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Zhai Y, Tong S, Chen L, Zhang Y, Amin FR, Khalid H, Liu F, Duan Y, Chen W, Chen G, Li D. The enhancement of energy supply in syngas-fermenting microorganisms. ENVIRONMENTAL RESEARCH 2024; 252:118813. [PMID: 38574985 DOI: 10.1016/j.envres.2024.118813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
After the second industrial revolution, social productivity developed rapidly, and the use of fossil fuels such as coal, oil, and natural gas increased greatly in industrial production. The burning of these fossil fuels releases large amounts of greenhouse gases such as CO2, which has caused greenhouse effects and global warming. This has endangered the planet's ecological balance and brought many species, including animals and plants, to the brink of extinction. Thus, it is crucial to address this problem urgently. One potential solution is the use of syngas fermentation with microbial cell factories. This process can produce chemicals beneficial to humans, such as ethanol as a fuel while consuming large quantities of harmful gases, CO and CO2. However, syngas-fermenting microorganisms often face a metabolic energy deficit, resulting in slow cell growth, metabolic disorders, and low product yields. This problem limits the large-scale industrial application of engineered microorganisms. Therefore, it is imperative to address the energy barriers of these microorganisms. This paper provides an overview of the current research progress in addressing energy barriers in bacteria, including the efficient capture of external energy and the regulation of internal energy metabolic flow. Capturing external energy involves summarizing studies on overexpressing natural photosystems and constructing semiartificial photosynthesis systems using photocatalysts. The regulation of internal energy metabolic flows involves two parts: regulating enzymes and metabolic pathways. Finally, the article discusses current challenges and future perspectives, with a focus on achieving both sustainability and profitability in an economical and energy-efficient manner. These advancements can provide a necessary force for the large-scale industrial application of syngas fermentation microbial cell factories.
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Affiliation(s)
- Yida Zhai
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Sheng Tong
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Limei Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Yuan Zhang
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Farrukh Raza Amin
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Habiba Khalid
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China; Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Wuxi Chen
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Demao Li
- Tianjin Key Laboratory for Industrial Biological System and Bioprocessing Engineering, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, PR China.
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2
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Greaves GE, Allison L, Machado P, Morfill C, Fleck RA, Porter AE, Phillips CC. Infrared nanoimaging of neuronal ultrastructure and nanoparticle interaction with cells. NANOSCALE 2024; 16:6190-6198. [PMID: 38445876 PMCID: PMC10956966 DOI: 10.1039/d3nr04948e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
Here we introduce scattering-type scanning near-field optical microscopy (s-SNOM) as a novel tool for nanoscale chemical-imaging of sub-cellular organelles, nanomaterials and of the interactions between them. Our setup uses a tuneable mid-infrared laser and a sharp scanning probe to image at a resolution substantially surpassing the diffraction limit. The laser can be tuned to excite vibrational modes of functional groups in biomolecules, (e.g. amide moieties), in a way that enables direct chemical mapping without the need for labelling. We, for the first time, chemically image neuronal ultrastructure, identify neuronal organelles and sub-organelle structures as small as 10 nm and validate our findings using transmission electron microscopy (TEM). We produce chemical and morphological maps of neurons treated with gold nanospheres and characterize nanoparticle size and intracellular location, and their interaction with the plasma membrane. Our results show that the label-free nature of s-SNOM means it has a 'true' chemical resolution of up to 20 nm which can be further improved. We argue that it offers significant potential in nanomedicine for nanoscale chemical imaging of cell ultrastructure and the subcellular distribution of nanomaterials within tissues.
