain better insight into the profile of tprK in primary syphilis patients. Our results showed that there was a mixture of distinct sequences within each V region of tprK. Except for the predominant sequence for each V region as previously reported using the clone-based Sanger approach, there were many minor variants of all strains that were mainly observed at a frequency of 1–5%. Interestingly, the identified distinct sequences within the regions were variable in length and differed by only 3 bp or multiples of 3 bp. In addition, amino acid sequence consistency within each V region was found among the 14 strains. Among the regions, the sequence IASDGGAIKH in V1 and the sequence DVGHKKENAANVNGTVGA in V4 showed a high stability of inter-strain redundancy. Conclusions The seven V regions of the tprK gene in primary syphilis infection demonstrated high diversity; they generally contained a high proportion sequence and numerous low-frequency minor variants, most of which are far below the detection limit of Sanger sequencing. The rampant variation in each V region was regulated by a strict gene conversion mechanism that maintained the length difference to 3 bp or multiples of 3 bp. The highly stable sequence of inter-strain redundancy may indicate that the sequences play a critical role in T. pallidum virulence. These highly stable peptides are also likely to be potential targets for vaccine development. Variations in tprK have been acknowledged to be the major contributors to persistent Treponema pallidum infections. Previous studies were based on the clone-based Sanger approach, and most of them were performed in propagated strains using rabbits, which could not reflect the actual heterogeneous characteristics of tprK in the context of human infection. In the present study, we employed next-generation sequencing (NGS) to explore the profile of tprK directly from 14 patients with primary syphilis. Our results showed a mixture of distinct sequences within each V region of tprK in these clinical samples. First, the length of identified distinct sequences within the region was variable, which differed by only 3 bp or multiples of 3 bp. Then, among the mixtures, a predominant sequence was usually observed for each V region, and the remaining minor variants were mainly observed at a frequency of 1–5%. In addition, there was a scenario of amino acid sequence consistency within the regions among the 14 primary syphilis strains. The identification of the profile of tprK in the context of human primary syphilis infection contributes to further exploration of the pathogenesis of syphilis.
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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
| | - Xi Luo
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Li-Li 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
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
- Institute of Infectious Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Hui-Lin Zhang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Yong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Jian-Jun Niu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medicine, Xiamen University, Xiamen, China
- Zhongshan Hospital, Fujian Medical 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
- * E-mail:
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Saranathan N, Vivekanandan P. G-Quadruplexes: More Than Just a Kink in Microbial Genomes. Trends Microbiol 2019; 27:148-163. [PMID: 30224157 PMCID: PMC7127049 DOI: 10.1016/j.tim.2018.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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Strouhal M, Mikalová L, Haviernik J, Knauf S, Bruisten S, Noordhoek GT, Oppelt J, Čejková D, Šmajs D. Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes. PLoS Negl Trop Dis 2018; 12:e0006867. [PMID: 30303967 PMCID: PMC6197692 DOI: 10.1371/journal.pntd.0006867] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/22/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes. METHODOLOGY/PRINCIPAL FINDINGS The genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126-TP0136, TP0856-TP0858, and TP0896 genes. CONCLUSIONS/SIGNIFICANCE Comparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
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Affiliation(s)
- Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Haviernik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology Unit, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
| | - Sylvia Bruisten
- Public Health Laboratory, Department of Infectious Diseases GGD Amsterdam, WT Amsterdam, the Netherlands
| | - Gerda T. Noordhoek
- Izore, Centrum Infectieziekten Friesland, EN Leeuwarden, the Netherlands
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Darina Čejková
- Department of Immunology, Veterinary Research Institute, Brno, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Abstract
Advances in understanding mechanisms of nucleic acids have revolutionized molecular biology and medicine, but understanding of nontraditional nucleic acid conformations is less developed. The guanine quadruplex (G4) alternative DNA structure was first described in the 1960s, but the existence of G4 structures (G4-S) and their participation in myriads of biological functions are still underappreciated. Despite many tools to study G4s and many examples of roles for G4s in eukaryotic molecular processes and issues with uncontrolled G4-S formation, there is relatively little knowledge about the roles of G4-S in viral or prokaryotic systems. This review summarizes the state of the art with regard to G4-S in eukaryotes and their potential roles in human disease before discussing the evidence that G4-S have equivalent importance in affecting viral and bacterial life.
