Programmed loading and rapid purification of engineered bacterial microcompartment shells
Abstract
Bacterial microcompartments (BMCs) are selectively permeable proteinaceous organelles which encapsulate segments of metabolic pathways across bacterial phyla. They consist of an enzymatic core surrounded by a protein shell composed of multiple distinct proteins. Despite great potential in varied biotechnological applications, engineering efforts have been stymied by difficulties in their isolation and characterization and a dearth of robust methods for programming cores and shell permeability. We address these challenges by functionalizing shell proteins with affinity handles, enabling facile complementation-based affinity purification (CAP) and specific cargo docking sites for efficient encapsulation via covalent-linkage (EnCo). These shell functionalizations extend our knowledge of BMC architectural principles and enable the development of minimal shell systems of precisely defined structure and composition. The generalizability of CAP and EnCo will enable their application to functionally diverse microcompartment systems to facilitate both characterization of natural functions and the development of bespoke shells for selectively compartmentalizing proteins.
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States). DOE Plant Research Laboratory
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1460586
- Alternate Identifier(s):
- OSTI ID: 1478349; OSTI ID: 1603659
- Grant/Contract Number:
- FG02-91ER20021; AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Name: Nature Communications Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Hagen, Andrew, Sutter, Markus, Sloan, Nancy, and Kerfeld, Cheryl A. Programmed loading and rapid purification of engineered bacterial microcompartment shells. United Kingdom: N. p., 2018.
Web. doi:10.1038/s41467-018-05162-z.
Hagen, Andrew, Sutter, Markus, Sloan, Nancy, & Kerfeld, Cheryl A. Programmed loading and rapid purification of engineered bacterial microcompartment shells. United Kingdom. https://doi.org/10.1038/s41467-018-05162-z
Hagen, Andrew, Sutter, Markus, Sloan, Nancy, and Kerfeld, Cheryl A. Mon .
"Programmed loading and rapid purification of engineered bacterial microcompartment shells". United Kingdom. https://doi.org/10.1038/s41467-018-05162-z.
@article{osti_1460586,
title = {Programmed loading and rapid purification of engineered bacterial microcompartment shells},
author = {Hagen, Andrew and Sutter, Markus and Sloan, Nancy and Kerfeld, Cheryl A.},
abstractNote = {Bacterial microcompartments (BMCs) are selectively permeable proteinaceous organelles which encapsulate segments of metabolic pathways across bacterial phyla. They consist of an enzymatic core surrounded by a protein shell composed of multiple distinct proteins. Despite great potential in varied biotechnological applications, engineering efforts have been stymied by difficulties in their isolation and characterization and a dearth of robust methods for programming cores and shell permeability. We address these challenges by functionalizing shell proteins with affinity handles, enabling facile complementation-based affinity purification (CAP) and specific cargo docking sites for efficient encapsulation via covalent-linkage (EnCo). These shell functionalizations extend our knowledge of BMC architectural principles and enable the development of minimal shell systems of precisely defined structure and composition. The generalizability of CAP and EnCo will enable their application to functionally diverse microcompartment systems to facilitate both characterization of natural functions and the development of bespoke shells for selectively compartmentalizing proteins.},
doi = {10.1038/s41467-018-05162-z},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United Kingdom},
year = {Mon Jul 23 00:00:00 EDT 2018},
month = {Mon Jul 23 00:00:00 EDT 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41467-018-05162-z
https://doi.org/10.1038/s41467-018-05162-z
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 70 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Biogenesis of a Bacterial Organelle: The Carboxysome Assembly Pathway
journal, November 2013
- Cameron, Jeffrey C.; Wilson, Steven C.; Bernstein, Susan L.
- Cell, Vol. 155, Issue 5
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
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
Stochastic reaction–diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway
journal, July 2007
- Conrado, Robert J.; Mansell, Thomas J.; Varner, Jeffrey D.
- Metabolic Engineering, Vol. 9, Issue 4
The Carboxysome Shell Is Permeable to Protons
journal, September 2010
- Menon, B. B.; Heinhorst, S.; Shively, J. M.
- Journal of Bacteriology, Vol. 192, Issue 22
A Catalytic Nanoreactor Based on in Vivo Encapsulation of Multiple Enzymes in an Engineered Protein Nanocompartment
journal, September 2016
- Giessen, Tobias W.; Silver, Pamela A.
- ChemBioChem, Vol. 17, Issue 20
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
Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%
journal, January 2012
- Goedhart, Joachim; von Stetten, David; Noirclerc-Savoye, Marjolaine
- Nature Communications, Vol. 3, Issue 1
Isolation and Characterization of High CO 2 -Requiring-Mutants of the Cyanobacterium Synechococcus PCC7942 : Two Phenotypes that Accumulate Inorganic Carbon but Are Apparently Unable to Generate CO
journal, October 1989
- Price, G. D.; Badger, M. R.
- Plant Physiology, Vol. 91, Issue 2
Molecular genetic analysis of a plant virus polyprotein cleavage site: A model
journal, August 1989
- Dougherty, William G.; Cary, Susan M.; Dawn Parks, T.
