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Stover EL, Little MB, Connolly KL, Li L, Nicholas RA, Sikora AE, Jerse AE, Hobbs MM, Duncan JA, Macintyre AN. Development and validation of multiplex assays for mouse and human IgG and IgA to Neisseria gonorrhoeae antigens. J Infect Dis 2024:jiae153. [PMID: 38526341 DOI: 10.1093/infdis/jiae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
There is an urgent need for vaccines against Neisseria gonorrhoeae (Ng), the causative agent of gonorrhea. Vaccination with an outer-membrane vesicle (OMV)-based Neisseria meningitidis (Nm) vaccine provides some protection from Ng; however, the mechanisms underlying this cross-protection are unknown. To address this need, we developed multiplexed bead-based assays for the relative quantification of human and mouse IgG and IgA against Ng antigens. The assays were evaluated for analyte independence, dilutional linearity, specificity, sensitivity, intra- and inter-assay variability, and robustness to sample storage conditions. The assay was then used to test samples from mice and humans immunized with an Nm-OMV vaccine.
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Affiliation(s)
- Erica L Stover
- Duke Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Marguerite B Little
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Kristie L Connolly
- Department of Microbiology and Immunology, Uniformed Services University, Maryland, USA
| | - Lixin Li
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Robert A Nicholas
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Ann E Jerse
- Department of Microbiology and Immunology, Uniformed Services University, Maryland, USA
| | - Marcia M Hobbs
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - J Alex Duncan
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Andrew N Macintyre
- Duke Human Vaccine Institute and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
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Martinez FG, Zielke RA, Fougeroux CE, Li L, Sander AF, Sikora AE. Development of a Tag/Catcher-mediated capsid virus-like particle vaccine presenting the conserved Neisseria gonorrhoeae SliC antigen that blocks human lysozyme. Infect Immun 2023; 91:e0024523. [PMID: 37916806 PMCID: PMC10715030 DOI: 10.1128/iai.00245-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Virus-like particles (VLPs) are promising nanotools for the development of subunit vaccines due to high immunogenicity and safety. Herein, we explored the versatile and effective Tag/Catcher-AP205 capsid VLP (cVLP) vaccine platform to address the urgent need for the development of an effective and safe vaccine against gonorrhea. The benefits of this clinically validated cVLP platform include its ability to facilitate unidirectional, high-density display of complex/full-length antigens through an effective split-protein Tag/Catcher conjugation system. To assess this modular approach for making cVLP vaccines, we used a conserved surface lipoprotein, SliC, that contributes to the Neisseria gonorrhoeae defense against human lysozyme, as a model antigen. This protein was genetically fused at the N- or C-terminus to the small peptide Tag enabling their conjugation to AP205 cVLP, displaying the complementary Catcher. We determined that SliC with the N-terminal SpyTag, N-SliC, retained lysozyme-blocking activity and could be displayed at high density on cVLPs without causing aggregation. In mice, the N-SliC-VLP vaccines, adjuvanted with AddaVax or CpG, induced significantly higher antibody titers compared to controls. In contrast, similar vaccine formulations containing monomeric SliC were non-immunogenic. Accordingly, sera from N-SliC-VLP-immunized mice also had significantly higher human complement-dependent serum bactericidal activity. Furthermore, the N-SliC-VLP vaccines administered subcutaneously with an intranasal boost elicited systemic and vaginal IgG and IgA, whereas subcutaneous delivery alone failed to induce vaginal IgA. The N-SliC-VLP with CpG (10 µg/dose) induced the most significant increase in total serum IgG and IgG3 titers, vaginal IgG and IgA, and bactericidal antibodies.
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Affiliation(s)
- Fabian G. Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | | | - Lixin Li
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Adam F. Sander
- AdaptVac Aps, Hørsholm, Denmark
- Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
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Sikora AE, Gomez C, Le Van A, Baarda BI, Darnell S, Martinez FG, Zielke RA, Bonventre JA, Jerse AE. A novel gonorrhea vaccine composed of MetQ lipoprotein formulated with CpG shortens experimental murine infection. Vaccine 2020; 38:8175-8184. [PMID: 33162204 DOI: 10.1016/j.vaccine.2020.10.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/15/2020] [Accepted: 10/23/2020] [Indexed: 11/18/2022]
Abstract
Bacterial surface lipoproteins are emerging as attractive vaccine candidates due to their biological importance and the feasibility of their large-scale production for vaccine manufacturing. The global prevalence of gonorrhea, resistance to antibiotics, and serious consequences to reproductive and neonatal health necessitate development of effective vaccines. Reverse vaccinology identified the surface-displayed L-methionine binding lipoprotein MetQ (NGO2139) and its homolog GNA1946 (NMB1946) as gonococcal and meningococcal vaccine candidates, respectively. Here, we assessed the suitability of MetQ for inclusion in a gonorrhea vaccine by examining MetQ conservation, its function inNeisseria gonorrhoeae (Ng) pathogenesis, and its ability to induce protective immune responses using a female murine model of lower genital tract infection. In-depth bioinformatics, phylogenetics and mapping the most prevalent Ng polymorphic amino acids to the GNA1946 crystal structure revealed remarkable MetQ conservation: ~97% Ng isolates worldwide possess a single MetQ variant. Mice immunized with rMetQ-CpG (n = 40), a vaccine containing a tag-free version of MetQ formulated with CpG, exhibited robust, antigen-specific antibody responses in serum and at the vaginal mucosae including IgA. Consistent with the activity of CpG as a Th1-stimulating adjuvant, the serum IgG1/IgG2a ratio of 0.38 suggested a Th1 bias. Combined data from two independent challenge experiments demonstrated that rMetQ-CpG immunized mice cleared infection faster than control animals (vehicle, p < 0.0001; CpG, p = 0.002) and had lower Ng burden (vehicle, p = 0.03; CpG, p < 0.0001). We conclude rMetQ-CpG induces a protective immune response that accelerates bacterial clearance from the murine lower genital tract and represents an attractive component of a gonorrhea subunit vaccine.
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Affiliation(s)
- Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97330, United States; Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States.
| | - Carolina Gomez
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, United States
| | - Adriana Le Van
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, United States
| | - Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97330, United States
| | - Stephen Darnell
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, United States
| | - Fabian G Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97330, United States
| | - Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97330, United States
| | - Josephine A Bonventre
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97330, United States
| | - Ann E Jerse
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, United States.
