RNA Processing

Types Of RNA Involved In RNA Processing

Let's start by looking at the definition of RNA.

In this article, we will tackle three types of RNA that are involved in RNA processing:

• Messenger RNA (mRNA): produced during transcription, this molecule contains the protein information of the gene that was encoded in DNA and will be used as a template in translation.

• Transfer RNA (tRNA): decodes mRNA into a protein during translation.

• Ribosomal RNA (rRNA): makes up the core of the ribosome, the organelle in which protein synthesis takes place.

What is RNA Processing?

RNA processing prepares the transcript (the product of transcription) so it can function in translation or protein synthesis. As such, it takes place after transcription and before translation.

When it is newly formed and unprocessed, “pre-” is attached to the name of the transcript: pre-mRNA, pre-tRNA, and pre-rRNA. After processing, the transcript is said to become “mature”, meaning it is ready for protein synthesis.

Before we proceed, let’s do a brief recap on transcription and translation.

Transcription: Process Of Making RNA from DNA

Transcription is where a gene's DNA sequence is copied and written into mRNA. Transcription has three basic steps: initiation, elongation, and termination. Transcription can be summed up as follows:

1. Initiation: an enzyme called RNA polymerase binds to the promoter, a site on the DNA strand that signifies the start of the gene. This causes the DNA to unwind.

2. Elongation: The RNA polymerase travels through the strand from 3′ → 5’. As it travels through the strand, it “copies” the strand by adding complementary base pairs from 5′ → 3′. Thymine (T) in DNA is encoded as uracil (U) in mRNA.

3. Termination: The RNA comes across a termination sequence in the gene which signals the end of transcription. Hydrogen bonds that join DNA with the newly formed mRNA break, releasing the mRNA molecule.

   • Whereas prokaryotic transcription ends here, eukaryotic pre-mRNA undergoes further processing: capping, polyadenylation, and splicing, all of which we will elaborate on later.

Translation: Process of Making Proteins from RNA

Translation is the process of “reading” the information contained in the mRNA and converting it into an amino acid sequence. Like transcription, translation takes place in three steps: initiation, elongation, and termination.

1. Initiation: the small ribosomal subunit binds to the charged initiator tRNA molecule (tRNAi) and together these traverse the mRNA strand up to the start codon “AUG”. The anticodon on the tRNAi binds to the start codon through base pairing.

2. Elongation: the ribosome continues to translate codons and add amino acids to the growing amino acid chain.

3. Termination: translation ends when nonsense or stop codon (UAA, UAG, or UGA) is encountered. Release factors call for the tRNA and the polypeptide chain to be hydrolyzed, releasing the newly formed protein.

Steps in RNA Processing

In the following section, we will discuss mRNA processing that takes place in eukaryotic cells. We will also discuss tRNA and rRNA processing that takes place in both prokaryotic and eukaryotic cells.

Messenger RNA (mRNA) Processing in Eukaryotes

In eukaryotic cells, the newly transcribed pre-mRNAs must undergo further processing before they can be moved from the nucleus to the cytoplasm and then translated into a protein. These additional steps give the eukaryotic mRNA a longer half-life compared to prokaryotic mRNA.

Pre-mRNAs undergo three additional steps before translation: 5’ capping, polyadenylation, and pre-mRNA splicing. Let’s go over each of these steps.

5’ capping in messenger RNA processing: description & diagram

While the pre-mRNA is being synthesized, the 5’ end of the pre-mRNA transcript will be covered with a functional group 7-methylguanosine cap through a triphosphate linkage. The functional group stabilizes it, preventing it from breaking down while it is being processed and transported out of the nucleus. Additionally, factors involved in protein synthesis can detect the cap and help initiate translation.

The process of 5’ capping is simplified in the diagram below (Fig. 1).

Polyadenylation in messenger RNA processing: description & diagram

After the elongation step in transcription, an enzyme called endonuclease creates a break between an AAUAAA sequence and a GU-rich sequence in the pre-mRNA. This leaves the AAUAAA on the pre-mRNA.

Then, a poly-A tail (a chain of around 200 adenine residues) will attach to the pre-mRNA. The poly-A tail will provide added protection and will signal the need for the pre-mRNA to be transported to the cytoplasm.

The process of polyadenylation is simplified in the diagram below (Fig. 2).

Splicing in messenger RNA processing: description & diagram

Splicing is the process of removing introns from pre-mRNA and then joining the exons. This is done by a complex of approximately 200 proteins and RNA molecules called spliceosomes.

Introns are intervening sequences, while exons are protein-coding sequences; both are found in eukaryotic genes. Splicing occurs while the pre-mRNA is still in the nucleus.

Introns in mRNA do not encode functional proteins; hence, it is important that they are removed from the pre-mRNA prior to protein synthesis to ensure that the exons are joined correctly for the encoding of amino acids.

Note that introns can be over 70 bases long and each of these has to undergo splicing to generate an mRNA molecule that can be properly translated. If there is a mistake in the splicing process (even by one nucleotide), the rejoined exons would shift and be read incorrectly. As a result, the protein to be encoded would be dysfunctional.

The process of pre-mRNA splicing is simplified in the diagram below (Fig. 3).

Transport RNA (tRNA) and Ribosomal RNA (rRNA) Processing

In addition to eukaryotic mRNAs, tRNAs and rRNAs that are found in both eukaryotes and prokaryotes also undergo processing before taking part in protein synthesis.

• Pre-tRNA is transcribed and processed in the nucleus before moving into the cytoplasm where it is attached to free amino acids for translation.

• Pre-rRNA is transcribed, processed, and combined to form ribosomes in the nucleolus.

Most prokaryotic and eukaryotic tRNAs and rRNAs are transcribed as a long precursor molecule made up of several tRNAs or rRNAs. Enzymes cut this precursor into subunits of tRNA or rRNA. Some pre-rRNAs are linked to a methyl functional group to stabilize them. Additionally, as with mRNAs, eukaryotic pre-tRNAs and pre-rRNAs undergo splicing.

Mature rRNAs account for almost half of each ribosome. Some RNA molecules in a ribosome are solely structural, while others include catalytic or binding activity. Through intramolecular hydrogen bonding, mature tRNAs develop a three-dimensional structure with the amino acid binding site at one end and the anticodon at the other. The anticodon is a codon in the tRNA that is complementary to a codon in the mRNA.

It is important to note that while these molecules participate in translation, they are not themselves translated.