1
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Gutierrez MDLP, Huckaby AB, Yang E, Weaver KL, Hall JM, Hudson M, Dublin SR, Sen-Kilic E, Rocuskie-Marker CM, Miller SJ, Pritchett CL, Mummadisetti MP, Zhang Y, Driscoll T, Barbier M. Antibody-mediated immunological memory correlates with long-term Lyme veterinary vaccine protection in mice. Vaccine 2024:S0264-410X(24)00725-4. [PMID: 38937181 DOI: 10.1016/j.vaccine.2024.06.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Lyme disease, caused by the bacterium Borrelia burgdorferi, is the most common tick-borne illness in the United States. Despite the rise in Lyme disease incidence, there is no vaccine against B. burgdorferi approved for human use. Little is known about the immune correlates of protection needed to prevent Lyme disease. In this work, a mouse model was used to characterize the immune response and compare the protection provided by two USDA-approved vaccines for use in canines: Duramune (bacterin vaccine) and Vanguard crLyme (subunit vaccine composed of two outer surface proteins, OspA and OspC). C3H/HeNCrl mice were immunized with two doses of either Duramune or Vanguard, and immune responses and protection against B. burgdorferi were assessed in short (35 days) and long-term (120 days) studies. Flow cytometry, ELISPOT detection of antibody-producing cells, and antibody affinity studies were performed to identify correlates of vaccine-mediated protection. Both vaccines induced humoral responses, with high IgG titers against B. burgdorferi. However, the levels of anti-B. burgdorferi antibodies decayed over time in Vanguard-vaccinated mice. While both vaccines triggered the production of antibodies against both OspA and OspC, antibody levels against these proteins were also lower in Vanguard-vaccinated mice 120 days post-vaccination. Both vaccines only provided partial protection against B. burgdorferi at the dose used in this model. The protection provided by Duramune was superior to Vanguard 120 days post-vaccination, and was characterized by higher antibody titers, higher abundance of long-lived plasma cells, and higher avidity antibodies than Vanguard. Overall, these studies provide insights into the importance of the humoral memory response to veterinary vaccines against Lyme disease and will help inform the development of future human vaccines.
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Affiliation(s)
- Maria de la Paz Gutierrez
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Annalisa B Huckaby
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Evita Yang
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Kelly L Weaver
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Joshua M Hall
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Matthew Hudson
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Spencer R Dublin
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Emel Sen-Kilic
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Carleena M Rocuskie-Marker
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | - Sarah Jo Miller
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA
| | | | | | - Ying Zhang
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Timothy Driscoll
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, USA; Vaccine Development Center, West Virginia University, Health Sciences Center, Morgantown, WV, USA.
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2
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Yamasaki Y, Singh P, Vimonish R, Ueti M, Bankhead T. Development and Application of an In Vitro Tick Feeding System to Identify Ixodes Tick Environment-Induced Genes of the Lyme Disease Agent, Borrelia burgdorferi. Pathogens 2024; 13:487. [PMID: 38921785 PMCID: PMC11207009 DOI: 10.3390/pathogens13060487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
The bacterial agent of Lyme disease, Borrelia burgdorferi, exists in an enzootic cycle by adapting to dissimilar mammalian and tick environments. The genetic elements necessary for host and vector adaptation are spread across a bacterial genome comprised of a linear chromosome and essential linear and circular plasmids. The promoter trap system, In Vivo Expression Technology (IVET), has been used to identify promoters of B. burgdorferi that are transcriptionally active specifically during infection of a murine host. However, an observed infection bottleneck effect in mice prevented the application of this system to study promoters induced in a tick environment. In this study, we adapted a membrane-based in vitro feeding system as a novel method to infect the Ixodes spp. vector with B. burgdorferi. Once adapted, we performed IVET screens as a proof of principle via an infected bloodmeal on the system. The screen yielded B. burgdorferi promoters that are induced during tick infection and verified relative expression levels using qRT-PCR. The results of our study demonstrate the potential of our developed in vitro tick feeding system and IVET systems to gain insight into the adaptive gene expression of the Lyme disease bacteria to the tick vector.
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Affiliation(s)
- Youki Yamasaki
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Preeti Singh
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Rubikah Vimonish
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
| | - Massaro Ueti
- Animal Disease Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164, USA;
| | - Troy Bankhead
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA; (Y.Y.); (P.S.); (R.V.)
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3
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Jusufovic N, Krusenstjerna AC, Savage CR, Saylor TC, Brissette CA, Zückert WR, Schlax PJ, Motaleb MA, Stevenson B. Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA and RNA binding protein. Mol Microbiol 2024; 121:1039-1062. [PMID: 38527857 DOI: 10.1111/mmi.15254] [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: 09/04/2023] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here, we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length and G-C content play a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.
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Affiliation(s)
- Nerina Jusufovic
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Andrew C Krusenstjerna
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Christina R Savage
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Timothy C Saylor
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | - Wolfram R Zückert
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Paula J Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, Maine, USA
| | - Md A Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Brian Stevenson
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
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Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth DR, Liao Y, Duggin IG, Marchfelder A, Erdmann S. Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proc Natl Acad Sci U S A 2024; 121:e2311321121. [PMID: 38408251 DOI: 10.1073/pnas.2311321121] [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: 07/14/2023] [Accepted: 01/14/2024] [Indexed: 02/28/2024] Open
Abstract
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.
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Affiliation(s)
- Joshua Mills
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - L Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daan R Speth
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Yan Liao
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Iain G Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
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5
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Zhang JJ, Raghunandanan S, Wang Q, Priya R, Alanazi F, Lou Y, Yang XF. BadR directly represses the expression of the glycerol utilization operon in the Lyme disease pathogen. J Bacteriol 2024; 206:e0034023. [PMID: 38214528 PMCID: PMC10882987 DOI: 10.1128/jb.00340-23] [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: 10/16/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024] Open
Abstract
Glycerol utilization as a carbohydrate source by Borreliella burgdorferi, the Lyme disease spirochete, is critical for its successful colonization and persistence in the tick vector. The expression of the glpFKD (glp) operon, which encodes proteins for glycerol uptake/utilization, must be tightly regulated during the enzootic cycle of B. burgdorferi. Previous studies have established that the second messenger cyclic di-GMP (c-di-GMP) is required for the activation of glp expression, while an alternative sigma factor RpoS acts as a negative regulator for glp expression. In the present study, we report identification of a cis element within the 5´ untranslated region of glp that exerts negative regulation of glp expression. Further genetic screen of known and predicted DNA-binding proteins encoded in the genome of B. burgdorferi uncovered that overexpressing Borrelia host adaptation regulator (BadR), a known global regulator, dramatically reduced glp expression. Similarly, the badR mutant significantly increased glp expression. Subsequent electrophoretic mobility shift assay analyses demonstrated that BadR directly binds to this cis element, thereby repressing glp independent of RpoS-mediated repression. The efficiency of BadR binding was further assessed in the presence of c-di-GMP and various carbohydrates. This finding highlights multi-layered positive and negative regulatory mechanisms employed by B. burgdorferi to synchronize glp expression throughout its enzootic cycle.IMPORTANCEBorreliella burgdorferi, the Lyme disease pathogen, must modulate its gene expression differentially to adapt successfully to its two disparate hosts. Previous studies have demonstrated that the glycerol uptake and utilization operon, glpFKD, plays a crucial role in spirochetal survival within ticks. However, the glpFKD expression must be repressed when B. burgdorferi transitions to the mammalian host. In this study, we identified a specific cis element responsible for the repression of glpFKD. We further pinpointed Borrelia host adaptation regulator as the direct binding protein to this cis element, thereby repressing glpFKD expression. This discovery paves the way for a deeper exploration of how zoonotic pathogens sense distinct hosts and switch their carbon source utilization during transmission.
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Affiliation(s)
- Jun-Jie Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sajith Raghunandanan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Qian Wang
- Department of Clinical Laboratory, Wenzhou People’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Fuad Alanazi
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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6
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Jusufovic N, Krusenstjerna AC, Savage CR, Saylor TC, Brissette CA, Zückert WR, Schlax PJ, Motaleb MA, Stevenson B. Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA and RNA binding protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.30.526351. [PMID: 36778503 PMCID: PMC9915621 DOI: 10.1101/2023.01.30.526351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length plays a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.
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Affiliation(s)
- Nerina Jusufovic
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Andrew C. Krusenstjerna
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Christina R. Savage
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Timothy C. Saylor
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, ND 58203-9061, USA
| | - Wolfram R. Zückert
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Paula J. Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, 04240-6030, USA
| | - Md A. Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834-435, USA
| | - Brian Stevenson
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, 40526-0001, USA
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7
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Zamba-Campero M, Soliman D, Yu H, Lasseter AG, Chang YY, Liu J, Aravind L, Jewett MW, Storz G, Adams PP. Broadly conserved FlgV controls flagellar assembly and Borrelia burgdorferi dissemination in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574855. [PMID: 38260563 PMCID: PMC10802407 DOI: 10.1101/2024.01.09.574855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Flagella propel pathogens through their environments yet are expensive to synthesize and are immunogenic. Thus, complex hierarchical regulatory networks control flagellar gene expression. Spirochetes are highly motile bacteria, but peculiarly in the Lyme spirochete Borrelia burgdorferi, the archetypal flagellar regulator σ28 is absent. We rediscovered gene bb0268 in B. burgdorferi as flgV, a broadly-conserved gene in the flagellar superoperon alongside σ28 in many Spirochaetes, Firmicutes and other phyla, with distant homologs in Epsilonproteobacteria. We found that B. burgdorferi FlgV is localized within flagellar motors. B. burgdorferi lacking flgV construct fewer and shorter flagellar filaments and are defective in cell division and motility. During the enzootic cycle, B. burgdorferi lacking flgV survive and replicate in Ixodes ticks but are attenuated for dissemination and infection in mice. Our work defines infection timepoints when spirochete motility is most crucial and implicates FlgV as a broadly distributed structural flagellar component that modulates flagellar assembly.