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Baarda BI, Zielke RA, Le Van A, Jerse AE, Sikora AE. Neisseria gonorrhoeae MlaA influences gonococcal virulence and membrane vesicle production. PLoS Pathog 2019; 15:e1007385. [PMID: 30845186 PMCID: PMC6424457 DOI: 10.1371/journal.ppat.1007385] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/19/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023] Open
Abstract
The six-component maintenance of lipid asymmetry (Mla) system is responsible for retrograde transport of phospholipids, ensuring the barrier function of the Gram-negative cell envelope. Located within the outer membrane, MlaA (VacJ) acts as a channel to shuttle phospholipids from the outer leaflet. We identified Neisseria gonorrhoeae MlaA (ngo2121) during high-throughput proteomic mining for potential therapeutic targets against this medically important human pathogen. Our follow-up phenotypic microarrays revealed that lack of MlaA results in a complex sensitivity phenome. Herein we focused on MlaA function in cell envelope biogenesis and pathogenesis. We demonstrate the existence of two MlaA classes among 21 bacterial species, characterized by the presence or lack of a lipoprotein signal peptide. Purified truncated N. gonorrhoeae MlaA elicited antibodies that cross-reacted with a panel of different Neisseria. Little is known about MlaA expression; we provide the first evidence that MlaA levels increase in stationary phase and under anaerobiosis but decrease during iron starvation. Lack of MlaA resulted in higher cell counts during conditions mimicking different host niches; however, it also significantly decreased colony size. Antimicrobial peptides such as polymyxin B exacerbated the size difference while human defensin was detrimental to mutant viability. Consistent with the proposed role of MlaA in vesicle biogenesis, the ΔmlaA mutant released 1.7-fold more membrane vesicles. Comparative proteomics of cell envelopes and native membrane vesicles derived from ΔmlaA and wild type bacteria revealed enrichment of TadA–which recodes proteins through mRNA editing–as well as increased levels of adhesins and virulence factors. MlaA-deficient gonococci significantly outcompeted (up to 16-fold) wild-type bacteria in the murine lower genital tract, suggesting the growth advantage or increased expression of virulence factors afforded by inactivation of mlaA is advantageous in vivo. Based on these results, we propose N. gonorrhoeae restricts MlaA levels to modulate cell envelope homeostasis and fine-tune virulence. The Gram-negative outer membrane is a formidable barrier, primarily because of its asymmetric composition. A layer of lipopolysaccharide is exposed to the external environment and phospholipids are on the internal face of the outer membrane. MlaA is part of a bacterial system that prevents phospholipid accumulation within the lipopolysaccharide layer. If MlaA is removed, membrane asymmetry is disrupted and bacteria become more vulnerable to certain antimicrobials. Neisseria gonorrhoeae causes millions of infections worldwide annually. A growing number are resistant to available antibiotics. Improving our understanding of gonococcal pathogenicity and basic biological processes is required to facilitate the discovery of new weapons against gonorrhea. We investigated the role of MlaA in N. gonorrhoeae and found that when MlaA was absent, bacteria were more sensitive to antibiotics and human defensins. However, the mutant bacteria produced more membrane vesicles–packages of proteins wrapped in membrane material. Mutant vesicles and cell envelopes were enriched in proteins that contribute to disease. These alterations significantly increased mutant fitness during experimental infection of the female mouse genital tract. Our results provide new insights into the processes N. gonorrhoeae uses to fine-tune its ability to stay fit in the hostile environment of the genital tract.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Adriana Le Van
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Ann E. Jerse
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
- * E-mail:
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Paraiso IL, Plagmann LS, Yang L, Zielke R, Gombart AF, Maier CS, Sikora AE, Blakemore PR, Stevens JF. Back cover: Reductive Metabolism of Xanthohumol and 8‐Prenylnaringenin by the Intestinal Bacterium
Eubacterium ramulus. Mol Nutr Food Res 2019. [DOI: 10.1002/mnfr.201970006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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El-Rami FE, Zielke RA, Wi T, Sikora AE, Unemo M. Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants. Mol Cell Proteomics 2019; 18:127-150. [PMID: 30352803 PMCID: PMC6317477 DOI: 10.1074/mcp.ra118.001125] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/23/2018] [Indexed: 12/27/2022] Open
Abstract
The sexually transmitted disease gonorrhea (causative agent: Neisseria gonorrhoeae) remains an urgent public health threat globally because of its reproductive health repercussions, high incidence, widespread antimicrobial resistance (AMR), and absence of a vaccine. To mine gonorrhea antigens and enhance our understanding of gonococcal AMR at the proteome level, we performed the first large-scale proteomic profiling of a diverse panel (n = 15) of gonococcal strains, including the 2016 World Health Organization (WHO) reference strains. These strains show all existing AMR profiles - established through phenotypic characterization and reference genome publication - and are intended for quality assurance in laboratory investigations. Herein, these isolates were subjected to subcellular fractionation and labeling with tandem mass tags coupled to mass spectrometry and multi-combinatorial bioinformatics. Our analyses detected 904 and 723 common proteins in cell envelope and cytoplasmic subproteomes, respectively. We identified nine novel gonorrhea vaccine candidates. Expression and conservation of new and previously selected antigens were investigated. In addition, established gonococcal AMR determinants were evaluated for the first time using quantitative proteomics. Six new proteins, WHO_F_00238, WHO_F_00635c, WHO_F_00745, WHO_F_01139, WHO_F_01144c, and WHO_F_01126, were differentially expressed in all strains, suggesting that they represent global proteomic AMR markers, indicate a predisposition toward developing or compensating gonococcal AMR, and/or act as new antimicrobial targets. Finally, phenotypic clustering based on the isolates' defined antibiograms and common differentially expressed proteins yielded seven matching clusters between established and proteome-derived AMR signatures. Together, our investigations provide a reference proteomics data bank for gonococcal vaccine and AMR research endeavors, which enables microbiological, clinical, or epidemiological projects and enhances the utility of the WHO reference strains.
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Affiliation(s)
- Fadi E El-Rami
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Ryszard A Zielke
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Teodora Wi
- §Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Aleksandra E Sikora
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon;; ¶Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon;.
| | - Magnus Unemo
- ‖World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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Baarda BI, Zielke RA, Jerse AE, Sikora AE. Lipid-Modified Azurin of Neisseria gonorrhoeae Is Not Surface Exposed and Does Not Interact With the Nitrite Reductase AniA. Front Microbiol 2018; 9:2915. [PMID: 30538694 PMCID: PMC6277709 DOI: 10.3389/fmicb.2018.02915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Lipid-modified cupredoxin azurin (Laz) is involved in electron transport in Neisseria and proposed to act as an electron donor to the surface-displayed nitrite reductase AniA. We identified Laz in Neisseria gonorrhoeae cell envelopes and naturally elaborated membrane vesicles in proteomic investigations focused on discovering new vaccine and therapeutic targets for this increasingly difficult to treat pathogen. Its surface exposure in N. meningitidis suggested Laz could be a vaccine candidate for N. gonorrhoeae. Here we characterized the localization, expression, and role of Laz within the gonococcal cell envelope and challenged the hypothesis that Laz and AniA interact. While we demonstrate that Laz indeed shows some good features of a vaccine antigen, such as stable expression, high conservation, and ability to elicit antibodies that cross-react with a diverse panel of Neisseria, it is not a surface-displayed lipoprotein in the gonococcus. This discovery eliminates Laz as a gonorrhea vaccine candidate, further highlighting the necessity of examining homologous protein localization between closely related species. Absence of Laz slightly altered cell envelope integrity but was not associated with growth defects in vitro, including during anoxia, implicating the presence of other electron pathways to AniA. To further dissect the implied AniA-Laz interaction, we utilized biolayer interferometry and optimized and executed chemical cross-linking coupled with immunoblotting to covalently link interacting protein partners in living gonococci. This method, applied for the first time in N. gonorrhoeae research to interrogate protein complexes, was validated by the appearance of the trimer form of AniA, as well as by increased formation of the β-barrel assembly machinery complex, in the presence of cross-linker. We conclude that Laz is not an electron donor to AniA based on their distinct subcellular localization, discordant expression during infection of the female mouse lower genital tract, and lack of interaction in vivo and in vitro.
