2-23 Inclusions and other internal structures are found in many prokaryotic cells

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• Prokaryotic cells do have some microscopically visible structures in their cytoplasm. They serve specific purposes for the cell.
• Inclusions are aggregates of specific chemical compounds and often serve as a reservoir of energy or carbon. Common inclusions are: poly-β-hydroxyalkanoate, sulfur globules, and polyphosphate.
• Gas vesicles are found in many aquatic microorganisms are serve to adjust the location of the microbe in the water column.
• Magnetosomes are structures that sense the magnetic field of the earth. Cells often use these to orient themselves appropriately in their environment.

We said before that there were few structures in the prokaryotic cytoplasm that are visible by microscopy. Some of those that are seen are discussed below. In general, they serve specific purposes in the cell and are often found only in certain cell types or under certain growth conditions.

Inclusions

Inclusions are dense aggregates of specific chemical compounds in the cell. Typically, the aggregated chemical serves as a reservoir of either energy-rich compounds or building blocks for the cell. Forming polymers costs energy and it may seem wiser for the cell to keep the excess monomers around for when they are needed. The benefit of polymerization is that it decreases the osmotic pressure on the cell, a serious problem as described later. Inclusions often accumulate under laboratory conditions when a cell is grown in the presence of excess nutrients. However, the role of some inclusions is unclear. Growth on rich medium causes their creation, but subsequent starvation in the test tube does not always result in the use of these reserves. This suggests that these inclusions, at least, are not storage bodies.

Poly-β-hydroxyalkanoate

One of the more common storage inclusions involves poly-β-hydroxyalkanoate (PHA). It is a long polymer of repeating hydrophobic units that can have various carbon chains attached to it. The most common form of this class of polymers is poly-β-hydroxybutyrate, which has a methyl group as the side chain to the molecule as shown in Figure 2-33. The function of PHA in bacteria is as a carbon and energy storage product. Just as we store fat, some bacteria store PHA. Some PHA polymers have plastic-like qualities and there is some interest in exploiting them as a form of biodegradable plastic.

Glycogen

Glycogen is another common carbon and energy storage product. Humans also synthesize and utilize glycogen, which is a polymer of repeating glucose units.

Phosphate granules and sulfur globules

Given the opportunity, many organisms accumulate granules containing long chains of phosphate, since this is often a limiting nutrient in the environment. These polyphosphate polymers, also called volutin, form visible granules in some microbes. These granules are readily stained by many basic dyes such as toluidine blue and turn reddish violet in color. These inclusions are often referred to as metachromatic granules because they become visible by "metachromasy" (a color change). Polyphosphate is found in all known cells (eukaryotes, bacteria and archaea) and appears to serve many important roles.

1. It serves as a phosphate reservoir
2. It is an alternative substrate in place of ATP when phosphorylating sugars during catabolism.
3. It is a chelator for divalent cations
4. It can be a buffer under alkaline stress
5. It is an important factor for DNA uptake.
6. Finally, phosphate polymers are important regulators in response to stress

Figure 2-34 depicts another visible structure, termed a sulfur globule, which is found in a variety of bacteria capable of oxidizing reduced sulfur compounds such as hydrogen sulfide and thiosulfate. Oxidation of these compounds is linked either to energy metabolism or photosynthesis. Oxidation of sulfide initially yields elemental sulfur, which accumulates in globules inside or outside the cell. If the sulfide is exhausted the sulfur may be further oxidized to sulfate.

Gas vesicles

Figure 2-35 shows an example of gas vesicles, also known as gas vacuoles, that are found in cyanobacteria. Cyanobacteria are photosynthetic and live in lakes and oceans. In these environments, the cyanobacteria use gas vesicles to control their position in the water column to obtain the optimum amount of light and nutrients.

Gas vesicles are often aggregates of hollow cylindrical structures composed of rigid proteins. They are impermeable to water, but permeable to gas. The amount of gas in the vesicle is under the control of the microorganism. Release of gas from the cell causes the bacteria to fall in the water column, while filling the vesicle with gas causes the cells to rise.

Magnetosomes

magnetosomes are intracellular crystals of iron magnetite (Fe₃O₄) that impart a permanent magnetic dipole to prokaryotic cells that have them. They allow these microbes to orient themselves in a magnetic field. This process does not appear to involve any special machinery beside the magnetosome, Each microbe can be thought of as having a tiny magnet that is responding to the magnetic field in the environment. These magnetosomes allow the microbes to follow the magnetic field of the earth. Some species of magnetotatic bacteria have the following behavior. In the northern hemisphere magnetotatic bacteria swim north along the magnetic field, while in the southern hemisphere they swim south. Because of the inclination of the earth's magnetic field, this causes the microbes to swim downward. Many microbes containing magnetosomes are aquatic organisms that do not grow well in the presence of atmospheric concentrations of oxygen and they move away from the oxygen higher up in the water column by detecting the magnetic field and swimming downward.

A special membrane surrounds magnetosomes that confines the magnetite to a defined area. The membrane likely plays a role in precipitating the iron as Fe₃O₄ in the developing magnetosome. Magnetosomes can be square, rectangular or even spike-shaped. Magnetosomes are primarily found in aquatic bacteria and in some unicellular algae (eukaryotes).

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