In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures

Hagen, Andrew R.; Plegaria, Jefferson S.; Sloan, Nancy; Ferlez, Bryan; Aussignargues, Clement; Burton, Rodney; Kerfeld, Cheryl A.

doi:10.1021/acs.nanolett.8b02991

Title: In Vitro Assembly of Diverse Bacterial Microcompartment Shell Architectures

Journal Article · Mon Oct 22 00:00:00 EDT 2018 · Nano Letters

DOI:https://doi.org/10.1021/acs.nanolett.8b02991· OSTI ID:1603663

^[1]; Plegaria, Jefferson S. ^[2]; Sloan, Nancy ^[1]; Ferlez, Bryan ^[2]; Aussignargues, Clement ^[2]; Burton, Rodney ^[2];

^[3]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Michigan State Univ., East Lansing, MI (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States)

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.

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Research Organization:: Michigan State Univ., East Lansing, MI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)

Grant/Contract Number:: FG02-91ER20021; 1R01AI14975-01

OSTI ID:: 1603663

Journal Information:: Nano Letters, Vol. 18, Issue 11; ISSN 1530-6984

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 35 works

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References (45)

Molecules into Cells: Specifying Spatial Architecture Harold, Franklin M. Microbiology and Molecular Biology Reviews, Vol. 69, Issue 4 https://doi.org/10.1128/MMBR.69.4.544-564.2005	journal	December 2005
Isolation and characterization of a novel ribonucleoprotein particle: large structures contain a single species of small RNA Kedersha, N. L. The Journal of Cell Biology, Vol. 103, Issue 3 https://doi.org/10.1083/jcb.103.3.699	journal	September 1986
Structural basis of enzyme encapsulation into a bacterial nanocompartment Sutter, Markus; Boehringer, Daniel; Gutmann, Sascha Nature Structural & Molecular Biology, Vol. 15, Issue 9 https://doi.org/10.1038/nsmb.1473	journal	August 2008
Widespread distribution of encapsulin nanocompartments reveals functional diversity Giessen, Tobias W.; Silver, Pamela A. Nature Microbiology, Vol. 2, Issue 6 https://doi.org/10.1038/nmicrobiol.2017.29	journal	March 2017
Bacterial microcompartments Kerfeld, Cheryl A.; Aussignargues, Clement; Zarzycki, Jan Nature Reviews Microbiology, Vol. 16, Issue 5 https://doi.org/10.1038/nrmicro.2018.10	journal	March 2018
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method Axen, Seth D.; Erbilgin, Onur; Kerfeld, Cheryl A. PLoS Computational Biology, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pcbi.1003898	journal	October 2014
Bacterial microcompartments and the modular construction of microbial metabolism Kerfeld, Cheryl A.; Erbilgin, Onur Trends in Microbiology, Vol. 23, Issue 1 https://doi.org/10.1016/j.tim.2014.10.003	journal	January 2015
Solution Structure of a Bacterial Microcompartment Targeting Peptide and Its Application in the Construction of an Ethanol Bioreactor Lawrence, Andrew D.; Frank, Stefanie; Newnham, Sarah ACS Synthetic Biology, Vol. 3, Issue 7 https://doi.org/10.1021/sb4001118	journal	November 2013
Bacterial microcompartment-directed polyphosphate kinase promotes stable polyphosphate accumulation in E. coli Liang, Mingzhi; Frank, Stefanie; Lünsdorf, Heinrich Biotechnology Journal, Vol. 12, Issue 3 https://doi.org/10.1002/biot.201600415	journal	February 2017
Bacterial microcompartments moving into a synthetic biological world Frank, Stefanie; Lawrence, Andrew D.; Prentice, Michael B. Journal of Biotechnology, Vol. 163, Issue 2 https://doi.org/10.1016/j.jbiotec.2012.09.002	journal	January 2013
Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell Sutter, Markus; Greber, Basil; Aussignargues, Clement Science, Vol. 356, Issue 6344 https://doi.org/10.1126/science.aan3289	journal	June 2017
