Life began with RNA

Nucleic acid research is one of the hot spots in biology. Due to the unique properties of RNA, they are increasingly being used in medicine and technology. But so far only a narrow circle of specialists knows about it.

Ribonucleic acid, otherwise - RNA - out of luck. It is not as widely known as its close "relative" - ​​DNA, despite the great chemical similarity. However, the discoveries of the last twenty years have radically changed our views on the role and function of these, as it turned out, very "skillful" molecules. The fruit of these discoveries was a fundamentally new idea that modern life was preceded by a completely self-sufficient ancient “RNA world”.

As it usually happens, new knowledge, expanding the horizon, gave rise to a lot of new questions. What were the mechanisms of "evolution" in the RNA world? Why, where and how did DNA and proteins appear? How did the transition from the "RNA world" to the modern world happen? Academician Valentin Viktorovich Vlasov and his son, Candidate of Chemical Sciences, Alexander Vlasov, tell readers about the searches being carried out in this direction.

Why does a series of articles devoted to the problem of the origin of life include an article about RNA, and not about other, more well-known organic molecules - DNA or proteins? Perhaps our readers have heard about RNA, but what? We are sure nothing remarkable - for one simple reason: so far only biologists know that it is RNA that is the "magic" molecules that gave rise to life. That once in antiquity, on a freshly cooled Earth, a mysterious "world of RNA" arose and existed...

Before heading to the "beginning of beginnings", let's stock up on the necessary knowledge about the structure of nucleic acids - DNA(deoxyribonucleic) and RNA (ribonucleic). In terms of its chemical composition, RNA is a twin, although not a complete twin, of DNA, the main keeper of genetic information in a living cell. Nucleic acids are polymeric macromolecules consisting of individual units - nucleotides. The skeleton of a macromolecule is a five-carbon sugar molecule connected by phosphoric acid residues. One nitrogenous base is attached to each sugar molecule. Nucleotides that differ from each other only by different nitrogenous bases are designated by the letters A, U, G, C (in RNA) and A, T, G, C (in DNA).

To be honest, no one thought about RNA for many years. There was a dogma that there is a cell, there are chromosomes in which there is DNA - the keeper of genetic information.
Eventually, proteins are synthesized on ribosomes. And RNA - it is somewhere in between, a carrier of information from DNA - and nothing more. And then discoveries rained down that made us look at RNA in a completely different way. The main difference between nucleic acids is their carbohydrate component. In RNA, the sugar is ribose, and in DNA, it is deoxyribose: where DNA has a hydrogen atom (H), RNA has an hydroxy group (OH). The results of such insignificant, to the untrained eye, differences are striking. So, DNA exists mainly in the form of well-known rigid helices, in which two strands of DNA are held together by the formation of hydrogen bonds between complementary nucleotides.

RNAs can also form double-stranded helices similar to those of DNA, but in most cases RNAs exist in complex coiled structures. These structures are formed not only due to the formation of the mentioned hydrogen bonds between different RNA regions, but also due to the ribose hydroxy group, which can form additional hydrogen bonds and interact with phosphoric acid and metal ions. The globular structures of RNA not only outwardly resemble protein structures, but also approach them in properties: they can interact with a wide variety of molecules, both small and polymeric.

Who is considered "Alive"?

Why do we call RNA the foremother of currently existing life? To answer this question, let's figure out where the border between living and non-living is.

Since scientists from different fields are working on the problem of the origin of life, each operates in terms of a science close to him. Chemists will definitely remember the word "catalyst", mathematicians - "information". Biologists will consider alive a system containing a substance (genetic program) that can be copied (or, in a simple way, multiply). At the same time, it is necessary that in the course of such copying some changes in hereditary information can occur and new variants of systems arise, i.e., there must be a possibility evolution. Biologists will also notice that such systems must be spatially isolated. Otherwise, the more advanced systems that have emerged will not be able to take advantage of their benefits, since their more efficient catalysts and other products will “float away” into the environment without hindrance.

How, then, were the first molecular systems isolated from the environment? Colonies of molecules could, for example, be held together by adsorption on some mineral surface or dust particles. However, it is possible that already the most primitive systems, like modern living cells, had a real membrane sheath. The fact is that such a “protocell” with a lipid membrane can be formed very simply. Many molecules with charged groups (for example, fatty acids) form microscopic bubbles in the aquatic environment - liposomes. This word should be well known to the beautiful half of our readers: liposomes are widely used in cosmetic creams - tiny fatty capsules are stuffed with vitamins and other biologically active substances. But what were the ancient "protocells" filled with? It turned out that it is RNA that claims to be the “stuffing”.

RNA can do everything?

Life, no doubt, had to begin with the formation of "skillful" molecules that could reproduce themselves and perform all the other "household work" necessary for the existence of the cell. However, neither DNA nor protein is suitable for the role of such craftsmen. DNA is an excellent store of genetic information, but it cannot reproduce itself. Proteins are unsurpassed catalysts, but cannot work as "genetic programs". A chicken-and-egg paradox arises: DNA cannot form without protein, and protein cannot form without DNA. And only RNA, as it turned out, can do EVERYTHING. But let's not get ahead of ourselves.

