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Before 1977, prokaryotes were phylogenetically organized into one group termed the Monera. The discovery of the extreme thermophile Thermus aquaticusin the hot springs of Yellowstone National Park by Tom Brock and the subsequent analysis by Carl Woese and others began a series of experiments that would change how scientists think about the organization of life on this planet. This revolution is the subject of later chapters, but here we will discuss the structural differences between this new group, the Archaea, and the Bacteria. "Bacteria" and "Archaea" refers to the formal phylogenetic classification of organisms, but we will typically refer to them more casually as groups of organisms and then use "bacteria" and "archaea". The third domain consists of eukaryotic organisms, both microbes and multi-cellular, and is referred to as Eukarya. As explained early in this chapter, it has become evident that eukaryotes arose when certain bacteria became engulfed in archaeal cells, eventually becoming organelles. Not surprisingly then, Archaea is a group of microbes that share some things in common with Bacteria, others with Eukarya, and still have other properties that are all their own. (see Table 2.5) In the following section, we highlight some of the major structural features of the Archaea.

The major differences between Archaea and other domains of life

RNA polymerase

DNA-dependent RNA polymerases in bacteria and archaea are different from each other. The primary RNA polymerase of all organisms is responsible for creating messenger RNA that the ribosome then translates into proteins. Bacterial RNA polymerase is relatively simple, containing five different proteins. In contrast, RNA polymerase from methanogens and halophiles (both Archaea) contains eight proteins. In hyperthermophiles (Archaea) RNA polymerase is even more complex, containing ten proteins. None of the archaeal RNA polymerases are affected by the antibiotic rifampicin, a known inhibitor of the bacterial RNA polymerase. The eukaryotic RNA polymerase responsible for most mRNA transcription (termed RNA polymerase II) contains 12 proteins and is similar to the RNA polymerase in the archaea.

RNA polymerases from all organisms recognize a variety of start sequences or promoters (Figure 3.37). A promoter for mRNA transcription in bacteria is recognized by the sigma protein and has two recognition zones about 10 and 35 bases before the transcription start site. In archaea and eukaryotes the transcription recognition sequence is a TATA sequence (termed the TATA box) and transcription is regulated by various protein transcription factors that bind to regions near the TATA box and then recruit RNA polymerase.

Translation and ribosomes

The structural make-up of the ribosomes of bacteria and archaea are similar in many respects. The ribosomes of archaea and bacteria are of the same size (70S) and are smaller than those of eukaryotes (80S). However, most of the archaea's ribosomal proteins, translation factors, and tRNAs more closely resemble their counterparts in eukaryotes. Mixing experiments with ribosomes from E. coli(Bacteria), Sulfolobus(Archaea) and yeast (Eukarya) have shown functional substitution between Archaea and Eukarya. Specifically, mixing a small subunit from a yeast ribosome with the large subunit from Sulfolobus, results in a ribosome that is capable of translation in vitro. In contrast, mixing a small subunit from yeast with the large subunit of E. coli resulted in no translation. Also, in all organisms translation begins at a start codon (typically an AUG in the mRNA). In bacteria, this codon causes the insertion of formylmethionine, while in archaea and eukaryotes, it results in insertion of an unmodified methionine.

Lipids

Archaeal membranes have features unlike those found in either eukaryotes or bacteria (Figure 3.38). In eukaryotes and bacteria, the fatty acids are attached to the glycerol backbone by ester bonds. In archaea, ether linkages link the polar groups to their long-chain alkyl groups. Also, the stereochemistry of lipids from archaea is primarily of the S form, while that of bacteria and eukaryotes is of the R form. In some archaea, the hydrophobic chains attached to the glycerol backbone are twice the normal length and pass completely through the membrane, attaching to a second backbone on the opposite side. This linked membrane adds extra stability, and these dual lipids are often found in archaea living in extreme environments.

Cell walls

Most microorganisms in the Bacteria domain contain cell walls with peptidoglycan, with N-acetyl muramic acid being the signature molecule for the presence of peptidoglycan. Archaea are considerably more diverse in the composition of their cell walls. They lack peptidoglycan, but some contain pseudomurein that has a similar structure, as shown in Figure 3.39. N-acetylalosaminuronic acid replaces N-acetylmuramic acid in the molecule's backbone, and each glycan unit is linked together using 1,3 glycosidic bonds instead of the 1,4 glycosidic bonds seen in peptidoglycan. Many archaea do not contain peptidoglycan in any form, instead covering the outside of the membrane with proteins, glycoproteins, or polysaccharides. Scientists refer to these cell walls as S-layers. In any case, the function of the cell wall remains the same, containing the cytoplasm and giving the microbe its shape.

These differences between archaea, bacteria, and eukaryotes indicate important differences between these life forms, and phylogenetic analysis bears out this conclusion. The archaea are more divergent from bacteria than we are from an amoeba. This significant divergence indicates that the common progenitor of these groups existed very early in evolution. Analysis and classification of the archaea has fundamentally changed how biologists think about organismal diversity.

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