The Biggest Evolutionary Jump: Restructuring of the Genome and Some Consequences © P

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THE BIGGEST EVOLUTIONARY JUMP: RESTRUCTURING OF THE GENOME AND SOME CONSEQUENCES © P. Omodeo

Dipartimento di Scienze Ambientali, Universita di Siena, Italy; e-mail: [email protected] Ï. Îìîäåî Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà In this paper, the evolution of the cell is investigated till the level of complexity obtained by protists. Part- icular attention is paid to the genomic compartment and to the question: why has the genome of prokaryotes remained so small over more than 3 billion years and more than 3 trillion generations? Constraints on their genome evolution may be attributed mainly to: 1) the fact that repetitions of nucleotide sequences longer than 12 to 15 bp are forbidden according to Thomas’ principle; 2) the high cost of the control of gene expression by means of regulatory proteins: this cost increases exponentially with chromosome elongation. The formation of chromatin, i. e. the wrapping of DNA around the nucleosomes, removed these constraints and allowed the increase of the genome and especially of the redundant sequences of DNA, whose role is discussed. The transformation and growth of the genome generated a trend towards separation of the various physiological functions and of their control. The formation of a nuclear envelope may have begun with the advent of mitosis, which replaced the simple but delicate device of pushing the newly formed DNA into the daughter prokaryotic cells. An increase of the O2 concentration in waters stimulated further evolution: the new cell established symbiosis with a bacterium capable of protecting against peroxides and performing aerobic respiration. The increased O2 concentration also led to the production of sterols, which became an important component of the cell membrane. The mutual adaptation of cells belonging to different domains involved further modifications, leading to the birth of proto-eukaryotic cells and facilitating the establishment of further symbioses with photosynthetic cyanobacteria. Pro- to-eukaryotic cells were devoid of motility and contractility, as are the cells of red algae, fungi and Zygnemata- les today. Both these faculties evolved when the protist eukaryotic cell acquired flagella, cytoplasmic contractility and sensors to govern them. K e y w o r d s: ñell evolution, genome evolution, constraints on genome growth, redundant DNA, pro- to-eukaryotes, protist motility and sensors.

The prokaryotic genome and its duplication point of the wall; hence, the entire process determines some aspects of cell morphology, particularly its length. The pro- The bacterial genome typically consists of an annular or cess is the same in the archaean cell, but in species without a linear chromosome, usually 0.25—2.0 mm long, formed by cell wall or with a deformable wall the centres (or centre) of one-nine million base pairs (bp) (fig. 1). The average number DNA duplication can find stable support only in the structure of nucleotides per gene is usually higher than 1000. In bacte- of the cytoskeleton, and the lack of bilateral symmetry in ria that became endocellular parasites, the size of the chromosome types of cells seems to make the process more preca- some is about an order of magnitude smaller, even in phyloge- rious. netically distant taxa. In procells with complex metabolic acti- The linear chromosomes of the procell divide in another vities and complicated shapes (cyanobacteria, streptomycetes manner because the DNA polymerase works in two different and others), the genome size can be up to 9 Mbp and beyond. ways on the two filaments of the double helix, which have op- Linear chromosomes are more common in such cases. posite polarity. Since the terminal tract of the nucleotide chain The genome of archaea differs significantly from that of cannot be duplicated entirely by the DNA polymerase, the li- bacteria: the nucleotide number is smaller by one third on ave- near chromosome would lose the terminal nucleotides and fa- rage; the number of nucleotides per gene is often less than tally shorten at each reproductive cycle. However, the enzyme 1000. It also differs in its relationships with histone molecu- telomerase adds a long appendix formed by repetitive les, which in some archaea form nucleosomes (Pereira et DNA sequences to the end of the chromosome. This appen- al., 1997), globular masses around which the DNA entwines, dix, called telomere,isnotentirely replicated by DNA po- plausibly for defence against heat denaturation. lymerase and is repaired by telomerase at each reproductive In the active procell, the chromosome duplicates continu- cycle. Thanks to this mechanism, the chromosomes are comp- ally and each new copy is apparently pushed by the replica- letely replicated without losing genetic information. In any ting apparatus to one of the two poles of the cell (which is a case, when the two new coils have reached separate centres in couple of mm long) without the thin filaments becoming en- the procell, cytodiaeresis takes place, involving the growth of tangled in the limited space. The operation proceeds in a surp- a diaphragm formed by the plasma membrane and cell wall (if risingly precise manner thanks to the activity of the two cent- it exists). During this process, mRNA transcription is not sus- res (or centre) of DNA polymerase (a multienzyme «replicati- pended, even though it must undergo momentary interrup- on machine») and to the fact that each centre is connected to a tions.

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Fig. 1. Comparison of the genome size of archaea and bacteria.

