RNA POLYMERASE: STRUCTURE, FUNCTIONS, PROKARYOTES, EUKARYOTES - BIOLOGY - 2025

The RNA polymerase is an enzyme complex that is responsible for mediating the polymerization of an RNA molecule, from a DNA sequence used as a template. This process is the first step in gene expression, and is called transcription. RNA polymerase binds to DNA in a very particular region, known as the promoter.

This enzyme - and the transcription process in general - is more complex in eukaryotes than in prokaryotes. Eukaryotes possess multiple RNA polymerases that specialize in certain types of genes, in contrast to prokaryotes where all genes are transcribed by a single class of polymerase.

Structure of RNA polymerase in action.

Source: I, Splette

The increased complexity within the eukaryotic lineage in elements related to transcription is presumably related to a more sophisticated gene regulation system, typical of multicellular organisms.

In archaea, transcription is similar to the process that occurs in eukaryotes, despite the fact that they only have one polymerase.

Polymerases do not act alone. For the transcription process to start correctly, the presence of protein complexes called transcription factors is necessary.

Structure

The best characterized RNA polymerase are the polymerases of bacteria. It consists of multiple polypeptide chains. The enzyme has several subunits, cataloged as α, β, β ′ and σ. It has been shown that this last subunit does not participate directly in catalysis, but is involved in specific binding to DNA.

In fact, if we remove the σ subunit the polymerase can still catalyze its associated reaction, but it does so in the wrong regions.

The α subunit has a mass of 40,000 daltons and there are two. Of the β and β ′ subunits there is only 1, and they have a mass of 155,000 and 160,000 daltons, respectively.

These three structures are located in the nucleus of the enzyme, while the σ subunit is further away, and is called the sigma factor. The complete enzyme - or holoenzyme - has a total weight close to 480,000 daltons.

The structure of RNA polymerase is widely variable, and depends on the group studied. However, in all organic beings it is a complex enzyme, made up of several units.

Features

The function of RNA polymerase is the polymerization of nucleotides of an RNA chain, built from a DNA template.

All the information necessary for the construction and development of an organism is written in its DNA. However, the information is not directly translated into proteins. The intermediate step to a messenger RNA molecule is necessary.

This transformation of the language from DNA to RNA is mediated by RNA polymerase and the phenomenon is called transcription. This process is similar to DNA replication.

In prokaryotes

Prokaryotes are unicellular organisms, without a defined nucleus. Of all the prokaryotes, the most studied organism has been Escherichia coli. This bacterium is a normal inhabitant of our microbiota and has been the ideal model for geneticists.

RNA polymerase was first isolated from this organism, and most transcription studies have been performed in E. coli. In a single cell of this bacterium we can find up to 7000 polymerase molecules.

Unlike eukaryotes that have three types of RNA polymerases, in prokaryotes all genes are processed by a single type of polymerase.

In eukaryotes

What is a gene?

Eukaryotes are organisms that have a nucleus delimited by a membrane and have different organelles. Eukaryotic cells are characterized by three types of nuclear RNA polymerases, and each type is responsible for the transcription of particular genes.

A "gene" is not an easy term to define. Usually, we are used to calling any DNA sequence that is finally translated into a protein “gene”. Although the previous statement is true, there are also genes whose final product is an RNA (and not a protein), or they are genes involved in the regulation of expression.

There are three types of polymerases, designated as I, II and III. We will describe its functions below:

RNA polymerase II

The genes that code for proteins - and involve a messenger RNA - are transcribed by RNA polymerase II. Due to its relevance in protein synthesis, it has been the polymerase most studied by researchers.

Transcription factors

These enzymes cannot direct the transcription process by themselves, they need the presence of proteins called transcription factors. Two types of transcription factors can be distinguished: general and additional.

The first group includes proteins that are involved in the transcription of all promoters of polymerases II. These constitute the basic machinery of transcription.

In in vitro systems, five general factors that are indispensable for the initiation of transcription by RNA polymerase II have been characterized. These promoters have a consensus sequence called the "TATA box".

The first step in transcription involves the binding of a factor called TFIID to the TATA box. This protein is a complex with multiple subunits - including a specific binding box. It is also made up of a dozen peptides called TAFs (TBP-associated factors).

A third factor involved is TFIIF. After polymerase II is recruited, the factors TFIIE and TFIIH are necessary for the initiation of transcription.

RNA polymerase I and III

Ribosomal RNAs are structural elements of ribosomes. In addition to ribosomal RNA, ribosomes are made up of proteins and are responsible for translating a messenger RNA molecule into protein.

Transfer RNAs also participate in this translation process, leading to the amino acid that will be incorporated into the forming polypeptide chain.

These RNAs (ribosomal and transfer) are transcribed by RNA polymerases I and III. RNA polymerase I is specific for the transcription of the largest ribosomal RNAs, known as 28S, 28S, and 5.8S. The S refers to the sedimentation coefficient, that is, the sedimentation rates during the centrifugation process.

RNA polymerase III is responsible for the transcription of the genes that code for the smallest ribosomal RNAs (5S).

In addition, a series of small RNAs (remember that there are multiple types of RNAs, not only the best known messenger, ribosomal and transfer RNAs) such as small nuclear RNAs, are transcribed by RNA polymerase III.

Transcription factors

RNA polymerase I, reserved exclusively for the transcription of ribosomal genes, requires several transcription factors for its activity. Genes encoding ribosomal RNA have a promoter located about 150 base pairs "upstream" from the transcriptional start site.

The promoter is recognized by two transcription factors: UBF and SL1. These cooperatively bind to the promoter and recruit polymerase I, forming the initiation complex.

These factors are made up of multiple protein subunits. Similarly, TBP appears to be a shared transcription factor for all three polymerases in eukaryotes.

For RNA polymerase III, the transcription factor TFIIIA, TFIIIB and TFIIIC have been identified. These bind sequentially to the transcription complex.

RNA polymerase in organelles

One of the distinguishing characteristics of eukaryotes is the subcellular compartments called organelles. Mitochondria and chloroplasts have a separate RNA polymerase that is reminiscent of this enzyme in bacteria. These polymerases are active, and they transcribe the DNA found in these organelles.

According to the endosymbiotic theory, eukaryotes come from a symbiosis event, where one bacterium engulfed a smaller one. This relevant evolutionary fact explains the similarity between the polymerases of mitochondria with the polymerase of bacteria.

In archaea

As in bacteria, in archaea there is only one type of polymerase responsible for the transcription of all the genes of the unicellular organism.

However, the RNA polymerase of archaea is very similar to the structure of polymerase in eukaryotes. They present a TATA box and transcription factors, TBP and TFIIB, specifically.

In general terms, the transcription process in eukaryotes is quite similar to that found in archaea.

Differences with DNA polymerase

DNA replication is orchestrated by an enzyme complex called DNA polymerase. Although this enzyme is often compared to RNA polymerase - both catalyze the polymerization of a nucleotide chain in the 5 ′ to 3 ′ direction - they differ in several respects.

DNA polymerase needs a short nucleotide fragment in order to start the replication of the molecule, called a primer or primer. RNA polymerase can start synthesis de novo, and does not need the primer for its activity.

DNA polymerase is capable of binding to various sites along a chromosome, whereas polymerase only binds to gene promoters.

As for the proofreading mechanisms of enzymes, those of DNA polymerase are much better known, being able to correct the wrong nucleotides that have been polymerized by mistake.

References

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