Anyone who studies molecular biology, biochemistry, genetic engineering and a number of other related sciences, sooner or later asks the question: what function does RNA polymerase perform? This is a rather complex topic that has not been fully investigated yet, but, nevertheless, what is known will be covered in the article.
general information
It is necessary to remember that there is an RNA polymerase of eukaryotes and prokaryotes. The first is further divided into three types, each of which is responsible for carrying out the transcription of a separate group of genes. These enzymes are numbered for simplicity as the first, second and third RNA polymerase. Prokaryotes, whose structure is non-nuclear, transcriptional acts according to a simplified scheme. Therefore, for clarity, to cover as much information as possible, eukaryotes will be considered. RNA polymerases are structurally similar. It is believed that they contain at least 10 polypeptide chains. In this case, RNA polymerase 1 synthesizes (transcribes) genes, which in the future will be translated into various proteins. The second deals with the transcription of genes, which are subsequently translated into proteins. RNA polymerase 3 is represented by a variety of low molecular weight stable enzymes that are moderately sensitive to alpha-amatin. But we did not decide what RNA polymerase is! So called enzymes, which are involved in the synthesis of ribonucleic acid molecules. In the narrow sense, this means DNA-dependent RNA polymerases that act on the basis of a matrix of deoxyribonucleic acid. Enzymes are of the greatest importance for the long and successful functioning of living organisms. RNA polymerase can be found in all cells and most viruses.
Division by features
Depending on the subunit composition, RNA polymerases are divided into two groups:
- The first is engaged in transcription of a small number of genes in simple genomes. To operate in this case, complex regulatory influences are not required. Therefore, all enzymes, which consist of only one subunit, are included here. RNA polymerases of bacteriophages and mitochondria can be used as an example.
- This group includes all RNA polymerases of eukaryotes and bacteria, which are complex arranged. They are intricate multi-subunit protein complexes that can transcribe thousands of different genes. During functioning these genes react to a large number of regulatory signals that come from protein factors and nucleotides.
This structural-functional division is a very conditional and strong simplification of the real state of affairs.
What does RNA polymerase I do?
Behind them, the function of formation of primary transcripts of rRNA genes is fixed, that is, they are the most important. The latter are more commonly known as 45S-RNA. Their length is about 13 thousand nucleotides. 28S-RNA, 18S-RNA and 5,8S-RNA are formed from it. Due to the fact that only one transcript is used for their creation, the organism receives a "guarantee" that the molecules will be formed in equal quantities. At the same time, only 7,000 nucleotides are created to create RNA directly. The rest of the transcript degrades in the nucleus. Concerning such a large residue, there is an opinion that it is necessary for the early stages of the formation of ribosomes. The number of these polymerases in the cells of higher creatures fluctuates around the mark of 40 thousand units.
How is it organized?
So, we already have a good look at the first RNA polymerase (prokaryotic-molecule structure). In this case, large subunits, as well as a large number of other high molecular weight polypeptides, have well distinguishable functional and structural domains. During the cloning of genes and the determination of their primary structure, scientists have identified evolutionarily conservative sections of the chains. Using a good expression, the researchers also carried out mutational analysis, which allows us to speak about the functional significance of individual domains. To do this, by directing the mutagenesis in the polypeptide chains, individual amino acids were changed and such altered subunits were used in the assembly of enzymes followed by analysis of the properties that were obtained in these constructs. It was noted that due to its organization, the first RNA polymerase for the presence of alpha-amatin (a highly toxic substance that is obtained from a pale toadstool) does not react at all.
Operation
Both the first and second RNA polymerases can exist in two forms. One of them can act to initiate a specific transcription. The second is DNA dependent RNA polymerase. This ratio is manifested in the magnitude of the activity of functioning. The topic is still under investigation, but it is already known that this depends on two transcription factors, which are denoted as SL1 and UBF. The peculiarity of the latter is that it can directly bind to the promoter, whereas SL1 requires the presence of UBF. Although it has been experimentally established that DNA-dependent RNA polymerase can participate in transcription at a minimal level and without the presence of the latter. But for the normal functioning of this mechanism UBF is still needed. Why so? For the time being, it is not possible to establish the reason for this behavior. One of the most popular explanations suggests that UBF acts as a stimulant for transcription of rDNA when it grows and develops. When the rest phase arrives, the minimum necessary level of functioning is maintained. And for him, the involvement of transcription factors is not critical. That's how RNA polymerase works. The functions of this enzyme allow us to support the reproduction of small "building blocks" of our body, thanks to which it has been continuously updated for decades.
The second group of enzymes
Their functioning is regulated by the assembly of a multi-protein pre-initiator complex of second-class promoters. Most often this is expressed in the work with special proteins - activators. An example is the TBP. These are the associated factors that make up TFIID. They are the target for p53, NF kappa B and so on. Their influence in the process of regulation is exerted by proteins called coactivators. As an example, you can cite GCN5. Why do we need these proteins? They act as adapters that adjust the interaction of activators and factors that enter the preinitiation complex. In order for transcription to take place correctly, it is necessary to have the necessary initiator factors. Despite the fact that there are six of them, only one can directly interact with the promoter. For other cases, a preformed complex of the second RNA polymerase is needed. Moreover, during these processes, the proximal elements are near - only in 50-200 pairs from the site where the transcription began. They contain an indication of the binding of protein activators.
