Everyone who studies molecular biology, biochemistry, genetic engineering and a number of other related sciences sooner or later asks the question: what is the function of RNA polymerase? This is a rather complex topic, which is still not fully explored, but, nevertheless, what is known will be covered within the framework of 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 the transcription of a separate group of genes. These enzymes are numbered for simplicity as the first, second, and third RNA polymerases. The prokaryote, whose structure is nuclear-free, during transcription acts according to a simplified scheme. Therefore, for clarity, in order to cover as much information as possible, eukaryotes will be considered. RNA polymerases are structurally similar to each other. They are believed to contain at least 10 polypeptide chains. At the same time, RNA polymerase 1 synthesizes (transcribes) genes that will subsequently be translated into various proteins. The second is transcribing genes, which are subsequently translated into proteins. RNA polymerase 3 is represented by a variety of low molecular weight stable enzymes that moderatelysensitive to alpha amatine. But we have not decided on what RNA polymerase is! This is the name of the enzymes that are involved in the synthesis of ribonucleic acid molecules. In a narrow sense, this refers to DNA-dependent RNA polymerases that act on the basis of a deoxyribonucleic acid template. Enzymes are of great importance for the long-term and successful functioning of living organisms. RNA polymerases are found in all cells and most viruses.
Division by features
Depending on the subunit composition, RNA polymerases are divided into two groups:
- The first deals with the transcription of a small number of genes in simple genomes. For functioning in this case, complex regulatory actions are not required. Therefore, this includes all enzymes that consist of only one subunit. An example is the RNA polymerase of bacteriophages and mitochondria.
- This group includes all RNA polymerases of eukaryotes and bacteria, which are complex. They are intricate multi-subunit protein complexes that can transcribe thousands of different genes. During their functioning, these genes respond to a large number of regulatory signals that come from protein factors and nucleotides.
Such a structural-functional division is a very conditional and strong simplification of the real state of affairs.
What does RNA polymerase I do?
They are assigned the function of forming primaryrRNA gene transcripts, that is, they are the most important. The latter are better known under the designation 45S-RNA. Their length is approximately 13 thousand nucleotides. 28S-RNA, 18S-RNA and 5,8S-RNA are formed from it. Due to the fact that only one transcriptor is used to create them, the body receives a “guarantee” that the molecules will be formed in equal quantities. At the same time, only 7 thousand nucleotides are used to create RNA directly. The rest of the transcript is degraded in the nucleus. Regarding such a large residue, there is an opinion that it is necessary for the early stages of ribosome formation. The number of these polymerases in the cells of higher beings fluctuates around the mark of 40 thousand units.
How is it organized?
So, we have already well considered the first RNA polymerase (prokaryotic structure of the molecule). At the same time, large subunits, as well as a large number of other high-molecular-weight polypeptides, have well-defined functional and structural domains. During the cloning of genes and the determination of their primary structure, scientists identified evolutionarily conservative sections of the chains. Using good expression, the researchers also carried out mutational analysis, which allows us to talk about the functional significance of individual domains. To do this, using site-directed mutagenesis, individual amino acids were changed in polypeptide chains, and such modified subunits were used in the assembly of enzymes with subsequent analysis of the properties that were obtained in these constructs. It was noted that due to its organization, the first RNA polymerase onthe presence of alpha-amatine (a highly toxic substance derived from the pale grebe) 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 specific transcription. The second is DNA dependent RNA polymerase. This relationship is manifested in the magnitude of the activity of functioning. The topic is still under investigation, but it is already known that it depends on two transcription factors, which are designated as SL1 and UBF. The peculiarity of the latter is that it can directly bind to the promoter, while SL1 requires the presence of UBF. Although it was experimentally found that DNA-dependent RNA polymerase can take part 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 exactly? So far, it has not been possible to establish the reason for this behavior. One of the most popular explanations suggests that UBF acts as a kind of rDNA transcription stimulator as it grows and develops. When the resting phase occurs, the minimum required level of functioning is maintained. And for him, the participation of transcription factors is not critical. This is how RNA polymerase works. The functions of this enzyme allow us to support the process of reproducing the small "building blocks" of our body, thanks to which it is constantly updated for decades.
Second group of enzymes
Their functioning is regulated by the assembly of a multiprotein pre-initiation complex of promoters of the second class. Most often this is expressed in work with special proteins - activators. An example is TVR. These are the associated factors that are part of TFIID. They are targets for p53, NF kappa B and so on. Proteins, which are called coactivators, also exert their influence in the process of regulation. An example is GCN5. Why are these proteins needed? They act as adapters that adjust the interaction of activators and factors that are included in the pre-initiation complex. In order for transcription to occur correctly, the presence of the necessary initiating factors is necessary. Despite the fact that there are six of them, only one can directly interact with the promoter. For other cases, a preformed second RNA polymerase complex is required. Moreover, during these processes, the proximal elements are nearby - only 50-200 pairs from the site where transcription began. They contain an indication of the binding of activator proteins.
