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In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography

Kaplan, Mohammed and Chreifi, Georges and Metskas, Lauren Ann and Liedtke, Janine and Wood, Cecily R. and Oikonomou, Catherine M. and Nicolas, William J. and Subramanian, Poorna and Zacharoff, Lori A. and Wang, Yuhang and Chang, Yi-Wei and Beeby, Morgan and Dobro, Megan and Zhu, Yongtao and McBride, Mark J. and Briegel, Ariane and Shaffer, Carrie L. and Jensen, Grant J. (2021) In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography. eLife . ISSN 2050-084X. doi:10.7554/eLife.73099. (In Press) https://resolver.caltech.edu/CaltechAUTHORS:20210715-193000687

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.7554/eLife.73099DOIArticle
https://doi.org/10.1101/2021.07.13.452161DOIDiscussion Paper
ORCID:
AuthorORCID
Kaplan, Mohammed0000-0002-0759-0459
Chreifi, Georges0000-0003-4194-1694
Metskas, Lauren Ann0000-0002-8073-6960
Liedtke, Janine0000-0003-2680-4130
Oikonomou, Catherine M.0000-0003-2312-4746
Nicolas, William J.0000-0001-5970-8626
Zacharoff, Lori A.0000-0001-8657-0968
Wang, Yuhang0000-0003-3715-8349
Chang, Yi-Wei0000-0003-2391-473X
Beeby, Morgan0000-0001-6413-9835
Dobro, Megan0000-0002-6464-3932
Zhu, Yongtao0000-0002-3069-6518
McBride, Mark J.0000-0002-3798-6761
Briegel, Ariane0000-0003-3733-3725
Shaffer, Carrie L.0000-0002-7457-7422
Jensen, Grant J.0000-0003-1556-4864
Alternate Title:In situ imaging of bacterial membrane projections and associated protein complexes using electron cryo-tomography
Additional Information:© 2021, Kaplan et al. This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited. Received: August 17, 2021; Accepted: August 23, 2021; Accepted Manuscript published: September 1, 2021 (version 1). This project was funded by the NIH (grant R35 GM122588 to G.J.J., and P20 GM130456 to C.L.S.) and a Baxter postdoctoral fellowship from Caltech to M.K. Cryo-ET work was done in the Beckman Institute Resource Center for Transmission Electron Microscopy at the California Institute of Technology. We are grateful to Prof. Martin Pilhofer for collecting the P. luteoviolacea data and for critically reading the manuscript. We thank Prof. Elitza I Tocheva for collecting the D. acidovorans data. We thank Prof. Mohamed El-Naggar for insights into preparing S. oneidensis samples and Dr. Yuxi Liu for discussions. Briegel lab data was collected at the Netherlands Center for Electron Nanoscopy with support from Dr. Wen Yang. This data was collected with support from the National Roadmap for Large-Scale Research Infrastructure 2017 – 2018 with project number 184.034.014, which is financed in part by the Dutch Research Council (NWO). This work was also supported by the NWO OCENW.GROOT.2019.063 grant. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Data availability: All data generated or analysed during this study are included in the manuscript and supporting files and movies.
Funders:
Funding AgencyGrant Number
NIHR35 GM122588
NIHP20 GM130456
Baxter FoundationUNSPECIFIED
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)184.034.014
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)OCENW.GROOT.2019.063
DOI:10.7554/eLife.73099
Record Number:CaltechAUTHORS:20210715-193000687
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210715-193000687
Official Citation:In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography. eLife 2021;10:e73099; DOI: 10.7554/eLife.73099
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109850
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Jul 2021 19:41
Last Modified:08 Sep 2021 15:54

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