right|thumb|460px|Electron micrographs showing alpha-carboxysomes from the chemoautotrophic bacterium [[Halothiobacillus|Halothiobacillus neapolitanus: (A) arranged within the cell, and (B) intact upon isolation. Scale bars indicate 100 nm.]]
Carboxysomes are bacterial microcompartments (BMCs) consisting of polyhedral protein shells filled with the enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)—the predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin cycle—and carbonic anhydrase.
Carboxysomes are an essential part of the broader metabolic network called the Carbon dioxide-Concentrating Mechanism (CCM), which functions in two parts: (1) Membrane transporters concentrate inorganic carbon (C<sub>i</sub>) in the cell cytosol which is devoid of carbonic anhydrases. Carbon is primarily stored in the form of HCO<sub>3</sub><sup>−</sup> which cannot re-cross the lipid membrane, as opposed to neutral CO<sub>2</sub> which can easily escape the cell. This stockpiles carbon in the cell, creating a disequilibrium between the intracellular and extracellular environments of about 30x the C<sub>i</sub> concentration in water. (2) Cytosolic HCO<sub>3</sub><sup>−</sup> diffuses into the carboxysome, where carboxysomal carbonic anhydrases dehydrate it back to CO<sub>2</sub> in the vicinity of Rubisco, allowing Rubisco to operate at its maximal rate.
Carboxysomes are the best studied example of bacterial microcompartments, the term for functionally diverse organelles that are alike in having a protein shell. The non-icosahedral faceted shapes of some carboxysomes can naturally be explained within the elastic theory of heterogeneous thin shells. Proteins known to form the shell have been structurally characterized by X-ray crystallography. The proteins that constitute the majority of the shell form cyclical hexamers or pseudo-hexamers and belong to the BMC protein family.
A number of capsids, protein shells of viruses, are also icosahedral, composed of hexameric and pentameric proteins, but currently there is no evidence suggesting any evolutionary relationship between the carboxysome shell and viral capsids.
Scaffold proteins
All carboxysomes contain scaffold proteins that nucleate carboxysome components together during the assembly process. These scaffold proteins are required for carboxysome assembly; without them, carboxysomes do not form. The α-carboxysomal scaffold protein is called CsoS2, and the β-carboxysomal scaffold protein is called CcmM. Though CsoS2 and CcmM have related functions, they have no evolutionary or sequence similarity. Both proteins bind to Rubisco, thereby ensuring that Rubisco gets packaged during carboxysome biogenesis. Remarkably, both proteins bind to Rubisco at a binding site that bridges two large subunits while maintaining contact with the small subunit, ensuring that only the 16-subunit Rubisco holoenzyme is encapsulated. Both CsoS2 and CcmM have repetitive domain structures giving them multi-valent modes of binding. CcmM has three small-subutnit-like (SSUL) domains that bind to Rubisco, In α-carboxysomes, the CsoS2 MR repeats have been shown to define the size of the carboxysome.
Two types of carboxysomes
There are two types of carboxysomes, alpha- and beta-carboxysomes. Although similar in appearance, they differ in their protein composition, including the form of RuBisCO they enclose. Furthermore, studies have revealed fundamental differences in their gene organization and possibly their assembly pathway. Based on bioinformatic studies of shell proteins, it appears that the two types of carboxysomes evolved independently. Repetitive motifs can be identified in all three regions; the N-terminal domain repeats bind to Rubisco, CsoSCA is a beta-carbonic anhydrase that binds to Rubisco and has been found to be allosterically regulated by the Rubisco substrate, ribulose,1-5,bisphosphate (RuBP) in alpha-cyanobacteria. Studies in Halothiobacillus neapolitanus have shown that empty shells of normal shape and composition are assembled in carboxysomal RuBisCO-lacking mutants, suggesting that alpha-carboxysome shell biogenesis and enzyme sequestration are two independent, but functionally linked processes.
The signature proteins of the beta-carboxysome are Form IB RuBisCO and a gamma carbonic anhydrase homolog.
The beta-carboxysome assembles from the inside out. First an enzymatic core forms that is subsequently encapsulated by the protein shell.
Potential uses of the carboxysome in biotechnology
As is the case with other BMCs, the carboxysome is attracting significant attention by researchers for applications in plant synthetic biology. The transfer of a genetic module coding for an alpha-carboxysome has been shown to produce carboxysome-like structures in E. coli.
- Engineer the carbon dioxide-concentrating mechanism (CCM) and carboxysomes into plants for increased CO<sub>2</sub> capture and enhanced growth.
- Engineer faster Rubiscos. The fastest form I prokaryotic Rubiscos are mostly found in α-carboxysomes.
- Engineer a minimal carboxysome gene set (Rubisco, carbonic anhydrase, scaffold protein, hexameric shell, pentameric shell) to facilitate facile engineering into alternative host organisms.
- Design in vitro carboxysomes for cell-free CO<sub>2</sub> fixation.
- Engineer carboxysomes to have alternative metabolisms.
Carboxysome reviews (by year)
Carboxysome research expands every year. Published reviews chart the rapid pace of discovery across the broad field of "carboxysomics".
