skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A designed bacterial microcompartment shell with tunable composition and precision cargo loading

Abstract

Microbes often augment their metabolism by conditionally constructing proteinaceous organelles, known as bacterial microcompartments (BMCs), that encapsulate enzymes to degrade organic compounds or assimilate CO2. BMCs self-assemble and are spatially delimited by a semi-permeable shell made up of hexameric, trimeric, and pentameric shell proteins. Bioengineers aim to recapitulate the organization and efficiency of these complex biological architectures by redesigning the shell to incorporate non-native enzymes from biotechnologically relevant pathways. To meet this challenge, a diverse set of synthetic biology tools are required, including methods to manipulate the properties of the shell as well as target and organize cargo encapsulation. We designed and determined the crystal structure of a synthetic shell protein building block with an inverted sidedness of its N- and C-terminal residues relative to its natural counterpart; the inversion targets genetically fused protein cargo to the lumen of the shell. Moreover, the titer of fluorescent protein cargo encapsulated using this strategy is controllable using an inducible tetracycline promoter. Furthermore, these results expand the available set of building blocks for precision engineering of BMC-based nanoreactors and are compatible with orthogonal methods which will facilitate the installation and organization of multi-enzyme pathways.

Authors:
 [1];  [2];  [2]
  1. Michigan State University, East Lansing, MI (United States)
  2. Michigan State University, East Lansing, MI (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (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, National Institute of Allergy and Infectious Diseases (NIAID)
OSTI Identifier:
1671303
Alternate Identifier(s):
OSTI ID: 1702961
Grant/Contract Number:  
FG02-91ER20021; 5 R01 AI114975-05; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Metabolic Engineering
Additional Journal Information:
Journal Volume: 54; Journal ID: ISSN 1096-7176
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bacterial microcompartments; protein design; metabolic engineering; synthetic biology

Citation Formats

Ferlez, Bryan, Sutter, Markus, and Kerfeld, Cheryl A. A designed bacterial microcompartment shell with tunable composition and precision cargo loading. United States: N. p., 2019. Web. https://doi.org/10.1016/j.ymben.2019.04.011.
Ferlez, Bryan, Sutter, Markus, & Kerfeld, Cheryl A. A designed bacterial microcompartment shell with tunable composition and precision cargo loading. United States. https://doi.org/10.1016/j.ymben.2019.04.011
Ferlez, Bryan, Sutter, Markus, and Kerfeld, Cheryl A. Tue . "A designed bacterial microcompartment shell with tunable composition and precision cargo loading". United States. https://doi.org/10.1016/j.ymben.2019.04.011. https://www.osti.gov/servlets/purl/1671303.
@article{osti_1671303,
title = {A designed bacterial microcompartment shell with tunable composition and precision cargo loading},
author = {Ferlez, Bryan and Sutter, Markus and Kerfeld, Cheryl A.},
abstractNote = {Microbes often augment their metabolism by conditionally constructing proteinaceous organelles, known as bacterial microcompartments (BMCs), that encapsulate enzymes to degrade organic compounds or assimilate CO2. BMCs self-assemble and are spatially delimited by a semi-permeable shell made up of hexameric, trimeric, and pentameric shell proteins. Bioengineers aim to recapitulate the organization and efficiency of these complex biological architectures by redesigning the shell to incorporate non-native enzymes from biotechnologically relevant pathways. To meet this challenge, a diverse set of synthetic biology tools are required, including methods to manipulate the properties of the shell as well as target and organize cargo encapsulation. We designed and determined the crystal structure of a synthetic shell protein building block with an inverted sidedness of its N- and C-terminal residues relative to its natural counterpart; the inversion targets genetically fused protein cargo to the lumen of the shell. Moreover, the titer of fluorescent protein cargo encapsulated using this strategy is controllable using an inducible tetracycline promoter. Furthermore, these results expand the available set of building blocks for precision engineering of BMC-based nanoreactors and are compatible with orthogonal methods which will facilitate the installation and organization of multi-enzyme pathways.},
doi = {10.1016/j.ymben.2019.04.011},
journal = {Metabolic Engineering},
number = ,
volume = 54,
place = {United States},
year = {2019},
month = {5}
}

Works referenced in this record:

Engineering and characterization of a superfolder green fluorescent protein
journal, December 2005

  • Pédelacq, Jean-Denis; Cabantous, Stéphanie; Tran, Timothy
  • Nature Biotechnology, Vol. 24, Issue 1, p. 79-88
  • DOI: 10.1038/nbt1172

A Simple Tagging System for Protein Encapsulation
journal, April 2006

  • Seebeck, Florian P.; Woycechowsky, Kenneth J.; Zhuang, Wei
  • Journal of the American Chemical Society, Vol. 128, Issue 14
  • DOI: 10.1021/ja058363s

The N-Terminal Regions of β and γ Subunits Lower the Solubility of Adenosylcobalamin-Dependent Diol Dehydratase
journal, January 2005

