For many decades, biologists, chemists and even mathematicians have been working on the problem of the origin of life. And although there are already scientifically substantiated and supported hypotheses of chemical evolution before the appearance of the first cell, work in this direction continues. "Lenta.ru" talks about a new study on the problem of the RNA world, the results of which were published in the journal Proceedings of the National Academy of Sciences.
Scientists at Portland State University, conducting experiments on ribozymes, found that the ability of these molecules to catalyze their own assembly depends on their interaction with other similar molecules. The study indirectly supports the hypothesis of the RNA world, which states that the first organic molecule that became the basis for the first cells was RNA. These RNA molecules were able to self-synthesize, compete with each other, and participate in prebiotic evolution, when the most successful compounds became the basis for more complex chemical complexes.
Many people know that living cells have their own special catalysts: enzymes, which are complexly folded protein molecules that carry out vital reactions. However, enzymes can be not only proteins, but also RNA chains. Recall that RNA is a nucleic acid very similar to DNA, but differs from it in that it contains ribose sugar (not deoxyribose), and one of the nitrogenous bases, thymine, is replaced by uracil. According to scientists, RNA appeared before DNA, because it is much more labile (its structure is more susceptible to changes) and can carry out catalytic reactions without the help of proteins. RNA molecules that are enzymes are called ribozymes. Typically, ribozymes catalyze the cleavage of themselves or other RNA molecules.
One of the most well-studied ribozymes is Azo, an enzyme made by scientists from self-cutting Group I introns found in the DNA of the bacterium Azoarcus. Introns are regions of genes that do not contain information about the sequence of a protein or nucleic acid, and are excised during messenger RNA (mRNA) maturation. All group I introns catalyze their own excision from the RNA sequence. The intron ribozyme Azo of interest to scientists is located in a gene that encodes a transport RNA (tRNA) that carries the amino acid isoleucine. Inside the cell, Azo, like other ribozymes, carries out its own excision from tRNA, but in laboratory conditions he was able to learn to carry out reverse splicing: the ribozyme cuts at a certain place the substrate - a short RNA molecule with a specific nucleotide sequence,pieces of which remain attached to Azo.
The structure of the ribozyme of the bacterium Azoarcus. Fragment IGS is marked in red
Image: Jessica AM Yeates et al. Department of Chemistry, Portland State University
Azo is roughly 200 nucleotides long and can break down into two, three, or four fragments that spontaneously come together at 42 degrees Celsius in the presence of MgCl2 solution. The self-assembly process begins with the interaction between two nucleotide triplets (triplets) belonging to different RNA fragments. When hydrogen bonds are formed between the triplets according to the principle of complementarity, the parts of the ribozyme change their spatial structure and reunite with each other. Scientists focused on the self-assembly reaction of two fragments, which were tentatively named WXY and Z, where W, X, Y and Z represent separate regions of the ribozyme approximately 50 nucleotides long (Fig. 1). On site W, at the front end of the RNA molecule, one of the triplets is located,which is involved in the initiation of self-assembly and is called the "internal guide sequence" (IGS). At the end of WXY, there is a tag triplet, which, interacting with IGS, forms a strong covalent bond with the Z fragment.
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The researchers created different variants (genotypes) of WXY fragments by changing the nucleotides located in the middle of the IGS and tag triplets (nucleotides M and N, respectively). Since RNA molecules are usually formed by only four types of nucleotides, there are 16 such variants. For example, one of the genotypes may be 5'-GGG-WXY-CAU-3 ', and the other 5'-GCG-WXY-CUU-3'. All of these variants of molecules can compete with each other, forming various metabolic networks, in which a common resource - the Z molecule - is required to restore a whole ribozyme.
The reaction between different fragments of the Azo ribozyme to form a whole molecule
Image: Jessica AM Yeates et al. Department of Chemistry, Portland State University.
In their experiments, scientists first tested the ability of each genotype to self-assemble separately. When M and N form Watson-Crick pairs (that is, according to the principle of complementarity, A - U, C - G), the ribozyme self-assembly rate becomes higher than for other types of pairs. The researchers then simulated a warm "small pond" environment in which various prebiotic molecules interact with each other to gain benefits from each other and accelerate self-organization. Biochemists tracked the behavior of genotypes paired with each other, in total, scientists studied 120 pairs, consisting of two dissimilar WXY variants. They measured the rate of each reaction that took place between molecules of the two WXY genotypes and Z fragments inside separate tubes for 30 minutes.
Interaction between sequences of different ribozyme fragments using hydrogen bonds
Image: Jessica AM Yeates et al. Department of Chemistry, Portland State University
By combining the results of both stages of the experiment and having obtained the self-assembly rates when two different genotypes interact, the researchers set up an evolutionary experiment. Pairs of genotypes were mixed in equal proportions, provided with Z-fragments and reacted with each other for five minutes. During this time, the scientists sampled 10 percent of the solution into a new test tube, which contained more unreacted WXY of each genotype and Z-fragments. Scientists tracked the ratios of each WXYZ genotype during eight such transfers. This made it possible to estimate the chemical equivalent of the evolutionary success of ribozymes over generations, which was observed as an "explosion" - that is, a strong increase in the rate of self-assembly of RNA. In an evolutionary experiment, biologists studied the interaction of seven pairs of ribozymes.
Based on all laboratory experiments, scientists have derived a mathematical model of differential equations that take into account the rate of self-assembly of genotypes with or without the presence of other genotypes. This model became the basis for a new evolutionary game theory, which defines several behaviors of RNA molecules. In one case, called "Dominance," one of the genotypes is always more common than the other, while its self-assembly rate always exceeds the speed of the competitor. In the other case - "Cooperation" - both genotypes that interact with each other receive benefits from "cooperation", and the speed of their self-assembly exceeds that which they would have separately from each other. The “Selfish Scenario” - the exact opposite of “Cooperation” - means that each ribozyme individually receives more than when interacting with someone else. And finallyin "Counter-dominance", the genotype with a low self-assembly rate suddenly begins to occur more often than its competitor.
This study is not aimed at directly proving the RNA world hypothesis, but it does represent another piece in the puzzle of scientific understanding of prebiotic evolution. It was shown for the first time that the enzymatic properties of individual molecules can be improved in the presence of other molecules that differ by only one or two nucleotides. In the gigantic solution that was the earth's oceans at the dawn of life, these molecules competed with each other for substrates, cooperated and intensified their action. On the basis of this, it can already be assumed why complex organic compounds sought to unite into systems that are prototypes of the first cells.
Alexander Enikeev