The appearance of the first eukaryotic cells occurred in the era. Evolution of cellular structures. The emergence of eukaryotes. The emergence of aerobes. major events of the Archean era

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) was analyzed in three superkingdoms: Archaea, Bacteria, and Eykaryota. Apparently, of the total number of eukaryotic protein domains, almost half was inherited from prokaryotic ancestors. From archaea, eukaryotes inherited the most important domains associated with the informational processes of the nucleocytoplasm (replication, transcription, translation). Bacteria inherited a significant portion of the domains associated with basic metabolism and signal-regulatory systems. Apparently, many signal-regulatory domains common to bacteria and eukaryotes performed synecological functions in the former (ensuring the interaction of the cell with other components of the prokaryotic community), while in the latter they began to be used to ensure the coordinated work of cell 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 for 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 Archaea, in which, under conditions of a crisis caused by an increase in the concentration of free oxygen in the prokaryotic community, the process of incorporation of alien genetic material from the external environment was sharply activated.

The symbiogenetic theory of the origin of eukaryotes is now practically universally recognized. The entire set of molecular genetic, cytological and other data indicates that the eukaryotic cell was formed by merging several prokaryotes into a single organism. The appearance of a eukaryotic cell should have been preceded by a more or less long period of co-evolution of its future components in one microbial community, during which a complex system of relationships and connections developed between species, necessary for coordinating various aspects of their life activity. The molecular mechanisms developed during the formation of these synecological bonds could play an important role in the subsequent process of association of several prokaryotes into a single cell. The appearance of eukaryotes (“eukaryotic integration”) should be considered as the end result of a long 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 proceed, 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, the archaea (Archaea) played the 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 eukaryotic nucleocytoplasm 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", how and why they acquired the 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 the result of the acquisition of bacterial endosymbionts (mitochondria and plastids), many of whose genes have moved into the nucleus, and proteins have begun to perform various functions in the nucleus and cytoplasm (Gabaldon and Huynen, 2003). The acquisition of mitochondria is often regarded as a key moment in the formation of eukaryotes, preceding the formation of the nucleus or occurring simultaneously with it. This opinion is supported by molecular data indicating the monophyletic origin of the mitochondria of all eukaryotes (Dyall and Johnson, 2000; Litoshenko, 2002). At the same time, currently living non-mitochondrial eukaryotes are interpreted as descendants of forms that had mitochondria, since their nuclear genomes contain genes of presumably mitochondrial origin (Vellai et al., 1998; Vellai and Vida, 1999; Gray et al., 1999).

An alternative point of view is that NCC was a chimeric organism of archaeal-bacterial nature even before the acquisition of mitochondria. According to one hypothesis, NCC was formed as a result of a unique evolutionary event - the fusion of an archaea with a proteobacterium (possibly a photosynthetic, close to Chlorobium). The resulting symbiotic complex received resistance to natural antibiotics from archaea, and aerotolerance from 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 which the host cell, which received the mitochondrial endosymbiont, was a prokaryotic nuclear-free organism formed by the fusion of an archaebacterium with a fermenting eubacterium, and the basic energy metabolism of this organism was eubacterial in 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 the archaea with the spirochete, and this event occurred before the acquisition of mitochondrial symbionts. Mitochondrial protozoa do not necessarily originate from ancestors that had mitochondria, and bacterial genes in their genome could have appeared as a result of symbiosis with other bacteria (Margulis et al., 2000; Dolan et al., 2002). There are other variations of the "chimeric" theory (Lupez-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 NCC belonged to "chronocytes" - a hypothetical extinct group of prokaryotes, equally distant from both bacteria and archaea ( Hartman and Fedorov, 2002).

Mitochondrial component

There is much more clarity on the nature of the mitochondrial component of the eukaryotic cell. Its ancestor, according to most authors, were 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, originally formed in these bacteria as part of the photosynthetic apparatus, subsequently began to be used for oxygen respiration.

On the basis of comparative proteomics, a reconstruction of the metabolism of "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 needed the supply of many important metabolites (lipids, amino acids, glycerols) from 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 (Gabaldun and Huynen, 2003). The main stimulus for the association of NCC with protomitochondria, according to most hypotheses, was the need for anaerobic NCC to protect itself from the toxic effects of molecular oxygen. The acquisition of symbionts utilizing this poisonous gas made it possible to successfully solve this problem (Kurland and 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). In this case, the host cell should be a methanogenic chemoautotrophic anaerobic archaea that needs hydrogen to synthesize methane from carbon dioxide. The hypothesis is based on the existence in some unicellular eukaryotes of the 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 a multiple, polyphyletic origin of eukaryotes. However, molecular evidence suggests they are monophyly (Gupta, 1998). The "hydrogen" hypothesis is also contradicted by the fact that the 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 the latest modification of ordinary mitochondria that perform 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 symbiosis of a cyanobacterium with a eukaryotic cell that already had mitochondria (Martin and Russel, 2003). It happened presumably from 1.5 to 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). Curiously, some enzymes of the Calvin cycle (the key metabolic pathway of photosynthesis) functioning in plastids are of proteobacterial rather than cyanobacterial origin (Martin and Schnarrenberger, 1997). The genes for these enzymes appear to be derived 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 great opportunities for the reconstruction of the processes of "eukaryotic integration".

At present, numerous and largely systematized data on the protein and nucleotide sequences of many organisms, including representatives of all three superkingdoms: Archaea, Bacteria, and Eukaryota, have been collected and are in the public domain (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 protein sequences and their encoding genes. Sequence comparisons are carried out both in representatives of the same species and between different taxa.

Using these data and analytical tools, it seems possible to collect and systematize a fairly massive material that will make it possible 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. In the course of such an analysis, it is also possible to obtain new data regarding specific groups of bacteria and archaea, which most likely could participate in the formation of the primary eukaryotic cell.

The ratio of common and unique protein domains in archaea, bacteria and eukaryotes

This paper presents the results of the analysis of functional spectra and taxonomic confinement of protein domains included in the 15th version of the Pfam system (the version was published on the Internet on August 20, 2004). This system, which is the most complete systematized catalog of its kind, currently includes 7503 protein domains.

The concept of "protein domain" is closely related to the currently actively developed natural classification of proteins. A domain is a more or less conservative 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 the functional blocks of protein molecules (for example, DNA-binding domains or catalytic domains of enzymes). The function of some domains is still unknown, but the conservatism and distribution pattern of these sequences suggests that they also have a 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 implemented by many different combinations of amino acids, therefore, in the case of the parallel appearance of functionally similar blocks in protein molecules in different organisms, the fact independent origin is usually fairly obvious.

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

Based on data from the Pfam system, the quantitative distribution of domains over three kingdoms of wildlife (Archaea, Bacteria, Eukaryota) was determined:

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 eukaryotic domains not found in the other two superkingdoms (2372);

2) Domains present in representatives of all three kingdoms (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 subsequent discussion is given to the domains of the third and fourth groups, since their taxonomic confinement makes it possible to speak with a certain degree of probability about their origin. Apparently, a significant part of the domains of the third group was inherited by eukaryotes from bacteria, the fourth - from archaea.

In some cases, the commonality of domains in different superkingdoms may be associated with a later horizontal transfer, but then in the “recipient” superkingdom, most likely, this domain will be found only in one or a few representatives. Such cases do exist. Compared to the previous, version 14 Pfam, in the new version 15, a number of purely bacterial domains have moved to the third group, for the reason that the corresponding sequences were found in the recently “decoded” genomes of individual eukaryotes (especially the mosquito Anopheles gambiae and the simplest Plasmodium yoelii). The presence in the genome of the malarial mosquito of genes encoding bacterial flagella proteins (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 (there are about 40 of them in the third group, and they are absent in the fourth group).