Why does the genome of prokaryotes remain The importance of Thomas’ principle becomes more evi- so small? dent when paraphrased in the following manner: in the prokaryotic chromosome, the repetition of DNA lengths containing Why has the prokaryotic genome remained so small thro- 12 or more nucleotides is forbidden; otherwise, the chromoso- ughout 3.8 billion years and at least a thousandfold higher me becomes unstable and its functionality is compromised. number of generations? This question comes to the fore insis- The situation postulated by Thomas’ principle finds an analo- tently in the mind of the biologist concerned with comparative gy in what philologists call a «jump from like to like», or ho- cytology. Why has the procell remained so small and simple moteleut: when on a page to be copied, one or more words are in this long period of time? This question is also raised by those concerned with evolution and who marvel that, in less than half that time and an incomparably smaller number of generations, eukaryotes showed a flowering of taxa and immensely larger forms of life. An answer to these questions can be found in a paper by Thomas (1966) dealing with recombinant DNA. He used phy- sico-chemical and biological evidence to formulate the following principle: «If freely recombining DNA molecules contain repetitious recognition lengths, they will be unstable under recombination» (p. 329). With the aid of collaborators from different scientific fields (see his appendixes), Thomas established that the repetitious recognition lengths should contain «at least twelve nucleotides» (p. 326). That implies that the chromosome, folding up inside the cell, can bring the two repeated sequences into contact; because they have complementary structures, they will adhere closely and the tract between Fig. 2. If A—C sequence of 12—15 base pairs (or longer) is repea- the two equal sequences can become detached and lost or un- ted along a bacterial chromosome, these sequences may come into dergo an «inversion» that compromises its functionality contact and adhere, forming a ring that may become detached; the- (fig. 2). refore, the chromosome becomes unstable (from: Thomas, 1966). Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 799 repeated not far from each other, the copyist omits the interve- synthetic apparatus are present in several grouped copies ning phrase (Omodeo, 1975). (Grossman et al., 1993; Kirby, 2004). At the time he wrote, Thomas had only one sure datum A third difficulty arises from data emerging from the se- concerning the instability of the chromosome of a mutant stra- quencing of prokaryotic genomes: in about 15 % of the cases, in of Escherichia coli in which a repetition had appeared. La- the nucleotide number exceeds the value considered compa- ter, other confirmatory cases came to light. Hansche (1975) tible with Thomas’ minimum length. reported: «However, duplicate genes that code for enzymes in It is possible that these exceptions have explanations that prokaryotes are generally unstable in the laboratory (Jackson, do not compromise Thomas’ principle. However, since we Yanofsky, 1973) and are unknown outside the laboratory now have about a thousand complete sequences of bacterial (Heyemen, Rosenberg, 1970)». genomes, it would be advisable to test the validity of the prin- If the prokaryotic chromosome cannot exceed this num- ciple and investigate if there are mechanisms that allow ex- ber of base pairs, we can say that — assuming there is propor- ceptions. tionality between the complexity of the organism and the size of its genome — prokaryotes cannot go further than the complexity attainable with only 1—2 megabytes of genetic infor- Control of the distribution of genetic information mation. This notion explains why there is such economy of and its problems codification in the prokaryotic genome and implies, above all, that the appearance of more complex cells, such as eukaryo- Examination of the bacterial genome reveals other inte- tes, was only made possible by a profound restructuring of the resting facts that supplement and confirm those discussed ear- genome. Indeed, the facts bear this out. lier. At the same time, they provide interesting perspectives on the evolutionary innovations which — after two billion years of history — allowed the prokaryotic cell to evolve into Implications of the principle of non-repeatability the eukaryotic cell and initiate its subsequent tumultuous proof DNA sequences in prokaryotes gress. However, before discussing this aspect, it is necessary to provide some preliminary indications. Thomas (1966) also made a suggestion that threw light on According to some trusty theoretical principles, we must a phenomenon that had remained obscure and had been the to- consider that the genome is an archive of programs, and such pic of many discussions following the discovery of the genetic an archive can work only on the condition that each program code: the «degeneracy» of this code, i. e. the fact that the is provided with its own address by which it can be activated 20 amino acids of proteins are coded for by a number of trip- or deactivated. The measurement of the parameters under con- lets that varies from two to six (only tryptophan and methioni- trol and the consequent activation or deactivation of the pro- ne are coded for by a single triplet). The consequent synthesis gram create an efficient self-control of the distribution of ge- of many more than 20 species of tRNA molecules, and as netic information. The addresses of the programs correspond many transport proteins, is a greater expense for the cell in to the «operator genes» (coordinated with «promoter genes»), terms of units of information. («Most amino acids have seve- which are nucleotide sequences with a receptor function able ral codons to represent them. Thus, „degeneracy” may be a to interact with special protein messengers to switch the infor- true „frequency suppressing device” employed to reconcile mation channel on and off. These messengers are called r e- the genetic requirement of nonrepetition with the structural repressors orco-repressors according to the type of in- quirements for enzyme function»). Moreover, degeneracy of tervention, or more generally regulatory proteins. the code allows much greater freedom in the planning of poly- Since reliability is a fundamental characteristic of a regu- peptide chain coding; because of it, the same sequence of fo- latory system, we should focus on the well-known molecular ur-five amino acids can be coded for in different ways in the genetics of bacteria. In this way, we can make four statements bacterial genome, and thus without having to repeat a sequen- concerning the reliability of the control and also its cost. ce of 12—15 nucleotides (the most abundant amino acid spe- 1. The sequences of each operator gene must be longer cies in proteins being those coded for by the highest number than the sequences that necessarily appear by a combinatory of triplets). event in a chromosome of given length; in the contrary case, the protein messengers could interact with them, with a consequent loss of reliability. Difficulties with Thomas’ principle 2. In a chromosome of given length, the more the structural genes subjected to control multiply, the more numerous A general principle in biology always runs into diffi- and longer must be the operator genes so that mistakes in the culties and exceptions and the Thomas’ principle is no excep- activation of the programs required in a given circumstance tion. do not occur. This affirmation is grounded on the fact, eviden- A first difficulty is substantial: the detachment of the seg- ced by combinatorial computation, that the total number ment between repetitions would not automatically follow their of strings having length n and an alphabet of k symbols is kn. pairing, but would require the intervention of endonucleases. This means that: when the numbers of customers grow, the te- These enzymes usually operate only upon recognizing a given lephone numbers (i. e. addresses) must become longer; signal that is a particular sequence of nucleotides. Therefore, when the total number of cars in a country grows, the alphanu- instability would be the result of not one but two conditions: meric code on the vehicle registration plates must become the repetition of a minimum recognition length and the pre- longer. sence of the appropriate signals. 3. As the DNA sequence of the operator gene becomes A second difficulty arises from the fact that the ribosomal longer, the precision with which it is recognized by the comp- genes in E. coli are present in 5 or 6 copies (Attardi, Amaldi, lementary structures in the protein messenger increases, and 1970); this report has been followed by many others. More- the risk that an identical sequence will appear following one over, in cyanobacteria, the genes for the proteins of the photo- or several mutations in another part of the chromosome beco- 800 Ï. Îìîäåî mes smaller. In other words, the reliability of the control inc- on single genes (often this is true for prokaryotes as well). It reases with the number of base pairs that make up the operator must also be mentioned that «house-keeping» genes, which gene. are continuously functioning in the cell, are not controlled, al- 4. As the DNA sequence of an operator gene becomes though the amount of their products is. longer, the cost of the messenger protein molecule that wraps Believing that the cost of the control would have caused and recognizes it becomes much greater, since its mass increa- insoluble problems, Britten and Davidson (Britten, Davidson, ses by the cube of the length of the receptor. 1969; Davidson, Britten, 1979) proposed a theory according This set of relationships triggers a perverse system with to which regulation in eukaryotes is carried out by repetitive regard to costs, whether they are calculated in terms of genetic segments of RNA complementary to the DNA of receptor (or memory employed or in terms of thermodynamics (Omodeo, operator) genes, thus light and economical molecules. After 1975, 1994). In the molecular genetics of bacteria (little is thirty years, this theory has proved true and we now know known for archaea), three different corrective measures that that, in the eukaryotic cell, in addition to the traditional regu- collaborate to moderate such disproportionate growth are re- latory proteins, whose complexity has become greater than in cognized. bacteria, there are innumerable segments of micro-RNA In many cases, the control is rarely performed on single with regulatory functions on both DNA sequences and on structural genes but on blocks of genes that work in synergy, mRNA sequences. i.e.onoperons.Theoperator gene consists of two (or even more) sequences in tandem or symmetrically inverted (i. e. palindromic), so that it will be recognized and then interact Disappearance of other constraints not with a single very large repressor molecule but with a pair in the molecular biology of prokaryotes of smaller molecules, coded for by a gene consisting of half the base pairs. The protein messengers can assume an oval rat- The appearance of nucleosomes removed the constraints her than a spherical shape, so that with equal effect their mass on the increase of genome size, i. e. of the information that di- is reduced. rects the development and functioning of the cell. The conse- Nevertheless, the ability to increase the quantity of gene- quent chromosome elongation, as well as the fact that the tic information while maintaining acceptable control of the chromatin mass is twice that of «naked» DNA, undoubtedly flow of this information increased only modestly and the bra- caused a loss of balance in the delicate mechanism of introdu- ke on growth of the genome continued to exist, causing a cing the newly formed chromosomes into the daughter cells: strong obstacle to the acquisition of new structural genes hence a new constraint appeared. The evolution of a mitotic (through transformation, or via other processes) and thus to apparatus made of tubulin and dynein and of a first anlage evolution by complexification. of nucleus sustaining it, as well as the breaking up of the chromosome into a set of shorter linear units, can be considered the primer of a series of adaptations in cascade. The The solution to constraints on growth first of which was the «maturation» process of eukaryotic of the prokaryotic genome mRNA.