Let us consider the long-known functions of RNA related to work ( expression) gene in the cell. When a gene is switched on, local DNA unwinding first occurs and an RNA copy of the genetic program is synthesized. As a result of complex processing with its special proteins, matrix RNA is obtained ( mRNA), which is the program for protein synthesis. This RNA is transferred from the nucleus to the cytoplasm of the cell, where it binds to special cellular structures - ribosomes, true molecular "machines" for protein synthesis. Protein is synthesized from activated amino acids attached to specific transfer RNAs (tRNAs), with each amino acid attached to its own specific tRNA. Thanks to tRNA, the amino acid is fixed in the catalytic center of the ribosome, where it is "sewn" to the synthesized protein chain. It can be seen from the considered sequence of events that RNA molecules play a key role in the decoding of genetic information and protein biosynthesis.

The more we delved into the study of various biosynthetic processes, the more often we discovered previously unknown functions of RNA. It turned out that in addition to the process transcriptions(RNA synthesis by copying a section of DNA) in some cases, on the contrary, DNA synthesis on RNA templates can occur. This process, called reverse transcription, use many viruses in their development, including the infamous oncogenic viruses and HIV-1, which causes AIDS.

Thus, it turned out that the flow of genetic information is not, as originally thought, unidirectional - from DNA to RNA. The role of DNA as originally the main carrier of genetic information began to be questioned. Moreover, many viruses (influenza, tick-borne encephalitis, and others) do not use DNA as a genetic material at all, their genome is built exclusively from RNA. And then, one after another, discoveries rained down that made us look at RNA in a completely different way.

On All "Molecules" Master

Most surprising was the discovery of the catalytic ability of RNA. Previously, it was thought that only proteins and enzymes could catalyze reactions. Scientists, for example, could not isolate the enzymes that cut and crosslink some RNA. After lengthy research, it turned out that RNAs do a great job of doing this on their own. RNA structures that act like enzymes are called ribozymes(by analogy with enzymes, catalytic proteins). A wide variety of ribozymes were soon discovered. They are especially widely used to manipulate their RNA by viruses and other simple infectious agents. Thus, RNAs turned out to be jacks of all trades: they can act as carriers of hereditary information, they can serve as catalysts, vehicles for amino acids, and form highly specific complexes with proteins.

The final confidence that the “RNA world” really existed came after the details of the structure of ribosome crystals were revealed by X-ray diffraction analysis. Scientists hoped to find there a protein that catalyzes the crosslinking of amino acids into a protein sequence. Imagine their surprise when it turned out that there are no protein structures in the catalytic center of ribosomes at all, that it is completely built from RNA! It turned out that all key stages of protein biosynthesis are carried out by RNA molecules. The point in the discussion about the possibility of the existence of the "RNA world" as a special stage of biological evolution was set.

Of course, the full picture has yet to be reconstructed - there are many unresolved issues. For example, in a modern cell, the activation of amino acids and their attachment to the corresponding tRNAs is carried out by specific enzyme proteins. Questions arise: could this reaction be carried out without the participation of proteins, only with the help of RNA? Could RNAs themselves catalyze the synthesis of RNA from nucleotides or the addition of nitrogenous bases to sugar? In general, after the discovery of ribozymes, such potential abilities of RNA were no longer in doubt. But science requires that hypotheses be experimentally verified.

Darwinian Evolution in Vitro

A good method often allows for a revolution in science. The same can be said about the method polymerase chain reaction (PCR), which allows you to multiply nucleic acids in unlimited quantities. Let us briefly describe the essence of the method. For DNA propagation in the PCR method, DNA enzymes are used. polymerase, i.e., those same enzymes that, during cell reproduction, synthesize complementary DNA chains from activated nucleotide monomers.

In the PCR method, a mixture of activated nucleotides, the enzyme DNA polymerase and the so-called primers- oligonucleotides complementary to the ends of the propagated DNA. When the solution is heated, the DNA strands separate. Then, upon cooling, primers bind to them, forming short fragments of helical structures. The enzyme attaches nucleotides to the primers and assembles a chain that is complementary to the chain of the original DNA. As a result of the reaction from one double-stranded DNA, two are obtained. If you repeat the process, you get four chains, and after n repetitions - 2n DNA molecules. Everything is very simple.

The invention of PCR and the development of methods for the chemical synthesis of DNA made it possible to create an amazing technology of molecular selection. The principle of molecular selection is also simple: first, many molecules with different properties are synthesized (the so-called molecular library), and then molecules with the desired property are selected from this mixture.