The quantitative ratio of common and unique domains in the three superkingdoms, it would seem, indicates a decisive predominance of the "bacterial" component in the eukaryotic cell compared to the "archaeal" one (eukaryotes have 831 "bacterial" domains and 114 "archaeal" domains). Similar results were obtained recently during comparative analysis genomes of yeast and various prokaryotes: it turned out that 75% of the total number of nuclear yeast genes with prokaryotic homologues are more similar to bacterial than to archaeal sequences (Esser et al., 2004). This conclusion, however, becomes less obvious if the mentioned figures are compared with the total number of common and unique domains in the two prokaryotic superkingdoms. 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 choosing one or another protein block from the available set, then it should be recognized that it preferred 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 by functional groups) and the physiological significance of the 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 the domains of this group is the high occurrence of such words and phrases as "essential" (key, vital) and "plays a key role" (plays key role). In annotations of domains from other groups, such indications are an order of magnitude less common.

This group is dominated by domains associated with the most basic, central processes of cell life, namely, with the processes of storage, reproduction, structural organization and reading of genetic information. This includes key domains responsible for the mechanism of replication (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 proteins associated with transcription showed that archaea show more similarity to eukaryotes than bacteria (Coulson et al., 2001, fig.1b).

Of interest are 6 domains associated with the synthesis (posttranscriptional modifications) of tRNA. Chemical changes, introduced by special enzymes into 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 thermophilic archaeal tRNAs increases with increasing temperature (Noon et al., 2003). The retention 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, while in eukaryotes it is a histone-like transcription factor.

Of particular note are 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), which in eukaryotes is 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), which 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. There are no proteins with such functions among the “domains of bacterial origin”. Domains that control membrane fusion and vesicle formation could play an important role in the symbiogenetic development of a eukaryotic cell, since they create the basis for the development of phagocytosis (the most likely way of acquiring intracellular symbionts - plastids and mitochondria), as well as for cell fusion (copulation) and the formation of various intracellular membrane structures eukaryotic, such as the endoplasmic reticulum (ER). Eukaryotic ER, according to one of the hypotheses, is of archabacterial 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). Recall that the ER of eukaryotes is closely related to the nuclear envelope, which allows us to assume a common genesis of these structures.

Attention should also be paid to the almost complete absence of metabolic domains in this group (which is in sharp contrast to the group of eukaryotic "domains of bacterial origin", where, on the contrary, metabolic proteins predominate sharply).

From the point of view of the problem of the emergence of eukaryotes, such domains of archaeal origin as the ZPR1 zinc-finger domain (PF03367) are of interest (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 functional spectra of eukaryotic domains present or absent in archaea (A), cyanobacteria (C), alphaproteobacteria (P), and bacteria in general, including C and P (B).

Functional group	A has it, B doesn't	B has it, A doesn't	C or P has it, A doesn't	B has it, A, C and P don't
protein synthesis
Including: ribosomal and biogenesis-related ribosomes
Broadcast
Synthesis, modification of tRNA
Post-translational modifications of proteins
Replication, transcription, modification and organization of NK
Including: basic replication and transcription
Histones and other proteins that organize DNA in chromosomes
NA modification (nucleases, topoisomerases, helicases, etc.)
reparation, recombination
NK-binding domains of unclear function or general purpose
Proteins associated with the formation and function of membrane vesicles
Transport and sorting proteins
Signaling and regulatory proteins
Including: transcription factors (regulation of gene expression)
Receptors
Intercellular interaction domains
Interprotein interaction domains
Protein-to-membrane binding domains
Protective and related to the immune system
Associated with the virulence of pathogenic bacteria and protozoa
Regulation of ontogeny
Hormone related domains
Replication regulation
Lectins (proteins that form complexes with carbohydrates)
Other signaling and regulatory proteins
Proteins associated with the cytoskeleton, microtubules
Proteins associated with cell division
Metabolism
Including: oxygen oxidation (oxygenases, peroxidases, etc.)
Metabolism of steroids, terpenes
Metabolism of nucleotides and nitrogenous bases
Carbohydrate metabolism
lipid metabolism
Amino acid metabolism
Protein metabolism (peptidases, proteases, etc.)
Photosynthesis, respiration, electron transport chain
Other basic energy (ATP synthase, NAD-H dehydrogenase, etc.)
Other metabolic domains

Rice. 2. Functional spectra of "archaeal" and "bacterial" eukaryotic domains. 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 proportion is much 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 mechanism of transcription), 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 mitochondrial DNA replication.

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 there is no data on localization in eukaryotic cells for one more domain. Thus, bacteria participating in eukaryotic integration apparently did not contribute practically anything to the structure of eukaryotic cytoplasmic ribosomes.

Among the domains of bacterial origin, the share of signal-regulatory proteins is much higher. However, if among the few regulatory domains of archaeal origin, basic transcription regulators of general purpose predominate (in fact, they do not so much regulate as organize the process), then signal-regulatory domains dominate in the bacterial group, 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 conditionally subdivided into "autecological" and "synecological", and both of them 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 overheating), such as HSP90 - PF00183. This also includes all kinds of receptor proteins (Receptor L domain - PF01030, Low-density lipoprotein receptor repeat class B - PF00058, etc.), 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 more. others

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 work of parts of the eukaryotic cell (primarily signaling and regulatory cascades) began to develop long before these parts actually existed. united under one cell membrane. Initially, they were formed as mechanisms that ensure the integrity of the microbial community (Markov, in press).

Of interest are domains of bacterial origin involved in the regulation of ontogeny or cell-tissue differentiation in eukaryotes (for example, Sterile alpha motif - PF00536; TIR domain - PF01582; ​​jmjC domain - PF02373, etc.). The very “idea” of the ontogenesis of multicellular eukaryotes is based primarily 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.

The analysis of the origin of such a domain as significant for eukaryotes as Ras is also indicative. Proteins of the Ras superfamily are the most important participants in signaling cascades in eukaryotic cells, transmitting a signal 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 second messengers , which controls 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 in the domains of the Elongation factor Tu GTP binding (GTP_EFTU) 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 signaling.

Formally, the Ras domain is one of the common domains for 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, isolated cases of its detection are observed. In the bacterial genome, the Ras domain has been identified in proteobacteria and cyanobacteria as part of low molecular weight peptides. At the same time, the structure of two peptides is similar to the structure of eukaryotic Ras proteins, and one of the Anabaena sp. additionally carries the LRR1 (Leucine Rich Repeat) domain involved in protein-to-protein interactions. In the archaeal genome, the Ras domain was found in the euarchaeots 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 aforementioned cyanobacterial Ras protein. In Methanopyrus kandleri AV19, the Ras domain is located next to the COG0218 domain, which indicates other functions of this protein compared to Ras proteins. These facts suggest 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 "archaeal" domains 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 (oxygenase, peroxidase, etc.) There are many such domains in the "bacterial" group (19), while 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.

Attention should be paid to 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). 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 bacterial (not archaeal) nature of the main component of the energy metabolism of the cytoplasm of eukaryotic cells - glycolysis. This conclusion is supported both 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 end product of glycolysis (pyruvate) with the formation of 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 with archaeal and bacterial proteins using BLAST. It turned out that this protein is almost identical to 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 from the genus Bacillus related to Clostridium (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 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 especially mitochondria (purple bacteria) were ecologically closely linked to the sulfur cycle. In this regard, of particular interest is the sulfide/quinone oxidoreductase enzyme found in mitochondria, which may be inherited by eukaryotes directly from photosynthetic alphaproteobacteria that 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 present in both bacteria and archaea; therefore, the corresponding family of Pfam proteins is in the 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 sulfide-quinone 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 for 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 then isomerizes and turns into lanosterol, from which cholesterol, all other sterols, steroid hormones, etc. are subsequently synthesized. bacteria or archaea. This enzyme contains, according to Pfam, the only 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 sarchaeal and bacterial proteins shows that this protein exhibits much more similarity with bacterial than with archaeal analogues (for the former, the minimum value of E=5*10 -9 , for the latter, E min =0.28). Of bacteria, the most similar proteins are possessed by the actinobacterium Streptomyces argillaceus, the bacillus Bacillus halodurans, and the gammaproteobacterium Pseudomonas aeruginosa. Only after them comes the cyanobacterium Nostoc sp. (E=3*10 -4). Thus, the key enzyme of sterol biosynthesis appears to have originated in early eukaryotes on the basis of 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 precursor of sterols, squalene. This enzyme belongs to the Pfam SQS_PSY - PF00494 family, present in all three superkingdoms. Human squalene synthase (http://www.genome.jp/dbget-bin/www_bget?hsa+2222) is very similar to the homologous proteins of bacteria, especially cyanobacteria and proteobacteria (E min =2*10 -16), but it is also similar to squalene synthase from the archaea Halobacterium sp. (E=2*10 -15).