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Affiliation(s)
- Maxime Zamba-Campero
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Soliman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaxin Yu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Amanda G. Lasseter
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Yuen-Yan Chang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, 32827, USA
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Melamed S, Zhang A, Jarnik M, Mills J, Silverman A, Zhang H, Storz G. σ 28-dependent small RNA regulation of flagella biosynthesis. eLife 2023; 12:RP87151. [PMID: 37843988 PMCID: PMC10578931 DOI: 10.7554/elife.87151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here, we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, the four sRNAs have varied effects on flagellin protein levels, flagella number and cell motility. UhpU, corresponding to the 3´ UTR of a metabolic gene, likely has hundreds of targets including a transcriptional regulator at the top flagella regulatory cascade connecting metabolism and flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs and act on ribosomal protein mRNAs connecting ribosome production and flagella synthesis. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.
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Affiliation(s)
- Sahar Melamed
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Aixia Zhang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Michal Jarnik
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Joshua Mills
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Aviezer Silverman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Hongen Zhang
- Bioinformatics and Scientific Computing Core, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentBethesdaUnited States
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9
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 2023; 14:3931. [PMID: 37402717 DOI: 10.1038/s41467-023-39576-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3' ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, 20892, USA.
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD, 20892, USA.
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10
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Van Gundy T, Patel D, Bowler BE, Rothfuss MT, Hall AJ, Davies C, Hall LS, Drecktrah D, Marconi RT, Samuels DS, Lybecker MC. c-di-GMP regulates activity of the PlzA RNA chaperone from the Lyme disease spirochete. Mol Microbiol 2023; 119:711-727. [PMID: 37086029 PMCID: PMC10330241 DOI: 10.1111/mmi.15066] [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: 04/03/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023]
Abstract
PlzA is a c-di-GMP-binding protein crucial for adaptation of the Lyme disease spirochete Borrelia (Borreliella) burgdorferi during its enzootic life cycle. Unliganded apo-PlzA is important for vertebrate infection, while liganded holo-PlzA is important for survival in the tick; however, the biological function of PlzA has remained enigmatic. Here, we report that PlzA has RNA chaperone activity that is inhibited by c-di-GMP binding. Holo- and apo-PlzA bind RNA and accelerate RNA annealing, while only apo-PlzA can strand displace and unwind double-stranded RNA. Guided by the crystal structure of PlzA, we identified several key aromatic amino acids protruding from the N- and C-terminal domains that are required for RNA-binding and unwinding activity. Our findings illuminate c-di-GMP as a switch controlling the RNA chaperone activity of PlzA, and we propose that complex RNA-mediated modulatory mechanisms allow PlzA to regulate gene expression during both the vector and host phases of the B. burgdorferi life cycle.
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Affiliation(s)
- Taylor Van Gundy
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Dhara Patel
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298, USA
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Michael T. Rothfuss
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Allie J. Hall
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Christopher Davies
- Department of Biochemistry and Molecular Biology, University of Southern Alabama, Mobile, AL 36688, USA
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA 23298, USA
| | - D. Scott Samuels
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C. Lybecker
- Bacterial Diseases Branch, Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Center for Disease Control and Prevention, Fort Collins, CO 80521, USA
- Department of Biology, University of Colorado, 1420 Austin Bluffs Parkway, Colorado Springs CO 80917, USA
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11
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Sze CW, Li C. Chemotaxis Coupling Protein CheW 2 Is Not Required for the Chemotaxis but Contributes to the Full Pathogenicity of Borreliella burgdorferi. Infect Immun 2023; 91:e0000823. [PMID: 36939335 PMCID: PMC10112267 DOI: 10.1128/iai.00008-23] [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: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 03/21/2023] Open
Abstract
The bacterial chemotaxis regulatory circuit mainly consists of coupling protein CheW, sensor histidine kinase CheA, and response regulator CheY. Most bacteria, such as Escherichia coli, have a single gene encoding each of these proteins. Interestingly, the Lyme disease pathogen, Borreliella burgdorferi, has multiple chemotaxis proteins, e.g., two CheA, three CheW, and three CheY proteins. The genes encoding these proteins mainly reside in two operons: cheW2-cheA1-cheB2-cheY2 (A-I) and cheA2-cheW3-cheX-cheY3 (A-II). Previous studies demonstrate that all the genes in A-II are essential for the chemotaxis of B. burgdorferi; however, the role of those genes in A-I remains unknown. This study aimed to fill this gap using the CheW2 gene, the first gene in A-I, as a surrogate. We first mapped the transcription start site of A-I upstream of cheW2 and identified a σ70-like promoter (PW2) and two binding sites (BS1 and BS2) of BosR, an unorthodox Fur/Per homolog. We then demonstrated that BosR binds to PW2 via BS1 and BS2 and that deletion of bosR significantly represses the expression of cheW2 and other genes in A-I, implying that BosR is a positive regulator of A-I. Deletion of cheW2 has no impact on the chemotaxis of B. burgdorferi in vitro but abrogates its ability to evade host adaptive immunity, because the mutant can establish systemic infection only in SCID mice and not in immunocompetent BALB/c mice. This report substantiates the previous proposition that A-I is not implicated in chemotaxis; rather, it may function as a signaling transduction pathway to regulate B. burgdorferi virulence gene expression.
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Affiliation(s)
- Ching Wooen Sze
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Chunhao Li
- Department of Oral Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, USA
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12
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Thompson C, Waldron C, George S, Ouyang Z. Role of the Hypothetical Protein BB0563 during Borrelia burgdorferi Infection in Animals. Infect Immun 2023; 91:e0053922. [PMID: 36744894 PMCID: PMC10016080 DOI: 10.1128/iai.00539-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The alternative sigma factor RpoS in Borrelia burgdorferi, the etiological agent of Lyme disease, has long been postulated to regulate virulence-associated genes other than ospC and dbpA. Here, we demonstrate that bb0563, a gene encoding a hypothetical protein, is regulated by RpoS and contributes to the optimal infectivity of B. burgdorferi. When B. burgdorferi was exposed to environmental stimuli, bb0563 showed similar expression patterns as rpoS, ospC, and dbpA. Expression of bb0563 was significantly downregulated when rpoS was inactivated and was restored in the complemented strain. By using rapid amplification of cDNA ends (RACE) and luciferase reporter assays, a functional promoter was identified in the regulatory region upstream of bb0563. Gene expression from this promoter was drastically decreased in the rpoS mutant. We next investigated the role of bb0563 during animal infection. By using quantitative reverse transcription-PCR (RT-PCR), we found that bb0563 was highly expressed in mouse tissues during infection. We further created a bb0563-deficient mutant in a bioluminescent B. burgdorferi strain and examined infection dynamics using in vivo imaging. Relative to the parental and complemented strains, the mutant showed a delayed infection pattern and bacterial load was reduced. Another bb0563 deletion mutant was also created in the strain 297 background, and quantitative PCR (qPCR) analysis revealed a significantly lower spirochetal burden in tissue samples collected from animals infected with the mutant. In addition, localization studies indicate that BB0563 is not exposed on the cell surface but is associated with outer membrane. Taken together, these results suggest that bb0563 is required for optimal infectivity of B. burgdorferi during experimental infection.
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Affiliation(s)
- Christina Thompson
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Connor Waldron
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Sierra George
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
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13
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Borrelia burgdorferi DnaA and the Nucleoid-Associated Protein EbfC Coordinate Expression of the dnaX-ebfC Operon. J Bacteriol 2023; 205:e0039622. [PMID: 36533911 PMCID: PMC9879097 DOI: 10.1128/jb.00396-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Borrelia burgdorferi, the spirochete agent of Lyme disease, has evolved within a consistent infectious cycle between tick and vertebrate hosts. The transmission of the pathogen from tick to vertebrate is characterized by rapid replication and a change in the outer surface protein profile. EbfC, a highly conserved nucleoid-associated protein, binds throughout the borrelial genome, affecting expression of many genes, including the Erp outer surface proteins. In B. burgdorferi, like many other bacterial species, ebfC is cotranscribed with dnaX, an essential component of the DNA polymerase III holoenzyme, which facilitates chromosomal replication. The expression of the dnaX-ebfC operon is tied to the spirochete's replication rate, but the underlying mechanism for this connection was unknown. In this work, we provide evidence that the expression of dnaX-ebfC is controlled by direct interactions of DnaA, the chromosomal replication initiator, and EbfC at the unusually long dnaX-ebfC 5' untranslated region (UTR). Both proteins bind to the 5' UTR DNA, with EbfC also binding to the RNA. The DNA binding of DnaA to this region was similarly impacted by ATP and ADP. In vitro studies characterized DnaA as an activator of dnaX-ebfC and EbfC as an antiactivator. We further found evidence that DnaA may regulate other genes essential for replication. IMPORTANCE The dual life cycle of Borrelia burgdorferi, the causative agent of Lyme disease, is characterized by periods of rapid and slowed replication. The expression patterns of many of the spirochete's virulence factors are impacted by these changes in replication rates. The connection between replication and virulence can be understood at the dnaX-ebfC operon. DnaX is an essential component of the DNA polymerase III holoenzyme, which replicates the chromosome. EbfC is a nucleoid-associated protein that regulates the infection-associated outer surface Erp proteins, as well as other transcripts. The expression of dnaX-ebfC is tied to replication rate, which we demonstrate is mediated by DnaA, the master chromosomal initiator protein and transcription factor, and EbfC.
