DNA TRANSCRIPTION: PROCESS IN EUKARYOTES AND PROKARYOTES - BIOLOGY - 2025

The transcription of the DNA is the process by which the information contained in the deoxyribonucleic acid is copied as a similar molecule, RNA, either as a step to protein synthesis or for the formation of RNA molecules involved in multiple cellular processes of great importance (regulation of gene expression, signaling, etc.).

Although it is not true that all the genes of an organism code for proteins, it is true that all the proteins of a cell, whether eukaryotic or prokaryotic, are encoded by one or more genes, where each amino acid is represented by a set of three DNA bases (codon).

Processing of eukaryotic genes (Source: Leonid 2 / CC BY-SA (https://creativecommons.org/licenses/by-sa/3.0) via Wikimedia Commons)

The synthesis of the polypeptide chain belonging to any cellular protein occurs thanks to two fundamental processes: transcription and translation; both highly regulated, since they are two processes of great importance for the functioning of any living organism.

What is DNA transcription?

Transcription involves the formation of a "template" for an RNA molecule known as "messenger RNA" (mRNA) from the "standard" sequence encoded in the region of DNA corresponding to the gene to be transcribed.

This process is carried out by an enzyme called RNA polymerase, which recognizes special places in the DNA sequence, binds to them, opens the DNA strand and synthesizes an RNA molecule using one of these complementary DNA strands as a template or pattern, even when it encounters another special stop sequence.

Translation, on the other hand, is the process through which protein synthesis occurs. It consists of the "reading" of the information contained in the mRNA that was transcribed from a gene, the "translation" of the DNA codons into amino acids and the formation of a polypeptide chain.

The translation of the nucleotide sequences of the mRNA is carried out by enzymes known as aminoacyl-tRNA synthetases, thanks to the participation of other RNA molecules known as "transfer RNA" (tRNA), which are anticodons of the codons contained in the MRNA, which are a faithful copy of the DNA sequence of a gene.

Transcription in eukaryotes (process)

During transcription in eukaryotes, DNA is used as a template to create a strand of messenger RNA with the help of the enzyme RNA polymerase.

In eukaryotic cells the transcription process occurs within the nucleus, which is the main intracellular organelle where DNA is contained in the form of chromosomes. It begins with the "copy" of the coding region of the gene that is transcribed into a single band molecule known as messenger RNA (mRNA).

Since the DNA is confined in said organelle, the mRNA molecules function as intermediaries or transporters in the transmission of the genetic message from the nucleus to the cytosol, where the translation of the RNA occurs and the entire biosynthetic machinery for protein synthesis (the ribosomes).

- What are eukaryotic genes like?

A gene consists of a DNA sequence whose characteristics determine its function, since the order of the nucleotides in said sequence is what determines its transcription and subsequent translation (in the case of those that code for proteins).

When a gene is transcribed, that is, when its information is copied in the form of RNA, the result can be a non-coding RNA (cRNA), which has direct functions in the regulation of gene expression, in cell signaling, etc. or it can be a messenger RNA (mRNA), which will then be translated into an amino acid sequence in a peptide.

Representation of the structure of a eukaryotic gene (Source: Thomas Shafee / CC BY (https://creativecommons.org/licenses/by/4.0) via Wikimedia Commons)

Whether a gene has a functional product in the form of RNA or protein depends on certain elements or regions present in its sequence.

Genes, eukaryotic or prokaryotic, have two strands of DNA, one known as the “sense” strand and the other “antisense”. The enzymes responsible for the transcription of these sequences "read" only one of the two strands, typically the "sense" or "coding" strand, which is "directed" 5'-3 '.

Every gene has regulatory sequences at its ends:

- if the sequences are before the coding region (the one that will be transcribed) they are known as "promoters"

- if they are separated by many kilobases, they can be "silencing" or "enhancing"

- those sequences that are closest to the 3 'region of genes are usually terminator sequences, which tell the polymerase that it must stop and end transcription (or replication, as the case may be)

The promoter region is divided into distal and proximal, according to its proximity to the coding region. It is at the 5 'end of the gene and is the site that the RNA polymerase enzyme and other proteins recognize to initiate transcription from DNA to RNA.