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Affiliation(s)
- H Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA;
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31
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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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Strouhal M, Oppelt J, Mikalová L, Arora N, Nieselt K, González-Candelas F, Šmajs D. Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes. BMC Res Notes 2018; 11:16. [PMID: 29325576 PMCID: PMC5765698 DOI: 10.1186/s13104-017-3106-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/19/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new "phylogenetic group" (called Lineage 2) among Chinese TPA strains. This lineage exhibited a "mosaic genomic structure" of Nichols-like and SS14-like lineages. RESULTS We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.
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Affiliation(s)
- Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO, Universidad de Valencia, Valencia, Spain.,Institute for Integrative Systems Biology (I2SysBio), Universidad de Valencia-CSIC, Valencia, Spain.,CIBER Epidemiologia y Salud Pública (CIBERESP), Valencia, Spain
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 625 00, Brno, Czech Republic.
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Sun J, Meng Z, Wu K, Liu B, Zhang S, Liu Y, Wang Y, Zheng H, Huang J, Zhou P. Tracing the origin of Treponema pallidum in China using next-generation sequencing. Oncotarget 2018; 7:42904-42918. [PMID: 27344187 PMCID: PMC5189996 DOI: 10.18632/oncotarget.10154] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/01/2016] [Indexed: 12/29/2022] Open
Abstract
Syphilis is a systemic sexually transmitted disease caused by Treponema pallidum ssp. pallidum (TPA). The origin and genetic background of Chinese TPA strains remain unclear. We identified a total of 329 single-nucleotide variants (SNVs) in eight Chinese TPA strains using next-generation sequencing. All of the TPA strains were clustered into three lineages, and Chinese TPA strains were grouped in Lineage 2 based on phylogenetic analysis. The phylogeographical data showed that TPA strains originated earlier than did T. pallidum ssp. pertenue (TPE) and T. pallidum ssp. endemicum (TPN) strains and that Chinese TPA strains might be derived from recombination between Lineage 1 and Lineage 3. Moreover, we found through a homology modeling analysis that a nonsynonymous substitution (I415F) in the PBP3 protein might affect the structural flexibility of PBP3 and the binding constant for substrates based on its possible association with penicillin resistance in T. pallidum. Our findings provide new insight into the molecular foundation of the evolutionary origin of TPA and support the development of novel diagnostic/therapeutic technology for syphilis.
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Affiliation(s)
- Jun Sun
- STD Institute, Shanghai Skin Disease Hospital, Shanghai, China
| | - Zhefeng Meng
- Oncology Bioinformatics Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Kaiqi Wu
- School of Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Biao Liu
- School of Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Sufang Zhang
- Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
| | - Yudan Liu
- Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
| | - Yuezhu Wang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Huajun Zheng
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Jian Huang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center and National Engineering Center for Biochip at Shanghai, Shanghai, China.,Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pingyu Zhou
- STD Institute, Shanghai Skin Disease Hospital, Shanghai, China.,Shanghai Skin Disease Hospital, Clinical School of Anhui Medical University, Shanghai, China
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Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart. PLoS Negl Trop Dis 2017; 11:e0005894. [PMID: 28886021 PMCID: PMC5607219 DOI: 10.1371/journal.pntd.0005894] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/20/2017] [Accepted: 08/22/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multi-stage disease, endemic in tropical regions of Africa, Asia, Oceania, and South America. To date, four TPE strains have been completely sequenced including three TPE strains of human origin (Samoa D, CDC-2, and Gauthier) and one TPE strain (Fribourg-Blanc) isolated from a baboon. All TPE strains are highly similar to T. pallidum subsp. pallidum (TPA) strains. The mutation rate in syphilis and related treponemes has not been experimentally determined yet. METHODOLOGY/PRINCIPAL FINDINGS Complete genomes of two TPE strains, CDC 2575 and Ghana-051, that infected patients in Ghana and were isolated in 1980 and 1988, respectively, were sequenced and analyzed. Both strains had identical consensus genome nucleotide sequences raising the question whether TPE CDC 2575 and Ghana-051 represent two different strains. Several lines of evidence support the fact that both strains represent independent samples including regions showing intrastrain heterogeneity (13 and 5 intrastrain heterogeneous sites in TPE Ghana-051 and TPE CDC 2575, respectively). Four of these heterogeneous sites were found in both genomes but the frequency of alternative alleles differed. The identical consensus genome sequences were used to estimate the upper limit of the yaws treponeme evolution rate, which was 4.1 x 10-10 nucleotide changes per site per generation. CONCLUSIONS/SIGNIFICANCE The estimated upper limit for the mutation rate of TPE was slightly lower than the mutation rate of E. coli, which was determined during a long-term experiment. Given the known diversity between TPA and TPE genomes and the assumption that both TPA and TPE have a similar mutation rate, the most recent common ancestor of syphilis and yaws treponemes appears to be more than ten thousand years old and likely even older.