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14
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522626. [PMID: 36712141 PMCID: PMC9881889 DOI: 10.1101/2023.01.04.522626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli , P. aeruginosa , and B. subtilis . We discovered 63% of B. burgdorferi RNA 3' ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5' derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi . We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis- acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.,Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA.,correspondence:
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15
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Ramos D, Lasseter AG, Richards CL, Schwarz B, Ghosh S, Victoria B, Bosio CM, Gherardini FC, Jewett MW. Riboflavin salvage by Borrelia burgdorferi supports carbon metabolism and is essential for survival in the tick vector. Mol Microbiol 2022; 118:443-456. [PMID: 36054485 PMCID: PMC9588712 DOI: 10.1111/mmi.14977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 10/20/2023]
Abstract
The Lyme disease agent, Borrelia burgdorferi, harbors a significantly reduced genome and relies on the scavenging of critical nutrients from its tick and mammalian hosts for survival. Riboflavin salvage has been shown to be important for B. burgdorferi infection of mice, yet the contributions of riboflavin to B. burgdorferi metabolism and survival in the tick remain unknown. Using a targeted mass spectrometry approach, we confirmed the importance of bb0318, the putative ATPase component of an ABC-type riboflavin transporter, for riboflavin salvage and the production of FMN and FAD. This analysis further revealed that Δbb0318 B. burgdorferi displayed increased levels of glycerol 3-phosphate compared to the wild-type. The glycerol 3-phosphate dehydrogenase activity of GlpD was found to be FAD-dependent and the transcription and translation of glpD were significantly decreased in Δbb0318 B. burgdorferi. Finally, gene bb0318 was found to be important for maximal spirochete burden in unfed larvae and essential for survival in feeding ticks. Together, these data demonstrate the importance of riboflavin salvage for B. burgdorferi carbon metabolism and survival in ticks.
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Affiliation(s)
- Darlene Ramos
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Amanda G. Lasseter
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Crystal L. Richards
- Laboratory of Bacteriology, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Benjamin Schwarz
- Laboratory of Bacteriology, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Susmita Ghosh
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
- Tectonic Therapeutics, Watertown, Massachusetts, USA
| | - Berta Victoria
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Catharine M. Bosio
- Laboratory of Bacteriology, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Frank C. Gherardini
- Laboratory of Bacteriology, Division of Intramural Research, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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16
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Probing the Role of bba30, a Highly Conserved Gene of the Lyme Disease Spirochete, Throughout the Mouse-Tick Infectious Cycle. Infect Immun 2021; 89:e0033321. [PMID: 34581605 DOI: 10.1128/iai.00333-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, has a complex and segmented genome consisting of a small linear chromosome and up to 21 linear and circular plasmids. Some of these plasmids are essential as they carry genes that are critical during the life cycle of the Lyme disease spirochete. Among these is a highly conserved linear plasmid, lp54, which is crucial for the mouse-tick infectious cycle of B. burgdorferi. However, the functions of most lp54-encoded open reading frames (ORFs) remain unknown. In this study, we investigate the contribution of a previously uncharacterized lp54 gene during the infectious cycle of B. burgdorferi. This gene, bba30, is conserved in the Borrelia genus but lacks any identified homologs outside the genus. Homology modeling of BBA30 ORF indicated the presence of a nucleic acid binding motif, helix-turn-helix (HTH), near the amino terminus of the protein, suggesting a putative regulatory function. A previous study reported that spirochetes with a transposon insertion in bba30 exhibited a noninfectious phenotype in mice. In the current study, however, we demonstrate that the highly conserved bba30 gene is not required by the Lyme disease spirochete at any stage of the experimental mouse-tick infectious cycle. We conclude that the undefined circumstances under which bba30 potentially confers a fitness advantage in the natural life cycle of B. burgdorferi are not factors of the experimental infectious cycle that we employ.
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17
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Felden B, Augagneur Y. Diversity and Versatility in Small RNA-Mediated Regulation in Bacterial Pathogens. Front Microbiol 2021; 12:719977. [PMID: 34447363 PMCID: PMC8383071 DOI: 10.3389/fmicb.2021.719977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression is under the control of a large set of molecules acting at multiple levels. In addition to the transcription factors (TFs) already known to be involved in global regulation of gene expression, small regulatory RNAs (sRNAs) are emerging as major players in gene regulatory networks, where they allow environmental adaptation and fitness. Developments in high-throughput screening have enabled their detection in the entire bacterial kingdom. These sRNAs influence a plethora of biological processes, including but not limited to outer membrane synthesis, metabolism, TF regulation, transcription termination, virulence, and antibiotic resistance and persistence. Almost always noncoding, they regulate target genes at the post-transcriptional level, usually through base-pair interactions with mRNAs, alone or with the help of dedicated chaperones. There is growing evidence that sRNA-mediated mechanisms of actions are far more diverse than initially thought, and that they go beyond the so-called cis- and trans-encoded classifications. These molecules can be derived and processed from 5' untranslated regions (UTRs), coding or non-coding sequences, and even from 3' UTRs. They usually act within the bacterial cytoplasm, but recent studies showed sRNAs in extracellular vesicles, where they influence host cell interactions. In this review, we highlight the various functions of sRNAs in bacterial pathogens, and focus on the increasing examples of widely diverse regulatory mechanisms that might compel us to reconsider what constitute the sRNA.
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Affiliation(s)
- Brice Felden
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
| | - Yoann Augagneur
- Inserm, Bacterial Regulatory RNAs and Medicine (BRM) - UMR_S 1230, Rennes, France
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18
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Kuhn HW, Lasseter AG, Adams PP, Avile CF, Stone BL, Akins DR, Jewett TJ, Jewett MW. BB0562 is a nutritional virulence determinant with lipase activity important for Borrelia burgdorferi infection and survival in fatty acid deficient environments. PLoS Pathog 2021; 17:e1009869. [PMID: 34415955 PMCID: PMC8409650 DOI: 10.1371/journal.ppat.1009869] [Citation(s) in RCA: 6] [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: 05/12/2021] [Revised: 09/01/2021] [Accepted: 08/05/2021] [Indexed: 11/22/2022] Open
Abstract
The Lyme disease spirochete Borrelia burgdorferi relies on uptake of essential nutrients from its host environments for survival and infection. Therefore, nutrient acquisition mechanisms constitute key virulence properties of the pathogen, yet these mechanisms remain largely unknown. In vivo expression technology applied to B. burgdorferi (BbIVET) during mammalian infection identified gene bb0562, which encodes a hypothetical protein comprised of a conserved domain of unknown function, DUF3996. DUF3996 is also found across adjacent encoded hypothetical proteins BB0563 and BB0564, suggesting the possibility that the three proteins could be functionally related. Deletion of bb0562, bb0563 and bb0564 individually and together demonstrated that bb0562 alone was important for optimal disseminated infection in immunocompetent and immunocompromised mice by needle inoculation and tick bite transmission. Moreover, bb0562 promoted spirochete survival during the blood dissemination phase of infection. Gene bb0562 was also found to be important for spirochete growth in low serum media and the growth defect of Δbb0562 B. burgdorferi was rescued with the addition of various long chain fatty acids, particularly oleic acid. In mammals, fatty acids are primarily stored in fat droplets in the form of triglycerides. Strikingly, addition of glyceryl trioleate, the triglyceride form of oleic acid, to the low serum media did not rescue the growth defect of the mutant, suggesting bb0562 may be important for the release of fatty acids from triglycerides. Therefore, we searched for and identified two canonical GXSXG lipase motifs within BB0562, despite the lack of homology to known bacterial lipases. Purified BB0562 demonstrated lipolytic activity dependent on the catalytic serine residues within the two motifs. In sum, we have established that bb0562 is a novel nutritional virulence determinant, encoding a lipase that contributes to fatty acid scavenge for spirochete survival in environments deficient in free fatty acids including the mammalian host. Borrelia burgdorferi, the causative agent of Lyme disease, has a small genome and lacks the ability to synthesize essential nutrients on its own as well as many of the virulence properties typical of bacterial pathogens that contribute to disease. The clinical manifestations of Lyme disease predominantly result from inflammation in response to the B. burgdorferi infection. Therefore, nutrient acquisition functions constitute key virulence factors for the pathogen. Fatty acids are critical components of B. burgdorferi membranes and lipoproteins, which the spirochete must scavenge from the host environment. Previously, through a genetic screen for B. burgdorferi genes that are expressed during mammalian infection we identified gene of unknown function, bb0562. Herein, we demonstrate that bb0562 encodes a lipase that plays a role in the release of free fatty acids from triglycerides. Furthermore, bb0562 contributes to B. burgdorferi survival and dissemination in the mammalian host. BB0562 is important for spirochete survival in environments low in free fatty acids thereby adding to B. burgdorferi’s arsenal of nutritional virulence determinants necessary for the pathogen to be maintained in the tick-mouse enzootic cycle and to cause disseminated disease.
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Affiliation(s)
- Hunter W. Kuhn
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Amanda G. Lasseter
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Philip P. Adams
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, United States of America
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institute of Health, Bethesda, Maryland, United States of America
| | - Carlos Flores Avile
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Brandee L. Stone
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Darrin R. Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Travis J. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, Florida, United States of America
- * E-mail:
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19
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Ante VM, Farris LC, Saputra EP, Hall AJ, O'Bier NS, Oliva Chávez AS, Marconi RT, Lybecker MC, Hyde JA. The Borrelia burgdorferi Adenylate Cyclase, CyaB, Is Important for Virulence Factor Production and Mammalian Infection. Front Microbiol 2021; 12:676192. [PMID: 34113333 PMCID: PMC8186283 DOI: 10.3389/fmicb.2021.676192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/16/2021] [Indexed: 12/21/2022] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, traverses through vastly distinct environments between the tick vector and the multiple phases of the mammalian infection that requires genetic adaptation for the progression of pathogenesis. Borrelial gene expression is highly responsive to changes in specific environmental signals that initiate the RpoS regulon for mammalian adaptation, but the mechanism(s) for direct detection of environmental cues has yet to be identified. Secondary messenger cyclic adenosine monophosphate (cAMP) produced by adenylate cyclase is responsive to environmental signals, such as carbon source and pH, in many bacterial pathogens to promote virulence by altering gene regulation. B. burgdorferi encodes a single non-toxin class IV adenylate cyclase (bb0723, cyaB). This study investigates cyaB expression along with its influence on borrelial virulence regulation and mammalian infectivity. Expression of cyaB was specifically induced with co-incubation of mammalian host cells that was not observed with cultivated tick cells suggesting that cyaB expression is influenced by cellular factor(s) unique to mammalian cell lines. The 3′ end of cyaB also encodes a small RNA, SR0623, in the same orientation that overlaps with bb0722. The differential processing of cyaB and SR0623 transcripts may alter the ability to influence function in the form of virulence determinant regulation and infectivity. Two independent cyaB deletion B31 strains were generated in 5A4-NP1 and ML23 backgrounds and complemented with the cyaB ORF alone that truncates SR0623, cyaB with intact SR0623, or cyaB with a mutagenized full-length SR0623 to evaluate the influence on transcriptional and posttranscriptional regulation of borrelial virulence factors and infectivity. In the absence of cyaB, the expression and production of ospC was significantly reduced, while the protein levels for BosR and DbpA were substantially lower than parental strains. Infectivity studies with both independent cyaB mutants demonstrated an attenuated phenotype with reduced colonization of tissues during early disseminated infection. This work suggests that B. burgdorferi utilizes cyaB and potentially cAMP as a regulatory pathway to modulate borrelial gene expression and protein production to promote borrelial virulence and dissemination in the mammalian host.
