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Pöhl S, Giacomelli G, Meyer FM, Kleeberg V, Cohen EJ, Biboy J, Rosum J, Glatter T, Vollmer W, van Teeseling MCF, Heider J, Bramkamp M, Thanbichler M. An outer membrane porin-lipoprotein complex modulates elongasome movement to establish cell curvature in Rhodospirillum rubrum. Nat Commun 2024; 15:7616. [PMID: 39223154 PMCID: PMC11369160 DOI: 10.1038/s41467-024-51790-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Curved cell shapes are widespread among bacteria and important for cellular motility, virulence and fitness. However, the underlying morphogenetic mechanisms are still incompletely understood. Here, we identify an outer-membrane protein complex that promotes cell curvature in the photosynthetic species Rhodospirillum rubrum. We show that the R. rubrum porins Por39 and Por41 form a helical ribbon-like structure at the outer curve of the cell that recruits the peptidoglycan-binding lipoprotein PapS, with PapS inactivation, porin delocalization or disruption of the porin-PapS interface resulting in cell straightening. We further demonstrate that porin-PapS assemblies act as molecular cages that entrap the cell elongation machinery, thus biasing cell growth towards the outer curve. These findings reveal a mechanistically distinct morphogenetic module mediating bacterial cell shape. Moreover, they uncover an unprecedented role of outer-membrane protein patterning in the spatial control of intracellular processes, adding an important facet to the repertoire of regulatory mechanisms in bacterial cell biology.
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Affiliation(s)
- Sebastian Pöhl
- Department of Biology, University of Marburg, Marburg, Germany
| | | | - Fabian M Meyer
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Volker Kleeberg
- Institut für Biologie II, University of Freiburg, Freiburg, Germany
- Pädagogische Forschungsstelle Kassel, Kassel, Germany
| | - Eli J Cohen
- Department of Life Sciences, Imperial College London, London, UK
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Julia Rosum
- Department of Biology, University of Marburg, Marburg, Germany
| | - Timo Glatter
- Mass Spectrometry and Proteomics Facility, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Muriel C F van Teeseling
- Department of Biology, University of Marburg, Marburg, Germany
- Institute of Microbiology, Friedrich-Schiller-Universität, Jena, Germany
| | - Johann Heider
- Department of Biology, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Marc Bramkamp
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
- Max Planck Fellow Group Bacterial Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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2
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Pöhl S, Osorio-Valeriano M, Cserti E, Harberding J, Hernandez-Tamayo R, Biboy J, Sobetzko P, Vollmer W, Graumann PL, Thanbichler M. A dynamic bactofilin cytoskeleton cooperates with an M23 endopeptidase to control bacterial morphogenesis. eLife 2024; 12:RP86577. [PMID: 38294932 PMCID: PMC10945521 DOI: 10.7554/elife.86577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Bactofilins have emerged as a widespread family of cytoskeletal proteins with important roles in bacterial morphogenesis, but their precise mode of action is still incompletely understood. In this study, we identify the bactofilin cytoskeleton as a key regulator of cell growth in the stalked budding alphaproteobacterium Hyphomonas neptunium. We show that, in this species, bactofilin polymers localize dynamically to the stalk base and the bud neck, with their absence leading to unconstrained growth of the stalk and bud compartments, indicating a central role in the spatial regulation of cell wall biosynthesis. Database searches reveal that bactofilin genes are often clustered with genes for cell wall hydrolases of the M23 peptidase family, suggesting a functional connection between these two types of proteins. In support of this notion, we find that the H. neptunium M23 peptidase homolog LmdC interacts directly with bactofilin in vitro and is required for proper cell shape in vivo. Complementary studies in the spiral-shaped alphaproteobacterium Rhodospirillum rubrum again reveal a close association of its bactofilin and LmdC homologs, which co-localize at the inner curve of the cell, modulating the degree of cell curvature. Collectively, these findings demonstrate that bactofilins and M23 peptidases form a conserved functional module that promotes local changes in the mode of cell wall biosynthesis, thereby driving cell shape determination in morphologically complex bacteria.
