Origin of eukaryotes. In what era and period did eukaryotes appear? The appearance of the first eukaryotic cells occurred in the era

Russian paleontologists planted a bomb under traditional views on the origin of life on the planet. The history of the Earth must be rewritten.

It is believed that life began on our planet approximately 4 billion years ago. And the first inhabitants of the Earth were bacteria. Billions of individuals formed colonies that covered the vast expanses of the seabed with a living film. Ancient organisms were able to adapt to the harsh realities of reality. High temperatures and an oxygen-free environment are conditions in which you are more likely to die than to survive. But the bacteria survived. The single-celled world was able to adapt to an aggressive environment due to its simplicity. A bacterium is a cell that does not have a nucleus inside. Such organisms are called prokaryotes. The next round of evolution is associated with eukaryotes - cells with a nucleus. The transition of life to the next stage of development occurred, as scientists were convinced until recently, about 1.5 billion years ago. But today the opinions of experts regarding this date are divided. The reason for this was a sensational statement by researchers from the Paleontological Institute of the Russian Academy of Sciences.

Give me some air!

Prokaryotes played an important role in the history of the evolution of the biosphere. Without them, there would be no life on Earth. But the world of nuclear-free creatures was deprived of the opportunity to develop progressively. What prokaryotes were like 3.5-4 billion years ago, they remain almost the same to this day. A prokaryotic cell is unable to create a complex organism. For evolution to move further and give rise to more complex forms of life, a different, more advanced type of cell was required - a cell with a nucleus.

The appearance of eukaryotes was preceded by one very important event: oxygen appeared in the Earth's atmosphere. Cells without nuclei could live in an oxygen-free environment, but eukaryotes could no longer live. The first producers of oxygen were most likely cyanobacteria, which found an efficient method of photosynthesis. What could he be? If before this bacteria used hydrogen sulfide as an electron donor, then at some point they learned to receive an electron from water.

“The transition to the use of such an almost unlimited resource as water has opened up evolutionary opportunities for cyanobacteria,” believes Alexander Markov, a researcher at the Paleontological Institute of the Russian Academy of Sciences. Instead of the usual sulfur and sulfates, oxygen began to be released during photosynthesis. And then, as they say, the fun began. The appearance of the first organism with a cell nucleus opened up vast opportunities for the evolution of all life on Earth. The development of eukaryotes led to the emergence of such complex forms as plants, fungi, animals and, of course, humans. They all have the same type of cell, with a nucleus at the center. This component is responsible for storing and transmitting genetic information. He also influenced the fact that eukaryotic organisms began to reproduce themselves through sexual reproduction.

Biologists and paleontologists have studied the eukaryotic cell in as much detail as possible. They assumed that they also knew the time of origin of the first eukaryotes. Experts gave figures of 1-1.5 billion years ago. But it suddenly turned out that this event happened much earlier.

An unexpected find

Back in 1982, paleontologist Boris Timofeev conducted an interesting study and published its results. In Archean and Lower Proterozoic rocks (2.9-3 billion years old) in Karelia, he discovered unusual fossilized microorganisms measuring about 10 micrometers (0.01 millimeters). Most of the finds were spherical in shape, the surface of which was covered with folds and patterns. Timofeev made the assumption that he discovered acritarchs - organisms that are classified as representatives of eukaryotes. Previously, paleontologists found similar samples of organic matter only in younger sediments - about 1.5 billion years old. The scientist wrote about this discovery in his book. “The quality of the printing of that edition was simply terrible. It was generally impossible to understand anything from the illustrations. The images were blurry gray spots,” says Alexander Markov, “so it is not surprising that most readers, having leafed through this work, threw it aside, safely about forgetting him." The sensation, as often happens in science, lay on a bookshelf for many years.

The director of the Paleontological Institute of the Russian Academy of Sciences, Doctor of Geological and Mineralogical Sciences, Corresponding Member of the Russian Academy of Sciences Alexey Rozanov, quite accidentally remembered Timofeev’s work. He decided once again, using modern devices, to explore the collection of Karelian samples. And he very quickly became convinced that these were indeed eukaryotic-like organisms. Rozanov is confident that the discovery of his predecessor is an important discovery, which is a compelling reason for revising existing views on the time of the first appearance of eukaryotes. Very quickly the hypothesis gained supporters and opponents. But even those who share Rozanov’s views speak with restraint on this issue: “In principle, the appearance of eukaryotes 3 billion years ago is possible. But this is difficult to prove,” says Alexander Markov. “The average size of prokaryotes ranges from 100 nanometers to 1 micron, "Eukaryotes range from 2-3 to 50 micrometers. In reality, the size ranges overlap. Researchers often find specimens of both giant prokaryotes and tiny eukaryotes. Size is not 100% proof." Testing a hypothesis is really not easy. There are no more specimens of eukaryotic organisms in the world obtained from Archean deposits. It is also not possible to compare ancient artifacts with their modern counterparts, because the descendants of the acritarchs did not survive to this day.

Revolution in science

Nevertheless, there was a big fuss in the scientific community around Rozanov’s idea. Some people categorically do not accept Timofeev’s find, because they are sure that 3 billion years ago there was no oxygen on Earth. Others are confused by the temperature factor. Researchers believe that if eukaryotic organisms appeared during the Archean era, then, roughly speaking, they would immediately cook. Alexey Rozanov says the following: “Usually parameters such as temperature, the amount of oxygen in the air, and water salinity are determined based on geological and geochemical data. I propose a different approach. First, use paleontological finds to estimate the level of biological organization. Then, based on these data, determine , how much oxygen should have been contained in the Earth's atmosphere for one or another form of life to feel normal. If eukaryotes appeared, then oxygen should already be present in the atmosphere, in the region of several percent of the current level. If a worm appeared, the oxygen content should "was already tens of percent. Thus, it is possible to draw up a graph reflecting the appearance of organisms of different levels of organization depending on the increase in oxygen and decrease in temperature." Alexey Rozanov is inclined to push back as far as possible the moment of the appearance of oxygen and to extremely reduce the temperature of the ancient Earth.

If it can be proven that Timofeev has found fossilized eukaryote-like microorganisms, this will mean that humanity will soon have to change its usual understanding of the course of evolution. This fact allows us to say that life on Earth appeared much earlier than expected. In addition, it turns out that it is necessary to revise the evolutionary chronology of life on Earth, which, it turns out, is almost 2 billion years older. But in this case, it remains unclear when, where, at what stage of development the evolutionary chain broke or why its progress slowed down. In other words, it is completely unclear what happened on Earth for 2 billion years, where eukaryotes were hiding all this time: too large a white spot is forming in the history of our planet. Another revision of the past is required, and this is a colossal work in scope, which may never end.

OPINIONS

Lifelong

Vladimir Sergeev, Doctor of Geological and Mineralogical Sciences, leading researcher at the Geological Institute of the Russian Academy of Sciences:

In my opinion, we need to be more careful with such conclusions. Timofeev's data are based on material that has secondary changes. And this is the main problem. The cells of eukaryotic-like organisms underwent chemical decomposition, and they could also be destroyed by bacteria. I consider it necessary to re-analyze Timofeev’s findings. As for the time of appearance of eukaryotes, most experts believe that they appeared 1.8-2 billion years ago. There are some finds whose biomarkers indicate the emergence of these organisms 2.8 billion years ago. In principle, this problem is associated with the appearance of oxygen in the Earth's atmosphere. According to the generally accepted opinion, it was formed 2.8 billion years ago. And Alexey Rozanov pushes this time back to 3.5 billion years. From my point of view, this is not true.

Alexander Belov, paleoanthropologist:

Everything that science finds today is only a particle of the material that may still exist on the planet. Preserved forms are very rare. The fact is that the preservation of organisms requires special conditions: a humid environment, lack of oxygen, mineralization. Microorganisms that lived on land may not have reached researchers at all. It is by mineralized or fossilized structures that scientists judge what kind of life there was on the planet. The material that falls into the hands of scientists is a mixture of fragments from different eras. Classic conclusions about the origin of life on Earth may not be true. In my opinion, it did not develop from simple to complex, but appeared at once.

Maya Prygunova, Itogi magazine No. 45 (595)

According to modern ideas, the first living beings of the Earth were single-celled prokaryotic organisms, to which archaebacteria are closest among modern living beings. It is believed that initially there was no free oxygen in the atmosphere and the World Ocean, and under these conditions only anaerobic heterotrophic microorganisms lived and developed, consuming ready-made organic matter of abiogenic origin. Gradually, the supply of organic matter was exhausted, and under these conditions, an important step in the evolution of life was the emergence of chemo- and photosynthetic bacteria, which, using the energy of light and inorganic compounds, converted carbon dioxide into carbohydrate compounds that served as food for other microorganisms. The first autotrophs were probably also anaerobes. A revolution in the historical development of the biosphere occurred with the advent of cyanides, which began to carry out photosynthesis with the release of oxygen. The accumulation of free oxygen, on the one hand, caused the massive death of primitive anaerobic prokaryotes, but, on the other hand, created conditions for the further progressive evolution of life, since aerobic organisms are capable of much more intense metabolism compared to anaerobic ones.

The appearance of a eukaryotic cell is the second most important event (after the origin of life itself) in biological evolution. Thanks to a more advanced system of genome regulation of eukaryotic organisms, the adaptability of single-celled organisms, their ability to adapt to changing conditions without introducing hereditary changes to the genome, has sharply increased. It was thanks to the ability to adapt, that is, to change depending on external conditions, that eukaryotes were able to become multicellular: after all, in a multicellular organism, cells with the same genome, depending on conditions, form tissues that are completely different in both morphology and function.

The evolution of eukaryotes led to the emergence of multicellularity and sexual reproduction, which in turn accelerated the pace of evolution.

The problem of the prevalence of life in the Universe

The question of the prevalence of life in the Universe has not been resolved by modern science. Postulating that in conditions similar to those that existed on the young Earth, the development of life is quite likely, we can come to the conclusion that life forms similar to those on Earth should be found in the infinite Universe. Many scientists take this principled position. Thus, Giordano Bruno’s idea about the plurality of inhabited worlds is picked up.

Firstly, in the metagalaxy there are a huge number of stars similar to our Sun, therefore, planetary systems can exist not only near the Sun. Moreover, studies have shown that some stars of certain spectral classes rotate slowly around their axis, which may be caused by the presence of planetary systems around these stars. Secondly, the molecular compounds necessary for the initial stage of the evolution of inanimate nature are quite common in the Universe and have been discovered even in the interstellar medium. Under appropriate conditions, life could arise on planets of other stars, similar to the evolutionary development of life on Earth. Thirdly, we cannot exclude the possibility of the existence of non-protein forms of life that are fundamentally different from those common on Earth.

On the other hand, many scientists believe that even primitive life is such a structurally and functionally complex system that even if all the conditions necessary for its emergence are present on any planet, the likelihood of its spontaneous emergence is extremely low. If these considerations are valid, then life should be an extremely rare and possibly, within the observable Universe, a unique phenomenon.

