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Hoang-Phou S, Pal S, Slepenkin A, Abisoye-Ogunniyun A, Zhang Y, Gilmore SF, Shelby M, Bourguet F, Mohagheghi M, Noy A, Rasley A, de la Maza LM, Coleman MA. Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597210. [PMID: 38895407 PMCID: PMC11185655 DOI: 10.1101/2024.06.04.597210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and de-centralized production of recombinant protein vaccine antigens. Here, we use CFPS to produce the putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for use as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were primed with CT584 adjuvanted with CpG-1826 intranasally (i.n.) or CpG-1826 + Montanide ISA 720 intramuscularly (i.m.), followed four-weeks later by an i.m. boost before respiratory challenge with 104 inclusion forming units (IFU) of Chlamydia muridarum. Immunization with CT584 generated robust antibody responses but weak cell mediated immunity and failed to protect against i.n. challenge as demonstrated by body weight loss, increased lungs' weights and the presence of high numbers of IFUs in the lungs. While CT584 alone may not be the ideal vaccine candidate, the speed and flexibility with which CFPS can be used to produce other potential chlamydial antigens makes it an attractive technique for antigen production.
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Affiliation(s)
- Steven Hoang-Phou
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Sukumar Pal
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Anatoli Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Abisola Abisoye-Ogunniyun
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Yuliang Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Sean F Gilmore
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Megan Shelby
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Feliza Bourguet
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Mariam Mohagheghi
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Amy Rasley
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Luis M de la Maza
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Matthew A Coleman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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2
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Lamanna MM, Maurelli AT. What Is Motion? Recent Advances in the Study of Molecular Movement Patterns of the Peptidoglycan Synthesis Machines. J Bacteriol 2022; 204:e0059821. [PMID: 34928180 PMCID: PMC9017339 DOI: 10.1128/jb.00598-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
How proteins move through space and time is a fundamental question in biology. While great strides have been made toward a mechanistic understanding of protein movement, many questions remain. We discuss the biological implications of motion in the context of the peptidoglycan (PG) synthesis machines. We reviewed systems in several bacteria, including Escherichia coli, Bacillus subtilis, and Streptococcus pneumoniae, and present a comprehensive view of our current knowledge regarding movement dynamics. Discrepancies are also addressed because "one size does not fit all". For bacteria to divide, new PG is synthesized and incorporated into the growing cell wall by complex multiprotein nanomachines consisting of PG synthases (transglycosylases [TG] and/or transpeptidases [TP]) as well as a variety of regulators and cytoskeletal factors. Advances in imaging capabilities and labeling methods have revealed that these machines are not static but rather circumferentially transit the cell via directed motion perpendicular to the long axis of model rod-shaped bacteria such as E. coli and B. subtilis. The enzymatic activity of the TG:TPs drives motion in some species while motion is mediated by FtsZ treadmilling in others. In addition, both directed and diffusive motion of the PG synthases have been observed using single-particle tracking technology. Here, we examined the biological role of diffusion regarding transit. Lastly, findings regarding the monofunctional transglycosylases (RodA and FtsW) as well as the Class A PG synthases are discussed. This minireview serves to showcase recent advances, broach mechanistic unknowns, and stimulate future areas of study.
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Affiliation(s)
- Melissa Mae Lamanna
- Department of Environmental & Global Health and Emerging Pathogens Institute, University of Floridagrid.15276.37, Gainesville, Florida, USA
| | - Anthony T. Maurelli
- Department of Environmental & Global Health and Emerging Pathogens Institute, University of Floridagrid.15276.37, Gainesville, Florida, USA
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3
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Huang Y, Wurihan W, Lu B, Zou Y, Wang Y, Weldon K, Fondell JD, Lai Z, Wu X, Fan H. Robust Heat Shock Response in Chlamydia Lacking a Typical Heat Shock Sigma Factor. Front Microbiol 2022; 12:812448. [PMID: 35046926 PMCID: PMC8762339 DOI: 10.3389/fmicb.2021.812448] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
Cells reprogram their transcriptome in response to stress, such as heat shock. In free-living bacteria, the transcriptomic reprogramming is mediated by increased DNA-binding activity of heat shock sigma factors and activation of genes normally repressed by heat-induced transcription factors. In this study, we performed transcriptomic analyses to investigate heat shock response in the obligate intracellular bacterium Chlamydia trachomatis, whose genome encodes only three sigma factors and a single heat-induced transcription factor. Nearly one-third of C. trachomatis genes showed statistically significant (≥1.5-fold) expression changes 30 min after shifting from 37 to 45°C. Notably, chromosomal genes encoding chaperones, energy metabolism enzymes, type III secretion proteins, as well as most plasmid-encoded genes, were differentially upregulated. In contrast, genes with functions in protein synthesis were disproportionately downregulated. These findings suggest that facilitating protein folding, increasing energy production, manipulating host activities, upregulating plasmid-encoded gene expression, and decreasing general protein synthesis helps facilitate C. trachomatis survival under stress. In addition to relieving negative regulation by the heat-inducible transcriptional repressor HrcA, heat shock upregulated the chlamydial primary sigma factor σ66 and an alternative sigma factor σ28. Interestingly, we show for the first time that heat shock downregulates the other alternative sigma factor σ54 in a bacterium. Downregulation of σ54 was accompanied by increased expression of the σ54 RNA polymerase activator AtoC, thus suggesting a unique regulatory mechanism for reestablishing normal expression of select σ54 target genes. Taken together, our findings reveal that C. trachomatis utilizes multiple novel survival strategies to cope with environmental stress and even to replicate. Future strategies that can specifically target and disrupt Chlamydia’s heat shock response will likely be of therapeutic value.
