Carboxysomes are
bacterial microcompartment ] Bacterial microcompartments (BMCs) are organelle-like structures, consisting of a protein shell that encloses enzymes and other proteins. BMCs are typically about 40–200 nanometers in diameter and are entirely made of proteins. The shell funct ...
s (BMCs) consisting of polyhedral protein shells filled with the enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (
RuBisCO Ribulose-1,5-bisphosphate carboxylase-oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is convert ...
)—the predominant enzyme in
carbon fixation Carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide Carbon dioxide (chemical formula ) is a colorless gas with a density about 53% higher than that of dry air. Carbon ...
and the rate limiting enzyme in the
Calvin cycle The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis Photosynthesis is a process used by plants and other organisms to into that, through , can ...

Calvin cycle
carbonic anhydrase The carbonic anhydrases (or carbonate dehydratases) form a family of enzymes that catalyst, catalyze the interconversion between carbon dioxide and water and the Dissociation (chemistry), dissociated ions of carbonic acid (i.e. bicarbonate and ...

carbonic anhydrase
. Carboxysomes are thought to have evolved as a consequence of the increase in oxygen concentration in the ancient atmosphere; this is because oxygen is a competing substrate to carbon dioxide in the RuBisCO reaction. To overcome the inefficiency of RuBisCO, carboxysomes concentrate carbon dioxide inside the shell by means of co-localized carbonic anhydrase activity, which produces carbon dioxide from the bicarbonate that diffuses into the carboxysome. The resulting concentration of carbon dioxide near RuBisCO decreases the proportion of ribulose-1,5-bisphosphate oxygenation and thereby avoids costly . The surrounding shell provides a barrier to carbon dioxide loss, helping to increase its concentration around RuBisCO. Carboxysomes are an essential part of the carbon dioxide-concentrating mechanism (CCM). Carboxysomes are the best studied example of bacterial microcompartments, the term for functionally diverse organelles that are alike in having a protein shell.


Polyhedral bodies were discovered by
transmission electron microscopy #REDIRECT Transmission electron microscopy #REDIRECT Transmission electron microscopy Transmission electron microscopy (TEM) is a technique in which a beam of s is transmitted through a specimen to form an image. The specimen is most often an u ...
in the
cyanobacterium Cyanobacteria (), also known as Cyanophyta, are a phylum (biology), phylum of Gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), giving them their other name, "blue-green algae", ...

''Phormidium uncinatum'' in 1956. These were later observed in other cyanobacteria and in some chemotrophic bacteria that fixed carbon dioxide—many of them are sulfur reducers or nitrogen fixers (for example, ''
Halothiobacillus ''Halothiobacillus'' is a genus in the ''Gammaproteobacteria''. Both species are obligate aerobic bacteria; they require oxygen to grow. They are also halotolerant; they live in environments with high concentrations of salt or other solutes, but ...
'', ''
Acidithiobacillus ''Acidithiobacillus'' is a genus of the ''Acidithiobacillia'' in the ''"Proteobacteria"''. The genus includes acidophilic organisms capable of iron and/or sulfur oxidation. Like all ''"Proteobacteria"'', ''Acidithiobacillus'' spp. are Gram-negat ...
'', ''
Nitrobacter ''Nitrobacter'' is a genus Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank In biological classification In biology, taxonomy () is the scientific study of naming, defining (Circumscription (taxonomy), cir ...
'' and ''Nitrococcus''; all belonging to
Proteobacteria Proteobacteria is a major phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The pl ...
). The polyhedral bodies were first purified from ''Thiobacillus neapolitanus'' (now ''Halothiobacillus neapolitanus'') in 1973 and shown to contain RuBisCO, held within a rigid outer covering. The authors proposed that since these appeared to be organelles involved in carbon fixation, they should be called ''carboxysomes''.


Structurally, carboxysomes are icosahedral, or quasi-
icosahedral In geometry Geometry (from the grc, γεωμετρία; ' "earth", ' "measurement") is, with , one of the oldest branches of . It is concerned with properties of space that are related with distance, shape, size, and relative position ...
. Electron cryo-tomography studies have confirmed the approximately icosahedral geometry of the carboxysome, and have imaged protein molecules inside (presumed to be RuBisCO), arranged in a few concentric layers. The non-icosahedral faceted shapes of some carboxysomes can naturally be explained within the elastic theory of heterogeneous thin shells. The carboxysome has an outer shell composed of a few thousand protein subunits, which encapsulates a CO2-producing enzyme (carbonic anhydrase) and a carbon-fixing enzyme (RuBisCO). Proteins known to form the shell have been structurally characterized by
X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract into many specific directions. By measurin ...