Based on astronomy data, we can clearly conclude that in the Solar System and other star systems closest to us, conditions for the formation of civilizations do not exist. But the existence of primitive life forms cannot be ruled out. Thus, a group of American scientists, based on an analysis of the structure of the so-called “Martian meteorite,” believes that they have discovered evidence of primitive single-cell life that existed on Mars in the distant past. Due to the scarcity of such material, it is now impossible to draw clear conclusions on this issue. Perhaps future Martian expeditions will help with this.

Development of life in the Proterozoic era. During the first half of the Proterozoic era (it began 2.5 billion years ago and ended about 0.6 billion years ago), prokaryotic ecosystems colonized the entire World Ocean. At this time (about 2 billion years ago), primitive unicellular eukaryotes (flagellates) arose, which quickly diverged into plants (algae), animals (protozoa) and fungi.

As a way to achieve biological progress, eukaryotes are characterized by increasing complexity of organization, which leads to more efficient absorption of vital resources.

The emergence of multicellular organisms- another manifestation of the ability of eukaryotes to complicate their structure. Most researchers believe that multicellular organisms evolved from colonial unicellular organisms due to the differentiation of their cells. Multicellularity in different groups of algae and fungi arose independently in different systematic groups: for example, multicellular green, brown and red algae evolved from different colonial (filamentous) forms. Among animals, all multicellular organisms that in embryonic development have two (ecto- and endoderm) or three (also mesoderm) germ layers (leaves) of cells are of monophyletic origin (i.e., origin from common ancestors).

Basic hypotheses of the origin of multicellular animals from colonial flagellates was put forward in the second half of the 19th century by the German biologist E. Haeckel and the Ukrainian scientist I. I. Mechnikov.

E. Haeckel, relying on the biogenetic law he discovered, believed that each stage of ontogenesis corresponds to a certain type of ancestral organisms. Studying the embryogenesis of some coelenterates, which he considered close to the original multicellular organisms, he established that gastrulation in them occurs due to the invagination of the blastoderm at the posterior end of the body (intussusception) with the formation of the primary mouth and sac-like intestine. Haeckel called this hypothetical animal “gastrea”. In his opinion, she captured food in her mouth and digested it in her intestines.

According to I.I. Mechnikov, the primary method of etching multicellular animals was phagocytosis, i.e. intracellular digestion, which is still characteristic of many groups with a low level of organization (sponges, some ciliated worms, some coelenterates, etc.). He also found that in some coelenterates, gastrulation occurs by migration of some blastoderm cells into the blastula. According to him, the original multicellular animals were hypoggetic “phagocytes”, covered with a layer of ciliated cells capable of capturing small nutrient particles using phagocytosis. Cells with digestive vacuoles migrated inside the phagocytele, losing their cilia, where they digested food. Organisms of the gastrea type arose from phagocytes in the later stages of evolution, when they acquired the ability to capture larger prey with their mouth opening, which arose due to differences in the outer layer of cells.

It should be noted that paleontologists have not found the remains of such organisms, so the real routes of origin of different types of multicellular animals have not yet been established.

Primordial eukaryotes(flagellated single-celled organisms) evolved from prokaryotes in the first half of the Proterozoic era and soon after split into single-celled plants (algae), animals (protozoa) and fungi. The formation of a complex genome, nuclear envelope, dominance of the sexual method of reproduction and the ability to complicate the organization of eukaryotes determined their wide adaptive capabilities and further rapid evolution.

According to most scientists, multicellular organisms evolved from colonial ancestors. The probable routes of origin of multicellular animals are explained by the hypotheses of the phagocytela of I.I. Mechnikov and the gastrea of ​​E. Haeckel.

According to modern concepts, life is the process of the existence of complex systems consisting of large organic molecules and inorganic substances and capable of self-reproduction, self-development and maintaining their existence as a result of the exchange of energy and matter with the environment.

With the accumulation of human knowledge about the world around us and the development of natural science, views on the origin of life changed, and new hypotheses were put forward. However, even today the question of the origin of life has not yet been finally resolved. There are many hypotheses about the origin of life. The most important of them are the following:

Ø Creationism (life was created by the Creator);

Ø Hypotheses of spontaneous generation (spontaneous generation; life arose repeatedly from inanimate matter);

Ø Steady State Hypothesis (life has always existed);

Ø Panspermia hypothesis (life was brought to Earth from other planets);

Ø Biochemical hypotheses (life arose under the conditions of the Earth as a result of processes that obey physical and chemical laws, i.e. as a result of biochemical evolution).

Creationism. According to this religious hypothesis, which has ancient roots, everything that exists in the Universe, including life, was created by a single Power - the Creator as a result of several acts of supernatural creation in the past. The organisms that inhabit the Earth today are descended from the individually created basic types of living beings. The created species were from the very beginning superbly organized and endowed with the capacity for some variability within certain limits (microevolution). This hypothesis is adhered to by followers of almost all the most widespread religious teachings.

The traditional Judeo-Christian view of creation, as set out in the Book of Genesis, has been and continues to be controversial. However, existing contradictions do not refute the concept of creation. Religion, considering the question of the origin of life, seeks answers mainly to the questions “why?” and “for what?”, and not to the question “how?”. If science makes extensive use of observation and experiment in its search for truth, then theology comprehends truth through divine revelation and faith.

The process of divine creation of the world is presented as having taken place only once and therefore inaccessible to observation. In this regard, the creation hypothesis can neither be proven nor disproved and will always exist along with scientific hypotheses of the origin of life.

Hypotheses of spontaneous generation. For thousands of years, people believed in the spontaneous generation of life, considering it the usual way for living beings to emerge from inanimate matter. It was believed that the source of spontaneous generation was either inorganic compounds or decaying organic remains (the concept of abiogenesis). This hypothesis was common in ancient China, Babylon and Egypt as an alternative to creationism, with which it coexisted. The idea of ​​spontaneous generation was also expressed by the philosophers of Ancient Greece and even earlier thinkers, i.e. it is apparently as old as humanity itself. Over such a long history, this hypothesis has been modified, but still remains erroneous. Aristotle, often hailed as the founder of biology, wrote that frogs and insects thrive in damp soil. In the Middle Ages, many “managed” to observe the birth of various living creatures, such as insects, worms, eels, mice, in the decomposing or rotting remains of organisms. These “facts” were considered very convincing until the Italian physician Francesco Redi (1626-1697) approached the problem of the origin of life more strictly and questioned the theory of spontaneous generation. In 1668, Redi performed the following experiment. He placed the dead snakes in different vessels, covering some vessels with muslin and leaving others open. The flies that swooped in laid eggs on dead snakes in open vessels; Soon the larvae hatched from the eggs. There were no larvae in the covered vessels (Fig. 5.1). Thus, Redi proved that the white worms appearing in the meat of snakes are the larvae of the Florence fly and that if the meat is covered and prevented from accessing the flies, it will not “produce” worms. Refuting the concept of spontaneous generation, Redi suggested that life can only arise from previous life (the concept of biogenesis).

Similar views were held by the Dutch scientist Anthony van Leeuwen Hoek (1632-1723), who, using a microscope, discovered tiny organisms invisible to the naked eye. These were bacteria and protists. Leeuwenhoek suggested that these tiny organisms, or “animalcules,” as he called them, were descended from their own kind.

Leeuwenhoek's opinion was shared by the Italian scientist Lazzaro Spallanzani (1729-1799), who decided to prove experimentally that microorganisms often found in meat broth do not spontaneously arise in it. For this purpose, he placed a liquid rich in organic substances (meat broth) into vessels, boiled this liquid over a fire, after which he sealed the vessels hermetically. As a result, the broth in the vessels remained clean and free of microorganisms. With his experiments, Spallanzani proved the impossibility of spontaneous generation of microorganisms.

Opponents of this point of view argued that life did not arise in flasks for the reason that the air in them deteriorates during boiling, so they still accepted the hypothesis of spontaneous generation.

A crushing blow to this hypothesis was dealt in the 19th century. French microbiologist Louis Pasteur (1822-1895) and English biologist John Tyndall (1820-1893). They showed that bacteria spread through the air and that if there are no bacteria in the air entering flasks with sterilized broth, then they will not appear in the broth itself. For this, Pasteur used flasks with a curved S-shaped neck, which served as a trap for bacteria, while air freely penetrated into and out of the flask (Fig. 5.3).

Tyndall sterilized the air entering the flasks by passing it through a flame or through cotton wool. By the end of the 70s. 19th century Almost all scientists recognized that living organisms come only from other living organisms, which meant returning to the original question: where did the first organisms come from?

Steady State Hypothesis. According to this hypothesis, the Earth never came into being, but existed forever; it was always capable of supporting life, and if it changed, it was very little; species have also always existed. This hypothesis is sometimes called the hypothesis of eternism (from the Latin eternus - eternal).

The hypothesis of eternism was put forward by the German scientist W. Preyer in 1880. Preyer’s views were supported by academician V.I. Vernadsky, author of the doctrine of the biosphere.

Panspermia hypothesis. The hypothesis about the appearance of life on Earth as a result of the transfer of certain embryos of life from other planets was called panspermia (from the Greek pan - all, everyone and sperma - seed). This hypothesis is adjacent to the stationary state hypothesis. Its adherents support the idea of ​​the eternal existence of life and put forward the idea of ​​its extraterrestrial origin. One of the first to express the idea of ​​the cosmic (extraterrestrial) origin of life was the German scientist G. Richter in 1865. According to Richter, life on Earth did not arise from inorganic substances, but was brought from other planets. In this regard, questions arose about how possible such a transfer from one planet to another was and how it could be accomplished. Answers were sought primarily in physics, and it is not surprising that the first defenders of these views were representatives of this science, outstanding scientists G. Helmholtz, S. Arrhenius, J. Thomson, P.P. Lazarev et al.

According to the ideas of Thomson and Helmholtz, spores of bacteria and other organisms could be brought to Earth with meteorites. Laboratory studies confirm the high resistance of living organisms to adverse effects, in particular to low temperatures. For example, plant spores and seeds did not die even after prolonged exposure to liquid oxygen or nitrogen.

Other scientists have expressed the idea of ​​transferring “spores of life” to Earth with light.

Modern adherents of the concept of panspermia (including Nobel Prize winner English biophysicist F. Crick) believe that life was brought to Earth either accidentally or intentionally by space aliens.

The panspermia hypothesis is supported by the point of view of astronomers C. Wickramasinghe (Sri Lanka) and F. Hoyle

(Great Britain). They believe that microorganisms are present in large numbers in outer space, mainly in gas and dust clouds, where, according to scientists, they are formed. Next, these microorganisms are captured by comets, which then, passing near the planets, “sow the germs of life.”

Life began in the Archean era. Since the first living organisms did not yet have any skeletal formations, almost no traces remained of them. However, the presence of rocks of organic origin among the Archean deposits - limestone, marble, graphite and others - indicates the existence of primitive living organisms in this era. They were single-celled prenuclear organisms (prokaryotes): bacteria and blue-green algae.

