eubacteria

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The Eubacteria, also called just "bacteria," are one of the three main domains of life, along with the Archaea and the Eukarya. Eubacteria are prokaryotic, meaning their cells do not have defined, membrane-limited nuclei. As a group they display an impressive range of biochemical diversity, and their numerous members are found in every habitat on Earth. Eubacteria are responsible for many human diseases, but also help maintain health and form vital parts of all of Earth's ecosystems.

Structure

Like archeans, eubacteria are prokaryotes, meaning their cells do not have nuclei in which their DNA is stored. This distinguishes both groups from the eukaryotes, whose DNA is contained in a nucleus. Despite this structural resemblance, the Eubacteria are not closely related to the Archaea, as shown by analysis of their RNA (see below).

Eubacteria are enclosed by a cell wall. The wall is made of cross-linked chains of peptidoglycan, a polymer that combines both amino acid and sugar chains. The network structure gives the wall the strength it needs to maintain its size and shape in the face of changing chemical and osmotic differences outside the cell. Penicillin and related antibiotics prevent bacterial cell growth by inactivating an enzyme that builds the cell wall. Penicillin-resistant bacteria contain an enzyme that chemically modifies penicillin, making it ineffective.

Some types of bacteria have an additional layer outside the cell wall. This layer is made from lipopolysaccharide (LPS), a combination of lipids and sugars. There are several consequences to possessing this outer layer. Of least import to the bacteria but significant for researchers, this layer prevents them from retaining a particular dye (called Gram stain) that is used to classify bacteria. Bacteria that have this LPS layer are called Gram-negative, in contrast to Gram-positive bacteria, which do not have an outer LPS layer and which do retain the stain. Of more importance to both the bacteria and the organisms they infect is that one portion of the LPS layer, called endotoxin, is particularly toxic to humans and other mammals. Endotoxin is partly to blame for the damage done by infection from Salmonella and other Gram-negative species.

Within the cell wall is the plasma membrane, which, like the eukaryotic plasma membrane, is a phospholipid bilayer studded with proteins. Embedded in the membrane and extending to the outside may be flagella, which are whiplike protein filaments. Powered by molecular motors at their base, these spin rapidly, propelling the bacterium through its environment.

Within the plasma membrane is the bacterial cytoplasm. Unlike eukaryotes, bacteria do not have any membrane-bound organelles, such as mitochondria or chloroplasts. In fact, these two organelles are believed to have evolved from eubacteria that took up residence inside an ancestral eukaryote.

Bacterial cells take on one of several common shapes, which until recently were used as a basis of classification. Bacilli are rod shaped; cocci are spherical; and spirilli are spiral or wavyshaped. After division, bacterial cells may remain linked, and these form a variety of other shapes, from clusters to filaments to tight coils.

Metabolism

Despite the lack of internal compartmentalization, bacterial metabolism is complex, and is far more diverse than eukaryotic metabolism. Within the Eubacteria there are species that perform virtually every biochemical reaction known (and much bacterial chemistry remains to be discovered). Most of the vitamins humans require in our diet can be synthesized by bacteria, including the vitamin K humans absorb from the Escherichia coli (E. coli) bacteria in our large intestines.

The broadest and most significant metabolic distinction among the Eubacteria is based on the source of energy they use to power their metabolism. Like humans, many bacteria are heterotrophs, consuming organic (carbon-containing) high-energy compounds made by other organisms. Other bacteria are chemolithotrophs, which use inorganic high-energy compounds, such as hydrogen gas, ammonia, or hydrogen sulfide. Still others are phototrophs, using sunlight to turn simple low-energy compounds into high-energy ones, which they then consume internally.

For all organisms, extraction of energy from high-energy compounds requires a chemical reaction in which electrons move from atoms that bind them loosely to atoms that bind them tightly. The difference in binding energy is the profit available for powering other cell processes. In almost all eukaryotes, the ultimate electron acceptor is oxygen, and water and carbon dioxide are the final waste products. Some bacteria use oxygen for this purpose as well. Others use sulfur (forming hydrogen sulfide, which has a strong odor), carbon (forming flammable methane, common in swamps), and a variety of other compounds.

Bacteria that use oxygen are called aerobes. Those that do not are called anaerobes. This distinction is not absolute, however, since many organisms can switch between the two modes of metabolism, and others can tolerate the presence of oxygen even if they do not use it. Some bacteria die in oxygen, however, including members of the Gram positiveClostridium genus. Clostridium botulinum produces botulinum toxin, the deadliest substance known. C. tetani produces tetanus toxin, responsible for tetanus and "lockjaw," while other Clostridium species cause gangrene.

Life Cycle

When provided with adequate nutrients at a suitable temperature and pH,E. coli bacteria can double in number within 20 minutes. This is faster than most species grow, and faster than E. coli grows under natural conditions. Regardless of the rate, the growth of a bacterium involves synthesizing double the quantity of all its parts, including membrane, proteins, ribosomes, and DNA. Separation of daughter cells, called binary fission, is accomplished by creating a wall between the two halves. The new cells may eventually separate, or may remain joined.

