Structure of Carboxysomes and Other Bacterial Microcompartments

Electron micrograph of carboxysomes (courtesy of Vim Vermaas, adapted from Kerfeld, et al., 2005)
Electron micrograph of carboxysomes (courtesy of Vim Vermaas, adapted from Kerfeld, et al., 2005)

Bacterial microcompartments are giant, polyhedrally shaped structures found within many bacteria. They consist of a thin outer protein shell assembled from a few thousand protein subunits — in a fashion reminiscent of a viral capsid — encapsulating a series of sequentially-acting enzymes. They function as simple protein-based metabolic organelles by sequestering key pathways within the cell. The carboxysome is the founding member; it encapsulates the enzymes carbonic anhydrase and RuBisCO in cyanabacteria and some chemoautotrophs in order to enhance CO2 fixation. Other types of microcompartments have been studied that metabolize two and three carbon compunds such as ethanolamine and 1,2-propanediol in various enteric bacteria. Those microcompartments serve to retain chemically reactive and/or volatile pathway intermediates like acetaldehyde and propionaldehyde so they can be converted to less reactive compounds before being released into the cytosol.

Metabolic functions of two kinds of microcompartments. (Adapted from Yeates, Crowley, & Tanaka, 2010)
Metabolic functions of two kinds of microcompartments. (Adapted from Yeates, Crowley, & Tanaka, 2010)

We have determined crystal structures of many of the shell proteins that compose various microcompartments, including from the carboxysome, the Pdu (propanediol utilization), and the Eut (ethanolamine) shells. These have been extremely helpful in illuminating form and function. From these studies we understand that the main shell proteins (known as BMC proteins) assemble as hexamers, which then further assemble side-by-side in a molecular sheet that forms the flat facets of the intact shell. In our models, special pentameric shell proteins are postulated to form the vertices of the icosahedral-like shell. These valuable structural findings are the result of efforts by numerous graduate students, postodocs and researchers in the laboratory over the years, beginning with Kerfeld et al. in 2005.

A simplified model of microcompartment assembly. (Adapted from Yeates, Thompson & Bobik, 2011)
A simplified model of microcompartment assembly. (Adapted from Yeates, Thompson & Bobik, 2011)

Each of the hexamers bears a narrow central pore. These pores are presumed to be the routes by which substrates and products — and likely cofactors for some of the enclosed enzymatic reactions — cross into and out of the microcompartment. Some of the shell proteins undergo conformational changes between open and closed forms, providing a clue about how transport might be controlled. We have also determined that certain special shell proteins bind an iron-sulfur metal cluster at the center of their pore, we presume in order to facilitate transport of electrons or possibly intact metal clusters; most microcompartment types involve internal redox reactions as well as internal iron-sulfur enzymes. Our collaborator, Tom Bobik at Iowa State, has established that some of the enzymes inside microcompartments are targeted to the interior surface of the shell by special N-terminal sequence extensions. An understanding of this mechanism has opened up prospects for engineering microcompartments with novel interior enzymes.

Open and closed pore forms of a BMC shell protein (EutL). (Adapted from Tanaka, et al., 2010)
Open and closed pore forms of a BMC shell protein (EutL). (Adapted from Tanaka, et al., 2010)

Our ongoing aims are: to provide futher structural data in order to establish more complete three-dimensional models of microcompartments; to engineer microcompartments with different properties; and to use bioinformatics methods to discover new types of compartments in bacteria.

References:

2017

Park J, Chun S, Bobik TA, Houk KN, Yeates TO
Molecular Dynamics Simulations of Selective Metabolite Transport across the Propanediol Bacterial Microcompartment Shell.
J Phys Chem B. Aug 2017. 121(34):8149-8154. 2017 PMID: 28829618
10.1021/acs.jpcb.7b07232

2016

Jorda J, Leibly DJ, Thompson MC, Yeates TO
Structure of a novel 13 nm dodecahedral nanocage assembled from a redesigned bacterial microcompartment shell protein.
Chem. Commun. (Camb.). Apr 2016. 52(28):5041-4. 2016 PMID: 26988700
10.1039/c6cc00851h

2015

Thompson MC, Cascio D, Leibly DJ, Yeates TO
An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein.
Protein Sci.. Jun 2015. 24(6):956-75. 2015 PMID: 25752492
PMC4456109 10.1002/pro.2672
Chowdhury C, Chun S, Pang A, Sawaya MR, Sinha S, Yeates TO, Bobik TA
Selective molecular transport through the protein shell of a bacterial microcompartment organelle.
Proc. Natl. Acad. Sci. U.S.A.. Mar 2015. 112(10):2990-5. 2015 PMID: 25713376
PMC4364225 10.1073/pnas.1423672112