Therefore, a structural obstacle and a functional obstacle opposed growth of the genome in prokaryotes. These obstac- Uncoupling of transcription les were overcome and the ability to store a larger amount of and translation of messenger RNA information and to accept repetition, even of long sequences, occurred when the naked DNA of the procell evolved into In the procell, as soon as transcription of mRNA on the chromatin,acomposite material unique to the eucell. This DNA template begins, ribosomes usually attach to it in suc- evolutionary step involved the wrapping of the double fila- cession and each one immediately begins translation of the ment of DNA around protein masses formed, in the eucell, by messenger. Accordingly, the polypeptide chain synthesized four pairs of histone molecules. These approximately cylindri- by the first-arriving ribosome will be the longest, while the cal masses, together with the two and a half coils of DNA wo- chains synthesized by ribosomes arriving later will be succes- und around them, are called nucleosomes. In electron sively shorter; finally, the chain adhering to the last ribosome micrographs of specially treated material, chromatin looks will be formed by one or a few amino acids. This is the man- like a series of globules arranged along the filament at short ner of formation of the triangular aggregates of progressively uniform distances. shorter peptide chains that electron microscopy has revealed For topological reasons, this structure prevents two equal to us. When the last-arriving ribosome has completed its linear segments of DNA, exceeding the critical length, from work, the proteins have detached and the mRNA has been de- interacting and causing the instability reported by Thomas. polymerized. For the same topological reasons, this wrapping modifies the In the eucell, transcription and translation proceed in relationships of the double DNA filament with the repressor another manner. The mRNA molecules are transcribed within or holorepressor macromolecules, to whose regulatory action the nucleus, where they are protected at each end (with a dif- the histone molecules add their own modulation of gene trans- ferent cap) so that they are not recognized by ribonuclease: af- cription while contributing to genome compaction, as they did ter such modification they are destined for transfer to the cy- in the cells of the thermophilic archaea from which they de- toplasm. There, depending on the proteins it codes for, the rived. mRNA can combine with some ribosomes to form polysomes This was a first important evolutionary step that allowed a and synthesize some proteins destined to remain free in the radical reduction of the costs of reliable control of the flow of cytoplasm. Otherwise, the mRNA reaches ribosomes adhering genetic information (i. e. control of gene expression). Due to to the nuclear envelope or endoplasmic reticulum, after which the reduction of costs in eukaryotes, this control is no longer the newly-formed proteins are moved to the place where they exerted on groups of synergic structural genes (operons) but will perform their function and also to the exterior. In other Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 801 cases, the protected mRNA is «archived» and it will be read Functional novelties in the genome of eukaryotes later at the appropriate moment, even after a rather long time. Therefore, the uncoupling of mRNA transcription and transla- The most conspicuous acquisition of the cell in the evolution means that the various activities of the eucell, those mation of the eukaryotic condition was not that of the nucleus, as naged by mRNA as well as its own production, can be regula- the name suggests, but rather the ability to increase its heredi- ted independently in time and in suitable sites. tary patrimony. In red algae and fungi, this patrimony is, on average, ten times that of bacteria. The DNA content increased further in the passage from The nuclear envelope red algae and fungi to protists, but in very different ways according to the phyla. We can say that, on average, it increased The most obvious attribute of the eukaryotic cell is the by 100 times with respect to bacteria and that the redun- nucleus, consisting of a very complex envelope containing dancy,i.e.therepetition of some DNA sequences, increased the chromatin. Its origin has been reconstructed by various even more with respect to the proto-eukaryotes; the increased authors in a similar way, involving several successive steps. chromatin mass of the protists was correlated with the appea- 1. An introflexion of the plasma membrane in a manner simi- rance of the histone H1 (absent in fungi and red algae), which lar to that in procells with intense metabolic activity which re- assured further packing of the chromatin. We can also add quires an extensive surface to support the corresponding enzy- that, in animals and plants, the DNA content increased by a matic apparatuses. 2. The nuclear envelope would have for- further order of magnitude. In protists, plants and animals, med in some part of the plasma membrane containing the there are large variations in nuclear DNA content (abbreviated apparatuses for DNA replication and the ribosomes dedicated as C). Because of this «C-value paradox» the idea of a precise to the synthesis of proteins to be released outside the cell. relationship between organismal complexity and genome size 3. Initially, the introflexion would have had the form of a cup does not hold up. The many examples of the C-value paradox and then would have closed like a ball provided with many include the lungfishes (Dipnoi), the Urodela amphibians and very complex selective passages, t h e nuclear pores,thro- many monocotyledonous plants, whose nuclear DNA exceeds ugh which the genome communicates with the cytoplasm, that of humans by an order of magnitude. To explain the phe- transferring to it ribosomes, mRNA, tRNA and receiving from nomenon, one can hypothesize that these variations are related it protein macromolecules (including histones, an integral part to more or less prolix or concise coding systems. In any case, of the chromatin) and messengers that regulate gene expressi- the C-value paradox does not invalidate the principle that an on. 4. Perhaps in relation to its mechanical role in mitosis, the increase of cell complexity is necessarily related to an increa- nuclear envelope acquired a robust internal layer formed by se of genetic information. This, however, is only part of the intermediate filaments andasimilar less robust exter- story, since the number of structural genes, i. e. the genes that nal layer. specify proteins with catalytic or structural functions, increa- The evolutionary appearance of the nuclear envelope is sed from bacteria to mammals (including man) only by about easy to imagine and explain, but it is less easy to understand tenfold, i. e. from two-three thousand to twenty-thirty thou- why, how and when it differentiated a system of very complex sand. This has caused many specialists to consider DNA with selective passages, each of which formed by no less than high or very high repetitiveness as «selfish DNA», «junk 50 protein species arranged according to a precise octagonal DNA» or, in the best of hypotheses, to assign this DNA a geometry. mechanical role. Yet, the genesis of the nuclear envelope as reported above appears too simple: a cup-shaped nucleus does not need pores provided with a selective apparatus; moreover, the idea that What was the use of the increased the nuclear pores, which precisely control the traffic of mole- memory capacity? cules entering and exiting the nucleus (one of the loveliest chapters in cell physiology), evolved immediately after closu- The increased memory capacity of the nuclear genome re of the cup is difficult to believe, especially since each mac- was employed by the earliest eucells to acquire part of the mi- romolecule allowed to enter bears an identification signal for tochondrial and plastidial genomes. In this way, the numbers entry (nuclear localization signal)while each macro- of structural genes and controlling genes also increased. Int- molecule allowed to exit bears a different signal. This indica- rons and redundant DNA, polynucleotide structures only ex- tes that evolution of the nuclear envelope and pores and evo- ceptionally seen in procells, also appeared and became com- lution of the traffic signals must have proceeded at the same mon in the earliest eucells; their amount particularly increased pace. Hence, we should infer a somewhat different order of in the cells of protists, animals and plants, where they now re- appearance of the key events during the evolution of the euka- ach and sometimes exceed 90 % of the total DNA. ryotic cell: formation of chromatin and consequent appearan- As the structure of redundant DNA became better unders- ce of a new mechanism for chromosomal duplication; endo- tood, it turned out to be organized as an array of characte- symbiosis with the precursor of mitochondria, which preser- ristic repetitive sequences that can be classified into four clas- ved its wall and its genetic and metabolic prerogatives; a long ses and more families: some of them are thoroughly intersper- period of reciprocal functional adaptation of the two compart- sed in the genome. Their functions remain obscure but ments; finally, completion of the nuclear envelope and of its previous hypotheses of them being parasite or junk DNA pores, and loss of the wall by the endosymbiont. now appear unsustainable and have been rejected by most It remains to understand the paradox of mitosis, which specialists. does not involve the entry of actin and tubulin into the nucleus Many efforts have been made to clarify the role of redun- through its intact envelope. In fact, these molecules, essential dant DNA. Particularly important have been studies on the for eukaryotic chromosomal division, polymerize in the cy- discharge of DNA fragments from the nuclei of cells pertai- toplasm usually and enter the nucleus via laceration of its en- ning to the somatic line, but not the germinal line, of animal velope. embryos. This phenomenon, called «chromatin diminution», 802 Ï. Îìîäåî has been observed in nematodes and in many arthropod gene- lained by biophysics and information theory; however, it is ra, particularly in copepods. Beermann (1977) and Beermann certain that the possibility of introducing and exploiting the and Meyer (1980) gave a detailed description of the chromatin potentialities of redundancy was a great event in the evolutio- diminution in Cyclops and found that it occurs between the 4th nary history of the eucell. and the 7th blastomere division, according to the species. The To explain why it is not at all surprising that the ratio same authors also investigated the genome size and chromo- of translated DNA to untranslated regulatory DNA is 3—5 % some number of the examined species. In my opinion, the in the cells of higher eukaryotes, I used a simile between most relevant results in the field are those by Akifyev and the construction of buildings and ontogeny: «Bricks, mortar, Grishanin (2005); they found that, in congeneric species of tiles, wood, glass and a few other materials can be used to copepods, DNA diminution may be either very strong or nil: construct either a shed or a cathedral: the difference in result 94 % in Cyclops kolensis,0%inC. insignis insignis.Byse- depends on the order in space and time in which these materi- quencing the excluded DNA of C. kolensis, these authors sho- als are arranged. The architect’s plan regards the latter aspect wed that it does not contain structural genes, but only repetiti- almost exclusively» and I added «True, the analogy is a rough ve untranscribed DNA. one, but I have proposed it not to maintain that ontogeny pro- These results do not prove that redundant DNA is useless ceeds along the lines of a building project, but rather to indica- but that, after it has accomplished its function, the cell may te a convenient point of view for evaluating certain quantitati- discharge it without any harm on the occasion of a pre-estab- ve and operative aspects of the genome» (Omodeo, 1975, lished blastomeric division. The fact that redundant DNA is p. 369). perpetuated in the germinal line suggests that its principal role The importance I gave in that paper to the control of ge- is in ontogeny. netic information may seem excessive. However, one can easily be convinced that it was not an exaggeration: in effect, the eucell differs from the procell not only in containing a gre- Role of redundancy ater variety of biochemical materials but mainly in having a much more complex design. The realization of this design re- Redundancy, which is very often looked at as a waste or quires that form and function is reconciled in the smallest de- as a plethora of tedious people, has some positive values. In tails, and to this end it is necessary that the genome not only technology, it is embedded in scientific instruments that must distribute but also receive and process a higher amount of in- work for as long as possible in extremely adverse conditions. formation. In physics and biophysics, as Gabor and Borselllino have ta- The hypothesis that, with the increase of DNA content of ught us, distributed redundancy is the basis of holographic er- an organism, an increasingly large proportion of this content ror-proof memories that contain the whole message in all their is used in control is supported by a very general notion that parts, with more reduced definition the smaller the part. Some emerged unexpectedly from research by Abrahamson and col- time ago, I hypothesized (Omodeo, 1987) that DNA sequen- leagues (1973) on the hazard of damage caused by ionizing ces repeated tens of thousands to millions of times and distri- radiation to operational genetic units of organisms buted throughout the genome constitute a holographic, and with different amounts of DNA in their cells. The trend of the thus error-proof, genetic memory. How these holographic me- phenomenon (fig. 3) does not leave any doubt that the increa- mories present in the genome are «read» will perhaps be exp- se in genome size corresponds to an increase in the amount of DNA used for the control and production of structures auxiliary to the single operational genetic units. In a way, we are wit- nessing the substitution of the operon by ever larger operational genetic units. This agrees with the results of the study of the genome of Chlamydomonas reinhardtii, showing that no less than twenty genes collaborate in the control of morphogenesis and motility of its flagella. This is but one of many examples.

To conclude this part

The formation of chromatin removed the constraints on growth of the genome: the consequent increase in genome size mostly involved a huge increase of redundant DNA. A plausible function for such redundancy could be both in im- proving the reliability of cell functioning and in developing a holographic genetic memory. The winning strategy in this evolutionary process was the separation and independent control of physiological functions formerly tied together. An important result was the harmoni- zing of the nuclear, mitochondrial and plastidial genomes. We Fig. 3. Frequency of mutations of single «operational genetic are in the dark concerning the characteristics of the host cell, units» per unit of X-radiation according to the DNA content of the but we can fill the void with at least partly testable hypo- cell; double logarithmic scale. theses. The curve demonstrates that as the size of the genome increases the size of the Hereafter I will discuss what I believe to be the most di- operation genetic units increases (from: Abrahamson et al., 1973). rect and least debatable path to follow. Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 803

