1
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Bourgeois JS, Hu LT. Hitchhiker's Guide to Borrelia burgdorferi. J Bacteriol 2024; 206:e0011624. [PMID: 39140751 PMCID: PMC11411949 DOI: 10.1128/jb.00116-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024] Open
Abstract
Don't Panic. In the nearly 50 years since the discovery of Lyme disease, Borrelia burgdorferi has emerged as an unlikely workhorse of microbiology. Interest in studying host-pathogen interactions fueled significant progress in making the fastidious microbe approachable in laboratory settings, including the development of culture methods, animal models, and genetic tools. By developing these systems, insight has been gained into how the microbe is able to survive its enzootic cycle and cause human disease. Here, we discuss the discovery of B. burgdorferi and its development as a model organism before diving into the critical lessons we have learned about B. burgdorferi biology at pivotal stages of its lifecycle: gene expression changes during the tick blood meal, colonization of a new vertebrate host, and developing a long-lasting infection in that vertebrate until a new tick feeds. Our goal is to highlight the advancements that have facilitated B. burgdorferi research and identify gaps in our current understanding of the microbe.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Biology and Microbiology, Tufts University Lyme Disease Initiative, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Linden T Hu
- Department of Molecular Biology and Microbiology, Tufts University Lyme Disease Initiative, Tufts University School of Medicine, Boston, Massachusetts, USA
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2
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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 PMCID: PMC10319736 DOI: 10.1038/s41467-023-39576-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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3
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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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4
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Wachter J, Cheff B, Hillman C, Carracoi V, Dorward DW, Martens C, Barbian K, Nardone G, Renee Olano L, Kinnersley M, Secor PR, Rosa PA. Coupled induction of prophage and virulence factors during tick transmission of the Lyme disease spirochete. Nat Commun 2023; 14:198. [PMID: 36639656 PMCID: PMC9839762 DOI: 10.1038/s41467-023-35897-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The alternative sigma factor RpoS plays a central role in the critical host-adaptive response of the Lyme disease spirochete, Borrelia burgdorferi. We previously identified bbd18 as a negative regulator of RpoS but could not inactivate bbd18 in wild-type spirochetes. In the current study we employed an inducible bbd18 gene to demonstrate the essential nature of BBD18 for viability of wild-type spirochetes in vitro and at a unique point in vivo. Transcriptomic analyses of BBD18-depleted cells demonstrated global induction of RpoS-dependent genes prior to lysis, with the absolute requirement for BBD18, both in vitro and in vivo, circumvented by deletion of rpoS. The increased expression of plasmid prophage genes and the presence of phage particles in the supernatants of lysing cultures indicate that RpoS regulates phage lysis-lysogeny decisions. Through this work we identify a mechanistic link between endogenous prophages and the RpoS-dependent adaptive response of the Lyme disease spirochete.
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Affiliation(s)
- Jenny Wachter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA. .,Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Britney Cheff
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Chad Hillman
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Valentina Carracoi
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - David W Dorward
- Electron Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Kent Barbian
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Glenn Nardone
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - L Renee Olano
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Margie Kinnersley
- Division of Biological Sciences, The University of Montana, Missoula, MT, USA
| | - Patrick R Secor
- Division of Biological Sciences, The University of Montana, Missoula, 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
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5
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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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6
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Freire de Melo F, Marques HS, Fellipe Bueno Lemos F, Silva Luz M, Rocha Pinheiro SL, de Carvalho LS, Souza CL, Oliveira MV. Role of nickel-regulated small RNA in modulation of Helicobacter pylori virulence factors. World J Clin Cases 2022; 10:11283-11291. [PMID: 36387830 PMCID: PMC9649571 DOI: 10.12998/wjcc.v10.i31.11283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/14/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative bacterium that infects about half of the world's population. H. pylori infection prevails by several mechanisms of adaptation of the bacteria and by its virulence factors including the cytotoxin associated antigen A (CagA). CagA is an oncoprotein that is the protagonist of gastric carcinogenesis associated with prolonged H. pylori infection. In this sense, small regulatory RNAs (sRNAs) are important macromolecules capable of inhibiting and activating gene expression. This function allows sRNAs to act in adjusting to unstable environmental conditions and in responding to cellular stresses in bacterial infections. Recent discoveries have shown that nickel-regulated small RNA (NikS) is a post-transcriptional regulator of virulence properties of H. pylori, including the oncoprotein CagA. Notably, high concentrations of nickel cause the reduction of NikS expression and consequently this increases the levels of CagA. In addition, NikS expression appears to be lower in clinical isolates from patients with gastric cancer when compared to patients without. With that in mind, this minireview approaches, in an accessible way, the most important and current aspects about the role of NikS in the control of virulence factors of H. pylori and the potential clinical repercussions of this modulation.