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Affiliation(s)
- Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Ann E Jerse
- Department of Microbiology and Immunology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States.,Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
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Baarda BI, Zielke RA, Nicholas RA, Sikora AE. PubMLST for Antigen Allele Mining to Inform Development of Gonorrhea Protein-Based Vaccines. Front Microbiol 2018; 9:2971. [PMID: 30581422 PMCID: PMC6292995 DOI: 10.3389/fmicb.2018.02971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/19/2018] [Indexed: 02/02/2023] Open
Abstract
Neisseria gonorrhoeae (Ng) is a human-specific pathogen and the etiological agent of gonorrhea, a sexually transmitted infection with a significant global health burden. While often asymptomatic, untreated gonorrhea can lead to pelvic inflammatory disease, ectopic pregnancy, infertility, and increased transmission/acquisition of HIV. A protective gonorrhea vaccine may be the only way to control disease transmission in the future due to the inexorable development of antibiotic resistance. Subunit antigens are proven candidates for vaccine development due to their safety, cost-effectiveness, and rapid preparation. To inform protein-based gonorrhea vaccine design by including different antigen variants, herein we present bioinformatics mining of alleles and single nucleotide/amino acid polymorphisms using DNA/protein sequences of all Ng isolates deposited into the PubMLST database and MtrE and BamA as model antigens. We also present phylogenetic analyses that can be performed using sequence data to gain insights into the evolutionary relationships between the polymorphisms found among the population of isolates using a convenient tool: Molecular Evolutionary Genetics Analysis (MEGA) software. Finally, we perform antigen polymorphism mapping onto the MtrE and BamA structures. This methodology can be applied for rational vaccine design to increase vaccine coverage and cross-protection by heteroligand presentation achieved via inclusion of diverse antigen variants and is relevant to over 100 different species and genera deposited into the PubMLST family of databases.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Robert A. Nicholas
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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Baarda BI, Martinez FG, Sikora AE. Proteomics, Bioinformatics and Structure-Function Antigen Mining For Gonorrhea Vaccines. Front Immunol 2018; 9:2793. [PMID: 30564232 PMCID: PMC6288298 DOI: 10.3389/fimmu.2018.02793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the serious health consequences combined with the prevalence and the dire possibility of untreatable gonorrhea. Reverse vaccinology, which includes genome and proteome mining, has proven successful in the discovery of vaccine candidates against many pathogenic bacteria. Here, we describe proteomic applications including comprehensive, quantitative proteomic platforms and immunoproteomics coupled with broad-ranging bioinformatics that have been applied for antigen mining to develop gonorrhea vaccine(s). We further focus on outlining the vaccine candidate decision tree, describe the structure-function of novel proteome-derived antigens as well as ways to gain insights into their roles in the cell envelope, and underscore new lessons learned about the fascinating biology of Neisseria gonorrhoeae.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Fabian G. Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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Paraiso IL, Plagmann LS, Yang L, Zielke R, Gombart AF, Maier CS, Sikora AE, Blakemore PR, Stevens JF. Reductive Metabolism of Xanthohumol and 8-Prenylnaringenin by the Intestinal Bacterium Eubacterium ramulus. Mol Nutr Food Res 2018; 63:e1800923. [PMID: 30471194 DOI: 10.1002/mnfr.201800923] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/14/2018] [Indexed: 12/16/2022]
Abstract
SCOPE The intestinal microbiota transforms a wide range of available substrates, including polyphenols. Microbial catabolites of polyphenols can contribute in significant ways to the health-promoting properties of their parent polyphenols. This work aims to identify intestinal metabolites of xanthohumol (XN), a prenylated flavonoid found in hops (Humulus lupulus) and beer, as well as to identify pathways of metabolism of XN in the gut. METHODS AND RESULTS To investigate intestinal metabolism, XN and related prenylated flavonoids, isoxanthohumol (IX), and 8-prenylnaringenin (8PN) were added to growing cultures of intestinal bacteria, Eubacterium ramulus and E. limosum. Liquid chromatography coupled with mass spectrometry was used to identify metabolites of the flavonoids from the cultures. The metabolic capacity of E. limosum appears to be limited to O-demethylation. Evidence from the study indicates that E. ramulus hydrogenates XN to form α,β-dihydroxanthohumol (DXN) and metabolizes the potent phytoestrogen 8PN into the chalcones, O-desmethylxanthohumol (DMX) and O-desmethyl-α,β-dihydroxanthohumol (DDXN). CONCLUSION Microbial metabolism is likely to affect both activity and toxicity of XN and derivatives. This study along with others highlights that attention should be focused on metabolites, in particular, products of intestinal microbial metabolism.
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Affiliation(s)
- Ines L Paraiso
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.,Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
| | - Layhna S Plagmann
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA.,Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Liping Yang
- Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Ryszard Zielke
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA
| | - Adrian F Gombart
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA.,Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Claudia S Maier
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA.,Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.,Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Paul R Blakemore
- Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA.,Department of Chemistry, Oregon State University, Corvallis, OR, 97331, USA
| | - Jan F Stevens
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97331, USA.,Linus Pauling Institute, Oregon State University, Corvallis, OR, 97331, USA
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Lam KC, Vyshenska D, Hu J, Rodrigues RR, Nilsen A, Zielke RA, Brown NS, Aarnes EK, Sikora AE, Shulzhenko N, Lyng H, Morgun A. Transkingdom network reveals bacterial players associated with cervical cancer gene expression program. PeerJ 2018; 6:e5590. [PMID: 30294508 PMCID: PMC6170155 DOI: 10.7717/peerj.5590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 08/15/2018] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is the fourth most common cancer in women worldwide with human papillomavirus (HPV) being the main cause the disease. Chromosomal amplifications have been identified as a source of upregulation for cervical cancer driver genes but cannot fully explain increased expression of immune genes in invasive carcinoma. Insight into additional factors that may tip the balance from immune tolerance of HPV to the elimination of the virus may lead to better diagnosis markers. We investigated whether microbiota affect molecular pathways in cervical carcinogenesis by performing microbiome analysis via sequencing 16S rRNA in tumor biopsies from 121 patients. While we detected a large number of intra-tumor taxa (289 operational taxonomic units (OTUs)), we focused on the 38 most abundantly represented microbes. To search for microbes and host genes potentially involved in the interaction, we reconstructed a transkingdom network by integrating a previously discovered cervical cancer gene expression network with our bacterial co-abundance network and employed bipartite betweenness centrality. The top ranked microbes were represented by the families Bacillaceae, Halobacteriaceae, and Prevotellaceae. While we could not define the first two families to the species level, Prevotellaceae was assigned to Prevotella bivia. By co-culturing a cervical cancer cell line with P. bivia, we confirmed that three out of the ten top predicted genes in the transkingdom network (lysosomal associated membrane protein 3 (LAMP3), STAT1, TAP1), all regulators of immunological pathways, were upregulated by this microorganism. Therefore, we propose that intra-tumor microbiota may contribute to cervical carcinogenesis through the induction of immune response drivers, including the well-known cancer gene LAMP3.
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Affiliation(s)
- Khiem Chi Lam
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.,Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Dariia Vyshenska
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Jialu Hu
- College of Pharmacy, Oregon State University, Corvallis, OR, USA.,School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | | | - Anja Nilsen
- Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ryszard A Zielke
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | | | - Eva-Katrine Aarnes
- Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | | | - Natalia Shulzhenko
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Heidi Lyng
- Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
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13
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Gallegos DA, Saurí J, Cohen RD, Wan X, Videau P, Vallota-Eastman AO, Shaala LA, Youssef DTA, Williamson RT, Martin GE, Philmus B, Sikora AE, Ishmael JE, McPhail KL. Jizanpeptins, Cyanobacterial Protease Inhibitors from a Symploca sp. Cyanobacterium Collected in the Red Sea. J Nat Prod 2018; 81:1417-1425. [PMID: 29808677 PMCID: PMC7847313 DOI: 10.1021/acs.jnatprod.8b00117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Jizanpeptins A-E (1-5) are micropeptin depsipeptides isolated from a Red Sea specimen of a Symploca sp. cyanobacterium. The planar structures of the jizanpeptins were established using NMR spectroscopy and mass spectrometry and contain 3-amino-6-hydroxy-2-piperidone (Ahp) as one of eight residues in a typical micropeptin motif, as well as a side chain terminal glyceric acid sulfate moiety. The absolute configurations of the jizanpeptins were assigned using a combination of Marfey's methodology and chiral-phase HPLC analysis of hydrolysis products compared to commercial and synthesized standards. Jizanpeptins A-E showed specific inhibition of the serine protease trypsin (IC50 = 72 nM to 1 μM) compared to chymotrypsin (IC50 = 1.4 to >10 μM) in vitro and were not overtly cytotoxic to HeLa cervical or NCI-H460 lung cancer cell lines at micromolar concentrations.
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Affiliation(s)
- David A. Gallegos
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Josep Saurí
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Ryan D. Cohen
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuemei Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Patrick Videau
- Department of Biology, College of Arts and Sciences, Dakota State University, Madison, SD 57042
| | - Alec O. Vallota-Eastman
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Lamiaa A. Shaala
- Suez Canal University Hospital, Suez Canal University, Ismailia 41522, Egypt
| | - Diaa T. A. Youssef
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - R. Thomas Williamson
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Gary E. Martin
- Structure Elucidation Group, Process and Analytical Research and Development, Merck & Co., Inc.,126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Jane E. Ishmael
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331, United States
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14
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Sikora AE, Wierzbicki IH, Zielke RA, Ryner RF, Korotkov KV, Buchanan SK, Noinaj N. Structural and functional insights into the role of BamD and BamE within the β-barrel assembly machinery in Neisseria gonorrhoeae. J Biol Chem 2018; 293:1106-1119. [PMID: 29229778 PMCID: PMC5787791 DOI: 10.1074/jbc.ra117.000437] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/18/2017] [Indexed: 12/22/2022] Open
Abstract
The β-barrel assembly machinery (BAM) is a conserved multicomponent protein complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Given its role in the production of OMPs for survival and pathogenesis, BAM represents an attractive target for the development of therapeutic interventions, including drugs and vaccines against multidrug-resistant bacteria such as Neisseria gonorrhoeae The first structure of BamA, the central component of BAM, was from N. gonorrhoeae, the etiological agent of the sexually transmitted disease gonorrhea. To aid in pharmaceutical targeting of BAM, we expanded our studies to BamD and BamE within BAM of this clinically relevant human pathogen. We found that the presence of BamD, but not BamE, is essential for gonococcal viability. However, BamE, but not BamD, was cell-surface-displayed under native conditions; however, in the absence of BamE, BamD indeed becomes surface-exposed. Loss of BamE altered cell envelope composition, leading to slower growth and an increase in both antibiotic susceptibility and formation of membrane vesicles containing greater amounts of vaccine antigens. Both BamD and BamE are expressed in diverse gonococcal isolates, under host-relevant conditions, and throughout different phases of growth. The solved structures of Neisseria BamD and BamE share overall folds with Escherichia coli proteins but contain differences that may be important for function. Together, these studies highlight that, although BAM is conserved across Gram-negative bacteria, structural and functional differences do exist across species, which may be leveraged in the development of species-specific therapeutics in the effort to combat multidrug resistance.