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Affiliation(s)
- George E Greaves
- Experimental Solid State Group, Department of Physics, Imperial College London, SW7 2BW, UK.
| | - Leanne Allison
- Centre for Ultrastructural Imaging, Kings College London, SE1 1UL, UK
| | - Pedro Machado
- Centre for Ultrastructural Imaging, Kings College London, SE1 1UL, UK
| | - Corinne Morfill
- Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ, UK
| | - Roland A Fleck
- Centre for Ultrastructural Imaging, Kings College London, SE1 1UL, UK
- Randall Centre for Cell and Molecular Biophysics, Kings College London, SE1 1YR, UK
| | - Alexandra E Porter
- Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ, UK
| | - Chris C Phillips
- Experimental Solid State Group, Department of Physics, Imperial College London, SW7 2BW, UK.
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3
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Worrall LJ, Majewski DD, Strynadka NCJ. Structural Insights into Type III Secretion Systems of the Bacterial Flagellum and Injectisome. Annu Rev Microbiol 2023; 77:669-698. [PMID: 37713458 DOI: 10.1146/annurev-micro-032521-025503] [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: 09/17/2023]
Abstract
Two of the most fascinating bacterial nanomachines-the broadly disseminated rotary flagellum at the heart of cellular motility and the eukaryotic cell-puncturing injectisome essential to specific pathogenic species-utilize at their core a conserved export machinery called the type III secretion system (T3SS). The T3SS not only secretes the components that self-assemble into their extracellular appendages but also, in the case of the injectisome, subsequently directly translocates modulating effector proteins from the bacterial cell into the infected host. The injectisome is thought to have evolved from the flagellum as a minimal secretory system lacking motility, with the subsequent acquisition of additional components tailored to its specialized role in manipulating eukaryotic hosts for pathogenic advantage. Both nanomachines have long been the focus of intense interest, but advances in structural and functional understanding have taken a significant step forward since 2015, facilitated by the revolutionary advances in cryo-electron microscopy technologies. With several seminal structures of each nanomachine now captured, we review here the molecular similarities and differences that underlie their diverse functions.
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Affiliation(s)
- Liam J Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
| | - Dorothy D Majewski
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
- Current affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada; , ,
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4
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Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ. Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Nat Microbiol 2023; 8:1267-1279. [PMID: 37349588 PMCID: PMC11061892 DOI: 10.1038/s41564-023-01401-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Bdellovibrio bacteriovorus is a microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here we used cryo-electron tomography to comprehensively image the lifecycle of B. bacteriovorus at nanometre-scale resolution. With high-resolution images of predation in a native (hydrated, unstained) state, we discover several surprising features of the process, including macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find that B. bacteriovorus does not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following growth and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensed B. bacteriovorus nucleoid.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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5
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Kaplan M, Yao Q, Jensen GJ. Structure and Assembly of the Proteus mirabilis Flagellar Motor by Cryo-Electron Tomography. Int J Mol Sci 2023; 24:8292. [PMID: 37176000 PMCID: PMC10179241 DOI: 10.3390/ijms24098292] [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: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Proteus mirabilis is a Gram-negative Gammaproteobacterium and a major causative agent of urinary tract infections in humans. It is characterized by its ability to switch between swimming motility in liquid media and swarming on solid surfaces. Here, we used cryo-electron tomography and subtomogram averaging to reveal the structure of the flagellar motor of P. mirabilis at nanometer resolution in intact cells. We found that P. mirabilis has a motor that is structurally similar to those of Escherichia coli and Salmonella enterica, lacking the periplasmic elaborations that characterize other more specialized gammaproteobacterial motors. In addition, no density corresponding to stators was present in the subtomogram average suggesting that the stators are dynamic. Finally, several assembly intermediates of the motor were seen that support the inside-out assembly pathway.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, USA
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6
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Diving into the complexity of the spirochetal endoflagellum. Trends Microbiol 2023; 31:294-307. [PMID: 36244923 DOI: 10.1016/j.tim.2022.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/27/2022]
Abstract
Spirochaetes, a phylum that includes medically important pathogens such as the causative agents of Lyme disease, syphilis, and leptospirosis, are in many ways highly unique bacteria. Their cell morphology, subcellular organization, and metabolism reveal atypical features. Spirochetal motility is also singular, dependent on the presence of periplasmic flagella or endoflagella, inserted subterminally at cell poles and not penetrating the outer membrane and elongating outside the cell as in enterobacteria. In this review we present a comprehensive comparative genomics analysis of endoflagellar systems in spirochetes, highlighting recent findings on the flagellar basal body and filament. Continued progress in understanding the function and architecture of spirochetal flagella is uncovering paradigm-shifting mechanisms of bacterial motility.