The results obtained do not, in principle, 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, NCC had to have a sufficiently elastic and mobile membrane to acquire a mitochondrial symbiont, and this is hardly possible without the synthesis of sterols, which just give eukaryotic membranes the properties necessary for phagocytosis, pseudopodia formation, 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 structures of the cytoskeleton. 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 evidence for this hypothesis would be the discovery of homology in the amino acid sequences of the contractile protein of spirochetes and proteins of the eukaryotic cytoskeleton. The same idea is developed in detail in a recent work by M.F. Dolan et al. (Dolan et al., 2002).

In eukaryotic cytoskeletal proteins, it has not yet been possible to detect features specific specifically for spirochetes. 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 the FtsZ proteins, which are widely distributed in bacteria and archaea. FtsZ proteins are able to polymerize into tubules, plates and rings and play an important role in cell division 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, which contains both of the above domains (http://us.expasy.org/cgi-bin/sprot-search-ac?Q72N68), shows a high similarity with plastid and mitochondrial eukaryotic proteins involved in the division of these organelles. but not with eukaryotic tubulin. Therefore, some researchers suggest that there must have been another prokaryotic tubulin precursor closer to eukaryotic homologues than FtsZ proteins. Recently, such proteins, indeed very similar to eukaryotic tubulins (Emin=10 -75), have been found in several bacterial species 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 by horizontal transfer from Prosthecobacter or another bacterium that had similar proteins (the possibility of fusion of an archaebacterium cell with a bacterium that had the tubulin gene is not excluded).

GTPases involved in the regulation of microtubule assembly also indicate the bacterial "roots" of the eukaryotic cytoskeleton. Thus, the Dynamin_N domain has a strictly bacterial origin (it is found in many groups of bacteria and is unknown in archaea).

Some proteins important for the formation of the cytoskeleton, eukaryotes could inherit from archaea. For example, prefoldin (PF02996) is involved in actin biogenesis; homologous proteins are found in many archaea, while only single small fragments of similar sequences have been found in bacteria. As for actin itself, no obvious homologues of this most important eukaryotic protein have yet been found in prokaryotes. Both bacteria and archaea have MreB/Mbl proteins 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 form of the cell (they are not found in coccoid forms), forming something like a "prokaryotic cytoskeleton". However, MreB/Mbl proteins bear little resemblance to actin in their primary structure. For example, MreB proteins of the spirochete Treponema pallidum ( http://us.expasy.org/cgi-bin/sprot-search-ac?O83510), Clostridium tetani ( http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi) and 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 between the primary structure of MreB proteins and actin is rather weak, but in archaeal proteins it is somewhat higher than in bacterial ones.

Origin of bacterial components of eukaryotic nucleocytoplasm.

This review confirms that NCC is a chimeric formation that combines features 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 development of the NCC, however, a significant part of its "peripheral" systems was lost and replaced by systems of bacterial origin. How could this happen?

The simplest explanation offered by many authors is the assumption that the bacterial elements of the NCC originate from endosymbionts - mitochondria and plastids, many of whose genes have indeed moved into the nucleus, and the proteins they encode have assumed many purely cytoplasmic functions. This explanation is convincingly supported by extensive factual material (Vellai and Vida, 1999; Gray et al., 1999; Gabaldon and Huynen, 2003). The only question is whether it is sufficient.

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

The table (two right columns) reflects the functional spectra of two groups of "bacterial" eukaryotic domains:

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

When comparing the functional spectra, it should be taken 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 that also have these domains. Thus, it can be expected that the real number of "bacterial" domains obtained by eukaryotes not from endosymbionts is significantly higher than the numbers in the right column of the table show. 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 those in the fourth.

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

The main distinguishing feature of the functional spectrum of domains of the second group is a sharply increased proportion of signal-regulatory proteins. This 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 provide 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 distinct unevenness in the quantitative distribution of the domains of the first and second groups in different parts of the metabolism. Thus, almost all domains associated with photosynthesis, aerobic respiration, and electron transport chains are apparently of mitochondrial or plastid origin. This is quite an 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 "communal economy" of the emerging eukaryotic cell.

Proteins associated with carbohydrate metabolism have the largest share among the metabolic domains of the second group. We have already mentioned above the similarity of eukaryotic lactate dehydrogenase with homologous proteins of fermenting bacteria such as Clostridium (i.e., taxonomically very distant from cyanobacteria 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, as well as lactate dehydrogenase, shows the greatest similarity with the proteins of representatives of the genus Clostridium (E = 10 -136), next in 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 \u003d 10 -113. Archaeal glyceraldehyde-3-phosphate dehydrogenases are much less similar, although the corresponding Pfam domains ( PF00044 and PF02800), of course, is found in all three kingdoms.

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 confirmed by the results of a recent detailed phylogenetic analysis of glycolytic enzyme sequences in a number of representatives of eukaryotes and bacteria (Canback et al., 2002).

Half of the eight "bacterial" domains of steroid metabolism and related compounds are missing from the ancestors of plastids and mitochondria, including the domain of the 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, while in bacteria they perform other catalytic functions, in particular, those associated with the metabolism of nucleotide sugars. The remaining three domains are found only in two or three bacterial species each (moreover, different domains are found in different species). What function these proteins perform in bacteria is unknown. But in general, these data suggest that the enzyme systems of steroid metabolism could have developed in early eukaryotes on the basis of bacterial precursor proteins that previously performed somewhat different functions, and the origin of these precursors cannot be associated exclusively with endosymbionts - plastids and mitochondria. Recall that the key enzyme of sterol synthesis in eukaryotes (squalene monooxygenase) also shows the greatest similarity to the proteins of actinobacteria, bacilli, and gammaproteobacteria, and not cyanobacteria or alphaproteobacteria.

Nature and genesis of the nuclear-cytoplasmic component of eukaryotes.

Let us try, on the basis of the given data, 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 (systems of replication, transcription and translation, including ribosomes) had a pronounced archaeal nature. However, it must be borne in mind that none of the living archaea (as well as bacteria) has intracellular symbionts. Moreover, all prokaryotes known to us, apparently, cannot acquire them in principle, because incapable of phagocytosis. Apparently, the only exception is the mysterious symbiotic bacterial complexes of insects of the Pseudococcidae family, consisting of spheres containing gammaproteobacteria. It is possible that these spheres themselves are betaproteobacteria, strongly modified during a long coevolution with insect hosts (Dohlen et al., 2001).

Note also that the emergence of the eukaryotic cell was a major evolutionary leap. In terms of 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, it should not be expected that NCC was a "normal prokaryotic organism". There are no direct analogues of this organism in modern biota.

The JCC would have to be a large enough organism to take over endosymbionts, whereas archaea are mostly small prokaryotes.

Many archaea are characterized by very small genomes, which may be the result of a narrow specialization in extreme habitats, where these organisms practically do not experience competitive pressure, and conditions, although extreme, do not change for billions of years. Rather, NCC should have lived 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 vital activity of the host and symbionts. Judging by the above data, a significant (possibly large) part of these genes was obtained by NCC from bacteria, and not from those that became endosymbionts, but from others.

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

The biosynthesis of sterols requires the presence of low 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, to have at least the rudiments of an actin-tubulin cytoskeleton. The origin of actin remains unclear, but JCC could borrow close tubulin homologues from bacteria not related to plastids and mitochondria.