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Mikalová L, Strouhal M, Oppelt J, Grange PA, Janier M, Benhaddou N, Dupin N, Šmajs D. Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively. PLoS Negl Trop Dis 2017; 11:e0005434. [PMID: 28263990 PMCID: PMC5354452 DOI: 10.1371/journal.pntd.0005434] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/16/2017] [Accepted: 02/23/2017] [Indexed: 11/25/2022] Open
Abstract
Background Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). An unusual human TEN 11q/j isolate was obtained from a syphilis-like primary genital lesion from a patient that returned to France from Pakistan. Methodology/Principal findings The TEN 11q/j isolate was characterized using nested PCR followed by Sanger sequencing and/or direct Illumina sequencing. Altogether, 44 chromosomal regions were analyzed. Overall, the 11q/j isolate clustered with TEN strains Bosnia A and Iraq B as expected from previous TEN classification of the 11q/j isolate. However, the 11q/j sequence in a 505 bp-long region at the TP0488 locus was similar to Treponema pallidum subsp. pallidum (TPA) strains, but not to TEN Bosnia A and Iraq B sequences, suggesting a recombination event at this locus. Similarly, the 11q/j sequence in a 613 bp-long region at the TP0548 locus was similar to Treponema pallidum subsp. pertenue (TPE) strains, but not to TEN sequences. Conclusions/Significance A detailed analysis of two recombinant loci found in the 11q/j clinical isolate revealed that the recombination event occurred just once, in the TP0488, with the donor sequence originating from a TPA strain. Since TEN Bosnia A and Iraq B were found to contain TPA-like sequences at the TP0548 locus, the recombination at TP0548 took place in a treponeme that was an ancestor to both TEN Bosnia A and Iraq B. The sequence of 11q/j isolate in TP0548 represents an ancestral TEN sequence that is similar to yaws-causing treponemes. In addition to the importance of the 11q/j isolate for reconstruction of the TEN phylogeny, this case emphasizes the possible role of TEN strains in development of syphilis-like lesions. Treponema pallidum subsp. endemicum (TEN) is an uncultivable pathogenic treponeme that causes bejel (endemic syphilis), a chronic human infection mostly affecting children under 15 years of age, occurring mainly in several African and Middle East countries. In this work, we characterized a TEN 11q/j isolate from France that was obtained from an adult male with genital lesions, who was suspected of having syphilis and who received benzathine penicillin G. DNA sequencing of the isolate revealed two loci that were, rather than to TEN, related either to T. pallidum subsp. pertenue or to T. pallidum subsp. pallidum and likely resulted from recombination events. The recombination event in TP0488 as well as the recombination in TP0548, of the 11q/j, helped clarify the phylogeny of the TEN strains indicating that the recombination in TP0548 took place in a treponeme that was ancestral of Bosnia A and Iraq B, but was not an ancestor of the 11q/j isolate. In contrast, a recombination event in TP0488 appeared in the ancestor of the 11q/j isolate after separation of the ancestral treponeme of Bosnia A and Iraq B. This case also points to a possible role of TEN strains in development of syphilis-like lesions in countries with endemic syphilis.