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Lloyd CJ, Klose KE. The Vibrio Polar Flagellum: Structure and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:77-97. [PMID: 36792872 DOI: 10.1007/978-3-031-22997-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Here we discuss the structure and regulation of the Vibrio flagellum and its role in the virulence of pathogenic species. We will cover some of the novel insights into the structure of this nanomachine that have recently been enabled by cryoelectron tomography. We will also highlight the recent genetic studies that have increased our understanding in flagellar synthesis specifically at the bacterial cell pole, temporal regulation of flagellar genes, and how the flagellum enables directional motility through Run-Reverse-Flick cycles.
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Affiliation(s)
- Cameron J Lloyd
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA.,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA
| | - Karl E Klose
- South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA. .,Department of Molecular Microbiology and Immunology, University of Texas San Antonio, San Antonio, TX, USA.
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8
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Lai L, Cheung YW, Martinez M, Kixmoeller K, Palao L, Steimle S, Ho MC, Black BE, Lai EM, Chang YW. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol 2023; 2646:211-248. [PMID: 36842118 DOI: 10.1007/978-1-0716-3060-0_18] [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: 04/13/2023]
Abstract
Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.
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Affiliation(s)
- Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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9
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Gibson K, Chu JK, Zhu S, Nguyen D, Mrázek J, Liu J, Hoover TR. A Tripartite Efflux System Affects Flagellum Stability in Helicobacter pylori. Int J Mol Sci 2022; 23:ijms231911609. [PMID: 36232924 PMCID: PMC9570263 DOI: 10.3390/ijms231911609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
Helicobacter pylori uses a cluster of polar, sheathed flagella for swimming motility. A search for homologs of H. pylori proteins that were conserved in Helicobacter species that possess flagellar sheaths but were underrepresented in Helicobacter species with unsheathed flagella identified several candidate proteins. Four of the identified proteins are predicted to form part of a tripartite efflux system that includes two transmembrane domains of an ABC transporter (HP1487 and HP1486), a periplasmic membrane fusion protein (HP1488), and a TolC-like outer membrane efflux protein (HP1489). Deleting hp1486/hp1487 and hp1489 homologs in H. pylori B128 resulted in reductions in motility and the number of flagella per cell. Cryo-electron tomography studies of intact motors of the Δhp1489 and Δhp1486/hp1487 mutants revealed many of the cells contained a potential flagellum disassembly product consisting of decorated L and P rings, which has been reported in other bacteria. Aberrant motors lacking specific components, including a cage-like structure that surrounds the motor, were also observed in the Δhp1489 mutant. These findings suggest a role for the H. pylori HP1486-HP1489 tripartite efflux system in flagellum stability. Three independent variants of the Δhp1486/hp1487 mutant with enhanced motility were isolated. All three motile variants had the same frameshift mutation in fliL, suggesting a role for FliL in flagellum disassembly.
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Affiliation(s)
- Katherine Gibson
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Joshua K. Chu
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Shiwei Zhu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
| | - Doreen Nguyen
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| | - Jan Mrázek
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
| | - Timothy R. Hoover
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
- Correspondence: ; Tel.: +1-706-542-2675
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10
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Discovery of a Novel Inner Membrane-Associated Bacterial Structure Related to the Flagellar Type III Secretion System. J Bacteriol 2022; 204:e0014422. [PMID: 35862756 PMCID: PMC9380563 DOI: 10.1128/jb.00144-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure. IMPORTANCE The type III secretion system (T3SS) is a fascinating suite of proteins involved in building diverse macromolecular systems, including the bacterial flagellar motility machine, the injectisome machinery that bacteria use to inject effector proteins into host cells, and probably membrane nanotubes which connect bacterial cells. Here, we accidentally discovered a novel inner membrane-associated complex related to the flagellar T3SS. Examining our lab database, which is comprised of more than 40,000 cryo-tomograms of dozens of species, we discovered that this novel structure is both ubiquitous and ancient, being present in highly divergent classes of bacteria. Discovering a novel, widespread structure related to what are among the best-studied molecular machines in bacteria will open new venues for research aiming at understanding the function and evolution of T3SS proteins.