Nucleic acid libraries are mixtures of molecules that are the same length but differ in nucleotide sequence. They can be obtained if, during chemical synthesis on an automatic synthesizer, all four nucleotides are added simultaneously at each stage of the nucleotide sequence elongation. Each of them will be included in the growing nucleic acid with equal probability, resulting in 4 variants of sequences at each stage of attachment. If a nucleic acid with a length of n links is synthesized in this way, then the variety of molecules obtained will be 4 to the power of n. Since sections with a length of 30-60 monomers are usually used, as a result of the synthesis, from 430 to 460 different molecules are obtained! Figures familiar only to astronomers.

Since, depending on the composition, nucleic acids fold into different spatial structures, the synthesis of statistical sequences gives a huge variety of molecules that differ in properties. From the resulting DNA - using the enzyme RNA polymerase - RNA is read. The result is a library of already single-stranded RNAs. Next, a selection procedure is performed: the RNA solution is passed through a column containing an insoluble carrier with chemically attached target molecules in order to "catch" the so-called future aptamer, i.e., RNA capable of binding certain molecules. The column is then washed to remove unbound RNA, and then the RNA retained on the column due to binding to target molecules is washed off (this can be done, for example, by heating the column).

DNA copies are made from isolated RNA using reverse transcription and ordinary double-stranded DNA molecules are obtained from them. From the latter, it is possible to read the desired RNA aptamers, and then multiply them by PCR in unlimited quantities. Of course, this happens in the ideal case, in practice everything turns out to be more complicated. Typically, the original RNA preparation contains a huge excess of "foreign" molecules, which is difficult to get rid of. Therefore, the resulting RNA is passed through the column again and again in order to isolate the RNAs that form the strongest complexes with the target molecules.

Using this method, thousands of different RNA aptamers were obtained, which form specific complexes with various organic compounds and molecules.

The considered scheme of molecular selection can be applied to obtain molecules with any properties. For example, RNAs have been obtained that can catalyze the reactions of synthesis of RNA and proteins: the addition of nitrogenous bases to ribose, the polymerization of activated nucleotides on RNA chains, the addition of amino acids to RNA. These studies once again confirmed that, under conditions of prebiological evolution, RNA molecules could arise from random polymers.
with specific structures and functions.

Place Your Order!

The method of molecular selection has very great potential. With its help, it is possible to solve the problem of finding the right molecules even if there is no initial idea of ​​how such molecules should be arranged. However, if you come up with a selection procedure, you can select them according to the principle of required properties, and then deal with the question of how these properties are achieved. Let us demonstrate this by the example of isolation of RNAs capable of binding to cell membranes and modulating their permeability.

Ancient ribocytes had to absorb "nutrients" from the environment, remove metabolic products and divide during reproduction.
And all these processes require control of membrane permeability. Since we believe that there were no other functional molecules, except for RNA, in ribocytes, some RNA must have interacted with membranes. However, from a chemical point of view, they are completely unsuitable for the role of membrane permeability regulators.

The membranes of modern cells and liposomes built from fatty acids carry a negative charge. Since RNAs are also negatively charged, according to Coulomb's law, they must be repelled from the lipid surface and, moreover, they cannot penetrate into the depth of the lipid layer. The only known way for nucleic acids to interact with the surface of membranes is through doubly charged metal ions. These positively charged ions can act as bridges between the negatively charged groups on the membrane surface and the phosphate groups of the nucleic acid. Since such bridging interactions are rather weak, only a very large nucleic acid can bind to the membrane due to the many weak bonds to the membrane surface. So small enemies tied Gulliver to the ground with many thin ropes.

Here the method of molecular selection helped the researchers. From the RNA library, it was possible to isolate several molecules that very successfully bind to membranes, and at a sufficiently high concentration, they even break them! These RNAs had unusual properties. They seemed to help each other: a mixture of molecules of different kinds bound to membranes much better than molecules of the same kind. Everything became clear after studying the secondary structures of these RNAs. It turned out that they have loops with complementary regions. Due to these sites, “membrane” RNAs can form community complexes that are able to form multiple contacts with the membrane and do things that a single RNA molecule cannot do.

This selection experiment suggested that RNA has an additional way of acquiring new properties through the formation of complex supramolecular complexes. This mechanism could also be used to keep evolving RNA systems in the form of colonies on surfaces even before these systems acquired an insulating membrane.

"World of RNA": Was, Is and Will Be!

Plenty of evidence suggests that an "RNA world" did exist. True, it is not entirely clear where. Some experts believe that the initial stages of evolution did not take place on Earth, that already functionally active systems were brought to Earth, which adapted to local conditions. However, with chemical
and from a biological point of view, this does not change the essence of the matter. In any case, it remains a mystery - as a result of what processes in the environment ribocytes were formed and due to what components they existed. After all, the nucleotides required for the life of ribocytes are complex molecules. It is difficult to imagine that these substances could be formed under the conditions of prebiotic synthesis.

It is possible that ancient RNAs were significantly different from modern ones. Unfortunately, traces of these ancient RNA cannot be experimentally detected; we are talking about times that are billions of years away from us. Even the rocks of those times "crumbled into sand" long ago. Therefore, we can only talk about experimental modeling of processes that could occur at the earliest stages of molecular evolution.