X-ray crystallography
. The protein that constitutes the majority of the shell forms a cyclical hexamer and belongs to BMC protein family. These hexamers, BMC-H proteins, are the basic building blocks of the shell. In some crystal forms the hexamers assemble further in a side-by-side fashion to form a tightly packed molecular layer, which presumably is how the facets of the shell are assembled. Small pores perforate many different types of BMC-H hexamers, and may serve as the route for diffusion of small substrates (e.g. bicarbonate) into and out of the carboxysome. Positively charged amino acids in the pores presumably help promote the diffusion of the negatively charged substrates and products. Other minor structural components of the shell that have been characterized include pentameric proteins ( BMC-P proteins), which have been proposed to occupy the vertices of the icosahedral shell. A third building block of the carboxysome shell is a protein composed of two BMC domains in tandem ( BMC-T proteins). Structurally, many of these are known to form trimers which are pseudohexameric. Some members of the BMC-T protein family stack in a face-to-face fashion and form tiny cages. Based on crystal structures, these protein cages have relatively large gated pores on both sides, and it has been proposed that the opening and closing of the pore could be controlled in a manner similar to an air-lock. Such an air-lock, in contrast to BMC-H proteins with constitutively open pores, has been suggested to serve as a route for larger substrates (ribulose-1,5-bisphosphate) and products (3-phosphoglycerate) that must cross the shell. A number of viral capsids 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.

Two Types of Carboxysomes

There are two types of carboxysomes. Although they may seem 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 in how they assemble.


Alpha-carboxysomes (aka α-carboxysomes) are also referred as the ''cso'' type of carboxysome. They contain Form IA RuBisCO; they are found in alpha-cyanobacteria, some nitrifying bacteria, some sulfur-oxidizing bacteria (for example, ''Halothiobacillus neapolitanus''), and some
purple bacteria Purple bacteria or purple photosynthetic bacteria are Gram-negative bacteria, Gram-negative proteobacteria that are phototrophic, capable of producing their own food via photosynthesis. They are pigmented with bacteriochlorophyll ''a'' or ''b'', ...
; these are all classified as
Proteobacteria Proteobacteria is a major phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical category of number. The pl ...
). The alpha-carboxysome was the first bacterial microcompartment to be purified and characterized. Electron microscopy studies on purified alpha-carboxysomes or cell sections containing alpha-carboxysomes revealed that they are typically 100-160 nm in diameter. Common building blocks for the shell of alpha-carboxysomes are called CsoS1A/B/C (BMC-H), CsoS4A/B (BMC-P), and CsoS1D (BMC-T). CsoS4A/B were the first BMC-P proteins to be experimentally demonstrated as minor components of the BMC shell (only 12 pentamers are required to cap the vertices of an icosahedron). CsoS1D is first BMC-T which has been structurally characterized; it is also the first example of dimerization of two BMC building blocks in a face-to-face fashion to create a tiny cage. The CsoS1D cage has gated pore at both end, which is proposed to facilitate large metabolites crossing the shell. In addition to the specific form of RuBisCO, other encapsulated proteins distinguish alpha-carboxysomes from beta-carboxysomes such as CsoS2 and CsoSCA. The CsoS2 protein has a very high pI and a unique primary structure. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle- and C-terminal regions. Repetitive motifs can be identified in the N-terminal and middle regions. Recently, it was proposed to be an intrinsically disordered protein with an essential role in alpha-carboxysome assembly. CsoSCA is a shell-associated beta-carbonic anhydrase. 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. Intriguingly, carboxysomes of ''Halothiobacillus neapolitanus'' have been found to accommodate chimeric and heterologous species of RuBisCO and it is the large subunit of RuBisCO which determines whether the enzyme is sequestered into carboxysomes or not.


Beta-carboxysomes (aka β-carboxysomes) can be found in
cyanobacteria Cyanobacteria (), also known as Cyanophyta, are a phylum In biology, a phylum (; plural The plural (sometimes list of glossing abbreviations, abbreviated ), in many languages, is one of the values of the grammatical number, grammatical ...

