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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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Chalifour B, Li J. A Review of the Molluscan Microbiome: Ecology, Methodology and Future. MALACOLOGIA 2021. [DOI: 10.4002/040.063.0208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Bridget Chalifour
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 334 UCB, Boulder, Colorado, 80309, U.S.A
| | - Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 334 UCB, Boulder, Colorado, 80309, U.S.A
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Porfírio S, Carlson RW, Azadi P. Elucidating Peptidoglycan Structure: An Analytical Toolset. Trends Microbiol 2019; 27:607-622. [DOI: 10.1016/j.tim.2019.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 01/04/2023]
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Brenzinger S, van der Aart LT, van Wezel GP, Lacroix JM, Glatter T, Briegel A. Structural and Proteomic Changes in Viable but Non-culturable Vibrio cholerae. Front Microbiol 2019; 10:793. [PMID: 31057510 PMCID: PMC6479200 DOI: 10.3389/fmicb.2019.00793] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/28/2019] [Indexed: 11/13/2022] Open
Abstract
Aquatic environments are reservoirs of the human pathogen Vibrio cholerae O1, which causes the acute diarrheal disease cholera. Upon low temperature or limited nutrient availability, the cells enter a viable but non-culturable (VBNC) state. Characteristic of this state are an altered morphology, low metabolic activity, and lack of growth under standard laboratory conditions. Here, for the first time, the cellular ultrastructure of V. cholerae VBNC cells raised in natural waters was investigated using electron cryo-tomography. This was complemented by a comparison of the proteomes and the peptidoglycan composition of V. cholerae from LB overnight cultures and VBNC cells. The extensive remodeling of the VBNC cells was most obvious in the passive dehiscence of the cell envelope, resulting in improper embedment of flagella and pili. Only minor changes of the peptidoglycan and osmoregulated periplasmic glucans were observed. Active changes in VBNC cells included the production of cluster I chemosensory arrays and change of abundance of cluster II array proteins. Components involved in iron acquisition and storage, peptide import and arginine biosynthesis were overrepresented in VBNC cells, while enzymes of the central carbon metabolism were found at lower levels. Finally, several pathogenicity factors of V. cholerae were less abundant in the VBNC state, potentially limiting their infectious potential. This study gives unprecedented insight into the physiology of VBNC cells and the drastically altered presence of their metabolic and structural proteins.
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Affiliation(s)
- Susanne Brenzinger
- Department of Microbial Biotechnology & Health, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Lizah T. van der Aart
- Department of Microbial Biotechnology & Health, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Gilles P. van Wezel
- Department of Microbial Biotechnology & Health, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Jean-Marie Lacroix
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR CNRS 8576, Université de Lille Sciences et Technologies, Villeneuve d'Ascq, France
| | - Timo Glatter
- Facility for Bacterial Proteomics and Mass Spectrometry, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ariane Briegel
- Department of Microbial Biotechnology & Health, Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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Ultee E, Schenkel F, Yang W, Brenzinger S, Depelteau JS, Briegel A. An Open-Source Storage Solution for Cryo-Electron Microscopy Samples. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:60-63. [PMID: 29345600 DOI: 10.1017/s143192761701279x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cryo-electron microscopy (cryo-EM) enables the study of biological structures in situ in great detail and to solve protein structures at Ångstrom level resolution. Due to recent advances in instrumentation and data processing, the field of cryo-EM is a rapidly growing. Access to facilities and national centers that house the state-of-the-art microscopes is limited due to the ever-rising demand, resulting in long wait times between sample preparation and data acquisition. To improve sample storage, we have developed a cryo-storage system with an efficient, high storage capacity that enables sample storage in a highly organized manner. This system is simple to use, cost-effective and easily adaptable for any type of grid storage box and dewar and any size cryo-EM laboratory.
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Affiliation(s)
- Eveline Ultee
- 1Institute of Biology,Leiden University of Leiden,2333 BE Leiden,The Netherlands
| | - Fred Schenkel
- 2Fine Mechanical Department,University of Leiden,2333 CA Leiden,The Netherlands
| | - Wen Yang
- 1Institute of Biology,Leiden University of Leiden,2333 BE Leiden,The Netherlands
| | - Susanne Brenzinger
- 1Institute of Biology,Leiden University of Leiden,2333 BE Leiden,The Netherlands
| | - Jamie S Depelteau
- 1Institute of Biology,Leiden University of Leiden,2333 BE Leiden,The Netherlands
| | - Ariane Briegel
- 1Institute of Biology,Leiden University of Leiden,2333 BE Leiden,The Netherlands
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Engelhardt H, Bollschweiler D. Cryo-Electron Microscopy of Extremely Halophilic Microbes. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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