Programmed loading and rapid purification of engineered bacterial microcompartment shells Hagen, Andrew; Sutter, Markus; Sloan, Nancy Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05162-z	journal	July 2018
Arginine-rich cell-penetrating peptides Schmidt, Nathan; Mishra, Abhijit; Lai, Ghee Hwee FEBS Letters, Vol. 584, Issue 9 https://doi.org/10.1016/j.febslet.2009.11.046	journal	November 2009
Use of the confined spaces of apo-ferritin and virus capsids as nanoreactors for catalytic reactions Maity, Basudev; Fujita, Kenta; Ueno, Takafumi Current Opinion in Chemical Biology, Vol. 25 https://doi.org/10.1016/j.cbpa.2014.12.026	journal	April 2015
Encapsulins: microbial nanocompartments with applications in biomedicine, nanobiotechnology and materials science Giessen, Tobias W. Current Opinion in Chemical Biology, Vol. 34 https://doi.org/10.1016/j.cbpa.2016.05.013	journal	October 2016
Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle Jakobson, Christopher M.; Tullman-Ercek, Danielle PLOS Pathogens, Vol. 12, Issue 5 https://doi.org/10.1371/journal.ppat.1005558	journal	May 2016
Analysis of Carboxysomes from Synechococcus PCC7942 Reveals Multiple Rubisco Complexes with Carboxysomal Proteins CcmM and CcaA Long, Benedict M.; Badger, Murray R.; Whitney, Spencer M. Journal of Biological Chemistry, Vol. 282, Issue 40 https://doi.org/10.1074/jbc.M703896200	journal	August 2007
Structural Insight into the Clostridium difficile Ethanolamine Utilisation Microcompartment Pitts, Alison C.; Tuck, Laura R.; Faulds-Pain, Alexandra PLoS ONE, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pone.0048360	journal	October 2012
Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy Sutter, Markus; Faulkner, Matthew; Aussignargues, Clément Nano Letters, Vol. 16, Issue 3 https://doi.org/10.1021/acs.nanolett.5b04259	journal	December 2015
Purification and Characterization of Protein Nanotubes Assembled from a Single Bacterial Microcompartment Shell Subunit Noël, Christopher R.; Cai, Fei; Kerfeld, Cheryl A. Advanced Materials Interfaces, Vol. 3, Issue 1 https://doi.org/10.1002/admi.201500295	journal	October 2015
Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization in Clostridium kluyveri Heldt, Dana; Frank, Stefanie; Seyedarabi, Arefeh Biochemical Journal, Vol. 423, Issue 2 https://doi.org/10.1042/BJ20090780	journal	September 2009
Structural Insights into Higher Order Assembly and Function of the Bacterial Microcompartment Protein PduA Pang, Allan; Frank, Stefanie; Brown, Ian Journal of Biological Chemistry, Vol. 289, Issue 32 https://doi.org/10.1074/jbc.M114.569285	journal	May 2014
UniProt: the universal protein knowledgebase Nucleic Acids Research, Vol. 45, Issue D1, p. D158-D169 https://doi.org/10.1093/nar/gkw1099	journal	November 2016
A new protease required for cell-cycle progression in yeast Li, Shyr-Jiann; Hochstrasser, Mark Nature, Vol. 398, Issue 6724 https://doi.org/10.1038/18457	journal	March 1999
Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function Lassila, Jonathan K.; Bernstein, Susan L.; Kinney, James N. Journal of Molecular Biology, Vol. 426, Issue 11 https://doi.org/10.1016/j.jmb.2014.02.025	journal	May 2014
Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications Young, Eric J.; Burton, Rodney; Mahalik, Jyoti P. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01441	journal	July 2017
Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm Lee, Matthew J.; Mantell, Judith; Hodgson, Lorna Nature Chemical Biology, Vol. 14, Issue 2 https://doi.org/10.1038/nchembio.2535	journal	December 2017
Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria: Bacterial Microcompartments Jorda, Julien; Lopez, David; Wheatley, Nicole M. Protein Science, Vol. 22, Issue 2 https://doi.org/10.1002/pro.2196	journal	January 2013
Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement Parsons, Joshua B.; Frank, Stefanie; Bhella, David Molecular Cell, Vol. 38, Issue 2 https://doi.org/10.1016/j.molcel.2010.04.008	journal	April 2010
