3-8 Archaeal Structure

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Learning Objectives

After reading this section, students will...

  1. Be able to explain the differences between the three domains of life.
  2. Be able to describe the unique properties of Archaea.

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 have still 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.

Table 2.5 Comparison of properties between Archaea, Bacteria and Eukarya

Property Bacteria Archaea Eukarya
RNA polymerase 4 proteins Rifampicin sensitive 8-10 proteins Rifampicin resistant 12 proteins (RNA pol II) Rifampicin resistant
Transcription start site Variable often contains a -35 and -10 region TATA box TATA box
Starting amino acid formylmethionine methionine methionine
Lipids ester-linked ether-linked ester-linked
Cell wall composition G+ peptidoglycan
G- peptidoglycan and outer membrane
pseudopeptidoglycan or
S-layer of proteins, glycoproteins, or polysaccharides
none or cellulose

Archaea are a unique form of life, as different phylogenetically from bacteria as they are from eukaryotes.

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 is then translated into proteins at the ribosome. Bacterial RNA polymerase is relatively simple, containing 5 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 (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.

Control elements in bacteria and archaea

Figure 3.37. Control elements in bacteria and archaea. The best-studied bacteria have promoters at two positions upstream of the transcription start site that are recognized by the σ factors associated with RNA polymerase. The transcriptional control elements in the archaea are much more like those found in eukaryotes, where RNA polymerase is recruited to a promoter by interaction with protein regulatory factors, and transcription begins downstream of a TATA box.

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.


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, while in archaea ether linkages are used to link 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 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.

Ether-linked lipids

Figure 3.38. Ether-linked lipids. Archaea have an ether linkage between the long alkyl chain and the glycerol backbone, which is in contrast to the ester linkage seen in bacteria and eukaryotes. (A) An ether-linked lipid show as the chemical structure and a space-filling model. (B) A tetraether lipid, showing a general chemical structure. An example of a tetraether lipid from the thermophilic archaeal species Thermoplasma acidophiliumis shown as a space-filling model.

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 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.

A comparison of cell wall structure in Archaea

Figure 3.39. A comparison of cell wall structure in Archaea. Archaea have several different types of cell wall. Some contain a structure reminiscent of peptidoglycan called pseudomurein. The chemical formula is pictured on the left. Other microbes will have a surface layer (S-layer) composed of repeating units of one or a few proteins, glycoproteins or sugar. These crystal lattices serve to protect the cell. The micrograph on the right shows the surface of Methanospirillum hungateicells. Note the regular repetition of the pattern on the outside surface. (Source: M. Firtel, et al.1993. J. Bacteriol. 175:7550-7560)

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.

Key Takeaways

  1. Archaea are a different life form, as different from bacteria as we are from E. coli.
  2. Archaea share traits that are similar to eukaryotes. The RNA polymerase of Archaea and the promoter structure is similar to eukaryotes.
  3. In addition, translation of proteins inserts a methionine as do eukaryotes, instead of a formylmethionine, as bacteria do.
  4. Archaea do have some unique traits, including ether-linked lipids and unique cell wall structures that can be formed from pseudopeptidoglycan or an S-layer.


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Quickcheck 3-8

Answer the questions below and then hit the Grade Exam button

1. The RNA polymerase of some archaea is more similar to that in the bacteria than to that in the eukaryotes.

  1. True
  2. False

2. For which of the following properties are archaea more similar to eukaryotes than to bacteria?

  1. RNA polymerase and transcription.
  2. Translation mechanisms.
  3. Lipid stereochemistry.
  4. Organismal complexity.

3. Archaeal membranes have several different properties in comparison to bacterial membranes. They are

  1. Three fatty acids are linked to the glycerol backbone.
  2. The alkyl chains are linked to glycerol by ether bonds instead of ester bonds.
  3. Some archeal lipids span the entire membrane.
  4. Propionate replaces glycerol as the backbone in some lipids of archaea