Metabolism of NCC and future mitochondria, especially energy, had to be complementary, otherwise the symbiotic system could not have developed. Mitochondria are obtained from the cytoplasm primarily pyruvate - a product of glycolysis. Enzymes of anaerobic digestion 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, NCC appears before us in the form of a chimeric organism with a distinctly archaeal "core" and a bacterial "periphery". This contradicts the idea that the ancestor of the NCC was a prokaryotic organism that is not directly related to either archaea or bacteria - a “chronocyte” (Hartman and 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 better correspond to the “chimeric” hypotheses, according to which, even before the acquisition of endosymbionts, the archaea merged with some kind of bacterium, for example, a spirochete (Margulis et al., 2000; Dolan et al., 2002), a photosynthetic proteobacterium (Gupta, 1998) or a fermenter (Emelyanov, 2003).

However, the set of nucleocytoplasmic domains that are of bacterial, but not endosymbiotic, origin does not allow us to unambiguously point to any one group of bacteria as their common source. More likely is the borrowing of individual genes and gene complexes by proto-eukaryotes 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, which became the basis of the NCC, had an abnormally high ability to incorporate foreign genetic material. Incorporation could occur by lateral transfer (viral or plasmid), direct absorption of DNA from the external environment, as well as by establishing various kinds 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 accomplish by acquiring individual genes one by one.

Normally, prokaryotes absorb foreign DNA in the process of conjugation, and the recipient cell must “recognize” the donor cell and come to a state of competence. So prokaryotes are protected from the exchange of 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 into 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 hyperpolymorphic bacterium Helicobacter pylori. Possibly, 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 (carried 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 there was a period (most likely short-term) in the evolution of NCC when the old, prokaryotic barriers to foreign genes were weakened, and new, eukaryotic, did not yet function in full force. During this period, NCC was a destabilized strain with sharply weakened mechanisms of genetic isolation. Moreover, it seems to have gradually developed additional mechanisms that ensured more intense and controlled recombination. Several such mechanisms can be proposed:

1) The ability to perforate the cell membranes of other prokaryotes and suck out their contents (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 associated with the “replacement” of archaeal membranes by bacterial ones and the appearance of membrane sterols.

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

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

5) Based on a single (albeit almost as complex as in eukaryotes) archaeal RNA polymerase, the development 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) The emergence of the nuclear envelope, which at first may have functioned as a filter to help limit and streamline the flow of genes from the cytoplasm, where foreign cells captured by phagocytosis fell, could also be caused by similar needs.

Of course, this is all just speculation. However, the very 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., deserves attention. 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 the corresponding mechanisms in eukaryotes.

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

Processing systems, introns, and more complex RNA polymerases, which are absent in bacteria, but are present in archaea and eukaryotes, apparently indicate a more complex, perfect, and controlled transcription mechanism (smarter, more legible 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 NCC 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 took place in the temporary vicinity of the turn 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 aged 2.7 billion years (Brocks et al., 1999), it can be assumed that many important milestones in the evolution of NCC were passed long before the end archean era.

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

Obviously, all the main stages in 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 opinion that an important driving force in the process of eukaryotic intergation was the increase in the concentration of molecular oxygen associated with the transition of cyanobacteria from oxygen-free to oxygen photosynthesis.

We assume that the "ancestral community" of eukaryotes consisted of at least three layers. Cyanobacteria (among which were the ancestors of plastids) lived in the upper one, using light waves up to 750 nm long for photosynthesis. These waves have little penetrating power, so the events had to unfold 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 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 wavelengths greater than 750nm (mostly red and infrared). These waves have better penetrating power, so they can easily pass through the layer of cyanobacteria. Purple bacteria still 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 the organic matter produced by photosynthetics; some of them released hydrogen as one of the end 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 sulfide-consuming photosynthetics), for methanogenic archaea (reduce carbon dioxide to methane) and other anaerobic life forms. . Among the archaea that lived here were also the ancestors of the YaCC.

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

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

Crisis transformations began with 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). Perhaps this was 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 it also had negative consequences. Instead of sulfur and sulfates during photosynthesis, molecular oxygen began to be released - an extremely toxic substance and poorly compatible with the most ancient terrestrial life.

The first to face the toxic effect 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 initial purpose of which, apparently, was not to obtain energy, but only to neutralize molecular oxygen, and they spent (oxidized) large quantities organics. Enzymatic systems of nitrogen fixation, for which the action of oxygen is especially detrimental, 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 of aerobic respiration based on photosynthetic electron transport chains. It was purple alphaproteobacteria that developed the most perfect respiratory chain, which now functions in the mitochondria of all eukaryotes. Apparently, in the same group, a closed cycle formed for the first time. tricarboxylic acids- the most efficient metabolic pathway for the complete oxidation of organics, allowing you to extract the maximum energy (Gusev, Mineeva, 1992). In living purple bacteria, photosynthesis and respiration are two alternative energy metabolisms that usually operate 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 cells switch to heterotrophic nutrition based on oxygen respiration. Apparently, the mechanisms of this "switching" were already formed in the epoch under consideration.

In the third layer of the community, the appearance of free oxygen must 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 hydrogen-producing bacteria, in turn, cannot grow in an environment where there are no hydrogen-utilizing microorganisms (Zavarzin, 1993). Of the fermenters, the community seems to have retained forms that emit low-organic compounds such as pyruvate, lactate, or acetate as end products. These fermenters developed some special means of protecting themselves from oxygen and became facultative anaerobes or microaerophiles. Archaea, the ancestors of the YaCC, were also among the survivors. Perhaps at first they "hid" in the lowest horizons of the community, below the layer of wanderers. Whatever their metabolism was originally, in the new conditions it no longer provided life support. Therefore, it was soon completely replaced, and no traces of it remain in modern eukaryotes. It cannot be ruled out that these were originally methanogenic forms, because they are the most coenophilic among modern archaea (primarily due to their dependence on molecular hydrogen produced by fermenters), and the ancestor of NCC, undoubtedly, must 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 at this moment of crisis that the key event occurred - the weakening of genetic isolation in the ancestors of the NCC and the beginning of rapid evolutionary experimentation. Ancestors of NCC (possibly switched to active predation) incorporated the 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 acids. Note that modern aerobic archaea apparently originated from methanogens, and acquired the enzyme systems necessary for oxygen respiration relatively late, with lateral gene transfer from aerobic bacteria playing an important role in this (Brochier et al., 2004).

During this period, membranes apparently changed in NCC (from "archaeal", containing esters of terpenoid acids, to "bacterial", based on esters of fatty acids), membrane sterols and rudiments of the actin-tubulin cytoskeleton appeared. This created the necessary prerequisites 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 oxygen 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 sought in layers older than 2.7 Ga, since disturbances in the sulfur cycle must 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, releasing lactate and pyruvate of the NCC - now directly contacted the new inhabitants of the second layer - aerobic alphaproteobacteria, which not only developed effective means of protecting against oxygen, but also learned how to use it to obtain energy through respiratory electron transport chain and tricarboxylic acid cycle. Thus, the metabolism of NCC and aerobic alphaproteobacteria became complementary, which created prerequisites for symbiosis. In addition, the very topographic location of alphaproteobacteria in the community (between the upper oxygen-releasing layer and the lower microaerophilic layer) predetermined their role as “defenders” of NCC from excess oxygen.

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

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

All proposed transformations of NCC, up to the acquisition of alphaproteobacteria endosymbionts, could hardly have occurred slowly, gradually and over vast territories. Rather, they happened quite quickly and locally, because organisms (NCC) were at that time in an extremely unstable state - the stage of destabilization (Rautian, 1988). It is possible that the return to an evolutionarily stable state and the restoration of insulating barriers occurred soon after the acquisition of mitochondria, and only in the NCC lineage in which this most successful symbiosis arose. All other lines, most likely, quickly died out.

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

Conclusion

A comparative analysis of protein domains in three superkingdoms (Archaea, Bacteria, Eukaryota) confirms the symbiogenetic theory of the origin of eukaryotes. Eukaryotes have inherited many key components from archaea. information systems nucleocytoplasm. Bacterial endosymbionts (mitochondria and plastids) have 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 by lateral transfer from various bacteria. Apparently, in the evolution of the ancestors of the nucleocytoplasm there was a period of destabilization, during which the insulating barriers were sharply weakened. During this period there was an intense incorporation of foreign genetic material. The “trigger” of 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.