Why did the transition from the "RNA world" to the modern world take place? Proteins, which have a much larger set of chemical groups than RNA, are the best catalysts and building blocks. Apparently, some ancient RNAs began to use protein molecules as "tools of labour". Such RNAs, which were also able to synthesize useful molecules from the environment for their own purposes, received advantages in reproduction. Appropriate aptamers and ribozymes were naturally selected.
And then evolution did its job: the translation apparatus arose, and gradually the responsibility for catalysis passed to proteins. The tools turned out to be so convenient that they forced their "masters" out of many areas of activity.

The reader has the right to ask: why is it necessary to study the evolution of RNA at all, since the ancient “RNA world” has disappeared? Is it really only for the sake of "pure art", to satisfy the interests of fanatical researchers? However, without knowing the past, it is impossible to understand the present. The study of the evolution and possibilities of RNA can suggest new directions in the search for processes occurring in modern living cells. For example, powerful double-stranded RNA gene regulation systems have recently been discovered, with the help of which the cell protects itself from viral infections. This ancient cellular defense system is likely to find its way into therapy soon.

Therefore, it is not surprising that in our time, nucleic acid research continues to be one of the hot spots in molecular biology. Due to the unique properties of RNA, they are increasingly being used in medicine and technology. The "RNA world" that emerged in time immemorial will not only continue to exist invisibly
in our cells, but also to be reborn in the form of new biotechnologies.

The editors would like to thank the staff of the Institute of Chemical Biology and Fundamental Medicine
SB RAS Ph.D. n. V.V. Kovalya, Ph.D. n. S. D. Myzin and K. Kh. n. A. A. Bondar for help in preparing the article

There is no generally accepted definition of life. We know only one life - earthly, and we do not know which of its properties are indispensable for any life in general. Two such properties can be assumed. This is, firstly, the presence of hereditary information, and secondly, the active implementation of functions aimed at self-maintenance and reproduction, as well as obtaining the energy necessary to perform all this work.

All life on Earth copes with the above tasks with the help of three classes of complex organic compounds: DNA, RNA and proteins. DNA took on the first task - the storage of hereditary information. Proteins are responsible for the second: they perform all kinds of active "work". Their division of labor is very strict.

Molecules of the third class of substances - RNA - serve as intermediaries between DNA and proteins, providing the reading of hereditary information. With the help of RNA, protein synthesis is carried out in accordance with the “instructions” recorded in the DNA molecule. Some of the functions performed by RNA are very similar to those of proteins (the active work of reading the genetic code and protein synthesis), others resemble the functions of DNA (storage and transmission of information). And RNA does all this not alone, but with the active assistance of proteins. At first glance, RNA seems like a “third wheel”. In principle, it is not difficult to imagine an organism in which there is no RNA at all, and all its functions are divided between DNA and proteins. True, such organisms do not exist in nature.

Which of the three molecules appeared first? Some scientists said: of course, proteins, because they do all the work in a living cell, life is impossible without them. They objected: proteins cannot store hereditary information, and without it, life is even more impossible! So DNA was the first!

The situation seemed insoluble: DNA is worthless without proteins, proteins without DNA. It turned out that they had to appear together, at the same time, and this is hard to imagine. About the "extra" RNA in these disputes almost forgotten.

Later, however, it turned out that in many viruses hereditary information is stored in the form of RNA molecules, not DNA. But this was considered a curiosity, an exception. The revolution took place in the 80s of the XX century, when ribozymes were discovered - RNA molecules with catalytic properties. Ribozymes are RNAs that do active work, that is, what proteins are supposed to do.

As a result, RNA went from “almost superfluous” to “almost the main one”. It turned out that she, and only she, can perform both main life tasks at once - storage of information and active work. It became clear that a full-fledged living organism is possible, having neither proteins nor DNA, in which all functions are performed only by RNA molecules. Of course, DNA is better at storing information, and proteins are better at “working,” but these are details. RNA organisms could acquire proteins and DNA later, and at first do without them.

This is how the theory of the RNA world appeared, according to which the first living beings were RNA organisms without proteins and DNA. And the first prototype of the future RNA organism could be an autocatalytic cycle formed by self-reproducing RNA molecules - ribozymes, capable of catalyzing the synthesis of their own copies.

Personally, I consider the theory of the RNA world one of the most outstanding achievements of theoretical thought in biology. To tell the truth, we could have thought of this earlier. After all, two types of ribozymes have been known since the 1960s, although they were not then called ribozymes. These are ribosomal RNA (rRNA), from which molecular "machines" for translation (protein synthesis) are made - ribosomes, and transfer RNA (tRNA), which bring the necessary amino acids to the ribosomes during translation.