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Affiliation(s)
- Vanessa M Ante
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Lauren C Farris
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Elizabeth P Saputra
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
| | - Allie J Hall
- Department of Biology, University of Colorado at Colorado Springs, Colorado Springs, CO, United States
| | - Nathaniel S O'Bier
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Adela S Oliva Chávez
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Richard T Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Meghan C Lybecker
- Department of Biology, University of Colorado at Colorado Springs, Colorado Springs, CO, United States
| | - Jenny A Hyde
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX, United States
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20
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Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT. Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. eLife 2021; 10:62438. [PMID: 33460557 PMCID: PMC7815308 DOI: 10.7554/elife.62438] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs. In most organisms, specific segments of a cell’s genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are ‘non-coding’ and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.
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Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, United States
| | - Gabriele Baniulyte
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Kavya Chegireddy
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Molly Monge
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, United States.,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
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21
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Coburn J, Garcia B, Hu LT, Jewett MW, Kraiczy P, Norris SJ, Skare J. Lyme Disease Pathogenesis. Curr Issues Mol Biol 2020; 42:473-518. [PMID: 33353871 DOI: 10.21775/cimb.042.473] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lyme disease Borrelia are obligately parasitic, tick- transmitted, invasive, persistent bacterial pathogens that cause disease in humans and non-reservoir vertebrates primarily through the induction of inflammation. During transmission from the infected tick, the bacteria undergo significant changes in gene expression, resulting in adaptation to the mammalian environment. The organisms multiply and spread locally and induce inflammatory responses that, in humans, result in clinical signs and symptoms. Borrelia virulence involves a multiplicity of mechanisms for dissemination and colonization of multiple tissues and evasion of host immune responses. Most of the tissue damage, which is seen in non-reservoir hosts, appears to result from host inflammatory reactions, despite the low numbers of bacteria in affected sites. This host response to the Lyme disease Borrelia can cause neurologic, cardiovascular, arthritic, and dermatologic manifestations during the disseminated and persistent stages of infection. The mechanisms by which a paucity of organisms (in comparison to many other infectious diseases) can cause varied and in some cases profound inflammation and symptoms remains mysterious but are the subjects of diverse ongoing investigations. In this review, we provide an overview of virulence mechanisms and determinants for which roles have been demonstrated in vivo, primarily in mouse models of infection.
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Affiliation(s)
- Jenifer Coburn
- Center For Infectious Disease Research, Medical College of Wisconsin, 8701 Watertown Plank Rd., TBRC C3980, Milwaukee, WI 53226, USA
| | - Brandon Garcia
- Department of Microbiology and Immunology, East Carolina University, Brody School of Medicine, Greenville, NC 27858, USA
| | - Linden T Hu
- Department of Molecular Biology and Microbiology, Vice Dean of Research, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
| | - Mollie W Jewett
- Immunity and Pathogenesis Division Head, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 6900 Lake Nona Blvd. Orlando, FL 32827, USA
| | - Peter Kraiczy
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University Frankfurt, Paul-Ehrlich-Str. 40, 60596 Frankfurt, Germany
| | - Steven J Norris
- Department of Pathology and Laboratory Medicine, University of Texas Medical School at Houston, P.O. Box 20708, Houston, TX 77225, USA
| | - Jon Skare
- Professor and Associate Head, Texas A and M University, 8447 Riverside Pkwy, Bryan, TX 77807, USA
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22
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Chaconas G, Moriarty TJ, Skare J, Hyde JA. Live Imaging. Curr Issues Mol Biol 2020; 42:385-408. [PMID: 33310914 PMCID: PMC7946808 DOI: 10.21775/cimb.042.385] [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] [Indexed: 11/05/2022] Open
Abstract
Being able to vizualize a pathogen at a site of interaction with a host is an aesthetically appealing idea and the resulting images can be both informative as well as enjoyable to view. Moreover, the approaches used to derive these images can be powerful in terms of offering data unobtainable by other methods. In this article, we review three primary modalities for live imaging Borrelia spirochetes: whole animal imaging, intravital microscopy and live cell imaging. Each method has strengths and weaknesses, which we review, as well as specific purposes for which they are optimally utilized. Live imaging borriliae is a relatively recent development and there was a need of a review to cover the area. Here, in addition to the methods themselves, we also review areas of spirochete biology that have been significantly impacted by live imaging and present a collection of images associated with the forward motion in the field driven by imaging studies.
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Affiliation(s)
- George Chaconas
- Department of Biochemistry and Molecular Biology and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Tara J. Moriarty
- Faculties of Dentistry and Medicine (Laboratory Medicine and Pathobiology), University of Toronto, Toronto, Ontario, M5G 1G6, Canada
| | - Jon Skare
- Department of Microbial Pathogenesis and Immunology, Texas A & M University Health Science Center, Bryan, Texas, 77807, USA
| | - Jenny A. Hyde
- Department of Microbial Pathogenesis and Immunology, Texas A & M University Health Science Center, Bryan, Texas, 77807, USA
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23
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Samuels DS, Lybecker MC, Yang XF, Ouyang Z, Bourret TJ, Boyle WK, Stevenson B, Drecktrah D, Caimano MJ. Gene Regulation and Transcriptomics. Curr Issues Mol Biol 2020; 42:223-266. [PMID: 33300497 DOI: 10.21775/cimb.042.223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.
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Affiliation(s)
- D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO 80918, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40536, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
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24
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Abstract
Genetic studies in Borrelia require special consideration of the highly segmented genome, complex growth requirements and evolutionary distance of spirochetes from other genetically tractable bacteria. Despite these challenges, a robust molecular genetic toolbox has been constructed to investigate the biology and pathogenic potential of these important human pathogens. In this review we summarize the tools and techniques that are currently available for the genetic manipulation of Borrelia, including the relapsing fever spirochetes, viewing them in the context of their utility and shortcomings. Our primary objective is to help researchers discern what is feasible and what is not practical when thinking about potential genetic experiments in Borrelia. We have summarized published methods and highlighted their critical elements, but we are not providing detailed protocols. Although many advances have been made since B. burgdorferi was first transformed over 25 years ago, some standard genetic tools remain elusive for Borrelia. We mention these limitations and why they persist, if known. We hope to encourage investigators to explore what might be possible, in addition to optimizing what currently can be achieved, through genetic manipulation of Borrelia.
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Affiliation(s)
- Patricia A. Rosa
- Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St. Hamilton, MT 59840 USA
| | - Mollie W. Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, 6900 Lake Nona Blvd, Orlando, FL 32827 USA
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25
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The BB0345 Hypothetical Protein of Borrelia burgdorferi Is Essential for Mammalian Infection. Infect Immun 2020; 88:IAI.00472-20. [PMID: 32928963 DOI: 10.1128/iai.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
During the natural enzootic life cycle of Borrelia burgdorferi (also known as Borreliella burgdorferi), the bacteria must sense conditions within the vertebrate and arthropod and appropriately regulate expression of genes necessary to persist within these distinct environments. bb0345 of B. burgdorferi encodes a hypothetical protein of unknown function that is predicted to contain an N-terminal helix-turn-helix (HTH) domain. Because HTH domains can mediate protein-DNA interactions, we hypothesized that BB0345 might represent a previously unidentified borrelial transcriptional regulator with the ability to regulate events critical for the B. burgdorferi enzootic cycle. To study the role of BB0345 within mammals, we generated a bb0345 mutant and assessed its virulence potential in immunocompetent mice. The bb0345 mutant was able to initiate localized infection and disseminate to distal tissues but was cleared from all sites by 14 days postinfection. In vitro growth curve analyses revealed that the bb0345 mutant grew similar to wild-type bacteria in standard Barbour-Stoenner-Kelley II (BSK-II) medium; however, the mutant was not able to grow in dilute BSK-II medium or dialysis membrane chambers (DMCs) implanted in rats. Proteinase K accessibility assays and whole-cell partitioning indicated that BB0345 was intracellular and partially membrane associated. Comparison of protein production profiles between the wild-type parent and the bb0345 mutant revealed no major differences, suggesting BB0345 may not be a global transcriptional regulator. Taken together, these data show that BB0345 is essential for B. burgdorferi survival in the mammalian host, potentially by aiding the spirochete with a physiological function that is required by the bacterium during infection.