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Affiliation(s)
- Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- CEITEC–Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Philippe Alain Grange
- Institut Cochin U1016, Laboratoire de Dermatologie—CNR Syphilis, Faculté de Médecine, Université Sorbonne Paris Descartes, Paris, France
| | - Michel Janier
- Centre des MST, Hôpital Saint-Louis, AP-HP, Paris, France
| | - Nadjet Benhaddou
- Institut Cochin U1016, Laboratoire de Dermatologie—CNR Syphilis, Faculté de Médecine, Université Sorbonne Paris Descartes, Paris, France
- Service de Bactériologie, Groupe Hospitalier Paris Centre Cochin-Hôtel Dieu-Broca, Paris, France
| | - Nicolas Dupin
- Institut Cochin U1016, Laboratoire de Dermatologie—CNR Syphilis, Faculté de Médecine, Université Sorbonne Paris Descartes, Paris, France
- Service de Dermatologie-Vénéréologie, Hôpital Cochin–Pavillon Tarnier, AP-HP, Paris, France
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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Abstract
Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within the mammalian host. Whereas viruses make use of a minimal proofreading capacity combined with large amounts of progeny to use random mutation for variant generation, antigenically variant bacteria have evolved mechanisms which use a stable genome, which aids in protecting the fitness of the progeny. Here, three well-characterized and highly antigenically variant bacterial pathogens are discussed: Anaplasma, Borrelia, and Neisseria. These three pathogens display a variety of mechanisms used to create the structural and antigenic variation needed for immune escape and long-term persistence. Intrahost antigenic variation is the focus; however, the role of these immune escape mechanisms at the population level is also presented.
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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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Radolf JD, Deka RK, Anand A, Šmajs D, Norgard MV, Yang XF. Treponema pallidum, the syphilis spirochete: making a living as a stealth pathogen. Nat Rev Microbiol 2016; 14:744-759. [PMID: 27721440 DOI: 10.1038/nrmicro.2016.141] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The past two decades have seen a worldwide resurgence in infections caused by Treponema pallidum subsp. pallidum, the syphilis spirochete. The well-recognized capacity of the syphilis spirochete for early dissemination and immune evasion has earned it the designation 'the stealth pathogen'. Despite the many hurdles to studying syphilis pathogenesis, most notably the inability to culture and to genetically manipulate T. pallidum, in recent years, considerable progress has been made in elucidating the structural, physiological, and regulatory facets of T. pallidum pathogenicity. In this Review, we integrate this eclectic body of information to garner fresh insights into the highly successful parasitic lifestyles of the syphilis spirochete and related pathogenic treponemes.
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Affiliation(s)
- Justin D Radolf
- Departments of Medicine, Pediatrics, Genetics and Genomic Science, Molecular Biology and Biophysics, and Immunology, UConn Health, 263 Farmington Avenue, Farmington, Connecticut 06030-3715, USA
| | - Ranjit K Deka
- Department of Microbiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9048, USA
| | - Arvind Anand
- Department of Medicine, UConn Health, 263 Farmington Avenue, Farmington, Connecticut 06030-3715, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Michael V Norgard
- Department of Microbiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9048, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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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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Houston S, Taylor JS, Denchev Y, Hof R, Zuerner RL, Cameron CE. Conservation of the Host-Interacting Proteins Tp0750 and Pallilysin among Treponemes and Restriction of Proteolytic Capacity to Treponema pallidum. Infect Immun 2015; 83:4204-16. [PMID: 26283341 PMCID: PMC4598410 DOI: 10.1128/iai.00643-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/06/2015] [Indexed: 12/13/2022] Open
Abstract
