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D'haeseleer P, Collette NM, Lao V, Segelke BW, Branda SS, Franco M. Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei. Front Immunol 2021; 12:716676. [PMID: 34659206 PMCID: PMC8513525 DOI: 10.3389/fimmu.2021.716676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.
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Affiliation(s)
- Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Nicole M Collette
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Victoria Lao
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Brent W Segelke
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Steven S Branda
- Molecular and Microbiology Department, Sandia National Laboratories, Livermore, CA, United States
| | - Magdalena Franco
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
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Klimentova J, Rehulka P, Pavkova I, Kubelkova K, Bavlovic J, Stulik J. Cross-Species Proteomic Comparison of Outer Membrane Vesicles and Membranes of Francisella tularensis subsp. tularensis versus subsp. holarctica. J Proteome Res 2021; 20:1716-1732. [PMID: 33543941 DOI: 10.1021/acs.jproteome.0c00917] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Release of outer membrane vesicles (OMV) is an important phenomenon in Gram-negative bacteria playing multiple roles in their lifestyle, including in relation to virulence and host-pathogen interaction. Francisella tularensis, unlike other bacteria, releases unusually shaped, tubular OMV. We present a proteomic comparison of OMV and membrane fractions from two F. tularensis strains: moderately virulent subsp. holarctica strain FSC200 and highly virulent subsp. tularensis strain SchuS4. Proteomic comparison studies routinely evaluate samples from the same proteome, but sometimes we must compare samples from closely related organisms. This raises quantification issues. We propose a novel approach to cross-species proteomic comparison based on an intersection protein database from the individual single-species databases. This is less prone to quantification errors arising from differences in the sequences. Consecutively comparing subproteomes of OMV and membranes of the two strains allows distinguishing differences in relative protein amounts caused by global expression changes from those caused by preferential protein packing to OMV or membranes. Among the proteins most differently packed into OMV between the two strains, we detected proteins involved in biosynthesis and metabolism of bacterial envelope components like O-antigen, lipid A, phospholipids, and fatty acids, as well as some major structural outer membrane proteins. The data are available via ProteomeXchange with identifier PXD022406.
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Affiliation(s)
- Jana Klimentova
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
| | - Pavel Rehulka
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
| | - Ivona Pavkova
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
| | - Klara Kubelkova
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
| | - Jan Bavlovic
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
| | - Jiri Stulik
- Faculty of Military Health Sciences, Department of Molecular Pathology and Biology, University of Defence, Hradec Kralove 500 01, Czech Republic
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Zook J, Shekhar M, Hansen D, Conrad C, Grant T, Gupta C, White T, Barty A, Basu S, Zhao Y, Zatsepin N, Ishchenko A, Batyuk A, Gati C, Li C, Galli L, Coe J, Hunter M, Liang M, Weierstall U, Nelson G, James D, Stauch B, Craciunescu F, Thifault D, Liu W, Cherezov V, Singharoy A, Fromme P. XFEL and NMR Structures of Francisella Lipoprotein Reveal Conformational Space of Drug Target against Tularemia. Structure 2020; 28:540-547.e3. [PMID: 32142641 DOI: 10.1016/j.str.2020.02.005] [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: 07/29/2019] [Revised: 12/23/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
Francisella tularensis is the causative agent for the potentially fatal disease tularemia. The lipoprotein Flpp3 has been identified as a virulence determinant of tularemia with no sequence homology outside the Francisella genus. We report a room temperature structure of Flpp3 determined by serial femtosecond crystallography that exists in a significantly different conformation than previously described by the NMR-determined structure. Furthermore, we investigated the conformational space and energy barriers between these two structures by molecular dynamics umbrella sampling and identified three low-energy intermediate states, transitions between which readily occur at room temperature. We have also begun to investigate organic compounds in silico that may act as inhibitors to Flpp3. This work paves the road to developing targeted therapeutics against tularemia and aides in our understanding of the disease mechanisms of tularemia.