The proto-eukaryotic cell. also present a zoospore stage with all the attributes of the ad- The cells involved in the birth of eukaryotes vanced eukaryotic cell. The only case described for non-parasitic organisms is the According to a widely accepted hypothesis, the first euka- profound regression from a mammal similar to a mole, thro- ryotic cell derived from an archaean cell that, when the O2 ugh various stages, to a form similar to a turbellarian flat- content of waters reached a convenient concentration, incor- worm. This is a caricature born from the satirical vein of the porated a bacterial cell able to use oxygen for cell respiration. German zoologist, Harald Stumpke [Gerholf Steiner], whose The idea that the host cell was archaean is supported by the aim was to dissuade the naturalist from proposing a too con- many characteristics shared by the two domains (other less venient process of reverse evolution (Steiner, 1991). important ones are omitted here): 1) several «families» of pro- Joking aside, it is rather implausible that the type of cell teins are common to archaea and eukaryotes but are absent or characteristic of many tens of thousands of species of eumy- poorly represented in bacteria; 2) RNA polymerase consists cetic fungi, which have very diverse ecological roles and ap- of four subunits in bacteria but of 8—12 subunits in archaea, peared over a billion years ago, derived from the cell of an as in eukaryotes; moreover, in eukaryotes there are three evolved eukaryote, which would have had to lose many of its known functional variants that coexist within the same cell; attributes. It is unrealistic to imagine an environmental situati- 3) the mRNA triplet that initiates translation is AUG in both on that would have required of the hypothetical precursor of prokaryotes and eukaryotes, but in archaea and eukaryotes eumycetic fungi: 1) the loss of the flagella and centrioles and, it specifies the amino acid methionine while in bacteria it spe- from the functional perspective, the possibility of swimming; cifies N-formyl-methionine; 4) the ribosomal composition 2) the loss of cellular contractility and thus the loss of the in archaea resembles that in eukaryotes more than that in bac- many functions that completely or partly depend on contracti- teria (Lecompte et al., 2002); 5) the archaea contain histones, lity: amoeboid motion, phagocytosis, active control of water whose molecules resemble those of eukaryotes and someti- content, etc.; 3) simplification of mitosis, without disappea- mes form nucleosomes around which the DNA entwines (Ta- rance of the nucleolus and nuclear envelope; 4) disappearance kayanagi et al., 1992; Pereira et al., 1997; Sandman, Reeve, of the gametes; 5) simplification of the sexuality, in many ca- 1999). ses reduced to parasexuality, which implies the exchange of It is hoped that the discovery and study of other archaean chromosomal material without the intervention of true meio- species will demonstrate that their cytoplasm contains tubulin, sis; 6) the loss of histone H1, used for DNA compaction, and dynein, and actin, typical proteins of eukaryotes that play de- of the respective gene. cisive roles in the eucell, especially in the dynamics of mito- Indeed, it is impossible to imagine that such a degraded sis. If this were to occur, the already rather solid hypothesis cell could have competed with the more advanced cells from could be considered a proven fact. Nevertheless, thus far the which it derived, could have insured the virtual monopoly on precursors of these proteins have been found only in bacteria the consumption of accumulations of organic material and co- (see: Larsen et al., 2009). uld have undergone symbiosis with cyanobacteria and unicellular algae to produce the lichens, pioneer organisms able to settle in terrestrial environments totally lacking other forms of Digression on primitive simplicity or simplicity life. Lastly, the oldest fungal fossil is dated to 1.25 Gyr while by regression of eumycetic fungi the oldest animal fossil is dated to about 0.6 Gyr (Fedonkin et al., 2007) Many authors believe that the cell of eumycetic fungi has the simplest organization among eukaryotes. Others are not explicit in this regard but do not raise objections. Neverthe- Phylogenetic and ecological relationships less, almost all cytologists reject the idea of the primitiveness between eumycetic fungi and red algae of this type of cell and maintain that the organizational and functional simplicity is due to regressive evolution from an- It is important to point out that almost all the presumed cestors close to the animal kingdom. simplifications and losses mentioned above are also found in Certainly, phenomena of regression have long been red algae, which instead are considered primitive by specia- known in parasitic animals. The most sensational case con- lists: absence of any form of motility and contractility, absen- cerns endoparasitic crustaceans of the genus Sacculina, which ce of gametes in the unicellular species, mitosis that occurs resemble fungi in their vegetative stage. However, these ani- within the nuclear envelope, etc. On the other hand, there is mals conserve the apparatus for crustacean morphogenesis in clear agreement in important details between fungi and red al- their genetic patrimony; in fact, simple nauplii hatch from the gae: for instance, in the filamentous multicellular forms of eggs and transform into cypridiform larvae, typical of the Cir- both taxa, the diaphragms that separate the cells have a hole ripedia. Less sensational cases of regression concern the Bran- that guarantees the flow of nutrients and the eventual passage chiura, crustacean ectoparasites of fishes, which conserve of materials and organelles; these holes differ only in name, only an uncertain affinity with the Copepoda. Other cases re- septal pores (dolipores) in fungi, p i t connections in gard the Pentastomida (derived from arthropods close to arac- red algae. The plugs of these holes also differ in name: V o- hnids), the Myzostomida (polychaete worms, parasites of ec- ronin bodies andpit plugs, even though they have the hinoderms), some molluscs and many insects. However, these same function: regulating the flow between two adjoining animals always conserve structural traits characteristic of the compartments and sealing the stumps if the filament breaks. family or order to which they belong. The same occurs for There are various forms of these plugs (fig. 4) (Rascio et al., Orobanche, Rafflesia and Cuscuta, genera of herbaceous 1991) but they do not help to distinguish the two taxa. There plants that are parasites of other plants. Among Protista, we is also a certain correspondence between the complicated thal- can cite the Oomycetes, relatives of the heterokont algae, li of red algae and the equally complicated fruit bodies of as- which became parasites of animals and higher plants; they comycetes and basidiomycetes, both formed by pseudotis- have a vegetative stage similar to the fungal mycelium but sues,i.e.a webof sometimes bifurcate filaments held toge- 804 Ï. Îìîäåî

vely, appeared toward 1.25 Gyr. Marine species of fungi are rare, mainly being «yeasts» that live in river mouths; their strong cell wall may have appeared as an adaptation to the va- rying osmolarity of that environment and then became a prea- daptation for subaerial habitats. On the basis of this evidence, the evolution of the eukaryotic cell can be divided into two successive steps. The first concerns the attainment of the typical structure of red algae and fungi; the second concerns the acquisition of mobility and contractility typical of protists. This distinction provides a better chronological arrangement and makes the evolution of the eukaryotic cell clearer and more plausible.

More proto-eukaryotes?

There is an order of algae, the Zygnematales or Conjuga- les, whose cells show some basic characters of the pro- to-eucells. They are enclosed in a mainly cellulosic wall, are devoid of motility and lack contractile vacuoles, even though they live in fresh water; they crawl by extending mucous thre- ads like some cyanobacteria. Unicellular Zygnematales have a symmetrical crescent or star-like form. Multicellular species form long chains that differ from fungal hyphae because the cells are not interconnected and detach from one another without damage. These algae produce enclosed in a two valves shell motionless gametes that conjugate, forming spheroidal zygotes (Fig. 5A); in multicellular ribbon-like species the pattern of conjugation is similar to that found in Zygomycetes. It is unknown whether they possess the histone H1. The most evident difference from proto-eukaryote species lies in the large cell size. Zygotes have a thick pluristratified wall, which in most species is decorated with equidistant thorns by means of ext- rusions through the pores. They remain quiescent on the bottom of the water body for many months before germinating. Fig. 4. Micrographs of a pit plugs in a red alga (courtesy of N. Ras- These zygotes are somewhat reminiscent of those of dinofla- cio; Rascio et al., 1991). gellates, but even more they resemble some Mesoproterozoic cw — cell wall, pc — pit connection. The high-resolution image shows the microfossils designated as acritarchs (fig. 5), particularly presence of long molecules, probably of actin, arranged palisade-like against the two concave surfaces. cysts named Tappania, Shuiyousphaerium, Appendisphaeri- um and Tanarium (see: Grey, 2007). ther by a mucilaginous matrix, which in some red algae can be impregnated with calcium carbonate. Functional organization More generally, we must note the complementarity of the of the proto-eukaryotic cell metabolic activities of the two groups. In early geological epochs, this complementarity would have created an environ- After ending the necessary digression on the systematic mental dynamics between photosynthetic red algae, which position and relatedness of the organisms that can be placed at transform CO2 into oxygen and organic carbon, and saprobic the base of the eukaryotic domain, I will describe the pro- fungi, which recycle dead material to produce CO2, which to-eukaryotic cell as it appears today. It has the typical euka- then supplies the red algae. This is a parallel situation to the ryotic nucleus whose envelope is provided with pores through one today involving the production of O2 and organic carbon which exchanges with the cytoplasm take place. The cytop- by algae and green plants and the oxidation of organic carbon lasm contains mitochondria with tubules instead of crests (Tay- by fungi and animals. lor, 1978) but otherwise they are no different from those fo- The relatedness of fungi and red algae has had impassio- und in the cells of more advanced taxa. The rhodoplasts in the ned and authoritative supporters (Dodge, 1914; Cain, 1962; most primitive unicellular forms (Cyanidium) conserve the Demoulin, 1985, and many others), whose ideas, however, peptidoglycan wall and resemble cyanelles, i. e. symbiotic cy- have had little support. Yet, this relatedness should be recon- anobacteria within animal tissues; in the slightly more evol- sidered by specialists since a mass of evidence speaks in its ved forms (Cyanophora), the rhodoplasts lack a wall and cy- favour and also in favour of the idea that the cell organization toplasm and their chromosome is small, while the photosyn- of both groups is primitive. The most interesting evidence inc- thetic apparatus remains the original one, provided with ludes palaeontological specimens from the Mesoproterozoic chlorophyll-a and the typical pigments phycobilin and phyco- period between 1.6 and 1.2 Gyr. Some species of acritarchs, erythrin; these are the pigments that give the entire cell the ty- dubitatively attributed to dinophycean algae, appeared in that pical red or purplish red colour. The chloroplasts of the Zyg- period, while Bangiomorpha and Eosaccharomyces, reliably nematales contain chlorophyll-a and -b and have unusual referred to advanced red algae and unicellular fungi respecti- forms: star-shaped, lobose, ribbon-shaped, helicoidal. In addi- Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 805

