2-38 The major differences between Archaea and other domains of life

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• The RNA polymerase in archaea is similar to RNA polymerase II in eukaryotes.
• The ribosomes of Archaea are similar in structure to those of Bacteria.
• Lipids in membranes from Archaea are unique, containing ether linkages between the glycerol backbone and the fatty acids, instead of ester linkages.
• The cells walls of Archaea are chemically and structurally diverse and do not contain peptidoglycan.

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 is then translated into proteins at the ribosome. Bacterial RNA polymerase is relatively simple, containing 4 different proteins. In contrast, RNA polymerase from methanogens and halophiles (both Archaea) contains 8 proteins. In hyperthermophiles (Archaea) RNA polymerase is even more complex, containing 10 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. 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. The exact sequence recognized by RNA polymerase depends upon the σ factor that has bound to the enzyme, and cells have different numbers of σ factors that bind to different types of promoter sequences. This allows regulation of mRNA expression by changing the levels of σ factors inside the cell. 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 ribosomal proteins, translation factors and tRNAs of archaea more closely resemble their counterparts in eukaryotes. In fact, mixing experiments with ribosomes from E. coli (Bacteria), Sulfolobus (Archaea) and yeast (Eukarya) have shown functional substitution between Archaea and Eukarya. Specifically, when the small subunit from a yeast ribosome was mixed with the large subunit from Sulfolobus, the hybrid ribosome was capable of translation in vitro. When the small subunit from yeast was mixed with the large subunit of E. coli, translation did not occur. 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. The lipids in archaea have a different chemical make-up in the following way. Remember that lipids in bacteria are amphipathic molecules (i.e. having both hydrophobic and hydrophilic portions) containing a backbone of glycerol connected to a hydrophilic head group and two hydrophobic long-chain fatty acids. In eukaryotes and bacteria the fatty acids are attached to the glycerol backbone by ester bonds, while in archaea ether linkages are used. 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 normal length and pass completely through the membrane, attaching to a second backbone on the opposite side. This adds extra stability to the membrane and these dual lipids are often found in archaea living in extreme environments.

Cell walls

As we have discussed, almost all bacteria have cell walls. These walls contain 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 2-54. N-acetylalosaminuronic acid replaces N-acetylmuramic acid in the backbone of the molecule 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 a peptidoglycan molecule 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 various differences between archaea, bacteria and eukaryotes indicate major differences between these life forms, and phylogenetic analysis bears out this conclusion. It is clear that the archaea are more divergent from bacteria than we are from an amoeba. This in turn 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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