Life in water was possible due to the fact that water protected organisms from the harmful effects of ultraviolet rays. That is why the sea could become the cradle of life.

4 major events of the Archean era

In the Archean era, four major events (aromorphosis) occurred in the evolution of the organic world and the development of life:

• Eukaryotes appeared;
• photosynthesis;
• sexual process;
• multicellularity.

The appearance of eukaryotes is associated with the formation of cells with a true nucleus (containing chromosomes) and mitochondria. Only such cells are capable of dividing mitotically, which ensures good preservation and transmission of genetic material. This was a prerequisite for the emergence of the sexual process.

The first inhabitants of our planet were heterotrophic and fed on organic substances of abiogenic origin dissolved in the primordial ocean. The progressive development of primary living organisms subsequently provided a huge leap (aromorphosis) in the development of life: the emergence of autotrophs that use solar energy to synthesize organic compounds from the simplest inorganic ones.

Of course, such a complex compound as chlorophyll did not arise immediately. Initially, simpler pigments appeared that facilitated the absorption of organic substances. From these pigments, chlorophyll apparently developed.

Over time, the primordial ocean began to dry out the organic substances that had accumulated in it abiogenically. The appearance of autotrophic organisms, primarily green plants capable of photosynthesis, ensured further continuous synthesis of organic substances, thanks to the use of solar energy (the cosmic role of plants), and, consequently, the existence and further development of life.

With the advent of photosynthesis, the organic world diverged into two trunks, differing in the way they feed. Thanks to the emergence of autotrophic photosynthetic plants, water and the atmosphere began to be enriched with free oxygen. This predetermined the possibility of the emergence of aerobic organisms capable of more efficient use of energy in the process of life.

The accumulation of oxygen in the atmosphere led to the formation of an ozone screen in its upper layers, which did not transmit life-destructive ultraviolet rays. This paved the way for life to reach land. The appearance of photosynthetic plants provided the possibility of the existence and progressive development of heterotrophic organisms.

The appearance of the sexual process led to the emergence of combinative variability supported by selection. Finally, apparently, in this era, multicellular organisms evolved from colonial flagellates. The emergence of the sexual process and multicellularity prepared the way for further progressive evolution.

Conclusions from the analysis of protein homologies in the three superkingdoms of living nature

The distribution of protein domains included in the 15th version of the Pfam database (August 2004) in three superkingdoms: Archaea, Bacteria and Eykaryota was analyzed. Apparently, of the total number of protein domains in eukaryotes, almost half were inherited from prokaryotic ancestors. From archaea, eukaryotes inherited the most important domains associated with the information processes of the nucleocytoplasm (replication, transcription, translation). A significant portion of domains associated with basic metabolism and signal-regulatory systems have been inherited from bacteria. Apparently, many signal-regulatory domains common to bacteria and eukaryotes in the former performed synecological functions (ensuring the interaction of the cell with other components of the prokaryotic community), and in the latter they began to be used to ensure the coordinated functioning of cellular organelles and individual cells of a multicellular organism. Many eukaryotic domains of bacterial origin (including “synecological”) could not be inherited from the ancestors of mitochondria and plastids, but were borrowed from other bacteria. A model of the formation of a eukaryotic cell through a series of successive symbiogenetic acts has been proposed. According to this model, the ancestor of the nuclear-cytoplasmic component of the eukaryotic cell was an archaea, in which, under conditions of crisis caused by an increase in the concentration of free oxygen in the prokaryotic community, the process of incorporation of foreign genetic material from the external environment sharply intensified.

The symbiogenetic theory of the origin of eukaryotes is now almost universally accepted. The entire set of molecular genetic, cytological and other data indicates that the eukaryotic cell was formed by the fusion of several prokaryotes into a single organism. The appearance of a eukaryotic cell should have been preceded by a more or less long period of coevolution of its future components in one microbial community, during which a complex system of relationships and connections developed between species, necessary to coordinate various aspects of their life activity. The molecular mechanisms that evolved during the formation of these synecological connections could play an important role in the subsequent process of combining several prokaryotes into a single cell. The emergence of eukaryotes (“eukaryotic integration”) should be considered as the end result of the long-term development of integration processes in the prokaryotic community (Markov, in press). The specific mechanisms of eukaryotic integration, its details and sequence of events, as well as the conditions under which it could occur, remain largely unclear.

It is generally accepted that at least three prokaryotic components took part in the formation of a eukaryotic cell: “nuclear-cytoplasmic”, “mitochondrial” and “plastid”.

Nuclear-cytoplasmic component (NCC)

The most difficult task is the identification of the nuclear-cytoplasmic component. Apparently, archaea (Archaea) played a leading role in its formation. This is evidenced by the presence of typically archaeal features in the most important structural and functional systems of the nucleus and cytoplasm of eukaryotes. Similarities can be traced in the organization of the genome (introns), in the basic mechanisms of replication, transcription and translation, and in the structure of ribosomes (Margulis and Bermudes, 1985; Slesarev et al., 1998; Ng et al., 2000; Cavalier-Smith, 2002). It has been noted that the molecular systems of the nucleocytoplasm of eukaryotes associated with the processing of genetic information are predominantly of archaeal origin (Gupta, 1998). However, it is not clear which archaebacteria gave rise to NCC, what ecological niche they occupied in the “ancestral community,” or how and why they acquired a mitochondrial endosymbiont.

In the structure of the nucleocytoplasm of eukaryotes, in addition to archaeal and specifically eukaryotic features, there are also bacterial ones. A number of hypotheses have been proposed to explain this fact. Some authors believe that these features are a consequence of the acquisition of bacterial endosymbionts (mitochondria and plastids), many of whose genes moved to the nucleus, and proteins began to perform various functions in the nucleus and cytoplasm (Gabaldon and Huynen, 2003). The acquisition of mitochondria is often considered a key moment in the formation of eukaryotes, either preceding or occurring simultaneously with the emergence of the nucleus. This opinion is supported by molecular data indicating the monophyletic origin of mitochondria in all eukaryotes (Dyall and Johnson, 2000; Litoshenko, 2002). At the same time, living non-mitochondrial eukaryotes are interpreted as descendants of forms that had mitochondria, since their nuclear genomes contain genes presumably of mitochondrial origin (Vellai et al., 1998; Vellai and Vida, 1999; Gray et al., 1999).

An alternative point of view is that JCC was a chimeric organism of archaeal-bacterial nature even before the acquisition of mitochondria. According to one hypothesis, JCC was formed as a result of a unique evolutionary event - the merger of an archaea with a proteobacterium (possibly a photosynthetic organism close to Chlorobium). The resulting symbiotic complex received resistance to natural antibiotics from the archaea, and aerotolerance from the proteobacteria. The cell nucleus was formed in this chimeric organism even before the incorporation of the mitochondrial symbiont (Gupta, 1998). Another version of the “chimeric” theory was proposed by V.V. Emelyanov (Emelyanov, 2003), according to whom the host cell that received the mitochondrial endosymbiont was a prokaryotic non-nuclear organism formed by the fusion of an archaebacterium with a fermenter eubacterium, and the basic energy metabolism This organism was of eubacterial nature (glycolysis, fermentation). According to the third version of the “chimeric” theory, the nucleus appeared simultaneously with undulipodia (eukaryotic flagella) as a result of the symbiosis of an archaea with a spirochete, and this event occurred before the acquisition of mitochondrial symbionts. Mitochondrial-free protozoa do not necessarily descend from ancestors that had mitochondria, and the bacterial genes in their genome may have arisen as a result of symbiosis with other bacteria (Margulis et al., 2000; Dolan et al., 2002). There are other variations of the “chimera” theory (Lуpez-Garcia, Moreira, 1999).

Finally, the presence in the nucleocytoplasm of eukaryotes of many unique features that are not characteristic of either bacteria or archaea formed the basis of another hypothesis, according to which the ancestor of the JCC belonged to the “chronocytes” - a hypothetical extinct group of prokaryotes, equally distant from both bacteria and archaea ( Hartman, Fedorov, 2002).

Mitochondrial component

There is much more clarity on the nature of the mitochondrial component of a eukaryotic cell. Its ancestor, according to most authors, was alphaproteobacteria (which include, in particular, purple bacteria that carry out oxygen-free photosynthesis and oxidize hydrogen sulfide to sulfate). Thus, it was recently shown that the mitochondrial genome of yeast is closest to the genome of the purple nonsulfur alphaproteobacterium Rhodospirillum rubrum(Esser et al., 2004). The electron transport chain, which was originally formed in these bacteria as part of the photosynthetic apparatus, subsequently began to be used for oxygen respiration.

Based on comparative proteomics, a metabolic reconstruction of the “protomitochondria,” a hypothetical alphaproteobacterium that gave rise to the mitochondria of all eukaryotes, has recently been compiled. According to these data, the ancestor of mitochondria was an aerobic heterotroph that received energy from the oxygen oxidation of organic matter and had a fully formed electron transport chain, but required the supply of many important metabolites (lipids, amino acids, glycerols) from the outside. This is evidenced, among other things, by the presence in the reconstructed “protomitochondria” of a large number of molecular systems that serve to transport these substances across the membrane (Gabaldún, Huynen, 2003). The main stimulus for the combination of NCC with protomitochondrion, according to most hypotheses, was the need for anaerobic NCC to protect itself from the toxic effects of molecular oxygen. The acquisition of symbionts that utilize this poisonous gas made it possible to successfully solve this problem (Kurland, Andersson, 2000).

There is another hypothesis, according to which the protomitochondrion was a facultative anaerobe, capable of oxygen respiration, but at the same time producing molecular hydrogen as a by-product of fermentation (Martin and Muller, 1998). The host cell in this case was supposed to be a methanogenic chemoautotrophic anaerobic archaea that needed hydrogen to synthesize methane from carbon dioxide. The hypothesis is based on the existence in some unicellular eukaryotes of so-called hydrogenosomes - organelles that produce molecular hydrogen. Although hydrogenosomes do not have their own genome, some of their properties indicate a relationship with mitochondria (Dyall and Johnson, 2000). Close symbiotic associations between methanogenic archaea and hydrogen-producing proteobacteria are quite common in modern biota, and apparently were common in the past, so if the “hydrogen” hypothesis were correct, one would expect multiple, polyphyletic origins of eukaryotes. However, molecular evidence suggests their monophyly (Gupta, 1998). The “hydrogen” hypothesis is also contradicted by the fact that specific protein domains of archaea associated with methanogenesis do not have homologues in eukaryotes. Most authors consider the “hydrogen” hypothesis of the origin of mitochondria to be untenable. Hydrogenosomes are most likely a later modification of ordinary mitochondria that carried out aerobic respiration (Gupta, 1998; Kurland and Andersson, 2000; Dolan et al., 2002).