Fig. 5. Comparison between acritarchs and zygotes of Zygnematales. A — a young zygote of Micrasterias crux-melitensis, note the thickness of the cell wall; AR — ripe zygote after extrusion of spines (nearby the valves of gametes); B — acritarch without spines of Leiosphaeridia; C — Tanarium conoideum from the dell’Ediacariano; D — Tappania plana from the Mesoproterozoic, with spines; E — Shuiyousphaerium macroreticulatum from the Mesoproterozoic, note the thickness of the cell wall. (A, AR — from: Strasburger, 1978; B, D, E — from: Knoll et al., 2006; C — from: Fedonkin et al., 2007). tion to the organelles of endosymbiotic origin, there are Golgi it is difficult to decide if it exists. In the case of fungi, electron bodies, which in some fungi look like poorly differentiated glo- microscopy reveals that radially arranged filaments of actin bules; they acquire the appearance of superimposed flattened accumulate under the plasma membrane. We can presume that cisternae only in red algae, in the most evolved Eumycetes and these accumulations have a role in water absorption in in Zygnematales, an appearance they present in all other euka- the forms that live both on arid soil and symbiotic with algae ryotes. The endoplasmic reticulum is modestly developed and within lichens, even if water is present in minimal amounts; a often appears connected with the nuclear envelope. The cyto- similar role is played by fungi in mycorrhizae, to the advanta- plasm contains two types of reserve polysaccharides: glycogen ge of the plant symbiont. It should also be mentioned that in the fungal cell, floridean starch in the red algae. In both ca- many fungi live on organic materials that are highly osmolar ses, there are lipid drops that help the cell to float. or dry and thus not attacked by bacteria. Absent in the proto-eucell is phagocytosis, which gives the ability to completely exploit nutrient particles without having to secrete digestive enzymes outside the cell and recover Karyology of the proto-eukaryotic cell only part of the digested products. Hence, there are no alimen- tary vacuoles and the lysosomes that «collaborate» with them. The nucleus contains a nucleolus of globular, or discoid, Many symbiotic and predaceous fungi are provided with h a- shape, sometimes adhering to the nuclear envelope; this struc- ustoria, thin ramifications, sometimes finely divided, that ture, with no precedents in the procell, is the site of ribosome penetrate inside the cells of the prey, and inside the cells of assembly. In the proto-eucell, the ribosomes resemble those of plant roots in the case of mycorrhizae. archaea, have virtually the same size and are composed of a In these cells, there is a simple form of endocytosis (Bry- higher number of RNA filaments and protein molecules. They ant, Stevens; 1998) although pinocytosis isunknown and are extruded through the pores of the nuclear envelope and 806 Ï. Îìîäåî

Fig. 6. Three examples of Warnowiaceae, predatory dinoflagellates. lf — longitudinal flagellum, p — piston, rt f — transverse flagellum. Below — two orthogonal sections through the ocelloid of Nematodinium. The shape of the re- tinoid is shown in the centre; the short axis of the occelloid is directed toward the centre of the cell (from micrographies of Greuet, 1970). then «decorate» its external side; in addition, they become fi- two separate places of the nucleus has been described, follo- xed to the cisternae of the endoplasmic reticulum. wed by the entry of microtubules; reabsorption of the wall of The chromosomes adhere to the internal wall of the nucle- the invagination sacks allows the microtubules to establish the ar envelope by means of a special structure. They are numero- necessary relationships with the chromosome. In these cells, us and very small, almost invisible under the light microsco- discs or rings of electron-opaque material situated outside the pe; during mitosis, they condense to a small degree. The geno- poles of the nucleus appear during mitosis; they could be pre- me is small, especially in the «yeasts» and in the red algae cursors of the centrioles (Scott, Broadwater, 2005). Cyanidiophyceae: 14—47 Mbp (Zolan, 1995; Maruyama et The nuclear cycle is known only for red algae. It differs al., 2007), although the size can be even smaller in the para- from that of the most evolved eukaryotes because the G2 pha- sitic species. The chromosomes of Zygnematales are small, se is missing; thus, in these organisms, the bichromatid condi- condensed and apparently monochromatidic in vegetative tion of the chromosome is momentary while the monochro- haploid mitoses; they have a «diffuse» centromere (King, matid condition is stable (see below). In yeasts, the presence 1959). ofcohesin,the protein that binds the two chromatids at the Mitosis occurs without disappearance of the nuclear enve- centromere (Losada, 2007), suggests the existence of a G2 lope and nucleolus, and in rather varied modes with regard to phase, whereas the morphology and size of the chromosomes formation of the mitotic spindle since the tubulin and actin are (Zolan, 1995) suggest that this phase is missing. It is impor- synthesized and polymerized outside the nucleus (Powell, tant to note that two physiological functions, DNA duplication 1980; Dave, Godward, 1982; Maruyama et al., 2007). In pro- and cell division (cytodiaeresis), are simultaneous and to-eukaryotes, laceration or invagination of the envelope in connected in prokaryotes, but become temporally disjunct and Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 807 independent with the progress of evolution. This process is tablishes the diploid state ofthe chromosomes in the re- parallel to that of the uncoupling of transcription and translati- sulting cell, called a zygote.Meiosis then re-establishes, on of mRNA. It appears that the establishment of independent through two successive divisions, the haploid state ofthe control of the physiological functions was the winning evolu- chromosomes. Meiosis can intervene immediately after kary- tionary strategy. ogamy or after a more or less high number of mitotic divisions: in this way, the alternation of generations typical of red algae, and also of various protists and plants, appea- All clear on the evolution of the genome? red. Key events of this process (with many consequences for the fields of evolution and genetics) were exchanges, between Not exactly, since a peculiar group of protists, the dinofla- two different strains, of: 1) chromosomes; 2) portions of chro- gellates, half autotrophes and half heterotrophes, have unusu- mosomes thanks to crossing-over; 3) portions of genes, thanks ally structured DNA which presents some similarities with to intragenic crossing-over. bacterial DNA. For this reason, the group was given the name In basidiomycetes and zygomycetes, karyogamy is not mesokaryotes (Dodge, 1965); this name was later abandoned carried out by specialized gametes;thetwopartners are eit- in systematics but it would be opportune to preserve it to de- her equal cells with opposite signs (+, –) or nuclei of opposi- signate a very unusual type of cell. The term «dinokaryote» te signs present within the same cell. Things are the same in has been proposed for this type of cell but «mesokaryote» has unicellular red algae, but in multicellular ones the cells invol- priority. ved in karyogamy are differentiated, even if both are non-mo- In the nucleus of the mesokaryotic cell, the chromosomes tile: the male spermatia detach from the alga and are trans- conserve the condensed form typical of mitosis in the eucell ported passively until they meet t h e oospheres (egg (Chatton, 1920) and the coiling into superimposed discs (or cells), which intercept them by means of a projection covered into helices?) even during the interphase. These chromosomes with viscous material called the trichogyne. Even in the do not consist of chromatin since they lack nucleosomes, even Zygnematales, which show many characters of the lower though they contain a small quantity of a bacterial-type basic eukaryotes, two non-motile subequal cells with opposite signs HU protein (Rizzo, 1981, 1991; Wong et al., 2003; Hackett, fuse. Bhattacharya, 2006), and they divide in their own typical In proto-eukaryotic cells, meiosis takes place in a simpler manner (Bhaud et al., 2000). As regards the structure of the manner than in evolved eucells, since the nuclear envelope cell, we can say that it has two very different and characteris- does not break down and, as already mentioned, there are tic flagella, and sometimes achieves surprising complexity two plaques or two polar rings giving rise to micro- (fig. 6). The dinoflagellate cell has a layer of alveoli un- tubules in place of the centrosomes at the two poles of the derneath the plasma membrane which contain plaques of the nucleus (Heywood, Magee, 1976). Nevertheless, there are wall. For this reason, Cavalier-Smith (1991) placed these or- many cases in which these special structures are missing or ganisms in the kingdom of Alveolata along with the ciliates have not been identified. and apicomplexa, which present the same characteristic; this In addition, there are two variants indicating two different taxon has been justified by molecular phylogeny and it is usu- primitive conditions. The first was described for a red alga ally given the rank of phylum. (Dodge, 1973) in which karyogamy occurs between nuclei Most ancient dinoflagellates date to the Silurian and per- with monochromatid chromosomes; these chromosomes pair haps to the preceding period. Some acritarchs, unicellular or- and then separate in the first meiotic telophase. In the two ganisms that lived between 1600 and 400 Myr, resemble the haploid daughter cells, the S phase restores the dichromatid cysts of dinoflagellates but lack the sulci that host the flagella condition of the chromosomes; then the second meiotic divisi- in most dinoflagellate species. on follows, which consists of a normal mitosis producing mo- The mesokaryotic cell presents some archaic traits in mi- nochromatid chromosomes. tosis (Rajkov, 1978), in lipid composition of the plasma mem- The other variant concerns Saccharomyces, in which the brane, in the ribosomes, in the lack of introns, and controls its whole meiotic process takes place within the same nuclear en- water content through an organelle of a different type. Howe- velope. The first meiotic metaphase is simultaneous with the ver, the affinity of dinoflagellates with ciliates and apicomple- second one in the mother cell of the spores, which presents xa, albeit not very evident, suggests that they have not been a two parallel spindles; in the subsequent double telophase, four group divergent from all other eukaryotes from the beginning. haploid nuclei with monochromatid chromosomes are formed, It seems plausible that the karyological characteristics of the which will form four meiospores (Moens, Rapport, 1971; Gal- mesokaryotic cell appeared via a different mutual adaptation braith et al., 1997). of the host cell with endosymbionts, particularly with plastids To complete the discussion of the modes of meiosis, it (Chatton, 1920; Hackett et al., 2004; Hackett, Bhattacharya, should be mentioned that, in ascomycetes and basidiomyce- 2006). This idea agrees with the fact that, in some cells of tes, the meiotic divisions are always followed by ordinary mi- other protists and animals, histones can be temporarily (but tosis, and thus there are eight ascospores and basidiospores. not permanently) replaced by smaller basic protein molecules, as described for the nuclei of Acetabularia gametes and for the nuclei of sperms. The synaptonemal complex