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Affiliation(s)
- Aleksandra E Sikora
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330,
| | - Igor H Wierzbicki
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Ryszard A Zielke
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Rachael F Ryner
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536
| | - Susan K Buchanan
- NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907
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15
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Sikora AE, Tehan R, McPhail K. Utilization of Vibrio cholerae as a Model Organism to Screen Natural Product Libraries for Identification of New Antibiotics. Methods Mol Biol 2018; 1839:135-146. [PMID: 30047060 DOI: 10.1007/978-1-4939-8685-9_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The development of antibiotic-resistant bacteria requires increasing research efforts in drug discovery. Vibrio cholerae can be utilized as a model gram-negative enteric pathogen in high- and medium-throughput screening campaigns to identify antimicrobials with different modes of action. In this chapter, we describe methods for the optimal growth of V. cholerae in 384-well plates, preparation of suitable microtiter natural product sample libraries, as well as their screening using measurements of bacterial density and activity of type II secretion-dependent protease as readouts. Concomitant LC-MS/MS profiling and spectral data networking of assay sample libraries facilitate dereplication of putative known and/or nuisance compounds and efficient prioritization of samples containing putative new natural products for further investigation.
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Affiliation(s)
- Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
| | - Richard Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Kerry McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
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16
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Liu Y, Hammer LA, Liu W, Hobbs MM, Zielke RA, Sikora AE, Jerse AE, Egilmez NK, Russell MW. Experimental vaccine induces Th1-driven immune responses and resistance to Neisseria gonorrhoeae infection in a murine model. Mucosal Immunol 2017; 10:1594-1608. [PMID: 28272393 PMCID: PMC5591041 DOI: 10.1038/mi.2017.11] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/23/2017] [Indexed: 02/04/2023]
Abstract
Female mice were immunized intravaginally with gonococcal outer membrane vesicles (OMVs) plus microencapsulated interleukin-12 (IL-12), and challenged using an established model of genital infection with Neisseria gonorrhoeae. Whereas sham-immunized and control animals cleared the infection in 10-13 days, those immunized with OMV plus IL-12 cleared infection with homologous gonococcal strains in 6-9 days. Significant protection was also seen after challenge with antigenically distinct strains of N. gonorrhoeae, and protective anamnestic immunity persisted for at least 6 months after immunization. Serum and vaginal immunoglobulin G (IgG) and IgA antibodies were generated against antigens expressed by homologous and heterologous strains. Iliac lymph node CD4+ T cells secreted interferon-γ (IFNγ), but not IL-4, in response to immunization, and produced IL-17 in response to challenge regardless of immunization. Antigens recognized by immunized mouse serum included several shared between gonococcal strains, including two identified by immunoproteomics approaches as elongation factor-Tu (EF-Tu) and PotF3. Experiments with immunodeficient mice showed that protective immunity depended upon IFNγ and B cells, presumably to generate antibodies. The results demonstrated that immunity to gonococcal infection can be induced by immunization with a nonliving gonococcal antigen, and suggest that efforts to develop a human vaccine should focus on strategies to generate type 1 T helper cell (Th1)-driven immune responses in the genital tract.
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Affiliation(s)
- Yingru Liu
- TherapyX, Inc., Buffalo, NY, USA,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | | | - Wensheng Liu
- Department of Pediatrics, Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, NY, USA
| | - Marcia M. Hobbs
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Ann E. Jerse
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Nejat K. Egilmez
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, USA
| | - Michael W. Russell
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
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17
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Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University Hospital and Örebro University, S. Grevrosengatan 2, SE-701 85 Örebro, Sweden
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330, USA
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18
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Dugovich BS, Peel MJ, Palmer AL, Zielke RA, Sikora AE, Beechler BR, Jolles AE, Epps CW, Dolan BP. Detection of bacterial-reactive natural IgM antibodies in desert bighorn sheep populations. PLoS One 2017; 12:e0180415. [PMID: 28662203 PMCID: PMC5491220 DOI: 10.1371/journal.pone.0180415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 05/29/2017] [Indexed: 12/25/2022] Open
Abstract
Ecoimmunology is a burgeoning field of ecology which studies immune responses in wildlife by utilizing general immune assays such as the detection of natural antibody. Unlike adaptive antibodies, natural antibodies are important in innate immune responses and often recognized conserved epitopes present in pathogens. Here, we describe a procedure for measuring natural antibodies reactive to bacterial antigens that may be applicable to a variety of organisms. IgM from desert bighorn sheep plasma samples was tested for reactivity to outer membrane proteins from Vibrio coralliilyticus, a marine bacterium to which sheep would have not been exposed. Immunoblotting demonstrated bighorn sheep IgM could bind to a variety of bacterial cell envelope proteins while ELISA analysis allowed for rapid determination of natural antibody levels in hundreds of individual animals. Natural antibody levels were correlated with the ability of plasma to kill laboratory strains of E. coli bacteria. Finally, we demonstrate that natural antibody levels varied in two distinct populations of desert bighorn sheep. These data demonstrate a novel and specific measure of natural antibody function and show that this varies in ecologically relevant ways.
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Affiliation(s)
- Brian S. Dugovich
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Melanie J. Peel
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Amy L. Palmer
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Brianna R. Beechler
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Anna E. Jolles
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
| | - Clinton W. Epps
- Department of Fisheries and Wildlife, College of Agricultural Sciences, Oregon State University, Corvallis, Oregon, United States of America
| | - Brian P. Dolan
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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19
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Wierzbicki IH, Zielke RA, Korotkov KV, Sikora AE. Functional and structural studies on the Neisseria gonorrhoeae GmhA, the first enzyme in the glycero-manno-heptose biosynthesis pathways, demonstrate a critical role in lipooligosaccharide synthesis and gonococcal viability. Microbiologyopen 2017; 6. [PMID: 28063198 PMCID: PMC5387315 DOI: 10.1002/mbo3.432] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/14/2016] [Accepted: 11/17/2016] [Indexed: 12/04/2022] Open
Abstract
Sedoheptulose‐7‐phosphate isomerase, GmhA, is the first enzyme in the biosynthesis of nucleotide‐activated‐glycero‐manno‐heptoses and an attractive, yet underexploited, target for development of broad‐spectrum antibiotics. We demonstrated that GmhA homologs in Neisseria gonorrhoeae and N. meningitidis (hereafter called GmhAGC and GmhANM, respectively) were interchangeable proteins essential for lipooligosaccharide (LOS) synthesis, and their depletion had adverse effects on neisserial viability. In contrast, the Escherichia coli ortholog failed to complement GmhAGC depletion. Furthermore, we showed that GmhAGC is a cytoplasmic enzyme with induced expression at mid‐logarithmic phase, upon iron deprivation and anaerobiosis, and conserved in contemporary gonococcal clinical isolates including the 2016 WHO reference strains. The untagged GmhAGC crystallized as a tetramer in the closed conformation with four zinc ions in the active site, supporting that this is most likely the catalytically active conformation of the enzyme. Finally, site‐directed mutagenesis studies showed that the active site residues E65 and H183 were important for LOS synthesis but not for GmhAGC function in bacterial viability. Our studies bring insights into the importance and mechanism of action of GmhA and may ultimately facilitate targeting the enzyme with small molecule inhibitors.