The spirochete Treponema pallidum subsp. pallidum is the causative agent of syphilis, a chronic, sexually transmitted infection characterized by multiple symptomatic and asymptomatic stages. Although several other species in the genus are able to cause or contribute to disease, T. pallidum differs in that it is able to rapidly disseminate via the bloodstream to tissue sites distant from the site of initial infection. It is also the only Treponema species able to cross both the blood-brain and placental barriers. Previously, the T. pallidum proteins, Tp0750 and Tp0751 (also called pallilysin), were shown to degrade host proteins central to blood coagulation and basement membrane integrity, suggesting a role for these proteins in T. pallidum dissemination and tissue invasion. In the present study, we characterized Tp0750 and Tp0751 sequence variation in a diversity of pathogenic and nonpathogenic treponemes. We also determined the proteolytic potential of the orthologs from the less invasive species Treponema denticola and Treponema phagedenis. These analyses showed high levels of sequence similarity among Tp0750 orthologs from pathogenic species. For pallilysin, lower levels of sequence conservation were observed between this protein and orthologs from other treponemes, except for the ortholog from the highly invasive rabbit venereal syphilis-causing Treponema paraluiscuniculi. In vitro host component binding and degradation assays demonstrated that pallilysin and Tp0750 orthologs from the less invasive treponemes tested were not capable of binding or degrading host proteins. The results show that pallilysin and Tp0750 host protein binding and degradative capability is positively correlated with treponemal invasiveness.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - John S Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Yavor Denchev
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Rebecca Hof
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Richard L Zuerner
- Bacterial Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Ames, Iowa, USA Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Research, Uppsala, Sweden
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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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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Abstract
PURPOSE OF REVIEW The past 15 years have seen a dramatic increase in syphilis diagnoses in several regions including China, North America, Western Europe and Australia. Worldwide, the disease remains prevalent, contributing to substantial adult morbidity and neonatal mortality. Testing and treatment strategies are largely informed by data from the early antibiotic era, but increasing use of molecular diagnostics and new screening strategies could improve the management of syphilis substantially. RECENT FINDINGS The review explores new testing strategies for syphilis, including the importance of screening test selection and advances in point-of-care diagnostics. It then examines molecular studies of Treponema pallidum, covering typing; macrolide resistance; association between genotype and phenotype and the use of PCR in testing and monitoring strategies. SUMMARY Clinicians should be aware of testing strategies employed by their laboratories to ensure optimal sensitivity and specificity. Locally available T. pallidum PCR assays may improve the diagnosis of early disease and inform antibiotic choice. Robust serologic follow-up is still required, but predictors of potential treatment failure, including PCR-measured bacterial load, have been identified. Re-treatment should be considered for patients in the serofast state. The publication of T. pallidum genomes would allow further and more detailed study of strains and disease pathogenesis.
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Holder IT, Hartig JS. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. ACTA ACUST UNITED AC 2015; 21:1511-21. [PMID: 25459072 DOI: 10.1016/j.chembiol.2014.09.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/13/2014] [Accepted: 09/17/2014] [Indexed: 01/01/2023]
Abstract
We provide important insights into secondary-structure-mediated regulation of gene expression in Escherichia coli. In a comprehensive survey, we show that the strand orientation and the exact position of a G-quadruplex sequence strongly influence its effect on transcription and translation. We generated a series of reporter gene constructs that contained systematically varied positions of quadruplexes and respective control sequences inserted into several positions within the promoter, 50-UTR, and 30-UTR regions. G-rich sequences at specific locations in the promoter and also in proximity to the ribosome-binding site (RBS) showed pronounced inhibitory effects. Additionally, we rationally designed a system where quadruplex formation showed a gene-activating behavior. Moreover, we characterized quadruplexes in proximity to the RBS that occur naturally in E. coli genes, demonstrating that some of these quadruplexes exert significant modulation of gene expression. Taken together, our data show strong position-dependent effects of quadruplex secondary structures on bacterial gene expression.