The crucial event of meiosis takes place in the prophase, Sexuality in the lower eukaryotes in particular during the zygotene andpachytene stages when the synaptonemal complex, which sets in exact In the eumycetic fungi and red algae, sexuality appeared alignment particular DNA sequences of homologous chromo- in a completely new manner with respect to the prokaryotes. somes, is formed. The synaptonemal complex is a temporary First, there is karyogamy, the fusion of two nuclei belo- structure typical of meiosis; it appeared in the meiosis of nging to different individuals of the same species, which es- yeasts (Engels, Croes, 1968) and remained virtually unchan- 808 Ï. Îìîäåî

Fig. 7. Synaptonemal complex. A — the synaptonemal complex that links homologous chromosomes of the eukaryotic cell during the diplotene and pachytene stages of meiosis, at it appears under the electron microscope; B — the current interpretation; C — how the synaptonemal complex could be structured if alignment of the homologous loci is medi- ated by repressor molecules, which in addition to recognizing the respective DNA sequences also recognize each other (from: Omodeo, 1994; redrawn). ged throughout the evolutionary history of the eukaryotic cell. This complex, easily identifiable by transmission electron The complex consists o f transverse filaments and a microscopy, reveals the existence of meiosis and thus proces- central element,sometimes double. Each transverse fila- ses of sexuality in taxa (Euglenophyta, for example) in which ment is linked by one end to a predetermined tract of a chro- sexuality have not been demonstrated by classic methods (He- mosome, while the other end meets (at the height of the cent- ywood, Magee, 1976). Various auxiliary proteins are known ral element) the terminal part of the corresponding filament, in the synaptonemal complex (some related to cros- which in turn is linked to the same tract of the homologous sing-over), but there has been no research to establish chromosome (fig. 7). which molecules recognize corresponding sequences of ho- Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 809 mologous chromosomes and how they interact to form a brid- that genetic engineering created a bacterial strain that acqui- ge between the two chromosomes. red the gene to produce human haemoglobin. I (Omodeo, 1994) have hypothesized that the transverse From the evolutionary point of view, transformation pro- filaments are molecules of the regulatory proteins discussed duces the so-called horizontal gene transfer, which on p. 8; one end of these proteins would recognize opera- renders the borders of bacterial species fluctuating and indistinct, tor genes, while the proteins would recognize each other at the and ensures that evolution proceeds not only in a descending other end (at the height of the central element). This hypothe- line, as one would expect, but also in a «horizontal» direction. sis, testable via molecular studies, has the advantage of clari- The processes of sexuality in eukaryotes exclude horizon- fying the evolutionary process by referring to pre-existing tal gene transfer by the modes described for bacteria and ar- molecules known in prokaryotes and already endowed with chaea, and thus species boundaries are clearer. However, the appropriate capabilities. Moreover, it is supported by the many primitive eukaryotic cells reiterated endosymbiosis with fact that meiosis, and with it the formation of the synaptone- other cells, even those that were distant systematically and of mal complex, is triggered in the lower eukaryotes by cell star- different types. There are many examples of this and of the vation, which inhibits transcription. consequent appearance of chimeras.Inthe case of Eugle- Therefore, the evolution of meiosis would have been initi- nophyta, dinoflagellates and other photosynthetic cells, it has ated by the quiescence triggered by starvation, during which been demonstrated that chloroplasts containing chlorophyll-a the structural genes were blocked by regulatory proteins; the and -b derived from endosymbiotic eukaryotic cells (Gibbs, regulatory proteins were joined in the course of evolution by 1981) that lost part of their eukaryotic genome to the advanta- other proteins that caused crossing-over and presided over the ge of the host cell but not their plasma membrane; thus, s e- other functions of meiosis. condary plastids are enveloped by three or four memb- ranes. In the case of cryptomonads, it is presumed that the plastids (rhodoplasts) derived from an endosymbiotic red alga Parasexuality provided with chlorophyll-a and phycobilisomes, which preserved a rudimentary nucleus with three chromosomes, called Parasexuality has been described by Pontecorvo a nucleomorph (Gillot, Gibbs, 1980); the same would (Pontecorvo et al., 1953) in Aspergillus, a mould belonging to have occurred for Chlorarachnium, an amoeba provided with the phylum Ascomycota. The process begins in a cell pro- flagella whose chloroplasts, containing chlorophyll-a and -b, vided with two nuclei of opposite signs (dikaryon)that ori- also preserved a nucleomorph with three chromosomes deri- ginated by the fusion of two adjoining hyphae. After a certa- ved not from a red alga but from an endosymbiotic green alga in number of synchronous divisions, these nuclei fuse (karyo- (Ludwig, Gibbs, 1987, 1989). Despite the different origins of gamy) giving rise to a zygote nucleus (with diploid number the endosymbiotic cells, the evolution of nucleomorphs was of chromosomes). During the following divisions, it may oc- surprisingly parallel, not only in terms of the form and number cur (but with low frequency) that two homologous chromoso- of chromosomes but in terms of the genes that preceded the mes exchange corresponding portions via a process called telomeres (2008). I will also mention the well-known case of mitotic crossing-over.Inthe subsequent mitoses, the the dinoflagellates Peridinium balticum and Kryptoperidini- diploid nuclei gradually lose a whole set of chromosomes um foliaceum: close to their nucleus containing their chroma- so that haploid cells provided with a new assortment of tin, they possess a second nucleus containing standard chro- gene alleles appear, as occurs in the more complex process of matin, perhaps deriving from an endosymbiotic golden alga meiosis. (Dodge, Bibby, 1973). Finally, I will cite the fungi of mycor- In Aspergillus and saccharomycetes, parasexuality alter- rhizae (Glomeraceae), which host two different types of bac- nates with the true sexuality discussed previously; it has also teria (Scannerini, Bonfante-Fasolo, 1990, 1991). This is of been recorded in various «imperfect» fungi, i. e. in species for great interest because it documents that endosymbiosis also which true sexuality is not known. For this reason and in light occurred in non-phagotrophic cells provided with a wall, a of the previous remarks on the primitiveness of the fungal fact that to some degree reduces the perplexity of Esser and cell, it can be hypothesized that parasexuality is the most pri- collaborators (Esser et al., 2004) regarding the presence of mitive manifestation of sexuality in eukaryotes. This is testab- many bacterial genes in the genome of yeasts, presumably ac- le by an examination of the molecules that trigger karyogamy quired by repeated horizontal transfer events. and of those that cause the gradual elimination of an entire The summation of two different genomes occurring seve- chromosomal set. ral times in such chimeras has generated progeny whose evolutionary history is difficult to unravel. The most detailed research on the topic concerns the cell of Apicomplexa, para- Endosymbiosis and «horizontal gene transfer» sitic protozoa provided with an organelle termed the apical complex or also apicoplast because it evolved from a Let us return to the prokaryotes, in which different me- plastid that conserved a minichromosome (of 35 Kbp in Plas- chanisms for the exchange of hereditary material between modium falciparum). Huang and Kissinger (2008) were able cells have been identified; these mechanisms represent forms to reconstruct part of the complicated history using the tools of sexuality, the best known being conjugation, trans- of molecular biology. duction andtransformation.Without entering into details, we can say that transformation is the process by which a procell takes in more or less long DNA sequences that are free The passage from proto-eukaryotic in the environment; these sequences replace the homologous cell to eukaryotic cell ones or are added to the other sequences in the genome. In this way, procells can acquire genes of different organisms (even The evolution from proto-eucell to eucell was primarily taxonomically distant ones) and can begin producing the cor- marked by the appearance of cytoplasmic contractility and responding proteins. For instance, it was via transformation structures for locomotion. It also involved an increase of ge- 810 Ï. Îìîäåî nome size and thus cell complexity, especially in relation to this anomaly as due to regression. Nevertheless, we should sensory structures and the respective behavioural programs. not be surprised since there is only a reason for motility if it is Mitosis and meiosis remained fairly uniform in the various controlled, otherwise it is a dangerous waste. And control is protist taxa, with the exception of Lobosea and Chlorophyta in only possible if there are adequate sensors. In effect, the pro- which there were modifications that foreshadowed the tists, assumed to have appeared not long after the proto-euka- well-known situation in animals and plants: mitosis with di- ryotes, are all provided (sometimes extravagantly) with or- sappearance of the nuclear envelope and nucleolus, and fema- gans for locomotion and sensors that regulate the taxes,es- le meiosis that produces one cell rich in reserves and three pecially phototaxis andchemotaxis.The receptors for cells without them and thus sterile. Multicellular or multinuc- chemotaxis are not identifiable and may be located in diffe- lear structures appeared in the biological cycle of photosyn- rent cell sites, but the behaviour of approaching a pheromone thetic protists, rather small in the case of palmellae but also of source or escaping from a noxious chemical is often easily ob- enormous size; indeed, tissues and organs, like those that ap- servable and has been described many times. peared in animals and plants, became differentiated in some photosynthetic protists. It is difficult to follow the evolutionary lineages of the The flagellar apparatus of the eukaryotic cell protist cell because of the many evolutionary trends and the complexity the cell could reach because of frequent and vari- The structure of the flagellum is well known in eucells, ed processes of endosymbiosis. For this reason, I will mainly and I will briefly describe it to discuss its evolution. The fla- discuss the evolution of contractility and motility, together gellum has a circular section. It is covered externally by the with the developments of the sensory apparatus that accompa- plasma membrane while internally it contains the axoneme, nied them. I will conclude by dealing with the appearance and formed by nine pairs of microtubules arranged around two evolutionary trend of apoptosis. central tubules and connected to them by nine radial spokes. Connecting the external pairs are large molecules of dynein, which in cross section appear to form an outer and an inner Support of the cell in the Protista arm. Dynein has ATPase activity, i. e. it releases «quanta» of I have already discussed the support of the proto-eukaryo- energy that produce the reciprocal sliding of microtubule pa- tic cell. This support becomes different in the much larger irs, which, being linked together, cause the whole structure to cells of the evolved Protista. In Chlamydomonas and related bend. The motion is propagated in various ways from the base genera, the cell is contained in a thin cellulosic shell open at toward the apex. The molecular structure of the flagellum ap- the anterior apex where the flagella emerge. In Euglenophyta, pears to be a very complex propulsive machine and the comp- Ciliata and some minor groups, the external shell is replaced lexity seems even greater when we consider how the machine by a rather robust protein pellicle situated below the plasma is supplied during its construction, maintenance and ope- membrane. In Euglenophyta, this pellicle is formed by struc- ration. In fact, the thin space between the axoneme and plas- tural modules that produce the helical architecture of the cell. ma membrane contains an apparatus (a kind of conveyor belt) In Ciliata, the pellicle gives support to the innumerable «cilia» that provides for the transport of tubulin dimers toward the covering these organisms. In amoeboid protists, there is inter- apex of the flagellum or in the opposite direction during the nal support formed by cylinders of tubulin and long filaments lengthening or shortening of the flagellum. The transport of of actin that shorten or lengthen to support the varied and un- ATP occurs in a similar way, as does the reverse transport of certain morphology of the cells. ADP, which forms when ATP has released the energy it trans- Other protists exhibit the most extraordinary bloom of ports. structures giving support and protection to the cell. The test of The flagellum is always inserted on a centriole (or some Sarcodina Filosea and the central capsule of Heliozoea basal body)shaped like a short cylinder formed by a crown are made of chitin; Heliozoea are provided with radial spicula of nine triplets of microtubules. The function of the centriole made of silica or of strontium sulphate; Foraminifera have a is debated but it would not be wrong to believe that it promo- mineralized calcareous test, while Radiolaria and diatoms are tes and governs the formation and growth of the axoneme, and provided, respectively, with a silica skeleton or with a «frustu- that it also regulates the length of the flagellum in relation to le», namely a silicate shell of admirable architecture. A trace the viscosity of the medium in which it acts. The centriole of these many extraordinary solutions remains only in spon- may also help to equalize the length of the flagella of cells ges. with two of them operating in synchrony. In these cells, in In no case is the cell of protists completely enclosed by an fact, if one flagellum breaks off, the other shortens to the inextensible wall; hence, the water content of the cell is alwa- length of the one with which it cooperates, after which they ys actively regulated by pulsating vacuoles orbypul- both grow to the optimal length. sules inthe case of dinoflagellates. In eukaryotic cells, the centriole is usually duplicated at each mitosis, but in algal cells the centriole can appear and di- sappear according to the phases of the biological cycle. In the The apparatus for motility and the taxes less evolved gymnosperms (cycads, Ginkgo), centrioles and flagella appear only in the male gametes; they are lacking The proteins tubulin, dynein and actin are present in the completely in the other gymnosperms and in angiosperms. In nucleus of the proto-eucell, where they control the transfer of animal cells, the centriole, wrapped in a protein matrix, forms chromatids during mitosis as well as cytodiaeresis at the cell thecentrosome,which participates in the formation of the equator (Yamamoto, Hiraoka, 2003); actin also is present and mitotic spindle; however, when it acts as a basal body, it appe- perhaps myosin. It seems strange, even incredible, that the ars the same as the others. functions corresponding to these molecules, i. e. contractility and motility, did not appear. We could be tempted to interpret Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 811