Bibliography

Gusev M.V., Mineeva L.A. Microbiology. Third edition. M.: Publishing House of Moscow State University, 1992.

Domaradsky I.V. Molecular biological bases of Helicobacter pylori variability // Journal of Microbiology, 2002, No. 3, p. 79-84.

Zavarzin G.A. Development of microbial communities in the history of the Earth // Problems of pre-anthropogenic evolution of the biosphere. M.: Nauka, 1993. S. 212-222.

Litoshenko A.I. Evolution of mitochondria // Tsitol. Genetics. 2002. V. 36. No. 5. S. 49-57.

Margelis L. 1983. The role of symbiosis in cell evolution. M.: Mir. 352 p.

Markov A.V. The problem of the origin of eukaryotes // Paleontol. magazine In the press.

Rautian A.S. Paleontology as a source of information about the regularities and factors of evolution // Modern paleontology. M.: Nedra, 1988. V.2. pp. 76-118.

Fedorov V.D. Blue-green algae and the evolution of photosynthesis // Biology of blue-green algae. 1964.

Bernhard J.M., Buck K.R., Farmer M.A., Bowser S.S. The Santa Barbara Basin is a symbiosis oasis // Nature. 2000. V. 403. No. 6765. P. 77-80.

Brocks J.J., Logan G.A., Buick R., Summons R.E. Archean molecular fossils and the early rise of eukaryotes // Science. 1999. V. 285. No. 5430. P. 1025-1027.

Brochier C., Forterre P., Gribaldo S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox // Genome Biol. 2004.V.5. No. 3. P. R17.

Canback B., Andersson S. G. E., Kurland, C. G. The global phylogeny of glycolytic enzymes // Proc. Natl. Acad. sci. U. S. A. 2002. No. 99. P. 6097-6102.

Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification // Int. J. Syst. Evol. microbiol. 2002. No. 52. Pt 1. P. 7-76.

Coulson R.M., Enright A.J., Ouzounis C.A. Transcription-associated protein families are primarily taxon-specific // Bioinformatics. 2001. V.17. No. 1. P. 95-97.

Dohlen C.D., von, Kohler S., Alsop S.T., McManus W.R. Mealybug beta-proteobacterial endosymbionts contain gamma-proteobacterial symbionts // Nature. 2001. V. 412. N 6845. P. 433-436.

Dolan M.F., Melnitsky H., Margulis L., Kolnicki R. Motility proteins and the origin of the nucleus // Anat. Rec. 2002. N 268. P. 290-301.

Duval B., Margulis L. The microbial community of Ophrydium versatile colonies: endosymbionts, residents, and tenants // Symbiosis. 1995. N 18. P. 181-210.

Dyall S.D., Brown M.T., Johnson P.J. Ancient Invasions: From Endosymbionts to Organelles // Science. 2004. V. 304. N 5668. P. 253-257.

Dyall S.D., Johnson P.J. Origins of hydrogenosomes and mitochondria: evolution and organelle biogenesis // Curr. Opin. microbiol. 2000. V. 3. N 4. P. 404-411.

Ent F., van den, Amos L.A., Löwe J. Prokaryotic origin of the actin cytoskeleton // Nature. 2001. V. 413. N 6851. P. 39-44.

Esser C., Ahmadinejad N., Wiegand C. et al. A Genome Phylogeny for Mitochondria Among Alpha-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes // Mol. Biol. Evol. 2004. V. 21. N 9. P.1643-1660.

Feng D.F., Cho G., Doolittle R.F. Determining divergence times with a protein clock: Update and reevaluation // Proc. Natl. Acad. sci. USA. 1997. V. 94. P. 13028-13033.

Gabaldun T., Huynen M.A. Reconstruction of the Proto-Mitochondrial Metabolism // Science. 2003. V. 301. N 5633. P. 609.

Gray M.W., Burger G., Lang B.F. Mitochondrial Evolution // Science. 1999. V. 283. N 5407. P. 1476-1481.

Gupta R.S. Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes // Microbiology and Molecular Biology Reviews. 1998. V. 62. N 4. P. 1435-1491.

Guerrero R., Pedros-Alio C., Esteve I. et al. Predatory prokaryotes: predation and primary consumption evolved in bacteria // Proc. Nat. Acad. sci. USA. 1986. N 83. P. 2138-2142.

Hartman H., Fedorov A. The origin of the eukaryotic cell: a genomic investigation // Proc. Nat. Acad. sci. USA. 2002. V. 99. N 3. P. 1420-1425.

Helenius A., Aebi M. Intracellular functions of N-linked glycans // Science. 2001. V. 291. N 5512. P. 2364-2369.

Jenkins C., Samudrala R., Anderson I. et al. Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. //Proc. Natl. Acad. sci. U S A. 2002. V. 99. N 26. P. 17049-17054.

Kurland C.G., Andersson S.G.E. Origin and Evolution of the Mitochondrial Proteome // Microbiology and Molecular Biology Reviews. 2000. V. 64. N. 4. P. 786-820.

Margulis L., Bermudes D. Symbiosis as a mechanism of evolution: status of cell symbiosis theory // Symbiosis. 1985. N 1. P. 101-124.

Margulis L., Dolan M.F., Guerrero R. The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists // Proc. Natl. Acad. sci. U S A. 2000. V. 97. N 13. P. 6954-6959.

Martin W. Gene transfer from organelles to the nucleus: Frequent and in big chunks // Proc. Natl. Acad. sci. U.S.A. 2003. V. 100. N 15. P. 8612-8614.

Martin W., Muller M. The hydrogen hypothesis for the first eukaryote // Nature. 1998. N 392. P.37-41.

Martin W., Russell M.J. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells // Phil. Trans. R. Soc. Lond. B. biol. sci. 2003. V. 358. N 1429. P. 59-85.

Martin W, Schnarrenberger C. The evolution of the Calvin cycle from prokaryotic to eukaryotic chromosomes: a case study of functional redundancy in ancient pathways through endosymbiosis // Curr Genet. 1997. V. 32. N 1. P. 1-18.

Mayer F. Cytoskeletons in prokaryotes // Cell. Biol. Int. 2003. V. 27. N 5. P. 429-438.

Ng W.V., Kennedy S.P., Mahairas G.G. et al. Genome sequence of Halobacterium species NRC-1 // Proc. Natl. Acad. sci. U S A. 2000. V. 97. N 22. P. 12176-12181.

Noon K.R., Guymon R., Crain P.F. et al. Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature , 23 degrees C) and Stetteria hydrogenophila (Topt, 95 degrees C) // J. Bacteriol. 2003. V. 185. N 18. P. 5483-5490.

Nugent J.M., Palmer J.D. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution // Cell. 1991. V. 66. N 3. P. 473-481.

Slesarev A.I., Belova G.I., Kozyavkin S.A., Lake J.A. Evidence for an early prokaryotic origin of histones H2A and H4 prior to the emergence of eukaryotes // Nucleic Acids Res. 1998. V. 26. N 2. P. 427-430.

Theissen U., Hoffmeister M., Grieshaber M., Martin W. Single Eubacterial Origin of Eukaryotic Sulfide: Quinone Oxidoreductase, a Mitochondrial Enzyme Preserved from the Early Evolution of Eukaryotes During Anoxic and Sulfidic Times // Mol. Biol. Evol. 2003. V. 20. N 9. P. 1564-1574.

Vellai T., Takacs K., Vida G. A new aspect to the origin and evolution of eukaryotes // J. Mol. Evol. 1998. V. 46. N 5. P. 499-507.

Vellai T., Vida G. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells // Proc. R. Soc. Lond. B Biol. sci. 1999. V. 266. N 1428. P. 1571-1577.

Walden W.E. From bacteria to mitochondria: Aconitase yields surprises // Proc. Natl. Acad. sci. U. S. A. 2002. No. 99. P. 4138-4140.