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Affiliation(s)
- Sebastian Pöhl
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Manuel Osorio-Valeriano
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Emöke Cserti
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Jannik Harberding
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
| | - Rogelio Hernandez-Tamayo
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle UniversityNewcastle upon TyneUnited Kingdom
- Institute for Molecular Bioscience, The University of QueenslandBrisbaneAustralia
| | - Peter L Graumann
- Department of Chemistry, University of MarburgMarburgGermany
- Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Martin Thanbichler
- Department of Biology, University of Marburg, Marburg, GermanyMarburgGermany
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
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3
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Lee J, Cox JV, Ouellette SP. The Unique N-Terminal Domain of Chlamydial Bactofilin Mediates Its Membrane Localization and Ring-Forming Properties. J Bacteriol 2023; 205:e0009223. [PMID: 37191556 PMCID: PMC10294636 DOI: 10.1128/jb.00092-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/01/2023] [Indexed: 05/17/2023] Open
Abstract
Chlamydia trachomatis is an obligate intracellular bacterial pathogen. In evolving to the intracellular niche, Chlamydia has reduced its genome size compared to other bacteria and, as a consequence, has a number of unique features. For example, Chlamydia engages the actin-like protein MreB, rather than the tubulin-like protein FtsZ, to direct peptidoglycan (PG) synthesis exclusively at the septum of cells undergoing polarized cell division. Interestingly, Chlamydia possesses another cytoskeletal element-a bactofilin ortholog, BacA. Recently, we reported BacA is a cell size-determining protein that forms dynamic membrane-associated ring structures in Chlamydia that have not been observed in other bacteria with bactofilins. Chlamydial BacA possesses a unique N-terminal domain, and we hypothesized this domain imparts the membrane-binding and ring-forming properties of BacA. We show that different truncations of the N terminus result in distinct phenotypes: removal of the first 50 amino acids (ΔN50) results in large ring structures at the membrane whereas removal of the first 81 amino acids (ΔN81) results in an inability to form filaments and rings and a loss of membrane association. Overexpression of the ΔN50 isoform altered cell size, similar to loss of BacA, suggesting that the dynamic properties of BacA are essential for the regulation of cell size. We further show that the region from amino acid 51 to 81 imparts membrane association as appending it to green fluorescent protein (GFP) resulted in the relocalization of GFP from the cytosol to the membrane. Overall, our findings suggest two important functions for the unique N-terminal domain of BacA and help explain its role as a cell size determinant. IMPORTANCE Bacteria use a variety of filament-forming cytoskeletal proteins to regulate and control various aspects of their physiology. For example, the tubulin-like FtsZ recruits division proteins to the septum whereas the actin-like MreB recruits peptidoglycan (PG) synthases to generate the cell wall in rod-shaped bacteria. Recently, a third class of cytoskeletal protein has been identified in bacteria-bactofilins. These proteins have been primarily linked to spatially localized PG synthesis. Interestingly, Chlamydia, an obligate intracellular bacterium, does not have PG in its cell wall and yet possesses a bactofilin ortholog. In this study, we characterize a unique N-terminal domain of chlamydial bactofilin and show that this domain controls two important functions that affect cell size: its ring-forming and membrane-associating properties.
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Affiliation(s)
- Junghoon Lee
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - John V. Cox
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Richter P, Melzer B, Müller FD. Interacting bactofilins impact cell shape of the MreB-less multicellular Rhodomicrobium vannielii. PLoS Genet 2023; 19:e1010788. [PMID: 37256900 DOI: 10.1371/journal.pgen.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/16/2023] [Indexed: 06/02/2023] Open
Abstract
Most non-spherical bacteria rely on the actin-like MreB cytoskeleton to control synthesis of a cell-shaping and primarily rod-like cell wall. Diverging from simple rod shape generally requires accessory cytoskeletal elements, which locally interfere with the MreB-guided cell wall synthesis. Conserved and widespread representatives of this accessory cytoskeleton are bactofilins that polymerize into static, non-polar bundles of filaments. Intriguingly, many species of the Actinobacteria and Rhizobiales manage to grow rod-like without MreB by tip extension, yet some of them still possess bactofilin genes, whose function in cell morphogenesis is unknown. An intricate representative of these tip-growing bacteria is Rhodomicrobium vannielii; a member of the hitherto genetically not tractable and poorly studied Hyphomicrobiaceae within the MreB-less Rhizobiales order. R. vannielii displays complex asymmetric cell shapes and differentiation patterns including filamentous hyphae to produce offspring and to build dendritic multicellular arrays. Here, we introduce techniques to genetically access R. vannielii, and we elucidate the role of bactofilins in its sophisticated morphogenesis. By targeted mutagenesis and fluorescence microscopy, protein interaction studies and peptidoglycan incorporation analysis we show that the R. vannielii bactofilins are associated with the hyphal growth zones and that one of them is essential to form proper hyphae. Another paralog is suggested to represent a novel hybrid and co-polymerizing bactofilin. Notably, we present R. vannielii as a powerful new model to understand prokaryotic cell development and control of multipolar cell growth in the absence of the conserved cytoskeletal element, MreB.