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11
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Sobe RC, Gilbert C, Vo L, Alexandre G, Scharf BE. FliL and its paralog MotF have distinct roles in the stator activity of the Sinorhizobium meliloti flagellar motor. Mol Microbiol 2022; 118:223-243. [PMID: 35808893 PMCID: PMC9541039 DOI: 10.1111/mmi.14964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The bacterial flagellum is a complex macromolecular machine that drives bacteria through diverse fluid environments. Although many components of the flagellar motor are conserved across species, the roles of FliL are numerous and species‐specific. Here, we have characterized an additional player required for flagellar motor function in Sinorhizobium meliloti, MotF, which we have identified as a FliL paralog. We performed a comparative analysis of MotF and FliL, identified interaction partners through bacterial two‐hybrid and pull‐down assays, and investigated their roles in motility and motor rotation. Both proteins form homooligomers, and interact with each other, and with the stator proteins MotA and MotB. The ∆motF mutant exhibits normal flagellation but its swimming behavior and flagellar motor activity are severely impaired and erratic. In contrast, the ∆fliL mutant is mostly aflagellate and nonmotile. Amino acid substitutions in cytoplasmic regions of MotA or disruption of the proton channel plug of MotB partially restored motor activity to the ∆motF but not the ∆fliL mutant. Altogether, our findings indicate that both, MotF and FliL, are essential for flagellar motor torque generation in S. meliloti. FliL may serve as a scaffold for stator integration into the motor, and MotF is required for proton channel modulation.
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Affiliation(s)
- Richard C Sobe
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
| | - Crystal Gilbert
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
| | - Lam Vo
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA.,Present address: Molecular Cellular and Developmental Biology and Physics, Yale Science Building, Yale University, New Haven, CT, USA
| | - Gladys Alexandre
- Department of Biochemistry and Cell and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, VA, USA
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12
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Kaplan M, Oikonomou CM, Wood CR, Chreifi G, Subramanian P, Ortega DR, Chang Y, Beeby M, Shaffer CL, Jensen GJ. Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors. EMBO J 2022; 41:e109523. [PMID: 35301732 PMCID: PMC9108667 DOI: 10.15252/embj.2021109523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/20/2022] Open
Abstract
The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Catherine M Oikonomou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Cecily R Wood
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
| | - Georges Chreifi
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Poorna Subramanian
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Davi R Ortega
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Yi‐Wei Chang
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Morgan Beeby
- Department of Life SciencesImperial College LondonLondonUK
| | - Carrie L Shaffer
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Grant J Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Chemistry and BiochemistryBrigham Young UniversityProvoUTUSA
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Abstract
The bacterial flagellum is a large macromolecular assembly that acts as propeller, providing motility through the rotation of a long extracellular filament. It is composed of over 20 different proteins, many of them highly oligomeric. Accordingly, it has attracted a huge amount of interest amongst researchers and the wider public alike. Nonetheless, most of its molecular details had long remained elusive.This however has changed recently, with the emergence of cryo-EM to determine the structure of protein assemblies at near-atomic resolution. Within a few years, the atomic details of most of the flagellar components have been elucidated, revealing not only its overall architecture but also the molecular details of its rotation mechanism. However, many questions remained unaddressed, notably on the complexity of the assembly of such an intricate machinery.In this chapter, we review the current state of our understanding of the bacterial flagellum structure, focusing on the recent development from cryo-EM. We also highlight the various elements that still remain to be fully characterized. Finally, we summarize the existing model for flagellum assembly and discuss some of the outstanding questions that are still pending in our understanding of the diversity of assembly pathways.