  • Tobimatsu, Takamasa; Kawata, Masahiro; Toraya, Tetsuo
  • Bioscience, Biotechnology, and Biochemistry, Vol. 69, Issue 3
  • DOI: 10.1271/bbb.69.455

A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration
journal, May 2017

  • Jakobson, Christopher M.; Tullman-Ercek, Danielle; Slininger, Marilyn F.
  • PLOS Computational Biology, Vol. 13, Issue 5
  • DOI: 10.1371/journal.pcbi.1005525

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

Self-Sorting of Foreign Proteins in a Bacterial Nanocompartment
journal, February 2014

  • Rurup, W. Frederik; Snijder, Joost; Koay, Melissa S. T.
  • Journal of the American Chemical Society, Vol. 136, Issue 10
  • DOI: 10.1021/ja410891c

Bacterial microcompartment assembly: The key role of encapsulation peptides
journal, May 2015

  • Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul
  • Communicative & Integrative Biology, Vol. 8, Issue 3
  • DOI: 10.1080/19420889.2015.1039755

In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures
journal, October 2018


Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Microcompartments for B12-Dependent 1,2-Propanediol Degradation Provide Protection from DNA and Cellular Damage by a Reactive Metabolic Intermediate
journal, February 2008

  • Sampson, E. M.; Bobik, T. A.
  • Journal of Bacteriology, Vol. 190, Issue 8, p. 2966-2971
  • DOI: 10.1128/JB.01925-07

Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

BglBrick vectors and datasheets: A synthetic biology platform for gene expression
journal, January 2011

  • Lee, Taek; Krupa, Rachel A.; Zhang, Fuzhong
  • Journal of Biological Engineering, Vol. 5, Issue 1
  • DOI: 10.1186/1754-1611-5-12

Modular interior loading and exterior decoration of a virus-like particle
journal, January 2017

  • Sharma, Jhanvi; Uchida, Masaki; Miettinen, Heini M.
  • Nanoscale, Vol. 9, Issue 29
  • DOI: 10.1039/C7NR03018E

Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin
journal, February 2012

  • Zakeri, B.; Fierer, J. O.; Celik, E.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 12
  • DOI: 10.1073/pnas.1115485109

Metal affinity precipitation of proteins carrying genetically attached polyhistidine affinity tails
journal, June 1991


A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
journal, October 2014


Short N-terminal sequences package proteins into bacterial microcompartments
journal, March 2010

  • Fan, C.; Cheng, S.; Liu, Y.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 16
  • DOI: 10.1073/pnas.0913199107

Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein
journal, January 2016

  • Jorda, J.; Leibly, D. J.; Thompson, M. C.
  • Chemical Communications, Vol. 52, Issue 28
  • DOI: 10.1039/C6CC00851H

Localization of Proteins to the 1,2-Propanediol Utilization Microcompartment by Non-native Signal Sequences Is Mediated by a Common Hydrophobic Motif
journal, August 2015

  • Jakobson, Christopher M.; Kim, Edward Y.; Slininger, Marilyn F.
  • Journal of Biological Chemistry, Vol. 290, Issue 40
  • DOI: 10.1074/jbc.M115.651919

The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle
journal, March 2016


Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell
journal, June 2017


Bacterial microcompartments
journal, March 2018

  • Kerfeld, Cheryl A.; Aussignargues, Clement; Zarzycki, Jan
  • Nature Reviews Microbiology, Vol. 16, Issue 5
  • DOI: 10.1038/nrmicro.2018.10

Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function
journal, May 2014

  • Lassila, Jonathan K.; Bernstein, Susan L.; Kinney, James N.
  • Journal of Molecular Biology, Vol. 426, Issue 11
  • DOI: 10.1016/j.jmb.2014.02.025

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy
journal, December 2015


XDS
journal, January 2010

  • Kabsch, Wolfgang
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2
  • DOI: 10.1107/S0907444909047337

De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments
journal, August 2018


Programmed loading and rapid purification of engineered bacterial microcompartment shells
journal, July 2018


Protein Structures Forming the Shell of Primitive Bacterial Organelles
journal, August 2005


Elucidating Essential Role of Conserved Carboxysomal Protein CcmN Reveals Common Feature of Bacterial Microcompartment Assembly
journal, March 2012

  • Kinney, James N.; Salmeen, Annette; Cai, Fei
  • Journal of Biological Chemistry, Vol. 287, Issue 21
  • DOI: 10.1074/jbc.M112.355305

    Works referencing / citing this record:

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

    • Huang, Jingcheng; Ferlez, Bryan H.; Young, Eric J.
    • Frontiers in Bioengineering and Biotechnology, Vol. 7
    • DOI: 10.3389/fbioe.2019.00432

    Encapsulin carrier proteins for enhanced expression of antimicrobial peptides
    journal, November 2019

    • Lee, Tek‐Hyung; Carpenter, Timothy S.; D'haeseleer, Patrik
    • Biotechnology and Bioengineering, Vol. 117, Issue 3
    • DOI: 10.1002/bit.27222

    Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella
    journal, December 2019


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