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

Russian paleontologists have 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 originated on our planet about 4 billion years ago. And the first inhabitants of the Earth were bacteria. Billions of individual individuals formed colonies that covered the vast expanses of the seabed with a living film. Ancient organisms were able to adapt to the realities of harsh reality. High temperatures and anoxic environments are conditions under which one would rather die than stay alive. But the bacteria survived. The unicellular 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 about this date are divided. The reason for this was the sensational statement of researchers from the Paleontological Institute of the Russian Academy of Sciences.

Give me air!

Prokaryotes have 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 beings was deprived of the opportunity to develop progressively. What prokaryotes were 3.5-4 billion years ago, they have remained almost the same to this day. A prokaryotic cell is unable to create a complex organism. In order for evolution to move on and give rise to more complex forms of life, another, more perfect 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 no longer could. The first producers of oxygen, most likely, were cyanobacteria, which found an efficient way of photosynthesis. What could he be? If before that bacteria used hydrogen sulfide as an electron donor, then at some point they learned how to get an electron from water.

"The transition to the use of such a virtually unlimited resource as water has opened up evolutionary opportunities for cyanobacteria," believes Researcher Paleontological Institute of the Russian Academy of Sciences Alexander Markov. Instead of the usual sulfur and sulfates, oxygen began to be released during photosynthesis. And then, as they say, the most interesting began. The appearance of the first organism with a cell nucleus opened up wide opportunities for the evolution of all life on Earth. The development of eukaryotes has led to the emergence of such complex forms as plants, fungi, animals and, of course, humans. All of them have the same type of cell, in the center of which is the nucleus. This component is responsible for the storage and transmission of 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 called the numbers 1-1.5 billion years ago. But it suddenly turned out that this event happened much earlier.

unexpected find

Back in 1982, paleontologist Boris Timofeev conducted an interesting study and published his results. In the Archean and Lower Proterozoic rocks (2.9-3 billion years) on the territory of Karelia, he discovered unusual fossilized microorganisms about 10 micrometers (0.01 millimeters) in size. Most of the finds had a spherical shape, the surface of which was covered with folds and patterns. Timofeev suggested that he discovered acritarchs - organisms that are classified as representatives of eukaryotes. Previously, paleontologists found similar samples of organic matter only in younger deposits - about 1.5 billion years old. The scientist wrote about this discovery in his book. “The print quality 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 for many years on a bookshelf.

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 Alexei Rozanov quite accidentally remembered Timofeev's work. He decided once again, using modern devices, to explore the collection of Karelian specimens. And very quickly he became convinced that he really had eukaryote-like organisms in front of him. Rozanov is sure that the discovery of his predecessor is an important discovery, which is a good reason to revise existing views on the time of the first appearance of eukaryotes. Very quickly, the hypothesis had 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,” Alexander Markov believes. eukaryotes - from 2-3 to 50 micrometers. In reality, the size intervals overlap. Researchers often find samples of both giant prokaryotes and tiny eukaryotes. Size is not one hundred percent proof." It's really hard to test the hypothesis. There are no more samples of eukaryotic organisms extracted from Archean deposits in the world. It is also impossible to compare ancient artifacts with their modern counterparts, because the descendants of the acritarchs did not survive to this day.

Revolution in science

However, in scientific community a big fuss arose around Rozanov's idea. Someone categorically does not accept Timofeev's find, because he is 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 had appeared during the time of the Archaean, then, roughly speaking, they would have been cooked immediately. Aleksey 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, assess the level of biological organization based on paleontological findings. Then, based on these data, determine , how much oxygen should have been contained in the Earth's atmosphere so that one or another form of life could feel normal.If eukaryotes appeared, then oxygen should already have been 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. " Aleksey Rozanov is inclined to move as far as possible into the past the moment of the appearance of oxygen and to reduce the temperature of the ancient Earth as much as possible.

If it is possible to prove that Timofeev found fossilized eukaryote-like microorganisms, this will mean that in the near future humanity will have to change the usual idea about the course of evolution. This fact will allow us to say that life on Earth appeared much earlier than it was supposed. 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 was broken or why its course 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 much white spot is formed in the history of our planet. Another revision of the past is required, and this is a colossal work in its scope, which, perhaps, will never end.

OPINIONS

Life long

Vladimir Sergeev, Doctor of Geology and Mineralogy, Leading Researcher at the Geological Institute of the Russian Academy of Sciences:

In my opinion, one should be more careful with such conclusions. Timofeev's data are based on material with secondary changes. And this is the main problem. The cells of eukaryote-like organisms were chemically degraded and could be destroyed by bacteria. I consider it necessary to re-examine the Timofeev finds. As for the time of the 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. It is generally accepted that it formed 2.8 billion years ago. And Alexei 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 fraction of the material that may still exist on the planet. Surviving forms are very rare. The fact is that special conditions are necessary for the preservation of organisms: a humid environment, lack of oxygen, and mineralization. Microorganisms that lived on land, in general, could not reach the researchers. It is by mineralized or petrified structures that scientists judge what kind of life was on the planet. The material that falls into the hands of scientists is a mixed fragments from different eras. Classical conclusions about the origin of life on Earth may not correspond to reality. In my opinion, it did not develop from simple to complex, but appeared at once.

Maya Prygunova, Itogi magazine No. 45 (595)

Development of life in the Proterozoic era. During the first half of the Proterozoic era (started 2.5 billion, ended - about 0.6 billion years ago), prokaryotic ecosystems mastered the entire oceans. 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 the complication of organization, which leads to a more efficient assimilation of vital resources.

The emergence of multicellular organisms- another manifestation of the ability of eukaryotes to complicate the structure. Most researchers believe that multicellular organisms evolved from colonial unicellular organisms due to the differentiation of their cells. Rich clitinism in various groups of algae and fungi arose independently in different systematic groups: for example, multicellular green, brown and red algae originated from various 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).

Main hypotheses of the origin of multicellular animals from the colonial flagella were 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 discovered by him, 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, he found that gastrulation in them occurs due to the insertion of the blastoderm at the posterior end of the body (invagination) with the formation of the primary mouth and sac-like intestine. Haeckel called such a hypothetical animal "gastreya". In his opinion, she captured food with her mouth and digested it in her intestines.

According to II 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 ciliary worms, some coelenterates, etc.). He also established that gastrulation in some coelenterates occurs by migration of some of the blastoderm cells into the blastula. According to him, the original multicellular animals were hypogetic "phagocytes", covered with a layer of ciliated cells capable of capturing small nutrient particles through phagocytosis. Cells with digestive vacuoles migrated into the phagocyte, losing cilia, where they digested food. Organisms such as gastrea originated from phagocytes on late stages evolution, when they acquired the ability to capture large-sized prey with the mouth opening, which arose due to the difference in the outer layer of cells.

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

primordial eukaryotes(flagellate unicellular organisms) originated from prokaryotes in the first half of the Proterozoic era and shortly thereafter split into single-celled plants (algae), animals (protozoa), and fungi. The formation of a complex genome, the nuclear envelope, the dominance of the sexual mode of reproduction and the ability to complicate the organization of eukaryotes led to their wide adaptive capabilities and further rapid evolution.

According to most scientists, multicellular organisms originated from colonial ancestors. The probable ways of origin of multicellular animals explain the hypotheses of the phagocyte of I.I. Mechnikov and the gastraea of ​​E. Haeckel.

By modern ideas, life is the process of the existence of complex systems consisting of large organic molecules and not organic matter and capable of self-reproducing, self-developing 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, the development of natural science, views on the origin of life changed, 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 for 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 Stationary state hypothesis (life has always existed);

Ø Panspermia hypothesis (life 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 Force - the Creator as a result of several acts of supernatural creation in the past. The organisms that inhabit the Earth today are descended from separately created basic types of living beings. The created species were from the very beginning excellently organized and endowed with the capacity for some variability within certain boundaries (microevolution). Followers of almost all the most common religious teachings adhere to this hypothesis.