- Virology, Vol. 171, Issue 2
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
Engineering nanoscale protein compartments for synthetic organelles
journal, August 2013
- Kim, Edward Y.; Tullman-Ercek, Danielle
- Current Opinion in Biotechnology, Vol. 24, Issue 4
Cyan and Yellow Super Fluorescent Proteins with Improved Brightness, Protein Folding, and FRET Förster Radius † , ‡
journal, May 2006
- Kremers, Gert-Jan; Goedhart, Joachim; van Munster, Erik B.
- Biochemistry, Vol. 45, Issue 21
The Distribution of Polyhedral Bacterial Microcompartments Suggests Frequent Horizontal Transfer and Operon Reassembly
journal, January 2013
- AbdulRahman, Farah
- Journal of Phylogenetics & Evolutionary Biology, Vol. 01, Issue 04
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
Engineered Protein Nano-Compartments for Targeted Enzyme Localization
journal, March 2012
- Choudhary, Swati; Quin, Maureen B.; Sanders, Mark A.
- PLoS ONE, Vol. 7, Issue 3
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
journal, October 2014
- Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A.
- PLoS Computational Biology, Vol. 10, Issue 10
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
The Structure of CcmP, a Tandem Bacterial Microcompartment Domain Protein from the β-Carboxysome, Forms a Subcompartment Within a Microcompartment
journal, April 2013
- Cai, Fei; Sutter, Markus; Cameron, Jeffrey C.
- Journal of Biological Chemistry, Vol. 288, Issue 22
Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell
journal, June 2017
- Sutter, Markus; Greber, Basil; Aussignargues, Clement
- Science, Vol. 356, Issue 6344
The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle
journal, March 2016
- Erbilgin, Onur; Sutter, Markus; Kerfeld, Cheryl A.
- PLOS Biology, Vol. 14, Issue 3
Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells
journal, July 2014
- Cai, Fei; Sutter, Markus; Bernstein, Susan L.
- ACS Synthetic Biology, Vol. 4, Issue 4
Evolution of Coenzyme B12 Synthesis Among Enteric Bacteria: Evidence for Loss and Reacquisition of a Multigene Complex
journal, January 1996
- Lawrence, Jeffrey G.; Roth, John R.
- Genetics, Vol. 142, Issue 1
Ferritin, cellular iron storage and regulation: FERRITIN AND IRON STORAGE
journal, March 2017
- Arosio, Paolo; Elia, Leonardo; Poli, Maura
- IUBMB Life, Vol. 69, Issue 6
Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis
journal, March 2008
- Parsons, Joshua B.; Dinesh, Sriramulu D.; Deery, Evelyne
- Journal of Biological Chemistry, Vol. 283, Issue 21
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
Bacterial microcompartments
journal, March 2018
- Kerfeld, Cheryl A.; Aussignargues, Clement; Zarzycki, Jan
- Nature Reviews Microbiology, Vol. 16, Issue 5
Atomic-Level Models of the Bacterial Carboxysome Shell
journal, February 2008
- Tanaka, S.; Kerfeld, C. A.; Sawaya, M. R.
- Science, Vol. 319, Issue 5866
Engineering nanoreactors using bacterial microcompartment architectures
journal, June 2018
- Plegaria, Jefferson S.; Kerfeld, Cheryl A.
- Current Opinion in Biotechnology, Vol. 51
Crystal structures of β-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore
journal, March 2017
- Larsson, Anna M.; Hasse, Dirk; Valegård, Karin
- Journal of Experimental Botany, Vol. 68, Issue 14
A synthetic system for expression of components of a bacterial microcompartment
journal, September 2013
- Sargent, F.; Davidson, F. A.; Kelly, C. L.
- Microbiology, Vol. 159, Issue Pt_11
Molecular Interaction Between the Strep-tag Affinity Peptide and its Cognate Target, Streptavidin
journal, February 1996
- Schmidt, Thomas G. M.; Koepke, Jürgen; Frank, Ronald
- Journal of Molecular Biology, Vol. 255, Issue 5
Identification and Structural Analysis of a Novel Carboxysome Shell Protein with Implications for Metabolite Transport
journal, September 2009
- Klein, Michael G.; Zwart, Peter; Bagby, Sarah C.
- Journal of Molecular Biology, Vol. 392, Issue 2
De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment : Design of Signal Sequences
journal, April 2017
- Jakobson, Christopher M.; Slininger Lee, Marilyn F.; Tullman-Ercek, Danielle
- Protein Science, Vol. 26, Issue 5
Specific Covalent Labeling of Recombinant Protein Molecules Inside Live Cells
journal, July 1998
- Griffin, B. Albert; Adams, Stephen R.; Tsien, Roger Y.
- Science, Vol. 281, Issue 5374, p. 269-272
Protein Structures Forming the Shell of Primitive Bacterial Organelles
journal, August 2005
- Kerfeld, C. A.
- Science, Vol. 309, Issue 5736
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
The Pentameric Vertex Proteins Are Necessary for the Icosahedral Carboxysome Shell to Function as a CO2 Leakage Barrier
journal, October 2009
- Cai, Fei; Menon, Balaraj B.; Cannon, Gordon C.
- PLoS ONE, Vol. 4, Issue 10