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Affiliation(s)
- Igor H. Wierzbicki
- Department of Pharmaceutical SciencesCollege of PharmacyOregon State UniversityCorvallisORUSA
| | - Ryszard A. Zielke
- Department of Pharmaceutical SciencesCollege of PharmacyOregon State UniversityCorvallisORUSA
| | - Konstantin V. Korotkov
- Department of Molecular & Cellular BiochemistryCollege of MedicineUniversity of KentuckyLexingtonKYUSA
| | - Aleksandra E. Sikora
- Department of Pharmaceutical SciencesCollege of PharmacyOregon State UniversityCorvallisORUSA
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20
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Greer RL, Dong X, Moraes ACF, Zielke RA, Fernandes GR, Peremyslova E, Vasquez-Perez S, Schoenborn AA, Gomes EP, Pereira AC, Ferreira SRG, Yao M, Fuss IJ, Strober W, Sikora AE, Taylor GA, Gulati AS, Morgun A, Shulzhenko N. Akkermansia muciniphila mediates negative effects of IFNγ on glucose metabolism. Nat Commun 2016; 7:13329. [PMID: 27841267 PMCID: PMC5114536 DOI: 10.1038/ncomms13329] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/23/2016] [Indexed: 12/19/2022] Open
Abstract
Cross-talk between the gut microbiota and the host immune system regulates host metabolism, and its dysregulation can cause metabolic disease. Here, we show that the gut microbe Akkermansia muciniphila can mediate negative effects of IFNγ on glucose tolerance. In IFNγ-deficient mice, A. muciniphila is significantly increased and restoration of IFNγ levels reduces A. muciniphila abundance. We further show that IFNγ-knockout mice whose microbiota does not contain A. muciniphila do not show improvement in glucose tolerance and adding back A. muciniphila promoted enhanced glucose tolerance. We go on to identify Irgm1 as an IFNγ-regulated gene in the mouse ileum that controls gut A. muciniphila levels. A. muciniphila is also linked to IFNγ-regulated gene expression in the intestine and glucose parameters in humans, suggesting that this trialogue between IFNγ, A. muciniphila and glucose tolerance might be an evolutionally conserved mechanism regulating metabolic health in mice and humans. Mice deficient in the pro-inflammatory cytokine IFNγ have improved glucose tolerance. Here, the authors show that this effect depends on the gut microbe Akkermansia muciniphila, whose abundance increases in the absence IFNγ, and which is known to have beneficial effects on host metabolism.
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Affiliation(s)
- Renee L Greer
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
| | - Xiaoxi Dong
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Ana Carolina F Moraes
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr Arnaldo, 715, São Paulo, SP 01246-904, Brazil
| | - Ryszard A Zielke
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Gabriel R Fernandes
- Oswaldo Cruz Foundation, René Rachou Research Center, Av. Augusto de Lima, 1715, Belo Horizonte, MG 30190-002, Brazil
| | - Ekaterina Peremyslova
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Stephany Vasquez-Perez
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
| | - Alexi A Schoenborn
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, 260 MacNider Building, CB# 7220, Chapel Hill, North Carolina 27599, USA
| | - Everton P Gomes
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, Av. Dr Eneas de Carvalho Aguiar, 44, São Paulo, SP 05403-000, Brazil
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, Av. Dr Eneas de Carvalho Aguiar, 44, São Paulo, SP 05403-000, Brazil
| | - Sandra R G Ferreira
- Department of Epidemiology, School of Public Health, University of São Paulo, Av. Dr Arnaldo, 715, São Paulo, SP 01246-904, Brazil
| | - Michael Yao
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Ivan J Fuss
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Warren Strober
- Mucosal Immunity Section, Laboratory of Immune Defenses, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA
| | - Aleksandra E Sikora
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Gregory A Taylor
- Geriatric Research, Education and Clinical Center, VA Medical Center, Departments of Medicine, Molecular Genetics and Microbiology and Immunology, Division of Geriatrics and Center for the Study of Aging and Human Development, Duke Box 3003, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Ajay S Gulati
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hill, 260 MacNider Building, CB# 7220, Chapel Hill, North Carolina 27599, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, 1601 SW Jefferson Way, Corvallis, Oregon 97331, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, 105 Dryden Hall, 450 SW 30th Street, Corvallis, Oregon 97331, USA
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21
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Unemo M, Golparian D, Sánchez-Busó L, Grad Y, Jacobsson S, Ohnishi M, Lahra MM, Limnios A, Sikora AE, Wi T, Harris SR. The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization. J Antimicrob Chemother 2016; 71:3096-3108. [PMID: 27432602 PMCID: PMC5079299 DOI: 10.1093/jac/dkw288] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/02/2016] [Accepted: 06/11/2016] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Gonorrhoea and MDR Neisseria gonorrhoeae remain public health concerns globally. Enhanced, quality-assured, gonococcal antimicrobial resistance (AMR) surveillance is essential worldwide. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) was relaunched in 2009. We describe the phenotypic, genetic and reference genome characteristics of the 2016 WHO gonococcal reference strains intended for quality assurance in the WHO global GASP, other GASPs, diagnostics and research worldwide. METHODS The 2016 WHO reference strains (n = 14) constitute the eight 2008 WHO reference strains and six novel strains. The novel strains represent low-level to high-level cephalosporin resistance, high-level azithromycin resistance and a porA mutant. All strains were comprehensively characterized for antibiogram (n = 23), serovar, prolyliminopeptidase, plasmid types, molecular AMR determinants, N. gonorrhoeae multiantigen sequence typing STs and MLST STs. Complete reference genomes were produced using single-molecule PacBio sequencing. RESULTS The reference strains represented all available phenotypes, susceptible and resistant, to antimicrobials previously and currently used or considered for future use in gonorrhoea treatment. All corresponding resistance genotypes and molecular epidemiological types were described. Fully characterized, annotated and finished references genomes (n = 14) were presented. CONCLUSIONS The 2016 WHO gonococcal reference strains are intended for internal and external quality assurance and quality control in laboratory investigations, particularly in the WHO global GASP and other GASPs, but also in phenotypic (e.g. culture, species determination) and molecular diagnostics, molecular AMR detection, molecular epidemiology and as fully characterized, annotated and finished reference genomes in WGS analysis, transcriptomics, proteomics and other molecular technologies and data analysis.
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Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Leonor Sánchez-Busó
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK
| | - Yonatan Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Diseases, Department of Microbiology, South Eastern Area Laboratory Services, The Prince of Wales Hospital, Randwick, Sydney, Australia
| | - Athena Limnios
- WHO Collaborating Centre for Sexually Transmitted Diseases, Department of Microbiology, South Eastern Area Laboratory Services, The Prince of Wales Hospital, Randwick, Sydney, Australia
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Teodora Wi
- Department of Reproductive Health and Research, World Health Organization, Geneva, Switzerland
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridgeshire, UK
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Zielke RA, Wierzbicki IH, Baarda BI, Gafken PR, Soge OO, Holmes KK, Jerse AE, Unemo M, Sikora AE. Proteomics-driven Antigen Discovery for Development of Vaccines Against Gonorrhea. Mol Cell Proteomics 2016; 15:2338-55. [PMID: 27141096 PMCID: PMC4937508 DOI: 10.1074/mcp.m116.058800] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/25/2016] [Indexed: 12/18/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the dire possibility of untreatable gonococcal infections. Reverse vaccinology, which includes genome and proteome mining, has proven very successful in the discovery of vaccine candidates against many pathogenic bacteria. However, progress with this approach for a gonorrhea vaccine remains in its infancy. Accordingly, we applied a comprehensive proteomic platform-isobaric tagging for absolute quantification coupled with two-dimensional liquid chromatography and mass spectrometry-to identify potential gonococcal vaccine antigens. Our previous analyses focused on cell envelopes and naturally released membrane vesicles derived from four different Neisseria gonorrhoeae strains. Here, we extended these studies to identify cell envelope proteins of N. gonorrhoeae that are ubiquitously expressed and specifically induced by physiologically relevant environmental stimuli: oxygen availability, iron deprivation, and the presence of human serum. Together, these studies enabled the identification of numerous potential gonorrhea vaccine targets. Initial characterization of five novel vaccine candidate antigens that were ubiquitously expressed under these different growth conditions demonstrated that homologs of BamA (NGO1801), LptD (NGO1715), and TamA (NGO1956), and two uncharacterized proteins, NGO2054 and NGO2139, were surface exposed, secreted via naturally released membrane vesicles, and elicited bactericidal antibodies that cross-reacted with a panel of temporally and geographically diverse isolates. In addition, analysis of polymorphisms at the nucleotide and amino acid levels showed that these vaccine candidates are highly conserved among N. gonorrhoeae strains. Finally, depletion of BamA caused a loss of N. gonorrhoeae viability, suggesting it may be an essential target. Together, our data strongly support the use of proteomics-driven discovery of potential vaccine targets as a sound approach for identifying promising gonococcal antigens.