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Affiliation(s)
- Pia Richter
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Faculty of Biology, University of Marburg, Marburg, Germany
| | - Brigitte Melzer
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Max Rubner-Institute, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
| | - Frank D Müller
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
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Cutler KJ, Stringer C, Lo TW, Rappez L, Stroustrup N, Brook Peterson S, Wiggins PA, Mougous JD. Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation. Nat Methods 2022; 19:1438-1448. [PMID: 36253643 PMCID: PMC9636021 DOI: 10.1038/s41592-022-01639-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 09/06/2022] [Indexed: 12/26/2022]
Abstract
Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors. We show that Omnipose achieves unprecedented segmentation performance on mixed bacterial cultures, antibiotic-treated cells and cells of elongated or branched morphology. Furthermore, the benefits of Omnipose extend to non-bacterial subjects, varied imaging modalities and three-dimensional objects. Finally, we demonstrate the utility of Omnipose in the characterization of extreme morphological phenotypes that arise during interbacterial antagonism. Our results distinguish Omnipose as a powerful tool for characterizing diverse and arbitrarily shaped cell types from imaging data.
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Affiliation(s)
- Kevin J Cutler
- Department of Physics, University of Washington, Seattle, WA, USA
| | | | - Teresa W Lo
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Luca Rappez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - S Brook Peterson
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Paul A Wiggins
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Joseph D Mougous
- Department of Microbiology, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Sichel SR, Bratton BP, Salama NR. Distinct regions of H. pylori's bactofilin CcmA regulate protein-protein interactions to control helical cell shape. eLife 2022; 11:e80111. [PMID: 36073778 PMCID: PMC9507126 DOI: 10.7554/elife.80111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/07/2022] [Indexed: 11/26/2022] Open
Abstract
The helical shape of Helicobacter pylori cells promotes robust stomach colonization; however, how the helical shape of H. pylori cells is determined is unresolved. Previous work identified helical-cell-shape-promoting protein complexes containing a peptidoglycan-hydrolase (Csd1), a peptidoglycan precursor synthesis enzyme (MurF), a non-enzymatic homolog of Csd1 (Csd2), non-enzymatic transmembrane proteins (Csd5 and Csd7), and a bactofilin (CcmA). Bactofilins are highly conserved, spontaneously polymerizing cytoskeletal bacterial proteins. We sought to understand CcmA's function in generating the helical shape of H. pylori cells. Using CcmA deletion analysis, in vitro polymerization, and in vivo co-immunoprecipitation experiments, we identified that the bactofilin domain and N-terminal region of CcmA are required for helical cell shape and the bactofilin domain of CcmA is sufficient for polymerization and interactions with Csd5 and Csd7. We also found that CcmA's N-terminal region inhibits interaction with Csd7. Deleting the N-terminal region of CcmA increases CcmA-Csd7 interactions and destabilizes the peptidoglycan-hydrolase Csd1. Using super-resolution microscopy, we found that Csd5 recruits CcmA to the cell envelope and promotes CcmA enrichment at the major helical axis. Thus, CcmA helps organize cell-shape-determining proteins and peptidoglycan synthesis machinery to coordinate cell wall modification and synthesis, promoting the curvature required to build a helical cell.