The theory of the RNA world, at first purely speculative, quickly "acquires" experimental data. Chemists have learned to create ribozymes with almost any desired characteristics. It is done like this. For example, we want to create an RNA molecule that can accurately recognize and bind to substance X. To do this, a large number of different RNA chains are synthesized by connecting ribonucleotides to each other in a random order. A solution containing the resulting mixture of RNA molecules is poured onto a surface coated with substance X. After that, it remains only to select and examine those RNA molecules that have adhered to the surface. The technology is simple, but it really works. Ribozymes that catalyze the synthesis of nucleotides, add amino acids to RNA, and perform many other biochemical functions were obtained in approximately this way.

The RNA world is a hypothetical stage in the origin of life on Earth, when ensembles of ribonucleic acid molecules performed both the function of storing genetic information and catalyzing chemical reactions. Subsequently, from their associations, modern DNA-RNA-protein life arose, isolated from the external environment by a membrane. The idea of ​​the RNA world was first expressed by Carl Woese in 1968, later developed by Leslie Orgel and finally formulated by Walter Gilbert in 1986.

Summary

In living organisms, almost all processes occur mainly due to protein enzymes. Proteins, however, cannot self-replicate and are synthesized de novo in the cell based on information stored in DNA. But the duplication of DNA occurs only due to the participation of proteins and RNA. A vicious circle is formed, because of which, within the framework of the theory of spontaneous generation of life, it was necessary to recognize the extreme importance of not only the abiogenic synthesis of both classes of molecules, but also the spontaneous emergence of a complex system of their interconnection.

In the early 1980s, the catalytic ability of RNA was discovered in the laboratory of T. Chek and S. Altman in the USA. By analogy with enzymes, RNA catalysts were called ribozymes, for their discovery Thomas Czek was awarded the Nobel Prize in Chemistry in 1989. Moreover, it turned out that the active center of ribosomes contains a large amount of rRNA. RNAs are also able to double strand and self-replicate.

Τᴀᴋᴎᴍ ᴏϬᴩᴀᴈᴏᴍ, RNA could exist completely autonomously, catalyzing ʼʼmetabolicʼʼ reactions, for example, the synthesis of new ribonucleotides and self-reproducing, retaining catalytic properties from ʼʼgenerationʼʼ to ʼʼgenerationʼʼ. The accumulation of random mutations led to the emergence of RNAs that catalyze the synthesis of certain proteins, which are a more efficient catalyst, and therefore these mutations were fixed in the course of natural selection. On the other hand, specialized repositories of genetic information - DNA - arose. RNA has been preserved between them as an intermediary.

The role of RNA in the modern world

Traces of the world of RNA have remained in modern living cells, and RNA is involved in critical processes of cell life:

1) The main energy carrier in cells - ATP - is a ribonucleotide, not a deoxyribonucleotide.

2) Protein biosynthesis is almost entirely carried out using various types of RNA:

messenger RNAs are the template for protein synthesis in ribosomes;

transfer RNAs deliver amino acids to ribosomes and implement the genetic code;

· Ribosomal RNA is the active center of ribosomes, catalyzing the formation of peptide bonds between amino acids.

3) RNA is also critical for DNA replication:

· to start the process of DNA duplication, RNA-ʼʼseedʼʼ (primer) is needed;

· for infinite duplication of DNA, not limited by the Hayflick limit, in eukaryotic cells, the end sections of chromosomes (telomeres) are constantly restored by the enzyme telomerase, which includes an RNA template.

4) In the process of reverse transcription, information from RNA is rewritten into DNA.

5) In the process of RNA maturation, various RNAs that do not code for proteins are used, including small nuclear RNAs, small nucleolar RNAs.

At the same time, many viruses store their genetic material in the form of RNA and deliver RNA-dependent RNA polymerase to the infected cell for its replication.

Abiogenic RNA synthesis

The abiogenic synthesis of RNA from simpler compounds has not been fully demonstrated experimentally. In 1975, Manfred Samper and Rudiger Lewis demonstrated in the Eigen laboratory that in a mixture containing no RNA at all, but containing only nucleotides and Qβ replicase, self-replicating RNA can spontaneously arise under certain conditions.

In 2009, a group of scientists from the University of Manchester, led by John Sutherland, managed to demonstrate the possibility of synthesizing uridine and cytidine with high efficiency and the degree of fixation of the reaction result (as well as with the possibility of accumulating end products) under the conditions of the early Earth. At the same time, although the abiogenic synthesis of purine bases was demonstrated quite a long time ago (in particular, adenine is a pentamer of hydrocyanic acid), their glycosylation by the free ribose of adenosine and guanosine has so far been shown only in an ineffective variant.

RNA evolution

The ability of RNA molecules to evolve has been clearly demonstrated in a number of experiments. Even before the discovery of the catalytic activity of RNA, such experiments were carried out by Leslie Orgel and colleagues in California. Οʜᴎ was added to a test tube with RNA poison - ethidium bromide, which inhibits RNA synthesis. At first, the rate of synthesis was slowed down by the poison, but after about nine "test-tube generations" of evolution, a new breed of poison-resistant RNA was bred by natural selection. By successively doubling the doses of the poison, a breed of RNA was bred that was resistant to its very high concentrations. In total, 100 test tube generations changed in the experiment (and many more RNA generations, since generations changed inside each test tube). Although in this experiment the RNA replicase was added to the solution by the experimenters themselves, Orgel found that RNAs are also capable of spontaneous self-copying, without the addition of an enzyme, albeit much more slowly.