Specific features
Does the subunit structure of enzymes of different origin affect their functional role in transcription? There is no exact answer to this question, but it is believed that it is, most likely, positive. How does RNA polymerase depend on this? Functions of simple enzymes are the transcription of a limited range of genes (or even their small parts). As an example, we can cite the synthesis of RNA primers of Okaucas fragments. The promoter specificity of RNA polymerase bacteria and phages is that the enzymes are possessed of a simple structure and do not differ in variety. This can be observed by the example of DNA replication in bacteria. Although we can also consider this: when the complex structure of the even T-phage genome was studied, during the development of which a multiple transcription of transcription between different groups of genes was noted, it was revealed that a complex RNA polymerase of the host was used for this. That is, a simple enzyme is not induced in such cases. This leads to a number of consequences:
- The RNA polymerase of eukaryotes and bacteria should be able to recognize different promoters.
- It is necessary that enzymes have a certain reaction to different regulatory proteins.
- RNA polymerase should also be able to change the specificity of recognition of the sequence of nucleotides of the template DNA. To do this, a variety of protein effectors are used.
Hence the need of the organism for additional "building" elements. The proteins of the transcription complex help the RNA polymerase to fully perform its functions. This applies, most of all, to enzymes of complex structure, in the capabilities of which the implementation of an extensive program for the realization of genetic information. Due to various tasks, we can observe a peculiar hierarchy of the structure of RNA polymerases.
How does the process of transcription take place?
Is there a gene responsible for the association with RNA polymerase? To begin with, about transcription: in eukaryotes, the process takes place in the nucleus. In prokaryotes, it flows inside the microorganism itself. The interaction of the polymerase is based on the fundamental structural principle of the complementary pairing of individual molecules. Concerning the issues of interaction, it can be said that DNA acts exclusively as a matrix and does not change during transcription. Since DNA is an integral enzyme, it is certain that a specific gene is responsible for this polymer, but it will be very long. It should not be forgotten that DNA contains 3.1 billion nucleotide residues. Therefore, it is more appropriate to say that each type of RNA has its own DNA. For the course of the polymerase reaction, energy sources and ribonucleotide-triphosphate substrates are needed. In their presence, 3 ', 5'-phosphodiester bonds between ribonucleoside monophosphates are formed. The RNA molecule begins to be synthesized in certain DNA sequences (promoters). This process ends in terminating sections (terminations). The site, which is involved here, is called transcripton. In eukaryotes, there is usually only one gene, whereas prokaryotes may have several parts of the code. Each transcript has a noninformative zone. They contain specific nucleotide sequences interacting with regulatory transcription factors mentioned earlier.
Bacterial RNA polymerases
In these microorganisms, one enzyme is responsible for the synthesis of mRNA, rRNA and tRNA. The average polymerase molecule has about 5 subunits. Two of them act as binding elements of the enzyme. Another subunit is involved in the initiation of synthesis. There is also an enzyme component for non-specific DNA binding. And the last subunit is engaged in bringing the RNA polymerase into a working form. It should be noted that the enzyme molecules are not in the "free" swimming in the cytoplasm of the bacterium. When RNA polymerases are not used, they are bound by nonspecific DNA regions and are waiting for an active promoter to be discovered. A little distraction from the topic, it should be said that it is very convenient on bacteria to study proteins and their effect on ribonucleic acid polymerases. It is especially convenient for them to put experiments on stimulation or inhibition of individual elements. Due to their high rate of reproduction, the desired result can be obtained relatively quickly. Alas, human research can not be carried out at such a rapid pace thanks to our structural diversity.
How did RNA polymerase "take root" in various forms?
So the article approaches the logical conclusion. The main attention was paid to eukaryotes. But there are archaea and viruses. Therefore, I want to give a little attention to these forms of life. In the life of the Archaeans there is only one group of RNA polymerases. But it is extremely similar in its properties to the three associations of eukaryotes. Many scientists speculate that what we can observe in the Archaeans is in fact an evolutionary ancestor of specialized polymerases. The structure of viruses is also interesting . As previously reported, not all such microorganisms have their polymerase. And where it is, it is one subunit. It is believed that viral enzymes originate from DNA polymerases, rather than from complex RNA constructs. Although due to the diversity of this group of microorganisms, a different realization of the biological mechanism under consideration is encountered.
Conclusion
Alas, now mankind does not yet have all the necessary information necessary for understanding the genome. And that only one could do! Virtually all diseases in their basis have a genetic basis - this applies primarily to viruses, which constantly deliver problems to us, to infections and so on. The most complex and incurable diseases - they too, in fact, directly or indirectly depend on the human genome. When we learn to understand ourselves and will apply this knowledge to the benefit, a large number of problems and diseases will simply cease to exist. Already many terrible diseases, such as smallpox, plague, have become a thing of the past. Prepare to go there mumps, whooping cough. But you should not relax, because before us there is still a lot of different challenges, to which you need to find the answer. And he will be found, for everything goes to this.