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Affiliation(s)
- Ryszard A Zielke
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Igor H Wierzbicki
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Benjamin I Baarda
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
| | - Philip R Gafken
- §Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olusegun O Soge
- ¶Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington
| | - King K Holmes
- ¶Neisseria Reference Laboratory, Department of Global Health, University of Washington, Seattle, Washington; ‖Departments of Medicine and Global Health, University of Washington, Seattle, Washington
| | - Ann E Jerse
- **Department of Microbiology and Immunology, F. Edward Herbert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Magnus Unemo
- ‡‡WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Aleksandra E Sikora
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon;
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Bonventre JA, Zielke RA, Korotkov KV, Sikora AE. Targeting an Essential GTPase Obg for the Development of Broad-Spectrum Antibiotics. PLoS One 2016; 11:e0148222. [PMID: 26848972 PMCID: PMC4743925 DOI: 10.1371/journal.pone.0148222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/14/2016] [Indexed: 11/19/2022] Open
Abstract
A promising new drug target for the development of novel broad-spectrum antibiotics is the highly conserved small GTPase Obg (YhbZ, CgtA), a protein essential for the survival of all bacteria including Neisseria gonorrhoeae (GC). GC is the agent of gonorrhea, a prevalent sexually transmitted disease resulting in serious consequences on reproductive and neonatal health. A preventive anti-gonorrhea vaccine does not exist, and options for effective antibiotic treatments are increasingly limited. To address the dire need for alternative antimicrobial strategies, we have designed and optimized a 384-well GTPase assay to identify inhibitors of Obg using as a model Obg protein from GC, ObgGC. The assay was validated with a pilot screen of 40,000 compounds and achieved an average Z’ value of 0.58 ± 0.02, which suggests a robust assay amenable to high-throughput screening. We developed secondary assessments for identified lead compounds that utilize the interaction between ObgGC and fluorescent guanine nucleotide analogs, mant-GTP and mant-GDP, and an ObgGC variant with multiple alterations in the G-domains that prevent nucleotide binding. To evaluate the broad-spectrum potential of ObgGC inhibitors, Obg proteins of Klebsiella pneumoniae and methicillin-resistant Staphylococcus aureus were assessed using the colorimetric and fluorescence-based activity assays. These approaches can be useful in identifying broad-spectrum Obg inhibitors and advancing the therapeutic battle against multidrug resistant bacteria.
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Affiliation(s)
- Josephine A. Bonventre
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
| | - Konstantin V. Korotkov
- Department of Molecular and Cellular Biochemistry, and Center for Structural Biology, University of Kentucky, Lexington, KY, 40536, United States of America
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, 97330, United States of America
- * E-mail:
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Baarda BI, Sikora AE. Proteomics of Neisseria gonorrhoeae: the treasure hunt for countermeasures against an old disease. Front Microbiol 2015; 6:1190. [PMID: 26579097 PMCID: PMC4620152 DOI: 10.3389/fmicb.2015.01190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/12/2015] [Indexed: 01/26/2023] Open
Abstract
Neisseria gonorrhoeae is an exquisitely adapted, strictly human pathogen and the causative agent of the sexually transmitted infection gonorrhea. This ancient human disease remains a serious problem, occurring at high incidence globally and having a major impact on reproductive and neonatal health. N. gonorrhoeae is rapidly evolving into a superbug and no effective vaccine exists to prevent gonococcal infections. Untreated or inadequately treated gonorrhea can lead to severe sequelae, including pelvic inflammatory disease and infertility in women, epididymitis in men, and sight-threatening conjunctivitis in infants born to infected mothers. Therefore, there is an immediate need for accelerated research toward the identification of molecular targets for development of drugs with new mechanisms of action and preventive vaccine(s). Global proteomic approaches are ideally suited to guide these studies. Recent quantitative proteomics (SILAC, iTRAQ, and ICAT) have illuminated the pathways utilized by N. gonorrhoeae to adapt to different lifestyles and micro-ecological niches within the host, while comparative 2D SDS-PAGE analysis has been used to elucidate spectinomycin resistance mechanisms. Further, high-throughput examinations of cell envelopes and naturally released membrane vesicles have unveiled the ubiquitous and differentially expressed proteins between temporally and geographically diverse N. gonorrhoeae isolates. This review will focus on these different approaches, emphasizing the role of proteomics in the search for vaccine candidates. Although our knowledge of N. gonorrhoeae has been expanded, still far less is known about this bacterium than the closely related N. meningitidis, where genomics- and proteomics-driven studies have led to the successful development of vaccines.
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Affiliation(s)
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
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Zielke RA, Wierzbicki IH, Baarda BI, Sikora AE. The Neisseria gonorrhoeae Obg protein is an essential ribosome-associated GTPase and a potential drug target. BMC Microbiol 2015; 15:129. [PMID: 26122105 PMCID: PMC4487204 DOI: 10.1186/s12866-015-0453-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Neisseria gonorrhoeae (GC) is a Gram-negative pathogen that most commonly infects mucosal surfaces, causing sexually transmitted urethritis in men and endocervicitis in women. Serious complications associated with these infections are frequent and include pelvic inflammatory disease, ectopic pregnancy, and infertility. The incidence of gonorrhea cases remains high globally while antibiotic treatment options, the sole counter measures against gonorrhea, are declining due to the remarkable ability of GC to acquire resistance. Evaluating of potential drug targets is essential to provide opportunities for developing antimicrobials with new mechanisms of action. We propose the GC Obg protein, belonging to the Obg/CgtA GTPase subfamily, as a potential target for the development of therapeutic interventions against gonorrhea, and in this study perform its initial functional and biochemical characterization. Results We report that NGO1990 encodes Obg protein, which is an essential factor for GC viability, associates predominantly with the large 50S ribosomal subunit, and is stably expressed under conditions relevant to infection of the human host. The anti-Obg antisera cross-reacts with a panel of contemporary GC clinical isolates, demonstrating the ubiquitous nature of Obg. The cellular levels of Obg reach a maximum in the early logarithmic phase and remain constant throughout bacterial growth. The in vitro binding and hydrolysis of the fluorescent guanine nucleotide analogs mant-GTP and mant-GDP by recombinant wild type and T192AT193A mutated variants of Obg are also assessed. Conclusions Characterization of the GC Obg at the molecular and functional levels presented herein may facilitate the future targeting of this protein with small molecule inhibitors and the evaluation of identified lead compounds for bactericidal activity against GC and other drug-resistant bacteria. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0453-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Igor H Wierzbicki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Benjamin I Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, 433 Weniger Hall, 103 SW Memorial Pl, Corvallis, OR, 97330, USA.