Hypothesis on the origin of the flagellum spectrum and endowed with less specialized metabolic resour- ces. However, although it may be correct to classify chytrids There has been much discussion on the origin of the fla- with the fungi, it must be clear that their evolutionary level is gellum and its evolution. Respecting the principle of economy exactly that of protists: they are motile, they produce gametes of hypotheses, we can conjecture that it derived from structu- attracted by pheromones, and some species exhibit photo- res like the mitotic spindle, which forms outside the nuclear accumulation.Infact, Phlyctochytrium possesses a struc- envelope in protists. Duplication of the spindle could have gi- ture that can be interpreted as a photoreceptor organelle (Ka- ven rise to the structures called axostyles, bundles of mic- zama, 1972) (fig. 8). rotubules alternating with dynein molecules that are part of Cytoplasmic contractility is not evident in chytrids, but it the cytoskeleton of the polymastigine protists and also of likely exists and regulates some activities of the cell. some others. The microtubules of the axostyle can slide past one another, shortening or lengthening the cell body, and they can also protrude from it. The axostyle could have evolved The acquisition of cytoplasmic contractility into the axoneme, acquiring the singular morphology summa- rized by the formula9+2.This formula seems to have been In all other protists, the water content is controlled by determined by reasons of spatial economy and energy output; rhythmic contractions of the pulsating vacuole, and it is the critical event would have been the fusion of the external known that the actin/myosin couple is involved in the cytodia- pairs of tubules. However, this formula is not the only one fo- eresis, i. e. constriction of the cytoplasm that separates the da- und in protists. For example, in the small cells of coccidia (pa- ughter cells during the telophase. This is easily seen when rasitic protists), the flagella are thinner and with formula freshwater protists treated with cytochalasin B, a substance 6 + 2, perhaps to adapt the mass of the flagellum to the small that inhibits the actin/myosin interaction, are observed under size of the cell. There are also very many variations of its the microscope: the pulsating vacuoles cease functioning im- structure in animal spermatozoa, especially in arthropods. mediately and with them the control of the water content of It is more difficult to understand the origin of the basal the cell, which swells until it bursts. Cytodiaeresis also halts body and its particular functions. and sister cells become monstrously attached to one another because the constricting ring, which completes the division of the cytoplasm after mitosis, has not functioned. Phagocytosis Chytrids, the first cells provided with a flagellum also stops, but this is difficult to observe. It should be noted that the presence of flagella in aquatic The most primitive cell with a flagellum is that of the protists requires the action of contractile vacuoles. Since the chytrids (or Chytridiomycota), saprobic, symbiotic or parasi- surface of the flagellum cannot be covered by impermeable tic organisms. They possess a single posterior flagellum, two material which would reduce its mechanical output, water en- in the zygote, or more than two, as in Neocallimastix and rela- ters and leaves through its membrane. The same holds for ted genera. (The number of flagella has been given too much freshwater amoebae, even when their body is protected by a importance in phylogeny: it is very likely that this number is shell, since at least part of the cell membrane must remain free correlated to the mass to be propelled or pulled and to the re- to contact the substratum. sistance of the medium. In smaller cells, one flagellum is suf- Regulation of the trajectories involved in taxes is only po- ficient but in larger ones two flagella may not be enough. Fla- ssible if the system is provided with sensors that perceive the gella that pull the cell are anchored to the interior by minuscu- appropriate signals and is able to analyse their intensity varia- le radicles often attached to the nuclear envelope.) tions. In more general terms, movement is made possible if Neocallimastix and related genera live as symbionts in the ru- the system, be it a missile or a spermatozoon, is endowed with men of artiodactyls, an oxygen-free environment, where they a taxis, with an elementary behavioural program that directs it digest cellulose. They lack true mitochondria, which have to the target, be it a ship or an oocyte. evolved into hydrogenosomes that release H2. The H2 is used by methanogenic archaeans that live with them to synthesize CH4. The ruminant frees itself from this gas by bel- Evolution of the flagellar apparatus ching. Such evolution of mitochondria involved the loss of the usual metabolic functions and also the loss of their whole ge- From a condition more or less corresponding to that of the nome. chytrids and the male gametes of diatoms, the flagellar appa- Chytrids present some biochemical features that are unu- ratus evolved in protists along two divergent paths. On the one sual in protists: 1) presence of chitin (and also cellulose) in the hand, the cells acquired two identical flagella acting in perfect cell wall; 2) a particular mode of synthesis of the amino acid symmetry, like the arms of a man swimming the «butterfly» lysine; 3) glycogen as reserve. Because of these characteris- or «breaststroke». This type of cell has been given the name tics, it has been proposed that they be included in the kingdom isokont.Ontheother hand, cells acquired two feathery fla- of fungi, together with ascomycetes, basidiomycetes and zy- gella that are slightly or very different and act in a comple- gomycetes which present the same characteristics: the propo- mentary way: one drags the cell, the other makes it swim, so sal has been supported by molecular phylogeny (Bowman et that it «spins» through the water. This type of cell has been gi- al., 1992). To this, we can add that their biological cycle has ven the name heterokont (fig. 9). similarities with that of some red algae and that mitosis occurs The path followed by the heterokont cell did not require in a very similar manner to that of fungi sensu stricto equality and synchronization of the two flagella, but needed (Dave, Godward, 1982). the presence along the flagella of short rigid hairs called Evidence against the primitiveness of chytrids comes mastigonemes. These hairs are synthesized in the Golgi from the fact that they live in fresh water and that many of apparatus and released to the exterior where they become po- them are symbionts or parasites of higher plants or animals. sitioned at fixed places on the membrane covering the flagel- They could be the survivors of a group with vast ecological lum. According to an idea mentioned also by Grell (1973), the 812 Ï. Îìîäåî