Plastid component

The ancestors of plastids were cyanobacteria. According to the latest data, plastids of all algae and higher plants are of monophyletic origin and arose as a result of the symbiosis of a cyanobacterium with a eukaryotic cell that already had mitochondria (Martin and Russel, 2003). This supposedly happened between 1.5 and 1.2 billion years ago. In this case, many of those integration molecular systems (signaling, transport, etc.) that had already been formed in eukaryotes to ensure interaction between the nuclear-cytoplasmic and mitochondrial components were used (Dyall et al., 2004). It is interesting that some enzymes of the Calvin cycle (a key metabolic pathway of photosynthesis) functioning in plastids are of proteobacterial rather than cyanobacterial origin (Martin and Schnarrenberger, 1997). Apparently, the genes for these enzymes come from a mitochondrial component whose ancestors were also once photosynthetic (purple bacteria).

Possibilities of comparative genomics and proteomics in the study of the origin of eukaryotes

Comparative analysis of genomic and proteomic data opens up great opportunities for reconstructing the processes of “eukaryotic integration”.

Currently, numerous and largely systematized data on protein and nucleotide sequences of many organisms, including representatives of all three superkingdoms: Archaea, Bacteria and Eukaryota, have been collected and are publicly available (on the Internet). Bases like COGs
(Phylogenetic classification of proteins encoded in complete genomes; http://www.ncbi.nlm.nih.gov/COG/), SMART(Simple Modular Architecture Research Tool; http://smart.embl-heidelberg.de/) , Pfam(Protein Domain Families Based on Seed Alignments;http://pfam.wustl.edu/index.html) , NCBI-CDD(http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) and others provide many tools for searching and comparing full-text sequences of proteins and their encoding genes. Sequence comparisons are made both within representatives of the same species and between different taxa.

Using these data and analytical tools, it seems possible to collect and systematize sufficiently massive material that will allow us to establish which structural and functional subsystems of the eukaryotic cell were inherited from Archaea, which from Bacteria, and which appeared later and are unique to Eukaryota. Such analysis can also provide new data regarding specific groups of bacteria and archaea that were most likely to participate in the formation of the primary eukaryotic cell.

Ratio of common and unique protein domains in archaea, bacteria and eukaryotes

This work reflects the results of an analysis of the functional spectra and taxonomic assignment of protein domains included in the 15th version of the Pfam system (version published on the Internet on August 20, 2004). This system, which is the most comprehensive systematic catalog of its kind, currently includes 7503 protein domains.

The concept of “protein domain” is closely related to the natural classification of proteins that is currently being actively developed. A domain is a more or less conserved sequence of amino acids (or the so-called “motif” - a sequence that includes alternating conservative and variable fragments) present in several (usually many) protein molecules in different organisms. Most of the domains included in the Pfam system are characterized by a strictly defined function and thus represent functional blocks of protein molecules (for example, DNA-binding domains or catalytic domains of enzymes). The function of some domains remains unknown to this day, but the conservation and distribution of these sequences suggests that they also have functional unity. It is assumed that the vast majority of domains are homologous sequences (i.e., having a single origin, and not arising in parallel in different branches of the evolutionary tree). This is evidenced by the significant length of these sequences, as well as the fact that almost any function (catalytic, signaling, structural, etc.) can be realized by many different combinations of amino acids, therefore, in the case of parallel appearance of functionally similar blocks in protein molecules in different organisms, it is a fact independent origin is usually quite obvious.

Proteins are grouped into families based on the presence of common domains in them, so the concepts of “protein family” and “domain” in the Pfam system largely coincide.

Based on data from the Pfam system, a quantitative distribution of domains was determined across three superkingdoms of living nature (Archaea, Bacteria, Eukaryota):

Rice. 1. Quantitative ratio of common and unique protein domains in archaea, bacteria and eukaryotes. The areas of the figures are approximately proportional to the number of domains.

In total, the 15th version of Pfam contains 4474 eukaryotic domains, which can be divided into 4 groups:

1) Specific domains of eukaryotes not found in the other two superkingdoms (2372);

2) Domains present among representatives of all three superkingdoms (1157);

3) Domains common to eukaryotes and bacteria, but absent in archaea (831);

4) Domains common to eukaryotes and archaea, but absent in bacteria (114).

The greatest attention in the following discussion is paid to the domains of the third and fourth groups, since their taxonomic location allows us to speak with a certain degree of probability about their origin. Apparently, a significant part of the domains of the third group were inherited by eukaryotes from bacteria, and the fourth - from archaea.

In some cases, the commonality of domains in different superkingdoms may be associated with later horizontal transfer, but then in the “recipient” superkingdom, most likely, this domain will be found in only one or a few representatives. There really are such cases. Compared to the previous, 14th version of Pfam, in the new, 15th version, a number of purely bacterial domains have moved to the third group for the reason that the corresponding sequences were discovered in the recently “deciphered” genomes of individual eukaryotes (especially the mosquito Anopheles gambiae and the simplest Plasmodium yoelii). The presence in the genome of the malaria mosquito of genes encoding proteins of bacterial flagella (despite the fact that these sequences have not been found in any other eukaryotes) naturally suggests horizontal transfer. Such domains were not taken into account in further discussion (in the third group there are about 40 of them, in the fourth group they are absent).

The quantitative ratio of common and unique domains in the three superkingdoms would seem to indicate a decisive predominance of the “bacterial” component in the eukaryotic cell compared to the “archaeal” one (eukaryotes have 831 “bacterial” domains and 114 “archaeal” ones). Similar results were recently obtained during a comparative analysis of the genomes of yeast and various prokaryotes: it turned out that 75% of the total number of yeast nuclear genes that have prokaryotic homologs are more similar to bacterial than to archaeal sequences (Esser et al., 2004). This conclusion, however, becomes less obvious if we compare the mentioned figures with the total number of common and unique domains in the two superkingdoms of prokaryotes. Thus, out of the total number of bacterial domains not found in archaea (2558), 831 were transferred to eukaryotic cells, which is 32.5%. Of the total number of archaeal domains not found in bacteria (224), 114, i.e. 48.7%, were found in eukaryotic cells. Thus, if we imagine the emerging eukaryotic cell as a system capable of freely selecting certain protein blocks from the available set, then it should be recognized that it gave preference to archaeal domains.

The significant role of the archaeal component in the formation of eukaryotes becomes even more obvious if we compare the “functional spectra” (distribution among functional groups) and the physiological significance of eukaryotic domains of “archaeal” and “bacterial” origin.

Functional spectrum of eukaryotic domains of “archaeal” origin

The first thing that catches your eye when looking at the descriptions of domains in this group is the high occurrence of words and phrases such as “essential” (key, vital) and “plays a key role” (plays a key role). In annotations of domains from other groups, such indications are much less common.

This group is dominated by domains associated with the most basic, central processes of cell life, namely the processes of storage, reproduction, structural organization and reading of genetic information. These include key domains responsible for the replication mechanism (DNA primase domains, etc.), transcription (including 7 domains of DNA-dependent RNA polymerases), translation (a large set of ribosomal proteins, domains associated with ribosome biogenesis, initiation factors and elongation, etc.), as well as with various modifications of nucleic acids (including rRNA processing in the nucleolus) and their organization in the nucleus (histones and other proteins associated with the organization of chromosomes). Note that a recent detailed comparative analysis of all known transcription-related proteins showed that archaea show more similarities to eukaryotes than bacteria (Coulson et al., 2001, fig. 1b).

Of interest are 6 domains associated with the synthesis (post-transcriptional modifications) of tRNA. Chemical changes made by special enzymes to tRNA nucleotides are one of the most important means of adaptation to high temperatures (they allow tRNA to maintain the correct tertiary structure when heated). It has been shown that the number of altered nucleotides in tRNA of thermophilic archaea increases with increasing temperature (Noon et al., 2003). The preservation of these archaeal domains in eukaryotes may indicate that the temperature conditions in the habitats of the first eukaryotes were unstable (there was a danger of overheating), which is typical for shallow-water habitats.

There are relatively few signal-regulatory domains, but among them are such important ones as the transcription factor TFIID (TATA-binding protein, PF00352), the domains of the transcription factors TFIIB, TFIIE, TFIIS (PF00382, PF02002, PF01096), general-purpose transcription regulators that play a central role in the activation of genes transcribed by RNA polymerase II. The domain CBFD_NFYB_HMF (PF00808) is also interesting: in archaea it is a histone, and in eukaryotes it is a histone-like transcription factor.

Of particular note are the eukaryotic domains of “archaeal origin” associated with membrane vesicles. These include the Adaptin N domain (PF01602), which is associated with endocytosis in eukaryotes; Aromatic-di-Alanine (AdAR) repeat (PF02071), in eukaryotes involved in the process of fusion of membrane vesicles with the cytoplasmic membrane and found in two species of archaea from the genus Pyrococcus; Syntaxin (PF00804), in eukaryotes, regulates, in particular, the attachment of intracellular membrane vesicles to the presynaptic membrane of neurons and was found in aerobic archaea of ​​the genus Aeropyrum, etc. Among the “domains of bacterial origin” there are no proteins with such functions. Domains that control membrane fusion and vesicle formation could play an important role in the symbiogenetic formation of a eukaryotic cell, since they create the basis for the development of phagocytosis (the most likely route for the acquisition of intracellular symbionts - plastids and mitochondria), as well as for cell fusion (copulation) and the formation of various intracellular membrane structures characteristic of eukaryotes, such as the endoplasmic reticulum (ER). The ER of eukaryotes, according to one hypothesis, is of archaebacterial origin (Dolan et al., 2002). The assumption is based, in particular, on the similarity of the synthesis of N-linked glycans in the ER with certain stages of cell wall formation in archaea (Helenius and Aebi, 2001). Let us recall that the ER of eukaryotes is closely related to the nuclear envelope, which allows us to assume a single genesis of these structures.

One should also pay attention to the almost complete absence of metabolic domains in this group (which represents a sharp contrast with the group of eukaryotic “domains of bacterial origin”, where metabolic proteins, on the contrary, sharply predominate).

From the point of view of the problem of the emergence of eukaryotes, such domains of archaeal origin are of interest as the ZPR1 zinc-finger domain (PF03367) (in eukaryotes, this domain is part of many key regulatory proteins, especially those responsible for the interaction between nuclear and cytoplasmic processes), and zf-RanBP (PF00641), which is one of the most important components of nuclear pores in eukaryotes (responsible for the transport of substances across the nuclear membrane).

All 28 domains of ribosomal proteins of archaeal origin are present in the cytoplasmic ribosomes of eukaryotes, and all of them are found in both plants and animals. This picture is well consistent with the fact that the NOG1 domain, which has specific GTPase activity and is used by auxiliary proteins of the nucleolar organizer (rRNA gene clusters), is also of archaeal origin.

Table. Comparison of the functional spectra of eukaryotic domains present or absent in archaea (A), cyanobacteria (C), alphaproteobacteria (P) and bacteria in general, including C and P (B).