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26
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Narra HP, Sahni A, Alsing J, Schroeder CLC, Golovko G, Nia AM, Fofanov Y, Khanipov K, Sahni SK. Comparative transcriptomic analysis of Rickettsia conorii during in vitro infection of human and tick host cells. BMC Genomics 2020; 21:665. [PMID: 32977742 PMCID: PMC7519539 DOI: 10.1186/s12864-020-07077-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/17/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pathogenic Rickettsia species belonging to the spotted fever group are arthropod-borne, obligate intracellular bacteria which exhibit preferential tropism for host microvascular endothelium in the mammalian hosts, resulting in disease manifestations attributed primarily to endothelial damage or dysfunction. Although rickettsiae are known to undergo evolution through genomic reduction, the mechanisms by which these pathogens regulate their transcriptome to ensure survival in tick vectors and maintenance by transovarial/transstadial transmission, in contrast to their ability to cause debilitating infections in human hosts remain unknown. In this study, we compare the expression profiles of rickettsial sRNAome/transcriptome and determine the transcriptional start sites (TSSs) of R. conorii transcripts during in vitro infection of human and tick host cells. RESULTS We performed deep sequencing on total RNA from Amblyomma americanum AAE2 cells and human microvascular endothelial cells (HMECs) infected with R. conorii. Strand-specific RNA sequencing of R. conorii transcripts revealed the expression 32 small RNAs (Rc_sR's), which were preferentially expressed above the limit of detection during tick cell infection, and confirmed the expression of Rc_sR61, sR71, and sR74 by quantitative RT-PCR. Intriguingly, a total of 305 and 132 R. conorii coding genes were differentially upregulated (> 2-fold) in AAE2 cells and HMECs, respectively. Further, enrichment for primary transcripts by treatment with Terminator 5'-Phosphate-dependent Exonuclease resulted in the identification of 3903 and 2555 transcription start sites (TSSs), including 214 and 181 primary TSSs in R. conorii during the infection to tick and human host cells, respectively. Seventy-five coding genes exhibited different TSSs depending on the host environment. Finally, we also observed differential expression of 6S RNA during host-pathogen and vector-pathogen interactions in vitro, implicating an important role for this noncoding RNA in the regulation of rickettsial transcriptome depending on the supportive host niche. CONCLUSIONS In sum, the findings of this study authenticate the presence of novel Rc_sR's in R. conorii, reveal the first evidence for differential expression of coding transcripts and utilization of alternate transcriptional start sites depending on the host niche, and implicate a role for 6S RNA in the regulation of coding transcriptome during tripartite host-pathogen-vector interactions.
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Affiliation(s)
- Hema P Narra
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Abha Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jessica Alsing
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Casey L C Schroeder
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anna M Nia
- Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Sanjeev K Sahni
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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27
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Snow S, Bacon E, Bergeron J, Katzman D, Wilhelm A, Lewis O, Syangtan D, Calkins A, Archambault L, Anacker ML, Schlax PJ. Transcript decay mediated by RNase III in Borrelia burgdorferi. Biochem Biophys Res Commun 2020; 529:386-391. [PMID: 32703440 DOI: 10.1016/j.bbrc.2020.05.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 11/29/2022]
Abstract
The causative agent of Lyme disease, Borrelia burgdorferi, requires shifts in gene expression to undergo its natural enzootic cycle between tick and vertebrate hosts. mRNA decay mechanisms play significant roles in governing gene expression in other bacteria, but are not yet characterized in B. burgdorferi. RNase III is an important enzyme in processing ribosomal RNA, but it also plays a role in mRNA decay in many bacteria. We compared RNA decay profiles and steady-state abundances of transcripts in wild-type Borrelia burgdorferi strain B31 and in an RNase III null (rnc-) mutant. Transcripts encoding RNA polymerase subunits (rpoA and rpoS), ribosomal proteins (rpsD, rpsK, rpsM, rplQ, and rpsO), a nuclease (pnp), a flagellar protein (flaB), and a translational regulator (bpuR) decayed more rapidly in the wild-type strain than in the slow growing rnc- mutant indicating that RNA turnover is mediated by RNase III in the bacterium that causes Lyme disease. Additionally, in wild type bacteria, RNA decay rates of rpoS, rpoN, ospA, ospC, bpuR and dbpA transcripts are only modestly affected by changes in the osmolarity.
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Affiliation(s)
- Santina Snow
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Emily Bacon
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Jennifer Bergeron
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - David Katzman
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Amelia Wilhelm
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Owen Lewis
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Deepsing Syangtan
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Andrew Calkins
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Linda Archambault
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA
| | - Melissa L Anacker
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Paula Jean Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME, USA.
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28
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Establishment of an in vitro RNA polymerase transcription system: a new tool to study transcriptional activation in Borrelia burgdorferi. Sci Rep 2020; 10:8246. [PMID: 32427963 PMCID: PMC7237435 DOI: 10.1038/s41598-020-65104-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/27/2020] [Indexed: 12/04/2022] Open
Abstract
The Lyme disease spirochete Borrelia burgdorferi exhibits dramatic changes in gene expression as it transits between its tick vector and vertebrate host. A major hurdle to understanding the mechanisms underlying gene regulation in B. burgdorferi has been the lack of a functional assay to test how gene regulatory proteins and sigma factors interact with RNA polymerase to direct transcription. To gain mechanistic insight into transcriptional control in B. burgdorferi, and address sigma factor function and specificity, we developed an in vitro transcription assay using the B. burgdorferi RNA polymerase holoenzyme. We established reaction conditions for maximal RNA polymerase activity by optimizing pH, temperature, and the requirement for divalent metals. Using this assay system, we analyzed the promoter specificity of the housekeeping sigma factor RpoD to promoters encoding previously identified RpoD consensus sequences in B. burgdorferi. Collectively, this study established an in vitro transcription assay that revealed RpoD-dependent promoter selectivity by RNA polymerase and the requirement of specific metal cofactors for maximal RNA polymerase activity. The establishment of this functional assay will facilitate molecular and biochemical studies on how gene regulatory proteins and sigma factors exert control of gene expression in B. burgdorferi required for the completion of its enzootic cycle.
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29
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Medina-Pérez DN, Wager B, Troy E, Gao L, Norris SJ, Lin T, Hu L, Hyde JA, Lybecker M, Skare JT. The intergenic small non-coding RNA ittA is required for optimal infectivity and tissue tropism in Borrelia burgdorferi. PLoS Pathog 2020; 16:e1008423. [PMID: 32365143 PMCID: PMC7224557 DOI: 10.1371/journal.ppat.1008423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/14/2020] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Post-transcriptional regulation via small regulatory RNAs (sRNAs) has been implicated in diverse regulatory processes in bacteria, including virulence. One class of sRNAs, termed trans-acting sRNAs, can affect the stability and/or the translational efficiency of regulated transcripts. In this study, we utilized a collaborative approach that employed data from infection with the Borrelia burgdorferi Tn library, coupled with Tn-seq, together with borrelial sRNA and total RNA transcriptomes, to identify an intergenic trans-acting sRNA, which we designate here as ittA for infectivity-associated and tissue-tropic sRNA locus A. The genetic inactivation of ittA resulted in a significant attenuation in infectivity, with decreased spirochetal load in ear, heart, skin and joint tissues. In addition, the ittA mutant did not disseminate to peripheral skin sites or heart tissue, suggesting a role for ittA in regulating a tissue-tropic response. RNA-Seq analysis determined that 19 transcripts were differentially expressed in the ittA mutant relative to its genetic parent, including vraA, bba66, ospD and oms28 (bba74). Subsequent proteomic analyses also showed a significant decrease of OspD and Oms28 (BBA74) proteins. To our knowledge this is the first documented intergenic sRNA that alters the infectivity potential of B. burgdorferi.
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Affiliation(s)
- Diana N. Medina-Pérez
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Beau Wager
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts, United States of America
| | - Erin Troy
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts, United States of America
| | - Lihui Gao
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Houston, Texas, United States of America
| | - Steven J. Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Houston, Texas, United States of America
| | - Tao Lin
- Department of Pathology and Laboratory Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Houston, Texas, United States of America
| | - Linden Hu
- Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts, United States of America
| | - Jenny A. Hyde
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, Texas, United States of America
| | - Meghan Lybecker
- Department of Biology, University of Colorado at Colorado Springs, Colorado Springs, Colorado, United States of America
| | - Jon T. Skare
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, Texas, United States of America
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30
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Adams PP, Storz G. Prevalence of small base-pairing RNAs derived from diverse genomic loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194524. [PMID: 32147527 DOI: 10.1016/j.bbagrm.2020.194524] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in fine-tuning the levels and translation of their target transcripts across a variety of model and pathogenic organisms. Work from many different groups in a wide range of bacterial species has provided evidence for the importance and complexity of sRNA regulatory networks, which allow bacteria to quickly respond to changes in their environment. However, despite the expansive literature, much remains to be learned about all aspects of sRNA-mediated regulation, particularly in bacteria beyond the well-characterized Escherichia coli and Salmonella enterica species. Here we discuss what is known, and what remains to be learned, about the identification of regulatory base-pairing RNAs produced from diverse genomic loci including how their expression is regulated. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA; Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892-6200, USA.
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892-5430, USA
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31
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Fitzgerald BL, Molins CR, Islam MN, Graham B, Hove PR, Wormser GP, Hu L, Ashton LV, Belisle JT. Host Metabolic Response in Early Lyme Disease. J Proteome Res 2020; 19:610-623. [PMID: 31821002 PMCID: PMC7262776 DOI: 10.1021/acs.jproteome.9b00470] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lyme disease is a tick-borne bacterial illness that occurs in areas of North America, Europe, and Asia. Early infection typically presents as generalized symptoms with an erythema migrans (EM) skin lesion. Dissemination of the pathogen Borrelia burgdorferi can result in multiple EM skin lesions or in extracutaneous manifestations such as Lyme neuroborreliosis. Metabolic biosignatures of patients with early Lyme disease can potentially provide diagnostic targets as well as highlight metabolic pathways that contribute to pathogenesis. Sera from well-characterized patients diagnosed with either early localized Lyme disease (ELL) or early disseminated Lyme disease (EDL), plus healthy controls (HC), from the United States were analyzed by liquid chromatography-mass spectrometry (LC-MS). Comparative analyses were performed between ELL, or EDL, or ELL combined with EDL, and the HC to develop biosignatures present in early Lyme disease. A direct comparison between ELL and EDL was also performed to develop a biosignature for stages of early Lyme disease. Metabolic pathway analysis and chemical identification of metabolites with LC-tandem mass spectrometry (LC-MS/MS) demonstrated alterations of eicosanoid, bile acid, sphingolipid, glycerophospholipid, and acylcarnitine metabolic pathways during early Lyme disease. These metabolic alterations were confirmed using a separate set of serum samples for validation. The findings demonstrated that infection of humans with B. burgdorferi alters defined metabolic pathways that are associated with inflammatory responses, liver function, lipid metabolism, and mitochondrial function. Additionally, the data provide evidence that metabolic pathways can be used to mark the progression of early Lyme disease.