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Affiliation(s)
- Fabrício Freire de Melo
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Hanna Santos Marques
- Campus Vitória da Conquista, Universidade Estadual do Sudoeste da Bahia, Vitória da Conquista 45083-900, Brazil
| | - Fabian Fellipe Bueno Lemos
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Marcel Silva Luz
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Samuel Luca Rocha Pinheiro
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Lorena Sousa de Carvalho
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Cláudio Lima Souza
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
| | - Márcio Vasconcelos Oliveira
- Institution Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista 45029-094, Brazil
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7
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Crowley MA, Bankhead T. Potential Regulatory Role in Mammalian Host Adaptation for a Small Intergenic Region of Lp17 in the Lyme Disease Spirochete. Front Cell Infect Microbiol 2022; 12:892220. [PMID: 35586252 PMCID: PMC9108270 DOI: 10.3389/fcimb.2022.892220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The bacterial agent of Lyme disease, Borrelia burgdorferi, relies on an intricate gene regulatory network to transit between the disparate Ixodes tick vector and mammalian host environments. We recently reported that a B. burgdorferi mutant lacking a transcriptionally active intergenic region of lp17 displayed attenuated murine tissue colonization and pathogenesis due to altered expression of multiple antigens. In this study, a more detailed characterization of the putative regulatory factor encoded by the intergenic region was pursued. In cis complemented strains featuring mutations aimed at eliminating potential protein translation were capable of full tissue colonization, suggesting that the functional product encoded by the intergenic region is not a protein as previously predicted. In trans complementation of the intergenic region resulted in elevated transcription of the sequence compared to wild type and was found to completely abolish infectivity in both immunocompetent "and immunodeficient mice. Quantitative analysis of transcription of the intergenic region by wild-type B. burgdorferi showed it to be highly induced during murine infection relative to in vitro culture. Lastly, targeted deletion of this intergenic region resulted in significant changes to the transcriptome, including genes with potential roles in transmission and host adaptation. The findings reported herein strongly suggest that this segment of lp17 serves a potentially critical role in the regulation of genes required for adaptation and persistence of the pathogen in a mammalian host.
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Affiliation(s)
| | - Troy Bankhead
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
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8
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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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9
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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: 18] [Impact Index Per Article: 4.5] [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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10
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Abstract
The genus Borrelia consists of evolutionarily and genetically diverse bacterial species that cause a variety of diseases in humans and domestic animals. These vector-borne spirochetes can be classified into two major evolutionary groups, the Lyme borreliosis clade and the relapsing fever clade, both of which have complex transmission cycles during which they interact with multiple host species and arthropod vectors. Molecular, ecological, and evolutionary studies have each provided significant contributions towards our understanding of the natural history, biology and evolutionary genetics of Borrelia species; however, integration of these studies is required to identify the evolutionary causes and consequences of the genetic variation within and among Borrelia species. For example, molecular and genetic studies have identified the adaptations that maximize fitness components throughout the Borrelia lifecycle and enhance transmission efficacy but provide limited insights into the evolutionary pressures that have produced them. Ecological studies can identify interactions between Borrelia species and the vertebrate hosts and arthropod vectors they encounter and the resulting impact on the geographic distribution and abundance of spirochetes but not the genetic or molecular basis underlying these interactions. In this review we discuss recent findings on the evolutionary genetics from both of the evolutionarily distinct clades of Borrelia species. We focus on connecting molecular interactions to the ecological processes that have driven the evolution and diversification of Borrelia species in order to understand the current distribution of genetic and molecular variation within and between Borrelia species.