Rice. 2. Functional spectra of “archaeal” and “bacterial” domains of eukaryotes. 1 - Protein synthesis, 2 - Replication, transcription, modification and organization of NK, 3 - Signaling and regulatory proteins, 4 - Proteins associated with the formation and functioning of membrane vesicles, 5 - Transport and sorting proteins, 6 - Metabolism

Functional spectrum of eukaryotic domains of “bacterial” origin

Domains associated with basic information processes (replication, transcription, RNA processing, translation, organization of chromosomes and ribosomes, etc.) are also present in this group, but their relative share is significantly less than that of “archaeal” domains (Fig. 2 ). Most of them are either of secondary importance or are associated with information processes in organelles (mitochondria and plastids). For example, among the eukaryotic domains of archaeal origin, there are 7 domains of DNA-dependent RNA polymerases (the basic transcription mechanism), while in the bacterial group there are only two such domains (PF00940 and PF03118), the first of which is associated with the transcription of mitochondrial DNA, and the second is plastid. Another example: the PF00436 domain (Single-strand binding protein family) in bacteria is part of multifunctional proteins that play an important role in replication, repair and recombination; in eukaryotes, this domain is involved only in the replication of mitochondrial DNA.

The situation with ribosomal proteins is very indicative. Of the 24 eukaryotic domains of ribosomal proteins of bacterial origin, 16 are present in the ribosomes of mitochondria and plastids, 7 are present only in plastids, and for another domain there is no data on localization in eukaryotic cells. Thus, bacteria - participants in eukaryotic integration, apparently, contributed practically nothing to the structure of cytoplasmic ribosomes of eukaryotes.

Among domains of bacterial origin, the proportion of signal-regulatory proteins is significantly higher. However, if among the few regulatory domains of archaeal origin, basic general-purpose transcription regulators predominate (in fact, they do not so much regulate as organize the process), then in the bacterial group, signal-regulatory domains predominate, responsible for specific mechanisms of cell response to environmental factors (biotic and abiotic). These domains define what can be figuratively called the “ecology of the cell.” They can be roughly divided into “autecological” and “synecological”, and both are widely represented.

“Autecological” domains responsible for cell adaptation to external abiotic factors include, in particular, domains of hit-shock proteins (responsible for cell survival under overheated conditions), such as HSP90 - PF00183. This also includes all kinds of receptor proteins (Receptor L domain - PF01030, Low-density lipoprotein receptor repeat class B - PF00058 and many others), as well as protective proteins, for example, those associated with protecting cells from heavy metal ions (TerC - PF03741 ), from other toxic substances (Toluene tolerance, Ttg2 - PF05494), from oxidative stress (Indigoidine synthase A - PF04227) and many others. etc.

The preservation of many bacterial domains of an “ecological” nature in eukaryotes confirms the previously stated assumption that many integrating mechanisms that ensure the integrity and coordinated operation of parts of the eukaryotic cell (primarily signaling and regulatory cascades) began to develop long before these parts actually united under one cell membrane. Initially, they were formed as mechanisms ensuring the integrity of the microbial community (Markov, in press).

Of interest are domains of bacterial origin that are involved in the regulation of ontogenesis or cell-tissue differentiation in eukaryotes (for example, Sterile alpha motif - PF00536; TIR domain - PF01582; ​​jmjC domain - PF02373, etc.). The very “idea” of ontogenesis of multicellular eukaryotes is based, first of all, on the ability of cells, with an unchanged genome, to change their structure and properties depending on external and internal factors. This ability for adaptive modifications originated in prokaryotic communities and initially served to adapt bacteria to changing biotic and abiotic factors.

An analysis of the origin of such a significant domain for eukaryotes as Ras is also indicative. Proteins of the Ras superfamily are the most important participants in signaling cascades in eukaryotic cells, transmitting signals from receptors, both protein kinase and G-protein coupled, to non-receptor kinases - participants in the MAPK kinase cascade to transcription factors, to phosphatidylinositol kinase to secondary messengers , controlling the stability of the cytoskeleton, the activity of ion channels and other vital cellular processes. One of the most important motifs of the Ras domain, the P-loop with GTPase activity, is known as part of the Elongation factor Tu GTP binding (GTP_EFTU) domains and its related COG0218 and is widely represented in both bacteria and archaea. However, these domains belong to high molecular weight GTPases and are not related to cytoplasmic signal transduction.

Formally, the Ras domain is one common to archaea, bacteria, and eukaryotes. However, if in the latter it is found in a huge number of highly specialized signaling proteins, then in the genomes of bacteria and archaea there are isolated cases of its detection. In the bacterial genome, the Ras domain has been identified in proteobacteria and cyanobacteria, as part of low molecular weight peptides. Moreover, the structure of two peptides is similar to the structure of eukaryotic Ras proteins, and one of the proteins of Anabaena sp. additionally carries the LRR1 (Leucine Rich Repeat) domain, which is involved in protein-protein interactions. In the archaeal genome, the Ras domain was found in euarchaeota Methanosarcinaceae (Methanosarcina acetivorans) and Methanopyraceae (Methanopyrus kandleri AV19). It turns out that in Methanosarcina acetivorans the Ras domain is also located next to the LRR1 domain, which has not yet been found in other archaeal proteins and is known in eukaryotes and bacteria, including the above-mentioned Ras protein of cyanobacteria. In Methanopyrus kandleri AV19, the Ras domain is located next to the COG0218 domain, indicating different functions of this protein compared to Ras proteins. These facts give reason to assume the secondary appearance of the Ras and LRR1 domains in methane-producing archaea and the primary formation and specialization of the Ras domain in bacteria.

The most important difference between the functional spectrum of domains of bacterial origin and those of “archaeal” origin is the sharp predominance of metabolic domains. Among them, it should be noted, first of all, a large number of domains associated with photosynthesis and oxygen respiration. This is not surprising, since, according to the generally accepted opinion, both photosynthesis and oxygen respiration were obtained by eukaryotes together with bacterial endosymbionts - the ancestors of plastids and mitochondria.

Important for understanding the origin of eukaryotes are domains that are not directly related to the mechanism of aerobic respiration, but are associated with the microaerophilic metabolism of the eukaryotic cytoplasm and with protection from the toxic effects of molecular oxygen (oxygenases, peroxidases, etc.) There are many such domains in the “bacterial” group (19), but in the “archaeal” they are absent. Most of these domains in eukaryotes function in the cytoplasm. This suggests that eukaryotes apparently inherited from bacteria not only mitochondrial oxygen respiration, but also a significant part of the “aerobic” (more precisely, microaerophilic) cytoplasmic metabolism.

Note the large number (93) of domains associated with carbohydrate metabolism. Most of them in eukaryotes work in the cytoplasm. These include fructose diphosphate aldolase (domains PF00274 And PF01116) is one of the key enzymes of glycolysis. Fructose diphosphate aldolase catalyzes the reversible cleavage of hexose (fructose diphosphate) into two three-carbon molecules (dihydroxyacetone phosphate and glyceraldehyde 3-phosphate). A comparison of other glycolytic enzymes in archaea, bacteria and eukaryotes (in particular, according to genomic data from the COG system http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=20) clearly confirms the bacterial (not archaeal) nature of the main component of the energy metabolism of the cytoplasm of a eukaryotic cell - glycolysis. This conclusion is confirmed by pairwise comparison of protein sequences using BLAST (Feng et al., 1997) and by the results of a detailed comparative phylogenetic analysis of complete sequences of glycolytic enzymes in several representatives of archaea, bacteria and eukaryotes (Canback et al., 2002).

The most important role in the cytoplasmic metabolism of carbohydrates in eukaryotes is played by lactate dehydrogenase, an enzyme that reduces the final product of glycolysis (pyruvate) to form lactate (sometimes this reaction is considered as the last step of glycolysis). This reaction is an “anaerobic alternative” to mitochondrial oxygen respiration (during the latter, pyruvate is oxidized to water and carbon dioxide). Lactate dehydrogenase from a primitive eukaryotic organism, the fungus Schizosaccharomyces pombe, was compared using BLAST with archaeal and bacterial proteins. It turned out that this protein is almost identical to the malate/lactate dehydrogenases of bacteria of the genus Clostridium - strictly anaerobic fermenters (E min = 2 * 10 -83) and, to a lesser extent, obligate or facultative aerobes related to clostridia of the genus Bacillus (E min = 10 - 75). The closest archaeal homologue is the protein of the aerobic archaea Aeropyrum pernix (E=10 -44). Thus, eukaryotes also inherited this key component of cytoplasmic metabolism from fermenting bacteria rather than from archaea.

Among the eukaryotic domains of bacterial origin, there are several domains associated with the metabolism of sulfur compounds. This is important because the putative bacterial ancestors of plastids and, in particular, mitochondria (purple bacteria) were ecologically closely linked to the sulfur cycle. In this regard, the enzyme sulfide/quinone oxidoreductase found in mitochondria is especially interesting, which may have been inherited by eukaryotes directly from photosynthetic alphaproteobacteria, which use hydrogen sulfide as an electron donor during photosynthesis (unlike plants and most cyanobacteria, which use water for this) ( Theissen et al., 2003). Quinone sulfide oxidoreductases and related proteins are found in both bacteria and archaea, so the corresponding Pfam family of proteins is found in a group of domains common to all three superkingdoms. However, in terms of the amino acid sequences of these enzymes, eukaryotes are much closer to bacteria than to archaea. For example, comparing human mitochondrial quinone sulfide oxidoreductase http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=27151704 with archaeal proteins using BLAST, we obtain minimum E values ​​of at least 4*10 - 36 (Thermoplasma), with bacterial - 10 -123 (Chloroflexus).

Bacterial “roots” of sterol biosynthesis

The “bacterial” group contains several domains associated with steroid metabolism (3-beta hydroxysteroid dehydrogenase/isomerase family - PF01073, Lecithin:cholesterol acyltransferase - PF02450, 3-oxo-5-alpha-steroid 4-dehydrogenase - PF02544, etc.) . Even L. Margelis (1983), one of the main creators of the symbiogenetic theory of the origin of eukaryotes, noted that it is very important to establish the origin of the key enzyme in the biosynthesis of sterols (including cholesterol) in eukaryotes - squalene monooxygenase, which catalyzes the reaction:

squalene + O 2 + AH 2 = (S)-squalene-2,3-epoxide + A + H 2 O

The product of this reaction is then isomerized and converted into lanosterol, from which cholesterol, all other sterols, steroid hormones, etc. are subsequently synthesized. The importance of the problem of the origin of squalene monooxygenase is due to the fact that the biosynthesis of sterols is one of the main distinctive features of the metabolism of eukaryotes, not characteristic of any bacteria or archaea. This enzyme contains, according to Pfam, a single conserved domain (Monooxygenase - PF01360), which is present in many proteins of all three superkingdoms. Comparison of the amino acid sequence of human squalene monooxygenase (NP_003120; http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=4507197) using BLAST with archaeal and bacterial proteins shows that this protein exhibits much more similar to bacterial than to archaeal analogues (for the former, the minimum value is E = 5*10 -9, for the latter, E min = 0.28). Among bacteria, the actinobacterium Streptomyces argillaceus, the bacillus Bacillus halodurans, and the gammaproteobacterium Pseudomonas aeruginosa have the most similar proteins. Only after them comes the cyanobacterium Nostoc sp. (E=3*10 -4). Thus, the key enzyme in sterol biosynthesis appears to have evolved in early eukaryotes from bacterial rather than archaeal precursor proteins.