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Affiliation(s)
| | - Claudia R. Molins
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - M. Nurul Islam
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80521, USA
| | - Barbara Graham
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80521, USA
| | - Petronella R. Hove
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80521, USA
| | - Gary P. Wormser
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, NY 10595, USA
| | - Linden Hu
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Laura V. Ashton
- Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - John T. Belisle
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80521, USA
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Melamed S, Adams PP, Zhang A, Zhang H, Storz G. RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles. Mol Cell 2020; 77:411-425.e7. [DOI: 10.1016/j.molcel.2019.10.022] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/09/2019] [Accepted: 10/15/2019] [Indexed: 01/22/2023]
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Jutras BL, Savage CR, Arnold WK, Lethbridge KG, Carroll DW, Tilly K, Bestor A, Zhu H, Seshu J, Zückert WR, Stewart PE, Rosa PA, Brissette CA, Stevenson B. The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase. Mol Microbiol 2019; 112:973-991. [PMID: 31240776 PMCID: PMC6736767 DOI: 10.1111/mmi.14336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2019] [Indexed: 12/24/2022]
Abstract
When the Lyme disease spirochete, Borrelia burgdorferi, transfers from a feeding tick into a human or other vertebrate host, the bacterium produces vertebrate‐specific proteins and represses factors needed for arthropod colonization. Previous studies determined that the B. burgdorferi BpuR protein binds to its own mRNA and autoregulates its translation, and also serves as co‐repressor of erp transcription. Here, we demonstrate that B. burgdorferi controls transcription of bpuR, expressing high levels of bpuR during tick colonization but significantly less during mammalian infection. The master regulator of chromosomal replication, DnaA, was found to bind specifically to a DNA sequence that overlaps the bpuR promoter. Cultured B. burgdorferi that were genetically manipulated to produce elevated levels of BpuR exhibited altered levels of several proteins, although BpuR did not impact mRNA levels. Among these was the SodA superoxide dismutase, which is essential for mammalian infection. BpuR bound to sodA mRNA in live B. burgdorferi, and a specific BpuR‐binding site was mapped 5′ of the sodA open reading frame. Recognition of posttranscriptional regulation of protein levels by BpuR adds another layer to our understanding of the B. burgdorferi regulome, and provides further evidence that bacterial protein levels do not always correlate directly with mRNA levels.
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Affiliation(s)
- Brandon L Jutras
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Christina R Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - William K Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Kathryn G Lethbridge
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Dustin W Carroll
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Kit Tilly
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Aaron Bestor
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Wolfram R Zückert
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Philip E Stewart
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patricia A Rosa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA.,Department of Entomology, University of Kentucky, Lexington, KY, USA
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Abstract
The spirochetes Borrelia (Borreliella) burgdorferi and Borrelia hermsii, the etiologic agents of Lyme disease and relapsing fever, respectively, cycle in nature between an arthropod vector and a vertebrate host. They have extraordinarily unusual genomes that are highly segmented and predominantly linear. The genetic analyses of Lyme disease spirochetes have become increasingly more sophisticated, while the age of genetic investigation in the relapsing fever spirochetes is just dawning. Molecular tools available for B. burgdorferi and related species range from simple selectable markers and gene reporters to state-of-the-art inducible gene expression systems that function in the animal model and high-throughput mutagenesis methodologies, despite nearly overwhelming experimental obstacles. This armamentarium has empowered borreliologists to build a formidable genetic understanding of the cellular physiology of the spirochete and the molecular pathogenesis of Lyme disease.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
| | - D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
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Zhang K, Qin Z, Chang Y, Liu J, Malkowski MG, Shipa S, Li L, Qiu W, Zhang JR, Li C. Analysis of a flagellar filament cap mutant reveals that HtrA serine protease degrades unfolded flagellin protein in the periplasm of Borrelia burgdorferi. Mol Microbiol 2019; 111:1652-1670. [PMID: 30883947 DOI: 10.1111/mmi.14243] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Unlike external flagellated bacteria, spirochetes have periplasmic flagella (PF). Very little is known about how PF are assembled within the periplasm of spirochaetal cells. Herein, we report that FliD (BB0149), a flagellar cap protein (also named hook-associated protein 2), controls flagellin stability and flagellar filament assembly in the Lyme disease spirochete Borrelia burgdorferi. Deletion of fliD leads to non-motile mutant cells that are unable to assemble flagellar filaments and pentagon-shaped caps (10 nm in diameter, 12 nm in length). Interestingly, FlaB, a major flagellin protein of B. burgdorferi, is degraded in the fliD mutant but not in other flagella-deficient mutants (i.e., in the hook, rod, or MS-ring). Biochemical and genetic studies reveal that HtrA, a serine protease of B. burgdorferi, controls FlaB turnover. Specifically, HtrA degrades unfolded but not polymerized FlaB, and deletion of htrA increases the level of FlaB in the fliD mutant. Collectively, we propose that the flagellar cap protein FliD promotes flagellin polymerization and filament growth in the periplasm. Deletion of fliD abolishes this process, which leads to leakage of unfolded FlaB proteins into the periplasm where they are degraded by HtrA, a protease that prevents accumulation of toxic products in the periplasm.
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Affiliation(s)
- Kai Zhang
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute, Virginia Commonwealth University, Richmond, VI, 23298, USA
| | - Zhuan Qin
- Department of Microbial Pathogenesis & Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, 06516, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis & Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, 06516, USA
| | - Jun Liu
- Department of Microbial Pathogenesis & Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, 06516, USA
| | - Michael G Malkowski
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, NY, 14203, USA
| | - Saimtun Shipa
- Department of Biological Sciences, City University of New York, New York, NY, 10021, USA
| | - Li Li
- Department of Biological Sciences, City University of New York, New York, NY, 10021, USA
| | - Weigang Qiu
- Department of Biological Sciences, City University of New York, New York, NY, 10021, USA
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute, Virginia Commonwealth University, Richmond, VI, 23298, USA
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Borrelia burgdorferi bbk13 Is Critical for Spirochete Population Expansion in the Skin during Early Infection. Infect Immun 2019; 87:IAI.00887-18. [PMID: 30782856 DOI: 10.1128/iai.00887-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/08/2019] [Indexed: 12/31/2022] Open
Abstract
Lyme disease is caused by the spirochete Borrelia burgdorferi and is transmitted via the bite of an infected tick. B. burgdorferi enters the skin, disseminates via the bloodstream, and infects various distal tissues, leading to inflammatory sequelae, such as Lyme arthritis and Lyme carditis. B. burgdorferi linear plasmid 36 (lp36) is critical for mammalian infectivity; however, the full complement of genes on lp36 that contribute to this process remains unknown. Through a targeted mutagenesis screen of the genes on lp36, we identified a novel infectivity gene of unknown function, bbk13, which encodes an immunogenic, non-surface-exposed membrane protein that is important for efficient mammalian infection. Loss of bbk13 resulted in reduced spirochete loads in distal tissues in a mouse model of infection. Through a detailed analysis of B. burgdorferi infection kinetics, we discovered that bbk13 is important for promoting spirochete proliferation in the skin inoculation site. The attenuated ability of Δbbk13 spirochetes to proliferate in the inoculation site was followed by reduced numbers of B. burgdorferi spirochetes in the bloodstream and, ultimately, consistently reduced spirochete loads in distal tissues. Together, our data indicate that bbk13 contributes to disseminated infection by promoting spirochete proliferation in the early phase of infection in the skin. This work not only increases the understanding of the contribution of the genes on lp36 to B. burgdorferi infection but also begins to define the genetic basis for B. burgdorferi expansion in the skin during localized infection and highlights the influence of the early expansion of spirochetes in the skin on the outcome of infection.
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Casselli T, Crowley MA, Highland MA, Tourand Y, Bankhead T. A small intergenic region of lp17 is required for evasion of adaptive immunity and induction of pathology by the Lyme disease spirochete. Cell Microbiol 2019; 21:e13029. [PMID: 30945408 DOI: 10.1111/cmi.13029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/07/2019] [Accepted: 03/30/2019] [Indexed: 01/15/2023]
Abstract
The causative agent of Lyme disease, Borrelia burgdorferi, harbours a single linear chromosome and upwards of 23 linear and circular plasmids. Only a minority of these plasmids, including linear plasmid 17, are maintained with near-absolute fidelity during extended in vitro passage, and characterisation of any putative virulence determinants they encode has only recently begun. In this work, a mutant lacking a ~4.7 kb fragment of lp17 was studied. Colonisation of murine tissues by this lp17 mutant was significantly impaired, as was the ability to induce carditis and arthritis. The deficiency in tissue colonisation was alleviated in severe combined immunodeficient (SCID) mice, implicating a role for this plasmid region in adaptive immune evasion. Through genetic complementation, the mutant phenotype could be fully attributed to a 317 bp intergenic region that corresponds to the discontinued bbd07 ORF and upstream sequence. The intergenic region was found to be transcriptionally active, and mutant spirochetes lacking this region exhibited an overall difference in the antigenic profile during infection of an immunocompetent murine host. Overall, this study is the first to provide evidence for the involvement of lp17 in colonisation of joint and heart tissues, along with the associated pathologies caused by the Lyme disease spirochete.
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Affiliation(s)
- Timothy Casselli
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Michael A Crowley
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Margaret A Highland
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA.,Animal Disease Research Unit, USDA Agricultural Research Service, Pullman, Washington, USA
| | - Yvonne Tourand
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Troy Bankhead
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
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38
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Martini MC, Zhou Y, Sun H, Shell SS. Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia. Front Microbiol 2019; 10:591. [PMID: 30984135 PMCID: PMC6448022 DOI: 10.3389/fmicb.2019.00591] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5′-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.