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Affiliation(s)
- James Zook
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Mrinal Shekhar
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; Center for the Development of TherapeuticsThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Debra Hansen
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Chelsie Conrad
- Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
| | - Thomas Grant
- Hauptman Woodward Institute, Jacobs School of Medicine and Biomedical Science, SUNY, Buffalo, NY 14260, USA
| | - Chitrak Gupta
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Thomas White
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Anton Barty
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble, Grenoble Cedex 9 38042, France
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Andrii Ishchenko
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Alex Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Cornelius Gati
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Lorenzo Galli
- DESY, Center for Free Electron Laser Science, Hamburg 22607, Germany
| | - Jesse Coe
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Meng Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Uwe Weierstall
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Garret Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Paul Scherrer Institute, 5232 Villigen, Switzerland
| | | | - Felicia Craciunescu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Darren Thifault
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Abhishek Singharoy
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Petra Fromme
- Center for Applied Structural Discovery, the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
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Madar M, Bencurova E, Mlynarcik P, Almeida AM, Soares R, Bhide K, Pulzova L, Kovac A, Coelho AV, Bhide M. Exploitation of complement regulatory proteins by Borrelia and Francisella. MOLECULAR BIOSYSTEMS 2016; 11:1684-95. [PMID: 25912816 DOI: 10.1039/c5mb00027k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pathogens have developed sophisticated mechanisms of complement evasion such as binding to the host complement regulatory proteins (CRPs) on their surface or expression of CRP mimicking molecules. The ability of pathogens to evade the complement system has been correlated with pathogenesis and host selectivity. Hitherto, little work has been undertaken to determine whether Borrelia and Francisella exploit various CRPs to block complement attack. Seventeen Borrelia (twelve species) and six Francisella (three subspecies) strains were used to assess their ability to bind human, sheep and cattle CRPs or mimic membrane associated complement regulators. A series of experiments including affinity ligand binding experiments, pull-down assays and mass spectrometry based protein identification, revealed an array of CRP binding proteins of Borrelia and Francisella. Unlike Francisella, Borrelia strains were able to bind multiple human CRPs. Three strains of Borrelia (SKT-4, SKT-2 and HO14) showed the presence of a human CD46-homologous motif, indicating their ability to possess putative human CD46 mimicking molecules. Similarly, five strains of Borrelia and two strains of Francisella may have surface proteins with human CD59-homologous motifs. Among ovine and bovine CRPs, the only CRP bound by Francisella (LVS, Tul4 strain) was vitronectin, while ovine C4BP, ovine factor H and bovine factor H were bound to Borrelia strains SKT-2, DN127 and Co53. This study presents an array of proteins of Borrelia and Francisella that bind CRPs or may mimic membrane-CRPs, thus enabling multiphasic complement evasion strategies of these pathogens.
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Affiliation(s)
- Marian Madar
- Laboratory of Biomedical Microbiology and Immunology, Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 04181, Košice, Slovakia.
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Peetermans M, Vanassche T, Liesenborghs L, Lijnen RH, Verhamme P. Bacterial pathogens activate plasminogen to breach tissue barriers and escape from innate immunity. Crit Rev Microbiol 2015; 42:866-82. [PMID: 26485450 DOI: 10.3109/1040841x.2015.1080214] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Both coagulation and fibrinolysis are tightly connected with the innate immune system. Infection and inflammation cause profound alterations in the otherwise well-controlled balance between coagulation and fibrinolysis. Many pathogenic bacteria directly exploit the host's hemostatic system to increase their virulence. Here, we review the capacity of bacteria to activate plasminogen. The resulting proteolytic activity allows them to breach tissue barriers and evade innate immune defense, thus promoting bacterial spreading. Yersinia pestis, streptococci of group A, C and G and Staphylococcus aureus produce a specific bacterial plasminogen activator. Moreover, surface plasminogen receptors play an established role in pneumococcal, borrelial and group B streptococcal infections. This review summarizes the mechanisms of bacterial activation of host plasminogen and the role of the fibrinolytic system in infections caused by these pathogens.
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Affiliation(s)
- Marijke Peetermans
- a Center for Molecular and Vascular Biology, KU Leuven , Leuven , Belgium
| | - Thomas Vanassche
- a Center for Molecular and Vascular Biology, KU Leuven , Leuven , Belgium
| | | | - Roger H Lijnen
- a Center for Molecular and Vascular Biology, KU Leuven , Leuven , Belgium
| | - Peter Verhamme
- a Center for Molecular and Vascular Biology, KU Leuven , Leuven , Belgium
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Bacterial plasminogen receptors: mediators of a multifaceted relationship. J Biomed Biotechnol 2012; 2012:272148. [PMID: 23118502 PMCID: PMC3478875 DOI: 10.1155/2012/272148] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/07/2012] [Indexed: 12/14/2022] Open
Abstract
Multiple species of bacteria are able to sequester the host zymogen plasminogen to the cell surface. Once localised to the bacterial surface, plasminogen can act as a cofactor in adhesion, or, following activation to plasmin, provide a source of potent proteolytic activity. Numerous bacterial plasminogen receptors have been identified, and the mechanisms by which they interact with plasminogen are diverse. Here we provide an overview of bacterial plasminogen receptors and discuss the diverse role bacterial plasminogen acquisition plays in the relationship between bacteria and the host.
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Subversion of host recognition and defense systems by Francisella spp. Microbiol Mol Biol Rev 2012; 76:383-404. [PMID: 22688817 DOI: 10.1128/mmbr.05027-11] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Francisella tularensis is a gram-negative intracellular pathogen and the causative agent of the disease tularemia. Inhalation of as few as 10 bacteria is sufficient to cause severe disease, making F. tularensis one of the most highly virulent bacterial pathogens. The initial stage of infection is characterized by the "silent" replication of bacteria in the absence of a significant inflammatory response. Francisella achieves this difficult task using several strategies: (i) strong integrity of the bacterial surface to resist host killing mechanisms and the release of inflammatory bacterial components (pathogen-associated molecular patterns [PAMPs]), (ii) modification of PAMPs to prevent activation of inflammatory pathways, and (iii) active modulation of the host response by escaping the phagosome and directly suppressing inflammatory pathways. We review the specific mechanisms by which Francisella achieves these goals to subvert host defenses and promote pathogenesis, highlighting as-yet-unanswered questions and important areas for future study.