Another important enzyme in the biosynthesis of sterols is squalene synthase (EC 2.5.1.21), which synthesizes the sterol precursor - squalene. This enzyme belongs to the Pfam family SQS_PSY - PF00494, present in all three superkingdoms. Human squalene synthase (http://www.genome.jp/dbget-bin/www_bget?hsa+2222) is very similar to homologous proteins of bacteria, especially cyanobacteria and proteobacteria (E min = 2*10 -16), but is also similar to squalene synthase from the archaea Halobacterium sp. (E=2*10 -15).

The results obtained, in principle, do not contradict the hypothesis of L. Margulis that squalene was already present in proto-eukaryotes, i.e. in the nuclear-cytoplasmic component before the acquisition of mitochondria, while the synthesis of lanosterol became possible only after this event. On the other hand, JCC had to have a sufficiently elastic and mobile membrane in order to acquire a mitochondrial symbiont, and this is hardly possible without the synthesis of sterols, which precisely give eukaryotic membranes the properties necessary for phagocytosis, the formation of pseudopodia, etc.

Cytoskeleton

The most important feature of a eukaryotic cell is the presence of microtubules that are part of the undulipodia (flagella), the mitotic spindle and other cytoskeletal structures. L. Margelis (1983) suggested that these structures were inherited by the ancestors of eukaryotes from symbiotic spirochetes that turned into undulipodia. B.M. Mednikov, in the preface to the Russian edition of the book by L. Margelis, indicated that the best proof of this hypothesis would be the discovery of homologies in the amino acid sequences of the contractile protein of spirochetes and the cytoskeletal proteins of eukaryotes. The same idea is developed in detail in the recent work of M.F. Dolan et al. (Dolan et al., 2002).

It has not yet been possible to detect features specific to spirochetes in the cytoskeletal proteins of eukaryotes. At the same time, possible precursors of these proteins have been found in both bacteria and archaea.

Tubulin contains two Pfam domains: Tubulin/FtsZ family, C-terminal domain (PF03953) and Tubulin/FtsZ family, GTPase domain (PF00091). The same two domains are present in FtsZ proteins, which are widespread in bacteria and archaea. FtsZ proteins are capable of polymerizing into tubes, plates and rings and play an important role in the cell division of prokaryotes.

Although eukaryotic tubulins and prokaryotic FtsZ proteins are homologues, their sequence similarity is very low. For example, the tubulin-like protein of the spirochete Leptospira interrogans, containing both of the above domains (http://us.expasy.org/cgi-bin/sprot-search-ac?Q72N68) shows high similarity to plastid and mitochondrial proteins of eukaryotes involved in the division of these organelles , but not with eukaryotic tubulin. Therefore, some researchers speculate that there must have been another prokaryotic precursor of tubulin, more closely related to its eukaryotic homologues than the FtsZ proteins. Recently, such proteins, indeed very similar to eukaryotic tubulins (Emin = 10 -75), were found in several species of bacteria of the genus Prosthecobacter (Jenkins et al., 2002). These bacteria, unlike spirochetes, are immobile. The authors of the mentioned work believe that proto-eukaryotes could acquire tubulin through horizontal transfer from Prosthecobacter or another bacterium that had similar proteins (the possibility of fusion of an archaebacterial cell with a bacterium that had the tubulin gene cannot be ruled out).

GTPases involved in the regulation of microtubule assembly also point to the bacterial “roots” of the eukaryotic cytoskeleton. Thus, the Dynamin_N domain is of strictly bacterial origin (found in many groups of bacteria and unknown in archaea).

Eukaryotes could have inherited some proteins important for the formation of the cytoskeleton from archaea. For example, prefoldin (PF02996) is involved in actin biogenesis; Homologous proteins are present in many archaea, while only a few small fragments of similar sequences are found in bacteria. As for actin itself, no obvious homologues of this important eukaryotic protein have yet been discovered in prokaryotes. In both bacteria and archaea, MreB/Mbl proteins are known, similar to actin in their properties (the ability to polymerize and form filaments) and tertiary structure (Ent et al., 2001; Mayer, 2003). These proteins serve to maintain the rod-shaped shape of the cell (they are not found in coccoid forms), forming something like a “prokaryotic cytoskeleton”. However, in their primary structure, the MreB/Mbl proteins bear little resemblance to actin. Thus, MreB proteins of the spirochete Treponema pallidum ( http://us.expasy.org/cgi-bin/sprot-search-ac?O83510), clostridium Clostridium tetani ( http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi) and the archaea Methanobacterium thermoautotrophicum ( http://us.expasy.org/cgi-bin/sprot-search-ac?O27103) and Methanopyrus kandleri ( http://us.expasy.org/cgi-bin/sprot-search-ac?Q8TYX3) of eukaryotic proteins show the greatest similarity to the hit-shock proteins of chloroplasts and mitochondria Hsp70 (chaperones; localized in the nucleoid of organelles, involved in translocations of protein molecules). The similarity of the primary structure of MreB proteins to actin is rather weak, but in archaeal proteins it is somewhat higher than in bacterial ones.

Origin of bacterial components of eukaryotic nucleocytoplasm.

The above review confirms that JCC is a chimeric formation that combines the characteristics of archaea and bacteria. Its “central” blocks associated with the storage, reproduction, organization and reading of genetic information are predominantly of archaeal origin, while a significant part of the “periphery” (metabolic, signal-regulatory and transport systems) clearly has bacterial roots.

The archaeal ancestor apparently played the main organizing role in the formation of the JCC, but a significant part of its “peripheral” systems was lost and replaced by systems of bacterial origin. How could this happen?

The simplest explanation proposed by many authors is the assumption that the bacterial elements of the JCC originate from endosymbionts - mitochondria and plastids, many of whose genes actually moved to the nucleus, and the proteins encoded by them took on many purely cytoplasmic functions. This explanation is convincingly supported by extensive factual material (Vellai, Vida, 1999; Gray et al., 1999; Gabaldon, Huynen, 2003). The only question is whether it is sufficient.

There is reason to believe that this is not the case. There are many known facts indicating the presence in the nucleocytoplasm of eukaryotes of bacterial components that are not derived from either plastid or mitochondrial endosymbionts (Gupta, 1998). This is also evident from the analysis of protein domains. The JCC contains quite a lot of “bacterial” domains, which are not characteristic of either cyanobacteria (the ancestors of plastids) or alphaproteobacteria (the ancestors of mitochondria). If we exclude from the number of “bacterial” domains of eukaryotes (831 domains) those found in cyanobacteria and alphaproteobacteria, another 229 domains remain. Their origin cannot be explained by migration from organelles to the cytoplasm. Similar results were obtained from a comparative analysis of the complete sequences of protein molecules: many proteins of bacterial origin were found in eukaryotes, which were not acquired by them together with endosymbionts, but originate from other groups of bacteria. Many of these proteins were re-entered into organelles, where they continue to function in modern eukaryotes (Kurland and Andersson, 2000; Walden, 2002).

The table (two right columns) shows the functional spectra of two groups of “bacterial” domains of eukaryotes:

1) domains found in cyanobacteria and/or alphaproteobacteria, i.e. those that could be acquired by eukaryotes together with endosymbionts - plastids and mitochondria (602 domains),
2) domains that are absent in cyanobacteria and alphaproteobacteria, i.e. those whose origin cannot be directly linked to the acquisition of plastids and mitochondria (229 domains).

When comparing functional spectra, one must take into account that many of the domains of the first group could in fact also be acquired by eukaryotes not from endosymbionts, but from other bacteria in which these domains are also present. Thus, we can expect that the actual number of “bacterial” domains obtained by eukaryotes other than from endosymbionts is significantly higher than the numbers in the right column of the table indicate. This is especially true for proteins from those functional groups for which the numbers in the third column of the table are less or slightly greater than in the fourth.

First of all, we note that almost all “bacterial” domains of eukaryotes associated with the basic mechanisms of replication, transcription and translation (including ribosomal proteins) belong to the first group. In other words, it is very likely that they were obtained by eukaryotes almost exclusively from endosymbionts that turned into plastids and mitochondria. This was to be expected, since the ancestors of these organelles were captured entirely by the nuclear-cytoplasmic component, along with their own systems for processing genetic information and protein synthesis. Plastids and mitochondria retained their bacterial circular chromosomes, RNA polymerases, ribosomes and other central life support systems. The “interference” of the NCC in the internal life of organelles was reduced to the transfer of most of their genes into the nucleus, where they came under the control of more advanced nuclear-cytoplasmic regulatory systems. Almost all “bacterial” domains of eukaryotes associated with information processes function in organelles, and not in the nucleus and cytoplasm.

The main distinctive feature of the functional spectrum of domains of the second group is a sharply increased proportion of signal-regulatory proteins. This also includes many domains of an “ecological” nature, that is, those that in prokaryotes were responsible for the relationship of the cell with the external environment and, in particular, with other members of the prokaryotic community (receptors, signaling and protective proteins, domains of intercellular interaction, etc.) . In multicellular eukaryotes, as already noted, these domains often ensure interaction between cells and tissues, and are also used in the immune system (relationships with foreign microorganisms are also a kind of “synecology”).

The proportion of metabolic domains in the second group is sharply reduced compared to the first. There is a clear unevenness in the quantitative distribution of domains of the first and second groups in different parts of metabolism. Thus, almost all domains associated with photosynthesis, aerobic respiration, and electron transport chains appear to be of mitochondrial or plastid origin. This is a completely expected result, since photosynthesis and aerobic respiration are the main functions of plastids and mitochondria. The corresponding molecular systems were the main contribution of endosymbionts to the “utilities” of the developing eukaryotic cell.

The largest share among the metabolic domains of the second group belongs to proteins associated with carbohydrate metabolism. We have already mentioned the similarity of eukaryotic lactate dehydrogenase with homologous proteins of fermenting bacteria, such as Clostridium (i.e., very distant in taxonomic terms from cyano- and alphaproteobacteria). The situation is similar with other glycolytic enzymes. For example, human glyceraldehyde-3-phosphate dehydrogenase ( http://us.expasy.org/cgi-bin/niceprot.pl?G3P1_HUMAN) of all bacterial homologues, like lactate dehydrogenase, also shows the greatest similarity with proteins of representatives of the genus Clostridium (E = 10 -136), followed by the degree of similarity are various gammaproteobacteria - facultative anaerobic fermenters (Escherichia, Shigella, Vibrio, Salmonella, etc. .d.), obligate anaerobic fermenters Bacteroides, and only after them - the cyanobacterium Synechocystis sp. with E=10 -113. The similarity to archaeal glyceraldehyde-3-phosphate dehydrogenases is much lower, although the corresponding Pfam domains ( PF00044 And PF02800), of course, is found in all three superkingdoms.