In the proximal part of the promoter region, transcription factors can bind, which have the ability to modify the affinity of the enzyme to the sequence to be transcribed, thus, they are in charge of positively or negatively regulating the transcription of genes.

The enhancer and silencing regions are also responsible for regulating gene transcription by modifying the "activity" of the promoter regions by their union with activator or repressor elements "upstream" of the coding sequence of the gene.

It is said that eukaryotic genes are always "turned off" or "repressed" by default, so they need to be activated by promoter elements in order to be expressed (transcribed).

- Who is in charge of the transcription?

Whatever the organism, transcription is carried out by a group of enzymes called RNA polymerases, which, similar to the enzymes responsible for DNA replication when a cell is about to divide, specialize in the synthesis of an RNA chain from one of the DNA strands of the gene being transcribed.

RNA polymerases are large enzyme complexes made up of many subunits. There are different types:

- RNA polymerase I (Pol I): which transcribe the genes that encode the "large" ribosomal subunit.

- RNA polymerase II (Pol II): which transcribe the genes encoding proteins and produce micro RNAs.

- RNA polymerase III (Pol III): which produce the transfer RNAs used during translation and also the RNA corresponding to the small subunit of the ribosome.

- RNA polymerase IV and V (Pol IV and Pol V): these are typical of plants and are responsible for the transcription of small interfering RNAs.

- What is the process?

Eukaryotic gene transcription (Source: Erinp.5000 / CC BY-SA (https://creativecommons.org/licenses/by-sa/4.0) via Wikimedia Commons)

Genetic transcription is a process that can be studied as divided into three phases: initiation, elongation, and termination.

Initiation

During initiation the promoter region the promoter region of the gene functions as a recognition site for RNA polymerase. This is where most of the genetic expression is controlled

RNA polymerase (say RNA polymerase II) binds to the sequence of the promoter region, which consists of a 6 to 10 base pair stretch at the 5 'end of the gene, usually about 35 base pairs of the transcription start site.

The union of RNA polymerase leads to the "opening" of the DNA double helix, separating the complementary strands. RNA synthesis begins at the site known as the "initiation site" and occurs in the 5'-3 'direction, that is, "downstream" or from left to right (by convention).

The initiation of transcription mediated by RNA polymerases depends on the concomitant presence of protein transcription factors known as general transcription factors, which contribute to the "location" of the enzyme in the promoter region.

After the enzyme has begun to polymerize, it is "shed" from both the promoter sequence and general transcription factors.

Elongation

During elongation, RNA polymerase slides down the chain that serves as a template

It occurs as RNA polymerase "moves" along the DNA sequence and adds ribonucleotides complementary to the DNA strand that serves as a "template" to the growing RNA. As RNA polymerase "passes" through the DNA strand, it rejoins its antisense strand.

The polymerization carried out by RNA polymerase consists of nucleophilic attacks of oxygen in position 3 'of the growing RNA chain to the phosphate "alpha" of the next nucleotide precursor to be added, with the consequent formation of phosphodiester bonds and the release of a pyrophosphate molecule (PPi).

The set comprised of the DNA strand, the RNA polymerase and the nascent RNA strand is known as a transcription bubble or complex.

Termination

When RNA polymerase reaches the terminal region of the gene, the transcriptional messenger RNA is complete. Then RNA polymerase, DNA strand, and transcription messenger RNA dissociate

Termination occurs when the polymerase reaches the termination sequence, which is logically located "downstream" from the transcription initiation site. When this occurs, both the enzyme and the synthesized RNA become "detached" from the DNA sequence being transcribed.

The termination region normally consists of a DNA sequence that is capable of "folding" on itself, forming a "hairpin loop" type structure.