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Affiliation(s)
- Sophie R Sichel
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleUnited States
- Molecular Medicine and Mechanisms of Disease Graduate Program, University of WashingtonSeattleUnited States
| | - Benjamin P Bratton
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
- Vanderbilt Institute for Infection, Immunology and InflammationNashvilleUnited States
| | - Nina R Salama
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleUnited States
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7
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Holtrup S, Greger M, Mayer B, Specht M, Waidner B. Insights Into the Helical Shape Complex of Helicobacter pylori. Front Microbiol 2022; 13:929194. [PMID: 36090072 PMCID: PMC9448923 DOI: 10.3389/fmicb.2022.929194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
One important factor that promotes the colonization of the upper digestive system of the human pathogen Helicobacter pylori is its helical cell shape. The bacteria cell shape is predominantly defined by its peptidoglycan cell wall. In rod-shaped species, PG synthesis is mediated by two dynamic molecular machines that facilitate growth along the perpendicular axis and the septum, called the elongasome and the divisome, respectively. Furthermore, many bacteria evolved additional mechanisms to locally change PG synthesis patterns to generate diverse cell shapes. Recent work characterizing cell shape mutants of Helicobacter pylori revealed a novel mechanism for the generation of a twisted helix from a rod, including PG-modifying enzymes as well as additional proteins such as the bactofilin homolog CcmA or the membrane proteins Csd5 and Csd7. In this study, we investigate the localization and dynamics of CcmA and Csd7 using live-cell imaging. We also address the question of how these change in the presence or absence of the putative interaction partners.
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Affiliation(s)
- Sven Holtrup
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Biochemistry and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Maximilian Greger
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Biochemistry and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Benjamin Mayer
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Biochemistry and Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Mara Specht
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Barbara Waidner
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
- Department of Biochemistry and Chemistry, Philipps University of Marburg, Marburg, Germany
- *Correspondence: Barbara Waidner,
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Ladant D. A Bacterial Two-Hybrid System for In Vivo Assays of Protein-Protein Interactions and Drug Discovery. Methods Mol Biol 2022; 2548:145-167. [PMID: 36151497 DOI: 10.1007/978-1-0716-2581-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The bacterial adenylate cyclase-based two-hybrid (BACTH) system is a robust and simple genetic assay used to monitor protein-protein interactions in vivo. This system is based on functional complementation between two fragments from the catalytic domain of Bordetella pertussis adenylate cyclase (AC) to reconstitute a cyclic AMP (cAMP)-signaling cascade in Escherichia coli. Interactions between two chimeric proteins result in the synthesis of cAMP, which activates the transcription of various catabolite operons, leading to selectable phenotypes. One advantageous feature of this signaling cascade is that the physical association between the two interacting hybrid proteins is spatially separated from the transcriptional activation readout. Consequently, the BACTH system can detect protein-protein interactions occurring at various subcellular localizations. The system has been used to characterize interactions between soluble or membrane proteins of prokaryotic, eukaryotic, or viral origin. The BACTH assay can be used to uncover the region(s), domain(s), or amino acid residue(s) of a protein involved in an interaction with a specific partner. The BACTH system can also be adapted for the high-throughput screening of small molecules able to interfere with protein-protein interactions.
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Affiliation(s)
- Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, Paris Cedex 15, France.
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9
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Bioengineering of Bordetella pertussis Adenylate Cyclase Toxin for Vaccine Development and Other Biotechnological Purposes. Toxins (Basel) 2021; 13:toxins13020083. [PMID: 33499260 PMCID: PMC7911819 DOI: 10.3390/toxins13020083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/15/2022] Open
Abstract
The adenylate cyclase toxin, CyaA, is one of the key virulent factors produced by Bordetella pertussis, the causative agent of whooping cough. This toxin primarily targets innate immunity to facilitate bacterial colonization of the respiratory tract. CyaA exhibits several remarkable characteristics that have been exploited for various applications in vaccinology and other biotechnological purposes. CyaA has been engineered as a potent vaccine vehicle to deliver antigens into antigen-presenting cells, while the adenylate cyclase catalytic domain has been used to design a robust genetic assay for monitoring protein-protein interactions in bacteria. These two biotechnological applications are briefly summarized in this chapter.
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10
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Abstract
Work identifying how stalk morphogenesis in a species of Alphaproteobacteria is controlled unveils an interesting mechanism that other bacteria may utilize to generate the variety of bacterial cell morphologies found across the bacterial domain.
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Affiliation(s)
- Sophie R Sichel
- Fred Hutchinson Cancer Research Center, Division of Human Biology, Seattle, WA 98109, USA; Molecular Medicine and Mechanisms of Disease Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Nina R Salama
- Fred Hutchinson Cancer Research Center, Division of Human Biology, Seattle, WA 98109, USA.
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