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Affiliation(s)
- M Carla Martini
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Ying Zhou
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Huaming Sun
- Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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Takacs CN, Kloos ZA, Scott M, Rosa PA, Jacobs-Wagner C. Fluorescent Proteins, Promoters, and Selectable Markers for Applications in the Lyme Disease Spirochete Borrelia burgdorferi. Appl Environ Microbiol 2018; 84:e01824-18. [PMID: 30315081 PMCID: PMC6275353 DOI: 10.1128/aem.01824-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/08/2018] [Indexed: 11/30/2022] Open
Abstract
Lyme disease is the most widely reported vector-borne disease in the United States. Its incidence is rapidly increasing, and disease symptoms can be debilitating. The need to understand the biology of the disease agent, the spirochete Borrelia burgdorferi, is thus evermore pressing. Despite important advances in B. burgdorferi genetics, the array of molecular tools available for use in this organism remains limited, especially for cell biological studies. Here, we adapt a palette of bright and mostly monomeric fluorescent proteins for versatile use and multicolor imaging in B. burgdorferi We also characterize two novel antibiotic selection markers and establish the feasibility of their use in conjunction with extant markers. Last, we describe a set of promoters of low and intermediate strengths that allow fine-tuning of gene expression levels. These molecular tools complement and expand current experimental capabilities in B. burgdorferi, which will facilitate future investigation of this important human pathogen. To showcase the usefulness of these reagents, we used them to investigate the subcellular localization of BB0323, a B. burgdorferi lipoprotein essential for survival in the host and vector environments. We show that BB0323 accumulates at the cell poles and future division sites of B. burgdorferi cells, highlighting the complex subcellular organization of this spirochete.IMPORTANCE Genetic manipulation of the Lyme disease spirochete B. burgdorferi remains cumbersome, despite significant progress in the field. The scarcity of molecular reagents available for use in this pathogen has slowed research efforts to study its unusual biology. Of interest, B. burgdorferi displays complex cellular organization features that have yet to be understood. These include an unusual morphology and a highly fragmented genome, both of which are likely to play important roles in the bacterium's transmission, infectivity, and persistence. Here, we complement and expand the array of molecular tools available for use in B. burgdorferi by generating and characterizing multiple fluorescent proteins, antibiotic selection markers, and promoters of varied strengths. These tools will facilitate investigations in this important human pathogen, as exemplified by the polar and midcell localization of the cell envelope regulator BB0323, which we uncovered using these reagents.
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Affiliation(s)
- Constantin N Takacs
- Microbial Sciences Institute, Yale West Campus, West Haven, Connecticut, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale West Campus, West Haven, Connecticut, USA
| | - Zachary A Kloos
- Microbial Sciences Institute, Yale West Campus, West Haven, Connecticut, USA
- Microbiology Program, Yale University, New Haven, Connecticut, USA
| | - Molly Scott
- Microbial Sciences Institute, Yale West Campus, West Haven, Connecticut, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale West Campus, West Haven, Connecticut, USA
| | - Patricia A Rosa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale West Campus, West Haven, Connecticut, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale West Campus, West Haven, Connecticut, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
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DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi. J Bacteriol 2018; 200:JB.00395-18. [PMID: 30249703 DOI: 10.1128/jb.00395-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/18/2018] [Indexed: 02/08/2023] Open
Abstract
Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The type strain of the causative agent of Lyme disease, Borrelia burgdorferi B31, possesses two RM systems with N6-methyladenosine (m6A) MTase activity, which are encoded by the bbe02 gene located on linear plasmid lp25 and bbq67 on lp56. The specific recognition and/or methylation sequences had not been identified for either of these B. burgdorferi MTases, and it was not previously known whether these RM systems influence transcript levels. In the current study, single-molecule real-time sequencing was utilized to map genome-wide m6A sites and to identify consensus modified motifs in wild-type B. burgdorferi as well as MTase mutants lacking either the bbe02 gene alone or both bbe02 and bbq67 genes. Four novel conserved m6A motifs were identified and were fully attributable to the presence of specific MTases. Whole-genome transcriptome changes were observed in conjunction with the loss of MTase enzymes, indicating that DNA methylation by the RM systems has effects on gene expression. Genes with altered transcription in MTase mutants include those involved in vertebrate host colonization (e.g., rpoS regulon) and acquisition by/transmission from the tick vector (e.g., rrp1 and pdeB). The results of this study provide a comprehensive view of the DNA methylation pattern in B. burgdorferi, and the accompanying gene expression profiles add to the emerging body of research on RM systems and gene regulation in bacteria.IMPORTANCE Lyme disease is the most prevalent vector-borne disease in North America and is classified by the Centers for Disease Control and Prevention (CDC) as an emerging infectious disease with an expanding geographical area of occurrence. Previous studies have shown that the causative bacterium, Borrelia burgdorferi, methylates its genome using restriction modification systems that enable the distinction from foreign DNA. Although much research has focused on the regulation of gene expression in B. burgdorferi, the effect of DNA methylation on gene regulation has not been evaluated. The current study characterizes the patterns of DNA methylation by restriction modification systems in B. burgdorferi and evaluates the resulting effects on gene regulation in this important pathogen.
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Yin X, Wu Orr M, Wang H, Hobbs EC, Shabalina SA, Storz G. The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels. Mol Microbiol 2018; 111:131-144. [PMID: 30276893 DOI: 10.1111/mmi.14143] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2018] [Indexed: 01/04/2023]
Abstract
In response to low levels of magnesium (Mg2+ ), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pairs with the eptB mRNA thus affecting lipopolysaccharide modification. Surprisingly, we found overexpression of the MgtS protein also leads to induction of the PhoRB regulon. Studies to understand this activation showed that MgtS forms a complex with a second protein, PitA, a cation-phosphate symporter. Given that the additive effect of ∆mgtA and ∆mgtS mutations on intracellular Mg2+ concentrations seen previously is lost in the ∆pitA mutant, we suggest that MgtS binds to and prevents Mg2+ leakage through PitA under Mg2+ -limiting conditions. Consistent with a detrimental role of PitA in low Mg2+ , we also observe MgrR sRNA repression of PitA synthesis. Thus, PhoQP induces the expression of two convergent small genes in response to Mg2+ limitation whose products act to modulate PitA at different levels to increase intracellular Mg2+ .
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Affiliation(s)
- Xuefeng Yin
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,Health Science Center, Peking University, Beijing, 100191, China
| | - Mona Wu Orr
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Hanbo Wang
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA.,School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Errett C Hobbs
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892-4417, USA
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Bontemps-Gallo S, Gaviard C, Richards CL, Kentache T, Raffel SJ, Lawrence KA, Schindler JC, Lovelace J, Dulebohn DP, Cluss RG, Hardouin J, Gherardini FC. Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. Front Microbiol 2018; 9:2036. [PMID: 30233522 PMCID: PMC6127242 DOI: 10.3389/fmicb.2018.02036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
The post-translational modification of proteins has been shown to be extremely important in prokaryotes. Using a highly sensitive mass spectrometry-based proteomics approach, we have characterized the acetylome of B. burgdorferi. As previously reported for other bacteria, a relatively low number (5%) of the potential genome-encoded proteins of B. burgdorferi were acetylated. Of these, the vast majority were involved in central metabolism and cellular information processing (transcription, translation, etc.). Interestingly, these critical cell functions were targeted during both ML (mid-log) and S (stationary) phases of growth. However, acetylation of target proteins in ML phase was limited to single lysine residues while these same proteins were acetylated at multiple sites during S phase. To determine the acetyl donor in B. burgdorferi, we used mutants that targeted the sole acetate metabolic/anabolic pathway in B. burgdorferi (lipid I synthesis). B. burgdorferi strains B31-A3, B31-A3 ΔackA (acetyl-P- and acetyl-CoA-) and B31-A3 Δpta (acetyl-P+ and acetyl-CoA-) were grown to S phase and the acetylation profiles were analyzed. While only two proteins were acetylated in the ΔackA mutant, 140 proteins were acetylated in the Δpta mutant suggesting that acetyl-P was the primary acetyl donor in B. burgdorferi. Using specific enzymatic assays, we were able to demonstrate that hyperacetylation of proteins in S phase appeared to play a role in decreasing the enzymatic activity of at least two glycolytic proteins. Currently, we hypothesize that acetylation is used to modulate enzyme activities during different stages of growth. This strategy would allow the bacteria to post-translationally stimulate the activity of key glycolytic enzymes by deacetylation rather than expending excessive energy synthesizing new proteins. This would be an appealing, low-energy strategy for a bacterium with limited metabolic capabilities. Future work focuses on identifying potential protein deacetylase(s) to complete our understanding of this important biological process.
