Specialized Internal Structures of Prokaryotes

Ribosomes

The purpose of the ribosome is to translate messenger RNA (mRNA) into proteins with the aid of tRNA.

Ribosomes are tiny spherical organelles that make proteins by joining amino acids together. Many ribosomes are found free in the cytosol, while others are attached to the rough endoplasmic reticulum. The purpose of the ribosome is to translate messenger RNA (mRNA) to proteins with the aid of tRNA. In eukaryotes, ribosomes can commonly be found in the cytosol of a cell, the endoplasmic reticulum or mRNA, as well as the matrix of the mitochondria. Proteins synthesized in each of these locations serve a different role in the cell. In prokaryotes, ribosomes can be found in the cytosol as well. This protein-synthesizing organelle is the only organelle found in both prokaryotes and eukaryotes, asserting the fact that the ribosome is a trait that evolved early on, most likely present in the common ancestor of eukaryotes and prokaryotes. Ribosomes are not membrane bound.

Ribosomes are composed of two subunits, one large and one small, that only bind together during protein synthesis. The purpose of the ribosome is to take the actual message and the charged aminoacyl-tRNA complex to generate the protein. To do so, they have three binding sites. One is for the mRNA; the other two are for the tRNA. The binding sites for tRNA are the A site, which holds the aminoacyl-tRNA complex, and the P site, which binds to the tRNA attached to the growing polypeptide chain.

In most bacteria, the most numerous intracellular structure is the ribosome which is the site of protein synthesis in all living organisms. All prokaryotes have 70S (where S=Svedberg units) ribosomes while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S ribosome is made up of a 50S and 30S subunits. The 50S subunit contains the 23S and 5S rRNA while the 30S subunit contains the 16S rRNA. These rRNA molecules differ in size in eukaryotes and are complexed with a large number of ribosomal proteins, the number and type of which can vary slightly between organisms. The ribosome is the most commonly observed intracellular multiprotein complex in bacteria.

Ribosome assembly consists of transcription, translation, the folding of rRNA and ribosomal proteins, the binding of ribosomal proteins, and the binding and release of the assembly components to make the ribosome. In vivo assembly of the 30S subunit has two intermediates (p130S and p230S) and the 50S subunit has three intermediates (p150S, p250S, and p350S). However, the reconstitution intermediates are not the same as in vitro. The intermediates of the 30S subunit yield 21S and 30S particles while the intermediates of the 50S subunit yield 32S, 43S, and 50S particles. The intermediates in the in vivo assembly are precursor rRNA which is different from in vitro which uses matured rRNA. To complete the mechanism of ribosome assembly, these precursor rRNA gets transformed in the polysomes.

Cell Inclusions and Storage Granules

Bacteria have different methods of nutrient storage that are employed in times of plenty, for use in times of want.

Cell Inclusions and Storage Granules

Bacteria, despite their simplicity, contain a well-developed cell structure responsible for many unique biological properties not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms, and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.

Most bacteria do not live in environments that contain large amounts of nutrients at all times. To accommodate these transient levels of nutrients, bacteria contain several different methods of nutrient storage that are employed in times of plenty, for use in times of want. For example, many bacteria store excess carbon in the form of polyhydroxyalkanoates or glycogen. Some microbes store soluble nutrients, such as nitrate in vacuoles. Sulfur is most often stored as elemental (S0) granules which can be deposited either intra- or extracellularly. Sulfur granules are especially common in bacteria that use hydrogen sulfide as an electron source. Most of the above mentioned examples can be viewed using a microscope, and are surrounded by a thin non-unit membrane to separate them from the cytoplasm.

Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell, and usually consist of viral capsid proteins. Inclusion bodies have a non-unit lipid membrane. Protein inclusion bodies are classically thought to contain misfolded protein. However, this has recently been contested, as green fluorescent protein will sometimes fluoresce in inclusion bodies, which indicates some resemblance of the native structure and researchers have recovered folded protein from inclusion bodies.

When genes from one organism are expressed in another the resulting protein sometimes forms inclusion bodies. This is often true when large evolutionary distances are crossed; for example, a cDNA isolated from Eukarya and expressed as a recombinant gene in a prokaryote, risks the formation of the inactive aggregates of protein known as inclusion bodies. While the cDNA may properly code for a translatable mRNA, the protein that results will emerge in a foreign microenvironment. This often has fatal effects, especially if the intent of cloning is to produce a biologically active protein. For example, eukaryotic systems for carbohydrate modification and membrane transport are not found in prokaryotes.

The internal microenvironment of a prokaryotic cell (pH, osmolarity) may differ from that of the original source of the gene. Mechanisms for folding a protein may also be absent, and hydrophobic residues that normally would remain buried may be exposed and available for interaction with similar exposed sites on other ectopic proteins. Processing systems for the cleavage and removal of internal peptides would also be absent in bacteria. The initial attempts to clone insulin in a bacterium suffered all of these deficits. In addition, the fine controls that may keep the concentration of a protein low will also be missing in a prokaryotic cell, and overexpression can result in filling a cell with ectopic protein that, even if it were properly folded, would precipitate by saturating its environment.

Carboxysomes

Carboxysomes are intracellular structures that contain enzymes involved in carbon fixation and found in many autotrophic bacteria.