An additional experiment was later carried out in the laboratory of the German school of Manfred Eigen. He discovered the spontaneous generation of an RNA molecule in a test tube with a substrate and RNA replicase. It was created by gradually increasing evolution.

After the discovery of the catalytic activity of RNAs (ribozymes), their evolution in a computer-controlled automated device was observed in experiments by Brian Pegel and Gerald Joyce of the Scripps Research Institute in California in 2008. The factor playing the role of selection pressure was the limitation of the substrate, which included oligonucleotides that the ribozyme recognized and attached to itself, and nucleotides for the synthesis of RNA and DNA. When building copies, sometimes there were defects - mutations - affecting their catalytic activity (to speed up the process, the mixture was mutated several times using a polymerase chain reaction using "inaccurate" polymerases). Molecules were selected on this basis: the most rapidly copied molecules quickly began to dominate in the medium. Next, 90% of the mixture was removed, and instead a fresh mixture with substrate and enzymes was added, and the cycle was repeated again. For 3 days, the catalytic activity of the molecules increased by 90 times due to a total of 11 mutations.

These experiments prove that the first RNA molecules did not need to have sufficiently good catalytic properties. Οʜᴎ developed later in the course of evolution under the influence of natural selection.

In 2009, Canadian biochemists from the University of Montreal K. Bokov and S. Steinberg, having studied the main component of the Escherichia coli ribosome, the 23S-rRNA molecule, showed how the mechanism of protein synthesis could develop from relatively small and simple ribozymes. The molecule was subdivided into 60 relatively independent structural blocks, the main of which is the catalytic center (peptidyl-transferase center, PTC, peptidyl-transferase centre), responsible for transpeptidation (formation of a peptide bond). It was shown that all these blocks can be sequentially detached from the molecule without destroying its remaining part until only one transpeptidation center remains.
Hosted on ref.rf
However, it retains the ability to catalyze transpeptidation. If each bond between the blocks of the molecule is represented as an arrow directed from the block that is not destroyed upon separation to the block that is destroyed, then such arrows do not form a single closed ring. If the direction of the connections were random, the probability of this would be less than one in a billion. Therefore, this nature of the bonds reflects the sequence of gradual addition of blocks in the evolution of the molecule, which the researchers were able to reconstruct in detail. Τᴀᴋᴎᴍ ᴏϬᴩᴀᴈᴏᴍ, a relatively simple ribozyme, the PTC center of the 23S-rRNA molecule, to which new blocks were then added, could be at the origins of life, improving the process of protein synthesis. PTC itself consists of two symmetrical blades, each of which holds the CCA "tail of one tRNA molecule. It is assumed that such a structure arose as a result of duplication (doubling) of one initial blade. Functional RNAs (ribozymes) capable of catalyzing transpeptidation were obtained by artificial evolution The structure of these artificially derived ribozymes is very close to the structure of the protoribosome that the authors ʼʼcalculatedʼʼ.

Properties of RNA World Objects

There are various assumptions about what self-replicating RNA systems looked like. Most often, the extreme importance of RNA-aggregating membranes or the placement of RNA on the surface of minerals and in the pore space of loose rocks is postulated. In the 1990s, A. B. Chetverin and co-workers demonstrated the ability of RNA to form molecular colonies on gels and solid substrates when it creates conditions for replication. There was a free exchange of molecules, which could exchange areas during a collision, which was shown experimentally. The whole set of colonies in connection with this rapidly evolved.

After the emergence of protein synthesis, colonies that could create enzymes developed more successfully. Even more successful were the colonies, which formed a more reliable mechanism for storing information in DNA and, finally, separated from the outside world by a lipid membrane that prevented the dispersion of their molecules.

Pre-RNA worlds

Biochemist R. Shapiro criticizes the RNA-world hypothesis, believing that the probability of spontaneous emergence of RNA with catalytic properties is very low. Instead of the hypothesis ʼʼin the beginning there was RNAʼʼ, he proposes the hypothesis ʼʼin the beginning there was metabolismʼʼ, that is, the occurrence of complexes of chemical reactions - analogues of metabolic cycles - with the participation of low-molecular compounds occurring inside compartments - spatially limited by spontaneously formed membranes or other phase boundaries - areas. This concept is close to the coacervate hypothesis of abiogenesis proposed by A. I. Oparin in 1924.

Another hypothesis of abiogenic RNA synthesis, designed to solve the problem of the low estimated probability of RNA synthesis, is the hypothesis of the world of polyaromatic hydrocarbons, proposed in 2004 and suggesting the synthesis of RNA molecules based on a stack of polyaromatic rings.