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Affiliation(s)
- Sébastien Bontemps-Gallo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Charlotte Gaviard
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Crystal L Richards
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Takfarinas Kentache
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Sandra J Raffel
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Kevin A Lawrence
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Joseph C Schindler
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Joseph Lovelace
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Daniel P Dulebohn
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
| | - Robert G Cluss
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Julie Hardouin
- CNRS UMR 6270 Polymères, Biopolymères, Surfaces Laboratory, Université de Rouen, Mont-Saint-Aignan, France.,PISSARO Proteomic Facility, Institut de Recherche et d'Innovation Biomédicale, Mont-Saint-Aignan, France
| | - Frank C Gherardini
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States
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Arnold WK, Savage CR, Lethbridge KG, Smith TC, Brissette CA, Seshu J, Stevenson B. Transcriptomic insights on the virulence-controlling CsrA, BadR, RpoN, and RpoS regulatory networks in the Lyme disease spirochete. PLoS One 2018; 13:e0203286. [PMID: 30161198 PMCID: PMC6117026 DOI: 10.1371/journal.pone.0203286] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 08/19/2018] [Indexed: 01/17/2023] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease, survives in nature through a cycle that alternates between ticks and vertebrates. To facilitate this defined lifestyle, B. burgdorferi has evolved a gene regulatory network that ensures transmission between those hosts, along with specific adaptations to niches within each host. Several regulatory proteins are known to be essential for the bacterium to complete these critical tasks, but interactions between regulators had not previously been investigated in detail, due to experimental uses of different strain backgrounds and growth conditions. To address that deficit in knowledge, the transcriptomic impacts of four critical regulatory proteins were examined in a uniform strain background. Pairs of mutants and their wild-type parent were grown simultaneously under a single, specific culture condition, permitting direct comparisons between the mutant strains. Transcriptomic analyses were strand-specific, and assayed both coding and noncoding RNAs. Intersection analyses identified regulatory overlaps between regulons, including transcripts involved in carbohydrate and polyamine metabolism. In addition, it was found that transcriptional units such as ospC and dbpBA, which were previously observed to be affected by alternative sigma factors, are transcribed by RNA polymerase using the housekeeping sigma factor, RpoD.
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Affiliation(s)
- William K. Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Christina R. Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Kathryn G. Lethbridge
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Trever C. Smith
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Catherine A. Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
- Department of Entomology, University of Kentucky, Lexington, KY, United States of America
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Drecktrah D, Hall LS, Rescheneder P, Lybecker M, Samuels DS. The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi. Front Cell Infect Microbiol 2018; 8:231. [PMID: 30027068 PMCID: PMC6041397 DOI: 10.3389/fcimb.2018.00231] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
The Lyme disease spirochete Borrelia (Borreliella) burgdorferi must tolerate nutrient stress to persist in the tick phase of its enzootic life cycle. We previously found that the stringent response mediated by RelBbu globally regulates gene expression to facilitate persistence in the tick vector. Here, we show that RelBbu regulates the expression of a swath of small RNAs (sRNA), affecting 36% of previously identified sRNAs in B. burgdorferi. This is the first sRNA regulatory mechanism identified in any spirochete. Threefold more sRNAs were RelBbu-upregulated than downregulated during nutrient stress and included antisense, intergenic and 5′ untranslated region sRNAs. RelBbu-regulated sRNAs associated with genes known to be important for host infection (bosR and dhhp) as well as persistence in the tick (glpF and hk1) were identified, suggesting potential mechanisms for post-transcriptional regulation of gene expression.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Laura S Hall
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Meghan Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO, United States
| | - D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT, United States.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, United States
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Abstract
Next-Generation Sequencing (NGS) has revolutionized transcriptomics studies in the last decade. Transcriptome analysis experiments using NGS-based RNA-sequencing have several advantages over DNA microarray analysis. Novel unannotated transcripts and transcriptional start sites can be identified. Differential gene expression can be determined on novel and annotated transcripts simultaneously, whereas DNA microarray analysis can only quantify changes of known genes. In the protocol below we describe an Illumina compatible ligation-based method for generating stranded cDNA libraries for total RNA and small RNA transcriptomes in Borrelia burgdorferi.
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Selection of Borrelia burgdorferi Promoter Sequences Active During Mammalian Infection Using In Vivo Expression Technology. Methods Mol Biol 2018; 1690:137-154. [PMID: 29032543 DOI: 10.1007/978-1-4939-7383-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
In vivo expression technology (IVET) has been applied to a variety of organisms to identify active promoters in specific environments or growth conditions of interest. Here, we describe modifications to employ this genome-wide screening method for Borrelia burgdorferi, the Lyme disease spirochete, during an active murine infection. Utilization of this technique provides valuable insights into the B. burgdorferi transcriptome during infection, despite the low bacterial numbers in the mammalian host environment.
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Borrelia burgdorferi SpoVG DNA- and RNA-Binding Protein Modulates the Physiology of the Lyme Disease Spirochete. J Bacteriol 2018; 200:JB.00033-18. [PMID: 29632088 DOI: 10.1128/jb.00033-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/02/2018] [Indexed: 11/20/2022] Open
Abstract
The SpoVG protein of Borrelia burgdorferi, the Lyme disease spirochete, binds to specific sites of DNA and RNA. The bacterium regulates transcription of spoVG during the natural tick-mammal infectious cycle and in response to some changes in culture conditions. Bacterial levels of spoVG mRNA and SpoVG protein did not necessarily correlate, suggesting that posttranscriptional mechanisms also control protein levels. Consistent with this, SpoVG binds to its own mRNA, adjacent to the ribosome-binding site. SpoVG also binds to two DNA sites in the glpFKD operon and to two RNA sites in glpFKD mRNA; that operon encodes genes necessary for glycerol catabolism and is important for colonization in ticks. In addition, spirochetes engineered to dysregulate spoVG exhibited physiological alterations.IMPORTANCEB. burgdorferi persists in nature by cycling between ticks and vertebrates. Little is known about how the bacterium senses and adapts to each niche of the cycle. The present studies indicate that B. burgdorferi controls production of SpoVG and that this protein binds to specific sites of DNA and RNA in the genome and transcriptome, respectively. Altered expression of spoVG exerts effects on bacterial replication and other aspects of the spirochete's physiology.
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48
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Bontemps-Gallo S, Lawrence KA, Richards CL, Gherardini FC. Borrelia burgdorferi genes, bb0639-0642, encode a putative putrescine/spermidine transport system, PotABCD, that is spermidine specific and essential for cell survival. Mol Microbiol 2018; 108:350-360. [PMID: 29476656 DOI: 10.1111/mmi.13940] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
Polyamines are an essential class of metabolites found throughout all kingdoms in life. Borrelia burgdorferi harbors no enzymes to synthesize or degrade polyamines yet does contain a polyamine uptake system, potABCD. In this report, we describe the initial characterization of this putative transport system. After several unsuccessful attempts to inactivate potABCD, we placed the operon under the control of an inducible LacI promoter expression system. Analyses of this construct confirmed that potABCD was required for in vitro survival. Additionally, we demonstrated that the potABCD operon were upregulated in vitro by low osmolarity. Previously, we had shown that low osmolarity triggers the activation of the Rrp2/RpoN/RpoS regulatory cascade, which regulates genes essential for the transmission of spirochetes from ticks to mammalian hosts. Interestingly, induction of the pot operon was only affected in an rpoS mutant but not in a rpoN mutant, suggesting that the genes were RpoS dependent and RpoN independent. Furthermore, potABCD was upregulated during tick feeding concomitant with the initiation of spirochete replication. Finally, uptake experiments determined the specificity of B. burgdorferi's PotABCD for spermidine.
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Affiliation(s)
- Sébastien Bontemps-Gallo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kevin A Lawrence
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Crystal L Richards
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Frank C Gherardini
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
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The Borrelia burgdorferi Glycosaminoglycan Binding Protein Bgp in the B31 Strain Is Not Essential for Infectivity despite Facilitating Adherence and Tissue Colonization. Infect Immun 2018; 86:IAI.00667-17. [PMID: 29158428 DOI: 10.1128/iai.00667-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/08/2017] [Indexed: 11/20/2022] Open
Abstract
The Lyme disease-causing organism Borrelia burgdorferi is transmitted into the mammalian host by an infected-tick bite. Successful infection relies on the ability of this extracellular pathogen to persist and colonize different tissues. B. burgdorferi encodes a large number of adhesins that are able to interact with host ligands to facilitate adherence and tissue colonization. Multiple glycosaminoglycan binding proteins present in B. burgdorferi offer a degree of redundancy of function during infection, and this highlights the importance of glycosaminoglycans as host cell receptors for spirochete adherence. Of particular interest in this study is Borrelia glycosaminoglycan binding protein (Bgp), which binds to heparin-related glycosaminoglycans. The properties of a bgp transposon mutant and a trans-complemented derivative were compared to those of the wild-type B. burgdorferi in the in vitro binding assays and in infection studies using a C3H/HeJ mouse infection model. We determined that the loss of Bgp impairs spirochete adherence, infectivity, and tissue colonization, resulting in a reduction of inflammatory manifestations of Lyme disease. Although Bgp is not essential for infectivity, it is an important virulence factor of B. burgdorferi that allows adherence and tissue colonization and contributes to disease severity.
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50
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Cabello FC, Godfrey HP, Bugrysheva J, Newman SA. Sleeper cells: the stringent response and persistence in the Borreliella (Borrelia) burgdorferi enzootic cycle. Environ Microbiol 2017; 19:3846-3862. [PMID: 28836724 PMCID: PMC5794220 DOI: 10.1111/1462-2920.13897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/12/2017] [Accepted: 08/17/2017] [Indexed: 12/27/2022]
Abstract
Infections with tick-transmitted Borreliella (Borrelia) burgdorferi, the cause of Lyme disease, represent an increasingly large public health problem in North America and Europe. The ability of these spirochetes to maintain themselves for extended periods of time in their tick vectors and vertebrate reservoirs is crucial for continuance of the enzootic cycle as well as for the increasing exposure of humans to them. The stringent response mediated by the alarmone (p)ppGpp has been determined to be a master regulator in B. burgdorferi. It modulates the expression of identified and unidentified open reading frames needed to deal with and overcome the many nutritional stresses and other challenges faced by the spirochete in ticks and animal reservoirs. The metabolic and morphologic changes resulting from activation of the stringent response in B. burgdorferi may also be involved in the recently described non-genetic phenotypic phenomenon of tolerance to otherwise lethal doses of antimicrobials and to other antimicrobial activities. It may thus constitute a linchpin in multiple aspects of infections with Lyme disease borrelia, providing a link between the micro-ecological challenges of its enzootic life-cycle and long-term residence in the tissues of its animal reservoirs, with the evolutionary side effect of potential persistence in incidental human hosts.
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Affiliation(s)
- Felipe C. Cabello
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Henry P. Godfrey
- Department of Pathology, New York Medical College, Valhalla, NY, USA
| | - Julia Bugrysheva
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart A. Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY, USA
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