When environmental conditions are harsh, some species (including members of the genus Clostridium) can form a special resistive structure within themselves called an endospore. The endospore contains DNA, ribosomes, and other structures needed for life, but is metabolically inactive. It has a protective outer coat and very low water content, which help it survive heating, freezing, radiation, and chemical attack. Endospores are known to have survived for several thousand years, and may be capable of surviving for much longer, possibly millions of years. When exposed to the right conditions (presence of warmth and nutrients), the endospore quickly undergoes conversion back into an active bacterial cell.

Dna

Most eubacteria have DNA that is present in a single large circular chromosome. In addition, there may be numerous much smaller circles, called plasmids. Plasmids usually carry one or a few genes. These often are for specialized functions, such as metabolism of a particular nutrient or antibiotic.

Despite the absence of a nucleus, the chromosome is usually confined to a small region of the cell, called the nucleoid, and is attached to the inner membrane. The bacterial genome is smaller than that of a eukaryote. For example, E. coli has only 4.6 million base pairs of DNA, versus three billion in humans. As in eukaryotes, the DNA is tightly coiled to fit it into the cell. Unlike eukaryotes, however, the DNA is not attached to histone proteins.

Much of what we know about DNA replication has come from study of bacteria, particularly E. coli, and the details of this process are discussed elsewhere in this encyclopedia. Unlike eukaryotic replication, prokaryotic replication begins at a single point, and proceeds around the circle in both directions. The result is two circular chromosomes, which are separated during cell division. Plasmids replicate by a similar process.

Gene Transfer

While bacteria do not have sex like multicellular organisms, there are several processes by which they obtain new genes: conjugation, transformation, and transduction. Conjugation can occur between two appropriate bacterial strains when one (or both) extends hairlike projections called pili to contact the other. The chromosome, or part of one, may be transferred from one bacterium to the other. In addition, plasmids can be exchanged through these pili. Some bacteria can take up DNA from the environment, a process called transformation. The DNA can then be incorporated into the host chromosome.

Some bacterial viruses, called phages, can carry out transduction. With some phages, the virus temporarily integrates into the host chromosome. When it releases itself, it may carry some part of the host DNA with it. When it goes on to infect another cell, this extra DNA may be left behind in the next round of integration and release. Other phages, called generalized transducers, package fragments of the chromosome into the phage instead of their own genome. When the transducing phage infects a new cell, they inject bacterial DNA. These phages lack their own genome and are unable to replicate in the new cell. The inserted bacterial DNA may recombine (join in with) the host bacterial chromosome.

Gene Regulation and Protein Synthesis

Gene expression in many bacteria is regulated through the existence of operons. An operon is a cluster of genes whose protein products have related functions. For instance, the lac operon includes one gene that transports lactose sugar into the cell and another that breaks it into two parts. These genes are under the control of the same promoter, and so are transcribed and translated into protein at the same time. RNA polymerase can only reach the promoter if a repressor is not blocking it; the lac repressor is dislodged by lactose. In this way, the bacterium uses its resources to make lactose-digesting enzymes only when lactose is available.

Other genes are expressed constantly at low levels; their protein products are required for "housekeeping" functions such as membrane synthesis and DNA repair. One such enzyme is DNA gyrase, which relieves strain in the double helix during replication and repair. DNA gyrase is the target for the antibiotic ciproflaxin (sold under the name Cipro), effective against Bacillus anthracis, the cause of anthrax. Since eukaryotes do not have this type of DNA gyrase, they are not harmed by the action of this antibiotic.

As in eukaryotes, translation (protein synthesis) occurs on the ribosome. Without a nucleus to exclude it, the ribosome can attach to the messenger RNA even while the RNA is still attached to the DNA. Multiple ribosomes can attach to the same mRNA, making multiple copies of the same protein.

The ribosomes of eubacteria are similar in structure to those in eukaryotes and archaea, but differ in molecular detail. This has two important consequences. First, sequencing ribosomal RNA molecules is a useful tool for understanding the evolutionary diversification of the Eubacteria. Organisms with more similar sequences are presumed to be more closely related. The same tool has been used to show that Archaea and Eubacteria are not closely related, despite their outward similarities. Indeed, Archaea are more closely related to eukaryotes (including humans) than they are to Eubacteria.

Second, the differences between bacterial and eukaryotic ribosomes can be exploited in designing antibacterial therapies. Various unique parts of the bacterial ribosome are the targets for numerous antibiotics, including streptomycin, tetracycline, and erythromycin.

Bibliography

Madigan, Michael T., John M. Martinko, and Jack Parker. Brock Biology of Micro-organisms, 9th ed. Upper Saddle River, NJ: Prentice Hall, 2000.

Margulis, Lynn, and Karlene Schwartz. Five Kingdoms, 3rd ed. New York: W. H.Freeman, 1998.

—Richard Robinson