The traditional Judeo-Christian idea of ​​the creation of the world, set forth in the Book of Genesis, has caused and continues to cause controversy. However, the 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 search of truth, then theology comprehends the truth through divine revelation and faith.

The process of the divine creation of the world is presented as having taken place only once and therefore inaccessible to observation. In this regard, the hypothesis of creation can neither be proved nor refuted 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 to be the usual way for the appearance of living beings from inanimate matter. It was believed that the source of spontaneous generation is either inorganic compounds or decaying organic residues (the concept of abiogenesis). This hypothesis was circulated in ancient China, Babylon, and Egypt as an alternative to the creationism with which it coexisted. The idea of ​​spontaneous generation was also expressed by the philosophers of Ancient Greece and even by earlier thinkers, i.e. it seems to be as old as humanity itself. Throughout such a long history, this hypothesis has been modified, but still remained 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 decaying 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 made the following experiment. He placed the dead snakes in different vessels, covering some vessels with muslin and leaving others open. The swarming flies laid their 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 that appear in the meat of snakes are the larvae of the Florentine fly and that if the meat is closed and the access of the flies is prevented, then it will not "produce" worms. Refuting the concept of spontaneous generation, Redi suggested that life can only arise from a 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. They were bacteria and protists. Leeuwenhoek suggested that these tiny organisms, or "animalcules," as he called them, are descended from their own kind.

Leeuwenhoek's opinion was shared by the Italian scientist Lazzaro Spallanzani (1729-1799), who decided to prove empirically that the microorganisms often found in meat broth do not spontaneously arise in it. To this end, he placed a liquid rich in organic matter (meat broth) into vessels, boiled this liquid over a fire, and then sealed the vessels hermetically. As a result, the broth in the vessels remained clean and free from 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, therefore they still recognized 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 Tyndale (1820-1893). They showed that bacteria spread through the air and that if they were not in the air entering the flasks with sterilized broth, then they would not arise in the broth itself. Pasteur used for this flasks with a curved S-shaped neck, which served as a trap for bacteria, while air freely entered and exited 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 practically all scientists recognized that living organisms are descended 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 has always been capable of sustaining life, and if it has changed, it has changed very little; species have always existed. This hypothesis is sometimes called the hypothesis of eternism (from 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 germs of life from other planets was called panspermia (from the Greek pan - all, everyone and sperma - seed). This hypothesis is adjacent to the steady 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 put forward the idea of ​​a cosmic (extraterrestrial) origin of life was the German scientist G. Richter in 1865. According to Richter, life on Earth did not originate from inorganic substances, but was introduced from other planets. In this regard, questions arose as to how possible such a transfer from one planet to another and how it could be carried out. The answers were sought primarily in physics, and it is not surprising that the first defenders of these views were the representatives of this science, the outstanding scientists G. Helmholtz, S. Arrhenius, J. Thomson, P.P. Lazarev and others.

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

Other scientists have expressed the idea of ​​transferring the "spores of life" to Earth by light.

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

The point of view of astronomers C. Vik-ramasingh (Sri Lanka) and F. Hoyle adjoins the panspermia hypothesis

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

Life originated in the Archean era. Since the first living organisms did not yet have any skeletal formations, there were almost no traces of them left. However, the presence among the Archean deposits of rocks of organic origin - limestone, marble, graphite and others - indicates the existence of primitive living organisms in this era. They were unicellular pre-nuclear 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 emergence of eukaryotes is associated with the formation of cells that have a real nucleus (containing chromosomes) and mitochondria. Only such cells are able to divide mitotically, which ensured good preservation and transfer 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 original 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 for the synthesis organic compounds from the simplest inorganic.

Of course, such a complex compound as chlorophyll did not immediately appear. Initially, more simply arranged pigments appeared, which contributed to the assimilation of organic substances. Chlorophyll apparently developed from these pigments.

Over time, organic matter accumulated in it abiogenically began to dry out in the primordial ocean. The emergence of autotrophic organisms, primarily green plants capable of photosynthesis, ensured the 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 stems, differing in the way of nutrition. 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 does not let in harmful ultraviolet rays. This paved the way for life to land on land. The appearance of photosynthetic plants made possible 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, multicellular organisms apparently evolved from colonial flagellates in this era. The appearance of the sexual process and multicellularity prepared further progressive evolution.

The emergence of eukaryotes is a major event. It changed the structure of the biosphere and opened up fundamentally new opportunities for progressive evolution. The eukaryotic cell is the result of a long evolution of the world of prokaryotes, a world in which diverse microbes adapted to each other and looked for ways to effectively cooperate.

timeline outline (reprise)

Photosynthetic prokaryotic complex Chlorochromatium aggregatum.

Eukaryotes arose as a result of symbiosis of several types of prokaryotes. Prokaryotes in general are quite prone to symbiosis (see Chapter 3 in The Birth of Complexity). Here is an interesting symbiotic system known as Chlorochromatium aggregatum. Lives in deep lakes, where there are anoxic conditions at depth. The central component is a mobile heterotrophic beta-proteobacterium. Around it, stacks are from 10 to 60 photosynthetic green sulfur bacteria. All components are connected by outgrowths of the outer membrane of the central bacterium. The meaning of the community is that the mobile beta-proteobacteria drags the whole company to places favorable for the life of fastidious sulfur bacteria, and sulfur bacteria are engaged in photosynthesis and provide food for themselves and beta-proteobacteria. Maybe some ancient microbial associations of approximately this type were the ancestors of eukaryotes.

Theory of symbiogenesis. Merezhkovsky, Margulis. Mitochondria are descendants of alpha-proteobacteria, plastids are descendants of cyanobacteria. It is more difficult to understand who was the ancestor of everything else, that is, the cytoplasm and the nucleus. The nucleus and cytoplasm of eukaryotes combine features of archaea and bacteria, and also have many unique features.

About mitochondria. Perhaps it was the acquisition of mitochondria (and not the nucleus) that was the key moment in the development of eukaryotes. Most of the ancestral mitochondrial genes were transferred to the nucleus, where they came under the control of nuclear regulatory systems. These nuclear genes of mitochondrial origin encode not only mitochondrial proteins, but also many proteins that work in the cytoplasm. This suggests that the mitochondrial symbiont played a more important role in the formation of the eukaryotic cell than expected.

The coexistence of two different genomes in one cell required the development of an effective system of their regulation. And in order to effectively manage the work of a large genome, it is necessary to isolate the genome from the cytoplasm, in which metabolism takes place and thousands of chemical reactions. The nuclear envelope just separates the genome from the turbulent chemical processes cytoplasm. The acquisition of symbionts (mitochondria) could become an important stimulus for the development of the nucleus and gene regulatory systems.

The same applies to sexual reproduction. You can live without sexual reproduction as long as your genome is small enough. Organisms with a large genome, but devoid of sexual reproduction, are doomed to rapid extinction, with rare exceptions.

Alphaproteobacteria - this group included the ancestors of mitochondria.

Rhodospirillum is an amazing microorganism that can live due to photosynthesis, including under anaerobic conditions, and as an aerobic heterotroph, and even as an aerobic chemoautotroph. It can, for example, grow by oxidizing carbon monoxide CO without using any other energy sources. In addition to all this, he also knows how to fix atmospheric nitrogen. That is, it is a highly versatile organism.

The immune system mistakes mitochondria for bacteria. When damaged mitochondria enter the blood during an injury, characteristic molecules are released from them that are found only in bacteria and mitochondria (bacterial-type circular DNA and proteins that carry a special modified amino acid formylmethionine at one of their ends). This is due to the fact that the protein synthesis apparatus in mitochondria remained the same as in bacteria. Cells of the immune system - neutrophils - react to these mitochondrial substances in the same way as to bacterial ones, and with the help of the same receptors. This is the clearest confirmation of the bacterial nature of mitochondria.

The main function of mitochondria is oxygen respiration. Most likely, the stimulus for the association of the anaerobic ancestor of the nucleus and cytoplasm with the "protomitochondria" was the need to protect themselves from the toxic effects of oxygen.