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Affiliation(s)
- Natalie S Al-Otaibi
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
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14
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Kaplan M, Chreifi G, Metskas LA, Liedtke J, Wood CR, Oikonomou CM, Nicolas WJ, Subramanian P, Zacharoff LA, Wang Y, Chang YW, Beeby M, Dobro MJ, Zhu Y, McBride MJ, Briegel A, Shaffer CL, Jensen GJ. In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography. eLife 2021; 10:73099. [PMID: 34468314 PMCID: PMC8455137 DOI: 10.7554/elife.73099] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/19/2022] Open
Abstract
The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: (1) tubes with a uniform diameter (with or without an internal scaffold), (2) tubes with irregular diameter, (3) tubes with a vesicular dilation at their tip, (4) pearling tubes, (5) connected chains of vesicles (with or without neck-like connectors), (6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Janine Liedtke
- Leiden University, Sylvius Laboratories, Leiden, Netherlands
| | - Cecily R Wood
- Department of Veterinary Science, University of Kentucky, Lexington, United States
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Yuhang Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Yongtao Zhu
- Department of Biological Sciences, Minnesota State University, Mankato, United States
| | - Mark J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, United States
| | - Ariane Briegel
- Leiden University, Sylvius Laboratories, Leiden, Netherlands
| | - Carrie L Shaffer
- Department of Veterinary Science, University of Kentucky, Lexington, United States.,Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, United States.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States
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15
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Structure of the molecular bushing of the bacterial flagellar motor. Nat Commun 2021; 12:4469. [PMID: 34294704 PMCID: PMC8298488 DOI: 10.1038/s41467-021-24715-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
The basal body of the bacterial flagellum is a rotary motor that consists of several rings (C, MS and LP) and a rod. The LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation without much friction. Here, we use electron cryomicroscopy to describe the LP ring structure around the rod, at 3.5 Å resolution, from Salmonella Typhimurium. The structure shows 26-fold rotational symmetry and intricate intersubunit interactions of each subunit with up to six partners, which explains the structural stability. The inner surface is charged both positively and negatively. Positive charges on the P ring (the part of the LP ring that is embedded within the peptidoglycan layer) presumably play important roles in its initial assembly around the rod with a negatively charged surface. In the basal body of the bacterial flagellum, the LP ring acts as a bushing supporting the distal rod for its rapid and stable rotation. Here, Yamaguchi et al. present the electron cryomicroscopy structure of the LP ring around the rod, shedding light into potential mechanisms involved in stability and assembly of the structure.
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16
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Abstract
The bacterial flagellar motor is a complex macromolecular machine whose function and self-assembly present a fascinating puzzle for structural biologists. Here, we report that in diverse bacterial species, cell lysis leads to loss of the cytoplasmic switch complex and associated ATPase before other components of the motor. This loss may be prevented by the formation of a cytoplasmic vesicle around the complex. These observations suggest a relatively loose association of the switch complex with the rest of the flagellar machinery. IMPORTANCE We show in eight different bacterial species (belonging to different phyla) that the flagellar motor loses its cytoplasmic switch complex upon cell lysis, while the rest of the flagellum remains attached to the cell body. This suggests an evolutionary conserved weak interaction between the switch complex and the rest of the flagellum which is important to understand how the motor evolved. In addition, this information is crucial for mimicking such nanomachines in the laboratory.
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Milne-Davies B, Wimmi S, Diepold A. Adaptivity and dynamics in type III secretion systems. Mol Microbiol 2020; 115:395-411. [PMID: 33251695 DOI: 10.1111/mmi.14658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 01/07/2023]
Abstract
The type III secretion system is the common core of two bacterial molecular machines: the flagellum and the injectisome. The flagellum is the most widely distributed prokaryotic locomotion device, whereas the injectisome is a syringe-like apparatus for inter-kingdom protein translocation, which is essential for virulence in important human pathogens. The successful concept of the type III secretion system has been modified for different bacterial needs. It can be adapted to changing conditions, and was found to be a dynamic complex constantly exchanging components. In this review, we highlight the flexibility, adaptivity, and dynamic nature of the type III secretion system.
