There are two genetically distinct lineages of prokaryotes, the "normal" bacteria or Eubacteria and the Archaebacteria (or Archaea). Although both have a prokary-otic cell without a nucleus, the Eubacteria and Archaebacteria are no more related to each other than either is to the eukaryotes. [See Ch. 20, Molecular Evolution,
Archaebacteria (or Archaea) Type of bacteria forming a genetically distinct domain of life. Includes many bacteria growing under extreme conditions conjugative transposon Type of transposon that can transfer themselves from one bacterial cell to another by conjugation Eubacteria Bacteria of the normal kind as opposed to the genetically distinct Archaebacteria
Phylogenetic tree of the Archaea lineage illustrating that different types of gene transfer can occur. The green zone contains salt tolerant organisms, the blue zone indicates methane producers and the red zone contains Archaea that grow at extremely high temperatures. Some Archaea use transformation whereas others use conjugation. Rare cases of viral transduction also occur. The modes of gene transfer seen within each family do not correlate well with either lifestyle or evolutionary relationships. The Crenarchaeota and the Euryarchaeota are the two major branches of the Archaea.
Archaebacteria are genetically distinct and often live under unusual or extreme conditions.
Gene transfer in Archaebacteria is widespread but still poorly understood.
for further discussion of these relationships.] The Eubacteria include most bacteria found in normal environments, including both the gram-negative and gram-positive bacteria discussed above. The Archaebacteria include the methane bacteria and a variety of less well-known bacteria found in extreme environments. Many have strange biochemical pathways and are adapted to extremes of temperature, pH or salinity. This makes Archaebacteria an attractive source of novel enzymes or proteins with unusual properties and/or resistance to extreme conditions. There are many possible industrial uses for enzymes capable of withstanding extreme temperatures, for example.
Although several complete genome sequences are available for members of the Archaebacteria, development of systems for gene transfer has lagged way behind the Eubacteria. There are many practical problems, including the need to grow many Archaebacteria under extreme conditions. For example, some extreme thermophiles grow at temperatures high enough to melt agar. Obtaining colonies on solid media has required the development of alternative materials.
Plasmids have been found in several Archaebacteria and some have been developed into cloning vectors (Fig. 18.21). Transformation procedures now exist for getting DNA into several Archaebacteria. They rely on removal of divalent cations, especially Mg2+, which results in the disassembly of the glycoprotein layer surrounding many Archaebacterial cells. (Note the contrast with the corresponding procedures for eubac-teria, which involve cold-shock in the presence of divalent cations!) It has been possible to express the lacZ reporter gene in methane bacteria under control of an archaebacterial promoter. However, staining of b-galactosidase with Xgal requires exposure to air, which kills methane bacteria! Consequently, colonies must first be replicated and one set sacrificed for analysis.
A major problem is choice of a selectable marker. Most standard antibiotics do not affect Archaebacteria due to their unusual biochemistry. For example, Archaebac-teria do not have cell walls made of peptidoglycan and are therefore not susceptible to penicillins. In addition, many resistance proteins from normal organisms are denatured at the extremes of temperature, salinity or pH under which many Archaebacteria grow. Novobiocin (a DNA gyrase inhibitor—see Ch. 5) and mevinolin (an inhibitor of the isoprenoid pathway) have been used to inhibit halophiles, and puromycin and neomycin (both protein synthesis inhibitors—see Ch. 16) will inhibit methane bacteria.
Viruses have been discovered that infect many Archaebacteria. So far only one, the YM1 phage of Methanobacterium thermoautotrophicum, has been shown to transduce genes of its host bacterium. Unfortunately this is of no practical use because of the low burst size—about six phage are liberated per cell after infection. The SSV1 phage of Sulfolobus solfataricus integrates into the bacterial chromosome and may be of future use.
Conjugation in Archaebacteria is of two types. Self-transferable plasmids that promote conjugation are found in Sulfolobus. In contrast, some halobacteria form conjugation bridges without the involvement of fertility plasmids. Moreover, in these cases DNA transfer is bi-directional. Neither of these phenomena has so far been developed into routine gene-transfer systems.
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