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Giacani L, Brandt SL, Ke W, Reid TB, Molini BJ, Iverson-Cabral S, Ciccarese G, Drago F, Lukehart SA, Centurion-Lara A. Transcription of TP0126, Treponema pallidum putative OmpW homolog, is regulated by the length of a homopolymeric guanosine repeat. Infect Immun 2015; 83:2275-89. [PMID: 25802057 PMCID: PMC4432754 DOI: 10.1128/iai.00360-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 03/17/2015] [Indexed: 12/12/2022] Open
Abstract
An effective mechanism for introduction of phenotypic diversity within a bacterial population exploits changes in the length of repetitive DNA elements located within gene promoters. This phenomenon, known as phase variation, causes rapid activation or silencing of gene expression and fosters bacterial adaptation to new or changing environments. Phase variation often occurs in surface-exposed proteins, and in Treponema pallidum subsp. pallidum, the syphilis agent, it was reported to affect transcription of three putative outer membrane protein (OMP)-encoding genes. When the T. pallidum subsp. pallidum Nichols strain genome was initially annotated, the TP0126 open reading frame was predicted to include a poly(G) tract and did not appear to have a predicted signal sequence that might suggest the possibility of its being an OMP. Here we show that the initial annotation was incorrect, that this poly(G) is instead located within the TP0126 promoter, and that it varies in length in vivo during experimental syphilis. Additionally, we show that TP0126 transcription is affected by changes in the poly(G) length consistent with regulation by phase variation. In silico analysis of the TP0126 open reading frame based on the experimentally identified transcriptional start site shortens this hypothetical protein by 69 amino acids, reveals a predicted cleavable signal peptide, and suggests structural homology with the OmpW family of porins. Circular dichroism of recombinant TP0126 supports structural homology to OmpW. Together with the evidence that TP0126 is fully conserved among T. pallidum subspecies and strains, these data suggest an important role for TP0126 in T. pallidum biology and syphilis pathogenesis.
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Affiliation(s)
- Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Stephanie L Brandt
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Wujian Ke
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA Graduate School, Southern Medical University, Guangzhou, People's Republic of China, and Division of STD, Guangdong Provincial Center for STI & Skin Diseases Control and Prevention, Guangzhou, People's Republic of China
| | - Tara B Reid
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Barbara J Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Stefanie Iverson-Cabral
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Giulia Ciccarese
- Department of Dermatology, IRCCS Azienda Universitaria Ospedaliera San Martino-IST, Genoa, Italy
| | - Francesco Drago
- Department of Dermatology, IRCCS Azienda Universitaria Ospedaliera San Martino-IST, Genoa, Italy
| | - Sheila A Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Arturo Centurion-Lara
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
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Ke W, Molini BJ, Lukehart SA, Giacani L. Treponema pallidum subsp. pallidum TP0136 protein is heterogeneous among isolates and binds cellular and plasma fibronectin via its NH2-terminal end. PLoS Negl Trop Dis 2015; 9:e0003662. [PMID: 25793702 PMCID: PMC4368718 DOI: 10.1371/journal.pntd.0003662] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/28/2015] [Indexed: 11/19/2022] Open
Abstract
Adherence-mediated colonization plays an important role in pathogenesis of microbial infections, particularly those caused by extracellular pathogens responsible for systemic diseases, such as Treponema pallidum subsp. pallidum (T. pallidum), the agent of syphilis. Among T. pallidum adhesins, TP0136 is known to bind fibronectin (Fn), an important constituent of the host extracellular matrix. To deepen our understanding of the TP0136-Fn interaction dynamics, we used two naturally-occurring sequence variants of the TP0136 protein to investigate which region of the protein is responsible for Fn binding, and whether TP0136 would adhere to human cellular Fn in addition to plasma Fn and super Fn as previously reported. Fn binding assays were performed with recombinant proteins representing the two full-length TP0136 variants and their discrete regions. As a complementary approach, we tested inhibition of T. pallidum binding to Fn by recombinant full-length TP0136 proteins and fragments, as well as by anti-TP0136 immune sera. Our results show that TP0136 adheres more efficiently to cellular Fn than to plasma Fn, that the TP0136 NH2-terminal conserved region of the protein is primarily responsible for binding to plasma Fn but that binding sites for cellular Fn are also present in the protein’s central and COOH-terminal regions. Additionally, message quantification studies show that tp0136 is highly transcribed during experimental infection, and that its message level increases in parallel to the host immune pressure on the pathogen, which suggests a possible role for this protein in T. pallidum persistence. In a time where syphilis incidence is high, our data will help in the quest to identify suitable targets for development of a much needed vaccine against this important disease. The study of Treponema pallidum subsp. pallidum (T. pallidum) proteins that mediate adhesion to host tissue components is pivotal to understand how the syphilis agent establishes infection and is able to invade virtually every organ system following dissemination from the site of entry. This study focuses on T. pallidum TP0136, a known plasma fibronectin (Fn) and super Fn binding protein that is heterogeneous in sequence among T. pallidum isolates. This study shows that TP0136 also mediates attachment to human cellular Fn, that TP0136 conserved NH2-terminus is primarily responsible for binding to plasma Fn, but that cellular Fn binding sites appears to be scattered throughout the molecule. Message quantification experiments reveal that tp0136 transcription is high during experimental syphilis and increases at the time of bacterial immune clearance, suggesting a role for this antigen in counteracting the host defenses during infection, as reported for other Fn binding proteins in other pathogens. Our data deepen the current knowledge of the function of T. pallidum TP0136 and further support a role for this virulence factor in syphilis pathogenesis.