Special 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? The functions of enzymes of a simple structure are the transcription of a limited range of genes (or even their small parts). An example is the synthesis of RNA primers of Okazaki fragments. The promoter specificity of the RNA polymerase of bacteria and phages is that the enzymes have a simple structure and do not differ in diversity. This can be seen in the process of DNA replication in bacteria. Although one can also consider this: when the complex structure of the genome of an even T-phage was studied, during the development of which multiple transcription switching between different groups of genes was noted, it was revealed that a complex host RNA polymerase was used for this. That is, a simple enzyme is not induced in such cases. A number of consequences follow from this:
- Eukaryotic and bacterial RNA polymerase should be able to recognize different promoters.
- It is necessary that enzymes have a certain response to different regulatory proteins.
- RNA polymerase should also be able to change the specificity of recognition of the nucleotide sequence of template DNA. For this, various protein effectors are used.
From here follows the body's need for additional "building" elements. The proteins of the transcription complex help the RNA polymerase to fully perform its functions. This applies, to the greatest extent, to enzymes of a complex structure, in the possibilities of which the implementation of an extensive program for the implementation of genetic information. Thanks to various tasks, we can observe a kind of hierarchy in the structure of RNA polymerases.
How does the transcription process work?
Is there a gene responsible for communication withRNA polymerase? First, about transcription: in eukaryotes, the process occurs in the nucleus. In prokaryotes, it takes place within the microorganism itself. The polymerase interaction is based on the fundamental structural principle of complementary pairing of individual molecules. With regard to interaction issues, we can say that DNA acts exclusively as a template and does not change during transcription. Since DNA is an integral enzyme, it is possible to say for sure that a particular 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 would be more appropriate to say that each type of RNA is responsible for its own DNA. For the polymerase reaction to proceed, energy sources and ribonucleoside triphosphate substrates are needed. In their presence, 3', 5'-phosphodiester bonds are formed between ribonucleoside monophosphates. The RNA molecule begins to be synthesized in certain DNA sequences (promoters). This process ends at the terminating sections (termination). The site that is involved here is called the transcripton. In eukaryotes, as a rule, there is only one gene here, while prokaryotes can have several sections of the code. Each transcripton has a non-informative zone. They contain specific nucleotide sequences that interact with the regulatory transcription factors mentioned earlier.
Bacterial RNA polymerases
Thesemicroorganisms one enzyme is responsible for the synthesis of mRNA, rRNA and tRNA. The average polymerase molecule has approximately 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 binding to DNA. And the last subunit is involved in bringing the RNA polymerase into a working form. It should be noted that the enzyme molecules are not "free" floating in the bacterial cytoplasm. When not in use, RNA polymerases bind to non-specific regions of DNA and wait for an active promoter to open. Slightly digressing from the topic, it should be said that it is very convenient to study proteins and their effect on ribonucleic acid polymerases on bacteria. It is especially convenient to experiment on them to stimulate or suppress individual elements. Due to their high multiplication rate, the desired result can be obtained relatively quickly. Alas, human research cannot proceed at such a rapid rate due to our structural diversity.
How did RNA polymerase "take root" in different forms?
This article is coming to its logical conclusion. The focus was on eukaryotes. But there are also archaea and viruses. Therefore, I would like to pay a little attention to these forms of life. In the life of archaea, there is only one group of RNA polymerases. But it is extremely similar in its properties to the three associations of eukaryotes. Many scientists have suggested that what we can observe in archaea is actuallyevolutionary ancestor of specialized polymerases. The structure of viruses is also interesting. As previously mentioned, not all such microorganisms have their own polymerase. And where it is, it is a single subunit. Viral enzymes are believed to be derived from DNA polymerases rather than complex RNA constructs. Although, due to the diversity of this group of microorganisms, there are different implementations of the considered biological mechanism.
Conclusion
Alas, right now mankind does not yet have all the necessary information needed to understand the genome. And what could be done! Almost all diseases basically have a genetic basis - this applies primarily to viruses that constantly cause us problems, to infections, and so on. The most complex and incurable diseases are also, in fact, directly or indirectly dependent on the human genome. When we learn to understand ourselves and apply this knowledge to our advantage, a large number of problems and diseases will simply cease to exist. Many previously terrible diseases, such as smallpox and plague, have already become a thing of the past. Preparing to go there mumps, whooping cough. But we should not relax, because we still face a large number of different challenges that need to be answered. And he will be found, for everything is heading towards this.