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Affiliation(s)
- Zachary J. Oppler
- Department of Biology, University of Pennsylvania, 433 South University Ave, Philadelphia, PA 19104, USA
| | - Kayleigh R. O’Keeffe
- Department of Biology, University of Pennsylvania, 433 South University Ave, Philadelphia, PA 19104, USA
| | - Karen D. McCoy
- Centre for Research on the Ecology and Evolution of Diseases (CREES), MiVEGEC, University of Montpellier – CNRS - IRD, Montpellier, France
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, 433 South University Ave, Philadelphia, PA 19104, USA
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11
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O'Keeffe KR, Oppler ZJ, Brisson D. Evolutionary ecology of Lyme Borrelia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104570. [PMID: 32998077 PMCID: PMC8349510 DOI: 10.1016/j.meegid.2020.104570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023]
Abstract
The bacterial genus, Borrelia, is comprised of vector-borne spirochete species that infect and are transmitted from multiple host species. Some Borrelia species cause highly-prevalent diseases in humans and domestic animals. Evolutionary, ecological, and molecular research on many Borrelia species have resulted in tremendous progress toward understanding the biology and natural history of these species. Yet, many outstanding questions, such as how Borrelia populations will be impacted by climate and land-use change, will require an interdisciplinary approach. The evolutionary ecology research framework incorporates theory and data from evolutionary, ecological, and molecular studies while overcoming common assumptions within each field that can hinder integration across these disciplines. Evolutionary ecology offers a framework to evaluate the ecological consequences of evolved traits and to predict how present-day ecological processes may result in further evolutionary change. Studies of microbes with complex transmission cycles, like Borrelia, which interact with multiple vertebrate hosts and arthropod vectors, are poised to leverage the power of the evolutionary ecology framework to identify the molecular interactions involved in ecological processes that result in evolutionary change. Using existing data, we outline how evolutionary ecology theory can delineate how interactions with other species and the physical environment create selective forces or impact migration of Borrelia populations and result in micro-evolutionary changes. We further discuss the ecological and molecular consequences of those micro-evolutionary changes. While many of the currently outstanding questions will necessitate new experimental designs and additional empirical data, many others can be addressed immediately by integrating existing molecular and ecological data within an evolutionary ecology framework.
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Affiliation(s)
| | - Zachary J Oppler
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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12
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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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13
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González Plaza JJ. Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases. Front Mol Biosci 2020; 7:101. [PMID: 32613006 PMCID: PMC7308464 DOI: 10.3389/fmolb.2020.00101] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/04/2020] [Indexed: 12/24/2022] Open
Abstract
Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.
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Affiliation(s)
- Juan José González Plaza
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
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14
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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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15
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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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16
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Drecktrah D, Hall LS, Brinkworth AJ, Comstock JR, Wassarman KM, Samuels DS. Characterization of 6S RNA in the Lyme disease spirochete. Mol Microbiol 2020; 113:399-417. [PMID: 31742773 PMCID: PMC7047579 DOI: 10.1111/mmi.14427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/05/2019] [Accepted: 11/16/2019] [Indexed: 12/31/2022]
Abstract