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Affiliation(s)
- Bailey Milne-Davies
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Stephan Wimmi
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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18
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Structural Conservation and Adaptation of the Bacterial Flagella Motor. Biomolecules 2020; 10:biom10111492. [PMID: 33138111 PMCID: PMC7693769 DOI: 10.3390/biom10111492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Many bacteria require flagella for the ability to move, survive, and cause infection. The flagellum is a complex nanomachine that has evolved to increase the fitness of each bacterium to diverse environments. Over several decades, molecular, biochemical, and structural insights into the flagella have led to a comprehensive understanding of the structure and function of this fascinating nanomachine. Notably, X-ray crystallography, cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) have elucidated the flagella and their components to unprecedented resolution, gleaning insights into their structural conservation and adaptation. In this review, we focus on recent structural studies that have led to a mechanistic understanding of flagellar assembly, function, and evolution.
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19
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Zhu S, Gao B. Bacterial Flagella Loss under Starvation. Trends Microbiol 2020; 28:785-788. [DOI: 10.1016/j.tim.2020.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 01/08/2023]
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20
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Garcez AS, Kaplan M, Jensen GJ, Scheidt FR, Oliveira EM, Suzuki SS. Effects of antimicrobial photodynamic therapy on antibiotic-resistant Escherichia coli. Photodiagnosis Photodyn Ther 2020; 32:102029. [PMID: 32980553 DOI: 10.1016/j.pdpdt.2020.102029] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/07/2023]
Abstract
This study used Electron Cryo-tomography (ECT) and fluorescent images to evaluate antimicrobial photodynamic therapy (aPDT) on the envelope architecture of a Gram-negative bacteria and the effects of combined therapy of aPDT and antibiotics. Standard and clinical suspension of Escherichia coli were submitted to photodynamic treatment with methylene blue solution (100μM) and a 100 mW LED emitting at 660 nm with 3 and 18 J of energy. As a control group, a suspension of E. coli was submitted to penicillin V for 60 min at 30 °C, to compare the damage in cell wall structure. After treatment, ECT images were collected and E. coli biofilms were grown in glass-cover slides and stained with live/dead staining for fluorescence analysis before and after treatments. Bacteria were also submitted to disc diffusion and MIC50 tests with Ampicillin, Amoxicillin + Clavulanic acid, Clindamycin and Erythromycin. For in vivo experiment Galleria mellonella larvae were infected with E. coli and treated with antibiotics, aPDT or combined therapy. ECT images presented damage to cell walls and vesicles structures inside and outside the bacteria and fluorescent images showed dose dependent effect of aPDT. Antibiotic or aPDT alone did not improve the survival of caterpillars, but the combined therapy significantly increased survival curve. ECT and fluorescent images shows that aPDT seems to promote micro-damages to cell envelope and causes the production of membrane vesicles permeabilizing cell membranes. The results showed that pre-treating bacterial cells with a photosensitizer and light make them more susceptible to antibiotics and could be an alternative to local infection treatment by resistant bacteria.
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Affiliation(s)
- Aguinaldo S Garcez
- Department of oral Microbiology, São Leopoldo Mandic Institute and Research Center, Campinas, Brazil.
| | - Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, USA
| | - Fábio R Scheidt
- Department of oral Microbiology, São Leopoldo Mandic Institute and Research Center, Campinas, Brazil
| | - Eduardo M Oliveira
- Department of oral Microbiology, São Leopoldo Mandic Institute and Research Center, Campinas, Brazil
| | - Selly S Suzuki
- Department of oral Microbiology, São Leopoldo Mandic Institute and Research Center, Campinas, Brazil
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