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Affiliation(s)
- Yehong Huang
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Bin Lu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China.,Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Yuxuan Wang
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Korri Weldon
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Joseph D Fondell
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
| | - Zhao Lai
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX, United States.,Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Xiang Wu
- Department of Parasitology, Xiangya School of Basic Medicine, Central South University, Changsha, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, United States
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4
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Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee T, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI. Wikidata as a knowledge graph for the life sciences. eLife 2020; 9:e52614. [PMID: 32180547 PMCID: PMC7077981 DOI: 10.7554/elife.52614] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/28/2020] [Indexed: 12/22/2022] Open
Abstract
Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We also demonstrate several use cases for Wikidata, including the crowdsourced curation of biomedical ontologies, phenotype-based diagnosis of disease, and drug repurposing.
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Affiliation(s)
| | - Gregory Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sebastian Burgstaller-Muehlbacher
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of ViennaViennaAustria
| | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of MedicineSt. LouisUnited States
| | - Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | | | - Toby S Hudson
- School of Chemistry, The University of SydneySydneyAustralia
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of WashingtonSeattleUnited States
| | - Sarah M Keating
- European Bioinformatics Institute (EMBL-EBI)HinxtonUnited Kingdom
| | - Magnus Manske
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Michael Mayers
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Daniel Mietchen
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Elvira Mitraka
- University of Maryland School of MedicineBaltimoreUnited States
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Timothy Putman
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Anders Riutta
- Institute of Data Science and Biotechnology, Gladstone InstitutesSan FranciscoUnited States
| | - Nuria Queralt-Rosinach
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Lynn M Schriml
- University of Maryland School of MedicineBaltimoreUnited States
| | - Thomas Shafee
- Department of Animal Plant and Soil Sciences, La Trobe UniversityMelbourneAustralia
| | - Denise Slenter
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | | | | | - Ginger Tsueng
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Roger Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Sabah Ul-Hasan
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht UniversityMaastrichtNetherlands
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
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Pillonel T, Tagini F, Bertelli C, Greub G. ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. Nucleic Acids Res 2020; 48:D526-D534. [PMID: 31665454 PMCID: PMC7145651 DOI: 10.1093/nar/gkz924] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/12/2023] Open
Abstract
ChlamDB is a comparative genomics database containing 277 genomes covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using accessions numbers of the most widely used databases including COG, KEGG ortholog, KEGG pathway, KEGG module, Pfam and InterPro. Gene annotations from multiple databases including UniProt (curated and automated protein annotations), KEGG (annotation of pathways), COG (orthology), TCDB (transporters), STRING (protein-protein interactions) and InterPro (domains and signatures) can be accessed in a comprehensive overview page. Candidate effectors of the Type III secretion system (T3SS) were identified using four in silico methods. The identification of orthologs among all PVC genomes allows users to perform large-scale comparative analyses and to identify orthologs of any protein in all genomes integrated in the database. Phylogenetic relationships of PVC proteins and their closest homologs in RefSeq, comparison of transmembrane domains and Pfam domains, conservation of gene neighborhood and taxonomic profiles can be visualized using dynamically generated graphs, available for download. As a central resource for researchers working on chlamydia, chlamydia-related bacteria, verrucomicrobia and planctomyces, ChlamDB facilitates the access to comprehensive annotations, integrates multiple tools for comparative genomic analyses and is freely available at https://chlamdb.ch/. Database URL: https://chlamdb.ch/.
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Affiliation(s)
- Trestan Pillonel
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Florian Tagini
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland
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