Where did bacteria, including alphaproteobacteria, get the molecular systems necessary for oxygen respiration? It seems that they were based on molecular systems of photosynthesis. The electron transport chain, which was formed in bacteria as part of the photosynthetic apparatus, was adapted for oxygen respiration. In some bacteria, parts of the electron transport chains are still used simultaneously in both photosynthesis and respiration. Most likely, the ancestors of mitochondria were aerobic heterotrophic alpha-proteobacteria, which, in turn, descended from photosynthetic alpha-proteobacteria, such as rhodospirillum.

The number of common and unique protein domains in archaea, bacteria and eukaryotes. A protein domain is a part of a protein molecule that has a specific function and characteristic structure, that is, a sequence of amino acids. Each protein, as a rule, contains one or more of these structural and functional units, or domains.

4.5 thousand protein domains that eukaryotes have can be divided into 4 groups: 1) available only in eukaryotes, 2) common to all three superkingdoms, 3) common to eukaryotes and bacteria, but absent in archaea; 4) common to eukaryotes and archaea, but absent in bacteria. We will consider the last two groups (they are highlighted in the figure), since for these proteins one can speak with some certainty about their origin: bacterial or archaeal, respectively.

The key point is that eukaryotic domains, thought to be inherited from bacteria and from archaea, have significantly different functions. Domains inherited from archaea (their functional spectrum is shown in the left graph) play a key role in the life of a eukaryotic cell. Among them, domains associated with the storage, reproduction, organization and reading of genetic information predominate. The majority of "archaeal" domains belong to those functional groups within which the horizontal exchange of genes in prokaryotes occurs least of all. Apparently, eukaryotes received this complex by direct (vertical) inheritance from archaea.

Among the domains of bacterial origin, there are also proteins associated with information processes, but they are few. Most of them work only in mitochondria or plastids. The eukaryotic ribosomes of the cytoplasm are of archaeal origin, the ribosomes of mitochondria and plastids are of bacterial origin.

Among the bacterial domains of eukaryotes, the share of signal-regulatory proteins is much higher. From bacteria, eukaryotes inherited many proteins responsible for the mechanisms of cell response to environmental factors. And also - many proteins associated with metabolism (for more details, see Chapter 3, "The Birth of Complexity").

Eukaryotes have:

Archaeal "core" (mechanisms for working with genetic information and protein synthesis)

Bacterial "periphery" (metabolism and signal-regulatory systems)

· The simplest scenario: ARCHEIA swallowed BACTERIA (ancestors of mitochondria and plastids) and acquired all its bacterial characteristics from them.

· This scenario is too simple because eukaryotes have many bacterial proteins that could not have been borrowed from mitochondrial or plastid ancestors.

Eukaryotes have many "bacterial" domains that are not characteristic of either cyanobacteria (ancestors of plastids) or alphaproteobacteria (ancestors of mitochondria). They were obtained from some other bacteria.

Birds and dinosaurs. Reconstructing proto-eukaryotes is difficult. It is clear that the group of ancient prokaryotes that gave rise to the nucleus and cytoplasm had a number of unique features that prokaryotes that have survived to this day do not have. And when we try to reconstruct the appearance of this ancestor, we are faced with the fact that the scope for hypotheses turns out to be too large.

Analogy. It is known that birds descended from dinosaurs, and not from some unknown dinosaurs, but from a very specific group - maniraptor dinosaurs, which belong to theropods, and theropods, in turn, are one of the groups of lizard dinosaurs. Many transitional forms between flightless dinosaurs and birds have been found.

But what could we say about the ancestors of birds if there were no fossil record? At best, we would find out that the closest relatives of birds are crocodiles. But could we recreate the appearance of the direct ancestors of birds, that is, dinosaurs? Unlikely. But it is precisely in this position that we find ourselves when we try to restore the appearance of the ancestor of the nucleus and cytoplasm. It is clear that this was a group of some prokaryotic dinosaurs, an extinct group that, unlike real dinosaurs, did not leave distinct traces in the geological record. Modern archaea are to eukaryotes what modern crocodiles are to birds. Try to reconstruct the structure of dinosaurs knowing only birds and crocodiles.

An argument in favor of the fact that many microbes lived in the Precambrian, not similar to the current ones. Proterozoic stromatolites were much more complex and diverse than modern ones. Stromatolites are the product of vital activity of microbial communities. Doesn't this mean that the Proterozoic microbes were also more diverse than modern ones, and that many groups of Proterozoic microbes simply did not survive to this day?

The ancestral community of eukaryotes and the origin of the eukaryotic cell (possible scenario)

The hypothetical "ancestral community" is a typical bacterial mat, only in its upper part lived the ancestors of cyanobacteria, which had not yet switched to oxygenic photosynthesis. They were engaged in anoxygenic photosynthesis. The electron donor was not water, but hydrogen sulfide. Sulfur and sulfates were isolated as by-products.

The second layer was inhabited by purple photosynthetic bacteria, including alphaproteobacteria, the ancestors of mitochondria. Purple bacteria use long wavelength light (red and infrared). These waves have the best penetrating power. Purple bacteria still often live under a layer of cyanobacteria. Purple alphaproteobacteria also use hydrogen sulfide as an electron donor.

In the third layer there were fermenting bacteria that processed organic matter; some of them emitted hydrogen as waste. This created a base for sulfate-reducing bacteria. There could also be methanogenic archaea. Among the archaea that lived here were the ancestors of the nucleus and cytoplasm.

Crisis events began with the transition of cyanobacteria to oxygen photosynthesis. As an electron donor, cyanobacteria began to be used instead of hydrogen sulfide plain water. This opened up great opportunities, but it also had negative consequences. Instead of sulfur and sulfates, oxygen began to be released during photosynthesis - a substance that is extremely toxic to all the ancient inhabitants of the earth.

The first to encounter this poison were its producers, cyanobacteria. They were probably the first to develop means of protection against it. The electron transport chains that served for photosynthesis were modified and began to serve for aerobic respiration. The original purpose, apparently, was not to obtain energy, but only to neutralize oxygen.

Soon, the inhabitants of the second layer of the community - purple bacteria - had to develop similar defense systems. Just like cyanobacteria, they have developed aerobic respiration systems based on photosynthetic systems. It was purple alphaproteobacteria that developed the most perfect respiratory chain, which now functions in the mitochondria of eukaryotes.

In the third layer of the community, the appearance of free oxygen must have caused a crisis. Methanogens and many sulfate reducers utilize molecular hydrogen with the help of hydrogenase enzymes. Such microbes cannot live under aerobic conditions because oxygen inhibits hydrogenases. Many bacteria that produce hydrogen, in turn, do not grow in an environment where there are no microorganisms that utilize it. Of the fermenters, the community apparently retained forms that emit low-organic compounds (pyruvate, lactate, acetate, etc.) as end products. These fermenters have developed their own means of protection from oxygen, less effective. Among the survivors were archaea - the ancestors of the nucleus and cytoplasm.

Perhaps, at this moment of crisis, a key event occurred - the weakening of genetic isolation in the ancestors of eukaryotes and the beginning of active borrowing of foreign genes. Proto-eukaryotes incorporated the genes of various fermenters until they became microaerophilic fermenters themselves, fermenting carbohydrates to pyruvate and lactic acid.

The inhabitants of the third layer - the ancestors of eukaryotes - were now in direct contact with the new inhabitants of the second layer - aerobic alphaproteobacteria, which had learned to use oxygen for energy. The metabolism of proto-eukaryotes and alphaproteobacteria became complementary, which created the prerequisites for symbiosis. And the very location of alphaproteobacteria in the community (between the upper layer, which releases oxygen, and the lower layer) predetermined their role as "defenders" of eukaryotic ancestors from excess oxygen.

It is likely that proto-eukaryotes ingested and acquired many different bacteria as endosymbionts. Experimentation of this kind is still going on in unicellular eukaryotes, which have a huge variety of intracellular symbionts. Of these experiments, the alliance with aerobic alphaproteobacteria proved to be the most successful.