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Inclusions and other internal structures

©2001 Timothy Paustian, University of Wisconsin-Madison

Internal structures are microscopically visible bodies in the cell that are distinguishable from the general cytoplasm. In most cases they serve some special purpose. In this section we look at some of the more common types of internal structures and their purpose.


Inclusions are aggregates of various compounds that are normally involved in storing energy reserves or building blocks for the cell. Inclusions accumilate when a cell is grown in the presence of excess nutrients and they are often observed under laboratory conditions.

Poly-beta-hydroxyalkanoate (PHA)

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

PHBEM.JPGChemical Structure of PHA
Figure 1 - Poly-beta-hydroxybutyrate (PHB) in a Rhodospirillum species. PHB is one type of PHA.The general structure of a PHA monomer


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

Phosphate and sulfur globules

Many organisms will accumilate granules of polyphosphate, since this is a limiting nutrient in the environment. The globules are long chains of phosphate. Photosynthetic bacteria that do not evolve oxygen will often use sulfides as their source of electrons, some of them accumilate sulfur globules. These globules may later be further oxidized and disapper if the sulfide pool dries up.

Gas vesicles


Figure 2 - A Gas vesicle

Gas vesicles are the exception to the rule that all bacterial cells have one contiguous membrane. Gas vesicles are found in Cyanobacteria, which are photosynthetic and live in aquatic systems. In these lakes and oceans, the Cyanonbacteria want to control their position in the water column to obtain the optimum amount of light and nutrients.


Gas vesicles are aggregates of hollow cylindrical structures composed of rigid proteins. They are impermeable to water, but permeable to gas. The amount of gas in the vacuole is under the control of the microorganism.


Gas vesicles regulate the buoancy of the microbes by changing the amount of gas contained within them. Release of gas from the vesicle causes the bacteria to fall in the water column, while filling the vesicle with gas increases their height in the water.


Endospores are highly resistant resting structures produced within cells. They are common to organisms which live in soil and may need to wait out some rough times such as >100°C heat, radiation, or drying.


Endospores are produced within cells and are refractile - light cannot penetrate them so that they are very easy to see in the phase microscope. See Figure below. They are resting structures, meaning that there is little or no metabolism inside the spore and it is a real form of suspended animation. Spores can survive for a very long time, and then regerminate. Spores that were dormant for thousands of years in the great tomes of the Egyption Pharohs were able to germinate and grow when placed in appropriate medium. There are even claims of spores that are over 250 million years old being able to germiinate when placed in appropriate medium. These results have yet to be validated.

Spores are resistant to heat, radiation, chemicals, and dessication. The mechanisms that acount for this include the dehydration of the protoplast and the production of special proteins that protect the spores DNA. Spores are capable of detecting their environment and under favorable nutrient conditions germinating and returning to the vegetative state.



Figure 3 - An Endospore

Parts of the Spore
  • Core - The core is dehydrated cytoplasm containing DNA, ribosomes, enzymes etc. Everything that is needed to function once returned to the vegetative state.

  • Cortex - The cortex is a modified cell wall/peptidoglycan layer that is not as cross-linked as in a vegetative cell.

  • Coats - Outside of the cortex are several protein layers that are impermeable to most chemcials. The coat is responsible for the spores resistance to chemicals

Spore life cycle

The formation of a spore is an expensive and complex process for the bacterial cell. Spores are only made under conditions where cell survival is threatened such as starvation for certain nutrients or accumulation of toxic wastes. Regulation of sporulation is tight and the first few steps are reversible. This helps the cell conserve energy and only sporulate when necessary.

Sporulation is a seven step process (although Stage I really doesn't seem to be genetically important). The first stages of sporulation are involved in forming a separate compartment for the spore in the mother cell. Once this occurs, sporulation is irreversible. The next stages involve laying down the various layers of the spore. Both the spore and the mother cell plays a role in this process. In the final stages, the spore dehydrates its cytoplasm and is released from the cell. Research on sporulation in Bacillus subtilis is intense. It is a wonderful model system for development, since the microbe is genetically tractible, allowing the isolation of many mutants in each stage of sporulation.


Figure 4 - The developmental cycle of the Endospore.

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