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Affiliation(s)
- Wujian Ke
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Harborview Medical Center, Seattle, Washington, United States of America
- Graduate School, Southern Medical University, Guangzhou, PR China
- Division of STD, Guangdong Provincial Center for STI & Skin Diseases Control and Prevention, Guangzhou, PR China
| | - Barbara J. Molini
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Harborview Medical Center, Seattle, Washington, United States of America
| | - Sheila A. Lukehart
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Harborview Medical Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Lorenzo Giacani
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Harborview Medical Center, 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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Reid TB, Molini BJ, Fernandez MC, Lukehart SA. Antigenic variation of TprK facilitates development of secondary syphilis. Infect Immun 2014; 82:4959-67. [PMID: 25225245 PMCID: PMC4249288 DOI: 10.1128/iai.02236-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/04/2014] [Indexed: 12/11/2022] Open
Abstract
Although primary syphilis lesions heal spontaneously, the infection is chronic, with subsequent clinical stages. Healing of the primary chancre occurs as antibodies against outer membrane antigens facilitate opsonophagocytosis of the bacteria by activated macrophages. TprK is an outer membrane protein that undergoes antigenic variation at 7 variable regions, and variants are selected by immune pressure. We hypothesized that individual TprK variants escape immune clearance and seed new disseminated lesions to cause secondary syphilis. As in human syphilis, infected rabbits may develop disseminated secondary skin lesions. This study explores the nature of secondary syphilis, specifically, the contribution of antigenic variation to the development of secondary lesions. Our data from the rabbit model show that the odds of secondary lesions containing predominately TprK variant treponemes is 3.3 times higher than the odds of finding TprK variants in disseminated primary lesions (odds ratio [OR] = 3.3 [95% confidence interval {CI}, 0.98 to 11.0]; P = 0.055) and that 96% of TprK variant secondary lesions are likely seeded by single treponemes. Analysis of antibody responses demonstrates significantly higher antibody titers to tprK variable region sequences found in the inoculum compared to reactivity to tprK variant sequences found in newly arising secondary lesions. This suggests that tprK variants escape the initial immune response raised against the V regions expressed in the inoculum. These data further support a role for TprK in immune evasion and suggest that the ability of TprK variants to persist despite a robust immune response is instrumental in the development of later stages of syphilis.