6S RNA binds to RNA polymerase and regulates gene expression, contributing to bacterial adaptation to environmental stresses. In this study, we examined the role of 6S RNA in murine infectivity and tick persistence of the Lyme disease spirochete Borrelia (Borreliella) burgdorferi. B. burgdorferi 6S RNA (Bb6S RNA) binds to RNA polymerase, is expressed independent of growth phase or nutrient stress in culture, and is processed by RNase Y. We found that rny (bb0504), the gene encoding RNase Y, is essential for B. burgdorferi growth, while ssrS, the gene encoding 6S RNA, is not essential, indicating a broader role for RNase Y activity in the spirochete. Bb6S RNA regulates expression of the ospC and dbpA genes encoding outer surface protein C and decorin binding protein A, respectively, which are lipoproteins important for host infection. The highest levels of Bb6S RNA are found when the spirochete resides in unfed nymphs. ssrS mutants lacking Bb6S RNA were compromised for infectivity by needle inoculation, but injected mice seroconverted, indicating an ability to activate the adaptive immune response. ssrS mutants were successfully acquired by larval ticks and persisted through fed nymphs. Bb6S RNA is one of the first regulatory RNAs identified in B. burgdorferi that controls the expression of lipoproteins involved in host infectivity.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | | | | | - Karen M. Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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17
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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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18
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Ding Z, Ma M, Tao L, Peng Y, Han Y, Sun L, Dai X, Ji Z, Bai R, Jian M, Chen T, Luo L, Wang F, Bi Y, Liu A, Bao F. Rhesus Brain Transcriptomic Landscape in an ex vivo Model of the Interaction of Live Borrelia Burgdorferi With Frontal Cortex Tissue Explants. Front Neurosci 2019; 13:651. [PMID: 31316336 PMCID: PMC6610209 DOI: 10.3389/fnins.2019.00651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Lyme neuroborreliosis (LNB) is the most dangerous manifestation of Lyme disease caused by the spirochete Borrelia burgdorferi which can reach the central nervous system most commonly presenting with lymphocytic meningitis; however, the molecular basis for neuroborreliosis is still poorly understood. We incubated explants from the frontal cortex of three rhesus brains with medium alone or medium with added live Borrelia burgdorferi for 6, 12, and 24 h and isolated RNA from each group was used for RNA sequencing with further bioinformatic analysis. Transcriptomic differences between the ex vivo model of live Borrelia burgdorferi with rhesus frontal cortex tissue explants and the controls during the progression of the infection were identified. A total of 2249, 1064, and 420 genes were significantly altered, of which 80.7, 52.9, and 19.8% were upregulated and 19.3, 47.1, 80.2% were downregulated at 6, 12, and 24 h, respectively. Gene ontology and KEGG pathway analyses revealed various pathways related to immune and inflammatory responses during the spirochete infection were enriched which is suggested to have a causal role in the pathogenesis of neurological Lyme disease. Moreover, we propose that the overexpressed FOLR2 which was demonstrated by the real-time PCR and western blotting could play a key role in neuroinflammation of the neuroborreliosis based on PPI analysis for the first time. To our knowledge, this is the first study to provide comprehensive information regarding the transcriptomic signatures that occur in the frontal cortex of the brain upon exposure to Borrelia burgdorferi, and suggest that FOLR2 is a promising target that is associated with neuroinflammation and may represent a new diagnostic or therapeutic marker in LNB.
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Affiliation(s)
- Zhe Ding
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Mingbiao Ma
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lvyan Tao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Yun Peng
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Luyun Sun
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Xiting Dai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Zhenhua Ji
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Ruolan Bai
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Miaomiao Jian
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Taigui Chen
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China
| | - Lisha Luo
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China
| | - Feng Wang
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Yunfeng Bi
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China
| | - Aihua Liu
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, China.,Yunnan Province Integrative Innovation Center for Public Health, Diseases Prevention and Control, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
| | - Fukai Bao
- Yunnan Province Key Laboratory for Tropical Infectious Diseases in Universities, Kunming Medical University, Kunming, China.,Department of Microbiology and Immunology, Kunming Medical University, Kunming, China.,Yunnan Province Integrative Innovation Center for Public Health, Diseases Prevention and Control, Kunming Medical University, Kunming, China.,Yunnan Demonstration Base of International Science and Technology Cooperation for Tropical Diseases, Kunming, China
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19
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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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20
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Phelan JP, Kern A, Ramsey ME, Lundt ME, Sharma B, Lin T, Gao L, Norris SJ, Hyde JA, Skare JT, Hu LT. Genome-wide screen identifies novel genes required for Borrelia burgdorferi survival in its Ixodes tick vector. PLoS Pathog 2019; 15:e1007644. [PMID: 31086414 PMCID: PMC6516651 DOI: 10.1371/journal.ppat.1007644] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/15/2019] [Indexed: 12/25/2022] Open