.Manuel Sommer, Fei Cai, Matthew Melnicki, Cheryl A Kerfeld
β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints
In: J Exp Bot. 68(14). 2017 Jun 22. Pp 3841–3855. Published online 2017 Apr 17. doi:10.1093/jxb/erx115. .
The signature proteins of the beta-carboxysome are Form IB RuBisCO and a gamma carbonic anhydrase homolog. Beta-carboxysomes are typically bigger than alpha-carboxysomes: the observed diameters for them vary from 200 to 400 nm. The structural proteins that are essential for carboxysome formation are encoded in the conserved carboxysome locus known as the ''ccm'' locus. The ''ccm'' locus includes genes for core proteins CcmM and CcmN and the shell proteins CcmK (a BMC-H protein), CcmL (a BMC-P protein) and CcmO (a BMC-T protein). A full length CcmM protein consists of a gamma-carbonic anhydrase domain on and three to five small subunit-like domains (SSLDs; which resemble RbcS, the small subunit of RuBisCO) on its C-terminus. The ccmM gene contains an internal translation site that produces a short form of CcmM (a protein which only consists of SSLDs); both long and short forms of CcmM are required for carboxysome assembly. CcmN contains multiple hexapeptide-repeat domains on its N-terminus and a short α-helical encapsulation peptide on the C-terminus. Other structural components of the carboxysomes are encoded outside of the ''ccm'' locus. CcmP is a BMC-T protein that is absolutely conserved among organisms that form beta-carboxysomes. CcmP pseudohexamer stacks to form a nanocompartment—an example of an air-lock forming protein. Likewise, in some cyanobacterial strains the beta-carboxysomes contain a beta-carbonic anhydrase that is not found in the ''ccm'' locus. The beta-carboxysome assembles from the inside out, first an enzymatic core forms that is subsequently encapsulated by a protein shell. Carboxysome assembly occurs through a series of protein-protein interactions: the enzyme RuBisCO and the two isoforms (full length and short form) of the CcmM protein interact by means of the SSLDs; in strains containing CcaA the beta-carbonic anhydrase is brought into the carboxysome core by interaction with the N-terminus of the full length CcmM. Once the procarboxysome (the carboxysome core) is formed, the N-terminus of the adapter protein CcmN interacts with the N-terminus of CcmM, while the C-terminus of CcmN recruits the shell proteins CcmK (BMC-H) and CcmO (BMC-T). The final step is the addition of the vertices formed by the BMC-P protein CcmL, which then fully cap the enzymatic core.

Potential uses of the carboxysome in biotechnology

As the case with other BMCs, the carboxysome is attracting significant attention by researchers for applications in
synthetic biology Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature. It is a branch of science that encompasses a broad ran ...
. The transfer of a genetic module coding for an alpha-carboxysome has been shown to produce carboxysome-like structures in ''E. coli''. Bioengineering of carboxysome shells have been shown feasible and beta-carboxysomes constructed with chimeric proteins or with chimeric shells has been reported. The introduction of carboxysomes into plant chloroplasts as part of a CO2 concentrating mechanism (such as that found in cyanobacteria) is predicted to have significant improvements on net CO2 fixation and yield. Expression of beta-carboxysomal shell proteins and Form IB Rubisco-CcmM complexes in tobacco chloroplasts has been achieved, but this did not result in compartments containing Rubisco. A further advance has been the construction of minimal alpha-carboxysomes from the cyanobacterium Cyanobium PCC7001 in tobacco chloroplasts containing Form IA Rubisco and the CsoS1A and CsoS2 proteins. As yet, identifiably functional carboxysomes have not yet been constructed in plant chloroplasts. Nonetheless, successful improvement of photosynthesis in plants using this approach is ultimately dependent on the operation of transporter proteins in the chloroplast inner envelope membrane to help generate a high concentration of bicarbonate inside the chloroplast.

See also

Bacterial microcompartment ] Bacterial microcompartments (BMCs) are organelle In cell biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, p ...
BMC domain In molecular biology the Bacterial Microcompartment (BMC) domain is a protein domain found in a variety of shell proteins, including CsoS1A, CsoS1B and CsoS1C of ''Thiobacillus neapolitanus'' (''Halothiobacillus neapolitanus'') and their Homology ( ...
RuBisCO Ribulose-1,5-bisphosphate carboxylase-oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is convert ...
Pyrenoid Pyrenoids are sub-cellular micro-compartments found in chloroplast A chloroplast is a type of membrane-bound organelle In cell biology, an organelle is a specialized subunit, usually within a cell (biology), cell, that has a specific fu ...


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Mysterious Bacterial Microcompartments Revealed By Biochemists

Cell anatomy Organelles Protein complexes