{| class="wikitable sortable mw-collapsible"
|+
!First Author
!Title
!Year
!Link
|-
|Shively et al.
|Inclusion bodies of prokaryotes
|1974
|[https://pubmed.ncbi.nlm.nih.gov/4372937/]
|-
|Badger and Price
|The CO<sub>2</sub> concentrating mechanism in cyanobacteria and microalgae
|1992
|[https://onlinelibrary.wiley.com/doi/10.1111/j.1399-3054.1992.tb04711.x]
|-
|Giordano et al.
|CO<sub>2</sub> Concentrating Mechanisms in Algae: Mechanisms, Environmental Modulation, and Evolution
|2005
|[https://www.annualreviews.org/doi/10.1146/annurev.arplant.56.032604.144052#abstractSection]
|-
|Heinhorst et al.
|Carboxysomes and Carboxysome-like Inclusions
|2006
|[https://link.springer.com/chapter/10.1007/7171_023]
|-
|Price et al.
|Advances in understanding the cyanobacterial CO<sub>2</sub>-concentrating-mechanism (CCM): functional components, Ci transporters, diversity, genetic regulation and prospects for engineering into plants
|2008
|[https://doi.org/10.1093/jxb/erm112]
|-
|Espie et al.
|Carboxysomes: cyanobacterial RubisCO comes in small packages
|2011
|[https://pubmed.ncbi.nlm.nih.gov/21556873/]
|-
|Kinney et al.
|Comparative analysis of carboxysome shell proteins
|2011
|[https://pubmed.ncbi.nlm.nih.gov/21279737/]
|-
|Moroney et al.
|Photorespiration and carbon concentrating mechanisms: two adaptations to high O2, low CO2 conditions
|2013
|[https://link.springer.com/article/10.1007/s11120-013-9865-7#Abs1]
|-
|Rae et al.
|Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO<sub>2</sub> Fixation in Cyanobacteria and Some Proteobacteria
|2013
|[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811607/]
|-
|Hanson et al.
|Towards engineering carboxysomes into C3 plants
|2016
|[https://onlinelibrary.wiley.com/doi/10.1111/tpj.13139]
|-
|Long et al.
|Cyanobacterial CO₂-concentrating mechanism components: function and prospects for plant metabolic engineering
|2016
|[https://www.sciencedirect.com/science/article/pii/S1369526616300292]
|-
|Kerfeld and Melnicki
|Assembly, function and evolution of cyanobacterial carboxysomes
|2016
|[https://pubmed.ncbi.nlm.nih.gov/27060669/]
|-
|Rae et al.
|Progress and challenges of engineering a biophysical CO<sub>2</sub>-concentrating mechanism into higher plants
|2017
|[https://academic.oup.com/jxb/article/68/14/3717/3750769#96316512]
|-
|Turmo et al.
|Carboxysomes: metabolic modules for CO<sub>2</sub> fixation
|2017
|[https://pubmed.ncbi.nlm.nih.gov/28934381/]
|-
|Hennacy and Jonikas
|Prospects for Engineering Biophysical CO2 Concentrating Mechanisms into Land Plants to Enhance Yields
|2020
|[https://www.annualreviews.org/doi/10.1146/annurev-arplant-081519-040100]
|-
|Borden and Savage
|New discoveries expand possibilities for carboxysome engineering
|2021
|[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169590/]
|-
|Huffine et al.
|Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments
|2021
|[https://pubmed.ncbi.nlm.nih.gov/34717259/]
|-
|Liu
|Advances in the bacterial organelles for CO<sub>2</sub> fixation
|2021
|[https://www.cell.com/trends/microbiology/fulltext/S0966-842X(21)00259-6]
|-
|Liu et al.
|Protein stoichiometry, structural plasticity and regulation of bacterial microcompartments
|2021
|[https://pubmed.ncbi.nlm.nih.gov/34340100/]
|-
|Trettel et al.
|Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation
|2024
|<nowiki>[20</nowiki>]
|-
|Trettel et al.
|Dynamic structural determinants in bacterial microcompartment shells
|2024
|<nowiki>[21</nowiki>]
|-
|Santos Correa et al.
|Carboxysomes: The next frontier in biotechnology and sustainable solutions
|2024
|<nowiki>[22</nowiki>]
|-
|Nguyen et al.
|Understanding carboxysomes to enhance carbon fixation in crops
|2025
|<nowiki>[23</nowiki>]
|-
|Nguyen et al.
|The Function, Evolution, and Future of Carboxysomes
|2025
|<nowiki>[24</nowiki>]
|-
|Hartzler et al.
|Recent insights into α-carboxysome structure, mechanism, and assembly
|2026
|<nowiki>[25</nowiki>]
|-
|Li et al.
|From fundamental understanding to engineering carboxysomes for biotechnological applications
|2026
|<nowiki>[26</nowiki>]
|}
See also
- Bacterial microcompartment
- BMC domain
- RuBisCO
- Pyrenoid
References
External links
- Mysterious Bacterial Microcompartments Revealed By Biochemists
- Not so simple after all. A renaissance of research into prokaryotic evolution and cell structure