A synthetic system for expression of components of a bacterial microcompartment Sargent, F.; Davidson, F. A.; Kelly, C. L. Microbiology, Vol. 159, Issue Pt_11 https://doi.org/10.1099/mic.0.069922-0	journal	September 2013
Engineered Protein Nano-Compartments for Targeted Enzyme Localization Choudhary, Swati; Quin, Maureen B.; Sanders, Mark A. PLoS ONE, Vol. 7, Issue 3 https://doi.org/10.1371/journal.pone.0033342	journal	March 2012
Engineering nanoreactors using bacterial microcompartment architectures Plegaria, Jefferson S.; Kerfeld, Cheryl A. Current Opinion in Biotechnology, Vol. 51 https://doi.org/10.1016/j.copbio.2017.09.005	journal	June 2018
Protein Structures Forming the Shell of Primitive Bacterial Organelles Kerfeld, C. A. Science, Vol. 309, Issue 5736 https://doi.org/10.1126/science.1113397	journal	August 2005
Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria Garcia-Alles, Luis F.; Lesniewska, Eric; Root, Katharina PLOS ONE, Vol. 12, Issue 9 https://doi.org/10.1371/journal.pone.0185109	journal	September 2017
Molecular Interaction Between the Strep-tag Affinity Peptide and its Cognate Target, Streptavidin Schmidt, Thomas G. M.; Koepke, Jürgen; Frank, Ronald Journal of Molecular Biology, Vol. 255, Issue 5 https://doi.org/10.1006/jmbi.1996.0061	journal	February 1996
Engineering and characterization of a superfolder green fluorescent protein Pédelacq, Jean-Denis; Cabantous, Stéphanie; Tran, Timothy Nature Biotechnology, Vol. 24, Issue 1, p. 79-88 https://doi.org/10.1038/nbt1172	journal	December 2005
Transcriptional Regulation of the Escherichia coli Gene rraB , Encoding a Protein Inhibitor of RNase E Zhou, Li; Zhao, Meng; Wolf, Rachel Z. Journal of Bacteriology, Vol. 191, Issue 21 https://doi.org/10.1128/JB.00344-09	journal	November 2009
Hyper-acidic protein fusion partners improve solubility and assist correct folding of recombinant proteins expressed in Escherichia coli Zou, Zhurong; Cao, Lijuan; Zhou, Pei Journal of Biotechnology, Vol. 135, Issue 4 https://doi.org/10.1016/j.jbiotec.2008.05.007	journal	July 2008
Encapsulation of multiple cargo proteins within recombinant Eut nanocompartments Quin, Maureen B.; Perdue, Sarah A.; Hsu, Szu-Yi Applied Microbiology and Biotechnology, Vol. 100, Issue 21 https://doi.org/10.1007/s00253-016-7737-8	journal	July 2016
De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment : Design of Signal Sequences Jakobson, Christopher M.; Slininger Lee, Marilyn F.; Tullman-Ercek, Danielle Protein Science, Vol. 26, Issue 5 https://doi.org/10.1002/pro.3144	journal	April 2017
Bacterial microcompartment assembly: The key role of encapsulation peptides Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul Communicative & Integrative Biology, Vol. 8, Issue 3 https://doi.org/10.1080/19420889.2015.1039755	journal	May 2015
Efficient in Vitro Encapsulation of Protein Cargo by an Engineered Protein Container Wörsdörfer, Bigna; Pianowski, Zbigniew; Hilvert, Donald Journal of the American Chemical Society, Vol. 134, Issue 2 https://doi.org/10.1021/ja211011k	journal	December 2011
Directed Evolution of a Protein Container Worsdorfer, B.; Woycechowsky, K. J.; Hilvert, D. Science, Vol. 331, Issue 6017 https://doi.org/10.1126/science.1199081	journal	February 2011
Quantitative Packaging of Active Enzymes into a Protein Cage Azuma, Yusuke; Zschoche, Reinhard; Tinzl, Matthias Angewandte Chemie International Edition, Vol. 55, Issue 4 https://doi.org/10.1002/anie.201508414	journal	December 2015
Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments Zarzycki, Jan; Erbilgin, Onur; Kerfeld, Cheryl A. Applied and Environmental Microbiology, Vol. 81, Issue 24 https://doi.org/10.1128/AEM.02587-15	journal	September 2015

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