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Affiliation(s)
- Tara B Reid
- Interdisciplinary Graduate Program in Pathobiology, Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barbara J Molini
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Mark C Fernandez
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sheila A Lukehart
- Interdisciplinary Graduate Program in Pathobiology, Department of Global Health, University of Washington, Seattle, Washington, USA Department of Medicine, University of Washington, Seattle, Washington, USA
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Staudová B, Strouhal M, Zobaníková M, Cejková D, Fulton LL, Chen L, Giacani L, Centurion-Lara A, Bruisten SM, Sodergren E, Weinstock GM, Smajs D. Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes. PLoS Negl Trop Dis 2014; 8:e3261. [PMID: 25375929 PMCID: PMC4222731 DOI: 10.1371/journal.pntd.0003261] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/10/2014] [Indexed: 02/03/2023] Open
Abstract
Background T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe. Methodology/Principal Findings The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6–2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes. Conclusions/Significance The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome. Uncultivable treponemes represent bacterial species and subspecies that are obligate pathogens of humans and animals causing diseases with distinct clinical manifestations. Treponema pallidum subsp. pallidum causes sexually transmitted syphilis, a multistage disease characterized in humans by localized, disseminated, and chronic forms of infection, whereas Treponema pallidum subsp. pertenue (agent of yaws) and Treponema pallidum subsp. endemicum (agent of bejel) cause milder, non-venereally transmitted diseases affecting skin, bones and joints. The genetic basis of the pathogenesis and evolution of these microorganisms are still unknown. In this study, a high quality whole genome sequence of the T. pallidum subsp. endemicum Bosnia A strain was obtained using a combination of next-generation sequencing approaches and compared to the genomes of available uncultivable pathogenic treponemes. Relative to all known genomes of Treponema pallidum subspecies, no major genome rearrangements were found in the Bosnia A. The Bosnia A strain clustered with other yaws-causing strains, while syphilis-causing strains clustered separately. In general, the Bosnia A genome showed similar genetic characteristics to yaws treponemes but also contained several sequences thought to be unique to syphilis-causing strains. This finding suggests a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.
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Affiliation(s)
- Barbora Staudová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Strouhal
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Marie Zobaníková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Darina Cejková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda L Fulton
- The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lei Chen
- The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lorenzo Giacani
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Arturo Centurion-Lara
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - Erica Sodergren
- The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - George M Weinstock
- The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - David Smajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Abstract
The endemic treponemal diseases, consisting of yaws, bejel (endemic syphilis) and pinta, are non-venereal infections closely related to syphilis, and are recognized by WHO as neglected tropical diseases (NTDs). Despite previous worldwide eradication efforts the prevalence of yaws has rebounded in recent years and the disease is now a major public health problem in 14 countries. Adequate data on the epidemiology of bejel and pinta is lacking. Each disease is restricted to a specific ecological niche but all predominantly affect poor, rural communities. As with venereal syphilis, the clinical manifestations of the endemic treponemal diseases are variable and can be broken down in to early stage and late stage disease. Current diagnostic techniques are unable to distinguish the different causative species but newer molecular techniques are now making this possible. Penicillin has long been considered the mainstay of treatment for the endemic treponemal diseases but the recent discovery that azithromycin is effective in the treatment of yaws has renewed interest in these most neglected of the NTDs, and raised hopes that global eradication may finally be possible.
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Affiliation(s)
- Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, WC1E 6JB, UK
| | - Anthony W Solomon
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, WC1E 6JB, UK
| | - David C Mabey
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK Hospital for Tropical Diseases, University College London Hospitals NHS Trust, London, WC1E 6JB, UK
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Nechvátal L, Pětrošová H, Grillová L, Pospíšilová P, Mikalová L, Strnadel R, Kuklová I, Kojanová M, Kreidlová M, Vaňousová D, Procházka P, Zákoucká H, Krchňáková A, Šmajs D. Syphilis-causing strains belong to separate SS14-like or Nichols-like groups as defined by multilocus analysis of 19 Treponema pallidum strains. Int J Med Microbiol 2014; 304:645-53. [DOI: 10.1016/j.ijmm.2014.04.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/14/2014] [Accepted: 04/21/2014] [Indexed: 11/24/2022] Open
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Complete Genome Sequence of the Treponema pallidum subsp. pallidum Sea81-4 Strain. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00333-14. [PMID: 24744342 PMCID: PMC3990758 DOI: 10.1128/genomea.00333-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Using the rabbit model of syphilis, the Sea81-4 strain of Treponema pallidum subsp. pallidum has been found to be more likely than other strains to invade the central nervous system (CNS). To identify possible explanations for this important phenotype at the genomic level, we sequenced the Sea81-4 strain genome.
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