Definition of Carboxysomes

Carboxysomes are intracellular structures found in many autotrophic bacteria, including Cyanobacteria, Knallgasbacteria, Nitroso- and Nitrobacteria. They are proteinaceous structures resembling phage heads in their morphology; they contain the enzymes of carbon dioxide fixation in these organisms. It is thought that the high local concentration of the enzymes, along with the fast conversion of bicarbonate to carbon dioxide by carbonic anhydrase, allows faster and more efficient carbon dioxide fixation than is possible inside the cytoplasm. Similar structures are known to harbor the B12-containing coenzyme glycerol dehydratase, the key enzyme of glycerol fermentation to 1,3-propanediol, in some Enterobacteriaceae, such as Salmonella.

Carboxysomes are bacterial microcompartments that contain enzymes involved in carbon fixation. Carboxysomes are made of polyhedral protein shells about 80 to 140 nanometres in diameter. These compartments are thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCo (ribulose bisphosphate carboxylase/oxygenase) - the predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin cycle. These organelles are found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide.

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. Using electron microscopy 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; over the next few years they were also discovered in some chemotrophic bacteria that fixed carbon dioxide. Among these are Halothiobacillus, Acidithiobacillus, Nitrobacter and Nitrococcus.

Carboxysomes were first purified from Thiobacillus neapolitanus in 1973, and were shown to contain RuBisCo held within a rigid outer covering.

Magnetosomes

Magnetosomes are intracellular organelles in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field.

Magnetosomes are intracellular organelles found in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field (magnetotaxis). They contain 15 to 20 magnetite crystals that together act like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments. Each magnetite crystal within a magnetosome is surrounded by a lipid bilayer. Specific soluble and transmembrane proteins are sorted to the membrane. Recent research has shown that magnetosomes are invaginations of the inner membrane and not freestanding vesicles. Magnetite-bearing magnetosomes have also been found in eukaryotic magnetotactic algae, with each cell containing several thousand crystals.

Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe₃O₄), or iron sulfide magnetosomes, which contain crystals of greigite (Fe₃S₄). Several other iron sulfide minerals have also been identified in iron sulfide magnetosomes — including mackinawite (tetragonal FeS) and a cubic FeS — which are thought to be precursors of Fe3S4. One type of magnetotactic bacterium present at the oxic-anoxic transition zone (OATZ) of the southern basin of the Pettaquamscutt River Estuary, Narragansett, Rhode Island is known to produce both iron oxide and iron sulfide magnetosomes.

The particle morphology of magnetosome crystals varies, but is consistent within cells of a single magnetotactic bacterial species or strain. Three general crystal morphologies have been reported in magnetotactic bacteria on the basis: roughly cuboidal, elongated prismatic (roughly rectangular), and tooth-, bullet-, or arrowhead-shaped. Magnetosome crystals are typically 35–120 nm long, which makes them single- domain. Single-domain crystals have the maximum possible magnetic moment per unit volume for a given composition. Smaller crystals are superparamagnetic–that is, not permanently magnetic at ambient temperature, and domain walls would form in larger crystals. In most magnetotactic bacteria, the magnetosomes are arranged in one or more chains.

Magnetic interactions between the magnetosome crystals in a chain cause their magnetic dipole moments to orientate parallel to each other along the length of the chain. The magnetic dipole moment of the cell is usually large enough so that its interaction with Earth's magnetic field overcomes thermal forces that tend to randomize the orientation of the cell in its aqueous surroundings. Magnetotactic bacteria also use aerotaxis, a response to changes in oxygen concentration that favors swimming toward a zone of optimal oxygen concentration. In lakes or oceans the oxygen concentration is commonly dependent on depth. As long as the Earth's magnetic field has a significant downward slant, the orientation along field lines aids the search for the optimal concentration. This process is called magneto-aerotaxis.

Gas Vesicles

Gas vesicles are spindle-shaped structures that provide buoyancy to cells by decreasing their overall cell density.

Gas vesicles are spindle-shaped structures found in some planktonic bacteria that provides buoyancy to these cells by decreasing their overall cell density. Positive buoyancy is needed to keep the cells in the upper reaches of the water column, so that they can continue to perform photosynthesis. They are made up of a shell of protein that has a highly hydrophobic inner surface, making it impermeable to water (and stopping water vapor from condensing inside), but permeable to most gases. Because the gas vesicle is a hollow cylinder, it is liable to collapse when the surrounding pressure becomes too great.

Natural selection has fine-tuned the structure of the gas vesicle to maximize its resistance to buckling by including an external strengthening protein, GvpC, rather like the green thread in a braided hosepipe. There is a simple relationship between the diameter of the gas vesicle and pressure at which it will collapse - the wider the gas vesicle the weaker it becomes. However, wider gas vesicles are more efficient. They provide more buoyancy per unit of protein than narrow gas vesicles. Different species produce gas vesicles of different diameters, allowing them to colonize different depths of the water column (fast growing, highly competitive species with wide gas vesicles in the top most layers; slow growing, dark-adapted, species with strong narrow gas vesicles in the deeper layers). The diameter of the gas vesicle will also help determine which species survive in different bodies of water. Deep lakes that experience winter mixing will expose the cells to the hydrostatic pressure generated by the full water column. This will select for species with narrower, stronger gas vesicles.