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Abstract
Neisseria gonorrhoeae (GC) is a strict human pathogen and the agent of the sexually transmitted disease gonorrhea. Gonococcal infections have been successfully treated with antibiotics; however, GC has repeatedly developed resistance to each new antibiotic used. Currently, third-generation cephalosporins are recommended, and resistance to these antimicrobials is emerging worldwide. Additionally, no vaccine is available to prevent GC infections. With the dire possibility of untreatable gonorrhea, there is a critical need to identify new therapeutic targets. Cell envelope and membrane vesicle proteins are key factors in pathogenesis, antibiotic resistance, biofilm formation, and general bacterial fitness. Here we describe methods for isolation and purification of GC cell envelopes and spontaneously released membrane vesicles. The isolated proteome fractions can be used in multiple downstream applications, including gel-based and gel-free quantitative proteomics, studies focused on subcellular localization of proteins, transmission electron microscopy, or strain characterization. Presented methods may be easily adapted to other bacterial species.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
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Zielke RA, Gafken PR, Sikora AE. Quantitative proteomic analysis of the cell envelopes and native membrane vesicles derived from gram-negative bacteria. ACTA ACUST UNITED AC 2014; 34:1F.3.1-16. [PMID: 25082006 DOI: 10.1002/9780471729259.mc01f03s34] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proteins localized to the cell envelope and naturally released membrane vesicles (MVs) play diverse functions in physiology and pathogenesis of Gram-negative bacteria. Study of these proteome fractions is essential for better understanding the basic physiological processes, development of vaccines, and identification of potential drug targets. This unit presents gel-free quantitative proteomic methods for comprehensive proteomic profiling of the cell envelopes and MVs. The procedure starts with the precipitation of the isolated proteome fractions to remove any potential compounds that may interfere with downstream experimental steps. Subsequently, the proteins are reduced, alkylated, and subjected to trypsin digestion. The trypsinized peptides are labeled using isobaric tagging for relative and absolute quantification (iTRAQ), and analyzed samples are pooled and subjected to rigorous prefractionations by strong cation exchange (SCX) and reversed-phase (RP) liquid chromatography (LC). Finally, the tandem mass spectrometry (MS/MS) fragmentation enables peptides identification and quantification.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon
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Zielke RA, Simmons RS, Park BR, Nonogaki M, Emerson S, Sikora AE. The type II secretion pathway in Vibrio cholerae is characterized by growth phase-dependent expression of exoprotein genes and is positively regulated by σE. Infect Immun 2014; 82:2788-801. [PMID: 24733097 PMCID: PMC4097608 DOI: 10.1128/iai.01292-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 04/10/2014] [Indexed: 01/08/2023] Open
Abstract
Vibrio cholerae, an etiological agent of cholera, circulates between aquatic reservoirs and the human gastrointestinal tract. The type II secretion (T2S) system plays a pivotal role in both stages of the lifestyle by exporting multiple proteins, including cholera toxin. Here, we studied the kinetics of expression of genes encoding the T2S system and its cargo proteins. We have found that under laboratory growth conditions, the T2S complex was continuously expressed throughout V. cholerae growth, whereas there was growth phase-dependent transcriptional activity of genes encoding different cargo proteins. Moreover, exposure of V. cholerae to different environmental cues encountered by the bacterium in its life cycle induced transcriptional expression of T2S. Subsequent screening of a V. cholerae genomic library suggested that σ(E) stress response, phosphate metabolism, and the second messenger 3',5'-cyclic diguanylic acid (c-di-GMP) are involved in regulating transcriptional expression of T2S. Focusing on σ(E), we discovered that the upstream region of the T2S operon possesses both the consensus σ(E) and σ(70) signatures, and deletion of the σ(E) binding sequence prevented transcriptional activation of T2S by RpoE. Ectopic overexpression of σ(E) stimulated transcription of T2S in wild-type and isogenic ΔrpoE strains of V. cholerae, providing additional support for the idea that the T2S complex belongs to the σ(E) regulon. Together, our results suggest that the T2S pathway is characterized by the growth phase-dependent expression of genes encoding cargo proteins and requires a multifactorial regulatory network to ensure appropriate kinetics of the secretory traffic and the fitness of V. cholerae in different ecological niches.
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Affiliation(s)
- Ryszard A Zielke
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Ryan S Simmons
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - Bo R Park
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Mariko Nonogaki
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Sarah Emerson
- Department of Statistics, Oregon State University, Corvallis, Oregon, USA
| | - Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
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29
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Zielke RA, Wierzbicki IH, Weber JV, Gafken PR, Sikora AE. Quantitative proteomics of the Neisseria gonorrhoeae cell envelope and membrane vesicles for the discovery of potential therapeutic targets. Mol Cell Proteomics 2014; 13:1299-317. [PMID: 24607996 PMCID: PMC4014286 DOI: 10.1074/mcp.m113.029538] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 02/28/2014] [Indexed: 01/29/2023] Open
Abstract
Neisseria gonorrhoeae (GC) is a human-specific pathogen, and the agent of a sexually transmitted disease, gonorrhea. There is a critical need for new approaches to study and treat GC infections because of the growing threat of multidrug-resistant isolates and the lack of a vaccine. Despite the implied role of the GC cell envelope and membrane vesicles in colonization and infection of human tissues and cell lines, comprehensive studies have not been undertaken to elucidate their constituents. Accordingly, in pursuit of novel molecular therapeutic targets, we have applied isobaric tagging for absolute quantification coupled with liquid chromatography and mass spectrometry for proteome quantitative analyses. Mining the proteome of cell envelopes and native membrane vesicles revealed 533 and 168 common proteins, respectively, in analyzed GC strains FA1090, F62, MS11, and 1291. A total of 22 differentially abundant proteins were discovered including previously unknown proteins. Among those proteins that displayed similar abundance in four GC strains, 34 were found in both cell envelopes and membrane vesicles fractions. Focusing on one of them, a homolog of an outer membrane protein LptD, we demonstrated that its depletion caused loss of GC viability. In addition, we selected for initial characterization six predicted outer membrane proteins with unknown function, which were identified as ubiquitous in the cell envelopes derived from examined GC isolates. These studies entitled a construction of deletion mutants and analyses of their resistance to different chemical probes. Loss of NGO1985, in particular, resulted in dramatically decreased GC viability upon treatment with detergents, polymyxin B, and chloramphenicol, suggesting that this protein functions in the maintenance of the cell envelope permeability barrier. Together, these findings underscore the concept that the cell envelope and membrane vesicles contain crucial, yet under-explored determinants of GC physiology, which may represent promising targets for designing new therapeutic interventions.
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Affiliation(s)
- Ryszard A. Zielke
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Igor H. Wierzbicki
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Jacob V. Weber
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
| | - Philip R. Gafken
- §Proteomics Facility, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024
| | - Aleksandra E. Sikora
- From the ‡Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97331
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Tran N, Zielke RA, Vining OB, Azevedo MD, Armstrong DJ, Banowetz GM, McPhail KL, Sikora AE. Development of a quantitative assay amenable for high-throughput screening to target the type II secretion system for new treatments against plant-pathogenic bacteria. ACTA ACUST UNITED AC 2013; 18:921-9. [PMID: 23580665 DOI: 10.1177/1087057113485426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Plant-pathogenic bacteria are the causative agents of diseases in important agricultural crops and ornamental plants. The severe economic burden of these diseases requires seeking new approaches for their control, particularly because phytopathogenic bacteria are often resistant to available treatments. The type II secretion (T2S) system is a key virulence factor used by major groups of phytopathogenic bacteria. The T2S machinery transports many hydrolytic enzymes responsible for degradation of the plant cell wall, thus enabling successful colonization and dissemination of the bacteria in the plant host. The genetic inactivation of the T2S system leads to loss of virulence, which strongly suggests that targeting the T2S could enable new treatments against plant-pathogenic bacteria. Accordingly, we have designed and optimized an assay to identify small-molecule inhibitors of the T2S system. This assay uses a double parametric output: measurement of bacterial growth and the enzymatic activity of cellulase, which is secreted via the T2S pathway in our model organism Dickeya dadantii. The assay was evaluated by screening natural extracts, culture filtrates isolated from rhizosphere bacteria, and a collection of pharmaceutically active compounds in LOPAC(1280). The calculated Z' values of 0.63, 0.63, and 0.58, respectively, strongly suggest that the assay is applicable for a high-throughput screening platform.
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Affiliation(s)
- Nini Tran
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
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31
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Affiliation(s)
- Aleksandra E Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America.