Apparently, the most important cytoplasmic enzyme systems associated with carbohydrate metabolism (including glycolysis) were obtained by proto-eukaryotes not from endosymbionts, but from other bacteria (possibly from obligate or facultative anaerobic fermenters). This conclusion is convincingly supported by the results of a recent detailed phylogenetic analysis of the sequences of glycolytic enzymes in a number of representatives of eukaryotes and bacteria (Canback et al., 2002).

Of the eight “bacterial” domains of metabolism of steroids and related compounds, the ancestors of plastids and mitochondria are missing half, including the domain 3-beta hydroxysteroid dehydrogenase/isomerase family (PF01073), widespread in both eukaryotes and bacteria. In eukaryotes, proteins of this family are involved in the synthesis of steroid hormones, and in bacteria they perform other catalytic functions, in particular those associated with the metabolism of nucleotide sugars. The remaining three domains are found in only two or three species of bacteria each (and different domains are found in different species). What function these proteins perform in bacteria is unknown. But in general, these data indicate that enzyme systems for steroid metabolism could have developed in early eukaryotes on the basis of bacterial precursor proteins that previously performed slightly different functions, and the origin of these precursors cannot be associated exclusively with endosymbionts - plastids and mitochondria. Let us remember that the key enzyme of sterol bisynthesis in eukaryotes (squalene monooxygenase) shows the greatest similarity with proteins of actinobacteria, bacilli and gammaproteobacteria, and not cyano- or alphaproteobacteria.

The nature and genesis of the nuclear-cytoplasmic component of eukaryotes.

Based on the data presented, let us try to restore the appearance of the NCC as it was on the eve of the acquisition of mitochondrial endosymbionts.

The “central,” or informational, part of the NCC (replication, transcription and translation systems, including ribosomes) had a clearly archaeal nature. However, it must be borne in mind that none of the living archaea (as well as bacteria) have intracellular symbionts. Moreover, all prokaryotes known to us, apparently, cannot acquire them in principle, because are not capable of phagocytosis. Apparently, the only exception is the mysterious symbiotic bacterial complexes of insects of the family Pseudococcidae, consisting of spheres containing gammaproteobacteria. It is possible that these spheres are themselves betaproteobacteria, highly modified during long coevolution with their insect hosts (Dohlen et al., 2001).

Let us also note that the emergence of the eukaryotic cell was a major evolutionary leap. In terms of its scale, this event is comparable only to the emergence of life itself. The organism that played a central role in this great transformation must have had unique properties. Therefore, one should not expect that JCC was a “common prokaryotic organism.” There are no direct analogues of this organism in modern biota.

JCC had to be a large enough organism to capture endosymbionts, whereas archaea are mostly small prokaryotes.

Many archaea are characterized by very small genomes, which may be a consequence of narrow specialization in extreme habitats, where these organisms experience virtually no competitive pressure, and conditions, although extreme, do not change for billions of years. JCC, rather, had to live in a complex biotic environment, be a coenophile, and have a fairly large genome, including genes for “synecological” protein systems necessary for successful interaction with other components of the microbial community. These same proteins subsequently formed the basis of intracellular coordination systems responsible for the coordinated life activity of the host and symbionts. Judging by the above data, a significant (perhaps most) part of these genes was obtained by JCC from bacteria, and not from those that became endosymbionts, but from others.

Apparently, JCC must have had sufficient membrane elasticity to capture endosymbionts. This suggests the presence of membrane sterols and, therefore, molecular systems for their biosynthesis. Possible precursors of some enzymes of sterol metabolism are again found in bacteria that are not related to the ancestors of mitochondria and plastids.

The biosynthesis of sterols requires the presence of small concentrations of molecular oxygen. Apparently, JCC was a microaerophilic rather than strictly anaerobic organism even before the acquisition of mitochondria. Some domains of microaerophilic metabolism were obtained by NCC from bacteria that did not become endosymbionts.

In order to capture endosymbionts, in addition to elastic membranes, NCC had to have cytoplasmic mobility, that is, have at least the rudiments of an actin-tubulin cytoskeleton. The origin of actin remains unclear, but JCC could have borrowed close homologues of tubulin from bacteria unrelated to plastids and mitochondria.

The metabolism of the NCC and future mitochondria, especially the energy metabolism, had to be complementary, otherwise the symbiotic system could not have developed. Mitochondria receive from the cytoplasm primarily pyruvate, a product of glycolysis. Enzymes for the anaerobic breakdown of sugars (glycolysis and lactic acid fermentation), as can be seen from the above data, were obtained by NCC most likely from bacteria not related to future endosymbionts.

Thus, on the eve of the acquisition of mitochondria, JCC appears to us in the guise of a chimeric organism with a distinctly archaeal “core” and a bacterial “periphery.” This contradicts the idea that the ancestor of JCC was a prokaryotic organism that is not directly related to either archaea or bacteria - a “chronocyte” (Hartman, Fedorov, 2002). This also contradicts those models of the origin of eukaryotes, according to which all bacterial features of the nucleocytoplasm appeared as a result of the acquisition of endosymbionts (primarily mitochondria). The available facts are better consistent with the “chimeric” hypotheses, according to which, even before the acquisition of endosymbionts, the archaea merged with some bacterium, for example, a spirochete (Margulis et al., 2000; Dolan et al., 2002), a photosynthetic proteobacterium (Gupta, 1998) or fermenter (Emelyanov, 2003).

However, the set of nucleocytoplasmic domains, which are of bacterial but not endosymbiotic origin, does not allow us to unambiguously indicate any one group of bacteria as their common source. It seems more likely that proto-eukaryotes borrowed individual genes and gene complexes from many different bacteria. A similar assumption was made earlier on the basis of a comparative analysis of proteomes, which showed the presence even in the mitochondria themselves of many proteins of bacterial, but not alphaproteobacterial, origin (Kurland and Andersson, 2000).

Apparently, the archaea that became the basis of the NCC had an abnormally high ability to incorporate foreign genetic material. Incorporation could occur through lateral transfer (viral or plasmid), direct absorption of DNA from the external environment, as well as through the establishment of various types of contacts between the recipient archaeal cell and bacterial donor cells (from ordinary conjugation to complete cell fusion). Apparently, entire enzyme systems were incorporated (for example, a complex of glycolytic enzymes, a system for the synthesis of plasma membranes), which would be very difficult to achieve by acquiring individual genes one by one.

Normally, prokaryotes absorb foreign DNA during the process of conjugation, and the recipient cell must “recognize” the donor cell and become competent. This is how prokaryotes are protected from exchanging genetic material with unrelated forms. However, there are prokaryotes capable of the so-called. "natural transformation". They absorb isolated DNA from the external environment, and for this they do not need to come to a state of competence. These prokaryotes are characterized by extremely high polymorphism and adaptability (for example, to antibiotics). An example of such an organism is the hyper-polymorphic bacterium Helicobacter pylori. Perhaps the extraordinary level of polymorphism of this species is associated with its recent adaptation to life in the human body (Domaradsky, 2002).

In prokaryotes, the influx of foreign genes (transported by viruses and plasmids, as well as absorbed from the external environment) is controlled by a restriction-modification system. Eukaryotes do not have this system; instead, other mechanisms of genetic isolation associated with sexual reproduction function (Gusev and Mineeva, 1992). We assume that in the evolution of JCC there was a period (most likely short-term) when the old, prokaryotic barriers to the path of foreign genes weakened, and the new, eukaryotic ones were not yet functioning at full strength. During this period, JCC was a destabilized strain with sharply weakened mechanisms of genetic isolation. Moreover, it apparently gradually developed additional mechanisms that ensured more intense and controlled recombination. Several such mechanisms can be hypothesized:

1) The ability to perforate the cell membranes of other prokaryotes and suck out the contents from them (an echo of this may be eukaryotic domains of bacterial origin associated with the virulence of pathogenic bacteria and membrane perforation, for example, the already mentioned MAC/Perforin domain);

2) The development of new forms of exchange of genetic material between closely related cells (possibly including the formation of cytoplasmic bridges between cells or even their fusion - copulation). This could be related to the “replacement” of archaeal membranes with bacterial ones and the appearance of membrane sterols.

3) Phagocytosis could have evolved as a further improvement in predation based on a new membrane structure.

4) The transition from a single circular chromosome to several linear ones could be associated with the activation of recombination processes.

5) The development, based on a single (albeit almost as complex as in eukaryotes) archaeal RNA polymerase, of three types of eukaryotic RNA polymerases responsible for reading different groups of genes, could be due to the urgent need to maintain the integrity of an unstable, rapidly changing chimeric genome.

6) Similar needs could have determined the appearance of the nuclear membrane, which at first may have functioned as a filter that helped limit and streamline the flow of genes from the cytoplasm, where foreign cells captured by phagocytosis entered.

Of course, all this is just speculation. However, noteworthy is the fact that the most important distinctive features of eukaryotes (membrane structure, phagocytosis, linear chromosomes, differentiated RNA polymerases, nuclear envelope) can be explained from the standpoint of the proposed model, i.e. as arising in connection with the activation of recombination processes in NCC. Note also that the incorporation of a significant part of plastid and mitochondrial genes into the nuclear genome (a process that continues to this day, especially in plants) (Dyall et al., 2004) confirms the presence of corresponding mechanisms in eukaryotes.

Why did archaea become the central organizing component of the JCC? Apparently, the molecular information systems of archaea (replication, transcription, translation, organization and modification of NK) were initially more plastic and stable than those of bacteria, which allowed archaea to adapt to the most extreme habitats.

Absent in bacteria, but present in archaea and eukaryotes, processing systems, introns, as well as more complex RNA polymerases, apparently indicate a more complex, perfect and controlled transcription mechanism (more “smart”, “readable” reading of genetic information) . Such a mechanism, apparently, was easier to adapt to various “emergency situations,” which include, in addition to high temperature, salinity and acidity, also the weakening of barriers that prevent the inclusion of foreign genes in the genome.

Such a specific evolutionary strategy, which we assume for the JCC in the era before the acquisition of mitochondria, could arise and exist only in extremely unstable, crisis conditions, when the highest level of variability and active evolutionary “experimentation” were required for survival. Similar conditions apparently occurred in the temporary vicinity of the boundary of the Archean and Proterozoic eras. We wrote earlier about the possible connection of these crisis events with the emergence of eukaryotes (Markov, in press).

Since the oldest fossils of sterols were found in sediments 2.7 Ga old (Brocks et al., 1999), it can be assumed that many important milestones in the evolution of JCC were passed long before the end of the Archean era.

The origin of eukaryotes as a natural result of the evolution of prokaryotic communities.

It is obvious that all the main stages of the formation of a eukaryotic cell could only occur in a complex and highly integrated prokaryotic community, which included various types of auto- and heterotrophic microbes. The data obtained are consistent with the generally accepted view that an important driving force in the process of eukaryotic integration was an increase in the concentration of molecular oxygen associated with the transition of cyanobacteria from anoxic to oxygenic photosynthesis.