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Silva MT, Pestana NTS. The in vivo extracellular life of facultative intracellular bacterial parasites: role in pathogenesis. Immunobiology 2012; 218:325-37. [PMID: 22795971 DOI: 10.1016/j.imbio.2012.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 03/23/2012] [Accepted: 05/16/2012] [Indexed: 01/14/2023]
Abstract
Classically labeled facultative intracellular pathogens are characterized by the ability to have an intracellular phase in the host, which is required for pathogenicity, while capable of extracellular growth in vitro. The ability of these bacteria to replicate in cell-free conditions is usually assessed by culture in artificial bacteriological media. However, the extracellular growth ability of these pathogens may also be expressed by a phase of extracellular infection in the natural setting of the host with pathologic consequences, an ability that adds to the pathogenic potential of the infectious agent. This infective capability to grow in the extracellular sites of the host represents an additional virulence attribute of those pathogens which may lead to severe outcomes. Here we discuss examples of infectious diseases where the in vivo infective extracellular life is well documented, including infections by Francisella tularensis, Yersinia pestis, Burkholderia pseudomallei, Burkholderia cenocepacia, Salmonella enterica serovar Typhimurium and Edwardsiella tarda. The occurrence of a phase of systemic dissemination with extracellular multiplication during progressive infections by facultative intracellular bacterial pathogens has been underappreciated, with most studies exclusively centered on the intracellular phase of the infections. The investigation of the occurrence of a dual lifestyle in the host among bacterial pathogens in general should be extended and likely will reveal more cases of infectious diseases with a dual infective intracellular/extracellular pattern.
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Affiliation(s)
- Manuel T Silva
- Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
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Zarrella TM, Singh A, Bitsaktsis C, Rahman T, Sahay B, Feustel PJ, Gosselin EJ, Sellati TJ, Hazlett KRO. Host-adaptation of Francisella tularensis alters the bacterium's surface-carbohydrates to hinder effectors of innate and adaptive immunity. PLoS One 2011; 6:e22335. [PMID: 21799828 PMCID: PMC3142145 DOI: 10.1371/journal.pone.0022335] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/27/2011] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The gram-negative bacterium Francisella tularensis survives in arthropods, fresh water amoeba, and mammals with both intracellular and extracellular phases and could reasonably be expected to express distinct phenotypes in these environments. The presence of a capsule on this bacterium has been controversial with some groups finding such a structure while other groups report that no capsule could be identified. Previously we reported in vitro culture conditions for this bacterium which, in contrast to typical methods, yielded a bacterial phenotype that mimics that of the bacterium's mammalian, extracellular phase. METHODS/FINDINGS SDS-PAGE and carbohydrate analysis of differentially-cultivated F. tularensis LVS revealed that bacteria displaying the host-adapted phenotype produce both longer polymers of LPS O-antigen (OAg) and additional HMW carbohydrates/glycoproteins that are reduced/absent in non-host-adapted bacteria. Analysis of wildtype and OAg-mutant bacteria indicated that the induced changes in surface carbohydrates involved both OAg and non-OAg species. To assess the impact of these HMW carbohydrates on the access of outer membrane constituents to antibody we used differentially-cultivated bacteria in vitro to immunoprecipitate antibodies directed against outer membrane moieties. We observed that the surface-carbohydrates induced during host-adaptation shield many outer membrane antigens from binding by antibody. Similar assays with normal mouse serum indicate that the induced HMW carbohydrates also impede complement deposition. Using an in vitro macrophage infection assay, we find that the bacterial HMW carbohydrate impedes TLR2-dependent, pro-inflammatory cytokine production by macrophages. Lastly we show that upon host-adaptation, the human-virulent strain, F. tularensis SchuS4 also induces capsule production with the effect of reducing macrophage-activation and accelerating tularemia pathogenesis in mice. CONCLUSION F. tularensis undergoes host-adaptation which includes production of multiple capsular materials. These capsules impede recognition of bacterial outer membrane constituents by antibody, complement, and Toll-Like Receptor 2. These changes in the host-pathogen interface have profound implications for pathogenesis and vaccine development.
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Affiliation(s)
- Tiffany M. Zarrella
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Anju Singh
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Constantine Bitsaktsis
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Tabassum Rahman
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Bikash Sahay
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Paul J. Feustel
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York, United States of America
| | - Edmund J. Gosselin
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Timothy J. Sellati
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Karsten R. O. Hazlett
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
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