Abstract
Borrelia burgdorferi, the causative agent of Lyme disease in humans, is maintained in a complex biphasic life cycle, which alternates between tick and vertebrate hosts. To successfully survive and complete its enzootic cycle, B. burgdorferi adapts to diverse hosts by regulating genes required for survival in specific environments. Here we describe the first ever use of transposon insertion sequencing (Tn-seq) to identify genes required for B. burgdorferi survival in its tick host. We found that insertions into 46 genes resulted in a complete loss of recovery of mutants from larval Ixodes ticks. Insertions in an additional 56 genes resulted in a >90% decrease in fitness. The screen identified both previously known and new genes important for larval tick survival. Almost half of the genes required for survival in the tick encode proteins of unknown function, while a significant portion (over 20%) encode membrane-associated proteins or lipoproteins. We validated the results of the screen for five Tn mutants by performing individual competition assays using mutant and complemented strains. To better understand the role of one of these genes in tick survival, we conducted mechanistic studies of bb0017, a gene previously shown to be required for resistance against oxidative stress. In this study we show that BB0017 affects the regulation of key borrelial virulence determinants. The application of Tn-seq to in vivo screening of B. burgdorferi in its natural vector is a powerful tool that can be used to address many different aspects of the host pathogen interaction. Borrelia burgdorferi, the causative agent of Lyme disease, must adjust to environmental changes as it moves between its tick and vertebrate hosts. We performed a screen of a B. burgdorferi transposon library using massively parallel sequencing (Tn-seq) to identify fitness defects involved in survival in its tick host. This screen accurately identified genes known to cause decreased fitness for tick survival and identified new genes involved in B. burgdorferi survival in ticks. All of the genes tested individually confirmed the Tn-seq results. One of the genes identified encodes a protein whose function was previously unknown that appears to be involved in regulating expression of proteins known to be involved in environmental adaptation. Tn-seq is a powerful tool for understanding vector-pathogen interactions and may reveal new opportunities for interrupting the infectious cycle of vector-borne diseases.
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Affiliation(s)
- James P. Phelan
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail: (JPP); (STH)
| | - Aurelie Kern
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Meghan E. Ramsey
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Maureen E. Lundt
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Bijaya Sharma
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Tao Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lihui Gao
- MD Anderson Cancer Center Thoracic & Cardiovascular Surgery, Houston, Texas, United States of America
| | - Steven J. Norris
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UT Health, Houston, Texas, 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
| | - Jon T. Skare
- Department of Microbial Pathogenesis and Immunology, Texas A & M University Health Science Center, Bryan, Texas, United States of America
| | - Linden T. Hu
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
- * E-mail: (JPP); (STH)
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21
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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: 8] [Impact Index Per Article: 1.6] [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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22
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Abstract
Lyme disease (LD) is the most common tick-borne disease in the Northern Hemisphere. As the most prevalent vector-borne disease in the USA, LD affects 300,000 human cases each year. LD is caused by inoculation of the bacterial spirochete, Borrelia burgdorferi sensu lato, from an infected tick. If not treated quickly and completely, the bacteria disseminate from the tick's biting site into multiple organs including the joints, heart, and brain. Thus, the best outcome from medical intervention can be expected with early detection and treatment with antibiotics, prior to multi-organ dissemination. In the absence of a characteristic rash, LD is diagnosed using serological testing involving enzyme-linked immunosorbent assay (ELISA) followed by western blotting, which is collectively known as the two-tier algorithm. These assays detect host antibodies against the bacteria, but are hampered by low sensitivity, which can miss early LD cases. This review discusses the application of some current assays for diagnosing LD clinically, thus providing a foundation for exploring newer techniques being developed in the laboratory for more sensitive detection of early LD.
