Carboxysome
Encyclopedia
Bacterial microcompartment
Bacterial microcompartments are widespread bacterial organelles that are made of a protein shell that surrounds and encloses various enzymes. These compartments are typically about 100-200 nanometres across and made of interlocking proteins. They do not contain lipids since they are not surrounded...
s that contain enzymes involved in carbon fixation
Carbon fixation
In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that...
. Carboxysomes are made of polyhedral
Polyhedron
In elementary geometry a polyhedron is a geometric solid in three dimensions with flat faces and straight edges...
protein shells about 80 to 140 nanometre
Nanometre
A nanometre is a unit of length in the metric system, equal to one billionth of a metre. The name combines the SI prefix nano- with the parent unit name metre .The nanometre is often used to express dimensions on the atomic scale: the diameter...
s in diameter. These compartments are thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCo
RuBisCO
Ribulose-1,5-bisphosphate carboxylase oxygenase, commonly known by the shorter name RuBisCO, is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is converted by plants to energy-rich molecules such as glucose. RuBisCo is an abbreviation...
- the predominant enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
in carbon fixation
Carbon fixation
In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that...
and the rate limiting enzyme in the Calvin cycle
Calvin cycle
The Calvin cycle or Calvin–Benson-Bassham cycle or reductive pentose phosphate cycle or C3 cycle or CBB cycle is a series of biochemical redox reactions that take place in the stroma of chloroplasts in photosynthetic organisms...
. These organelles are found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide
Carbon fixation
In biology, carbon fixation is the reduction of carbon dioxide to organic compounds by living organisms. The obvious example is photosynthesis. Carbon fixation requires both a source of energy such as sunlight, and an electron donor such as water. All life depends on fixed carbon. Organisms that...
.
Carboxysomes are an example of a wider group of protein micro-compartments that have dissimilar functions, but similar structures, based on homology of the two shell protein families.
Discovery
Using electron microscopyElectron microscope
An electron microscope is a type of microscope that uses a beam of electrons to illuminate the specimen and produce a magnified image. Electron microscopes have a greater resolving power than a light-powered optical microscope, because electrons have wavelengths about 100,000 times shorter than...
the first carboxysomes were seen in 1956, in the cyanobacterium Phormidium uncinatum in the early 1960s similar polyhedral objects were observed in other cyanobacteria. These structures were named polyhedral bodies in 1961 and over the next few years were also discovered in some chemotrophic bacteria that fixed carbon dioxide (for example, Halothiobacillus
Halothiobacillus
Halothiobacillus is a genus of Proteobacteria. All species are obligate aerobic bacteria, they requires oxygen to grow. They are also halophile, they live in environments with high concentrations of salt....
, Acidithiobacillus
Acidithiobacillus
Acidithiobacillus is a genus of Proteobacteria. Like all Proteobacteria, Acidithiobacillus is Gram-negative. The members of this genus used to belong to Thiobacillus, before they were reclassified in the year 2000....
, Nitrobacter
Nitrobacter
Nitrobacter is genus of mostly rod-shaped, gram-negative, and chemoautotrophic bacteria.Nitrobacter plays an important role in the nitrogen cycle by oxidizing nitrite into nitrate in soil...
and Nitrococcus).
Carboxysomes were first purified from Thiobacillus 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.
Architecture
Structurally, carboxysomes are icosahedralIcosahedron
In geometry, an icosahedron is a regular polyhedron with 20 identical equilateral triangular faces, 30 edges and 12 vertices. It is one of the five Platonic solids....
, or quasi-icosahedral, typically around 80 to 120 nm
Nanometre
A nanometre is a unit of length in the metric system, equal to one billionth of a metre. The name combines the SI prefix nano- with the parent unit name metre .The nanometre is often used to express dimensions on the atomic scale: the diameter...
in diameter. The carboxysome has an outer shell composed of a few thousand protein subunits, which encapsulates the two carbon fixing enzymes, carbonic anhydrase and RuBisCO. Proteins known to form the shell have been structurally characterized by X-ray crystallography. The protein that constitutes the majority of the shell forms a cyclical hexamer. These hexamers constitute the basic building blocks of the shell. X-ray structural data suggest that the hexamers assemble further in a side-by-side fashion to form a tightly packed molecular layer, which represents the outer shell. Small pores are present through the hexamers and may serve as the route for diffusion of substrates (bicarbonate
Bicarbonate
In inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid...
and ribulose-1,5-bisphosphate
Ribulose-1,5-bisphosphate
Ribulose-1,5-bisphosphate is an organic substance that is involved in photosynthesis. The anion is a double phosphate ester of the ketose called ribulose. Salts of this species can be isolated, but its crucial biological function involves this colourless anion in solution...
) and products (3-phosphoglycerate) into and out of the carboxysome. Positively charged amino acids in the pores might 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, which have been proposed to occupy the vertices of the icosahedral shell.
A number of viral capsids are also constructed from hexameric and pentameric proteins, but whether any evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary relationship exists between the carboxysome and viral capsids is unknown. Electron cryo-tomography studies have confirmed the approximately icosahedral geometry of the carboxysome, and have visualized enzymes molecules inside, presumed to be RuBisCO, arranged in a few concentric layers. In addition, non-icosahedral faceted shapes of some caroxysomes can naturally be explained within the elastic theory of heterogeneous thin shells.
Studies in Halothiobacillus neapolitanus
Halothiobacillus
Halothiobacillus is a genus of Proteobacteria. All species are obligate aerobic bacteria, they requires oxygen to grow. They are also halophile, they live in environments with high concentrations of salt....
have shown that empty shells of normal shape and composition are assembled in carboxysomal RuBisCO-lacking mutants suggesting that carboxysome shell biogenesis and enzyme sequestration are two independent, but functionally linked processes. Intriguingly, carboxysomes of Halothiobacillus neapolitanus
Halothiobacillus
Halothiobacillus is a genus of Proteobacteria. All species are obligate aerobic bacteria, they requires oxygen to grow. They are also halophile, they live in environments with high concentrations of salt....
have been found to accommodate chimeric and heterologous species of RuBisCO and it is the large subunit of RuBisCO that determines whether the enzyme is sequestered into carboxysomes or not.