We propose that the “ancestral community” of eukaryotes consisted of at least three layers. The upper one was inhabited by cyanobacteria (among which were the ancestors of plastids), which used light waves up to 750 nm long for photosynthesis. These waves have little penetrating power, so the events must have unfolded in shallow water. Initially, the electron donor was not water, but reduced sulfur compounds, primarily hydrogen sulfide. Hydrogen sulfide oxidation products (sulfur and sulfates) were released into the external environment as a by-product.

The second layer was inhabited by purple photosynthetic bacteria, including alphaproteobacteria, the ancestors of mitochondria. Purple bacteria use light with a wavelength greater than 750 nm (mainly red and infrared). These waves have better penetrating power, so they easily passed through the layer of cyanobacteria. Purple bacteria even now usually live in water bodies under a more or less thick layer of aerobic photosynthetics (cyanobacteria, algae, higher plants) (Fedorov, 1964). Purple alphaproteobacteria usually use hydrogen sulfide as an electron donor, oxidizing it to sulfate (and this does not require molecular oxygen).

The third layer was inhabited by non-photosynthetic bacteria and archaea. Among them could be a variety of fermenting bacteria that process organic matter produced by photosynthetics; some of them released hydrogen as one of the final products of fermentation. This created the basis for the existence of sulfate-reducing bacteria and archaea (they reduce sulfates to sulfides with the help of molecular hydrogen and therefore represent a useful “addition” to the community of anoxic photosynthetics that consume sulfide), for methanogenic archaea (they reduce carbon dioxide to methane) and other anaerobic life forms . Among the archaea that lived here were the ancestors of the JCC.

A community similar to the one described above could exist in well-lit shallow water at an average temperature of 30-40 0 C. This temperature is optimal for the vast majority of prokaryotes, including the groups that were part of this community. The idea that the origin of eukaryotes was associated with extremely thermophilic habitats arose due to the fact that the first prokaryotic organism in which histones were discovered was the archaea Thermoplasma acidophila, an acidothermophile. This suggested that the appearance of histones (one of the important distinguishing characteristics of eukaryotes) was associated with adaptation to high temperatures. Histones have now been found in many archaea with very different ecologies. Currently, there is no reason to believe that the temperature in the “primary biotope” of eukaryotes was higher than 30-40 degrees. This temperature appears to be optimal for most eukaryotic organisms. This is indirectly confirmed by the fact that exactly this temperature was “chosen” for themselves by those eukaryotes that managed to achieve a level of organization sufficient for the transition to homeothermy. The biotope of the “ancestral community” may have been overheated from time to time, as evidenced by the preservation in eukaryotes of several bacterial hit-shock domains and archaeal proteins involved in post-transcriptional modifications of tRNA. Susceptibility to periodic overheating is consistent with the assumption that the “ancestral biotope” of eukaryotes was shallow.

A prokaryotic community of the type described above can remain quite stable until its resource base is undermined.

The beginning of the crisis transformations was the transition of cyanobacteria to oxygen photosynthesis. The essence of the transformation was that cyanobacteria began to use water instead of hydrogen sulfide as an electron donor (Fedorov, 1964). This may have been due to a decrease in the concentration of hydrogen sulfide in the ocean. The transition to the use of such an almost unlimited resource as water opened up great evolutionary and ecological opportunities for cyanobacteria, but also had negative consequences. Instead of sulfur and sulfates, molecular oxygen began to be released during photosynthesis - a substance that is extremely toxic and poorly compatible with ancient earthly life.

The first to encounter the toxic effects of oxygen were its direct producers - cyanobacteria. They were probably the first to develop means of protection against the new poison. The electron transport chains created for photosynthesis were modified and began to serve for aerobic respiration, the original purpose of which, apparently, was not to obtain energy, but only to neutralize molecular oxygen, and large amounts of organic matter were spent (oxidized) for this. Enzymatic nitrogen fixation systems, for which the action of oxygen is especially destructive, were “hidden” in specialized cells - heterocysts, protected by a thick membrane and not photosynthesizing.

Soon, the inhabitants of the second layer of the community - purple bacteria - had to develop similar defense systems. Just like cyanobacteria, they formed enzyme complexes for aerobic respiration based on photosynthetic electron transport chains. It was the purple alphaproteobacteria that developed the most advanced respiratory chain, which now functions in the mitochondria of all eukaryotes. Apparently, in this same group, a closed cycle of tricarboxylic acids was first formed - the most effective metabolic pathway for the complete oxidation of organic matter, allowing for the extraction of maximum energy (Gusev, Mineeva, 1992). In living purple bacteria, photosynthesis and respiration are two alternative energy metabolism options, usually operating in antiphase. Under oxygen-free conditions, these organisms photosynthesize, and in the presence of oxygen, the synthesis of substances necessary for photosynthesis (bacteriochlorophylls and Calvin cycle enzymes) is suppressed, and the cells switch to heterotrophic nutrition based on oxygen respiration. Apparently, the mechanisms of this “switching” were formed already in the era under consideration.

In the third layer of the community, the appearance of free oxygen should have caused a serious crisis. Methanogenic, sulfate-reducing and other forms that utilize molecular hydrogen with the help of hydrogenase enzymes cannot exist under aerobic conditions, since oxygen has an inhibitory effect on hydrogenases. Many bacteria that produce hydrogen, in turn, cannot grow in an environment where there are no microorganisms that utilize it (Zavarzin, 1993). Of the fermenters in the community, apparently, there remained forms that secrete low-organic compounds as final products, such as pyruvate, lactate or acetate. These fermenters have developed some special defenses against oxygen and have become facultative anaerobes or microaerophiles. Among the survivors were the archaea, the ancestors of the JCC. Perhaps at first they “hid” in the lowest horizons of the community, below the layer of wanderers. Whatever their original metabolism may have been, under the new conditions it no longer ensured the maintenance of life. Therefore, it was soon completely replaced, and no traces of it remain in modern eukaryotes. It is possible that these were originally methanogenic forms, because among modern archaea they are the most coenophilic (primarily due to their dependence on the molecular hydrogen produced by fermenters), and the ancestor of the YCC must undoubtedly have been an obligate coenophile. Methanogenesis is the most common type of energy metabolism in modern archaea and is not found in the other two superkingdoms.

Perhaps it was precisely at this moment of crisis that a key event occurred - the weakening of genetic isolation in the ancestors of the JCC and the beginning of rapid evolutionary experimentation. The ancestors of JCC (possibly switching to active predation) incorporated gene complexes of various fermenters until they replaced a significant part of the archaeal “periphery” and became microaerophilic fermenters themselves, fermenting carbohydrates along the Embden-Meyerhof-Parnas glycolytic pathway to pyruvate and lactic acid. acids. Note that modern aerobic archaea apparently originated from methanogens, and acquired the enzyme systems necessary for oxygen respiration relatively late, and lateral gene transfer from aerobic bacteria played an important role in this (Brochier et al., 2004).

During this period, the JCC apparently changed membranes (from “archaeal”, containing esters of terpenoid acids, to “bacterial”, based on esters of fatty acids), membrane sterols and the rudiments of the actin-tubulin cytoskeleton appeared. This created the necessary preconditions for the development of phagocytosis and the acquisition of endosymbionts.

In the fossil record, the beginning of the events described, associated with the emergence of oxygenic photosynthesis and the release of several groups of bacteria from the active sulfur cycle, can probably be marked by more or less sharp fluctuations in the content of sulfides and sulfates in biogenic sediments, especially in stromatolites. Such markers should be looked for in layers older than 2.7 billion years, since disturbances in the sulfur cycle should have preceded the appearance of sterols.

Thus, the appearance of molecular oxygen changed the structure of the “ancestral community.” The inhabitants of the third layer of the community - microaerophilic, capable of phagocytosis, secreting lactate and pyruvate of NCC - were now in direct contact with the new inhabitants of the second layer - aerobic alphaproteobacteria, which not only developed effective means of protecting against oxygen, but also learned to use it to obtain energy using respiratory electron transport chain and tricarboxylic acid cycle. Thus, the metabolism of JCC and aerobic alphaproteobacteria became complementary, which created the preconditions for symbiosis. In addition, the very topographic location of alphaproteobacteria in the community (between the upper, oxygen-producing, and lower microaerophilic layer) predetermined their role as “protectors” of the NCC from excess oxygen.

It is likely that NCCs were ingested and acquired as endosymbionts by many different bacteria. Active experimentation of this kind continues today in unicellular eukaryotes, which have a huge variety of intracellular symbionts (Duval and Margulis, 1995; Bernhard et al., 2000). Of all these experiments, the alliance with aerobic alphaproteobacteria turned out to be the most successful and opened up enormous evolutionary prospects for new symbiotic organisms.

Apparently, in the first time after the acquisition of mitochondria, there was a massive transfer of endosymbiont genes into the central genome of the JCC (Dyall et al., 2004). This process was obviously based on the mechanisms of incorporation of foreign genetic material that had developed in the JCC during the previous period. Extremely interesting are recent data indicating that the transfer of mitochondrial genes to the nuclear genome could occur in large blocks (Martin, 2003), i.e. exactly as, according to our assumptions, the incorporation of foreign genes by the nuclear-cytoplasmic component occurred even before the acquisition of mitochondria. Another possible mechanism of gene incorporation into the central genome of JCC involved reverse transcription (Nugent and Palmer, 1991).

All the supposed transformations of the JCC, up to the acquisition of endosymbionts-alphaproteobacteria, could hardly occur slowly, gradually and over vast territories. Rather, they happened quite quickly and locally, because organisms (YCC) were at this time in an extremely unstable state - the stage of destabilization (Rautian, 1988). Perhaps the return to an evolutionarily stable state and the restoration of isolation barriers occurred soon after the acquisition of mitochondria, and only in the JCC line in which this most successful symbiosis arose. All other lineages most likely quickly died out.

The acquisition of mitochondria made eukaryotes completely aerobic organisms, which now possessed all the necessary prerequisites for the final act of integration - the acquisition of plastids.

Conclusion

Comparative analysis of protein domains in three superkingdoms (Archaea, Bacteria, Eukaryota) confirms the symbiogenetic theory of the origin of eukaryotes. From archaea, eukaryotes inherited many key components of nucleocytoplasmic information systems. Bacterial endosymbionts (mitochondria and plastids) made a great contribution to the formation of metabolic and signal-regulatory systems not only in organelles, but also in the cytoplasm. However, even before the acquisition of endosymbionts, archaea - the ancestors of nucleocytoplasm - received many protein complexes with metabolic and signal-regulatory functions through lateral transfer from various bacteria. Apparently, in the evolution of the ancestors of nucleocytoplasm there was a period of destabilization, during which the insulation barriers were sharply weakened. During this period, intensive incorporation of foreign genetic material occurred. The “trigger” for the chain of events that led to the emergence of eukaryotes was the crisis of prokaryotic communities caused by the transition of cyanobacteria to oxygen photosynthesis.

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Hereinafter, “domains of archaeal origin” will conventionally be called domains that are present in eukaryotes and archaea, but absent in bacteria. Accordingly, domains that are present in bacteria and eukaryotes, but absent in archaea, will be called “domains of bacterial origin.”