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Affiliation(s)
- Eunice Chou
- Vassar College in Poughkeepsie, NY SUNY Downstate Medical School and SUNY Polytechnic Institute
| | - Yi-Pin Lin
- University in Ithaca, NY and postdoctoral training from Tufts University in Boston, MA
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23
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Ten-Caten F, Vêncio RZN, Lorenzetti APR, Zaramela LS, Santana AC, Koide T. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA Biol 2018; 15:1119-1132. [PMID: 30175688 PMCID: PMC6161675 DOI: 10.1080/15476286.2018.1509661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.
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Affiliation(s)
- Felipe Ten-Caten
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ricardo Z N Vêncio
- b Department of Computation and Mathematics, Faculdade de Filosofia , Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Alan Péricles R Lorenzetti
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Livia Soares Zaramela
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ana Carolina Santana
- c Department of Cell and Molecular Biology and Pathogenic Bioagents , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Tie Koide
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
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24
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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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25
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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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26
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Malge A, Ghai V, Reddy PJ, Baxter D, Kim TK, Moritz RL, Wang K. mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles. FEMS Microbiol Lett 2018; 365:5017443. [PMID: 29846577 PMCID: PMC5995203 DOI: 10.1093/femsle/fny135] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/26/2018] [Indexed: 12/20/2022] Open
Abstract
Borrelia burgdorferi, a bacterium in the spirochete phylum, is the causative agent of Lyme disease. Borrelia burgdorferi has a linear chromosome with a number of circular and linear plasmids. Bacteria, including B. burgdorferi, release spherical outer membrane vesicles (OMVs) that are known to carry secretory products including metabolites, nucleic acids and proteins. Herein, we provide the first comparative transcriptomic analysis of the vesicles released from B. burgdorferi. We identified a total of ∼1200 unique transcripts with at least one mapped read from the bacterial cell and its OMVs. We compared the spectrum of transcripts between bacterial cell and its OMVs, and found a biased distribution based on the source of transcripts, i.e. plasmid-encoded transcripts are more likely to be enriched in the OMVs. We validated the distribution for some of the transcripts by qPCR. This analysis provides the first evidence that some of the B. burgdorferi transcripts are preferentially packaged in OMV, which further suggest that the bacteria might use its OMVs for bacteria-bacteria or bacteria-host communications. This report also suggests a possible involvement of Borrelia-derived OMVs in the development of Lyme disease in both early and post disease syndromes.
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Affiliation(s)
- Anjali Malge
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - Vikas Ghai
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - Panga Jaipal Reddy
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - David Baxter
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - Taek-Kyun Kim
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
| | - Kai Wang
- Institute for Systems Biology, 401 Terry Avenue North Seattle, WA 98109-5263, USA
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27
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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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28
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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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29
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Lybecker MC, Samuels DS. Small RNAs of Borrelia burgdorferi: Characterizing Functional Regulators in a Sea of sRNAs
. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2017; 90:317-323. [PMID: 28656017 PMCID: PMC5482307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Borrelia (Borreliella) burgdorferi and closely related genospecies are the causative agents of Lyme disease, the most common tick-borne disease north of the equator. The bacterium, a member of the spirochete phylum, is acquired by a tick vector that feeds on an infected vertebrate host and is transmitted to another vertebrate during subsequent feeding by the next tick stage. The precise navigation of this enzootic cycle entails the regulation of genes required for these two host-specific phases as well as the transitions between them. Recently, an expansive swath of small RNAs has been identified in B. burgdorferi and likely many, if not most, are involved in regulating gene expression. Regardless, with only a few exceptions, the functions of these RNAs are completely unknown. However, several state-of-the-art approaches are available to identify the targets of these RNAs and provide insight into their role in the enzootic cycle and infection.