In fact, both hypotheses of the ʼʼpre-RNA worldsʼʼ do not reject the RNA world hypothesis, but modify it by postulating the initial synthesis of replicating RNA macromolecules in primary metabolic compartments or on the surface of associates, pushing the ʼʼRNA worldʼʼ to the second stage of abiogenesis.

Academician of the Russian Academy of Sciences A. S. Spirin believes that the RNA world could not have appeared and existed on Earth, and considers the option of an extraterrestrial (primarily on comets) origin and evolution of the RNA world.

Candidate of Biological Sciences S. GRIGOROVICH.

At the earliest dawn of his history, when man acquired reason, and with it the ability to think abstractly, he became a prisoner of an irresistible need to explain everything. Why do the sun and moon shine? Why do rivers flow? How is the world? Of course, one of the most important was the question of the essence of the living. The sharp difference between the living, growing, and the dead, motionless, was too striking to be ignored.

The first virus described by D. Ivanovsky in 1892 is the tobacco mosaic virus. Thanks to this discovery, it became clear that there are living creatures more primitive than the cell.

Russian microbiologist D.I. Ivanovsky (1864-1920), founder of virology.

In 1924, A. I. Oparin (1894-1980) suggested that in the atmosphere of the young Earth, which consisted of hydrogen, methane, ammonia, carbon dioxide and water vapor, amino acids could be synthesized, which then spontaneously combined into proteins.

The American biologist Oswald Avery convincingly demonstrated in experiments with bacteria that it is nucleic acids that are responsible for the transmission of hereditary properties.

Comparative structure of RNA and DNA.

Two-dimensional spatial structure of the ribozyme of the simplest organism Tetrahymena.

Schematic representation of the ribosome, a molecular machine for protein synthesis.

Scheme of the "evolution in vitro" process (Selex method).

Louis Pasteur (1822-1895) was the first to discover that crystals of the same substance - tartaric acid - can have two mirror-symmetrical spatial configurations.

In the early 1950s, Stanley Miller of the University of Chicago (USA) did the first experiment that simulated the chemical reactions that could take place under the conditions of a young Earth.

Chiral molecules, such as amino acids, are mirror-symmetrical, like left and right hands. The term "chirality" itself comes from the Greek word "chiros" - hand.

Theory of the RNA world.

Science and life // Illustrations

At every stage of history, people have offered their own solution to the riddle of the appearance of life on our planet. The ancients, who did not know the word "science", found a simple and accessible explanation for the unknown: "Everything that is around was once created by someone." This is how the gods appeared.

From the time of the birth of ancient civilizations in Egypt, China, and then in the cradle of modern science - Greece, up to the Middle Ages, observations and opinions of "authorities" served as the main method of knowing the world. Constant observations unequivocally testified that the living, under certain conditions, appears from the inanimate: mosquitoes and crocodiles - from swamp mud, flies - from rotting food, and mice - from dirty laundry sprinkled with wheat. It is only important to observe a certain temperature and humidity.

European "scientists" of the Middle Ages, relying on the religious dogma of the creation of the world and the incomprehensibility of divine plans, considered it possible to argue about the origin of life only within the framework of the Bible and religious writings. The essence of what God created cannot be comprehended, but can only be "specified" using information from sacred texts or being under the influence of divine inspiration. Testing hypotheses at that time was considered bad manners, and any attempt to question the opinion of the holy church was considered as an unpleasing deed, heresy and sacrilege.

The knowledge of life was treading water. The achievements of the philosophers of ancient Greece remained the pinnacle of scientific thought for two thousand years. The most significant of these were Plato (428/427 - 347 BC) and his disciple Aristotle (384 - 322 BC). Plato, among other things, proposed the idea of ​​animating initially inanimate matter due to the infusion into it of an immortal non-material soul - "psyche". This is how the theory of spontaneous generation of living things from non-living things appeared.

The great word for science "experiment" came with the Renaissance. It took two thousand years for a person to decide to doubt the immutability of the authoritative statements of ancient scientists. One of the first daredevils known to us was the Italian physician Francisco Redi (1626 - 1698). He conducted an extremely simple but effective experiment: placing a piece of meat in several vessels, one of them was covered with a dense cloth, others with gauze, and the third left open. The fact that fly larvae developed only in open vessels (on which flies could land), but not in closed ones (which still had access to air), sharply contradicted the beliefs of the supporters of Plato and Aristotle about an incomprehensible life force rushing through the air and transforming inanimate matter into living matter.

This and similar experiments marked the beginning of a period of fierce battles between two groups of scientists: the vitalists and the mechanists. The essence of the dispute was the question: "Can the functioning (and appearance) of living things be explained by physical laws that are also applicable to inanimate matter?" The vitalists answered him in the negative. "A cell - only from a cell, all living things - only from a living one!" This position, put forward in the middle of the 19th century, became the banner of vitalism. The most paradoxical in this dispute is that even today, knowing about the "inanimate" nature of the atoms and molecules that make up our body and generally agreeing with the mechanistic point of view, scientists do not have experimental confirmation of the possibility of the origin of cellular life from inanimate matter. No one has yet succeeded in "composing" even the most primitive cell from "inorganic" "details" present outside living organisms. So, the final point in this epoch-making dispute has yet to be put.

