MICROBIOLOGY: THE BIOLOGY OF PROKARYOTES, VOLUME I - A. V. PINEVICH - 2006

CHAPTER 4. THE POSITION OF ARCHAEA IN THE BIOLOGICAL MEGASYSTEM

FROM "STRANGE BACTERIA" AND STANIER'S PROKARYOTES TO WOESE'S PHYLOGENETIC DOMAIN ARCHAEA

Class="center">Qui no sap cosselh prendre i’ora que Га mestier, ja a la cort del Poi no prengra l’espervier.

(Let him who cannot make the right decision at a critical moment not expect to win a falcon at the tournament in Pau).

Simon de Montfort (1208-1265).

Archaea were first discovered in the early 1920s. However, it was not until the late 1970s that they were found to possess a range of unique PHYSIOLOGICAL AND BIOCHEMICAL properties. Despite this, they continued to be regarded as Bacteria—albeit "peculiar" ones—and were grouped with "ordinary" bacteria based on shared morphophysiological traits.

After Roger Stanier developed a dichotomous megasystem, bacteria acquired the taxonomic status of prokaryotes. Therefore, prior to the era of molecular phylogenetics, archaeal prokaryotes were not separated from bacterial prokaryotes.

The first doubts regarding the bacterial nature of methanogens arose in 1976. By analyzing the distribution spectrum of mercaptoethanesulfonate, a coenzyme unique to methanogenesis, Ralph Wolfe demonstrated that this compound is exclusive to methanogens. This fact contradicted Albert Kluyver's paradigm of the biochemical unity of life. Suspecting that the unusual features of methanogens did not end there, Wolfe invited Carl Woese—his colleague at the University of Illinois at Urbana—in 1977 to compare their rRNA Structure with that of "ordinary" bacteria to determine just how distinct they were from one another. The result proved paradoxical: based on this marker, methanogens were so distant from "ordinary" bacteria that Woese proposed viewing them as "archaebacteria," representatives of a separate evolutionary branch or domain, "Archaebacteria." Following screening conducted by Woese and other researchers in 1978, extreme halophiles, the acidophilic Thermoplasma, and hyperthermophiles were also assigned to this domain.

As a result of a study carried out in 1977 at the request of Ralph Wolfe and Carl Woese, Munich biochemist Otto Kandler established that methanogens possess a Chemical composition of Cell walls uncharacteristic of bacteria. Long before this, in 1956, A. L. Houwink discovered that The Cell surface of *Halobacterium salinarium* is covered with a paracrystalline protein layer that acts as a rigid framework or exoskeleton. Throughout the 1970s and 1980s, Otto Kandler, J. B. Jones, M. F. Mescher, and L. R. Weiss conclusively demonstrated that extreme halophiles, methanogens, and hyperthermophiles differ from bacteria in their Cell wall composition.

A unique feature of archaea is their Membrane Lipids, which are glycerol diethes composed of glycerol and the fully saturated isoprenoid alcohol phytanol (see Section 8.3.3.2). This was revealed by the classic studies of M. Kates on *H. salinarium* in 1965—even before Woese formulated his concept of archaea. In the late 1970s, M. De Rosa and A. Gambacorta found identical lipids in the hyperthermophile *Sulfolobus*, and T. A. Langworthy found them in the thermoacidophile *Thermoplasma*. In 1978, T. G. Tornabene and R. A. Makula investigated the lipids of methanogens and obtained the same result as for extreme halophiles and thermoacidophiles. From that point on, these lipids came to be regarded as a chemotaxonomic marker distinguishing archaea from both bacteria and eukaryotes.

Throughout the 1960s and 1970s, the dichotomy between PROKARYOTES AND EUKARYOTES was considered obvious and indisputable. However, the situation changed dramatically after Carl Woese used the semantic characteristics of rRNA to determine evolutionary relationships. When this criterion was applied to extremophilic prokaryotes (previously assumed to be bacteria), it unexpectedly turned out that they are equally distanced on the universal tree from both "ordinary" bacteria and eukaryotes. Thus, the universal tree proved to be tritomous rather than dichotomous. Based on this, Woese arrived at a Conclusion that has become one of the paradigms of modern biology: at the highest taxonomic level, there are not two, but three "primary kingdoms":

— bacterial prokaryotes;

— archaeal prokaryotes;

— eukaryotes.

Initially, Woese gave these "primary kingdoms" quasi-taxonomic names (two Latin and one English): "Eubacteria," "Archaebacteria," and "Eukaryotes." He later renamed them Bacteria, Archaea, and Eucarya, respectively.

We have already noted that the cell walls and membrane lipids of archaea differ structurally from those of bacteria. Furthermore, crucial Proteins such as RNA polymerase, elongation factors, and membrane ATPases also exhibit distinct structures in archaea compared to bacteria.

Thus, the prokaryotic type of Organization is represented by two Branches of the universal tree. At Carl Woese's initiative, the term "archaea" has been used since 1990 instead of "archaebacteria," emphasizing that archaebacteria-archaea must be viewed not as "other" bacteria, but as "other" prokaryotes.

By the early 1990s, the tritomous STRUCTURE OF THE tree of life, reconstructed through primary rRNA structure analysis, had become a "totem pole" of biology and was no longer doubted in its objectivity. However, in the final decade of the 20th century, following the sequencing of several dozen bacterial genomes, molecular paleontological data emerged that allowed researchers to put forward alternative hypotheses regarding the genealogical relationships among archaea, bacteria, and eukaryotes.

In the late 1990s, analysis of archaeal genome structure revealed that they are characterized by a chimeric genomic organization.

In 1998, American molecular biologist J. A. Lake divided all genes into two major groups: "informational" and "operational." This corresponds to their two primary functional spheres.

"Informational genes" are responsible for copying and Processing Genetic information during Replication, METABOLISM/31.html">Transcription, and Translation.

"Operational genes," or "housekeeping genes," are responsible for transport, metabolic, and regulatory Functions.

As it turned out, archaeal informational genes show a predominant similarity to corresponding eukaryotic genes. In turn, archaeal operational genes are largely similar to bacterial operational genes. Finally, two-thirds of archaeal genes are unique, meaning they lack homologs in bacterial or Eukaryotic Genomes.

Due to the ambiguous interpretation of ribosomal Gene sequencing results, as well as the subjective analysis of combined geochemical, molecular-biochemical, and cytophysiological data, two ideological camps have formed, whose representatives hold differing views on archaeal phylogeny.

Proponents of the "canonical" scenario, notably Carl Woese, believe that archaea diverged from bacteria and eukaryotes at the very dawn of cellular evolution. Subsequently, The properties of archaea stabilized at a level reflecting adaptation to the environmental conditions of the primordial biosphere. In this case, the similarities between archaeal and bacterial genes are attributed to "horizontal" gene transfer, which could have occurred with high frequency during the early "pre-genealogical" stage of cellular evolution.

Proponents of the "heretical" scenario view archaea and eukaryotes as descendants of bacteria that secondarily adapted to extreme conditions, particularly high temperatures. English protistologist Thomas Cavalier-Smith regards archaea and eukaryotes as sister megataxa and proposes grouping them under the name "neomura" (from the Greek neos, meaning new, and Latin murus, meaning wall; "possessing a new type of cell wall"). According to his hypothesis, neomurans evolved from Gram-positive bacteria through the replacement of the murein layer with a proteinaceous S-layer.

Further research will reveal which of these Perspectives is closer to reality.