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Affiliation(s)
- Meghan C. Lybecker
- University of Colorado Colorado Springs, Department of Biology, Colorado Springs, CO,To whom all correspondence should be addressed: Meghan Lybecker, Department of Biology, University of Colorado, Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80917, Tel: 719-255-4101, .
| | - D. Scott Samuels
- University of Montana, Division of Biological Sciences, Missoula, MT
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30
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Adams PP, Flores Avile C, Jewett MW. A Dual Luciferase Reporter System for B. burgdorferi Measures Transcriptional Activity during Tick-Pathogen Interactions. Front Cell Infect Microbiol 2017; 7:225. [PMID: 28620587 PMCID: PMC5449462 DOI: 10.3389/fcimb.2017.00225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/16/2017] [Indexed: 12/23/2022] Open
Abstract
Knowledge of the transcriptional responses of vector-borne pathogens at the vector-pathogen interface is critical for understanding disease transmission. Borrelia (Borreliella) burgdorferi, the causative agent of Lyme disease in the United States, is transmitted by the bite of infected Ixodes sp. ticks. It is known that B. burgdorferi has altered patterns of gene expression during tick acquisition, persistence and transmission. Recently, we and others have discovered in vitro expression of RNAs found internal, overlapping, and antisense to annotated open reading frames in the B. burgdorferi genome. However, there is a lack of molecular genetic tools for B. burgdorferi for quantitative, strand-specific, comparative analysis of these transcripts in distinct environments such as the arthropod vector. To address this need, we have developed a dual luciferase reporter system to quantify B. burgdorferi promoter activities in a strand-specific manner. We demonstrate that constitutive expression of a B. burgdorferi codon-optimized Renilla reniformis luciferase gene (rlucBb ) allows normalization of the activity of a promoter of interest when fused to the B. burgdorferi codon-optimized Photinus pyralis luciferase gene (flucBb) on the same plasmid. Using the well characterized, differentially regulated, promoters for flagellin (flaBp), outer surface protein A (ospAp) and outer surface protein C (ospCp), we document the efficacy of the dual luciferase system for quantitation of promoter activities during in vitro growth and in infected ticks. Cumulatively, the dual luciferase method outlined herein is the first dual reporter system for B. burgdorferi, providing a novel and highly versatile approach for strand-specific molecular genetic analyses.
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Affiliation(s)
- Philip P Adams
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of MedicineOrlando, FL, United States
| | - Carlos Flores Avile
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of MedicineOrlando, FL, United States
| | - Mollie W Jewett
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, University of Central Florida College of MedicineOrlando, FL, United States
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31
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Stewart PE, Rosa PA. Physiologic and Genetic Factors Influencing the Zoonotic Cycle of Borrelia burgdorferi. Curr Top Microbiol Immunol 2017; 415:63-82. [PMID: 28864829 DOI: 10.1007/82_2017_43] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Borrelia burgdorferi is a symbiont of ticks of the Ixodes ricinus complex. These ticks serve as vectors to disseminate the spirochete to a variety of susceptible vertebrate hosts, which, in turn, act as reservoirs for naïve ticks to become infected, perpetuating the infectious life cycle of B. burgdorferi. The pivotal role of ticks in this life cycle and tick-spirochete interactions are the focus of this chapter. Here, we describe the challenging physiological environment that spirochetes encounter within Ixodes ticks, and the genetic factors that B. burgdorferi uses to successfully infect, persist, and be transmitted from the vector.
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Affiliation(s)
- Philip E Stewart
- Laboratory of Zoonotic Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th St., Hamilton, MT, 59840, USA.
| | - Patricia A Rosa
- Laboratory of Zoonotic Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th St., Hamilton, MT, 59840, USA.
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32
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Regulation of Gene and Protein Expression in the Lyme Disease Spirochete. Curr Top Microbiol Immunol 2017; 415:83-112. [PMID: 29064060 DOI: 10.1007/82_2017_49] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The infectious cycle of Borrelia burgdorferi necessitates persistent infection of both vertebrates and ticks, and efficient means of transmission between those two very different types of hosts. The Lyme disease spirochete has evolved mechanisms to sense its location in the infectious cycle, and use that information to control production of the proteins and other factors required for each step. Numerous components of borrelial regulatory pathways have been characterized to date. Their effects are being pieced together, thereby providing glimpses into a complex web of cooperative and antagonistic interactions. In this chapter, we present a broad overview of B. burgdorferi gene and protein regulation during the natural infectious cycle, discussions of culture-based methods for elucidating regulatory mechanisms, and summaries of many of the known regulatory proteins and small molecules. We also highlight areas that are in need of substantially more research.
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