So how could life have arisen on Earth? Sharing the positions of the mechanists, it is certainly easiest to imagine that life first had to arise in some very simple, primitively arranged form. But, despite the simplicity of the structure, it must still be Life, that is, something that has a minimum set of properties that distinguish living from non-living.

What are they, these critical properties for life? What actually distinguishes the living from the non-living?

Until the end of the 19th century, scientists were convinced that all living things are built from cells, and this is the most obvious difference between it and inanimate matter. This was considered before the discovery of viruses, which, although smaller than all known cells, can actively infect other organisms, multiply in them and produce offspring with the same (or very similar) biological properties. The first virus to be discovered, tobacco mosaic virus, was described by the Russian scientist Dmitry Ivanovsky (1864-1920) in 1892. Since then, it has become clear that creatures more primitive than cells can also claim the right to be called Life.

The discovery of viruses, and then even more primitive forms of living things - viroids, eventually made it possible to formulate the minimum set of properties that are necessary and sufficient for the object under study to be called alive. First, it must be capable of reproducing its own kind. This, however, is not the only condition. If the hypothetical primordial substance of life (for example, a primitive cell or molecule) were only capable of simply producing exact copies of itself, it would ultimately not be able to survive in the changing environmental conditions on the young Earth and the formation of other, more complex forms (evolution) would become impossible. Therefore, our supposed primitive "substance of the first life" can be defined as something that is arranged as simply as possible, but at the same time capable of changing and transmitting its properties to descendants.

In living organisms, almost all processes occur mainly due to enzymes of a protein nature. Proteins, however, cannot self-replicate and are synthesized de novo in the cell based on information stored in DNA. But the duplication of DNA occurs only due to the participation of proteins and RNA. A vicious circle is formed, because of which, within the framework of the theory of spontaneous generation of life, it was necessary to recognize the need not only for the abiogenic synthesis of both classes of molecules, but also for the spontaneous emergence of a complex system of their interconnection, the probability of which is extremely small.

In the early 1980s, the catalytic ability of RNA was discovered in the laboratory of T. Chek and S. Altman in the USA. By analogy with enzymes, RNA catalysts were called ribozymes, for their discovery Thomas Check was awarded the Nobel Prize in Chemistry in 1989. Moreover, it turned out that the active center of ribosomes contains a large amount of rRNA. RNAs are also able to double strand and self-replicate.

Thus, RNA could exist completely autonomously, catalyzing "metabolic" reactions, for example, the synthesis of new ribonucleotides and self-reproducing, retaining catalytic properties from "generation" to "generation". The accumulation of random mutations led to the emergence of RNAs that catalyze the synthesis of certain proteins, which are a more efficient catalyst, and therefore these mutations were fixed in the course of natural selection. On the other hand, specialized repositories of genetic information - DNA - arose. RNA was preserved between them as an intermediary.

There are various assumptions about what self-replicating RNA systems looked like. The need for RNA-aggregating membranes or placement of RNA on the surface of minerals and in the pore space of loose rocks is most often postulated. In the 1990s, A. B. Chetverin and co-workers demonstrated the ability of RNA to form molecular colonies on gels and solid substrates when it creates conditions for replication. There was a free exchange of molecules, which could exchange areas during a collision, which was shown experimentally. The whole set of colonies in connection with this rapidly evolved.

After the emergence of protein synthesis, colonies that could create enzymes developed more successfully. Even more successful were the colonies, which formed a more reliable mechanism for storing information in DNA and, finally, separated from the outside world by a lipid membrane that prevented the dispersion of their molecules.

Biochemist R. Shapiro criticizes the RNA-world hypothesis, believing that the probability of spontaneous emergence of RNA with catalytic properties is very low. Instead of the hypothesis “in the beginning there was RNA”, he proposes the hypothesis “in the beginning there was metabolism”, that is, the emergence of complexes of chemical reactions - analogues of metabolic cycles - with the participation of low-molecular compounds occurring inside compartments - spatially limited by spontaneously formed membranes or other phase boundaries - areas. This concept is close to the coacervate hypothesis of abiogenesis proposed by A. I. Oparin in 1924.

Another hypothesis of abiogenic RNA synthesis, designed to solve the problem of the low estimated probability of RNA synthesis, is the hypothesis of the world of polyaromatic hydrocarbons, proposed in 2004 and suggesting the synthesis of RNA molecules based on a stack of polyaromatic rings.

In fact, both hypotheses of "pre-RNA worlds" do not reject the hypothesis of the RNA world, but modify it, postulating the initial synthesis of replicating RNA macromolecules in primary metabolic compartments or on the surface of associates, pushing the "RNA world" to the second stage of abiogenesis.