Fig. 8. The zoospore of chytrids has a single flagellum lacking mastigonemes and a complicated phototactic apparatus formed by a lipid drop acting as a lens, a rumposome and a mass of electron-opaque material (from electron microphotographs of Kazama, 1972). mastigonemes reverse the direction of the motion that the fla- of either flagellum is cut off, the cell proceeds in a circular path gellum, in their absence, would impart on the cell. In the hete- until the undamaged flagellum shortens to the length of the am- rokont cell, the photoreceptor is always situated at the base of putated one, after which both flagella grow to the optimal one flagellum. length. The basal bodies, are anchored to the cytoplasm by me- The evolutionary path followed by the isokont cell invol- ans of radicles that sometimes fuse with the nuclear envelope. ved perfect isochrony and synergy of the two flagella. If part Isokont cells can reverse the direction of flagellar beating, and thus move backward. Their stigma is situated laterally. In isokont cells, when the cell mass to be pulled is very light and (or) the viscosity of medium is low, the flagella can become thinner, losing three of the nine peripheral doublets and reducing the formula as previously mentioned. If the cell mass increases, the number of flagellar pairs doubles or trip- les. This does not occur in heterokont cells, in which motility is exclusive to small vegetative cells, gametes and propagules.

The flagellar and phototactic apparatuses

Knowledge of the phototactic apparatus of protists helps us interpret the evolutionary processes that led photoautotrophic cells and some of their predator descendants to a high level of complexity. All photosynthetic protists present a motile unicellular stage (which can be of a vegetative cell, propagule or gamete) and this stage is always provided with a phototactic apparatus. In the motile cells of Chromophyta (brown algae), Euglenophyta and Eustigmophyta, this apparatus is Fig. 9. In the isokont cell (A), the particular movement of the two composed of the following elements: 1) a sensor consisting of flagella drags the cell forward, but when necessary can push it a small mass of photopigment, rhodopsin in Euglena (Gualtie- backward. In the heterokont cell (B), the motion of the major flagellum, thanks to the presence of mastigonemes, drags the cell for- ri et al., 1989), sometimes stratified or divided, visible under ward, while the minor flagellum does not contribute to cell move- the electron microscope, always situated at the base of one of ment. the two flagella; 2) a screen formed by drops of bright red ca- Âåëè÷àéøèé ýâîëþöèîííûé ñêà÷îê: ðåñòðóêòóðèçàöèÿ ãåíîìà 813

Fig. 10. Phototactic apparatus of motile photoautotrophic cells. Above — three cells (zoospores of Xanthophyceae and Phaeophyceae) in which the photoreceptor is on the minor flagellum lacking mastigonemes and the stigma (cup of dicarotenoid globules) is in the plastid; below — similar situation in the gametes of two Chrysophyceae. Detail of the relationships among the photoreceptor (grey), cell membrane and stigma: note the broad contact between photoreceptor and membrane and the thin cleft, here interpreted as a «synaptic cleft». rotenoids in front of the sensor, called the stigma,described ments, the mastigonemes, only one of which moves the for various unicellular algae by Ehrenberg (1838), which can cell while the other imparts a rotating motion or acts as a rud- be within a chloroplast or outside it; 3) a thin cleft (filled with der or is reduced to a stump supporting the photoreceptor ambient water) separating a rather large surface of cell memb- (Piccinni, Omodeo, 1975; Omodeo, 1980). rane from the membrane covering the sensor, which functions The relationships between stigma and chloroplasts and asanautosynapsis;4)twoflagella covered with thin fila- between sensor and flagella vary from taxon to taxon, but the 814 Ï. 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ÂÅËÈ×ÀÉØÈÉ ÝÂÎËÞÖÈÎÍÍÛÉ ÑÊÀ×ÎÊ: ÐÅÑÒÐÓÊÒÓÐÈÇÀÖÈß ÃÅÍÎÌÀ È ÍÅÊÎÒÎÐÛÅ ÂÛÂÎÄÛ

Ï. Îìîäåî

Îòäåë íàóê îá îêðóæàþùåé ñðåäå Ñèåíñêîãî óíèâåðñèòåòà, Èòàëèÿ; ýëåêòðîííûé àäðåñ: [email protected]

Â ñòàòüå èññëåäóåòñÿ ýâîëþöèÿ êëåòêè äî óðîâíÿ ñëîæíîñòè, ïðèîáðåòåííîãî ïðîñòåéøèìè. Îñîáîå âíèìàíèå óäåëÿåòñÿ è âîïðîñó î òîì, ïî÷åìó ãåíîì ïðîêàðèîò îñòàåòñÿ ñòîëü ìàëûì áîëåå ÷åì 3 ìëðä ëåò è áîëåå 3 òðëí ïîêîëåíèé. Îãðàíè÷åíèå ýâîëþöèè èõ ãåíîìà ìîæåò áûòü ñâÿçàíî â îñíîâíîì ñ òåì, ÷òî ïîâòîðû íóêëåîòèäíûõ ïîñëåäîâàòåëüíîñòåé äëèííåå 12—15 ï. î. çàïðåùåíû ñîãëàñíî ïðèíöèïó Òîìàñà, è ñ òåì, ÷òî öåíà êîíòðîëÿ ýêñïðåññèè ãåíîâ ñ ïîìîùüþ ðåãóëÿòîðíûõ áåëêîâ âûñîêà: ýòà öåíà âîçðàñòàåò ýêñïîíåíöèàëüíî ñ óäëèíåíèåì õðîìîñîì. Ôîðìèðîâàíèå õðîìàòèíà, ò. å. óïàêîâêà ÄÍÊ âî- êðóã íóêëåîñîì, ñíÿëî ýòè îãðàíè÷åíèÿ è ïîçâîëèëî óâåëè÷èâàòü ãåíîì è îñîáåííî èçáûòî÷íûå ïîñëå- äîâàòåëüíîñòè ÄÍÊ, ðîëü êîòîðûõ îáñóæäàåòñÿ. Ïðåîáðàçîâàíèå è ðîñò ãåíîìà ïîðîäèëè òåíäåíöèþ ê ðàçäåëåíèþ ðàçëè÷íûõ ôèçèîëîãè÷åñêèõ ôóíêöèéèêèõêîíòðîëþ. Îáðàçîâàíèå ÿäåðíîé îáîëî÷êè, âîç- ìîæíî, íà÷àëîñü ñ ïðèõîäîì ìèòîçà, êîòîðûé çàìåíèë ñîáîé ïðîñòîé, íî õðóïêèé ìåõàíèçì âûòàëêèâà- íèÿ íîâîîáðàçîâàííîé ÄÍÊ â äî÷åðíèå ïðîêàðèîòè÷åñêèå êëåòêè. Óâåëè÷åíèå êîíöåíòðàöèè O2 â âîäå ñòèìóëèðîâàëî äàëüíåéøåå ðàçâèòèå: íîâàÿ êëåòêà îáðàçîâàëà ñèìáèîç ñ áàêòåðèÿìè, ñïîñîáíûìè çàùè- òèòü îò ïåðîêñèäîâ è îñóùåñòâëÿòü àýðîáíîå äûõàíèå. Ïîâûøåííàÿ êîíöåíòðàöèÿ O2 ïðèâåëà òàêæå ê ïðîèçâîäñòâó ñòåðèíîâ, êîòîðûå ñòàëè âàæíûì êîìïîíåíòîì êëåòî÷íûõ ìåìáðàí. Âçàèìíàÿ àäàïòàöèÿ êëåòîê, ïðèíàäëåæàùèõ ê ðàçíûì äîìåíàì, âûçâàëà äàëüíåéøèå èçìåíåíèÿ, ïðèâåäøèå ê âîçíèêíîâå- íèþ ïðîòîýóêàðèîòè÷åñêèõ êëåòîê è ñïîñîáñòâîâàâøèå ñîçäàíèþ íîâûõ ñèìáèîçîâ ñ ôîòîñèíòåòè÷åñêè- ìè öèàíîáàêòåðèÿìè. Ïðîòîýóêàðèîòè÷åñêèå êëåòêè áûëè ëèøåíû ïîäâèæíîñòè è ñîêðàòèìîñòè, êàê è êëåòêè ñîâðåìåííûõ êðàñíûõ âîäîðîñëåé, ãðèáîâ è Zygnematales. Îáå ýòè ñïîñîáíîñòè ðàçâèëèñü, êîãäà ïðîñòåéøàÿ ýóêàðèîòè÷åñêàÿ êëåòêà ïðèîáðåëà æãóòèêè è ñîêðàòèìîñòü öèòîïëàçìû, à òàêæå ñåíñîðû, ÷òîáû èìè óïðàâëÿòü. Êëþ÷åâûå ñëîâà: ýâîëþöèÿ êëåòêè, ýâîëþöèÿ ãåíîìà, îãðàíè÷åíèÿ ðàçìåðà ãåíîìà, èçáûòî÷íàÿ ÄÍÊ, ïðîòîýóêàðèîòû, ïîäâèæíîñòü è ñåíñîðû ïðîñòåéøèõ.