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Title: In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures

Abstract

Bacterial Microcompartments (BMCs) are organelles composed of a selectively permeable protein shell that encapsulates enzymes involved in CO2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Confinement of sequential reactions by the BMC shell presumably increases the efficiency of the pathway by reducing the crosstalk of metabolites, release of toxic intermediates, and accumulation of inhibitory products. Because BMCs are composed entirely of protein and self-assemble, they are an emerging platform for engineering nanoreactors and molecular scaffolds. However, testing designs for assembly and function through in vivo expression is labor-intensive and has limited the potential of BMCs in bioengineering. Here, we developed a new method for in vitro assembly of defined nanoscale BMC architectures: shells and nanotubes. By inserting a “protecting group”, a short ubiquitin-like modifier (SUMO) domain, self-assembly ofshell proteins in vivo was thwarted, enabling preparation of concentrates of shell building blocks. Addition of the cognate protease removes the SUMO domain and subsequent mixing of the constituent shell proteins in vitro results in the self-assembly of three types of supramolecular architectures: a metabolosome shell, a carboxysome shell, and a BMC protein-based nanotube. We next applied our method to generate a metabolosome shell engineered with a hyper-basic luminal surface, allowing for the encapsulationmore » of biotic or abiotic cargos functionalized with an acidic accessory group. This is the first demonstration of using charge complementarity to encapsulate diverse cargos in BMC shells. Finally, our work provides a generally applicable method for in vitro assembly of natural and engineered BMC-based architectures.« less

Authors:
ORCiD logo [1];  [2];  [1];  [2];  [2];  [2]; ORCiD logo [3]
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  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Michigan State Univ., East Lansing, MI (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States)
Publication Date:
Research Org.:
Michigan State Univ., East Lansing, MI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
OSTI Identifier:
1603663
Grant/Contract Number:  
FG02-91ER20021; 1R01AI14975-01
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Nano Letters
Additional Journal Information:
Journal Volume: 18; Journal Issue: 11; Journal ID: ISSN 1530-6984
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Bacterial microcompartments; structural biology; protein engineering; in vitro supramolecular self-assembly; shells; nanotubes; electrostatic-based encapsulation

Citation Formats

Hagen, Andrew R., Plegaria, Jefferson S., Sloan, Nancy, Ferlez, Bryan, Aussignargues, Clement, Burton, Rodney, and Kerfeld, Cheryl A. In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures. United States: N. p., 2018. Web. doi:10.1021/acs.nanolett.8b02991.
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Hagen, Andrew R., Plegaria, Jefferson S., Sloan, Nancy, Ferlez, Bryan, Aussignargues, Clement, Burton, Rodney, & Kerfeld, Cheryl A. In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures. United States. https://doi.org/10.1021/acs.nanolett.8b02991
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Hagen, Andrew R., Plegaria, Jefferson S., Sloan, Nancy, Ferlez, Bryan, Aussignargues, Clement, Burton, Rodney, and Kerfeld, Cheryl A. Mon . "In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures". United States. https://doi.org/10.1021/acs.nanolett.8b02991. https://www.osti.gov/servlets/purl/1603663.
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@article{osti_1603663,
title = {In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures},
author = {Hagen, Andrew R. and Plegaria, Jefferson S. and Sloan, Nancy and Ferlez, Bryan and Aussignargues, Clement and Burton, Rodney and Kerfeld, Cheryl A.},
abstractNote = {Bacterial Microcompartments (BMCs) are organelles composed of a selectively permeable protein shell that encapsulates enzymes involved in CO2 fixation (carboxysomes) or carbon catabolism (metabolosomes). Confinement of sequential reactions by the BMC shell presumably increases the efficiency of the pathway by reducing the crosstalk of metabolites, release of toxic intermediates, and accumulation of inhibitory products. Because BMCs are composed entirely of protein and self-assemble, they are an emerging platform for engineering nanoreactors and molecular scaffolds. However, testing designs for assembly and function through in vivo expression is labor-intensive and has limited the potential of BMCs in bioengineering. Here, we developed a new method for in vitro assembly of defined nanoscale BMC architectures: shells and nanotubes. By inserting a “protecting group”, a short ubiquitin-like modifier (SUMO) domain, self-assembly ofshell proteins in vivo was thwarted, enabling preparation of concentrates of shell building blocks. Addition of the cognate protease removes the SUMO domain and subsequent mixing of the constituent shell proteins in vitro results in the self-assembly of three types of supramolecular architectures: a metabolosome shell, a carboxysome shell, and a BMC protein-based nanotube. We next applied our method to generate a metabolosome shell engineered with a hyper-basic luminal surface, allowing for the encapsulation of biotic or abiotic cargos functionalized with an acidic accessory group. This is the first demonstration of using charge complementarity to encapsulate diverse cargos in BMC shells. Finally, our work provides a generally applicable method for in vitro assembly of natural and engineered BMC-based architectures.},
doi = {10.1021/acs.nanolett.8b02991},
url = {https://www.osti.gov/biblio/1603663}, journal = {Nano Letters},
issn = {1530-6984},
number = 11,
volume = 18,
place = {United States},
year = {2018},
month = {10}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1021/acs.nanolett.8b02991
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Works referencing / citing this record:

Bio-engineering of bacterial microcompartments: a mini review
journal, June 2019

Structural organization of biocatalytic systems: the next dimension of synthetic metabolism
journal, September 2019

Self-Assembly Stability and Variability of Bacterial Microcompartment Shell Proteins in Response to the Environmental Change
journal, February 2019

Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components
journal, October 2019

Functionalization of Bacterial Microcompartment Shell Proteins With Covalently Attached Heme
journal, January 2020

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