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32
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Johnson TL, Sikora AE, Zielke RA, Sandkvist M. Fluorescence microscopy and proteomics to investigate subcellular localization, assembly, and function of the type II secretion system. Methods Mol Biol 2013; 966:157-172. [PMID: 23299734 DOI: 10.1007/978-1-62703-245-2_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Investigation of secretion systems is often critical to understanding the virulence mechanisms of bacterial pathogens. With estimates as high as 30-40% of proteins secreted or localized to the cell envelope, information about the subcellular localization and organization of secretion complexes and identification and functional characterization of their substrates are key steps toward understanding these intricate systems. Here we describe a protocol using fluorescent live-cell imaging of fusion proteins that can provide a powerful tool to potentially examine the localization, assembly, and role of each component in the secretion complex. In addition, we describe protocols for the identification of secreted substrates using 1D SDS-PAGE coupled with nano-liquid chromatography (LC) and tandem mass spectrometry (MS/MS), and isobaric tagging for absolute quantification (iTRAQ) coupled with two-dimensional LC and MS/MS. Both experimental approaches are applicable to any similar study of membrane transport systems.
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Affiliation(s)
- Tanya L Johnson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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Sikorska J, Parker-Nance S, Davies-Coleman MT, Vining OB, Sikora AE, McPhail KL. Antimicrobial rubrolides from a South African species of Synoicum tunicate. J Nat Prod 2012; 75:1824-7. [PMID: 23030848 PMCID: PMC3549467 DOI: 10.1021/np300580z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The CH₂Cl₂-MeOH extract of a South African tunicate described as the new Synoicum globosum Parker-Nance sp. nov. (Ascidiacea, Aplousobranchia) was subjected to ¹H NMR-guided fractionation. This resulted in the identification of new 3″-bromorubrolide F (1), 3'-bromorubrolide E (2), 3'-bromorubrolide F (3), and 3',3″-dibromorubrolide E (4) and reisolation of known rubrolides E (5) and F (6), based on NMR spectroscopic and mass spectrometric data. Biological testing of both new and known members of this reported antimicrobial family of halogenated, aryl-substituted furanones indicated moderate antibacterial properties for 3'-bromorubrolide E (2), 3',3″-dibromorubrolide E (4), and rubrolide F (6) against methicillin-resistant Staphylococcus aureus (MRSA) and S. epidermidis.
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Affiliation(s)
- Justyna Sikorska
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
| | - Shirley Parker-Nance
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
| | - Michael T. Davies-Coleman
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
| | - Oliver B. Vining
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, 203 Pharmacy Building, Oregon State University, Corvallis, Oregon 97331, United States
- Corresponding Author Tel: 541 737 5808. Fax: 541 737 3999.
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Sikora AE, Zielke RA, Lawrence DA, Andrews PC, Sandkvist M. Proteomic analysis of the Vibrio cholerae type II secretome reveals new proteins, including three related serine proteases. J Biol Chem 2011; 286:16555-66. [PMID: 21385872 DOI: 10.1074/jbc.m110.211078] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The type II secretion (T2S) system is responsible for extracellular secretion of a broad range of proteins, including toxins and degradative enzymes that play important roles in the pathogenesis and life cycle of many gram-negative bacteria. In Vibrio cholerae, the etiological agent of cholera, the T2S machinery transports cholera toxin, which induces profuse watery diarrhea, a hallmark of this life-threatening disease. Besides cholera toxin, four other proteins have been shown to be transported by the T2S machinery, including hemagglutinin protease, chitinase, GbpA, and lipase. Here, for the first time, we have applied proteomic approaches, including isotope tagging for relative and absolute quantification coupled with multidimensional liquid chromatography and tandem mass spectrometry, to perform an unbiased and comprehensive analysis of proteins secreted by the T2S apparatus of the V. cholerae El Tor strain N16961 under standard laboratory growth conditions. This analysis identified 16 new putative T2S substrates, including sialidase, several proteins participating in chitin utilization, two aminopeptidases, TagA-related protein, cytolysin, RbmC, three hypothetical proteins encoded by VCA0583, VCA0738, and VC2298, and three serine proteases VesA, VesB, and VesC. Focusing on the initial characterization of VesA, VesB, and VesC, we have confirmed enzymatic activities and T2S-dependent transport for each of these proteases. In addition, analysis of single, double, and triple protease knock-out strains indicated that VesA is the primary protease responsible for processing the A subunit of cholera toxin during in vitro growth of the V. cholerae strain N16961.
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Affiliation(s)
- Aleksandra E Sikora
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA
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35
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Abstract
The type II secretion (T2S) system of Vibrio cholerae is a multiprotein complex that spans the cell envelope and secretes proteins important for pathogenesis as well as survival in different environments. Here we report that, in addition to the loss of extracellular secretion, removal or inhibition of expression of the T2S genes, epsC-N, results in growth defects and a broad range of alterations in the outer membrane that interfere with its barrier function. Specifically, the sensitivity to membrane-perturbing agents such as bile salts and the antimicrobial peptide polymyxin B is increased, and periplasmic constituents leak out into the culture medium. As a consequence, the sigma(E) stress response is induced. Furthermore, due to the defects caused by inactivation of the T2S system, the Deltaeps deletion mutant of V. cholerae strain N16961 is incapable of surviving the passage through the infant mouse gastrointestinal tract. The growth defect and leaky outer membrane phenotypes are suppressed when the culture medium is supplemented with 5% glucose or sucrose, although the eps mutants remain sensitive to membrane-damaging agents. This suggests that the sugars do not restore the integrity of the outer membrane in the eps mutant strains per se but may provide osmoprotective functions.
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Affiliation(s)
- Aleksandra E Sikora
- University of Michigan Medical School, Department of Microbiology and Immunology, 1150 West Medical Center Drive, 6741 Medical Science Building II, Ann Arbor, MI 48109-0620, USA
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36
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Abstract
It was previously reported that unlike the other obg/cgtA GTPases, the Vibrio harveyi cgtAV is not essential. Here we show that cgtAV was not disrupted in these studies and is, in fact, essential for viability. Depletion of CgtAV did not result in cell elongation. CgtAV is associated with the large ribosomal particle. In light of our results, we predict that the V. harveyi CgtAV protein plays a similar essential role to that seen for Obg/CgtA proteins in other bacteria.
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Affiliation(s)
- A E Sikora
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, USA
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37
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Sikora AE, Zielke R, Wegrzyn A, Wegrzyn G. DNA replication defect in the Escherichia coli cgtA(ts) mutant arising from reduced DnaA levels. Arch Microbiol 2006; 185:340-7. [PMID: 16518617 DOI: 10.1007/s00203-006-0099-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 01/27/2006] [Accepted: 02/13/2006] [Indexed: 11/29/2022]
Abstract
In Escherichia coli and other bacteria, the ribosome-associated CgtA GTP-binding protein plays a critical role in many basic cellular processes, including the control of DNA replication and/or segregation. However, the mechanism of this control is largely unknown. Here we report that ectopic expression of the dnaA gene partially restored both early growth in liquid medium and DNA synthesis defects of the cgtA(ts) mutant. Amounts of DnaA protein in the cgtA(ts) mutant incubated at elevated (42 degrees C) temperature were significantly lower relative to wild-type bacteria. Both level of dnaA mRNA and transcriptional activity of the dnaA promoter-lacZ fusion were decreased in the CgtA-deficient cells. The effects of ectopic expression of dnaA were specific as analogous expression of another gene coding for a replication regulator, seqA, had no significant changes in growth and DNA synthesis in the cgtA mutant. Thus, it appears that the DNA replication defect in this mutant is a consequence of reduced DnaA levels.
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Affiliation(s)
- Aleksandra E Sikora
- Department of Molecular Biology, University of Gdansk, Kładki 24, 80-822, Gdansk, Poland
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38
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Abstract
Bacteria encode a number of relatively poorly characterized GTPases, including the essential, ribosome-associated Obg/CgtA proteins. In contrast to Ras-like proteins, it appears that the Obg/CgtA proteins bind guanine nucleotides with modest affinity and hydrolyze GTP relatively slowly. We show here that the Vibrio harveyi CgtA(V) exchanges guanine nucleotides rapidly and has a modest affinity for nucleotides, suggesting that these features are a universal property of the Obg/CgtA family. Interestingly, CgtA(V) possesses a significantly more rapid GTP hydrolysis rate than is typical of other family members, perhaps reflecting the diversity and specificity of bacterial ecological niches.
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Affiliation(s)
- A E Sikora
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109, USA
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