2014

Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA
Diverse bacterial microcompartment organelles.
Microbiol. Mol. Biol. Rev.. Sep 2014. 78(3):438-68. 2014 PMID: 25184561
PMC4187681 10.1128/MMBR.00009-14
Thompson MC, Wheatley NM, Jorda J, Sawaya MR, Gidaniyan SD, Ahmed H, Yang Z, McCarty KN, Whitelegge JP, Yeates TO
Identification of a unique Fe-S cluster binding site in a glycyl-radical type microcompartment shell protein.
J. Mol. Biol.. Sep 2014. 426(19):3287-304. 2014 PMID: 25102080
PMC4175982 10.1016/j.jmb.2014.07.018 NIHMS617253

2013

Yeates TO, Jorda J, Bobik TA
The shells of BMC-type microcompartment organelles in bacteria.
J. Mol. Microbiol. Biotechnol.. 2013. 23(4-5):290-9. 2013 PMID: 23920492
10.1159/000351347

2011

Yeates TO, Thompson MC, Bobik TA
The protein shells of bacterial microcompartment organelles.
Curr. Opin. Struct. Biol.. Apr 2011. 21(2):223-31. 2011 PMID: 21315581
PMC3070793 10.1016/j.sbi.2011.01.006 NIHMS274656

2010

Crowley CS, Cascio D, Sawaya MR, Kopstein JS, Bobik TA, Yeates TO
Structural insight into the mechanisms of transport across the Salmonella enterica Pdu microcompartment shell.
J. Biol. Chem.. Nov 2010. 285(48):37838-46. 2010 PMID: 20870711
PMC2988387 10.1074/jbc.M110.160580
Fan C, Cheng S, Liu Y, Escobar CM, Crowley CS, Jefferson RE, Yeates TO, Bobik TA
Short N-terminal sequences package proteins into bacterial microcompartments.
Proc. Natl. Acad. Sci. U.S.A.. Apr 2010. 107(16):7509-14. 2010 PMID: 20308536
PMC2867708 10.1073/pnas.0913199107
Tanaka S, Sawaya MR, Yeates TO
Structure and mechanisms of a protein-based organelle in Escherichia coli.
Science. Jan 2010. 327(5961):81-4. 2010 PMID: 20044574
10.1126/science.1179513

2009

Dryden KA, Crowley CS, Tanaka S, Yeates TO, Yeager M
Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals.
Protein Sci.. Dec 2009. 18(12):2629-35. 2009 PMID: 19844993
PMC2821281 10.1002/pro.272
Tanaka S, Sawaya MR, Phillips M, Yeates TO
Insights from multiple structures of the shell proteins from the beta-carboxysome.
Protein Sci.. Jan 2009. 18(1):108-20. 2009 PMID: 19177356
PMC2708042 10.1002/pro.14
Beeby M, Bobik TA, Yeates TO
Exploiting genomic patterns to discover new supramolecular protein assemblies.
Protein Sci.. Jan 2009. 18(1):69-79. 2009 PMID: 19177352
PMC2708037 10.1002/pro.1

2008

Cheng S, Liu Y, Crowley CS, Yeates TO, Bobik TA
Bacterial microcompartments: their properties and paradoxes.
Bioessays. Nov 2008. 30(11-12):1084-95. 2008 PMID: 18937343
PMC3272490 10.1002/bies.20830 NIHMS348799
Crowley CS, Sawaya MR, Bobik TA, Yeates TO
Structure of the PduU shell protein from the Pdu microcompartment of Salmonella.
Structure. Sep 2008. 16(9):1324-32. 2008 PMID: 18786396
10.1016/j.str.2008.05.013
Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM
Protein-based organelles in bacteria: carboxysomes and related microcompartments.
Nat. Rev. Microbiol.. Sep 2008. 6(9):681-91. 2008 PMID: 18679172
10.1038/nrmicro1913
Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO
Atomic-level models of the bacterial carboxysome shell.
Science. Feb 2008. 319(5866):1083-6. 2008 PMID: 18292340
10.1126/science.1151458

2007

Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, Heinhorst S, Kerfeld CA, Yeates TO
Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome.
PLoS Biol.. Jun 2007. 5(6):e144. 2007 PMID: 17518518
PMC1872035 10.1371/journal.pbio.0050144
Yeates TO, Tsai Y, Tanaka S, Sawaya MR, Kerfeld CA
Self-assembly in the carboxysome: a viral capsid-like protein shell in bacterial cells.
Biochem. Soc. Trans.. Jun 2007. 35(Pt 3):508-11. 2007 PMID: 17511640
10.1042/BST0350508

2006

Sawaya MR, Cannon GC, Heinhorst S, Tanaka S, Williams EB, Yeates TO, Kerfeld CA
The structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two.
J. Biol. Chem.. Mar 2006. 281(11):7546-55. 2006 PMID: 16407248
10.1074/jbc.M510464200

2005

Kerfeld CA, Sawaya MR, Tanaka S, Nguyen CV, Phillips M, Beeby M, Yeates TO
Protein structures forming the shell of primitive bacterial organelles.
Science. Aug 2005. 309(5736):936-8. 2005 PMID: 16081736
10.1126/science.1113397

structural, computational, and synthetic biology