After termination, the synthesized RNA strand is known as the primary transcript, which is released from the transcription complex, after which it may or may not be post-transcriptionally processed (prior to its translation into protein, if applicable) through a process called "cutting and splicing".

Transcription in prokaryotes (process)

Since prokaryotic cells do not have a membrane-enclosed nucleus, transcription occurs in the cytosol, specifically in the "nuclear" region, where chromosomal DNA is concentrated (bacteria have a circular chromosome).

In this way, the increase in the cytosolic concentration of a given protein is substantially faster in prokaryotes than in eukaryotes, since the transcription and translation processes occur in the same compartment.

- What are prokaryotic genes like?

Prokaryotic organisms have genes that are very similar to eukaryotes: the former also make use of promoter and regulatory regions for their transcription, although an important difference has to do with the fact that the promoter region is often sufficient to achieve a "strong" expression of the genes.

In this sense, it is important to mention that, in general, prokaryotic genes are always "on" by default.

The promoter region is associated with another region, usually "upstream", which is regulated by repressor molecules and is known as the "operator region."

Representation of the structure of a prokaryotic gene (Source: Thomas Shafee / CC BY (https://creativecommons.org/licenses/by/4.0) via Wikimedia Commons)

A difference in transcription between prokaryotes and eukaryotes is that normally the messenger RNAs of eukaryotes are monocistronic, that is, each one contains the information to synthesize a single protein, while in prokaryotes these can be monocistronic or polycistronic, where only one MRNA can contain the information for two or more proteins.

Thus, it is well known that prokaryotic genes encoding proteins with similar metabolic functions, for example, are found in groups known as operons, which are simultaneously transcribed into a single molecule form of messenger RNA.

Prokaryotic genes are densely packed, without many non-coding regions between them, so once transcribed into linear messenger RNA molecules, they can be translated into protein immediately (eukaryotic mRNAs often need further processing).

- How is prokaryotic RNA polymerase?

Prokaryotic organisms such as bacteria, for example, use the same RNA polymerase enzyme to transcribe all their genes, that is, those that code for ribosomal subunits and those that code for different cellular proteins.

In E. coli bacteria, RNA polymerase is composed of 5 polypeptide subunits, two of which are identical. The α, α, β, β 'subunits comprise the central portion of the enzyme and assemble and disassemble during each transcription event.

The α subunits are those that allow the union between the DNA and the enzyme; the β subunit binds to the triphosphate ribonucleotides that will be polymerized according to the DNA template in the nascent mRNA molecule and the β 'subunit binds to said template DNA strand.

The fifth subunit, known as σ participates in the initiation of transcription and is the one that confers specificity to the polymerase.

- What is the process?

Transcription in prokaryotes is very similar to that of eukaryotes (it is also divided into initiation, elongation, and termination), with some differences in the identity of the promoter regions and the transcription factors necessary for RNA polymerase exercise their functions.

Although the promoter regions can vary between different prokaryotic species, there are two conserved "consensus" sequences that can be easily identified in the -10 region (TATAAT) and in the -35 region (TTGACA) upstream of the coding sequence.

Initiation

It depends on the σ subunit of RNA polymerase, as it mediates the interaction between DNA and the enzyme, making it capable of recognizing promoter sequences. The initiation ends when some abortifacient transcripts of about 10 nucleotides are produced that are released.

Elongation

When the σ subunit is detached from the enzyme, the elongation phase begins, which consists of the synthesis of an mRNA molecule in the 5'-3 'direction (approximately 40 nucleotides per second).

Termination

Termination in prokaryotes depends on two different types of signals, it can be Rho-dependent and Rho-independent.

The Rho-dependent protein is controlled by this protein that "follows" the polymerase as it advances in RNA synthesis until the latter achieves a sequence rich in guanines (G), stops and comes into contact with the Rho protein. dissociating from DNA and mRNA.

Rho-independent termination is controlled by specific sequences of the gene, usually rich in guanine-cytosine (GC) repeats.

References

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